Add tools from CR copier template and some restructuring of code folders. Also some smaller fixes e.g. automatic file retrieval when running crf test reads

.copier-answers.yml

@@ -0,0 +1,18 @@
+# Changes here will be overwritten by Copier
+_commit: v0.3.0
+_src_path: ../../../helper_tools/copier-core-python-repository/
+email: mail@johannes-guetschow.de
+initial_setup: true
+name: Johannes Gütschow
+notebook_dependencies: false
+pandas_doctests: false
+plot_dependencies: true
+project_description_short: Reading country greenhouse gas data submitted to the United
+    Nations Framework Convention on Climate Change (UNFCCC)in different submissions
+    and formats and providing it in a standadized nc and csv format compatible with
+    primap2. Data are read using different methods from APIs, xlsx and csv files as
+    well as pdf files.
+project_name_human: Country greenhouse gas data submitted to the UNFCCC
+project_name_pip: unfccc-ghg-data
+project_name_python: unfccc_ghg_data
+project_url: https://github.com/JGuetschow/UNFCCC_non-AnnexI_data

.github/actions/setup/action.yml

@@ -0,0 +1,57 @@
+name: "Setup Python and Poetry"
+description: "setup Python and Poetry with caches"
+
+inputs:
+  python-version:
+    description: "Python version to use"
+    required: true
+  venv-id:
+    description: "ID to identify cached environment (should be unique from other steps)"
+    required: true
+  poetry-dependency-install-flags:
+    description: "Flags to pass to poetry when running `poetry install --no-interaction --no-root`"
+    required: true
+  run-poetry-install:
+    description: "Should we run the poetry install steps"
+    required: false
+    default: true
+
+
+runs:
+  using: "composite"
+  steps:
+    - name: Set up Python ${{ inputs.python-version }}
+      id: setup-python
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ inputs.python-version }}
+    - name: Load cached Poetry installation
+      id: cached-poetry
+      uses: actions/cache@v3
+      with:
+        path: ~/.local  # the path depends on the OS
+        key: poetry-2  # increment to reset cache
+    - name: Install Poetry
+      if: steps.cached-poetry.outputs.cache-hit != 'true'
+      uses: snok/install-poetry@v1
+    - name: Load cached venv
+      if: ${{ inputs.run-poetry-install == 'true' }}
+      id: cached-poetry-dependencies
+      uses: actions/cache@v3
+      with:
+        path: .venv
+        key: "venv-${{ inputs.venv-id }}-${{ inputs.python-version }}-${{ hashFiles('**/poetry.lock') }}"
+    # Install dependencies first so that our package doesn't appear in the cache by accident
+    - name: Install dependencies
+      if: ${{ inputs.run-poetry-install == 'true' }}
+      shell: bash
+      run: |
+        poetry config virtualenvs.create true
+        poetry config virtualenvs.in-project true
+        poetry env use ${{ inputs.python-version }}
+        poetry install --no-interaction --no-root ${{ inputs.poetry-dependency-install-flags }}
+    # Now run same command but let the package install too
+    - name: Install package
+      if: ${{ inputs.run-poetry-install == 'true' }}
+      shell: bash
+      run: poetry install --no-interaction ${{ inputs.poetry-dependency-install-flags }}

.github/workflows/bump.yaml

@@ -0,0 +1,60 @@
+name: Bump version
+
+on:
+  workflow_dispatch:
+    inputs:
+      bump_rule:
+        type: choice
+        description: How to bump the project's version (see https://python-poetry.org/docs/cli/#version)
+        options:
+          - patch
+          - minor
+          - major
+          - prepatch
+          - preminor
+          - premajor
+          - prerelease
+        required: true
+
+jobs:
+  bump_version:
+    name: "Bump version and create changelog"
+    if: "!startsWith(github.event.head_commit.message, 'bump:')"
+    runs-on: ubuntu-latest
+    env:
+      CI_COMMIT_EMAIL: "ci-runner@unfccc-ghg-data.invalid"
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+          token: "${{ secrets.PERSONAL_ACCESS_TOKEN }}"
+
+      # towncrier imports the package as part of building so we have to
+      # install the pacakage (to keep things slim, we only install the main
+      # dependencies, which also means that we get a test that we can import
+      # the package with only the compulsory dependencies installed for free)
+      - uses: ./.github/actions/setup
+        with:
+          python-version: "3.11"
+          venv-id: "bump"
+          poetry-dependency-install-flags: "--only main"
+
+      - name: Install towncrier
+        run: |
+          poetry run pip install towncrier
+
+      - name: Create bump and changelog
+
+        run: |
+          BASE_VERSION=`poetry version -s`
+          NEW_VERSION=`poetry version -s ${{ github.event.inputs.bump_rule }}`
+          poetry run towncrier build --yes --version v$NEW_VERSION
+
+          git config --global user.name "$GITHUB_ACTOR"
+          git config --global user.email "$CI_COMMIT_EMAIL"
+
+          git commit -a -m "bump: version $BASE_VERSION -> $NEW_VERSION"
+          git tag v$NEW_VERSION
+          git push && git push --tags
+          echo "Bumped to version $NEW_VERSION"

.github/workflows/ci.yaml

@@ -0,0 +1,112 @@
+name: CI
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+    tags: ['v*']
+
+jobs:
+  mypy:
+    if: ${{ !github.event.pull_request.draft }}
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v3
+      - uses: ./.github/actions/setup
+        with:
+          python-version: "3.9"
+          venv-id: "docs"
+          poetry-dependency-install-flags: "--all-extras --only 'main,dev'"
+      - name: mypy
+        run: MYPYPATH=stubs poetry run mypy src
+
+  docs:
+    if: ${{ !github.event.pull_request.draft }}
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v3
+      - uses: ./.github/actions/setup
+        with:
+          python-version: "3.9"
+          venv-id: "docs"
+          poetry-dependency-install-flags: "--all-extras --only 'main,docs'"
+      - name: docs
+        run: poetry run sphinx-build -W --keep-going -T -b html docs/source docs/build
+
+  tests:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ "ubuntu-latest" ]
+        python-version: [ "3.9", "3.10", "3.11" ]
+    runs-on: "${{ matrix.os }}"
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v3
+      - uses: ./.github/actions/setup
+        with:
+          python-version: "${{ matrix.python-version }}"
+          venv-id: "tests-${{ runner.os }}"
+          poetry-dependency-install-flags: "--all-extras"
+      - name: Run tests
+        run: |
+          poetry run pytest -r a -v src tests --doctest-modules --cov=src --cov-report=term-missing --cov-report=xml
+          poetry run coverage report
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v3
+
+  imports-without-extras:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ "ubuntu-latest" ]
+        python-version: [ "3.9", "3.10", "3.11" ]
+    runs-on: "${{ matrix.os }}"
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v3
+      - uses: ./.github/actions/setup
+        with:
+          python-version: "${{ matrix.python-version }}"
+          venv-id: "imports-without-extras-${{ runner.os }}"
+          poetry-dependency-install-flags: "--only main"
+      - name: Check importable without extras
+        run: poetry run python scripts/test-install.py
+
+  check-build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v3
+      - uses: ./.github/actions/setup
+        with:
+          python-version: "3.9"
+          venv-id: "check-build-${{ runner.os }}"
+          run-poetry-install: false
+          poetry-dependency-install-flags: "not used"
+      - name: Build package
+        run: |
+          poetry build --no-interaction
+      - name: Check build
+        run: |
+          tar -tvf dist/unfccc_ghg_data-*.tar.gz --wildcards '*unfccc_ghg_data/py.typed'
+
+  check-dependency-licences:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v3
+      - uses: ./.github/actions/setup
+        with:
+          python-version: "3.9"
+          venv-id: "licence-check"
+          poetry-dependency-install-flags: "--all-extras"
+      - name: Check licences of dependencies
+        shell: bash
+        run: |
+          TEMP_FILE=$(mktemp)
+          poetry export --without=tests --without=docs --without=dev > $TEMP_FILE
+          poetry run liccheck -r $TEMP_FILE -R licence-check.txt
+          cat licence-check.txt

.github/workflows/deploy.yaml

@@ -0,0 +1,33 @@
+name: Deploy
+
+on:
+  release:
+    types: [published]
+
+defaults:
+  run:
+    shell: bash
+
+jobs:
+  deploy-pypi:
+    name: Deploy to PyPI
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - uses: ./.github/actions/setup
+        with:
+          python-version: "3.9"
+          venv-id: "deploy"
+          poetry-dependency-install-flags: "--all-extras"
+      - name: Run tests
+        run: |
+          poetry run pytest -r a src tests --doctest-modules
+      - name: Publish to PyPI
+        env:
+          PYPI_TOKEN: "${{ secrets.PYPI_TOKEN }}"
+        run: |
+          poetry config pypi-token.pypi $PYPI_TOKEN
+          poetry publish --build --no-interaction

.github/workflows/install.yaml

@@ -0,0 +1,30 @@
+name: Install
+
+on:
+  schedule:
+    # * is a special character in YAML so you have to quote this string
+    - cron:  '0 0 * * 3'
+
+jobs:
+  test-pypi-install:
+    runs-on: "${{ matrix.os }}"
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
+        python-version: [ "3.9", "3.10", "3.11" ]
+    steps:
+    - name: Set up Python "${{ matrix.python-version }}"
+      id: setup-python
+      uses: actions/setup-python@v4
+      with:
+        python-version: "${{ matrix.python-version }}"
+    - name: Install
+      run: |
+        pip install --upgrade pip
+        pip install unfccc-ghg-data
+    - name: Checkout repository
+      uses: actions/checkout@v3
+    - name: Test installation (${{ matrix.os }} Python ${{ matrix.python-version }})
+      run: |
+        python scripts/test-install.py

.github/workflows/release.yaml

@@ -0,0 +1,47 @@
+name: Release
+
+on:
+  push:
+    tags: ['v*']
+
+defaults:
+  run:
+    shell: bash
+
+jobs:
+  draft-release:
+    name: Create draft release
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - uses: ./.github/actions/setup
+        with:
+          python-version: "3.9"
+          venv-id: "release"
+          poetry-dependency-install-flags: "--all-extras"
+      - name: Add version to environment
+        run: |
+          PROJECT_VERSION=$(poetry version --short)
+          echo "PROJECT_VERSION=$PROJECT_VERSION" >> $GITHUB_ENV
+      - name: Run tests
+        run: |
+          poetry run pytest -r a -v src tests --doctest-modules
+      - name: Build package
+        run: |
+          poetry build --no-interaction
+      - name: Generate Release Notes
+        run: |
+          git log $(git describe --tags --abbrev=0 HEAD^)..HEAD --pretty='format:* %h %s' --no-merges >> ".github/release_template.md"
+      - name: Create Release Draft
+        uses: softprops/action-gh-release@v1
+        with:
+          body_path: ".github/release_template.md"
+          draft: true
+          files: |
+            dist/unfccc_ghg_data-${{ env.PROJECT_VERSION }}-py3-none-any.whl
+            dist/unfccc_ghg_data-${{ env.PROJECT_VERSION }}.tar.gz
+        env:
+          GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"

.gitignore

@@ -1,16 +1,157 @@
-.idea
-venv
+# temporary
+src/unfccc_ghg_data/datasets
+
+# loging
+log/*
 geckodriver.log
-__pycache__
+
+# private dev code
 /JG_test_code/
-.doit.db
-log/*
-UNFCCC_GHG_data/datasets
-UNFCCC_GHG_data/UNFCCC_DI_reader/test_UNFCCC_DI_reader.ipynb
-UNFCCC_GHG_data/UNFCCC_DI_reader/.ipynb_checkpoints/
-*.autosave
-#UNFCCC_GHG_data/UNFCCC_DI_reader
-build
-UNFCCC_GHG_data.egg-info
 
+# Notebooks
+*.ipynb
+
+# Databases
+*.db
+
+# Jupyter cache
+.jupyter_cache
+
+# Licence check
+licence-check.txt
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# pycharm settings
+.idea
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
 
+# Mac stuff
+*.DS_Store

.pre-commit-config.yaml

@@ -0,0 +1,50 @@
+# See https://pre-commit.com for more information
+ci:
+  autofix_prs: false
+  autoupdate_schedule: quarterly
+  autoupdate_branch: pre-commit-autoupdate
+
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: 'v4.4.0'
+    hooks:
+      - id: check-added-large-files
+      - id: check-ast
+      - id: check-case-conflict
+      - id: check-json
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-yaml
+      - id: debug-statements
+      - id: detect-private-key
+      - id: end-of-file-fixer
+      - id: fix-byte-order-marker
+      - id: mixed-line-ending
+      - id: trailing-whitespace
+  - repo: local
+    hooks:
+      # Prevent committing .rej files
+      - id: forbidden-files
+        name: forbidden files
+        entry: found Copier update rejection files; review them and remove them
+        language: fail
+        files: "\\.rej$"
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: 'v0.0.263'
+    hooks:
+      - id: ruff
+        args: [ --fix, --exit-non-zero-on-fix ]
+  - repo: https://github.com/psf/black
+    rev: '23.3.0'
+    hooks:
+      - id: black
+  # additional to the above, apply black to doctests in source code
+  - repo: https://github.com/keewis/blackdoc
+    rev: v0.3.8
+    hooks:
+      - id: blackdoc
+  - repo: https://github.com/python-poetry/poetry
+    rev: '1.4.2'
+    hooks:
+      - id: poetry-check

.readthedocs.yaml

@@ -0,0 +1,24 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Thank you also https://browniebroke.com/blog/specify-docs-dependency-groups-with-poetry-and-read-the-docs/
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.9"
+  jobs:
+    post_create_environment:
+      - pip install poetry
+      - poetry config virtualenvs.create false
+    post_install:
+      - poetry install --with docs --all-extras
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/source/conf.py

Makefile

@@ -1,10 +1,76 @@
-.SILENT: help
-help:
-	echo Options:
-	echo make venv: create virtual environment
-
-venv: UNFCCC_GHG_data
-	[ -d ./venv ] || python3 -m venv venv
-	./venv/bin/pip install --upgrade pip
-	./venv/bin/pip install -Ur code/requirements.txt
-	touch venv
+# Makefile to help automate key steps
+
+.DEFAULT_GOAL := help
+# Will likely fail on Windows, but Makefiles are in general not Windows
+# compatible so we're not too worried
+TEMP_FILE := $(shell mktemp)
+
+# A helper script to get short descriptions of each target in the Makefile
+define PRINT_HELP_PYSCRIPT
+import re, sys
+
+for line in sys.stdin:
+	match = re.match(r'^([\$$\(\)a-zA-Z_-]+):.*?## (.*)$$', line)
+	if match:
+		target, help = match.groups()
+		print("%-30s %s" % (target, help))
+endef
+export PRINT_HELP_PYSCRIPT
+
+
+help:  ## print short description of each target
+	@python3 -c "$$PRINT_HELP_PYSCRIPT" < $(MAKEFILE_LIST)
+
+.PHONY: checks
+checks:  ## run all the linting checks of the codebase
+	@echo "=== pre-commit ==="; poetry run pre-commit run --all-files || echo "--- pre-commit failed ---" >&2; \
+		echo "=== mypy ==="; MYPYPATH=stubs poetry run mypy src || echo "--- mypy failed ---" >&2; \
+		echo "======"
+
+.PHONY: black
+black:  ## format the code using black
+	poetry run black src tests docs/source/conf.py scripts docs/source/notebooks/*.py
+	poetry run blackdoc src
+
+.PHONY: ruff-fixes
+ruff-fixes:  ## fix the code using ruff
+	poetry run ruff src tests scripts docs/source/conf.py docs/source/notebooks/*.py --fix
+
+
+.PHONY: test
+test:  ## run the tests
+	poetry run pytest src tests -r a -v --doctest-modules --cov=src
+
+# Note on code coverage and testing:
+# You must specify cov=src as otherwise funny things happen when doctests are
+# involved.
+# If you want to debug what is going on with coverage, we have found
+# that adding COVERAGE_DEBUG=trace to the front of the below command
+# can be very helpful as it shows you if coverage is tracking the coverage
+# of all of the expected files or not.
+# We are sure that the coverage maintainers would appreciate a PR that improves
+# the coverage handling when there are doctests and a `src` layout like ours.
+
+.PHONY: docs
+docs:  ## build the docs
+	poetry run sphinx-build -T -b html docs/source docs/build/html
+
+.PHONY: changelog-draft
+changelog-draft:  ## compile a draft of the next changelog
+	poetry run towncrier build --draft
+
+.PHONY: licence-check
+licence-check:  ## Check that licences of the dependencies are suitable
+	# Will likely fail on Windows, but Makefiles are in general not Windows
+	# compatible so we're not too worried
+	poetry export --without=tests --without=docs --without=dev > $(TEMP_FILE)
+	poetry run liccheck -r $(TEMP_FILE) -R licence-check.txt
+	rm -f $(TEMP_FILE)
+
+.PHONY: virtual-environment
+virtual-environment:  ## update virtual environment, create a new one if it doesn't already exist
+	poetry lock
+	# Put virtual environments in the project
+	poetry config virtualenvs.in-project true
+	poetry install --all-extras
+	poetry run pre-commit install

README.md

@@ -1,7 +1,86 @@
-# Collaborative UNFCCC non-AnnexI dataset
+# Country greenhouse gas data submitted to the UNFCCC
 This repository aims to organize a collective effort to bring GHG emissions and related data submitted by developing countries (non-AnnexI) to the UNFCCC into a standardized machine readable format. We focus on data not available through the [UNFCCC DI interface](https://di.unfccc.int/) which is mostly data submitted in IPCC 2006 categories.
 
-The code is based on [national-inventory-submissions](https://github.com/openclimatedata/national-inventory-submisions)
+<!--- sec-begin-description -->
+
+Reading country greenhouse gas data submitted to the United Nations Framework Convention on Climate Change (UNFCCC)in different submissions and formats and providing it in a standadized nc and csv format compatible with primap2. Data are read using different methods from APIs, xlsx and csv files as well as pdf files.
+
+
+
+[![CI](https://github.com/JGuetschow/UNFCCC_non-AnnexI_data/actions/workflows/ci.yaml/badge.svg?branch=main)](https://github.com/JGuetschow/UNFCCC_non-AnnexI_data/actions/workflows/ci.yaml)
+[![Coverage](https://codecov.io/gh/climate-resource/UNFCCC_non-AnnexI_data/branch/main/graph/badge.svg)](https://codecov.io/gh/climate-resource/UNFCCC_non-AnnexI_data)
+[![Docs](https://readthedocs.org/projects/unfccc-ghg-data/badge/?version=latest)](https://unfccc-ghg-data.readthedocs.io)
+
+**PyPI :**
+[![PyPI](https://img.shields.io/pypi/v/unfccc-ghg-data.svg)](https://pypi.org/project/unfccc-ghg-data/)
+[![PyPI: Supported Python versions](https://img.shields.io/pypi/pyversions/unfccc-ghg-data.svg)](https://pypi.org/project/unfccc-ghg-data/)
+[![PyPI install](https://github.com/JGuetschow/UNFCCC_non-AnnexI_data/actions/workflows/install.yaml/badge.svg?branch=main)](https://github.com/JGuetschow/UNFCCC_non-AnnexI_data/actions/workflows/install.yaml)
+
+**Other info :**
+[![License](https://img.shields.io/github/license/JGuetschow/UNFCCC_non-AnnexI_data.svg)](https://github.com/JGuetschow/UNFCCC_non-AnnexI_data/blob/main/LICENSE)
+[![Last Commit](https://img.shields.io/github/last-commit/JGuetschow/UNFCCC_non-AnnexI_data.svg)](https://github.com/JGuetschow/UNFCCC_non-AnnexI_data/commits/main)
+[![Contributors](https://img.shields.io/github/contributors/JGuetschow/UNFCCC_non-AnnexI_data.svg)](https://github.com/JGuetschow/UNFCCC_non-AnnexI_data/graphs/contributors)
+
+
+<!--- sec-end-description -->
+
+Full documentation can be found at:
+[unfccc-ghg-data.readthedocs.io](https://unfccc-ghg-data.readthedocs.io/en/latest/).
+We recommend reading the docs there because the internal documentation links
+don't render correctly on GitHub's viewer.
+
+## Installation
+
+<!--- sec-begin-installation -->
+
+Country greenhouse gas data submitted to the UNFCCC can be installed with conda or pip:
+
+```bash
+pip install unfccc-ghg-data
+conda install -c conda-forge unfccc-ghg-data
+```
+
+Additional dependencies can be installed using
+
+```bash
+# To add plotting dependencies
+pip install unfccc-ghg-data[plots]
+
+# If you are installing with conda, we recommend
+# installing the extras by hand because there is no stable
+# solution yet (issue here: https://github.com/conda/conda/issues/7502)
+```
+
+<!--- sec-end-installation -->
+
+### For developers
+
+<!--- sec-begin-installation-dev -->
+
+For development, we rely on [poetry](https://python-poetry.org) for all our
+dependency management. To get started, you will need to make sure that poetry
+is installed
+([instructions here](https://python-poetry.org/docs/#installing-with-the-official-installer),
+we found that pipx and pip worked better to install on a Mac).
+
+For all of work, we use our `Makefile`.
+You can read the instructions out and run the commands by hand if you wish,
+but we generally discourage this because it can be error prone.
+In order to create your environment, run `make virtual-environment`.
+
+If there are any issues, the messages from the `Makefile` should guide you
+through. If not, please raise an issue in the [issue tracker][issue_tracker].
+
+For the rest of our developer docs, please see [](development-reference).
+
+[issue_tracker]: https://github.com/JGuetschow/UNFCCC_non-AnnexI_data/issues
+
+<!--- sec-end-installation-dev -->
+
+
+TODO: old README below. reorganize into proper docs.
+
+The code for downloading submissions is based on [national-inventory-submissions](https://github.com/openclimatedata/national-inventory-submisions)
 
 
 **The repository is currently under initial development so a lot of things are still subject to change.**

UNFCCC_GHG_data/UNFCCC_CRF_reader/crf_specifications/__init__.py

@@ -1,10 +0,0 @@
-"""
-Define the CRF specifications here for easy access
-"""
-
-from .CRF2021_specification import CRF2021
-from .CRF2022_specification import CRF2022
-from .CRF2023_specification import CRF2023
-from .CRF2023_AUS_specification import CRF2023_AUS
-
-__all__ = ["CRF2021", "CRF2022", "CRF2023", "CRF2023_AUS"]

UNFCCC_GHG_data/UNFCCC_DI_reader/__init__.py

@@ -1,30 +0,0 @@
-# submodule to read data from UNFCCC DI API using the unfccc_di_api package
-
-#import unfccc_di_api
-from .UNFCCC_DI_reader_core import read_UNFCCC_DI_for_country,  \
-    convert_DI_data_to_pm2_if, convert_DI_IF_data_to_pm2, \
-    read_UNFCCC_DI_for_country_group
-
-from .UNFCCC_DI_reader_proc import process_UNFCCC_DI_for_country, \
-    process_and_save_UNFCCC_DI_for_country, process_UNFCCC_DI_for_country_group
-
-from .UNFCCC_DI_reader_datalad import read_DI_for_country_datalad, \
-read_DI_for_country_group_datalad, process_DI_for_country_datalad, \
-    process_DI_for_country_group_datalad
-
-from .UNFCCC_DI_reader_helper import determine_filename
-
-__all__ = [
-    "read_UNFCCC_DI_for_country",
-    "convert_DI_data_to_pm2_if",
-    "convert_DI_IF_data_to_pm2",
-    "read_UNFCCC_DI_for_country_group",
-    "process_UNFCCC_DI_for_country",
-    "process_and_save_UNFCCC_DI_for_country",
-    "process_UNFCCC_DI_for_country_group",
-    "process_DI_for_country_group_datalad",
-    "read_DI_for_country_datalad",
-    "process_DI_for_country_datalad",
-    "read_DI_for_country_group_datalad",
-    "determine_filename",
-]

UNFCCC_GHG_data/helper/__init__.py

@@ -1,33 +0,0 @@
-from .definitions import root_path, code_path, log_path
-from .definitions import extracted_data_path, extracted_data_path_UNFCCC
-from .definitions import legacy_data_path
-from .definitions import downloaded_data_path, downloaded_data_path_UNFCCC
-from .definitions import dataset_path, dataset_path_UNFCCC
-from .definitions import custom_country_mapping, custom_folders
-from .definitions import GWP_factors, gas_baskets
-from .functions import get_country_code, get_country_name, convert_categories
-from .functions import create_folder_mapping, process_data_for_country, get_code_file
-from .functions import fix_rows
-
-__all__ = [
-    "root_path",
-    "code_path",
-    "log_path",
-    "extracted_data_path",
-    "extracted_data_path_UNFCCC",
-    "legacy_data_path",
-    "downloaded_data_path",
-    "downloaded_data_path_UNFCCC",
-    "dataset_path",
-    "dataset_path_UNFCCC",
-    "custom_country_mapping",
-    "custom_folders",
-    "GWP_factors",
-    "gas_baskets",
-    "get_country_code",
-    "get_country_name",
-    "convert_categories",
-    "create_folder_mapping",
-    "process_data_for_country",
-    "fix_rows",
-]

changelog/README.md

@@ -0,0 +1,41 @@
+# CHANGELOG
+
+This directory contains "news fragments", i.e. short files that contain a small markdown-formatted bit of text that will be
+added to the CHANGELOG when it is next compiled.
+
+The CHANGELOG will be read by users, so this description should be aimed to Country greenhouse gas data submitted to the UNFCCC users instead of
+describing internal changes which are only relevant to developers. Merge requests in combination with our git history provides additional
+developer-centric information.
+
+Make sure to use phrases in the past tense and use punctuation, examples:
+
+```
+Improved verbose diff output with sequences.
+
+Terminal summary statistics now use multiple colors.
+```
+
+Each file should have a name of the form `<MR>.<TYPE>.md`, where `<MR>` is the merge request number, and `<TYPE>` is one of:
+
+* `feature`: new user facing features, like new command-line options and new behaviour.
+* `improvement`: improvement of existing functionality, usually without requiring user intervention
+* `fix`: fixes a bug.
+* `docs`: documentation improvement, like rewording an entire section or adding missing docs.
+* `deprecation`: feature deprecation.
+* `breaking`: a change which may break existing uses, such as feature removal or behaviour change.
+* `trivial`: fixing a small typo or internal change that might be noteworthy.
+
+So for example: `123.feature.md`, `456.fix.md`.
+
+Since you need the merge request number for the filename, you must submit a MR first. From this MR, you can get the MR number and then create the news file. A single MR can also have multiple news items, for example a given MR may add a feature as well as
+deprecate some existing functionality.
+
+If you are not sure what issue type to use, don't hesitate to ask in your MR.
+
+`towncrier` preserves multiple paragraphs and formatting (code blocks, lists, and so on), but for entries other than
+features it is usually better to stick to a single paragraph to keep it concise. You may also use `MyST` [style
+cross-referencing](https://myst-parser.readthedocs.io/en/latest/syntax/cross-referencing.html) within your news items to link to other
+documentation.
+
+You can also run `towncrier build --draft` to see the draft changelog that will be appended to [docs/source/changelog.md]()
+on the next release.

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/api/unfccc_ghg_data.operations.rst

@@ -0,0 +1,13 @@
+unfccc\_ghg\_data.operations
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. automodule:: unfccc_ghg_data.operations
+
+.. currentmodule:: unfccc_ghg_data.operations
+
+
+
+add\_two
+========
+
+.. autofunction:: add_two

docs/source/api/unfccc_ghg_data.rst

@@ -0,0 +1,12 @@
+API Reference
+~~~~~~~~~~~~~
+
+.. automodule:: unfccc_ghg_data
+
+.. currentmodule:: unfccc_ghg_data
+
+
+.. autosummary::
+  :toctree: ./
+
+  unfccc_ghg_data.operations

docs/source/changelog.md

@@ -0,0 +1,20 @@
+# Changelog
+
+Versions follow [Semantic Versioning](https://semver.org/) (`<major>.<minor>.<patch>`).
+
+Backward incompatible (breaking) changes will only be introduced in major versions
+with advance notice in the **Deprecations** section of releases.
+
+
+<!--
+You should *NOT* be adding new changelog entries to this file, this
+file is managed by towncrier. See changelog/README.md.
+
+You *may* edit previous changelogs to fix problems like typo corrections or such.
+To add a new changelog entry, please see
+https://pip.pypa.io/en/latest/development/contributing/#news-entries,
+noting that we use the `changelog` directory instead of news, md instead
+of rst and use slightly different categories.
+-->
+
+<!-- towncrier release notes start -->

docs/source/conf.py

@@ -0,0 +1,168 @@
+"""
+Configuration file for the Sphinx documentation builder.
+
+For the full list of built-in configuration values, see the documentation:
+https://www.sphinx-doc.org/en/master/usage/configuration.html
+"""
+from functools import wraps
+
+from sphinxcontrib_autodocgen import AutoDocGen
+
+from src import unfccc_ghg_data
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = "Country greenhouse gas data submitted to the UNFCCC"
+# put the authors in their own variable, so they can be reused later
+authors = ", ".join(["Johannes Gütschow"])
+# add a copyright year variable, we can extend this over time in future as
+# needed
+copyright_year = "2023"
+copyright = f"{copyright_year}, {authors}"
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    # create documentation automatically from source code
+    # https://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html
+    "sphinx.ext.autodoc",
+    # automatic summary
+    "sphinx.ext.autosummary",
+    # automatic summary with better control
+    "sphinxcontrib_autodocgen",
+    # tell sphinx that we're using numpy style docstrings
+    # https://www.sphinx-doc.org/en/master/usage/extensions/napoleon.html
+    "sphinx.ext.napoleon",
+    # add support for type hints too (so type hints are included next to
+    # argument and return types in docs)
+    # https://github.com/tox-dev/sphinx-autodoc-typehints
+    # this must come after napoleon
+    # in the list for things to work properly
+    # https://github.com/tox-dev/sphinx-autodoc-typehints#compatibility-with-sphinxextnapoleon
+    "sphinx_autodoc_typehints",
+    # jupytext rendered notebook support (also loads myst_parser)
+    "myst_nb",
+    # links to other docs
+    "sphinx.ext.intersphinx",
+    # add source code to docs
+    "sphinx.ext.viewcode",
+    # add copy code button to code examples
+    "sphinx_copybutton",
+    # math support
+    "sphinx.ext.mathjax",
+]
+
+# general sphinx settings
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+# Don't include module names in object names (can also be left on,
+# depends a bit how your project is structured and what you prefer)
+add_module_names = False
+# Other global settings which we've never used but are included by default
+templates_path = ["_templates"]
+# Avoid sphinx thinking that conf.py is a source file because we use .py
+# endings for notebooks
+exclude_patterns = ["conf.py"]
+# Stop sphinx doing funny things with byte order markers
+source_encoding = "utf-8"
+
+# configure default settings for autodoc directives
+# https://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html#directives
+autodoc_default_options = {
+    # Show the inheritance of classes
+    "show-inheritance": True,
+}
+
+# autosummary with autodocgen
+# make sure autosummary doesn't interfere
+autosummary_generate = True
+autosummary_generate_overwrite = False
+
+autodocgen_config = [
+    {
+        "modules": [unfccc_ghg_data],
+        "generated_source_dir": "docs/source/api",
+        # choose a different title for specific modules, e.g. the toplevel one
+        "module_title_decider": lambda modulename: "API Reference"
+        if modulename == "unfccc_ghg_data"
+        else modulename,
+    }
+]
+
+# monkey patch to remove leading newlines
+generate_module_rst_orig = AutoDocGen.generate_module_rst
+
+
+@wraps(generate_module_rst_orig)
+def _generate_module_rst_new(*args, **kwargs):
+    default = generate_module_rst_orig(*args, **kwargs)
+    out = default.lstrip("\n")
+    if not out.endswith("\n"):
+        out = f"{out}\n"
+
+    return out
+
+
+AutoDocGen.generate_module_rst = _generate_module_rst_new
+
+# napoleon extension settings
+# https://www.sphinx-doc.org/en/master/usage/extensions/napoleon.html
+# We use numpy style docstrings
+napoleon_numpy_docstring = True
+# We don't use google docstrings
+napoleon_google_docstring = False
+# Don't use separate rtype for the return documentation
+napoleon_use_rtype = False
+
+# autodoc type hints settings
+# https://github.com/tox-dev/sphinx-autodoc-typehints
+# include full name of classes when expanding type hints?
+typehints_fully_qualified = True
+# Add rtype directive if needed
+typehints_document_rtype = True
+# Put the return type as part of the return documentation
+typehints_use_rtype = False
+
+# Left-align maths equations
+mathjax3_config = {"chtml": {"displayAlign": "center"}}
+
+# myst configuration
+myst_enable_extensions = ["amsmath", "dollarmath"]
+# cache because we save our notebooks as `.py` files i.e. without output
+# stored so auto doesn't work (it just ends up being run every time)
+nb_execution_mode = "cache"
+nb_execution_raise_on_error = True
+nb_execution_show_tb = True
+nb_execution_timeout = 120
+nb_custom_formats = {".py": ["jupytext.reads", {"fmt": "py:percent"}]}
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+# Pick your theme for html output, we typically use the read the docs theme
+html_theme = "sphinx_rtd_theme"
+html_static_path = ["_static"]
+
+
+# Ignore ipynb files when building (see https://github.com/executablebooks/MyST-NB/issues/363).
+def setup(app):
+    """
+    Set up the Sphinx app
+    """
+    app.registry.source_suffix.pop(".ipynb", None)
+
+
+# Intersphinx mapping
+intersphinx_mapping = {
+    "numpy": ("https://docs.scipy.org/doc/numpy", None),
+    "pandas": ("https://pandas.pydata.org/pandas-docs/stable", None),
+    "python": ("https://docs.python.org/3", None),
+    "pyam": ("https://pyam-iamc.readthedocs.io/en/latest", None),
+    "scmdata": ("https://scmdata.readthedocs.io/en/latest", None),
+    "xarray": ("http://xarray.pydata.org/en/stable", None),
+    "pint": (
+        "https://pint.readthedocs.io/en/latest",
+        None,
+    ),
+}

docs/source/development.md

@@ -0,0 +1,55 @@
+(development-reference)=
+# Development
+
+Notes for developers. If you want to get involved, please do!
+
+## Language
+
+We use British English for our development.
+We do this for consistency with the broader work context of our lead developers.
+
+## Versioning
+
+This package follows the version format described in [PEP440](https://peps.python.org/pep-0440/) and
+[Semantic Versioning](https://semver.org/) to describe how the version should change depending on the updates to the
+code base. Our commit messages are written using written to follow the
+[conventional commits](https://www.conventionalcommits.org/en/v1.0.0/) standard which makes it easy to find the
+commits that matter when traversing through the commit history.
+
+(releasing-reference)=
+## Releasing
+
+Releasing is semi-automated via a CI job. The CI job requires the type of version bump that will be performed to be
+manually specified. See the poetry docs for the [list of available bump rules](https://python-poetry.org/docs/cli/#version).
+
+### Standard process
+
+The steps required are the following:
+
+
+1. Bump the version: manually trigger the "bump" workflow from the main branch
+   (see here: https://github.com/JGuetschow/UNFCCC_non-AnnexI_data/actions/workflows/bump.yaml).
+   A valid "bump_rule" (see https://python-poetry.org/docs/cli/#version) will need to be specified.
+   This will then trigger a draft release.
+
+1. Edit the draft release which has been created
+   (see here:
+   https://github.com/JGuetschow/UNFCCC_non-AnnexI_data/releases).
+   Once you are happy with the release (removed placeholders, added key
+   announcements etc.) then hit 'Publish release'. This triggers a release to
+   PyPI (which you can then add to the release if you want).
+
+
+1. That's it, release done, make noise on social media of choice, do whatever
+   else
+
+1. Enjoy the newly available version
+
+## Read the Docs
+
+Our documentation is hosted by
+[Read the Docs (RtD)](https://www.readthedocs.org/), a service for which we are
+very grateful. The RtD configuration can be found in the `.readthedocs.yaml`
+file in the root of this repository. The docs are automatically
+deployed at
+[unfccc-ghg-data.readthedocs.io](https://unfccc-ghg-data.readthedocs.io/en/latest/).

docs/source/index.md

@@ -0,0 +1,42 @@
+% Country greenhouse gas data submitted to the UNFCCC documentation master file
+% This was based on a sphinx-quickstart from Mon May  1 20:20:44 2023.
+% If you're having issues with sphinx, you may need to regenerate this doc.
+% You can adapt this file completely to your liking, but it should at least
+% contain the root `toctree` directive.
+
+# Country greenhouse gas data submitted to the UNFCCC
+
+```{include} ../../README.md
+:start-after: <!--- sec-begin-description -->
+:end-before: <!--- sec-end-description -->
+```
+
+## Installation
+
+```{include} ../../README.md
+:start-after: <!--- sec-begin-installation -->
+:end-before: <!--- sec-end-installation -->
+```
+
+### For developers
+
+```{include} ../../README.md
+:start-after: <!--- sec-begin-installation-dev -->
+:end-before: <!--- sec-end-installation-dev -->
+```
+
+```{toctree}
+:caption: Contents
+:maxdepth: 2
+notebooks
+development
+api/unfccc_ghg_data
+changelog
+```
+
+Index
+-----
+
+- :ref:`genindex`
+- :ref:`modindex`
+- :ref:`search`

docs/source/notebooks.md

@@ -0,0 +1,21 @@
+(notebooks-reference)=
+# Notebooks
+
+Here we provide various examples of how to use Country greenhouse gas data submitted to the UNFCCC.
+They  are derived from
+[jupyter notebooks](https://docs.jupyter.org/en/latest/start/index.html),
+but are saved using [jupytext](https://jupytext.readthedocs.io/en/latest/)
+to keep our repository slim and make it easier to track changes.
+
+## Basic demos
+
+```{toctree}
+:caption: Contents
+:maxdepth: 1
+notebooks/basic-demo.py
+```
+
+## Notebook execution info
+
+```{nb-exec-table}
+```

docs/source/notebooks/basic-demo.py

@@ -0,0 +1,24 @@
+# ---
+# jupyter:
+#   jupytext:
+#     text_representation:
+#       extension: .py
+#       format_name: percent
+#       format_version: '1.3'
+#       jupytext_version: 1.14.5
+#   kernelspec:
+#     display_name: Python 3 (ipykernel)
+#     language: python
+#     name: python3
+# ---
+
+# %% [markdown]
+# # Basic demo
+#
+# This notebook gives a basic demonstration of how to use Country greenhouse gas data submitted to the UNFCCC.
+
+# %%
+from src import unfccc_ghg_data
+
+# %%
+print(f"You are using unfccc_ghg_data version {unfccc_ghg_data.__version__}")

dodo.py

@@ -1,24 +1,35 @@
 # define tasks for UNFCCC data repository
 from doit import get_var
 import os
+import sys
 
 # TODO: task for folder mapping
 
 # create virtual environment
-def task_setup_venv():
-    """Create virtual environment"""
+# def task_setup_venv():
+#     """Create virtual environment"""
+#     return {
+#         'file_dep': ['requirements_dev.txt', 'setup.cfg', 'pyproject.toml'],
+#         'actions': ['python3 -m venv venv',
+#                     './venv/bin/pip install --upgrade pip wheel',
+#                     #'./venv/bin/pip install -Ur unfccc_ghg_data/requirements.txt',
+#                     './venv/bin/pip install --upgrade --upgrade-strategy '
+#                     'eager -e .[dev]',
+#                     'touch venv',],
+#         'targets': ['venv'],
+#         'verbosity': 2,
+#     }
+
+def task_in_venv():
+    def in_venv():
+        if sys.prefix == sys.base_prefix:
+            raise ValueError("You need to run the code from the virtual environment.")
+
     return {
-        'file_dep': ['requirements_dev.txt', 'setup.cfg', 'pyproject.toml'],
-        'actions': ['python3 -m venv venv',
-                    './venv/bin/pip install --upgrade pip wheel',
-                    #'./venv/bin/pip install -Ur UNFCCC_GHG_data/requirements.txt',
-                    './venv/bin/pip install --upgrade --upgrade-strategy '
-                    'eager -e .[dev]',
-                    'touch venv',],
-        'targets': ['venv'],
-        'verbosity': 2,
+        'actions': [in_venv],
     }
 
+
 # set UNFCCC_GHG_ROOT_PATH environment variable
 def task_set_env():
     """
@@ -42,11 +53,11 @@ def task_map_folders():
     Create or update the folder mapping in the given folder
     """
     return {
-        'actions': [f"./venv/bin/python UNFCCC_GHG_data/helper/folder_mapping.py "
+        'actions': [f"python src/unfccc_ghg_data/helper/folder_mapping.py "
                     f"--folder={read_config_folder['folder']}"],
         'task_dep': ['set_env'],
         'verbosity': 2,
-        'setup': ['setup_venv'],
+        'setup': ['in_venv'],
     }
 
 
@@ -57,10 +68,10 @@ def task_update_bur():
         'targets': ['downloaded_data/UNFCCC/submissions-bur.csv'],
         'actions': ['datalad run -m "Fetch BUR submissions" '
                     '-o downloaded_data/UNFCCC/submissions-bur.csv '
-                    './venv/bin/python UNFCCC_GHG_data/UNFCCC_downloader/fetch_submissions_bur.py'],
+                    'python src/unfccc_ghg_data/unfccc_downloader/fetch_submissions_bur.py'],
         'task_dep': ['set_env'],
         'verbosity': 2,
-        'setup': ['setup_venv'],
+        'setup': ['in_venv'],
     }
 
 
@@ -72,13 +83,13 @@ def task_download_bur():
         # before download
         'actions': ['datalad run -m "Download BUR submissions" '
                     '-i downloaded_data/UNFCCC/submissions-bur.csv '
-                    './venv/bin/python UNFCCC_GHG_data/UNFCCC_downloader/download_non-annexI.py --category=BUR',
-                    f"./venv/bin/python UNFCCC_GHG_data/helper/folder_mapping.py "
+                    'python src/unfccc_ghg_data/unfccc_downloader/download_non-annexI.py --category=BUR',
+                    f"python src/unfccc_ghg_data/helper/folder_mapping.py "
                     f"--folder=downloaded_data/UNFCCC"
                     ],
         'task_dep': ['set_env'],
         'verbosity': 2,
-        'setup': ['setup_venv'],
+        'setup': ['in_venv'],
     }
 
 
@@ -88,10 +99,10 @@ def task_update_nc():
         'targets': ['downloaded_data/UNFCCC/submissions-nc.csv'],
         'actions': ['datalad run -m "Fetch NC submissions" '
                     '-o downloaded_data/UNFCCC/submissions-nc.csv '
-                    './venv/bin/python UNFCCC_GHG_data/UNFCCC_downloader/fetch_submissions_nc.py'],
+                    'python src/unfccc_ghg_data/unfccc_downloader/fetch_submissions_nc.py'],
         'task_dep': ['set_env'],
         'verbosity': 2,
-        'setup': ['setup_venv'],
+        'setup': ['in_venv'],
     }
 
 
@@ -103,13 +114,13 @@ def task_download_nc():
         # before download
         'actions': ['datalad run -m "Download NC submissions" '
                     '-i downloaded_data/UNFCCC/submissions-nc.csv '
-                    './venv/bin/python UNFCCC_GHG_data/UNFCCC_downloader/download_non-annexI.py --category=NC',
-                    f"./venv/bin/python UNFCCC_GHG_data/helper/folder_mapping.py "
+                    'python src/unfccc_ghg_data/unfccc_downloader/download_non-annexI.py --category=NC',
+                    f"python src/unfccc_ghg_data/helper/folder_mapping.py "
                     f"--folder=downloaded_data/UNFCCC"
                     ],
         'task_dep': ['set_env'],
         'verbosity': 2,
-        'setup': ['setup_venv'],
+        'setup': ['in_venv'],
     }
 
 # annexI data: one update call for all data types (as they are on one page)
@@ -128,11 +139,11 @@ def task_update_annexi():
         'actions': [f"datalad run -m 'Fetch AnnexI submissions for {update_aI_config['year']}' "
                     "--explicit "
                     f"-o downloaded_data/UNFCCC/submissions-annexI_{update_aI_config['year']}.csv "
-                    f"./venv/bin/python UNFCCC_GHG_data/UNFCCC_downloader/fetch_submissions_annexI.py "
+                    f"python src/unfccc_ghg_data/unfccc_downloader/fetch_submissions_annexI.py "
                     f"--year={update_aI_config['year']}"],
         'task_dep': ['set_env'],
         'verbosity': 2,
-        'setup': ['setup_venv'],
+        'setup': ['in_venv'],
     }
 
 
@@ -145,14 +156,14 @@ def task_download_annexi():
         'actions': [f"datalad run -m 'Download AnnexI submissions for "
                     f"{update_aI_config['category']}{update_aI_config['year']}' "
                     f"-i downloaded_data/UNFCCC/submissions-annexI_{update_aI_config['year']}.csv "
-                    f"./venv/bin/python UNFCCC_GHG_data/UNFCCC_downloader/download_annexI.py "
+                    f"python src/unfccc_ghg_data/unfccc_downloader/download_annexI.py "
                     f"--category={update_aI_config['category']} --year={update_aI_config['year']}",
-                    f"./venv/bin/python UNFCCC_GHG_data/helper/folder_mapping.py "
+                    f"python src/unfccc_ghg_data/helper/folder_mapping.py "
                     f"--folder=downloaded_data/UNFCCC"
                     ],
         'task_dep': ['set_env'],
         'verbosity': 2,
-        'setup': ['setup_venv'],
+        'setup': ['in_venv'],
     }
 
 
@@ -160,13 +171,13 @@ def task_download_ndc():
     """ Download NDC submissions """
     return {
         'actions': ['datalad run -m "Download NDC submissions" '
-                    './venv/bin/python UNFCCC_GHG_data/UNFCCC_downloader/download_ndc.py',
-                    f"./venv/bin/python UNFCCC_GHG_data/helper/folder_mapping.py "
+                    'python src/unfccc_ghg_data/unfccc_downloader/download_ndc.py',
+                    f"python src/unfccc_ghg_data/helper/folder_mapping.py "
                     f"--folder=downloaded_data/UNFCCC"
                     ],
         'task_dep': ['set_env'],
         'verbosity': 2,
-        'setup': ['setup_venv'],
+        'setup': ['in_venv'],
     }
 
 
@@ -180,16 +191,16 @@ read_config = {
 
 # TODO: make individual task for non-UNFCCC submissions
 def task_read_unfccc_submission():
-    """ Read submission for a country (if UNFCCC_GHG_data exists) (not for CRF)"""
+    """ Read submission for a country (if code exists) (not for CRF)"""
     return {
-        'actions': [f"./venv/bin/python UNFCCC_GHG_data/UNFCCC_reader/read_UNFCCC_submission.py "
+        'actions': [f"python src/unfccc_ghg_data/unfccc_reader/read_UNFCCC_submission.py "
                     f"--country={read_config['country']} --submission={read_config['submission']}",
-                    f"./venv/bin/python UNFCCC_GHG_data/helper/folder_mapping.py "
+                    f"python src/unfccc_ghg_data/helper/folder_mapping.py "
                     f"--folder=extracted_data/UNFCCC"
                     ],
         'task_dep': ['set_env'],
         'verbosity': 2,
-        'setup': ['setup_venv'],
+        'setup': ['in_venv'],
     }
 
 
@@ -208,11 +219,12 @@ read_config_crf = {
 def task_read_unfccc_crf_submission():
     """ Read CRF submission for a country """
     actions = [
-        f"./venv/bin/python UNFCCC_GHG_data/UNFCCC_CRF_reader/read_UNFCCC_CRF_submission_datalad.py "
+        f"python src/unfccc_ghg_data/unfccc_crf_reader"
+        f"/read_unfccc_crf_submission_datalad.py "
         f"--country={read_config_crf['country']} "
         f"--submission_year={read_config_crf['submission_year']} "
         f"--submission_date={read_config_crf['submission_date']} ",
-        f"./venv/bin/python UNFCCC_GHG_data/helper/folder_mapping.py "
+        f"python src/unfccc_ghg_data/helper/folder_mapping.py "
         f"--folder=extracted_data/UNFCCC"
         ]
     if read_config_crf["re_read"] == "True":
@@ -221,16 +233,17 @@ def task_read_unfccc_crf_submission():
         'actions': actions,
         'task_dep': ['set_env'],
         'verbosity': 2,
-        'setup': ['setup_venv'],
+        'setup': ['in_venv'],
     }
 
 
 def task_read_new_unfccc_crf_for_year():
     """ Read CRF submission for all countries for given submission year. by default only reads
     data not present yet. Only reads the latest updated submission for each country."""
-    actions = [f"./venv/bin/python UNFCCC_GHG_data/UNFCCC_CRF_reader/read_new_UNFCCC_CRF_for_year_datalad.py "
+    actions = [f"python src/unfccc_ghg_data/unfccc_crf_reader"
+               f"/read_new_unfccc_crf_for_year_datalad.py "
                f"--submission_year={read_config_crf['submission_year']} ",
-               f"./venv/bin/python UNFCCC_GHG_data/helper/folder_mapping.py "
+               f"python src/unfccc_ghg_data/helper/folder_mapping.py "
                f"--folder=extracted_data/UNFCCC"
                ]
     # specifying countries is currently disabled duo to problems with command line
@@ -244,16 +257,16 @@ def task_read_new_unfccc_crf_for_year():
         'actions': actions,
         'task_dep': ['set_env'],
         'verbosity': 2,
-        'setup': ['setup_venv'],
+        'setup': ['in_venv'],
     }
 
 
 def task_test_read_unfccc_crf_for_year():
     """ Read CRF submission for all countries for given submission year. by default only reads
     data not present yet. Only reads the latest updated submission for each country."""
-    actions = [f"./venv/bin/python "
-               f"UNFCCC_GHG_data/UNFCCC_CRF_reader"
-               f"/test_read_UNFCCC_CRF_for_year.py "
+    actions = [f"python "
+               f"src/unfccc_ghg_data/unfccc_crf_reader"
+               f"/test_read_unfccc_crf_for_year.py "
                f"--submission_year={read_config_crf['submission_year']} "
                f"--country={read_config_crf['country']} "
                ]
@@ -267,26 +280,26 @@ def task_test_read_unfccc_crf_for_year():
         'actions': actions,
         'task_dep': ['set_env'],
         'verbosity': 2,
-        'setup': ['setup_venv'],
+        'setup': ['in_venv'],
     }
 
 
 def task_compile_raw_unfccc_crf_for_year():
     """ Read CRF submission for all countries for given submission year. by default only reads
     data not present yet. Only reads the latest updated submission for each country."""
-    actions = [f"./venv/bin/python "
-               f"UNFCCC_GHG_data/UNFCCC_CRF_reader/CRF_raw_for_year.py "
+    actions = [f"python "
+               f"src/unfccc_ghg_data/unfccc_crf_reader/crf_raw_for_year.py "
                f"--submission_year={read_config_crf['submission_year']} "
                ]
     return {
         'actions': actions,
         'task_dep': ['set_env'],
         'verbosity': 2,
-        'setup': ['setup_venv'],
+        'setup': ['in_venv'],
     }
 
 # tasks for DI reader
-# datalad run is called from within the read_UNFCCC_DI_for_country.py script
+# datalad run is called from within the read_unfccc_di_for_country.py script
 read_config_di = {
     "country": get_var('country', None),
     "date": get_var('date', None),
@@ -297,41 +310,43 @@ read_config_di = {
 def task_read_unfccc_di_for_country():
     """ Read DI data for a country """
     actions = [
-        f"./venv/bin/python "
-        f"UNFCCC_GHG_data/UNFCCC_DI_reader/read_UNFCCC_DI_for_country_datalad.py "
+        f"python "
+        f"src/unfccc_ghg_data/unfccc_di_reader/read_unfccc_di_for_country_datalad.py "
         f"--country={read_config_di['country']}",
-        f"./venv/bin/python UNFCCC_GHG_data/helper/folder_mapping.py "
+        f"python src/unfccc_ghg_data/helper/folder_mapping.py "
         f"--folder=extracted_data/UNFCCC"
         ]
     return {
         'actions': actions,
         'task_dep': ['set_env'],
         'verbosity': 2,
-        'setup': ['setup_venv'],
+        'setup': ['in_venv'],
     }
 
 def task_process_unfccc_di_for_country():
     """ Process DI data for a country """
     actions = [
-        f"./venv/bin/python "
-        f"UNFCCC_GHG_data/UNFCCC_DI_reader/process_UNFCCC_DI_for_country_datalad.py "
+        f"python "
+        f"src/unfccc_ghg_data/unfccc_di_reader/process_unfccc_di_for_country_datalad"
+        f".py "
         f"--country={read_config_di['country']} --date={read_config_di['date']}",
-        f"./venv/bin/python UNFCCC_GHG_data/helper/folder_mapping.py "
+        f"python src/unfccc_ghg_data/helper/folder_mapping.py "
         f"--folder=extracted_data/UNFCCC"
         ]
     return {
         'actions': actions,
         'task_dep': ['set_env'],
         'verbosity': 2,
-        'setup': ['setup_venv'],
+        'setup': ['in_venv'],
     }
 
 def task_read_unfccc_di_for_country_group():
     """ Read DI data for a country group """
     actions = [
-        f"./venv/bin/python "
-        f"UNFCCC_GHG_data/UNFCCC_DI_reader/read_UNFCCC_DI_for_country_group_datalad.py",
-        f"./venv/bin/python UNFCCC_GHG_data/helper/folder_mapping.py "
+        f"python "
+        f"src/unfccc_ghg_data/unfccc_di_reader/read_unfccc_di_for_country_group_datalad"
+        f".py",
+        f"python src/unfccc_ghg_data/helper/folder_mapping.py "
         f"--folder=extracted_data/UNFCCC"
         ]
     if read_config_di["annexI"] == "True":
@@ -341,15 +356,16 @@ def task_read_unfccc_di_for_country_group():
         'actions': actions,
         'task_dep': ['set_env'],
         'verbosity': 2,
-        'setup': ['setup_venv'],
+        'setup': ['in_venv'],
     }
 
 
 def task_process_unfccc_di_for_country_group():
     """ Process DI data for a country group """
     actions = [
-        f"./venv/bin/python "
-        f"UNFCCC_GHG_data/UNFCCC_DI_reader/process_UNFCCC_DI_for_country_group_datalad"
+        f"python "
+        f"src/unfccc_ghg_data/unfccc_di_reader"
+        f"/process_unfccc_di_for_country_group_datalad"
         f".py",
         ]
     if read_config_di["annexI"] == "True":
@@ -361,7 +377,7 @@ def task_process_unfccc_di_for_country_group():
         'actions': actions,
         'task_dep': ['set_env'],
         'verbosity': 2,
-        'setup': ['setup_venv'],
+        'setup': ['in_venv'],
     }
 
 # general tasks
@@ -369,10 +385,10 @@ def task_country_info():
     """ Print information on submissions and datasets
     available for given country"""
     return {
-        'actions': [f"./venv/bin/python UNFCCC_GHG_data/helper/country_info.py "
+        'actions': [f"python src/unfccc_ghg_data/helper/country_info.py "
                     f"--country={read_config['country']}"],
         'task_dep': ['set_env'],
         'verbosity': 2,
-        'setup': ['setup_venv'],
+        'setup': ['in_venv'],
     }
 

poetry.lock

@@ -0,0 +1,4263 @@
+# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
+
+[[package]]
+name = "alabaster"
+version = "0.7.13"
+description = "A configurable sidebar-enabled Sphinx theme"
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "alabaster-0.7.13-py3-none-any.whl", hash = "sha256:1ee19aca801bbabb5ba3f5f258e4422dfa86f82f3e9cefb0859b283cdd7f62a3"},
+    {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"},
+]
+
+[[package]]
+name = "annexremote"
+version = "1.6.4"
+description = "git annex special remotes made easy"
+optional = false
+python-versions = "*"
+files = [
+    {file = "annexremote-1.6.4-py3-none-any.whl", hash = "sha256:74fdf4d4e20fd3b5a5bc827b4c488dd5de95cb8161cda77ad06a6b5fbd22e82b"},
+    {file = "annexremote-1.6.4.tar.gz", hash = "sha256:da4198a25b36c699216fd5f1e93ba0e655e167b6822b64284a4bf90388ea69ae"},
+]
+
+[package.extras]
+doc = ["sphinx"]
+tests = ["coverage", "pytest"]
+
+[[package]]
+name = "appnope"
+version = "0.1.3"
+description = "Disable App Nap on macOS >= 10.9"
+optional = false
+python-versions = "*"
+files = [
+    {file = "appnope-0.1.3-py2.py3-none-any.whl", hash = "sha256:265a455292d0bd8a72453494fa24df5a11eb18373a60c7c0430889f22548605e"},
+    {file = "appnope-0.1.3.tar.gz", hash = "sha256:02bd91c4de869fbb1e1c50aafc4098827a7a54ab2f39d9dcba6c9547ed920e24"},
+]
+
+[[package]]
+name = "asttokens"
+version = "2.4.1"
+description = "Annotate AST trees with source code positions"
+optional = false
+python-versions = "*"
+files = [
+    {file = "asttokens-2.4.1-py2.py3-none-any.whl", hash = "sha256:051ed49c3dcae8913ea7cd08e46a606dba30b79993209636c4875bc1d637bc24"},
+    {file = "asttokens-2.4.1.tar.gz", hash = "sha256:b03869718ba9a6eb027e134bfdf69f38a236d681c83c160d510768af11254ba0"},
+]
+
+[package.dependencies]
+six = ">=1.12.0"
+
+[package.extras]
+astroid = ["astroid (>=1,<2)", "astroid (>=2,<4)"]
+test = ["astroid (>=1,<2)", "astroid (>=2,<4)", "pytest"]
+
+[[package]]
+name = "attrs"
+version = "23.1.0"
+description = "Classes Without Boilerplate"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "attrs-23.1.0-py3-none-any.whl", hash = "sha256:1f28b4522cdc2fb4256ac1a020c78acf9cba2c6b461ccd2c126f3aa8e8335d04"},
+    {file = "attrs-23.1.0.tar.gz", hash = "sha256:6279836d581513a26f1bf235f9acd333bc9115683f14f7e8fae46c98fc50e015"},
+]
+
+[package.extras]
+cov = ["attrs[tests]", "coverage[toml] (>=5.3)"]
+dev = ["attrs[docs,tests]", "pre-commit"]
+docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"]
+tests = ["attrs[tests-no-zope]", "zope-interface"]
+tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+
+[[package]]
+name = "babel"
+version = "2.13.1"
+description = "Internationalization utilities"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "Babel-2.13.1-py3-none-any.whl", hash = "sha256:7077a4984b02b6727ac10f1f7294484f737443d7e2e66c5e4380e41a3ae0b4ed"},
+    {file = "Babel-2.13.1.tar.gz", hash = "sha256:33e0952d7dd6374af8dbf6768cc4ddf3ccfefc244f9986d4074704f2fbd18900"},
+]
+
+[package.dependencies]
+setuptools = {version = "*", markers = "python_version >= \"3.12\""}
+
+[package.extras]
+dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
+
+[[package]]
+name = "beautifulsoup4"
+version = "4.12.2"
+description = "Screen-scraping library"
+optional = false
+python-versions = ">=3.6.0"
+files = [
+    {file = "beautifulsoup4-4.12.2-py3-none-any.whl", hash = "sha256:bd2520ca0d9d7d12694a53d44ac482d181b4ec1888909b035a3dbf40d0f57d4a"},
+    {file = "beautifulsoup4-4.12.2.tar.gz", hash = "sha256:492bbc69dca35d12daac71c4db1bfff0c876c00ef4a2ffacce226d4638eb72da"},
+]
+
+[package.dependencies]
+soupsieve = ">1.2"
+
+[package.extras]
+html5lib = ["html5lib"]
+lxml = ["lxml"]
+
+[[package]]
+name = "black"
+version = "23.3.0"
+description = "The uncompromising code formatter."
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "black-23.3.0-cp310-cp310-macosx_10_16_arm64.whl", hash = "sha256:0945e13506be58bf7db93ee5853243eb368ace1c08a24c65ce108986eac65915"},
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+io = ["cftime", "fsspec", "h5netcdf", "netCDF4", "pooch", "pydap", "scipy", "zarr"]
+parallel = ["dask[complete]"]
+viz = ["matplotlib", "nc-time-axis", "seaborn"]
+
+[[package]]
+name = "zipp"
+version = "3.17.0"
+description = "Backport of pathlib-compatible object wrapper for zip files"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "zipp-3.17.0-py3-none-any.whl", hash = "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31"},
+    {file = "zipp-3.17.0.tar.gz", hash = "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0"},
+]
+
+[package.extras]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
+testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
+
+[extras]
+plots = ["matplotlib"]
+
+[metadata]
+lock-version = "2.0"
+python-versions = "^3.9"
+content-hash = "8043af104d30423894a6db97a68468e72fe0530b735247ca8d19b81292ece705"

pyproject.toml

@@ -1,11 +1,218 @@
+[tool.poetry]
+name = "unfccc-ghg-data"
+version = "0.1.0"
+description = "Reading country greenhouse gas data submitted to the United Nations Framework Convention on Climate Change (UNFCCC)in different submissions and formats and providing it in a standadized nc and csv format compatible with primap2. Data are read using different methods from APIs, xlsx and csv files as well as pdf files."
+authors = ["Johannes Gütschow <mail@johannes-guetschow.de>"]
+readme = "README.md"
+packages = [{include = "unfccc_ghg_data", from = "src"}]
+
+[tool.poetry.dependencies]
+python = "^3.9"
+matplotlib = { version = "^3.7.1", optional = true }
+doit = "^0.36.0"
+primap2 = "^0.9.8"
+pycountry = "^22.3.5"
+datalad = "^0.19.3"
+treelib = "^1.7.0"
+camelot-py = "^0.11.0"
+selenium = "^4.15.2"
+bs4 = "^0.0.1"
+requests = "^2.31.0"
+opencv-python = "^4.8.1.78"
+unfccc-di-api = "^4.0.0"
+
+[tool.poetry.extras]
+plots = ["matplotlib"]
+
+[tool.poetry.group.tests.dependencies]
+pytest = "^7.3.1"
+
+[tool.poetry.group.docs.dependencies]
+myst-nb = "^0.17.0"
+sphinx-rtd-theme = "^1.2.0"
+sphinx-autodoc-typehints = "^1.23.0"
+sphinx-autodocgen = "^1.3"
+jupytext = "^1.14.5"
+sphinx-copybutton = "^0.5.2"
+
+[tool.poetry.group.dev.dependencies]
+pytest-cov = "^4.0.0"
+coverage = "^7.2.0"
+black = "23.3.0"
+blackdoc = "0.3.8"
+mypy = "^1.2.0"
+ruff = "0.0.264"
+pre-commit = "^3.3.1"
+towncrier = "^23.6.0"
+liccheck = "^0.9.1"
+
 [build-system]
-requires = [
-    "setuptools>=42",
-    "wheel",
-    "setuptools_scm[toml]>=3.4"
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.coverage.run]
+source = ["src"]
+branch = true
+
+[tool.coverage.report]
+fail_under = 95
+skip_empty = true
+show_missing = true
+# Regexes for lines to exclude from consideration in addition to the defaults
+exclude_also = [
+    # Don't complain about missing type checking code:
+    "if TYPE_CHECKING",
 ]
-build-backend = "setuptools.build_meta"
 
-[tool.black]
-line-length = 88
+[tool.mypy]
+strict = true
+# prevent unimported libraries silently being treated as Any
+disallow_any_unimported = true
+# show error codes on failure with context
+show_error_codes = true
+show_error_context = true
+# warn if code can't be reached
+warn_unreachable = true
+# importing following uses default settings
+follow_imports = "normal"
 
+[tool.jupytext]
+formats = "ipynb,py:percent"
+
+[tool.pytest.ini_options]
+addopts = [
+    "--import-mode=importlib",
+]
+
+[tool.ruff]
+src = ["src"]
+target-version = "py39"
+select = [
+    "E",  # pycodestyle error
+    "W",  # pycodestyle warning
+    "F",  # pyflakes
+    "I",  # isort
+    "D",  # pydocstyle
+    "PL",  # pylint
+    "TRY",  # tryceratops
+    "NPY",  # numpy rules
+    "RUF",  # ruff specifics
+    "UP",  # pyupgrade
+    "S",  # flake8-bandit
+    # pandas support via pandas-vet. In some cases we will want to disable
+    # this because it can lead to too many false positives.
+    "PD",
+]
+unfixable = [
+    "PD002",  # Disable autofix for inplace as this often introduces bugs
+]
+ignore = [
+    "D200",  # One-line docstring should fit on one line with quotes
+    "D400",  # First line should end with a period
+]
+# Provide some leeway for long docstring, this is otherwise handled by black
+line-length = 110
+
+[tool.ruff.per-file-ignores]
+"test*.py" = [
+    "D",  # Documentation not needed in tests
+    "S101",  # S101 Use of `assert` detected
+    "PLR2004" # Magic value used in comparison
+]
+"docs/source/notebooks/*" = [
+    "D100",  # Missing docstring at the top of file
+    "E402",  # Module level import not at top of file
+    "S101",  # Use of `assert` detected
+]
+"scripts/*" = [
+    "S101" # S101 Use of `assert` detected
+]
+
+[tool.ruff.isort]
+known-first-party = ["src"]
+
+[tool.ruff.pydocstyle]
+convention = "numpy"
+
+[tool.towncrier]
+package = "unfccc-ghg-data"
+package_dir = "src"
+filename = "docs/source/changelog.md"
+directory = "changelog/"
+title_format = "## unfccc-ghg-data {version} ({project_date})"
+underlines = ["", "", ""]
+issue_format = "[#{issue}](https://github.com/JGuetschow/UNFCCC_non-AnnexI_data/pulls/{issue})"
+
+  [[tool.towncrier.type]]
+  directory = "breaking"
+  name = "Breaking Changes"
+  showcontent = true
+
+  [[tool.towncrier.type]]
+  directory = "deprecation"
+  name = "Deprecations"
+  showcontent = true
+
+  [[tool.towncrier.type]]
+  directory = "feature"
+  name = "Features"
+  showcontent = true
+
+  [[tool.towncrier.type]]
+  directory = "improvement"
+  name = "Improvements"
+  showcontent = true
+
+  [[tool.towncrier.type]]
+  directory = "fix"
+  name = "Bug Fixes"
+  showcontent = true
+
+  [[tool.towncrier.type]]
+  directory = "docs"
+  name = "Improved Documentation"
+  showcontent = true
+
+  [[tool.towncrier.type]]
+  directory = "trivial"
+  name = "Trivial/Internal Changes"
+  showcontent = false
+
+[tool.liccheck]
+authorized_licenses = [
+    "bsd",
+    "bsd license",
+    "BSD 3-Clause",
+    "CC0",
+    "apache",
+    "apache 2.0",
+    "apache software",
+    "apache software license",
+    "Apache License, Version 2.0",
+    "Historical Permission Notice and Disclaimer (HPND)",
+    "isc license",
+    "isc license (iscl)",
+    "gnu lgpl",
+    "lgpl with exceptions or zpl",
+    "LGPLv2+",
+    "GNU Lesser General Public License v2 (LGPLv2)",
+    "GNU Lesser General Public License v2 or later (LGPLv2+)",
+    "mit",
+    "mit license",
+    "Mozilla Public License 2.0 (MPL 2.0)",
+    "python software foundation",
+    "python software foundation license",
+    "zpl 2.1",
+]
+# This starting list is relatively conservative. Depending on the project, it
+# may make sense to move some of these into the authorized list
+unauthorized_licenses = [
+    "agpl",
+    "gnu agpl",
+    "gpl v3",
+    "gplv3",
+    "gpl v2",
+    "gplv2",
+    "gpl v1",
+    "gplv1",
+]

requirements.txt

@@ -1 +0,0 @@
-.

requirements_dev.txt

@@ -1 +0,0 @@
-.[dev]

scripts/test-install.py

@@ -0,0 +1,28 @@
+"""
+Test that all of our modules can be imported
+
+Also test that associated constants are set correctly
+
+Thanks https://stackoverflow.com/a/25562415/10473080
+"""
+import importlib
+import pkgutil
+
+import unfccc_ghg_data
+
+
+def import_submodules(package_name):
+    """
+    Test import of submodules
+    """
+    package = importlib.import_module(package_name)
+
+    for _, name, is_pkg in pkgutil.walk_packages(package.__path__):
+        full_name = package.__name__ + "." + name
+        importlib.import_module(full_name)
+        if is_pkg:
+            import_submodules(full_name)
+
+
+import_submodules("unfccc_ghg_data")
+print(unfccc_ghg_data.__version__)

setup.cfg

@@ -1,79 +0,0 @@
-[metadata]
-name = UNFCCC_GHG_data
-version = 0.2
-author = Johannes Gütschow
-author_email = mail@johannes-guetschow.de
-description = Tools to read GHG data submitted to the UNFCCC using various methods
-long_description = file: README.md
-long_description_content_type = text/md
-url = https://github.com/JGuetschow/UNFCCC_non-AnnexI_data
-#project_urls =
-classifiers =
-    Development Status :: 3 - Alpha
-    Intended Audience :: Science/Research
-    Topic :: Scientific/Engineering :: Atmospheric Science
-    License :: OSI Approved :: Apache Software License
-    Natural Language :: English
-    Programming Language :: Python :: 3
-    Programming Language :: Python :: 3.8
-    Programming Language :: Python :: 3.9
-    Programming Language :: Python :: 3.10
-license = Apache Software License 2.0
-license_file = LICENSE
-
-[options]
-packages =
-    UNFCCC_GHG_data
-    UNFCCC_GHG_data.UNFCCC_CRF_reader
-    UNFCCC_GHG_data.UNFCCC_CRF_reader.crf_specifications
-    UNFCCC_GHG_data.UNFCCC_reader
-    UNFCCC_GHG_data.UNFCCC_downloader
-    UNFCCC_GHG_data.UNFCCC_DI_reader
-    UNFCCC_GHG_data.helper
-#UNFCCC_GHG_data.datasets
-python_requires = >=3.8
-setup_requires =
-    setuptools_scm
-install_requires =
-    bs4
-    requests
-    pandas
-    selenium
-    primap2
-    countrynames
-    pycountry
-    datalad
-    treelib
-    camelot-py
-    opencv-python
-    ghostscript
-    unfccc_di_api >=4.0.0
-    dask
-
-[options.extras_require]
-dev =
-    pip
-    wheel
-    bs4
-    requests
-    pandas
-    selenium
-    primap2
-    countrynames
-    pycountry
-    datalad
-    treelib
-    camelot-py
-    opencv-python
-    ghostscript
-    ipykernel
-    jupyter
-    dask
-    ipympl
-    black
-
-
-[options.package_data]
-* =
-    *.csv
-    *.nc

setup.py

@@ -1,5 +0,0 @@
-#!/usr/bin/env python
-
-import setuptools
-
-setuptools.setup()

UNFCCC_GHG_data/__init__.py → src/unfccc_ghg_data/__init__.py

@@ -1,10 +1,6 @@
-####
+"""unfccc_ghg_data package"""
 
 from . import helper
-from . import UNFCCC_reader
-from . import UNFCCC_CRF_reader
-from . import UNFCCC_DI_reader
-from . import UNFCCC_downloader
 
 __all__ = [
     "helper",
@@ -12,4 +8,4 @@ __all__ = [
     "UNFCCC_CRF_reader",
     "UNFCCC_DI_reader",
     "UNFCCC_downloader"
-]
+]

src/unfccc_ghg_data/helper/__init__.py

@@ -0,0 +1,54 @@
+"""
+helper functions and definitions
+
+helper functions and definitions used by the different readers and downloader in
+the unfccc_ghg_data package
+"""
+
+from .definitions import (
+    GWP_factors,
+    code_path,
+    custom_country_mapping,
+    custom_folders,
+    dataset_path,
+    dataset_path_UNFCCC,
+    downloaded_data_path,
+    downloaded_data_path_UNFCCC,
+    extracted_data_path,
+    extracted_data_path_UNFCCC,
+    gas_baskets,
+    legacy_data_path,
+    log_path,
+    root_path,
+)
+from .functions import (
+    convert_categories,
+    create_folder_mapping,
+    fix_rows,
+    get_country_code,
+    get_country_name,
+    process_data_for_country,
+)
+
+__all__ = [
+    "root_path",
+    "code_path",
+    "log_path",
+    "extracted_data_path",
+    "extracted_data_path_UNFCCC",
+    "legacy_data_path",
+    "downloaded_data_path",
+    "downloaded_data_path_UNFCCC",
+    "dataset_path",
+    "dataset_path_UNFCCC",
+    "custom_country_mapping",
+    "custom_folders",
+    "GWP_factors",
+    "gas_baskets",
+    "get_country_code",
+    "get_country_name",
+    "convert_categories",
+    "create_folder_mapping",
+    "process_data_for_country",
+    "fix_rows",
+]

UNFCCC_GHG_data/helper/country_info.py → src/unfccc_ghg_data/helper/country_info.py

@@ -1,14 +1,18 @@
-# this script takes country as input (from doit) and
-# runs displays available submissions and datasets
+"""
+script to display information on country
+
+This script takes country as input (from doit) and displays available
+submissions and datasets both read and not read
+"""
 
 import argparse
-from UNFCCC_GHG_data.helper.functions import get_country_submissions
-from UNFCCC_GHG_data.helper.functions import get_country_datasets
+
+from unfccc_ghg_data.helper.functions import get_country_datasets, get_country_submissions
 
 # Find the right function and possible input and output files and
 # read the data using datalad run.
 parser = argparse.ArgumentParser()
-parser.add_argument('--country', help='Country name or UNFCCC_GHG_data')
+parser.add_argument('--country', help='Country name or code')
 args = parser.parse_args()
 country = args.country
 
@@ -19,4 +23,4 @@ print("")
 
 #print available datasets
 print("="*15 + " Available datasets " + "="*15)
-get_country_datasets(country, True)
+get_country_datasets(country, True)

UNFCCC_GHG_data/helper/definitions.py → src/unfccc_ghg_data/helper/definitions.py

@@ -1,18 +1,21 @@
+"""definitions like folders, mappings etc."""
+
 import os
 from pathlib import Path
 
 
 def get_root_path() -> Path:
-    """ get the root_path from an environment variable """
+    """Get the root_path from an environment variable"""
     root_path_env = os.getenv('UNFCCC_GHG_ROOT_PATH', None)
     if root_path_env is None:
-        raise ValueError('UNFCCC_GHG_ROOT_PATH environment variable needs to be set')
+        raise ValueError('UNFCCC_GHG_ROOT_PATH environment '
+                         'variable needs to be set') # noqa: TRY003
     else:
         root_path = Path(root_path_env).resolve()
     return root_path
 
 root_path = get_root_path()
-code_path = root_path / "UNFCCC_GHG_data"
+code_path = root_path / "unfccc_ghg_data"
 log_path = root_path / "log"
 extracted_data_path = root_path / "extracted_data"
 extracted_data_path_UNFCCC = extracted_data_path / "UNFCCC"
@@ -42,7 +45,7 @@ custom_folders = {
     'Bolivia_(Plurinational_State_of)': 'BOL',
     'Türkiye': 'TUR',
     'Iran_(Islamic_Republic_of)': 'IRN',
-    'Côte_d’Ivoire': 'CIV',
+    'Côte_d`Ivoire': 'CIV',
     'Democratic_Republic_of_the_Congo': "COD",
     'European_Union': 'EUA',
     'Taiwan': 'TWN',
@@ -154,4 +157,4 @@ gas_baskets = {
                             'PFCS (AR5GWP100)'],
     'KYOTOGHG (AR6GWP100)': ['CO2', 'CH4', 'N2O', 'SF6', 'NF3', 'HFCS (AR6GWP100)',
                             'PFCS (AR6GWP100)'],
-}
+}

UNFCCC_GHG_data/helper/folder_mapping.py → src/unfccc_ghg_data/helper/folder_mapping.py

@@ -1,9 +1,13 @@
-# this script takes a folder as input (from doit) and
-# runs creates the mapping of subfolders to country codes
-# oir that folder
+""" create mapping of folder to countries
+
+this script takes a folder as input (from doit) and
+runs creates the mapping of subfolders to country codes
+for that folder
+"""
 
 import argparse
-from UNFCCC_GHG_data.helper import create_folder_mapping
+
+from unfccc_ghg_data.helper import create_folder_mapping
 
 # Find the right function and possible input and output files and
 # read the data using datalad run.

UNFCCC_GHG_data/helper/functions.py → src/unfccc_ghg_data/helper/functions.py

@@ -1,30 +1,42 @@
-import copy
+""" common functions for unfccc_ghg_data
 
-import pycountry
+Functions used by the different readers and downloaders in the unfccc_ghg_data package
+"""
+
+import copy
 import json
 import re
-import xarray as xr
-import pandas as pd
-import numpy as np
-from datetime import date
 from copy import deepcopy
-from typing import Dict, List, Optional
+from datetime import date
 from pathlib import Path
-from .definitions import custom_country_mapping, custom_folders
-from .definitions import root_path, downloaded_data_path, extracted_data_path
-from .definitions import legacy_data_path, code_path
-from .definitions import GWP_factors
+from typing import Optional
+
+import numpy as np
+import pandas as pd
+import pycountry
+import xarray as xr
+
+from .definitions import (
+    GWP_factors,
+    code_path,
+    custom_country_mapping,
+    custom_folders,
+    downloaded_data_path,
+    extracted_data_path,
+    legacy_data_path,
+    root_path,
+)
 
 
 def process_data_for_country(
     data_country: xr.Dataset,
-    entities_to_ignore: List[str],
-    gas_baskets: Dict[str, List[str]],
-    filter_dims: Optional[Dict[str, List[str]]] = None,
+    entities_to_ignore: list[str],
+    gas_baskets: dict[str, list[str]],
+    filter_dims: Optional[dict[str, list[str]]] = None,
     cat_terminology_out: Optional[str] = None,
-    category_conversion: Dict[str, Dict] = None,
-    sectors_out: List[str] = None,
-    processing_info_country: Dict = None,
+    category_conversion: dict[str, dict] = None,
+    sectors_out: list[str] = None,
+    processing_info_country: dict = None,
 ) -> xr.Dataset:
     """
     Process data from DI interface (where necessary).
@@ -32,8 +44,38 @@ def process_data_for_country(
     * country specific sector aggregation
     * Conversion to IPCC2006 categories
     * general sector and gas basket aggregation (in new categories)
+
+    Parameters
+    ----------
+    data_country: xr.Dataset
+        data to process
+    entities_to_ignore: list[str]
+        Which entities should be ignored. They will not be in the returned dataset
+    gas_baskets: dict[str, list[str]
+        Gas baskets to create. Each entry consists of the basket as key and a list of
+        gases that make up the basket as value
+    filter_dims: Optional[dict[str, list[str]]] = None
+        filter data before processing. Filter is in the format taken by PRIMAP2's
+        ds.pr.loc[] functionality
+    cat_terminology_out: Optional[str] = None
+        Category terminology for the output dataset
+    category_conversion: dict[str, dict] = None
+        Definition of category conversion. The dict has two possible fields:
+        * "conversion" where the value is a dict[str, str] with 1 to 1 category code
+        mapping (key is category from and value is category to)
+        * "aggregation" TODO
+    sectors_out: list[str] = None
+        Categories to return
+    processing_info_country
+        more detailed processing info TODO: explain format
+
+    Returns
+    -------
+    xr.Dataset: processed dataset
+
     """
 
+
     # 0: gather information
     countries = list(data_country.coords[data_country.attrs["area"]].values)
     if len(countries) > 1:
@@ -79,7 +121,7 @@ def process_data_for_country(
     # remove unused cats
     data_country = data_country.dropna(f"category ({cat_terminology_in})", how="all")
     # remove unused years
-    data_country = data_country.dropna(f"time", how="all")
+    data_country = data_country.dropna("time", how="all")
     # remove variables only containing nan
     nan_vars_country = [
         var
@@ -367,7 +409,7 @@ def process_data_for_country(
 
 def convert_categories(
     ds_input: xr.Dataset,
-    conversion: Dict[str, Dict[str, str]],
+    conversion: dict[str, dict[str, str]],
     # terminology_from: str,
     terminology_to: str,
     debug: bool = False,
@@ -431,7 +473,7 @@ def convert_categories(
             nan_vars = [
                 var
                 for var in data_agg.data_vars
-                if data_agg[var].isnull().all().data == True
+                if data_agg[var].isnull().all().data is True
             ]
             data_agg = data_agg.drop(nan_vars)
             if len(data_agg.data_vars) > 0:
@@ -464,7 +506,7 @@ def convert_categories(
 def get_country_name(
     country_code: str,
 ) -> str:
-    """get country name from code"""
+    """Get country name from code"""
     if country_code in custom_country_mapping:
         country_name = custom_country_mapping[country_code]
     else:
@@ -488,6 +530,7 @@ def get_country_code(
     is not a three letter code a search will be performed
 
     Parameters
+    ----------
     __________
     country_name: str
         Country code or name to get the three-letter code for.
@@ -502,7 +545,7 @@ def get_country_code(
         country_code = country_name
     else:
         try:
-            # check if it's a 3 letter UNFCCC_GHG_data
+            # check if it's a 3 letter code
             country = pycountry.countries.get(alpha_3=country_name)
             country_code = country.alpha_3
         except:
@@ -513,7 +556,7 @@ def get_country_code(
             except:
                 raise ValueError(
                     f"Country name {country_name} can not be mapped to "
-                    f"any country UNFCCC_GHG_data. Try using the ISO3 UNFCCC_GHG_data directly."
+                    f"any country code. Try using the ISO3 code directly."
                 )
             if len(country) > 1:
                 country_code = None
@@ -552,7 +595,6 @@ def create_folder_mapping(folder: str, extracted: bool = False) -> None:
         Nothing
 
     """
-
     folder = root_path / folder
     folder_mapping = {}
     # if not extracted:
@@ -595,16 +637,16 @@ def create_folder_mapping(folder: str, extracted: bool = False) -> None:
 def get_country_submissions(
     country_name: str,
     print_sub: bool = True,
-) -> Dict[str, List[str]]:
+) -> dict[str, list[str]]:
     """
-    Input is a three letter ISO UNFCCC_GHG_data for a country, or the countries name.
-    The function tries to map the country name to an ISO UNFCCC_GHG_data and then
+    Input is a three letter ISO code for a country, or the countries name.
+    The function tries to map the country name to an ISO code and then
     queries the folder mapping files for folders.
 
     Parameters
     ----------
         country_name: str
-            String containing the country name or ISO 3 letter UNFCCC_GHG_data
+            String containing the country name or ISO 3 letter code
 
         print_sub: bool
             If True information on submissions will be written to stdout
@@ -615,7 +657,6 @@ def get_country_submissions(
         Each value is a list of folders
 
     """
-
     data_folder = downloaded_data_path
 
     country_code = get_country_code(country_name)
@@ -625,7 +666,7 @@ def get_country_submissions(
 
     country_submissions = {}
     if print_sub:
-        print(f"#" * 80)
+        print("#" * 80)
         print(f"The following submissions are available for {country_name}")
     for item in data_folder.iterdir():
         if item.is_dir():
@@ -634,7 +675,7 @@ def get_country_submissions(
                 print("-" * 80)
                 print(f"Data folder {item.name}")
                 print("-" * 80)
-            with open(item / "folder_mapping.json", "r") as mapping_file:
+            with open(item / "folder_mapping.json") as mapping_file:
                 folder_mapping = json.load(mapping_file)
             if country_code in folder_mapping:
                 country_folders = folder_mapping[country_code]
@@ -664,11 +705,11 @@ def get_country_submissions(
 def get_country_datasets(
     country_name: str,
     print_ds: bool = True,
-) -> Dict[str, List[str]]:
+) -> dict[str, list[str]]:
     """
     Input is a three letter ISO code for a country, or the country's name.
-    The function tries to map the country name to an ISO UNFCCC_GHG_data and then
-    checks the UNFCCC_GHG_data and data folders for content on the country.
+    The function tries to map the country name to an ISO code and then
+    checks the code and data folders for content on the country.
 
     Parameters
     ----------
@@ -684,11 +725,10 @@ def get_country_datasets(
         Each value is a list of folders
 
     """
-
     data_folder = extracted_data_path
     data_folder_legacy = legacy_data_path
 
-    # obtain country UNFCCC_GHG_data
+    # obtain country code
     country_code = get_country_code(country_name)
 
     if print_ds:
@@ -697,7 +737,7 @@ def get_country_datasets(
     rep_data = {}
     # data
     if print_ds:
-        print(f"#" * 80)
+        print("#" * 80)
         print(f"The following datasets are available for {country_name}")
     for item in data_folder.iterdir():
         if item.is_dir():
@@ -706,7 +746,7 @@ def get_country_datasets(
                 print("-" * 80)
                 print(f"Data folder {item.name}")
                 print("-" * 80)
-            with open(item / "folder_mapping.json", "r") as mapping_file:
+            with open(item / "folder_mapping.json") as mapping_file:
                 folder_mapping = json.load(mapping_file)
             if country_code not in folder_mapping:
                 if print_ds:
@@ -757,7 +797,7 @@ def get_country_datasets(
                         if code_file:
                             data_info = data_info + f"code: {code_file.name}"
                         else:
-                            data_info = data_info + f"code: not found"
+                            data_info = data_info + "code: not found"
 
                         cleaned_datasets_current_folder[key] = data_info
 
@@ -775,7 +815,7 @@ def get_country_datasets(
 
     # legacy data
     if print_ds:
-        print(f"#" * 80)
+        print("#" * 80)
         print(f"The following legacy datasets are available for {country_name}")
     legacy_data = {}
     for item in data_folder_legacy.iterdir():
@@ -785,7 +825,7 @@ def get_country_datasets(
                 print("-" * 80)
                 print(f"Data folder {item.name}")
                 print("-" * 80)
-            with open(item / "folder_mapping.json", "r") as mapping_file:
+            with open(item / "folder_mapping.json") as mapping_file:
                 folder_mapping = json.load(mapping_file)
             if country_code not in folder_mapping:
                 if print_ds:
@@ -815,7 +855,7 @@ def get_country_datasets(
                     parts = dataset.split("_")
                     if parts[0] != country_code:
                         cleaned_datasets_current_folder[
-                            f"Wrong UNFCCC_GHG_data: {parts[0]}"
+                            f"Wrong code: {parts[0]}"
                         ] = dataset
                     else:
                         terminology = "_".join(parts[3:])
@@ -865,42 +905,41 @@ def get_code_file(
     Parameters
     ----------
         country_name: str
-            String containing the country name or ISO 3 letter UNFCCC_GHG_data
+            String containing the country name or ISO 3 letter code
 
         submission: str
             String of the submission
 
         print_info: bool = False
-            If True print information on UNFCCC_GHG_data found
+            If True print information on code found
 
     Returns
     -------
-        returns a pathlib Path object for the UNFCCC_GHG_data file
+        returns a pathlib Path object for the code file
     """
-
     code_file_path = None
-    UNFCCC_reader_path = code_path / "UNFCCC_reader"
+    UNFCCC_reader_path = code_path / "unfccc_reader"
 
-    # CRF is an exception as it's read using the UNFCCC_CRF_reader module
+    # CRF is an exception as it's read using the unfccc_crf_reader module
     # so we return the path to that.
     if submission[0:3] == "CRF":
-        return root_path / "UNFCCC_CRF_reader"
+        return root_path / "unfccc_crf_reader"
 
     if submission[0:2] == "DI":
-        return root_path / "UNFCCC_DI_reader"
+        return root_path / "unfccc_di_reader"
 
-    # obtain country UNFCCC_GHG_data
+    # obtain country code
     country_code = get_country_code(country_name)
 
     if print_info:
-        print(f"Country name {country_name} maps to ISO UNFCCC_GHG_data {country_code}")
+        print(f"Country name {country_name} maps to ISO code {country_code}")
 
-    with open(UNFCCC_reader_path / "folder_mapping.json", "r") as mapping_file:
+    with open(UNFCCC_reader_path / "folder_mapping.json") as mapping_file:
         folder_mapping = json.load(mapping_file)
 
     if country_code not in folder_mapping:
         if print_info:
-            print("No UNFCCC_GHG_data available")
+            print("No code available")
             print("")
     else:
         country_folder = UNFCCC_reader_path / folder_mapping[country_code]
@@ -910,7 +949,7 @@ def get_code_file(
             if file.match(code_file_name_candidate):
                 if code_file_path is not None:
                     raise ValueError(
-                        f"Found multiple UNFCCC_GHG_data candidates: "
+                        f"Found multiple code candidates: "
                         f"{code_file_path} and file.name. "
                         f"Please use only one file with name "
                         f"'read_ISO3_submission_XXX.YYY'."
@@ -918,7 +957,7 @@ def get_code_file(
                 else:
                     if print_info:
                         print(
-                            f"Found UNFCCC_GHG_data file {file.relative_to(root_path)}"
+                            f"Found code file {file.relative_to(root_path)}"
                         )
                 code_file_path = file
 
@@ -972,7 +1011,8 @@ def fix_rows(
         new_row = new_row.str.replace("- ", "-")
         # replace spaces in numbers
         pat = r"^(?P<first>[0-9\.,]*)\s(?P<last>[0-9\.,]*)$"
-        repl = lambda m: f"{m.group('first')}{m.group('last')}"
+        def repl(m):
+            return f"{m.group('first')}{m.group('last')}"
         new_row = new_row.str.replace(pat, repl, regex=True)
         data.loc[indices_to_merge[0]] = new_row
         data = data.drop(indices_to_merge[1:])

UNFCCC_GHG_data/UNFCCC_CRF_reader/__init__.py → src/unfccc_ghg_data/unfccc_crf_reader/__init__.py

@@ -4,7 +4,7 @@ CRF reader module
 
 #from pathlib import Path
 from . import crf_specifications
-from .UNFCCC_CRF_reader_prod import read_crf_for_country, read_crf_for_country_datalad
+from .unfccc_crf_reader_prod import read_crf_for_country, read_crf_for_country_datalad
 
 __all__ = ["crf_specifications",
            "read_crf_for_country",

UNFCCC_GHG_data/UNFCCC_CRF_reader/CRF_raw_for_year.py → src/unfccc_ghg_data/unfccc_crf_reader/crf_raw_for_year.py

@@ -9,14 +9,17 @@ submission are available in the downloaded data folder.
 # TODO: integrate into doit
 
 import argparse
-import primap2 as pm2
-from pathlib import Path
 from datetime import date
-from UNFCCC_GHG_data.helper import dataset_path_UNFCCC
+from pathlib import Path
+
+import primap2 as pm2
 
-from UNFCCC_GHG_data.UNFCCC_CRF_reader.util import all_crf_countries
-from UNFCCC_GHG_data.UNFCCC_CRF_reader.UNFCCC_CRF_reader_prod import get_input_and_output_files_for_country
-from UNFCCC_GHG_data.UNFCCC_CRF_reader.UNFCCC_CRF_reader_prod import submission_has_been_read
+from unfccc_ghg_data.helper import dataset_path_UNFCCC
+from unfccc_ghg_data.unfccc_crf_reader.unfccc_crf_reader_prod import (
+    get_input_and_output_files_for_country,
+    submission_has_been_read,
+)
+from unfccc_ghg_data.unfccc_crf_reader.util import all_crf_countries
 
 parser = argparse.ArgumentParser()
 parser.add_argument('--submission_year', help='Submission round to read', type=int)
@@ -89,4 +92,4 @@ ds_all_CRF.pr.to_netcdf(output_folder / (output_filename + ".nc"),
 # show info
 print(f"The following countries are included in the dataset: {included_countries}")
 print(f"The following countries have updated submission not yet read "
-      f"and not included in the dataset: {outdated_countries}")
+      f"and not included in the dataset: {outdated_countries}")

src/unfccc_ghg_data/unfccc_crf_reader/crf_specifications/__init__.py

@@ -0,0 +1,10 @@
+"""
+Define the CRF specifications here for easy access
+"""
+
+from .crf2021_specification import CRF2021
+from .crf2022_specification import CRF2022
+from .crf2023_aus_specification import CRF2023_AUS
+from .crf2023_specification import CRF2023
+
+__all__ = ["CRF2021", "CRF2022", "CRF2023", "CRF2023_AUS"]

UNFCCC_GHG_data/UNFCCC_CRF_reader/crf_specifications/CRF2021_specification.py → src/unfccc_ghg_data/unfccc_crf_reader/crf_specifications/crf2021_specification.py

@@ -1,4 +1,4 @@
-""" CRF2021 specification.
+"""CRF2021 specification.
 Currently not all tables are included. Extend if you need all country
 specific items in categories 2, 3.H-G, 4
 
@@ -39,6 +39,7 @@ TODO:
 """
 
 import numpy as np
+
 from .util import unit_info
 
 CRF2021 = {
@@ -117,7 +118,7 @@ CRF2021 = {
             ['1. Transport of CO2', ['1.C.1']],
             ['2. Injection and storage', ['1.C.2']],
             ['3. Other', ['1.C.3']],
-            ['Memo items: (1)', ['\IGNORE']],
+            ['Memo items: (1)', ['\\IGNORE']],
             ['International bunkers', ['M.Memo.Int']],
             ['Aviation', ['M.Memo.Int.Avi']],
             ['Navigation', ['M.Memo.Int.Mar']],
@@ -450,8 +451,8 @@ CRF2021 = {
             # 1.A.2.g.viii Other (please specify)
             ['1.A.2.g.viii Other (please specify)', ['1.A.2.g.viii', 'Total'], 2],
             # DKE
-            ['Construction', ['\IGNORE', '\IGNORE'], 3],  # (empty)
-            ['Mining', ['\IGNORE', '\IGNORE'], 3],  # (empty)
+            ['Construction', ['\\IGNORE', '\\IGNORE'], 3],  # (empty)
+            ['Mining', ['\\IGNORE', '\\IGNORE'], 3],  # (empty)
             # DNK, DKE, USA, CZE
             ['Other non-specified', ['1.A.2.g.viii.1', 'Total'], 3],
             ['Liquid Fuels', ['1.A.2.g.viii.1', 'Liquid'], 4],
@@ -501,7 +502,7 @@ CRF2021 = {
             ['Peat', ['1.A.2.g.viii.1', 'Peat'], 4],
             ['Biomass', ['1.A.2.g.viii.1', 'Biomass'], 4],
             # DKE
-            ['Textile', ['\IGNORE', '\IGNORE'], 3],  # (empty)
+            ['Textile', ['\\IGNORE', '\\IGNORE'], 3],  # (empty)
             # DNK, DNM, FIN, DKE
             ['Other manufacturing industries', ['1.A.2.g.viii.3', 'Total'], 3],
             ['Liquid Fuels', ['1.A.2.g.viii.3', 'Liquid'], 4],
@@ -1390,10 +1391,10 @@ CRF2021 = {
             ['Biomass', ['1.A.5.b.iii', 'Biomass'], 3],
             # ESP, FIN
             # Information Item
-            ['Information item:(15)', ['\IGNORE', '\IGNORE'], 0],
-            ['Waste incineration with energy recovery included as:', ['\IGNORE', '\IGNORE'], 1],
-            ['Biomass(6)', ['\IGNORE', '\IGNORE'], 1],
-            ['Fossil fuels(4)', ['\IGNORE', '\IGNORE'], 1],
+            ['Information item:(15)', ['\\IGNORE', '\\IGNORE'], 0],
+            ['Waste incineration with energy recovery included as:', ['\\IGNORE', '\\IGNORE'], 1],
+            ['Biomass(6)', ['\\IGNORE', '\\IGNORE'], 1],
+            ['Fossil fuels(4)', ['\\IGNORE', '\\IGNORE'], 1],
         ],
         "entity_mapping": {
             'EMISSIONS CH4': "CH4",
@@ -1537,7 +1538,7 @@ CRF2021 = {
             ['a. Injection', ['1.C.2.a']],
             ['b. Storage', ['1.C.2.b']],
             ['3. Other', ['1.C.3']],
-            ['Information item(4, 5)', ['\IGNORE']],
+            ['Information item(4, 5)', ['\\IGNORE']],
             ['Total amount captured for storage', ['M.Info.A.TACS']],
             ['Total amount of imports for storage', ['M.Info.A.TAIS']],
             ['Total A', ['M.Info.A']],
@@ -1545,7 +1546,7 @@ CRF2021 = {
             ['Total amount of CO2 injected at storage sites', ['M.Info.B.TAI']],
             ['Total leakage from transport, injection and storage', ['M.Info.B.TLTIS']],
             ['Total B', ['M.Info.B']],
-            ['Difference (A-B)(6)', ['\IGNORE']],
+            ['Difference (A-B)(6)', ['\\IGNORE']],
         ],
         "entity_mapping": {
             'EMISSIONS CO2(2)': 'CO2',
@@ -1804,61 +1805,61 @@ CRF2021 = {
             # A. Enteric fermentation
             ['A. Enteric fermentation', ['3.A'], 2],
             ['1. Cattle(1)', ['3.A.1'], 3],
-            ['Option A:', ['\IGNORE'], 4],
+            ['Option A:', ['\\IGNORE'], 4],
             ['Dairy cattle', ['3.A.1.Aa'], 5],
             ['Non-dairy cattle', ['3.A.1.Ab'], 5],
-            ['Option B:', ['\IGNORE'], 4],
+            ['Option B:', ['\\IGNORE'], 4],
             ['Mature dairy cattle', ['3.A.1.Ba'], 5],
             ['Other mature cattle', ['3.A.1.Bb'], 5],
             ['Growing cattle', ['3.A.1.Bc'], 5],
-            ['Option C (country-specific):', ['\IGNORE'], 4],
+            ['Option C (country-specific):', ['\\IGNORE'], 4],
             # all countries not specified explcitly
-            ['\C!-AUS-MLT-LUX-POL-SVN-USA\ Other (as specified in table 3(I).A)', ['3.A.1.C'], 5],
+            ['\\C!-AUS-MLT-LUX-POL-SVN-USA\\ Other (as specified in table 3(I).A)', ['3.A.1.C'], 5],
             # Australia
-            ['\C-AUS\ Other (as specified in table 3(I).A)', ['3.A.1.C'], 5],
-            ['\C-AUS\ Dairy Cattle', ['3.A.1.C-AUS-a'], 6],
-            ['\C-AUS\ Beef Cattle - Pasture', ['3.A.1.C-AUS-b'], 6],
-            ['\C-AUS\ Beef Cattle - Feedlot', ['3.A.1.C-AUS-c'], 6],
+            ['\\C-AUS\\ Other (as specified in table 3(I).A)', ['3.A.1.C'], 5],
+            ['\\C-AUS\\ Dairy Cattle', ['3.A.1.C-AUS-a'], 6],
+            ['\\C-AUS\\ Beef Cattle - Pasture', ['3.A.1.C-AUS-b'], 6],
+            ['\\C-AUS\\ Beef Cattle - Feedlot', ['3.A.1.C-AUS-c'], 6],
             # malta
-            ['\C-MLT\ Other (as specified in table 3(I).A)', ['3.A.1.C'], 5],
-            ['\C-MLT\ dairy cows', ['3.A.1.C-MLT-a'], 6],
-            ['\C-MLT\ non-lactating cows', ['3.A.1.C-MLT-b'], 6],
-            ['\C-MLT\ bulls', ['3.A.1.C-MLT-c'], 6],
-            ['\C-MLT\ calves', ['3.A.1.C-MLT-d'], 6],
-            ['\C-MLT\ growing cattle 1-2 years', ['3.A.1.C-MLT-e'], 6],
+            ['\\C-MLT\\ Other (as specified in table 3(I).A)', ['3.A.1.C'], 5],
+            ['\\C-MLT\\ dairy cows', ['3.A.1.C-MLT-a'], 6],
+            ['\\C-MLT\\ non-lactating cows', ['3.A.1.C-MLT-b'], 6],
+            ['\\C-MLT\\ bulls', ['3.A.1.C-MLT-c'], 6],
+            ['\\C-MLT\\ calves', ['3.A.1.C-MLT-d'], 6],
+            ['\\C-MLT\\ growing cattle 1-2 years', ['3.A.1.C-MLT-e'], 6],
             # Luxembourg
-            ['\C-LUX\ Other (as specified in table 3(I).A)', ['3.A.1.C'], 5],
-            ['\C-LUX\ Bulls', ['3.A.1.C-LUX-a'], 6],
-            ['\C-LUX\ Calves', ['3.A.1.C-LUX-b'], 6],
-            ['\C-LUX\ Young Cattle', ['3.A.1.C-LUX-c'], 6],
-            ['\C-LUX\ Suckler Cows', ['3.A.1.C-LUX-d'], 6],
-            ['\C-LUX\ Bulls under 2 years', ['3.A.1.C-LUX-e'], 6],
-            ['\C-LUX\ Dairy Cows', ['3.A.1.C-LUX-f'], 6],
+            ['\\C-LUX\\ Other (as specified in table 3(I).A)', ['3.A.1.C'], 5],
+            ['\\C-LUX\\ Bulls', ['3.A.1.C-LUX-a'], 6],
+            ['\\C-LUX\\ Calves', ['3.A.1.C-LUX-b'], 6],
+            ['\\C-LUX\\ Young Cattle', ['3.A.1.C-LUX-c'], 6],
+            ['\\C-LUX\\ Suckler Cows', ['3.A.1.C-LUX-d'], 6],
+            ['\\C-LUX\\ Bulls under 2 years', ['3.A.1.C-LUX-e'], 6],
+            ['\\C-LUX\\ Dairy Cows', ['3.A.1.C-LUX-f'], 6],
             # Poland
-            ['\C-POL\ Other (as specified in table 3(I).A)', ['3.A.1.C'], 5],
-            ['\C-POL\ Bulls (older than 2 years)', ['3.A.1.C-POL-a'], 6],
-            ['\C-POL\ Non-dairy Heifers (older than 2 years)', ['3.A.1.C-POL-b'], 6],
-            ['\C-POL\ Non-dairy Young Cattle (younger than 1 year)', ['3.A.1.C-POL-c'], 6],
-            ['\C-POL\ Dairy Cattle', ['3.A.1.C-POL-d'], 6],
-            ['\C-POL\ Non-dairy Young Cattle (1-2 years)', ['3.A.1.C-POL-e'], 6],
+            ['\\C-POL\\ Other (as specified in table 3(I).A)', ['3.A.1.C'], 5],
+            ['\\C-POL\\ Bulls (older than 2 years)', ['3.A.1.C-POL-a'], 6],
+            ['\\C-POL\\ Non-dairy Heifers (older than 2 years)', ['3.A.1.C-POL-b'], 6],
+            ['\\C-POL\\ Non-dairy Young Cattle (younger than 1 year)', ['3.A.1.C-POL-c'], 6],
+            ['\\C-POL\\ Dairy Cattle', ['3.A.1.C-POL-d'], 6],
+            ['\\C-POL\\ Non-dairy Young Cattle (1-2 years)', ['3.A.1.C-POL-e'], 6],
             # Slovenia
-            ['\C-SVN\ Other (as specified in table 3(I).A)', ['3.A.1.C'], 5],
-            ['\C-SVN\ Dairy cows', ['3.A.1.C-SVN-a'], 6],
-            ['\C-SVN\ Non-dairy cattle', ['3.A.1.C-SVN-b'], 6],
-            ['\C-SVN\ Other cows', ['3.A.1.C-SVN-c'], 6],
+            ['\\C-SVN\\ Other (as specified in table 3(I).A)', ['3.A.1.C'], 5],
+            ['\\C-SVN\\ Dairy cows', ['3.A.1.C-SVN-a'], 6],
+            ['\\C-SVN\\ Non-dairy cattle', ['3.A.1.C-SVN-b'], 6],
+            ['\\C-SVN\\ Other cows', ['3.A.1.C-SVN-c'], 6],
             # USA
-            ['\C-USA\ Other (as specified in table 3(I).A)', ['3.A.1.C'], 5],
-            ['\C-USA\ Steer Stocker', ['3.A.1.C-USA-a'], 6],
-            ['\C-USA\ Heifer Stocker', ['3.A.1.C-USA-b'], 6],
-            ['\C-USA\ Beef Cows', ['3.A.1.C-USA-c'], 6],
-            ['\C-USA\ Dairy Replacements', ['3.A.1.C-USA-d'], 6],
-            ['\C-USA\ Beef Replacements', ['3.A.1.C-USA-e'], 6],
-            ['\C-USA\ Steer Feedlot', ['3.A.1.C-USA-f'], 6],
-            ['\C-USA\ Heifer Feedlot', ['3.A.1.C-USA-g'], 6],
-            ['\C-USA\ Bulls', ['3.A.1.C-USA-h'], 6],
-            ['\C-USA\ Dairy Cows', ['3.A.1.C-USA-i'], 6],
-            ['\C-USA\ Beef Calves', ['3.A.1.C-USA-j'], 6],
-            ['\C-USA\ Dairy Calves', ['3.A.1.C-USA-k'], 6],
+            ['\\C-USA\\ Other (as specified in table 3(I).A)', ['3.A.1.C'], 5],
+            ['\\C-USA\\ Steer Stocker', ['3.A.1.C-USA-a'], 6],
+            ['\\C-USA\\ Heifer Stocker', ['3.A.1.C-USA-b'], 6],
+            ['\\C-USA\\ Beef Cows', ['3.A.1.C-USA-c'], 6],
+            ['\\C-USA\\ Dairy Replacements', ['3.A.1.C-USA-d'], 6],
+            ['\\C-USA\\ Beef Replacements', ['3.A.1.C-USA-e'], 6],
+            ['\\C-USA\\ Steer Feedlot', ['3.A.1.C-USA-f'], 6],
+            ['\\C-USA\\ Heifer Feedlot', ['3.A.1.C-USA-g'], 6],
+            ['\\C-USA\\ Bulls', ['3.A.1.C-USA-h'], 6],
+            ['\\C-USA\\ Dairy Cows', ['3.A.1.C-USA-i'], 6],
+            ['\\C-USA\\ Beef Calves', ['3.A.1.C-USA-j'], 6],
+            ['\\C-USA\\ Dairy Calves', ['3.A.1.C-USA-k'], 6],
             # Other livestock
             ['2. Sheep', ['3.A.2'], 3],
             ['3. Swine', ['3.A.3'], 3],
@@ -1879,60 +1880,60 @@ CRF2021 = {
             # Manure Management
             ['B. Manure management', ['3.B'], 2],
             ['1. Cattle(1)', ['3.B.1'], 3],
-            ['Option A:', ['\IGNORE'], 4],
+            ['Option A:', ['\\IGNORE'], 4],
             ['Dairy cattle', ['3.B.1.Aa'], 5],
             ['Non-dairy cattle', ['3.B.1.Ab'], 5],
-            ['Option B:', ['\IGNORE'], 4],
+            ['Option B:', ['\\IGNORE'], 4],
             ['Mature dairy cattle', ['3.B.1.Ba'], 5],
             ['Other mature cattle', ['3.B.1.Bb'], 5],
             ['Growing cattle', ['3.B.1.Bc'], 5],
-            ['Option C (country-specific):', ['\IGNORE'], 4],
+            ['Option C (country-specific):', ['\\IGNORE'], 4],
             # all countries not specified explicitly
-            ['\C!-AUS-MLT-LUX-POL-SVN-USA\ Other (as specified in table 3(I).B)', ['3.B.1.C'], 5],
+            ['\\C!-AUS-MLT-LUX-POL-SVN-USA\\ Other (as specified in table 3(I).B)', ['3.B.1.C'], 5],
             # Australia
-            ['\C-AUS\ Other (as specified in table 3(I).B)', ['3.B.1.C'], 5],
-            ['\C-AUS\ Dairy Cattle', ['3.B.1.C-AUS-a'], 6],
-            ['\C-AUS\ Beef Cattle - Pasture', ['3.B.1.C-AUS-b'], 6],
-            ['\C-AUS\ Beef Cattle - Feedlot', ['3.B.1.C-AUS-c'], 6],
+            ['\\C-AUS\\ Other (as specified in table 3(I).B)', ['3.B.1.C'], 5],
+            ['\\C-AUS\\ Dairy Cattle', ['3.B.1.C-AUS-a'], 6],
+            ['\\C-AUS\\ Beef Cattle - Pasture', ['3.B.1.C-AUS-b'], 6],
+            ['\\C-AUS\\ Beef Cattle - Feedlot', ['3.B.1.C-AUS-c'], 6],
             # Malta
-            ['\C-MLT\ Other (as specified in table 3(I).B)', ['3.B.1.C'], 5],
-            ['\C-MLT\ dairy cows', ['3.B.1.C-MLT-a'], 6],
-            ['\C-MLT\ non-lactating cows', ['3.B.1.C-MLT-b'], 6],
-            ['\C-MLT\ bulls', ['3.B.1.C-MLT-c'], 6],
-            ['\C-MLT\ calves', ['3.B.1.C-MLT-d'], 6],
-            ['\C-MLT\ growing cattle 1-2 years', ['3.B.1.C-MLT-e'], 6],
+            ['\\C-MLT\\ Other (as specified in table 3(I).B)', ['3.B.1.C'], 5],
+            ['\\C-MLT\\ dairy cows', ['3.B.1.C-MLT-a'], 6],
+            ['\\C-MLT\\ non-lactating cows', ['3.B.1.C-MLT-b'], 6],
+            ['\\C-MLT\\ bulls', ['3.B.1.C-MLT-c'], 6],
+            ['\\C-MLT\\ calves', ['3.B.1.C-MLT-d'], 6],
+            ['\\C-MLT\\ growing cattle 1-2 years', ['3.B.1.C-MLT-e'], 6],
             # Luxembourg
-            ['\C-LUX\ Other (as specified in table 3(I).B)', ['3.B.1.C'], 5],
-            ['\C-LUX\ Bulls', ['3.B.1.C-LUX-a'], 6],
-            ['\C-LUX\ Calves', ['3.B.1.C-LUX-b'], 6],
-            ['\C-LUX\ Young Cattle', ['3.B.1.C-LUX-c'], 6],
-            ['\C-LUX\ Suckler Cows', ['3.B.1.C-LUX-d'], 6],
-            ['\C-LUX\ Bulls under 2 years', ['3.B.1.C-LUX-e'], 6],
-            ['\C-LUX\ Dairy Cows', ['3.B.1.C-LUX-f'], 6],
+            ['\\C-LUX\\ Other (as specified in table 3(I).B)', ['3.B.1.C'], 5],
+            ['\\C-LUX\\ Bulls', ['3.B.1.C-LUX-a'], 6],
+            ['\\C-LUX\\ Calves', ['3.B.1.C-LUX-b'], 6],
+            ['\\C-LUX\\ Young Cattle', ['3.B.1.C-LUX-c'], 6],
+            ['\\C-LUX\\ Suckler Cows', ['3.B.1.C-LUX-d'], 6],
+            ['\\C-LUX\\ Bulls under 2 years', ['3.B.1.C-LUX-e'], 6],
+            ['\\C-LUX\\ Dairy Cows', ['3.B.1.C-LUX-f'], 6],
             # Poland
-            ['\C-POL\ Other (as specified in table 3(I).B)', ['3.B.1.C'], 5],
-            ['\C-POL\ Non-dairy Cattle', ['3.B.1.C-POL-a'], 6],
-            ['\C-POL\ Dairy Cattle', ['3.B.1.C-POL-b'], 6],
+            ['\\C-POL\\ Other (as specified in table 3(I).B)', ['3.B.1.C'], 5],
+            ['\\C-POL\\ Non-dairy Cattle', ['3.B.1.C-POL-a'], 6],
+            ['\\C-POL\\ Dairy Cattle', ['3.B.1.C-POL-b'], 6],
             # Slovenia
-            ['\C-SVN\ Other (as specified in table 3(I).B)', ['3.B.1.C'], 5],
-            ['\C-SVN\ Dairy cows', ['3.B.1.C-SVN-a'], 6],
-            ['\C-SVN\ Non-dairy cattle', ['3.B.1.C-SVN-b'], 6],
-            ['\C-SVN\ Other cows', ['3.B.1.C-SVN-c'], 6],
+            ['\\C-SVN\\ Other (as specified in table 3(I).B)', ['3.B.1.C'], 5],
+            ['\\C-SVN\\ Dairy cows', ['3.B.1.C-SVN-a'], 6],
+            ['\\C-SVN\\ Non-dairy cattle', ['3.B.1.C-SVN-b'], 6],
+            ['\\C-SVN\\ Other cows', ['3.B.1.C-SVN-c'], 6],
             # USA
-            ['\C-USA\ Other (as specified in table 3(I).B)', ['3.B.1.C'], 5],
-            ['\C-USA\ Dairy Cattle', ['\IGNORE'], 6],
-            ['\C-USA\ Non-Dairy Cattle', ['\IGNORE'], 6],
-            ['\C-USA\ Steer Stocker', ['3.B.1.C-USA-a'], 6],
-            ['\C-USA\ Heifer Stocker', ['3.B.1.C-USA-b'], 6],
-            ['\C-USA\ Beef Cows', ['3.B.1.C-USA-c'], 6],
-            ['\C-USA\ Dairy Replacements', ['3.B.1.C-USA-d'], 6],
-            ['\C-USA\ Beef Replacements', ['3.B.1.C-USA-e'], 6],
-            ['\C-USA\ Steer Feedlot', ['3.B.1.C-USA-f'], 6],
-            ['\C-USA\ Heifer Feedlot', ['3.B.1.C-USA-g'], 6],
-            ['\C-USA\ Bulls', ['3.B.1.C-USA-h'], 6],
-            ['\C-USA\ Dairy Cows', ['3.B.1.C-USA-i'], 6],
-            ['\C-USA\ Beef Calves', ['3.B.1.C-USA-j'], 6],
-            ['\C-USA\ Dairy Calves', ['3.B.1.C-USA-k'], 6],
+            ['\\C-USA\\ Other (as specified in table 3(I).B)', ['3.B.1.C'], 5],
+            ['\\C-USA\\ Dairy Cattle', ['\\IGNORE'], 6],
+            ['\\C-USA\\ Non-Dairy Cattle', ['\\IGNORE'], 6],
+            ['\\C-USA\\ Steer Stocker', ['3.B.1.C-USA-a'], 6],
+            ['\\C-USA\\ Heifer Stocker', ['3.B.1.C-USA-b'], 6],
+            ['\\C-USA\\ Beef Cows', ['3.B.1.C-USA-c'], 6],
+            ['\\C-USA\\ Dairy Replacements', ['3.B.1.C-USA-d'], 6],
+            ['\\C-USA\\ Beef Replacements', ['3.B.1.C-USA-e'], 6],
+            ['\\C-USA\\ Steer Feedlot', ['3.B.1.C-USA-f'], 6],
+            ['\\C-USA\\ Heifer Feedlot', ['3.B.1.C-USA-g'], 6],
+            ['\\C-USA\\ Bulls', ['3.B.1.C-USA-h'], 6],
+            ['\\C-USA\\ Dairy Cows', ['3.B.1.C-USA-i'], 6],
+            ['\\C-USA\\ Beef Calves', ['3.B.1.C-USA-j'], 6],
+            ['\\C-USA\\ Dairy Calves', ['3.B.1.C-USA-k'], 6],
             # other animals
             ['2. Sheep', ['3.B.2'], 3],
             ['3. Swine', ['3.B.3'], 3],
@@ -2023,15 +2024,15 @@ CRF2021 = {
             ['Flood prone', ['3.C.2.a']],
             ['Drought prone', ['3.C.2.b']],
             ['3. Deep water', ['3.C.3']],
-            ['Water depth 50–100 cm', ['3.C.3.a']],
+            ['Water depth 50-100 cm', ['3.C.3.a']],
             ['Water depth > 100 cm', ['3.C.3.b']],
             ['4. Other (please specify)', ['3.C.4']],
             ['Non-specified', ['3.C.4.a']],  # EST
             ['Other', ['3.C.4.a']],  # DEU
             ['other', ['3.C.4.a']],  # LVA
             ['Other cultivation', ['3.C.4.a']],  # CZE
-            ['Upland rice(4)', ['\IGNORE']],
-            ['Total(4)', ['\IGNORE']],
+            ['Upland rice(4)', ['\\IGNORE']],
+            ['Total(4)', ['\\IGNORE']],
         ],
         "entity_mapping": {
             'EMISSIONS CH4': 'CH4',
@@ -2267,7 +2268,7 @@ CRF2021 = {
             ['Sludge spreading', ['5.E.7']],  # ESP
             ['Accidental combustion', ['5.E.3']],  # ESP
             ['Other waste', ['5.E.5']],  # CZE
-            ['Memo item:(2)', ['\IGNORE']],
+            ['Memo item:(2)', ['\\IGNORE']],
             ['Long-term storage of C in waste disposal sites', ['M.Memo.LTSW']],
             ['Annual change in total long-term C storage', ['M.Memo.ACLT']],
             ['Annual change in total long-term C storage in HWP waste(3)', ['M.Memo.ACLTHWP']],

UNFCCC_GHG_data/UNFCCC_CRF_reader/crf_specifications/CRF2022_specification.py → src/unfccc_ghg_data/unfccc_crf_reader/crf_specifications/crf2022_specification.py

@@ -1,4 +1,4 @@
-""" CRF2022 specification.
+"""CRF2022 specification.
 Currently not all tables are included. Extend if you need all country
 specific items in categories 2, 3.H-G, 4
 
@@ -39,6 +39,7 @@ TODO:
 """
 
 import numpy as np
+
 from .util import unit_info
 
 CRF2022 = {
@@ -117,7 +118,7 @@ CRF2022 = {
             ['1. Transport of CO2', ['1.C.1']],
             ['2. Injection and storage', ['1.C.2']],
             ['3. Other', ['1.C.3']],
-            ['Memo items: (1)', ['\IGNORE']],
+            ['Memo items: (1)', ['\\IGNORE']],
             ['International bunkers', ['M.Memo.Int']],
             ['Aviation', ['M.Memo.Int.Avi']],
             ['Navigation', ['M.Memo.Int.Mar']],
@@ -450,8 +451,8 @@ CRF2022 = {
             # 1.A.2.g.viii Other (please specify)
             ['1.A.2.g.viii Other (please specify)', ['1.A.2.g.viii', 'Total'], 2],
             # DKE
-            ['Construction', ['\IGNORE', '\IGNORE'], 3],  # (empty)
-            ['Mining', ['\IGNORE', '\IGNORE'], 3],  # (empty)
+            ['Construction', ['\\IGNORE', '\\IGNORE'], 3],  # (empty)
+            ['Mining', ['\\IGNORE', '\\IGNORE'], 3],  # (empty)
             # DNK, DKE, USA, CZE
             ['Other non-specified', ['1.A.2.g.viii.1', 'Total'], 3],
             ['Liquid Fuels', ['1.A.2.g.viii.1', 'Liquid'], 4],
@@ -501,7 +502,7 @@ CRF2022 = {
             ['Peat', ['1.A.2.g.viii.1', 'Peat'], 4],
             ['Biomass', ['1.A.2.g.viii.1', 'Biomass'], 4],
             # DKE
-            ['Textile', ['\IGNORE', '\IGNORE'], 3],  # (empty)
+            ['Textile', ['\\IGNORE', '\\IGNORE'], 3],  # (empty)
             # DNK, DNM, FIN, DKE
             ['Other manufacturing industries', ['1.A.2.g.viii.3', 'Total'], 3],
             ['Liquid Fuels', ['1.A.2.g.viii.3', 'Liquid'], 4],
@@ -1405,10 +1406,10 @@ CRF2022 = {
             ['iii. Mobile (other)', ['1.A.5.b.iv', 'Total'], 2],
             ['Liquid Fuels', ['1.A.5.b.iv', 'Liquid'], 3],
             # Information Item
-            ['Information item:(15)', ['\IGNORE', '\IGNORE'], 0],
-            ['Waste incineration with energy recovery included as:', ['\IGNORE', '\IGNORE'], 1],
-            ['Biomass(6)', ['\IGNORE', '\IGNORE'], 1],
-            ['Fossil fuels(4)', ['\IGNORE', '\IGNORE'], 1],
+            ['Information item:(15)', ['\\IGNORE', '\\IGNORE'], 0],
+            ['Waste incineration with energy recovery included as:', ['\\IGNORE', '\\IGNORE'], 1],
+            ['Biomass(6)', ['\\IGNORE', '\\IGNORE'], 1],
+            ['Fossil fuels(4)', ['\\IGNORE', '\\IGNORE'], 1],
         ],
         "entity_mapping": {
             'EMISSIONS CH4': "CH4",
@@ -1554,7 +1555,7 @@ CRF2022 = {
             ['a. Injection', ['1.C.2.a']],
             ['b. Storage', ['1.C.2.b']],
             ['3. Other', ['1.C.3']],
-            ['Information item(4, 5)', ['\IGNORE']],
+            ['Information item(4, 5)', ['\\IGNORE']],
             ['Total amount captured for storage', ['M.Info.A.TACS']],
             ['Total amount of imports for storage', ['M.Info.A.TAIS']],
             ['Total A', ['M.Info.A']],
@@ -1562,7 +1563,7 @@ CRF2022 = {
             ['Total amount of CO2 injected at storage sites', ['M.Info.B.TAI']],
             ['Total leakage from transport, injection and storage', ['M.Info.B.TLTIS']],
             ['Total B', ['M.Info.B']],
-            ['Difference (A-B)(6)', ['\IGNORE']],
+            ['Difference (A-B)(6)', ['\\IGNORE']],
         ],
         "entity_mapping": {
             'EMISSIONS CO2(2)': 'CO2',
@@ -1821,61 +1822,61 @@ CRF2022 = {
             # A. Enteric fermentation
             ['A. Enteric fermentation', ['3.A'], 2],
             ['1. Cattle(1)', ['3.A.1'], 3],
-            ['Option A:', ['\IGNORE'], 4],
+            ['Option A:', ['\\IGNORE'], 4],
             ['Dairy cattle', ['3.A.1.Aa'], 5],
             ['Non-dairy cattle', ['3.A.1.Ab'], 5],
-            ['Option B:', ['\IGNORE'], 4],
+            ['Option B:', ['\\IGNORE'], 4],
             ['Mature dairy cattle', ['3.A.1.Ba'], 5],
             ['Other mature cattle', ['3.A.1.Bb'], 5],
             ['Growing cattle', ['3.A.1.Bc'], 5],
-            ['Option C (country-specific):', ['\IGNORE'], 4],
+            ['Option C (country-specific):', ['\\IGNORE'], 4],
             # all countries not specified explcitly
-            ['\C!-AUS-MLT-LUX-POL-SVN-USA\ Other (as specified in table 3(I).A)', ['3.A.1.C'], 5],
+            ['\\C!-AUS-MLT-LUX-POL-SVN-USA\\ Other (as specified in table 3(I).A)', ['3.A.1.C'], 5],
             # Australia
-            ['\C-AUS\ Other (as specified in table 3(I).A)', ['3.A.1.C'], 5],
-            ['\C-AUS\ Dairy Cattle', ['3.A.1.C-AUS-a'], 6],
-            ['\C-AUS\ Beef Cattle - Pasture', ['3.A.1.C-AUS-b'], 6],
-            ['\C-AUS\ Beef Cattle - Feedlot', ['3.A.1.C-AUS-c'], 6],
+            ['\\C-AUS\\ Other (as specified in table 3(I).A)', ['3.A.1.C'], 5],
+            ['\\C-AUS\\ Dairy Cattle', ['3.A.1.C-AUS-a'], 6],
+            ['\\C-AUS\\ Beef Cattle - Pasture', ['3.A.1.C-AUS-b'], 6],
+            ['\\C-AUS\\ Beef Cattle - Feedlot', ['3.A.1.C-AUS-c'], 6],
             # malta
-            ['\C-MLT\ Other (as specified in table 3(I).A)', ['3.A.1.C'], 5],
-            ['\C-MLT\ dairy cows', ['3.A.1.C-MLT-a'], 6],
-            ['\C-MLT\ non-lactating cows', ['3.A.1.C-MLT-b'], 6],
-            ['\C-MLT\ bulls', ['3.A.1.C-MLT-c'], 6],
-            ['\C-MLT\ calves', ['3.A.1.C-MLT-d'], 6],
-            ['\C-MLT\ growing cattle 1-2 years', ['3.A.1.C-MLT-e'], 6],
+            ['\\C-MLT\\ Other (as specified in table 3(I).A)', ['3.A.1.C'], 5],
+            ['\\C-MLT\\ dairy cows', ['3.A.1.C-MLT-a'], 6],
+            ['\\C-MLT\\ non-lactating cows', ['3.A.1.C-MLT-b'], 6],
+            ['\\C-MLT\\ bulls', ['3.A.1.C-MLT-c'], 6],
+            ['\\C-MLT\\ calves', ['3.A.1.C-MLT-d'], 6],
+            ['\\C-MLT\\ growing cattle 1-2 years', ['3.A.1.C-MLT-e'], 6],
             # Luxembourg
-            ['\C-LUX\ Other (as specified in table 3(I).A)', ['3.A.1.C'], 5],
-            ['\C-LUX\ Bulls', ['3.A.1.C-LUX-a'], 6],
-            ['\C-LUX\ Calves', ['3.A.1.C-LUX-b'], 6],
-            ['\C-LUX\ Young Cattle', ['3.A.1.C-LUX-c'], 6],
-            ['\C-LUX\ Suckler Cows', ['3.A.1.C-LUX-d'], 6],
-            ['\C-LUX\ Bulls under 2 years', ['3.A.1.C-LUX-e'], 6],
-            ['\C-LUX\ Dairy Cows', ['3.A.1.C-LUX-f'], 6],
+            ['\\C-LUX\\ Other (as specified in table 3(I).A)', ['3.A.1.C'], 5],
+            ['\\C-LUX\\ Bulls', ['3.A.1.C-LUX-a'], 6],
+            ['\\C-LUX\\ Calves', ['3.A.1.C-LUX-b'], 6],
+            ['\\C-LUX\\ Young Cattle', ['3.A.1.C-LUX-c'], 6],
+            ['\\C-LUX\\ Suckler Cows', ['3.A.1.C-LUX-d'], 6],
+            ['\\C-LUX\\ Bulls under 2 years', ['3.A.1.C-LUX-e'], 6],
+            ['\\C-LUX\\ Dairy Cows', ['3.A.1.C-LUX-f'], 6],
             # Poland
-            ['\C-POL\ Other (as specified in table 3(I).A)', ['3.A.1.C'], 5],
-            ['\C-POL\ Bulls (older than 2 years)', ['3.A.1.C-POL-a'], 6],
-            ['\C-POL\ Non-dairy Heifers (older than 2 years)', ['3.A.1.C-POL-b'], 6],
-            ['\C-POL\ Non-dairy Young Cattle (younger than 1 year)', ['3.A.1.C-POL-c'], 6],
-            ['\C-POL\ Dairy Cattle', ['3.A.1.C-POL-d'], 6],
-            ['\C-POL\ Non-dairy Young Cattle (1-2 years)', ['3.A.1.C-POL-e'], 6],
+            ['\\C-POL\\ Other (as specified in table 3(I).A)', ['3.A.1.C'], 5],
+            ['\\C-POL\\ Bulls (older than 2 years)', ['3.A.1.C-POL-a'], 6],
+            ['\\C-POL\\ Non-dairy Heifers (older than 2 years)', ['3.A.1.C-POL-b'], 6],
+            ['\\C-POL\\ Non-dairy Young Cattle (younger than 1 year)', ['3.A.1.C-POL-c'], 6],
+            ['\\C-POL\\ Dairy Cattle', ['3.A.1.C-POL-d'], 6],
+            ['\\C-POL\\ Non-dairy Young Cattle (1-2 years)', ['3.A.1.C-POL-e'], 6],
             # Slovenia
-            ['\C-SVN\ Other (as specified in table 3(I).A)', ['3.A.1.C'], 5],
-            ['\C-SVN\ Dairy cows', ['3.A.1.C-SVN-a'], 6],
-            ['\C-SVN\ Non-dairy cattle', ['3.A.1.C-SVN-b'], 6],
-            ['\C-SVN\ Other cows', ['3.A.1.C-SVN-c'], 6],
+            ['\\C-SVN\\ Other (as specified in table 3(I).A)', ['3.A.1.C'], 5],
+            ['\\C-SVN\\ Dairy cows', ['3.A.1.C-SVN-a'], 6],
+            ['\\C-SVN\\ Non-dairy cattle', ['3.A.1.C-SVN-b'], 6],
+            ['\\C-SVN\\ Other cows', ['3.A.1.C-SVN-c'], 6],
             # USA
-            ['\C-USA\ Other (as specified in table 3(I).A)', ['3.A.1.C'], 5],
-            ['\C-USA\ Steer Stocker', ['3.A.1.C-USA-a'], 6],
-            ['\C-USA\ Heifer Stocker', ['3.A.1.C-USA-b'], 6],
-            ['\C-USA\ Beef Cows', ['3.A.1.C-USA-c'], 6],
-            ['\C-USA\ Dairy Replacements', ['3.A.1.C-USA-d'], 6],
-            ['\C-USA\ Beef Replacements', ['3.A.1.C-USA-e'], 6],
-            ['\C-USA\ Steer Feedlot', ['3.A.1.C-USA-f'], 6],
-            ['\C-USA\ Heifer Feedlot', ['3.A.1.C-USA-g'], 6],
-            ['\C-USA\ Bulls', ['3.A.1.C-USA-h'], 6],
-            ['\C-USA\ Dairy Cows', ['3.A.1.C-USA-i'], 6],
-            ['\C-USA\ Beef Calves', ['3.A.1.C-USA-j'], 6],
-            ['\C-USA\ Dairy Calves', ['3.A.1.C-USA-k'], 6],
+            ['\\C-USA\\ Other (as specified in table 3(I).A)', ['3.A.1.C'], 5],
+            ['\\C-USA\\ Steer Stocker', ['3.A.1.C-USA-a'], 6],
+            ['\\C-USA\\ Heifer Stocker', ['3.A.1.C-USA-b'], 6],
+            ['\\C-USA\\ Beef Cows', ['3.A.1.C-USA-c'], 6],
+            ['\\C-USA\\ Dairy Replacements', ['3.A.1.C-USA-d'], 6],
+            ['\\C-USA\\ Beef Replacements', ['3.A.1.C-USA-e'], 6],
+            ['\\C-USA\\ Steer Feedlot', ['3.A.1.C-USA-f'], 6],
+            ['\\C-USA\\ Heifer Feedlot', ['3.A.1.C-USA-g'], 6],
+            ['\\C-USA\\ Bulls', ['3.A.1.C-USA-h'], 6],
+            ['\\C-USA\\ Dairy Cows', ['3.A.1.C-USA-i'], 6],
+            ['\\C-USA\\ Beef Calves', ['3.A.1.C-USA-j'], 6],
+            ['\\C-USA\\ Dairy Calves', ['3.A.1.C-USA-k'], 6],
             # Other livestock
             ['2. Sheep', ['3.A.2'], 3],
             ['3. Swine', ['3.A.3'], 3],
@@ -1896,60 +1897,60 @@ CRF2022 = {
             # Manure Management
             ['B. Manure management', ['3.B'], 2],
             ['1. Cattle(1)', ['3.B.1'], 3],
-            ['Option A:', ['\IGNORE'], 4],
+            ['Option A:', ['\\IGNORE'], 4],
             ['Dairy cattle', ['3.B.1.Aa'], 5],
             ['Non-dairy cattle', ['3.B.1.Ab'], 5],
-            ['Option B:', ['\IGNORE'], 4],
+            ['Option B:', ['\\IGNORE'], 4],
             ['Mature dairy cattle', ['3.B.1.Ba'], 5],
             ['Other mature cattle', ['3.B.1.Bb'], 5],
             ['Growing cattle', ['3.B.1.Bc'], 5],
-            ['Option C (country-specific):', ['\IGNORE'], 4],
+            ['Option C (country-specific):', ['\\IGNORE'], 4],
             # all countries not specified explicitly
-            ['\C!-AUS-MLT-LUX-POL-SVN-USA\ Other (as specified in table 3(I).B)', ['3.B.1.C'], 5],
+            ['\\C!-AUS-MLT-LUX-POL-SVN-USA\\ Other (as specified in table 3(I).B)', ['3.B.1.C'], 5],
             # Australia
-            ['\C-AUS\ Other (as specified in table 3(I).B)', ['3.B.1.C'], 5],
-            ['\C-AUS\ Dairy Cattle', ['3.B.1.C-AUS-a'], 6],
-            ['\C-AUS\ Beef Cattle - Pasture', ['3.B.1.C-AUS-b'], 6],
-            ['\C-AUS\ Beef Cattle - Feedlot', ['3.B.1.C-AUS-c'], 6],
+            ['\\C-AUS\\ Other (as specified in table 3(I).B)', ['3.B.1.C'], 5],
+            ['\\C-AUS\\ Dairy Cattle', ['3.B.1.C-AUS-a'], 6],
+            ['\\C-AUS\\ Beef Cattle - Pasture', ['3.B.1.C-AUS-b'], 6],
+            ['\\C-AUS\\ Beef Cattle - Feedlot', ['3.B.1.C-AUS-c'], 6],
             # Malta
-            ['\C-MLT\ Other (as specified in table 3(I).B)', ['3.B.1.C'], 5],
-            ['\C-MLT\ dairy cows', ['3.B.1.C-MLT-a'], 6],
-            ['\C-MLT\ non-lactating cows', ['3.B.1.C-MLT-b'], 6],
-            ['\C-MLT\ bulls', ['3.B.1.C-MLT-c'], 6],
-            ['\C-MLT\ calves', ['3.B.1.C-MLT-d'], 6],
-            ['\C-MLT\ growing cattle 1-2 years', ['3.B.1.C-MLT-e'], 6],
+            ['\\C-MLT\\ Other (as specified in table 3(I).B)', ['3.B.1.C'], 5],
+            ['\\C-MLT\\ dairy cows', ['3.B.1.C-MLT-a'], 6],
+            ['\\C-MLT\\ non-lactating cows', ['3.B.1.C-MLT-b'], 6],
+            ['\\C-MLT\\ bulls', ['3.B.1.C-MLT-c'], 6],
+            ['\\C-MLT\\ calves', ['3.B.1.C-MLT-d'], 6],
+            ['\\C-MLT\\ growing cattle 1-2 years', ['3.B.1.C-MLT-e'], 6],
             # Luxembourg
-            ['\C-LUX\ Other (as specified in table 3(I).B)', ['3.B.1.C'], 5],
-            ['\C-LUX\ Bulls', ['3.B.1.C-LUX-a'], 6],
-            ['\C-LUX\ Calves', ['3.B.1.C-LUX-b'], 6],
-            ['\C-LUX\ Young Cattle', ['3.B.1.C-LUX-c'], 6],
-            ['\C-LUX\ Suckler Cows', ['3.B.1.C-LUX-d'], 6],
-            ['\C-LUX\ Bulls under 2 years', ['3.B.1.C-LUX-e'], 6],
-            ['\C-LUX\ Dairy Cows', ['3.B.1.C-LUX-f'], 6],
+            ['\\C-LUX\\ Other (as specified in table 3(I).B)', ['3.B.1.C'], 5],
+            ['\\C-LUX\\ Bulls', ['3.B.1.C-LUX-a'], 6],
+            ['\\C-LUX\\ Calves', ['3.B.1.C-LUX-b'], 6],
+            ['\\C-LUX\\ Young Cattle', ['3.B.1.C-LUX-c'], 6],
+            ['\\C-LUX\\ Suckler Cows', ['3.B.1.C-LUX-d'], 6],
+            ['\\C-LUX\\ Bulls under 2 years', ['3.B.1.C-LUX-e'], 6],
+            ['\\C-LUX\\ Dairy Cows', ['3.B.1.C-LUX-f'], 6],
             # Poland
-            ['\C-POL\ Other (as specified in table 3(I).B)', ['3.B.1.C'], 5],
-            ['\C-POL\ Non-dairy Cattle', ['3.B.1.C-POL-a'], 6],
-            ['\C-POL\ Dairy Cattle', ['3.B.1.C-POL-b'], 6],
+            ['\\C-POL\\ Other (as specified in table 3(I).B)', ['3.B.1.C'], 5],
+            ['\\C-POL\\ Non-dairy Cattle', ['3.B.1.C-POL-a'], 6],
+            ['\\C-POL\\ Dairy Cattle', ['3.B.1.C-POL-b'], 6],
             # Slovenia
-            ['\C-SVN\ Other (as specified in table 3(I).B)', ['3.B.1.C'], 5],
-            ['\C-SVN\ Dairy cows', ['3.B.1.C-SVN-a'], 6],
-            ['\C-SVN\ Non-dairy cattle', ['3.B.1.C-SVN-b'], 6],
-            ['\C-SVN\ Other cows', ['3.B.1.C-SVN-c'], 6],
+            ['\\C-SVN\\ Other (as specified in table 3(I).B)', ['3.B.1.C'], 5],
+            ['\\C-SVN\\ Dairy cows', ['3.B.1.C-SVN-a'], 6],
+            ['\\C-SVN\\ Non-dairy cattle', ['3.B.1.C-SVN-b'], 6],
+            ['\\C-SVN\\ Other cows', ['3.B.1.C-SVN-c'], 6],
             # USA
-            ['\C-USA\ Other (as specified in table 3(I).B)', ['3.B.1.C'], 5],
-            ['\C-USA\ Dairy Cattle', ['\IGNORE'], 6],
-            ['\C-USA\ Non-Dairy Cattle', ['\IGNORE'], 6],
-            ['\C-USA\ Steer Stocker', ['3.B.1.C-USA-a'], 6],
-            ['\C-USA\ Heifer Stocker', ['3.B.1.C-USA-b'], 6],
-            ['\C-USA\ Beef Cows', ['3.B.1.C-USA-c'], 6],
-            ['\C-USA\ Dairy Replacements', ['3.B.1.C-USA-d'], 6],
-            ['\C-USA\ Beef Replacements', ['3.B.1.C-USA-e'], 6],
-            ['\C-USA\ Steer Feedlot', ['3.B.1.C-USA-f'], 6],
-            ['\C-USA\ Heifer Feedlot', ['3.B.1.C-USA-g'], 6],
-            ['\C-USA\ Bulls', ['3.B.1.C-USA-h'], 6],
-            ['\C-USA\ Dairy Cows', ['3.B.1.C-USA-i'], 6],
-            ['\C-USA\ Beef Calves', ['3.B.1.C-USA-j'], 6],
-            ['\C-USA\ Dairy Calves', ['3.B.1.C-USA-k'], 6],
+            ['\\C-USA\\ Other (as specified in table 3(I).B)', ['3.B.1.C'], 5],
+            ['\\C-USA\\ Dairy Cattle', ['\\IGNORE'], 6],
+            ['\\C-USA\\ Non-Dairy Cattle', ['\\IGNORE'], 6],
+            ['\\C-USA\\ Steer Stocker', ['3.B.1.C-USA-a'], 6],
+            ['\\C-USA\\ Heifer Stocker', ['3.B.1.C-USA-b'], 6],
+            ['\\C-USA\\ Beef Cows', ['3.B.1.C-USA-c'], 6],
+            ['\\C-USA\\ Dairy Replacements', ['3.B.1.C-USA-d'], 6],
+            ['\\C-USA\\ Beef Replacements', ['3.B.1.C-USA-e'], 6],
+            ['\\C-USA\\ Steer Feedlot', ['3.B.1.C-USA-f'], 6],
+            ['\\C-USA\\ Heifer Feedlot', ['3.B.1.C-USA-g'], 6],
+            ['\\C-USA\\ Bulls', ['3.B.1.C-USA-h'], 6],
+            ['\\C-USA\\ Dairy Cows', ['3.B.1.C-USA-i'], 6],
+            ['\\C-USA\\ Beef Calves', ['3.B.1.C-USA-j'], 6],
+            ['\\C-USA\\ Dairy Calves', ['3.B.1.C-USA-k'], 6],
             # other animals
             ['2. Sheep', ['3.B.2'], 3],
             ['3. Swine', ['3.B.3'], 3],
@@ -2040,15 +2041,15 @@ CRF2022 = {
             ['Flood prone', ['3.C.2.a']],
             ['Drought prone', ['3.C.2.b']],
             ['3. Deep water', ['3.C.3']],
-            ['Water depth 50–100 cm', ['3.C.3.a']],
+            ['Water depth 50-100 cm', ['3.C.3.a']],
             ['Water depth > 100 cm', ['3.C.3.b']],
             ['4. Other (please specify)', ['3.C.4']],
             ['Non-specified', ['3.C.4.a']],  # EST
             ['Other', ['3.C.4.a']],  # DEU
             ['other', ['3.C.4.a']],  # LVA
             ['Other cultivation', ['3.C.4.a']],  # CZE
-            ['Upland rice(4)', ['\IGNORE']],
-            ['Total(4)', ['\IGNORE']],
+            ['Upland rice(4)', ['\\IGNORE']],
+            ['Total(4)', ['\\IGNORE']],
         ],
         "entity_mapping": {
             'EMISSIONS CH4': 'CH4',
@@ -2286,7 +2287,7 @@ CRF2022 = {
             ['Other waste', ['5.E.5']],  # CZE
             ['5.E.1 Industrial Wastewater', ['5.E.8']],  # CAN, new in 2022
             ['Accidental Fires at SWDS', ['5.E.9']],  # AUS, new in 2022
-            ['Memo item:(2)', ['\IGNORE']],
+            ['Memo item:(2)', ['\\IGNORE']],
             ['Long-term storage of C in waste disposal sites', ['M.Memo.LTSW']],
             ['Annual change in total long-term C storage', ['M.Memo.ACLT']],
             ['Annual change in total long-term C storage in HWP waste(3)', ['M.Memo.ACLTHWP']],
@@ -2641,7 +2642,7 @@ CRF2022 = {
             "unit_info": unit_info["summary"],
         },
         "sector_mapping": [
-            ['Memo items:(7)', ['\IGNORE']],
+            ['Memo items:(7)', ['\\IGNORE']],
             ['International bunkers', ['M.Memo.Int']],
             ['Aviation', ['M.Memo.Int.Avi']],
             ['Navigation', ['M.Memo.Int.Mar']],

UNFCCC_GHG_data/UNFCCC_CRF_reader/crf_specifications/CRF2023_AUS_specification.py → src/unfccc_ghg_data/unfccc_crf_reader/crf_specifications/crf2023_aus_specification.py

@@ -1,4 +1,4 @@
-""" CRF2023 specification for Australia.
+"""CRF2023 specification for Australia.
 Currently not all tables are included. Extend if you need all country
 specific items in categories 2, 3.H-G, 4
 
@@ -40,6 +40,7 @@ TODO:
 """
 
 import numpy as np
+
 from .util import unit_info
 
 CRF2023_AUS = {
@@ -104,7 +105,7 @@ CRF2023_AUS = {
             ["1.C.1. Transport of CO2", ["1.C.1"]],
             ["1.C.2. Injection and storage", ["1.C.2"]],
             ["1.C.3. Other", ["1.C.3"]],
-            ["1.D. Memo items: (3)", ["\IGNORE"]],
+            ["1.D. Memo items: (3)", ["\\IGNORE"]],
             ["1.D.1. International bunkers", ["M.Memo.Int"]],
             ["1.D.1.a. Aviation", ["M.Memo.Int.Avi"]],
             ["1.D.1.b.Navigation", ["M.Memo.Int.Mar"]],
@@ -169,7 +170,7 @@ CRF2023_AUS = {
             ["Other fossil fuels (7)", ["1.A.1.a", "OtherFF"], 3],
             ["Peat (8)", ["1.A.1.a", "Peat"], 3],
             ["Biomass (3)", ["1.A.1.a", "Biomass"], 3],
-            ["Drop-down list:", ["\IGNORE", "\IGNORE"], 3],  # (empty)
+            ["Drop-down list:", ["\\IGNORE", "\\IGNORE"], 3],  # (empty)
             # 1.A.1.a.i Electricity Generation
             ["1.A.1.a.i. Electricity generation", ["1.A.1.a.i", "Total"], 3],
             ["Liquid fuels", ["1.A.1.a.i", "Liquid"], 4],
@@ -218,7 +219,7 @@ CRF2023_AUS = {
             ["Other fossil fuels (7)", ["1.A.1.c", "OtherFF"], 3],
             ["Peat (8)", ["1.A.1.c", "Peat"], 3],
             ["Biomass (3)", ["1.A.1.c", "Biomass"], 3],
-            ["Drop-down list:", ["\IGNORE", "\IGNORE"], 3],  # (empty)
+            ["Drop-down list:", ["\\IGNORE", "\\IGNORE"], 3],  # (empty)
             # 1.A.1.c.i Manufacture of solid fuels
             ["1.A.1.c.i. Manufacture of solid fuels", ["1.A.1.c.i", "Total"], 3],
             ["Liquid fuels", ["1.A.1.c.i", "Liquid"], 4],
@@ -331,7 +332,7 @@ CRF2023_AUS = {
             ["Biomass (3)", ["1.A.2.f", "Biomass"], 2],
             # g. other
             ["1.A.2.g. Other (please specify) (11)", ["1.A.2.g", "Total"], 1],
-            ["Dropdown list", ["\IGNORE", "\IGNORE"], 2],
+            ["Dropdown list", ["\\IGNORE", "\\IGNORE"], 2],
             # 1.A.2.g.i Manufacturing of machinery
             ["1.A.2.g.i. Manufacturing of machinery", ["1.A.2.g.i", "Total"], 2],
             ["Liquid fuels", ["1.A.2.g.i", "Liquid"], 3],
@@ -398,7 +399,7 @@ CRF2023_AUS = {
             ["Diesel oil", ["1.A.2.g.vii", "DieselOil"], 3],
             ["Liquefied petroleum gases (LPG)", ["1.A.2.g.vii", "LPG"], 3],
             ["Other liquid fuels (please specify)", ["1.A.2.g.vii", "OtherLiquid"], 3],
-            ["NA", ["\IGNORE", "\IGNORE"], 3],
+            ["NA", ["\\IGNORE", "\\IGNORE"], 3],
             ["Gaseous fuels (6)", ["1.A.2.g.vii", "Gaseous"], 3],
             ["Other fossil fuels (7)", ["1.A.2.g.vii", "OtherFF"], 3],
             ["Biomass (3)", ["1.A.2.g.vii", "Biomass"], 3],
@@ -454,7 +455,7 @@ CRF2023_AUS = {
             ["Diesel oil", ["1.A.3.b", "DieselOil"], 2],
             ["Liquefied petroleum gases (LPG)", ["1.A.3.b", "LPG"], 2],
             ["Other liquid fuels (please specify)", ["1.A.3.b", "OtherLiquid"], 2],
-            ["NA", ["\IGNORE", "\IGNORE"], 3],
+            ["NA", ["\\IGNORE", "\\IGNORE"], 3],
             ["Gaseous fuels (6)", ["1.A.3.b", "Gaseous"], 2],
             ["Biomass (3)", ["1.A.3.b", "Biomass"], 2],
             ["Other fossil fuels (please specify) (7)", ["1.A.3.b", "OtherFF"], 2],
@@ -465,7 +466,7 @@ CRF2023_AUS = {
             ["Diesel oil", ["1.A.3.b.i", "DieselOil"], 3],
             ["Liquefied petroleum gases (LPG)", ["1.A.3.b.i", "LPG"], 3],
             ["Other liquid fuels (please specify)", ["1.A.3.b.i", "OtherLiquid"], 3],
-            ["NA", ["\IGNORE", "\IGNORE"], 4],
+            ["NA", ["\\IGNORE", "\\IGNORE"], 4],
             ["Gaseous fuels (6)", ["1.A.3.b.i", "Gaseous"], 3],
             ["Biomass (3)", ["1.A.3.b.i", "Biomass"], 3],
             ["Other fossil fuels (please specify)(7)", ["1.A.3.b.i", "OtherFF"], 3],
@@ -476,7 +477,7 @@ CRF2023_AUS = {
             ["Diesel oil", ["1.A.3.b.ii", "DieselOil"], 3],
             ["Liquefied petroleum gases (LPG)", ["1.A.3.b.ii", "LPG"], 3],
             ["Other liquid fuels (please specify)", ["1.A.3.b.ii", "OtherLiquid"], 3],
-            ["NA", ["\IGNORE", "\IGNORE"], 4],
+            ["NA", ["\\IGNORE", "\\IGNORE"], 4],
             ["Gaseous fuels (6)", ["1.A.3.b.ii", "Gaseous"], 3],
             ["Biomass (3)", ["1.A.3.b.ii", "Biomass"], 3],
             ["Other fossil fuels (please specify)(7)", ["1.A.3.b.ii", "OtherFF"], 3],
@@ -487,7 +488,7 @@ CRF2023_AUS = {
             ["Diesel oil", ["1.A.3.b.iii", "DieselOil"], 3],
             ["Liquefied petroleum gases (LPG)", ["1.A.3.b.iii", "LPG"], 3],
             ["Other liquid fuels (please specify)", ["1.A.3.b.iii", "OtherLiquid"], 3],
-            ["NA", ["\IGNORE", "\IGNORE"], 4],
+            ["NA", ["\\IGNORE", "\\IGNORE"], 4],
             ["Gaseous fuels (6)", ["1.A.3.b.iii", "Gaseous"], 3],
             ["Biomass (3)", ["1.A.3.b.iii", "Biomass"], 3],
             ["Other fossil fuels (please specify)(7)", ["1.A.3.b.iii", "OtherFF"], 3],
@@ -498,19 +499,19 @@ CRF2023_AUS = {
             ["Diesel oil", ["1.A.3.b.iv", "DieselOil"], 3],
             ["Liquefied petroleum gases (LPG)", ["1.A.3.b.iv", "LPG"], 3],
             ["Other liquid fuels (please specify)", ["1.A.3.b.iv", "OtherLiquid"], 3],
-            ["NA", ["\IGNORE", "\IGNORE"], 4],
+            ["NA", ["\\IGNORE", "\\IGNORE"], 4],
             ["Gaseous fuels (6)", ["1.A.3.b.iv", "Gaseous"], 3],
             ["Biomass (3)", ["1.A.3.b.iv", "Biomass"], 3],
             ["Other fossil fuels (please specify)(7)", ["1.A.3.b.iv", "OtherFF"], 3],
             ["Lubricants", ["1.A.3.b.iv", "OFFLubricants"], 4],
             # v. Other
             ["1.A.3.b.v. Other (please specify)", ["1.A.3.b.v", "Total"], 2],
-            ["NA", ["\IGNORE", "\IGNORE"], 3],
+            ["NA", ["\\IGNORE", "\\IGNORE"], 3],
             ["Gasoline", ["1.A.3.b.v", "Gasoline"], 4],
             ["Diesel oil", ["1.A.3.b.v", "DieselOil"], 4],
             ["Liquefied petroleum gases (LPG)", ["1.A.3.b.v", "LPG"], 4],
             ["Other liquid fuels (please specify)", ["1.A.3.b.v", "OtherLiquid"], 4],
-            ["NA", ["\IGNORE", "\IGNORE"], 5],
+            ["NA", ["\\IGNORE", "\\IGNORE"], 5],
             ["Gaseous fuels (6)", ["1.A.3.b.v", "Gaseous"], 4],
             ["Biomass (3)", ["1.A.3.b.v", "Biomass"], 4],
             ["Other fossil fuels (please specify)(7)", ["1.A.3.b.v", "OtherFF"], 4],
@@ -529,7 +530,7 @@ CRF2023_AUS = {
             ["Gas/diesel oil", ["1.A.3.d", "GasDieselOil"], 2],
             ["Gasoline", ["1.A.3.d", "Gasoline"], 2],
             ["Other liquid fuels (please specify)", ["1.A.3.d", "OtherLiquid"], 2],
-            ["NA", ["\IGNORE", "\IGNORE"], 3],
+            ["NA", ["\\IGNORE", "\\IGNORE"], 3],
             ["Gaseous fuels (6)", ["1.A.3.d", "Gaseous"], 2],
             ["Biomass (3)", ["1.A.3.d", "Biomass"], 2],
             ["Other fossil fuels (please specify)(7)", ["1.A.3.d", "OtherFF"], 2],
@@ -557,7 +558,7 @@ CRF2023_AUS = {
             ["Diesel oil", ["1.A.3.e.ii.1", "DieselOil"], 4],
             ["Liquefied petroleum gases (LPG)", ["1.A.3.e.ii.1", "LPG"], 4],
             ["Other liquid fuels (please specify)", ["1.A.3.e.ii.1", "OtherLiquid"], 4],
-            ["NA", ["\IGNORE", "\IGNORE"], 5],
+            ["NA", ["\\IGNORE", "\\IGNORE"], 5],
             ["Solid fuels", ["1.A.3.e.ii.1", "Solid"], 4],
             ["Gaseous fuels (6)", ["1.A.3.e.ii.1", "Gaseous"], 4],
             ["Biomass (3)", ["1.A.3.e.ii.1", "Biomass"], 4],
@@ -605,7 +606,7 @@ CRF2023_AUS = {
             ["Other fossil fuels (7)", ["1.A.4.a", "OtherFF"], 2],
             ["Peat (8)", ["1.A.4.a", "Peat"], 2],
             ["Biomass (3)", ["1.A.4.a", "Biomass"], 2],
-            ["Drop-down list:", ["\IGNORE", "\IGNORE"], 2],  # (empty)
+            ["Drop-down list:", ["\\IGNORE", "\\IGNORE"], 2],  # (empty)
             # 1.A.4.a.i Stationary combustion
             ["1.A.4.a.i. Stationary combustion", ["1.A.4.a.i", "Total"], 2],
             ["Liquid fuels", ["1.A.4.a.i", "Liquid"], 3],
@@ -633,7 +634,7 @@ CRF2023_AUS = {
             ["Other fossil fuels (7)", ["1.A.4.b", "OtherFF"], 2],
             ["Peat (8)", ["1.A.4.b", "Peat"], 2],
             ["Biomass (3)", ["1.A.4.b", "Biomass"], 2],
-            ["Drop-down list:", ["\IGNORE", "\IGNORE"], 2],  # (empty)
+            ["Drop-down list:", ["\\IGNORE", "\\IGNORE"], 2],  # (empty)
             # 1.A.4.b.i Stationary combustion
             ["1.A.4.b.i. Stationary combustion", ["1.A.4.b.i", "Total"], 2],
             ["Liquid fuels", ["1.A.4.b.i", "Liquid"], 3],
@@ -680,22 +681,22 @@ CRF2023_AUS = {
             ["Diesel oil", ["1.A.4.c.ii", "DieselOil"], 3],
             ["Liquefied petroleum gases (LPG)", ["1.A.4.c.ii", "LPG"], 3],
             ["Other liquid fuels (please specify)", ["1.A.4.c.ii", "OtherLiquid"], 3],
-            ["NA", ["\IGNORE", "\IGNORE"], 4],
+            ["NA", ["\\IGNORE", "\\IGNORE"], 4],
             ["Gaseous fuels (6)", ["1.A.4.c.ii", "Gaseous"], 3],
             ["Biomass (3)", ["1.A.4.c.ii", "Biomass"], 3],
             ["Other fossil fuels (please specify)(7)", ["1.A.4.c.ii", "OtherFF"], 3],
-            ["NA", ["\IGNORE", "\IGNORE"], 4],
+            ["NA", ["\\IGNORE", "\\IGNORE"], 4],
             # iii. Fishing
             ["1.A.4.c.iii. Fishing", ["1.A.4.c.iii", "Total"], 2],
             ["Residual fuel oil", ["1.A.4.c.iii", "ResFuelOil"], 3],
             ["Gas/diesel oil", ["1.A.4.c.iii", "GasDieselOil"], 3],
             ["Gasoline", ["1.A.4.c.iii", "Gasoline"], 3],
             ["Other liquid fuels (please specify)", ["1.A.4.c.iii", "OtherLiquid"], 3],
-            ["NA", ["\IGNORE", "\IGNORE"], 4],
+            ["NA", ["\\IGNORE", "\\IGNORE"], 4],
             ["Gaseous fuels (6)", ["1.A.4.c.iii", "Gaseous"], 3],
             ["Biomass(3)", ["1.A.4.c.iii", "Biomass"], 3],
             ["Other fossil fuels (please specify)(7)", ["1.A.4.c.iii", "OtherFF"], 3],
-            ["NA", ["\IGNORE", "\IGNORE"], 4],
+            ["NA", ["\\IGNORE", "\\IGNORE"], 4],
             # 1.A.5 Other (Not specified elsewhere)(14)
             ["1.A.5 Other (Not specified elsewhere)(15)", ["1.A.5", "Total"], 0],
             ["Liquid fuels", ["1.A.5", "Liquid"], 1],
@@ -706,7 +707,7 @@ CRF2023_AUS = {
             ["Biomass (3)", ["1.A.5", "Biomass"], 1],
             # a. Stationary (please specify)
             ["1.A.5.a. Stationary (please specify)", ["1.A.5.a", "Total"], 1],
-            ["NA", ["\IGNORE", "\IGNORE"], 2],
+            ["NA", ["\\IGNORE", "\\IGNORE"], 2],
             ["Liquid fuels", ["1.A.5.a", "Liquid"], 2],
             ["Solid fuels", ["1.A.5.a", "Solid"], 2],
             ["Gaseous fuels (6)", ["1.A.5.a", "Gaseous"], 2],
@@ -722,14 +723,14 @@ CRF2023_AUS = {
             ["Other fossil fuels (7)", ["1.A.5.b.xii", "OtherFF"], 3],
             ["Biomass(3)", ["1.A.5.b.xii", "Biomass"], 3],
             # Information Item
-            ["Information item: (16)", ["\IGNORE", "\IGNORE"], 0],
+            ["Information item: (16)", ["\\IGNORE", "\\IGNORE"], 0],
             [
                 "Waste incineration with energy recovery included as:",
-                ["\IGNORE", "\IGNORE"],
+                ["\\IGNORE", "\\IGNORE"],
                 1,
             ],
-            ["Biomass (3)", ["\IGNORE", "\IGNORE"], 1],
-            ["Fossil fuels (7)", ["\IGNORE", "\IGNORE"], 1],
+            ["Biomass (3)", ["\\IGNORE", "\\IGNORE"], 1],
+            ["Fossil fuels (7)", ["\\IGNORE", "\\IGNORE"], 1],
         ],
         "entity_mapping": {
             "EMISSIONS CH4": "CH4",
@@ -766,22 +767,22 @@ CRF2023_AUS = {
                 2,
             ],
             ["1.B.1.a.i.5. Other (please specify)", ["1.B.1.a.i.5"], 2],
-            ["NA", ["\IGNORE"], 3],
+            ["NA", ["\\IGNORE"], 3],
             ["1.B.1.a.ii. Surface mines (4)", ["1.B.1.a.ii"], 1],
             ["1.B.1.a.ii.1. Mining activities", ["1.B.1.a.ii.1"], 2],
             ["1.B.1.a.ii.2. Post-mining activities", ["1.B.1.a.ii.2"], 2],
             ["1.B.1.a.ii.3. Other (please specify)", ["1.B.1.a.ii.3"], 2],
-            ["NA", ["\IGNORE"], 3],
+            ["NA", ["\\IGNORE"], 3],
             ["1. B. 1. b. Fuel transformation (6)", ["1.B.1.b"], 0],
-            ["Drop down list:", ["\IGNORE"], 1],
+            ["Drop down list:", ["\\IGNORE"], 1],
             ["1.B.1.b.i. Charcoal and biochar production (7)", ["1.B.1.b.i"], 1],
             ["1.B.1.b.ii. Coke production", ["1.B.1.b.ii"], 1],
             ["1.B.1.b.iii. Coal to liquids", ["1.B.1.b.iii"], 1],
             ["1.B.1.b.iv. Gas to liquids", ["1.B.1.b.iv"], 1],
             ["1.B.1.b.v. Other (please specify)", ["1.B.1.b.v"], 1],
-            ["NA", ["\IGNORE"], 2],
+            ["NA", ["\\IGNORE"], 2],
             ["1. B. 1. c. Other (please specify) (8)", ["1.B.1.c"], 0],
-            ["NA", ["\IGNORE"], 1],
+            ["NA", ["\\IGNORE"], 1],
         ],
         "entity_mapping": {
             "EMISSIONS (1) CH4": "CH4 emissions", # this is necessary because there
@@ -822,10 +823,10 @@ CRF2023_AUS = {
             ["1.B.2.a.iv. Refining/storage", ["1.B.2.a.4"], 1],
             ["1.B.2.a.v. Distribution of oil products", ["1.B.2.a.5"], 1],
             ["1.B.2.a.vi. Other", ["1.B.2.a.6"], 1],
-            ["Drop down list:", ["\IGNORE"], 2],
+            ["Drop down list:", ["\\IGNORE"], 2],
             ["1.B.2.a.vi.1. Abandoned wells", ["1.B.2.a.6.1"], 2],
             ["1.B.2.a.vi.2. Other (please specify)", ["1.B.1.a.6.2"], 2],
-            ["NA", ["\IGNORE"], 3],
+            ["NA", ["\\IGNORE"], 3],
             ["1.B.2.b. Natural gas", ["1.B.2.b"], 0],
             ["1.B.2.b.i. Exploration", ["1.B.2.b.1"], 1],
             ["1.B.2.b.ii. Production and gathering (8)", ["1.B.2.b.2"], 1],
@@ -833,7 +834,7 @@ CRF2023_AUS = {
             ["1.B.2.b.iv. Transmission and storage", ["1.B.2.b.4"], 1],
             ["1.B.2.b.v. Distribution", ["1.B.2.b.5"], 1],
             ["1.B.2.b.vi. Other", ["1.B.2.b.6"], 1],
-            ["Drop down list:", ["\IGNORE"], 2],
+            ["Drop down list:", ["\\IGNORE"], 2],
             ["1.B.2.b.vi.1. Gas post-meter", ["1.B.2.b.6.1"], 3],
             ["1.B.2.b.vi.2. Abandoned wells", ["1.B.2.b.6.2"], 3],
             ["1.B.2.b.vi.3. Other (please specify)", ["1.B.2.b.6.3"], 3],
@@ -850,7 +851,7 @@ CRF2023_AUS = {
             ["1.B.2.c.ii.2. Gas", ["1.B.2.c-fla.ii"], 2],
             ["1.B.2.c.ii.3. Combined", ["1.B.2.c-fla.iii"], 2],
             ["1.B.2.d. Other (please specify) (10)", ["1.B.2.d"], 0],
-            ["NA", ["\IGNORE"], 1],
+            ["NA", ["\\IGNORE"], 1],
         ],
         "entity_mapping": {
             "EMISSIONS CH4 (5)": "CH4",
@@ -882,13 +883,13 @@ CRF2023_AUS = {
             ["1.C.1.a. Pipelines", ["1.C.1.a"], 1],
             ["1.C.1.b. Ships", ["1.C.1.b"], 1],
             ["1.C.1.c. Other (please specify)", ["1.C.1.c"], 1],
-            ["NA", ["\IGNORE"], 2],
+            ["NA", ["\\IGNORE"], 2],
             ["1.C.2. Injection and storage (3)", ["1.C.2"], 0],
             ["1.C.2.a. Injection", ["1.C.2.a"], 1],
             ["1.C.2.b. Storage", ["1.C.2.b"], 1],
             ["1.C.3. Other (please specify)", ["1.C.3"], 0],
-            ["NA", ["\IGNORE"], 1],
-            ["Information item (4, 5, 6)", ["\IGNORE"], 0],
+            ["NA", ["\\IGNORE"], 1],
+            ["Information item (4, 5, 6)", ["\\IGNORE"], 0],
             ["Total amount captured for storage (7)", ["M.Info.A.TACS"], 1],
             ["Total amount of imports for storage (7)", ["M.Info.A.TAIS"], 1],
             ["Total A", ["M.Info.A"], 1],
@@ -901,7 +902,7 @@ CRF2023_AUS = {
                 1,
             ],
             ["Total B", ["M.Info.B"], 1],
-            ["Difference (A-B)(6)", ["\IGNORE"], 1],
+            ["Difference (A-B)(6)", ["\\IGNORE"], 1],
         ],
         "entity_mapping": {
             "EMISSIONS CO2 (2)": "CO2",
@@ -1097,10 +1098,10 @@ CRF2023_AUS = {
             ["3. Total agriculture", ["3"], 0],
             # A. Enteric fermentation
             ["3.A. Enteric fermentation", ["3.A"], 1],
-            ["Option A:", ["\IGNORE"], 2],
+            ["Option A:", ["\\IGNORE"], 2],
             ["3.A.1.a. Dairy cattle", ["3.A.1.Aa"], 3],
             ["3.A.1.b. Non-dairy cattle", ["3.A.1.Ab"], 3],
-            ["Option B (country-specific):", ["\IGNORE"], 2],
+            ["Option B (country-specific):", ["\\IGNORE"], 2],
             ["3.A.1.a. Other", ["3.A.1.C"], 3],
             # Other livestock
             ["3.A.2. Sheep", ["3.A.2"], 2],
@@ -1109,10 +1110,10 @@ CRF2023_AUS = {
             # Manure Management
             ["3.B. Manure management", ["3.B"], 1],
             ["3.B.1. Cattle(3)", ["3.B.1"], 2],
-            ["Option A:", ["\IGNORE"], 3],
+            ["Option A:", ["\\IGNORE"], 3],
             ["3.B.1.a. Dairy cattle", ["3.B.1.Aa"], 4],
             ["3.B.1.b. Non-dairy cattle", ["3.B.1.Ab"], 4],
-            ["Option B (country-specific):", ["\IGNORE"], 3],
+            ["Option B (country-specific):", ["\\IGNORE"], 3],
             ["3.B.1.a. Other", ["3.B.1.C"], 4],
             ["3.B.2. Sheep", ["3.B.2"], 2],
             ["3.B.3. Swine", ["3.B.3"], 2],
@@ -1140,7 +1141,7 @@ CRF2023_AUS = {
             ["3.H. Urea application", ["3.H"], 1],
             ["3.I. Other carbon-containing fertilizers", ["3.I"], 1],
             ["3.J. Other (please specify)", ["3.J"], 1],
-            ["NA", ["\IGNORE"], 2],
+            ["NA", ["\\IGNORE"], 2],
         ],
         "entity_mapping": {"Total GHG emissions (1)": "KYOTOGHG (AR4GWP100)"},
         "coords_defaults": {
@@ -1166,27 +1167,27 @@ CRF2023_AUS = {
         },
         "sector_mapping": [
             ["3.A.1. Cattle", ["3.A.1"], 0],
-            ["Option A:", ["\IGNORE"], 1],
+            ["Option A:", ["\\IGNORE"], 1],
             ["3.A.1.a. Dairy cattle", ["3.A.1.Aa"], 2],
             ["3.A.1.b. Non-dairy cattle", ["3.A.1.Ab"], 2],
-            ["Option B (country-specific): (3)", ["\IGNORE"], 1],
-            ["3.A.1.a. Other", ["\IGNORE"], 2],
-            ["Drop-down list:", ["\IGNORE"], 3],
-            ["3.A.1.a.i. Mature dairy cattle", ["\IGNORE"], 3],
-            ["3.A.1.a.ii. Other mature cattle", ["\IGNORE"], 3],
-            ["3.A.1.a.iii. Growing cattle", ["\IGNORE"], 3],
+            ["Option B (country-specific): (3)", ["\\IGNORE"], 1],
+            ["3.A.1.a. Other", ["\\IGNORE"], 2],
+            ["Drop-down list:", ["\\IGNORE"], 3],
+            ["3.A.1.a.i. Mature dairy cattle", ["\\IGNORE"], 3],
+            ["3.A.1.a.ii. Other mature cattle", ["\\IGNORE"], 3],
+            ["3.A.1.a.iii. Growing cattle", ["\\IGNORE"], 3],
             ["3.A.1.a.iv. Other (please specify)", ["3.A.1.C"], 3],
             ["Dairy Cattle", ["3.A.1.C-AUS-a"], 4],
             ["Beef Cattle - Pasture", ["3.A.1.C-AUS-b"], 4],
             ["Beef Cattle - Feedlot", ["3.A.1.C-AUS-c"], 4],
             ["3.A.2. Sheep", ["3.A.2"], 0],
-            ["3.A.2.a. Other (please specify)", ["\IGNORE"], 1],
-            ["Sheep", ["\IGNORE"], 2],
+            ["3.A.2.a. Other (please specify)", ["\\IGNORE"], 1],
+            ["Sheep", ["\\IGNORE"], 2],
             ["3.A.3. Swine", ["3.A.3"], 0],
-            ["3.A.3.a. Other (please specify)", ["\IGNORE"], 1],
-            ["Swine", ["\IGNORE"], 2],
+            ["3.A.3.a. Other (please specify)", ["\\IGNORE"], 1],
+            ["Swine", ["\\IGNORE"], 2],
             ["3.A.4. Other livestock (please specify) (4)", ["3.A.4"], 0],
-            ["Drop down list:", ["\IGNORE"], 1],
+            ["Drop down list:", ["\\IGNORE"], 1],
             ["3.A.4.a. Buffalo", ["3.A.4.a"], 2],
             ["3.A.4.b. Camels", ["3.A.4.b"], 2],
             ["3.A.4.c. Deer", ["3.A.4.c"], 2],
@@ -1200,7 +1201,7 @@ CRF2023_AUS = {
             ["3.A.4.h.iii. Ostrich", ["3.A.4.h.iii"], 3],
             ["3.A.4.h.iv. Fur-bearing animals (5)", ["3.A.4.h.iv"], 3],
             ["3.A.4.h.v. Other (please specity)", ["3.A.4.h.v"], 3],
-            ["Alpacas", ["\IGNORE"], 4],
+            ["Alpacas", ["\\IGNORE"], 4],
         ],
         "entity_mapping": {"EMISSIONS CH4": "CH4"},
         "coords_defaults": {
@@ -1230,27 +1231,27 @@ CRF2023_AUS = {
         },
         "sector_mapping": [
             ["3.B.1. Cattle", ["3.B.1"], 0],
-            ["Option A:", ["\IGNORE"], 1],
+            ["Option A:", ["\\IGNORE"], 1],
             ["3.B.1.a. Dairy cattle", ["3.B.1.Aa"], 2],
             ["3.B.1.b. Non-dairy cattle", ["3.B.1.Ab"], 2],
-            ["Option B (country-specific): (3)", ["\IGNORE"], 1],
-            ["3.B.1.a. Other", ["\IGNORE"], 2],
-            ["Drop down list:", ["\IGNORE"], 3],
-            ["3.B.1.a.i. Mature dairy cattle", ["\IGNORE"], 3],
-            ["3.B.1.a.ii. Other mature cattle", ["\IGNORE"], 3],
-            ["3.B.1.a.iii. Growing cattle", ["\IGNORE"], 3],
+            ["Option B (country-specific): (3)", ["\\IGNORE"], 1],
+            ["3.B.1.a. Other", ["\\IGNORE"], 2],
+            ["Drop down list:", ["\\IGNORE"], 3],
+            ["3.B.1.a.i. Mature dairy cattle", ["\\IGNORE"], 3],
+            ["3.B.1.a.ii. Other mature cattle", ["\\IGNORE"], 3],
+            ["3.B.1.a.iii. Growing cattle", ["\\IGNORE"], 3],
             ["3.B.1.a.iv. Other (please specify)", ["3.B.1.C"], 3],
             ["Dairy Cattle", ["3.B.1.C-AUS-a"], 4],
             ["Beef Cattle - Pasture", ["3.B.1.C-AUS-b"], 4],
             ["Beef Cattle - Feedlot", ["3.B.1.C-AUS-c"], 4],
             ["3.B.2. Sheep", ["3.B.2"], 0],
-            ["3.B.2.a. Other (please specify)", ["\IGNORE"], 1],
-            ["Sheep", ["\IGNORE"], 2],
+            ["3.B.2.a. Other (please specify)", ["\\IGNORE"], 1],
+            ["Sheep", ["\\IGNORE"], 2],
             ["3.B.3. Swine", ["3.B.3"], 0],
-            ["3.B.3.a. Other (please specify)", ["\IGNORE"], 1],
-            ["Swine", ["\IGNORE"], 2],
+            ["3.B.3.a. Other (please specify)", ["\\IGNORE"], 1],
+            ["Swine", ["\\IGNORE"], 2],
             ["3.B.4. Other livestock (4)", ["3.B.4"], 0],
-            ["Drop-down list:", ["\IGNORE"], 1],
+            ["Drop-down list:", ["\\IGNORE"], 1],
             ["3.B.4.a. Buffalo", ["3.B.4.a"], 2],
             ["3.B.4.b. Camels", ["3.B.4.b"], 2],
             ["3.B.4.c. Deer", ["3.B.4.c"], 2],
@@ -1264,7 +1265,7 @@ CRF2023_AUS = {
             ["3.B.4.h.iii. Ostrich", ["3.B.4.h.iii"], 3],
             ["3.B.4.h.iv. Fur-bearing animals (5)", ["3.B.4.h.iv"], 3],
             ["3.B.4.h.v. Other (please specity)", ["3.B.4.h.v"], 3],
-            ["Alpacas", ["\IGNORE"], 4],
+            ["Alpacas", ["\\IGNORE"], 4],
         ],
         "entity_mapping": {
             "EMISSIONS CH4 producing potential (Bo) (2) (average) CH4": "CH4"
@@ -1330,27 +1331,27 @@ CRF2023_AUS = {
         },
         "sector_mapping": [
             ["3.B.1. Cattle", ["3.B.1"], 0],
-            ["Option A:", ["\IGNORE"], 1],
+            ["Option A:", ["\\IGNORE"], 1],
             ["3.B.1.a. Dairy cattle", ["3.B.1.Aa"], 2],
             ["3.B.1.b. Non-dairy cattle", ["3.B.1.Ab"], 2],
-            ["Option B (country-specific): (5)", ["\IGNORE"], 1],
-            ["3.B.1.a. Other", ["\IGNORE"], 2],
-            ["Drop-down list", ["\IGNORE"], 3],
-            ["3.B.1.a.i. Mature dairy cattle", ["\IGNORE"], 3],
-            ["3.B.1.a.ii. Other mature cattle", ["\IGNORE"], 3],
-            ["3.B.1.a.iii. Growing cattle", ["\IGNORE"], 3],
+            ["Option B (country-specific): (5)", ["\\IGNORE"], 1],
+            ["3.B.1.a. Other", ["\\IGNORE"], 2],
+            ["Drop-down list", ["\\IGNORE"], 3],
+            ["3.B.1.a.i. Mature dairy cattle", ["\\IGNORE"], 3],
+            ["3.B.1.a.ii. Other mature cattle", ["\\IGNORE"], 3],
+            ["3.B.1.a.iii. Growing cattle", ["\\IGNORE"], 3],
             ["3.B.1.a.iv. Other (please specify)", ["3.B.1.C"], 3],
             ["Dairy Cattle", ["3.B.1.C-AUS-a"], 4],
             ["Beef Cattle - Pasture", ["3.B.1.C-AUS-b"], 4],
             ["Beef Cattle - Feedlot", ["3.B.1.C-AUS-c"], 4],
             ["3.B.2. Sheep", ["3.B.2"], 0],
-            ["3.B.2.a. Other (please specify)", ["\IGNORE"], 1],
-            ["Sheep", ["\IGNORE"], 2],
+            ["3.B.2.a. Other (please specify)", ["\\IGNORE"], 1],
+            ["Sheep", ["\\IGNORE"], 2],
             ["3.B.3. Swine", ["3.B.3"], 0],
-            ["3.B.3.a. Other (please specify)", ["\IGNORE"], 1],
-            ["Swine", ["\IGNORE"], 2],
+            ["3.B.3.a. Other (please specify)", ["\\IGNORE"], 1],
+            ["Swine", ["\\IGNORE"], 2],
             ["3.B.4. Other livestock (6)", ["3.B.4"], 0],
-            ["Drop-down list", ["\IGNORE"], 1],
+            ["Drop-down list", ["\\IGNORE"], 1],
             ["3.B.4.a. Buffalo", ["3.B.4.a"], 2],
             ["3.B.4.b. Camels", ["3.B.4.b"], 2],
             ["3.B.4.c. Deer", ["3.B.4.c"], 2],
@@ -1364,7 +1365,7 @@ CRF2023_AUS = {
             ["3.B.4.h.iii. Ostrich", ["3.B.4.h.iii"], 3],
             ["3.B.4.h.iv Fur-bearing animals (7)", ["3.B.4.h.iv"], 3],
             ["3.B.4.h.v. Other (please specity)", ["3.B.4.h.v"], 3],
-            ["Alpacas", ["\IGNORE"], 4],
+            ["Alpacas", ["\\IGNORE"], 4],
         ],
         "entity_mapping": {
             "EMISSIONS N2O Direct Nitrogen leaching and run-off": "N2O",
@@ -1400,12 +1401,12 @@ CRF2023_AUS = {
             ["3.C.2.a. Flood-prone", ["3.C.2.a"]],
             ["3.C.2.b. Drought-prone", ["3.C.2.b"]],
             ["3.C.3. Deep water", ["3.C.3"]],
-            ["3.C.3.a. Water depth 50–100 cm", ["3.C.3.a"]],
+            ["3.C.3.a. Water depth 50-100 cm", ["3.C.3.a"]],
             ["3.C.3.b. Water depth > 100 cm", ["3.C.3.b"]],
             ["3.C.4. Other (please specify)", ["3.C.4"]],
-            ["NA", ["\IGNORE"]],
-            ["Upland rice(4)", ["\IGNORE"]],
-            ["Total(4)", ["\IGNORE"]],
+            ["NA", ["\\IGNORE"]],
+            ["Upland rice(4)", ["\\IGNORE"]],
+            ["Total(4)", ["\\IGNORE"]],
         ],
         "entity_mapping": {
             "EMISSIONS CH4": "CH4",
@@ -1484,9 +1485,9 @@ CRF2023_AUS = {
         },
         "sector_mapping": [
             ["3.E.1. Forest land (specify ecological zone) (2)", ["3.E.1"], 0],
-            ["NA", ["\IGNORE"], 1],
+            ["NA", ["\\IGNORE"], 1],
             ["3.E.2. Grassland (specify ecological zone) (2)", ["3.E.2"], 0],
-            ["NA", ["\IGNORE"], 1],
+            ["NA", ["\\IGNORE"], 1],
         ],
         "entity_mapping": {
             "EMISSIONS (2) CH4": "CH4",
@@ -1612,7 +1613,7 @@ CRF2023_AUS = {
             ["5.D.3. Other", ["5.D.3"]],
             ["5.E. Other (please specify)", ["5.E"]],
             ["Accidential fires at Solid Waste Disposal Sites", ["5.E.9"]],
-            ["Memo item: (3)", ["\IGNORE"]],
+            ["Memo item: (3)", ["\\IGNORE"]],
             ["5.F.1. Long-term storage of C in waste disposal sites", ["M.Memo.LTSW"]],
             ["5.F.1.a. Annual change in total long-term C storage", ["M.Memo.ACLT"]],
             [
@@ -1693,10 +1694,10 @@ CRF2023_AUS = {
             ["5.D. Wastewater treatment and discharge", ["5.D"]],
             ["5.E. Other (6)", ["5.E"]],
             ["6. Other (please specify) (7)", ["6"]],
-            ["NA", ["\IGNORE"]],
-            ["", ["\IGNORE"]],
-            [np.nan, ["\IGNORE"]],
-            ["Memo items: (8)", ["\IGNORE"]],
+            ["NA", ["\\IGNORE"]],
+            ["", ["\\IGNORE"]],
+            [np.nan, ["\\IGNORE"]],
+            ["Memo items: (8)", ["\\IGNORE"]],
             ["1.D.1. International bunkers", ["M.Memo.Int"]],
             ["1.D.1.a. Aviation", ["M.Memo.Int.Avi"]],
             ["1.D.1.b. Navigation", ["M.Memo.Int.Mar"]],

UNFCCC_GHG_data/UNFCCC_CRF_reader/crf_specifications/CRF2023_specification.py → src/unfccc_ghg_data/unfccc_crf_reader/crf_specifications/crf2023_specification.py

@@ -1,4 +1,4 @@
-""" CRF2022 specification.
+"""CRF2022 specification.
 Currently not all tables are included. Extend if you need all country
 specific items in categories 2, 3.H-G, 4
 
@@ -40,6 +40,7 @@ TODO:
 """
 
 import numpy as np
+
 from .util import unit_info
 
 # TODO: GWPs now differ by country. This has to be implemented (maybe giving
@@ -122,7 +123,7 @@ CRF2023 = {
             ['1. Transport of CO2', ['1.C.1']],
             ['2. Injection and storage', ['1.C.2']],
             ['3. Other', ['1.C.3']],
-            ['Memo items: (1)', ['\IGNORE']],
+            ['Memo items: (1)', ['\\IGNORE']],
             ['International bunkers', ['M.Memo.Int']],
             ['Aviation', ['M.Memo.Int.Avi']],
             ['Navigation', ['M.Memo.Int.Mar']],
@@ -455,8 +456,8 @@ CRF2023 = {
             # 1.A.2.g.viii Other (please specify)
             ['1.A.2.g.viii Other (please specify)', ['1.A.2.g.viii', 'Total'], 2],
             # DKE
-            ['Construction', ['\IGNORE', '\IGNORE'], 3],  # (empty)
-            ['Mining', ['\IGNORE', '\IGNORE'], 3],  # (empty)
+            ['Construction', ['\\IGNORE', '\\IGNORE'], 3],  # (empty)
+            ['Mining', ['\\IGNORE', '\\IGNORE'], 3],  # (empty)
             # DNK, DKE, USA, CZE
             ['Other non-specified', ['1.A.2.g.viii.1', 'Total'], 3],
             ['Liquid Fuels', ['1.A.2.g.viii.1', 'Liquid'], 4],
@@ -506,7 +507,7 @@ CRF2023 = {
             ['Peat', ['1.A.2.g.viii.1', 'Peat'], 4],
             ['Biomass', ['1.A.2.g.viii.1', 'Biomass'], 4],
             # DKE
-            ['Textile', ['\IGNORE', '\IGNORE'], 3],  # (empty)
+            ['Textile', ['\\IGNORE', '\\IGNORE'], 3],  # (empty)
             # DNK, DNM, FIN, DKE
             ['Other manufacturing industries', ['1.A.2.g.viii.3', 'Total'], 3],
             ['Liquid Fuels', ['1.A.2.g.viii.3', 'Liquid'], 4],
@@ -1419,10 +1420,10 @@ CRF2023 = {
             ['iii. Mobile (other)', ['1.A.5.b.iv', 'Total'], 2],
             ['Liquid Fuels', ['1.A.5.b.iv', 'Liquid'], 3],
             # Information Item
-            ['Information item:(15)', ['\IGNORE', '\IGNORE'], 0],
-            ['Waste incineration with energy recovery included as:', ['\IGNORE', '\IGNORE'], 1],
-            ['Biomass(6)', ['\IGNORE', '\IGNORE'], 1],
-            ['Fossil fuels(4)', ['\IGNORE', '\IGNORE'], 1],
+            ['Information item:(15)', ['\\IGNORE', '\\IGNORE'], 0],
+            ['Waste incineration with energy recovery included as:', ['\\IGNORE', '\\IGNORE'], 1],
+            ['Biomass(6)', ['\\IGNORE', '\\IGNORE'], 1],
+            ['Fossil fuels(4)', ['\\IGNORE', '\\IGNORE'], 1],
         ],
         "entity_mapping": {
             'EMISSIONS CH4': "CH4",
@@ -1570,7 +1571,7 @@ CRF2023 = {
             ['a. Injection', ['1.C.2.a']],
             ['b. Storage', ['1.C.2.b']],
             ['3. Other', ['1.C.3']],
-            ['Information item(4, 5)', ['\IGNORE']],
+            ['Information item(4, 5)', ['\\IGNORE']],
             ['Total amount captured for storage', ['M.Info.A.TACS']],
             ['Total amount of imports for storage', ['M.Info.A.TAIS']],
             ['Total A', ['M.Info.A']],
@@ -1578,7 +1579,7 @@ CRF2023 = {
             ['Total amount of CO2 injected at storage sites', ['M.Info.B.TAI']],
             ['Total leakage from transport, injection and storage', ['M.Info.B.TLTIS']],
             ['Total B', ['M.Info.B']],
-            ['Difference (A-B)(6)', ['\IGNORE']],
+            ['Difference (A-B)(6)', ['\\IGNORE']],
         ],
         "entity_mapping": {
             'EMISSIONS CO2(2)': 'CO2',
@@ -1837,61 +1838,61 @@ CRF2023 = {
             # A. Enteric fermentation
             ['A. Enteric fermentation', ['3.A'], 2],
             ['1. Cattle(1)', ['3.A.1'], 3],
-            ['Option A:', ['\IGNORE'], 4],
+            ['Option A:', ['\\IGNORE'], 4],
             ['Dairy cattle', ['3.A.1.Aa'], 5],
             ['Non-dairy cattle', ['3.A.1.Ab'], 5],
-            ['Option B:', ['\IGNORE'], 4],
+            ['Option B:', ['\\IGNORE'], 4],
             ['Mature dairy cattle', ['3.A.1.Ba'], 5],
             ['Other mature cattle', ['3.A.1.Bb'], 5],
             ['Growing cattle', ['3.A.1.Bc'], 5],
-            ['Option C (country-specific):', ['\IGNORE'], 4],
+            ['Option C (country-specific):', ['\\IGNORE'], 4],
             # all countries not specified explcitly
-            ['\C!-AUS-MLT-LUX-POL-SVN-USA\ Other (as specified in table 3(I).A)', ['3.A.1.C'], 5],
+            ['\\C!-AUS-MLT-LUX-POL-SVN-USA\\ Other (as specified in table 3(I).A)', ['3.A.1.C'], 5],
             # Australia
-            ['\C-AUS\ Other (as specified in table 3(I).A)', ['3.A.1.C'], 5],
-            ['\C-AUS\ Dairy Cattle', ['3.A.1.C-AUS-a'], 6],
-            ['\C-AUS\ Beef Cattle - Pasture', ['3.A.1.C-AUS-b'], 6],
-            ['\C-AUS\ Beef Cattle - Feedlot', ['3.A.1.C-AUS-c'], 6],
+            ['\\C-AUS\\ Other (as specified in table 3(I).A)', ['3.A.1.C'], 5],
+            ['\\C-AUS\\ Dairy Cattle', ['3.A.1.C-AUS-a'], 6],
+            ['\\C-AUS\\ Beef Cattle - Pasture', ['3.A.1.C-AUS-b'], 6],
+            ['\\C-AUS\\ Beef Cattle - Feedlot', ['3.A.1.C-AUS-c'], 6],
             # malta
-            ['\C-MLT\ Other (as specified in table 3(I).A)', ['3.A.1.C'], 5],
-            ['\C-MLT\ dairy cows', ['3.A.1.C-MLT-a'], 6],
-            ['\C-MLT\ non-lactating cows', ['3.A.1.C-MLT-b'], 6],
-            ['\C-MLT\ bulls', ['3.A.1.C-MLT-c'], 6],
-            ['\C-MLT\ calves', ['3.A.1.C-MLT-d'], 6],
-            ['\C-MLT\ growing cattle 1-2 years', ['3.A.1.C-MLT-e'], 6],
+            ['\\C-MLT\\ Other (as specified in table 3(I).A)', ['3.A.1.C'], 5],
+            ['\\C-MLT\\ dairy cows', ['3.A.1.C-MLT-a'], 6],
+            ['\\C-MLT\\ non-lactating cows', ['3.A.1.C-MLT-b'], 6],
+            ['\\C-MLT\\ bulls', ['3.A.1.C-MLT-c'], 6],
+            ['\\C-MLT\\ calves', ['3.A.1.C-MLT-d'], 6],
+            ['\\C-MLT\\ growing cattle 1-2 years', ['3.A.1.C-MLT-e'], 6],
             # Luxembourg
-            ['\C-LUX\ Other (as specified in table 3(I).A)', ['3.A.1.C'], 5],
-            ['\C-LUX\ Bulls', ['3.A.1.C-LUX-a'], 6],
-            ['\C-LUX\ Calves', ['3.A.1.C-LUX-b'], 6],
-            ['\C-LUX\ Young Cattle', ['3.A.1.C-LUX-c'], 6],
-            ['\C-LUX\ Suckler Cows', ['3.A.1.C-LUX-d'], 6],
-            ['\C-LUX\ Bulls under 2 years', ['3.A.1.C-LUX-e'], 6],
-            ['\C-LUX\ Dairy Cows', ['3.A.1.C-LUX-f'], 6],
+            ['\\C-LUX\\ Other (as specified in table 3(I).A)', ['3.A.1.C'], 5],
+            ['\\C-LUX\\ Bulls', ['3.A.1.C-LUX-a'], 6],
+            ['\\C-LUX\\ Calves', ['3.A.1.C-LUX-b'], 6],
+            ['\\C-LUX\\ Young Cattle', ['3.A.1.C-LUX-c'], 6],
+            ['\\C-LUX\\ Suckler Cows', ['3.A.1.C-LUX-d'], 6],
+            ['\\C-LUX\\ Bulls under 2 years', ['3.A.1.C-LUX-e'], 6],
+            ['\\C-LUX\\ Dairy Cows', ['3.A.1.C-LUX-f'], 6],
             # Poland
-            ['\C-POL\ Other (as specified in table 3(I).A)', ['3.A.1.C'], 5],
-            ['\C-POL\ Bulls (older than 2 years)', ['3.A.1.C-POL-a'], 6],
-            ['\C-POL\ Non-dairy Heifers (older than 2 years)', ['3.A.1.C-POL-b'], 6],
-            ['\C-POL\ Non-dairy Young Cattle (younger than 1 year)', ['3.A.1.C-POL-c'], 6],
-            ['\C-POL\ Dairy Cattle', ['3.A.1.C-POL-d'], 6],
-            ['\C-POL\ Non-dairy Young Cattle (1-2 years)', ['3.A.1.C-POL-e'], 6],
+            ['\\C-POL\\ Other (as specified in table 3(I).A)', ['3.A.1.C'], 5],
+            ['\\C-POL\\ Bulls (older than 2 years)', ['3.A.1.C-POL-a'], 6],
+            ['\\C-POL\\ Non-dairy Heifers (older than 2 years)', ['3.A.1.C-POL-b'], 6],
+            ['\\C-POL\\ Non-dairy Young Cattle (younger than 1 year)', ['3.A.1.C-POL-c'], 6],
+            ['\\C-POL\\ Dairy Cattle', ['3.A.1.C-POL-d'], 6],
+            ['\\C-POL\\ Non-dairy Young Cattle (1-2 years)', ['3.A.1.C-POL-e'], 6],
             # Slovenia
-            ['\C-SVN\ Other (as specified in table 3(I).A)', ['3.A.1.C'], 5],
-            ['\C-SVN\ Dairy cows', ['3.A.1.C-SVN-a'], 6],
-            ['\C-SVN\ Non-dairy cattle', ['3.A.1.C-SVN-b'], 6],
-            ['\C-SVN\ Other cows', ['3.A.1.C-SVN-c'], 6],
+            ['\\C-SVN\\ Other (as specified in table 3(I).A)', ['3.A.1.C'], 5],
+            ['\\C-SVN\\ Dairy cows', ['3.A.1.C-SVN-a'], 6],
+            ['\\C-SVN\\ Non-dairy cattle', ['3.A.1.C-SVN-b'], 6],
+            ['\\C-SVN\\ Other cows', ['3.A.1.C-SVN-c'], 6],
             # USA
-            ['\C-USA\ Other (as specified in table 3(I).A)', ['3.A.1.C'], 5],
-            ['\C-USA\ Steer Stocker', ['3.A.1.C-USA-a'], 6],
-            ['\C-USA\ Heifer Stocker', ['3.A.1.C-USA-b'], 6],
-            ['\C-USA\ Beef Cows', ['3.A.1.C-USA-c'], 6],
-            ['\C-USA\ Dairy Replacements', ['3.A.1.C-USA-d'], 6],
-            ['\C-USA\ Beef Replacements', ['3.A.1.C-USA-e'], 6],
-            ['\C-USA\ Steer Feedlot', ['3.A.1.C-USA-f'], 6],
-            ['\C-USA\ Heifer Feedlot', ['3.A.1.C-USA-g'], 6],
-            ['\C-USA\ Bulls', ['3.A.1.C-USA-h'], 6],
-            ['\C-USA\ Dairy Cows', ['3.A.1.C-USA-i'], 6],
-            ['\C-USA\ Beef Calves', ['3.A.1.C-USA-j'], 6],
-            ['\C-USA\ Dairy Calves', ['3.A.1.C-USA-k'], 6],
+            ['\\C-USA\\ Other (as specified in table 3(I).A)', ['3.A.1.C'], 5],
+            ['\\C-USA\\ Steer Stocker', ['3.A.1.C-USA-a'], 6],
+            ['\\C-USA\\ Heifer Stocker', ['3.A.1.C-USA-b'], 6],
+            ['\\C-USA\\ Beef Cows', ['3.A.1.C-USA-c'], 6],
+            ['\\C-USA\\ Dairy Replacements', ['3.A.1.C-USA-d'], 6],
+            ['\\C-USA\\ Beef Replacements', ['3.A.1.C-USA-e'], 6],
+            ['\\C-USA\\ Steer Feedlot', ['3.A.1.C-USA-f'], 6],
+            ['\\C-USA\\ Heifer Feedlot', ['3.A.1.C-USA-g'], 6],
+            ['\\C-USA\\ Bulls', ['3.A.1.C-USA-h'], 6],
+            ['\\C-USA\\ Dairy Cows', ['3.A.1.C-USA-i'], 6],
+            ['\\C-USA\\ Beef Calves', ['3.A.1.C-USA-j'], 6],
+            ['\\C-USA\\ Dairy Calves', ['3.A.1.C-USA-k'], 6],
             # Other livestock
             ['2. Sheep', ['3.A.2'], 3],
             ['3. Swine', ['3.A.3'], 3],
@@ -1912,60 +1913,60 @@ CRF2023 = {
             # Manure Management
             ['B. Manure management', ['3.B'], 2],
             ['1. Cattle(1)', ['3.B.1'], 3],
-            ['Option A:', ['\IGNORE'], 4],
+            ['Option A:', ['\\IGNORE'], 4],
             ['Dairy cattle', ['3.B.1.Aa'], 5],
             ['Non-dairy cattle', ['3.B.1.Ab'], 5],
-            ['Option B:', ['\IGNORE'], 4],
+            ['Option B:', ['\\IGNORE'], 4],
             ['Mature dairy cattle', ['3.B.1.Ba'], 5],
             ['Other mature cattle', ['3.B.1.Bb'], 5],
             ['Growing cattle', ['3.B.1.Bc'], 5],
-            ['Option C (country-specific):', ['\IGNORE'], 4],
+            ['Option C (country-specific):', ['\\IGNORE'], 4],
             # all countries not specified explicitly
-            ['\C!-AUS-MLT-LUX-POL-SVN-USA\ Other (as specified in table 3(I).B)', ['3.B.1.C'], 5],
+            ['\\C!-AUS-MLT-LUX-POL-SVN-USA\\ Other (as specified in table 3(I).B)', ['3.B.1.C'], 5],
             # Australia
-            ['\C-AUS\ Other (as specified in table 3(I).B)', ['3.B.1.C'], 5],
-            ['\C-AUS\ Dairy Cattle', ['3.B.1.C-AUS-a'], 6],
-            ['\C-AUS\ Beef Cattle - Pasture', ['3.B.1.C-AUS-b'], 6],
-            ['\C-AUS\ Beef Cattle - Feedlot', ['3.B.1.C-AUS-c'], 6],
+            ['\\C-AUS\\ Other (as specified in table 3(I).B)', ['3.B.1.C'], 5],
+            ['\\C-AUS\\ Dairy Cattle', ['3.B.1.C-AUS-a'], 6],
+            ['\\C-AUS\\ Beef Cattle - Pasture', ['3.B.1.C-AUS-b'], 6],
+            ['\\C-AUS\\ Beef Cattle - Feedlot', ['3.B.1.C-AUS-c'], 6],
             # Malta
-            ['\C-MLT\ Other (as specified in table 3(I).B)', ['3.B.1.C'], 5],
-            ['\C-MLT\ dairy cows', ['3.B.1.C-MLT-a'], 6],
-            ['\C-MLT\ non-lactating cows', ['3.B.1.C-MLT-b'], 6],
-            ['\C-MLT\ bulls', ['3.B.1.C-MLT-c'], 6],
-            ['\C-MLT\ calves', ['3.B.1.C-MLT-d'], 6],
-            ['\C-MLT\ growing cattle 1-2 years', ['3.B.1.C-MLT-e'], 6],
+            ['\\C-MLT\\ Other (as specified in table 3(I).B)', ['3.B.1.C'], 5],
+            ['\\C-MLT\\ dairy cows', ['3.B.1.C-MLT-a'], 6],
+            ['\\C-MLT\\ non-lactating cows', ['3.B.1.C-MLT-b'], 6],
+            ['\\C-MLT\\ bulls', ['3.B.1.C-MLT-c'], 6],
+            ['\\C-MLT\\ calves', ['3.B.1.C-MLT-d'], 6],
+            ['\\C-MLT\\ growing cattle 1-2 years', ['3.B.1.C-MLT-e'], 6],
             # Luxembourg
-            ['\C-LUX\ Other (as specified in table 3(I).B)', ['3.B.1.C'], 5],
-            ['\C-LUX\ Bulls', ['3.B.1.C-LUX-a'], 6],
-            ['\C-LUX\ Calves', ['3.B.1.C-LUX-b'], 6],
-            ['\C-LUX\ Young Cattle', ['3.B.1.C-LUX-c'], 6],
-            ['\C-LUX\ Suckler Cows', ['3.B.1.C-LUX-d'], 6],
-            ['\C-LUX\ Bulls under 2 years', ['3.B.1.C-LUX-e'], 6],
-            ['\C-LUX\ Dairy Cows', ['3.B.1.C-LUX-f'], 6],
+            ['\\C-LUX\\ Other (as specified in table 3(I).B)', ['3.B.1.C'], 5],
+            ['\\C-LUX\\ Bulls', ['3.B.1.C-LUX-a'], 6],
+            ['\\C-LUX\\ Calves', ['3.B.1.C-LUX-b'], 6],
+            ['\\C-LUX\\ Young Cattle', ['3.B.1.C-LUX-c'], 6],
+            ['\\C-LUX\\ Suckler Cows', ['3.B.1.C-LUX-d'], 6],
+            ['\\C-LUX\\ Bulls under 2 years', ['3.B.1.C-LUX-e'], 6],
+            ['\\C-LUX\\ Dairy Cows', ['3.B.1.C-LUX-f'], 6],
             # Poland
-            ['\C-POL\ Other (as specified in table 3(I).B)', ['3.B.1.C'], 5],
-            ['\C-POL\ Non-dairy Cattle', ['3.B.1.C-POL-a'], 6],
-            ['\C-POL\ Dairy Cattle', ['3.B.1.C-POL-b'], 6],
+            ['\\C-POL\\ Other (as specified in table 3(I).B)', ['3.B.1.C'], 5],
+            ['\\C-POL\\ Non-dairy Cattle', ['3.B.1.C-POL-a'], 6],
+            ['\\C-POL\\ Dairy Cattle', ['3.B.1.C-POL-b'], 6],
             # Slovenia
-            ['\C-SVN\ Other (as specified in table 3(I).B)', ['3.B.1.C'], 5],
-            ['\C-SVN\ Dairy cows', ['3.B.1.C-SVN-a'], 6],
-            ['\C-SVN\ Non-dairy cattle', ['3.B.1.C-SVN-b'], 6],
-            ['\C-SVN\ Other cows', ['3.B.1.C-SVN-c'], 6],
+            ['\\C-SVN\\ Other (as specified in table 3(I).B)', ['3.B.1.C'], 5],
+            ['\\C-SVN\\ Dairy cows', ['3.B.1.C-SVN-a'], 6],
+            ['\\C-SVN\\ Non-dairy cattle', ['3.B.1.C-SVN-b'], 6],
+            ['\\C-SVN\\ Other cows', ['3.B.1.C-SVN-c'], 6],
             # USA
-            ['\C-USA\ Other (as specified in table 3(I).B)', ['3.B.1.C'], 5],
-            ['\C-USA\ Dairy Cattle', ['\IGNORE'], 6],
-            ['\C-USA\ Non-Dairy Cattle', ['\IGNORE'], 6],
-            ['\C-USA\ Steer Stocker', ['3.B.1.C-USA-a'], 6],
-            ['\C-USA\ Heifer Stocker', ['3.B.1.C-USA-b'], 6],
-            ['\C-USA\ Beef Cows', ['3.B.1.C-USA-c'], 6],
-            ['\C-USA\ Dairy Replacements', ['3.B.1.C-USA-d'], 6],
-            ['\C-USA\ Beef Replacements', ['3.B.1.C-USA-e'], 6],
-            ['\C-USA\ Steer Feedlot', ['3.B.1.C-USA-f'], 6],
-            ['\C-USA\ Heifer Feedlot', ['3.B.1.C-USA-g'], 6],
-            ['\C-USA\ Bulls', ['3.B.1.C-USA-h'], 6],
-            ['\C-USA\ Dairy Cows', ['3.B.1.C-USA-i'], 6],
-            ['\C-USA\ Beef Calves', ['3.B.1.C-USA-j'], 6],
-            ['\C-USA\ Dairy Calves', ['3.B.1.C-USA-k'], 6],
+            ['\\C-USA\\ Other (as specified in table 3(I).B)', ['3.B.1.C'], 5],
+            ['\\C-USA\\ Dairy Cattle', ['\\IGNORE'], 6],
+            ['\\C-USA\\ Non-Dairy Cattle', ['\\IGNORE'], 6],
+            ['\\C-USA\\ Steer Stocker', ['3.B.1.C-USA-a'], 6],
+            ['\\C-USA\\ Heifer Stocker', ['3.B.1.C-USA-b'], 6],
+            ['\\C-USA\\ Beef Cows', ['3.B.1.C-USA-c'], 6],
+            ['\\C-USA\\ Dairy Replacements', ['3.B.1.C-USA-d'], 6],
+            ['\\C-USA\\ Beef Replacements', ['3.B.1.C-USA-e'], 6],
+            ['\\C-USA\\ Steer Feedlot', ['3.B.1.C-USA-f'], 6],
+            ['\\C-USA\\ Heifer Feedlot', ['3.B.1.C-USA-g'], 6],
+            ['\\C-USA\\ Bulls', ['3.B.1.C-USA-h'], 6],
+            ['\\C-USA\\ Dairy Cows', ['3.B.1.C-USA-i'], 6],
+            ['\\C-USA\\ Beef Calves', ['3.B.1.C-USA-j'], 6],
+            ['\\C-USA\\ Dairy Calves', ['3.B.1.C-USA-k'], 6],
             # other animals
             ['2. Sheep', ['3.B.2'], 3],
             ['3. Swine', ['3.B.3'], 3],
@@ -2056,15 +2057,15 @@ CRF2023 = {
             ['Flood prone', ['3.C.2.a']],
             ['Drought prone', ['3.C.2.b']],
             ['3. Deep water', ['3.C.3']],
-            ['Water depth 50–100 cm', ['3.C.3.a']],
+            ['Water depth 50-100 cm', ['3.C.3.a']],
             ['Water depth > 100 cm', ['3.C.3.b']],
             ['4. Other (please specify)', ['3.C.4']],
             ['Non-specified', ['3.C.4.a']],  # EST
             ['Other', ['3.C.4.a']],  # DEU
             ['other', ['3.C.4.a']],  # LVA
             ['Other cultivation', ['3.C.4.a']],  # CZE
-            ['Upland rice(4)', ['\IGNORE']],
-            ['Total(4)', ['\IGNORE']],
+            ['Upland rice(4)', ['\\IGNORE']],
+            ['Total(4)', ['\\IGNORE']],
         ],
         "entity_mapping": {
             'EMISSIONS CH4': 'CH4',
@@ -2304,7 +2305,7 @@ CRF2023 = {
             ['Other waste', ['5.E.5']],  # CZE
             ['5.E.1 Industrial Wastewater', ['5.E.8']],  # CAN, new in 2022
             ['Accidental Fires at SWDS', ['5.E.9']],  # AUS, new in 2022
-            ['Memo item:(2)', ['\IGNORE']],
+            ['Memo item:(2)', ['\\IGNORE']],
             ['Long-term storage of C in waste disposal sites', ['M.Memo.LTSW']],
             ['Annual change in total long-term C storage', ['M.Memo.ACLT']],
             ['Annual change in total long-term C storage in HWP waste(3)', ['M.Memo.ACLTHWP']],
@@ -2663,7 +2664,7 @@ CRF2023 = {
             "unit_info": unit_info["summary"],
         },
         "sector_mapping": [
-            ['Memo items:(7)', ['\IGNORE']],
+            ['Memo items:(7)', ['\\IGNORE']],
             ['International bunkers', ['M.Memo.Int']],
             ['Aviation', ['M.Memo.Int.Avi']],
             ['Navigation', ['M.Memo.Int.Mar']],

UNFCCC_GHG_data/UNFCCC_CRF_reader/crf_specifications/util.py → src/unfccc_ghg_data/unfccc_crf_reader/crf_specifications/util.py

@@ -1,4 +1,4 @@
-""" Some definitions used for several CRF specifications"""
+"""Some definitions used for several CRF specifications"""
 
 unit_info = {
     "default": {
@@ -46,4 +46,4 @@ unit_info = {
         },
         "default_unit": "kt",
     },
-}
+}

UNFCCC_GHG_data/UNFCCC_CRF_reader/read_new_UNFCCC_CRF_for_year.py → src/unfccc_ghg_data/unfccc_crf_reader/read_new_unfccc_crf_for_year.py

@@ -3,10 +3,10 @@ This script is a wrapper around the read_crf_for_country
 function such that it can be called from datalad
 """
 
-from UNFCCC_GHG_data.UNFCCC_CRF_reader.UNFCCC_CRF_reader_prod import \
-    read_new_crf_for_year
 import argparse
 
+from unfccc_ghg_data.unfccc_crf_reader.unfccc_crf_reader_prod import read_new_crf_for_year
+
 parser = argparse.ArgumentParser()
 #parser.add_argument('--countries', help='List of country codes', default=None)
 parser.add_argument('--submission_year', help='Submission round to read', type=int)

UNFCCC_GHG_data/UNFCCC_CRF_reader/read_new_UNFCCC_CRF_for_year_datalad.py → src/unfccc_ghg_data/unfccc_crf_reader/read_new_unfccc_crf_for_year_datalad.py

@@ -4,10 +4,11 @@ from doit in the current setup where doit runs on system python and
 not in the venv.
 """
 
-from UNFCCC_GHG_data.UNFCCC_CRF_reader.UNFCCC_CRF_reader_prod import read_new_crf_for_year_datalad
-from UNFCCC_GHG_data.UNFCCC_CRF_reader.util import NoCRFFilesError
 import argparse
 
+from unfccc_ghg_data.unfccc_crf_reader.unfccc_crf_reader_prod import read_new_crf_for_year_datalad
+from unfccc_ghg_data.unfccc_crf_reader.util import NoCRFFilesError
+
 parser = argparse.ArgumentParser()
 #parser.add_argument('--countries', help='List of country codes', default=None)
 parser.add_argument('--submission_year', help='Submission round to read')
@@ -29,4 +30,4 @@ try:
         re_read=re_read
     )
 except NoCRFFilesError as err:
-    print(f"NoCRFFilesError: {err}")
+    print(f"NoCRFFilesError: {err}")

UNFCCC_GHG_data/UNFCCC_CRF_reader/read_UNFCCC_CRF_submission.py → src/unfccc_ghg_data/unfccc_crf_reader/read_unfccc_crf_submission.py

@@ -3,9 +3,10 @@ This script is a wrapper around the read_crf_for_country
 function such that it can be called from datalad
 """
 
-from UNFCCC_GHG_data.UNFCCC_CRF_reader.UNFCCC_CRF_reader_prod import read_crf_for_country
 import argparse
 
+from unfccc_ghg_data.unfccc_crf_reader.unfccc_crf_reader_prod import read_crf_for_country
+
 parser = argparse.ArgumentParser()
 parser.add_argument('--country', help='Country name or code')
 parser.add_argument('--submission_year', help='Submission round to read', type=int)

UNFCCC_GHG_data/UNFCCC_CRF_reader/read_UNFCCC_CRF_submission_datalad.py → src/unfccc_ghg_data/unfccc_crf_reader/read_unfccc_crf_submission_datalad.py

@@ -4,9 +4,10 @@ from doit in the current setup where doit runs on system python and
 not in the venv.
 """
 
-from UNFCCC_GHG_data.UNFCCC_CRF_reader.UNFCCC_CRF_reader_prod import read_crf_for_country_datalad
 import argparse
 
+from unfccc_ghg_data.unfccc_crf_reader.unfccc_crf_reader_prod import read_crf_for_country_datalad
+
 parser = argparse.ArgumentParser()
 parser.add_argument('--country', help='Country name or code')
 parser.add_argument('--submission_year', help='Submission round to read')
@@ -30,4 +31,4 @@ read_crf_for_country_datalad(
     submission_year=int(submission_year),
     submission_date=submission_date,
     re_read=re_read
-)
+)

UNFCCC_GHG_data/UNFCCC_CRF_reader/test_read_UNFCCC_CRF_for_year.py → src/unfccc_ghg_data/unfccc_crf_reader/test_read_unfccc_crf_for_year.py

@@ -3,9 +3,10 @@ This script is a wrapper around the read_year_to_test_specs
 function such that it can be called from datalad
 """
 
-from UNFCCC_GHG_data.UNFCCC_CRF_reader.UNFCCC_CRF_reader_devel import read_year_to_test_specs
 import argparse
 
+from unfccc_ghg_data.unfccc_crf_reader.unfccc_crf_reader_devel import read_year_to_test_specs
+
 parser = argparse.ArgumentParser()
 parser.add_argument('--submission_year', help='Submission round to read', type=int)
 parser.add_argument('--data_year', help='Data year to read', type=int, default=2010)

UNFCCC_GHG_data/UNFCCC_CRF_reader/UNFCCC_CRF_reader_core.py → src/unfccc_ghg_data/unfccc_crf_reader/unfccc_crf_reader_core.py

@@ -4,36 +4,42 @@ Core function are used both for reading for final datasets as
 well as for test-reading to check for new categories etc.
 """
 
-import re
-import os
 import json
+import os
+import re
+from collections import Counter
+from datetime import datetime, timedelta
+from operator import itemgetter
+from pathlib import Path
+from typing import Optional, Union
+
+import datalad as dl
 import numpy as np
 import pandas as pd
 import primap2 as pm2
-from pathlib import Path
 from treelib import Tree
-from operator import itemgetter
-from collections import Counter
-from typing import Dict, List, Optional, Tuple, Union
-from datetime import datetime, timedelta
+
+from unfccc_ghg_data.helper import downloaded_data_path_UNFCCC, root_path
+
 from . import crf_specifications as crf
 from .util import NoCRFFilesError
-from UNFCCC_GHG_data.helper import downloaded_data_path_UNFCCC
+
 
 ### reading functions
 def convert_crf_table_to_pm2if(
         df_table: pd.DataFrame,
         submission_year: int,
-        entity_mapping: Optional[Dict[str,str]]=None,
-        coords_defaults_input: Optional[Dict[str,str]]=None,
-        filter_remove_input: Optional[Dict[str,Dict[str,Union[str,List]]]]=None,
-        filter_keep_input: Optional[Dict[str,Dict[str,Union[str,List]]]]=None,
-        meta_data_input: Optional[Dict[str,str]]=None,
+        entity_mapping: Optional[dict[str,str]]=None,
+        coords_defaults_input: Optional[dict[str,str]]=None,
+        filter_remove_input: Optional[dict[str,dict[str,Union[str,list]]]]=None,
+        filter_keep_input: Optional[dict[str,dict[str,Union[str,list]]]]=None,
+        meta_data_input: Optional[dict[str,str]]=None,
 ) -> pd.DataFrame:
     """
     Converts a given pandas long format crf table to PRIMAP2 interchange format
 
     Parameters
+    ----------
     __________
         df_table: pd.DataFrame
             Data to convert
@@ -60,12 +66,12 @@ def convert_crf_table_to_pm2if(
             are given as input the automatic values are overwritten.
 
     Returns
+    -------
     _______
         pd.DataFrame:
             Pandas DataFrame containing the data in PRIMAP2 interchange format
             Metadata is stored as attrs in the DataFrame
     """
-
     coords_cols = {
         "category": "category",
         "entity": "entity",
@@ -107,7 +113,7 @@ def convert_crf_table_to_pm2if(
 
     filter_remove = {
         "f1": {
-            "category": ["\IGNORE"],
+            "category": ["\\IGNORE"],
         }
     }
     if filter_remove_input is not None:
@@ -150,14 +156,14 @@ def convert_crf_table_to_pm2if(
 
 
 def read_crf_table(
-        country_codes: Union[str, List[str]],
+        country_codes: Union[str, list[str]],
         table: str,
         submission_year: int,
-        data_year: Optional[Union[int, List[int]]]=None,
+        data_year: Optional[Union[int, list[int]]]=None,
         date: Optional[str]=None,
         folder: Optional[str]=None,
         debug: Optional[bool]=False,
-) -> Tuple[pd.DataFrame, List[List], List[List]]:
+) -> tuple[pd.DataFrame, list[list], list[list]]:
     """
     Read CRF table for given submission year and country / or countries
     This function can read for multiple years and countries but only a single
@@ -168,10 +174,11 @@ def read_crf_table(
     from the submission_year and country_code variables
 
     Parameters
+    ----------
     __________
 
     country_codes: str or list[str]
-        ISO 3-letter country UNFCCC_GHG_data or list of country codes
+        ISO 3-letter country code or list of country codes
 
     table: str
         name of the table sheet in the CRF xlsx file
@@ -194,6 +201,7 @@ def read_crf_table(
         if true print some debug information like column headers
 
     Returns
+    -------
     _______
         Tuple[pd.DataFrame, List[List], List[List]]:
         * First return parameter is the data as a pandas DataFrame in long format
@@ -223,7 +231,7 @@ def read_crf_table(
         if len(input_files) < expected_files:
             print(f"Found only {len(input_files)} input files for {country_codes}. "
                   f"Expected {expected_files}.")
-            print(f"Possibly exporting run overnight and some files have the previous day as date.")
+            print("Possibly exporting run overnight and some files have the previous day as date.")
             date_datetime = datetime.strptime(date, "%d%m%Y")
             date_datetime = date_datetime - timedelta(days=1)
             prv_date = date_datetime.strftime("%d%m%Y")
@@ -236,7 +244,7 @@ def read_crf_table(
                 print(f"Found {len(more_input_files)} additional input files.")
                 input_files = input_files + more_input_files
             else:
-                print(f"Found no additional input files")
+                print("Found no additional input files")
 
     if input_files == []:
         raise NoCRFFilesError(f"No files found for {country_codes}, "
@@ -251,7 +259,7 @@ def read_crf_table(
     if len(country_codes) == 1:
         try:
             crf_spec = getattr(crf, f"CRF{submission_year}_{country_codes[0]}")
-            print(f"Using country specific specification: " 
+            print(f"Using country specific specification: "
                   f"CRF{submission_year}_{country_codes[0]}")
         except:
             # no country specific specification, check for general specification
@@ -294,14 +302,15 @@ def read_crf_table(
 def read_crf_table_from_file(
         file: Path,
         table: str,
-        table_spec: Dict[str, Dict],
+        table_spec: dict[str, dict],
         debug: Optional[bool]=False,
-) -> Tuple[pd.DataFrame, List[List], List[List]]:
+) -> tuple[pd.DataFrame, list[list], list[list]]:
     """
     Read a single CRF table from a given file. This is the core function of the CRF
     reading process as it reads the data from xls and performs the category mapping.
 
     Parameters
+    ----------
     __________
     file: Path
         file to read from
@@ -316,6 +325,7 @@ def read_crf_table_from_file(
         if true print some debug information like column headers
 
     Returns
+    -------
     _______
         Tuple[pd.DataFrame, List[List], List[List]]:
         * First return parameter is the data as a pandas DataFrame in long format
@@ -326,6 +336,12 @@ def read_crf_table_from_file(
 
     TODO: add verbosity option for debugging?
     """
+    # check if file exists and if not download
+    if file.is_symlink():
+        if not file.exists():
+            dlds = dl.api.Dataset(root_path)
+            dlds.get(file.relative_to(root_path))
+
 
     table_properties = table_spec["table"]
     file_info = get_info_from_crf_filename(file.name)
@@ -366,7 +382,7 @@ def read_crf_table_from_file(
         last_row_nan = True
     else:
         last_row_nan = False
-    
+
 
     cols_to_drop = []
     # remove empty first column (for Australia tables start with an empty column)
@@ -433,7 +449,7 @@ def read_crf_table_from_file(
 
     # remove double spaces
     entities = [entity.strip() for entity in entities]
-    entities = [re.sub('\s+', ' ', entity) for entity in entities]
+    entities = [re.sub('\\s+', ' ', entity) for entity in entities]
 
     # replace the old header
     if len(header) > 2:
@@ -451,7 +467,7 @@ def read_crf_table_from_file(
     # remove double spaces
     for col in cols_for_space_stripping:
         df_current[col] = df_current[col].str.strip()
-        df_current[col] = df_current[col].replace('\s+', ' ', regex=True)
+        df_current[col] = df_current[col].replace('\\s+', ' ', regex=True)
 
     # prepare for sector mapping by initializing result lists and
     # variables
@@ -571,20 +587,21 @@ def read_crf_table_from_file(
 
 
 def get_crf_files(
-        country_codes: Union[str, List[str]],
+        country_codes: Union[str, list[str]],
         submission_year: int,
-        data_year: Optional[Union[int, List[int]]] = None,
+        data_year: Optional[Union[int, list[int]]] = None,
         date: Optional[str] = None,
         folder: Optional[str] = None,
-) -> List[Path]:
+) -> list[Path]:
     """
     Finds all files according to given parameters
 
     Parameters
+    ----------
     __________
 
     country_codes: str or list[str]
-        ISO 3-letter country UNFCCC_GHG_data or list of country codes
+        ISO 3-letter country code or list of country codes
 
     submission_year: int
         Year of the submission of the data
@@ -601,6 +618,7 @@ def get_crf_files(
         submissions_year and country_code variables
 
     Returns
+    -------
     _______
         List[Path]: list of Path objects for the files
     """
@@ -615,7 +633,7 @@ def get_crf_files(
         data_folder = downloaded_data_path_UNFCCC
         submission_folder = f"CRF{submission_year}"
 
-        with open(data_folder / "folder_mapping.json", "r") as mapping_file:
+        with open(data_folder / "folder_mapping.json") as mapping_file:
             folder_mapping = json.load(mapping_file)
 
         # use country default folders
@@ -625,8 +643,7 @@ def get_crf_files(
                 new_country_folders = folder_mapping[country_code]
                 if isinstance(new_country_folders, str):
                     # only one folder
-                    country_folders = country_folders + \
-                                      [data_folder / new_country_folders / submission_folder]
+                    country_folders = [*country_folders, data_folder / new_country_folders / submission_folder]
                 else:
                     country_folders = country_folders + \
                                       [data_folder / folder / submission_folder
@@ -683,21 +700,23 @@ def get_crf_files(
 
 def get_info_from_crf_filename(
         filename: str,
-) -> Dict[str, Union[int, str]]:
+) -> dict[str, Union[int, str]]:
     """
     Parse given file name and return a dict with information
     on the contained data.
 
     Parameters
+    ----------
     __________
 
     filename: str
         The file to analyze (without path)
 
     Returns
+    -------
     _______
     dict with fields:
-        party: the party that submitted the data (3 letter UNFCCC_GHG_data)
+        party: the party that submitted the data (3 letter code)
         submission_year: year of submission
         data_year: year in which the emissions took place
         date: date of the submission
@@ -724,22 +743,23 @@ def get_info_from_crf_filename(
 
 
 def filter_filenames(
-        files_to_filter: List[Path],
-        party: Optional[Union[str, List[str]]] = None,
-        data_year: Optional[Union[int, List[int]]] = None,
+        files_to_filter: list[Path],
+        party: Optional[Union[str, list[str]]] = None,
+        data_year: Optional[Union[int, list[int]]] = None,
         submission_year: Optional[str] = None,
         date: Optional[str] = None,
-) -> List[Path]:
-    """ Filter a list of filenames of CRF files
+) -> list[Path]:
+    """Filter a list of filenames of CRF files
 
     Parameters
+    ----------
     __________
     files_to_filter: List[Path]
         List with pathlib.Path objects for the filenames to filter
 
     party: Optional[Union[str, List[str]]] (default: None)
-        List of country codes or single country UNFCCC_GHG_data. If given only files
-        for this(these) country-UNFCCC_GHG_data(s) will be returned.
+        List of country codes or single country code. If given only files
+        for this(these) country-code(s) will be returned.
 
     data_year: Optional[Union[int, List[int]]] (default: None)
         List of data years or single year. If given only files for this
@@ -774,13 +794,14 @@ def filter_filenames(
 
 
 def check_crf_file_info(
-        file_info: Dict,
-        file_filter: Dict,
+        file_info: dict,
+        file_filter: dict,
 ) -> bool:
     """
     Check if a CRF file has given properties
 
     Parameters
+    ----------
     __________
     file_info: Dict
         the file info dict of a CRF xlsx file as returned by
@@ -791,6 +812,7 @@ def check_crf_file_info(
         with functionality as in `filter_filenames`
 
     Returns
+    -------
     _______
         bool: `True` if the file info matches the filter and `False` if not
 
@@ -819,7 +841,7 @@ def check_crf_file_info(
 
 
 def create_category_tree(
-        specification: List[List],
+        specification: list[list],
         table: str,
         country: Optional[str] = None,
 ) -> Tree:
@@ -831,6 +853,7 @@ def create_category_tree(
     correct categories to non-unique row headers.
 
     Parameters
+    ----------
     __________
 
     specification: List[List]
@@ -874,7 +897,7 @@ def create_category_tree(
                          for mapping in specification]
         # remove the categories for other countries
         specification = [mapping for mapping in specification
-                         if mapping[0] != "\REMOVE"]
+                         if mapping[0] != "\\REMOVE"]
 
     # build a tree from specification
     # when looping over the categories present in the table
@@ -922,31 +945,33 @@ def create_category_tree(
 
 
 def filter_category(
-        mapping: List,
+        mapping: list,
         country: str,
-) -> List[str]:
+) -> list[str]:
     """
     This function checks if a category mapping is suitable for the given country.
     If it is the country information will be removed and the new mapping returned.
-    If it is not suitable it will be returned with category name "\REMOVE" such that
+    If it is not suitable it will be returned with category name "\\REMOVE" such that
     it can be removed from the mapping by the calling function.
 
     Parameters
+    ----------
     __________
         mapping: List
             mapping for a single category
         country: str
-            iso 3-letter UNFCCC_GHG_data of the country
+            iso 3-letter code of the country
 
     Returns
+    -------
     _______
         List: updated mapping
 
     """
-    string_exclude = f"\C!-"
+    string_exclude = "\\C!-"
     regex_exclude = r"\\C!-([A-Z\-]+)\\"
     regex_exclude_full = r"(\\C!-[A-Z\-]+\\)"
-    string_country = f"\C-{country}\\"
+    string_country = f"\\C-{country}\\"
     regex_countries = r"^\\C-[A-Z]{3}\\"
     new_mapping = mapping.copy()
     if mapping[0].startswith(string_exclude):
@@ -954,14 +979,14 @@ def filter_category(
         countries_ex = re_result.group(1)
         countries_ex = countries_ex.split("-")
         if country in countries_ex:
-            new_mapping[0] = "\REMOVE"
+            new_mapping[0] = "\\REMOVE"
         else:
             re_result = re.search(regex_exclude_full, mapping[0])
             new_mapping[0] = mapping[0][len(re_result.group(1)) + 1:]
     elif mapping[0].startswith(string_country):
         new_mapping[0] = mapping[0][len(string_country) + 1:]
     elif re.match(regex_countries, mapping[0]):
-        new_mapping[0] = "\REMOVE"
+        new_mapping[0] = "\\REMOVE"
 
     return new_mapping
 
@@ -974,19 +999,20 @@ def get_latest_date_for_country(
     Find the latest submission date for a country
 
     Parameters
+    ----------
     __________
     country: str
-        3-letter country UNFCCC_GHG_data
+        3-letter country code
 
     submission_year: int
         Year of the submission to find the l;atest date for
 
     Returns
+    -------
     _______
         str: string with date
     """
-
-    with open(downloaded_data_path_UNFCCC / "folder_mapping.json", "r") as mapping_file:
+    with open(downloaded_data_path_UNFCCC / "folder_mapping.json") as mapping_file:
         folder_mapping = json.load(mapping_file)
 
     if country_code in folder_mapping:
@@ -1014,12 +1040,13 @@ def get_latest_date_for_country(
 
 def get_submission_dates(
         folder: Path,
-        file_filter: Dict[str, Union[str, int, List]],
-)->List[str]:
+        file_filter: dict[str, Union[str, int, list]],
+)->list[str]:
     """
     Returns all submission dates available in a folder
 
     Parameters
+    ----------
     __________
     folder: Path
         Folder to analyze
@@ -1028,14 +1055,14 @@ def get_submission_dates(
         Dict with possible fields "party", "submission_year", "data_year"
 
     Returns
+    -------
     _______
         List[str]:
             List of dates as str
     """
-
     if "date" in file_filter:
-        raise ValueError(f"'date' present in 'file_filter'. This makes no sense as "
-                         f"the function's purpose is to return available dates.")
+        raise ValueError("'date' present in 'file_filter'. This makes no sense as "
+                         "the function's purpose is to return available dates.")
 
     if folder.exists():
         files = filter_filenames(folder.glob("*.xlsx"), **file_filter)
@@ -1050,12 +1077,13 @@ def get_submission_dates(
 
 def get_submission_parties(
         folder: Path,
-        file_filter: Dict[str, Union[str, int, List]],
-)->List[str]:
+        file_filter: dict[str, Union[str, int, list]],
+)->list[str]:
     """
     Returns all submission dates available in a folder
 
     Parameters
+    ----------
     __________
     folder: Path
         Folder to analyze
@@ -1064,14 +1092,14 @@ def get_submission_parties(
         Dict with possible fields "submission_year", "data_year", "date"
 
     Returns
+    -------
     _______
         List[str]:
             List of parties as str
     """
-
     if "party" in file_filter:
-        raise ValueError(f"'party' present in 'file_filter'. This makes no sense as "
-                         f"the function's purpose is to return available parties.")
+        raise ValueError("'party' present in 'file_filter'. This makes no sense as "
+                         "the function's purpose is to return available parties.")
 
     if folder.exists():
         files = filter_filenames(list(folder.glob("*.xlsx")), **file_filter)
@@ -1085,7 +1113,7 @@ def get_submission_parties(
 
 
 def find_latest_date(
-        dates: List[str],
+        dates: list[str],
         date_format: str='%d%m%Y',
 )-> str:
     """
@@ -1093,21 +1121,22 @@ def find_latest_date(
     ddmmyyyy
 
     Parameters
+    ----------
     __________
     dates: List[str]
         List of dates
 
     Returns
+    -------
     _______
         str: latest date
     """
-
     if len(dates) > 0:
         dates_datetime = [[date, datetime.strptime(date, date_format)] for date in
                           dates]
         dates_datetime = sorted(dates_datetime, key=itemgetter(1))
     else:
-        raise ValueError(f"Passed list of dates is empty")
+        raise ValueError("Passed list of dates is empty")
 
     return dates_datetime[-1][0]
 

UNFCCC_GHG_data/UNFCCC_CRF_reader/UNFCCC_CRF_reader_devel.py → src/unfccc_ghg_data/unfccc_crf_reader/unfccc_crf_reader_devel.py

@@ -6,18 +6,20 @@ of single years in contrast to the production functions which are tailored
 towards the creation of full datasets including storage in the
 """
 
+from datetime import date
+from pathlib import Path
+from typing import Optional
+
 import pandas as pd
-import xarray as xr
 import primap2 as pm2
-from typing import List, Optional
-from pathlib import Path
-from datetime import date
+import xarray as xr
+
+from unfccc_ghg_data.helper import get_country_name, log_path
 
-from .util import all_crf_countries
-from UNFCCC_GHG_data.helper import log_path, get_country_name
 from . import crf_specifications as crf
-from .UNFCCC_CRF_reader_core import get_latest_date_for_country, read_crf_table
-from .UNFCCC_CRF_reader_core import convert_crf_table_to_pm2if
+from .unfccc_crf_reader_core import convert_crf_table_to_pm2if, get_latest_date_for_country, read_crf_table
+from .util import all_crf_countries
+
 
 def read_year_to_test_specs(
         submission_year: int,
@@ -35,6 +37,9 @@ def read_year_to_test_specs(
     if data_year is None:
         data_year=2000
 
+    if country_code=="None":
+        country_code=None
+
     unknown_categories = []
     last_row_info = []
     ds_all = None
@@ -43,43 +48,6 @@ def read_year_to_test_specs(
         print("Reading only tables to test.")
     print("#"*80)
 
-
-    # get specification
-    # if we only have a single country check if we might have a country specific
-    # specification (currently only Australia, 2023)
-    if country_code is not None:
-        try:
-            crf_spec = getattr(crf, f"CRF{submission_year}_{country_code}")
-            print(
-                f"Using country specific specification: "
-                f"CRF{submission_year}_{country_code}"
-            )
-        except:
-            # no country specific specification, check for general specification
-            try:
-                crf_spec = getattr(crf, f"CRF{submission_year}")
-            except:
-                raise ValueError(
-                    f"No terminology exists for submission year " f"{submission_year}"
-                )
-    else:
-        try:
-            crf_spec = getattr(crf, f"CRF{submission_year}")
-        except:
-            raise ValueError(
-                f"No terminology exists for submission year " f"{submission_year}"
-            )
-
-    if totest:
-        tables = [table for table in crf_spec.keys()
-                  if crf_spec[table]["status"] == "totest"]
-    else:
-        tables = [table for table in crf_spec.keys()
-                  if crf_spec[table]["status"] == "tested"]
-    print(f"The following tables are available in the " \
-          f"CRF{submission_year} specification: {tables}")
-    print("#" * 80)
-
     if country_code is not None:
         countries_to_read = [country_code]
     else:
@@ -87,8 +55,42 @@ def read_year_to_test_specs(
     for country_code in countries_to_read:
         # get country name
         country_name = get_country_name(country_code)
-        print(f"Reading for {country_name}")
+        print(f"reading for country: {country_code}")
         # get specification and available tables
+           # if we only have a single country check if we might have a country specific
+        # specification (currently only Australia, 2023)
+        if country_code is not None:
+            try:
+                crf_spec = getattr(crf, f"CRF{submission_year}_{country_code}")
+                print(
+                    f"Using country specific specification: "
+                    f"CRF{submission_year}_{country_code}"
+                )
+            except:
+                # no country specific specification, check for general specification
+                try:
+                    crf_spec = getattr(crf, f"CRF{submission_year}")
+                except:
+                    raise ValueError(
+                        f"No terminology exists for submission year " f"{submission_year}"
+                    )
+        else:
+            try:
+                crf_spec = getattr(crf, f"CRF{submission_year}")
+            except:
+                raise ValueError(
+                    f"No terminology exists for submission year " f"{submission_year}"
+                )
+
+        if totest:
+            tables = [table for table in crf_spec.keys()
+                      if crf_spec[table]["status"] == "totest"]
+        else:
+            tables = [table for table in crf_spec.keys()
+                      if crf_spec[table]["status"] == "tested"]
+        print(f"The following tables are available in the " \
+              f"CRF{submission_year} specification: {tables}")
+        print("#" * 80)
 
         try:
             submission_date = get_latest_date_for_country(country_code, submission_year)
@@ -98,7 +100,7 @@ def read_year_to_test_specs(
 
         if submission_date is not None:
             for table in tables:
-                # read table for all years
+                # read table for given years
                 ds_table, new_unknown_categories, new_last_row_info = read_crf_table(
                     country_code, table, submission_year, date=submission_date,
                     data_year=[data_year], debug=True)
@@ -134,8 +136,7 @@ def read_year_to_test_specs(
                     # if individual data for emissions and removals / recovery exist combine
                     # them
                     if (('CO2 removals' in ds_table_pm2.data_vars) and
-                            ('CO2 emissions' in ds_table_pm2.data_vars) and not
-                            ('CO2' in ds_table_pm2.data_vars)):
+                            ('CO2 emissions' in ds_table_pm2.data_vars) and "CO2" not in ds_table_pm2.data_vars):
                         # we can just sum to CO2 as we made sure that it doesn't exist.
                         # If we have CO2 and removals but not emissions, CO2 already has
                         # removals subtracted and we do nothing here
@@ -146,8 +147,7 @@ def read_year_to_test_specs(
                         ds_table_pm2["CO2"].attrs["entity"] = "CO2"
 
                     if (('CH4 removals' in ds_table_pm2.data_vars) and
-                            ('CH4 emissions' in ds_table_pm2.data_vars) and not
-                            ('CH4' in ds_table_pm2.data_vars)):
+                            ('CH4 emissions' in ds_table_pm2.data_vars) and "CH4" not in ds_table_pm2.data_vars):
                         # we can just sum to CH4 as we made sure that it doesn't exist.
                         # If we have CH4 and removals but not emissions, CH4 already has
                         # removals subtracted and we do nothing here
@@ -227,13 +227,14 @@ def read_year_to_test_specs(
 
 
 def save_unknown_categories_info(
-        unknown_categories: List[List],
+        unknown_categories: list[list],
         file: Path,
 ) -> None:
     """
     Save information on unknown categories to a csv file.
 
     Parameters
+    ----------
     __________
 
     unknown_categories: List[List]
@@ -277,7 +278,7 @@ def save_unknown_categories_info(
 
 
 def save_last_row_info(
-        last_row_info: List[List],
+        last_row_info: list[list],
         file: Path,
     ) -> None:
     """
@@ -287,6 +288,7 @@ def save_last_row_info(
     given in the specification and thus we might not read the full table.
 
     Parameters
+    ----------
     __________
 
     last_row_info: List[List]
@@ -325,4 +327,4 @@ def save_last_row_info(
     if not file.parents[0].exists():
         file.parents[0].mkdir()
     df_processed_lost_row_info = pd.DataFrame(processed_last_row_info, columns=["Table", "Country", "Categories"])
-    df_processed_lost_row_info.to_csv("test_last_row_info.csv", index=False)
+    df_processed_lost_row_info.to_csv("test_last_row_info.csv", index=False)

UNFCCC_GHG_data/UNFCCC_CRF_reader/UNFCCC_CRF_reader_prod.py → src/unfccc_ghg_data/unfccc_crf_reader/unfccc_crf_reader_prod.py

@@ -1,22 +1,30 @@
-import xarray as xr
-import primap2 as pm2
-import datalad.api
+
 from datetime import date
-from typing import Optional, List, Dict, Union
+from typing import Optional, Union
 
-from . import crf_specifications as crf
+import datalad.api
+import primap2 as pm2
+import xarray as xr
 
-from .UNFCCC_CRF_reader_core import read_crf_table
-from .UNFCCC_CRF_reader_core import convert_crf_table_to_pm2if
-from .UNFCCC_CRF_reader_core import get_latest_date_for_country
-from .UNFCCC_CRF_reader_core import get_crf_files
-from .UNFCCC_CRF_reader_devel import save_unknown_categories_info
-from .UNFCCC_CRF_reader_devel import save_last_row_info
+from unfccc_ghg_data.helper import (
+    code_path,
+    custom_country_mapping,
+    extracted_data_path_UNFCCC,
+    get_country_code,
+    get_country_name,
+    log_path,
+    root_path,
+)
 
-from UNFCCC_GHG_data.helper import code_path, log_path, root_path
-from UNFCCC_GHG_data.helper import custom_country_mapping, extracted_data_path_UNFCCC
-from UNFCCC_GHG_data.helper import get_country_code, get_country_name
-from .util import all_crf_countries, NoCRFFilesError
+from . import crf_specifications as crf
+from .unfccc_crf_reader_core import (
+    convert_crf_table_to_pm2if,
+    get_crf_files,
+    get_latest_date_for_country,
+    read_crf_table,
+)
+from .unfccc_crf_reader_devel import save_last_row_info, save_unknown_categories_info
+from .util import NoCRFFilesError, all_crf_countries
 
 #import sys
 #sys.path.append(code_path.name)
@@ -31,7 +39,7 @@ from .util import all_crf_countries, NoCRFFilesError
 # TODO: add function to read several / all countries
 
 # general approach:
-# main UNFCCC_GHG_data in a function that reads on table from one file.
+# main code in a function that reads on table from one file.
 # return raw pandas DF for use in different functions
 # wrappers around this function to read for a whole country or for test reading where we also
 # write files with missing sectors etc.
@@ -67,10 +75,11 @@ def read_crf_for_country(
 
 
     Parameters
+    ----------
     __________
 
     country_codes: str
-        ISO 3-letter country UNFCCC_GHG_data
+        ISO 3-letter country code
 
     submission_year: int
         Year of the submission of the data
@@ -83,10 +92,10 @@ def read_crf_for_country(
         Read the data also if it's already present
 
     Returns
+    -------
     _______
         return value is a Pandas DataFrame with the read data in PRIMAP2 format
     """
-
     # get country name
     country_name = get_country_name(country_code)
 
@@ -160,8 +169,7 @@ def read_crf_for_country(
             # if individual data for emissions and removals / recovery exist combine
             # them
             if (('CO2 removals' in ds_table_pm2.data_vars) and
-                    ('CO2 emissions' in ds_table_pm2.data_vars) and not
-                    ('CO2' in ds_table_pm2.data_vars)):
+                    ('CO2 emissions' in ds_table_pm2.data_vars) and "CO2" not in ds_table_pm2.data_vars):
                 # we can just sum to CO2 as we made sure that it doesn't exist.
                 # If we have CO2 and removals but not emissions, CO2 already has
                 # removals subtracted and we do nothing here
@@ -172,11 +180,10 @@ def read_crf_for_country(
                 ds_table_pm2["CO2"].attrs["entity"] = "CO2"
 
             if (('CH4 removals' in ds_table_pm2.data_vars) and
-                    ('CH4 emissions' in ds_table_pm2.data_vars) and not
-                    ('CH4' in ds_table_pm2.data_vars)):
+                    ('CH4 emissions' in ds_table_pm2.data_vars) and "CH4" not in ds_table_pm2.data_vars):
                 # we can just sum to CH4 as we made sure that it doesn't exist.
                 # If we have CH4 and removals but not emissions, CH4 already has
-                # removals subtracted and we do nothing here 
+                # removals subtracted and we do nothing here
                 ds_table_pm2["CH4"] = ds_table_pm2[["CH4 emissions",
                                                 "CH4 removals"]].pr.sum(
                     dim="entity", skipna=True, min_count=1
@@ -240,10 +247,11 @@ def read_crf_for_country_datalad(
     and output files and using datalad run to trigger the data reading
 
     Parameters
+    ----------
     __________
 
     country_codes: str
-        ISO 3-letter country UNFCCC_GHG_data
+        ISO 3-letter country code
 
     submission_year: int
         Year of the submission of the data
@@ -253,7 +261,6 @@ def read_crf_for_country_datalad(
         If not specified latest data will be read
 
     """
-
     # get all the info for the country
     country_info = get_input_and_output_files_for_country(
         country, submission_year=submission_year, verbose=True)
@@ -261,15 +268,15 @@ def read_crf_for_country_datalad(
     print(f"Attempting to read data for CRF{submission_year} from {country}.")
     print("#"*80)
     print("")
-    print(f"Using the UNFCCC_CRF_reader")
+    print("Using the unfccc_crf_reader")
     print("")
-    print(f"Run the script using datalad run via the python api")
-    script = code_path / "UNFCCC_CRF_reader" / "read_UNFCCC_CRF_submission.py"
+    print("Run the script using datalad run via the python api")
+    script = code_path / "unfccc_crf_reader" / "read_unfccc_crf_submission.py"
 
     cmd = f"./venv/bin/python3 {script.as_posix()} --country={country} "\
           f"--submission_year={submission_year} --submission_date={submission_date}"
     if re_read:
-        cmd = cmd + f" --re_read"
+        cmd = cmd + " --re_read"
     datalad.api.run(
         cmd=cmd,
         dataset=root_path,
@@ -283,7 +290,7 @@ def read_crf_for_country_datalad(
 
 def read_new_crf_for_year(
         submission_year: int,
-        countries: Optional[List[str]]=None,
+        countries: Optional[list[str]]=None,
         re_read: Optional[bool]=False,
 ) -> dict:
     """
@@ -302,6 +309,7 @@ def read_new_crf_for_year(
     read from different tables
 
     Parameters
+    ----------
     __________
 
     submission_year: int
@@ -317,11 +325,11 @@ def read_new_crf_for_year(
     TODO: write log with failed countries and what has been read
 
     Returns
+    -------
     _______
         list[str]: list with country codes for which the data has been read
 
     """
-
     if countries is None:
         countries = all_crf_countries
 
@@ -356,7 +364,7 @@ def read_new_crf_for_year(
 
 def read_new_crf_for_year_datalad(
         submission_year: int,
-        countries: Optional[List[str]] = None,
+        countries: Optional[list[str]] = None,
         re_read: Optional[bool] = False,
 ) -> None:
     """
@@ -364,6 +372,7 @@ def read_new_crf_for_year_datalad(
     and output files and using datalad run to trigger the data reading
 
     Parameters
+    ----------
     __________
 
     submission_year: int
@@ -377,11 +386,10 @@ def read_new_crf_for_year_datalad(
         If true data will be read even if already read before.
 
     """
-
     if countries is not None:
-        print(f"Reading CRF{submission_year} for countries {countries} using UNFCCC_CRF_reader.")
+        print(f"Reading CRF{submission_year} for countries {countries} using unfccc_crf_reader.")
     else:
-        print(f"Reading CRF{submission_year} for all countries using UNFCCC_CRF_reader.")
+        print(f"Reading CRF{submission_year} for all countries using unfccc_crf_reader.")
         countries = all_crf_countries
     print("#" * 80)
     print("")
@@ -417,8 +425,8 @@ def read_new_crf_for_year_datalad(
             # no error handling here as that is done in the function that does the actual reading
             pass
 
-    print(f"Run the script using datalad run via the python api")
-    script = code_path / "UNFCCC_CRF_reader" / "read_new_UNFCCC_CRF_for_year.py"
+    print("Run the script using datalad run via the python api")
+    script = code_path / "unfccc_crf_reader" / "read_new_unfccc_crf_for_year.py"
 
     #cmd = f"./venv/bin/python3 {script.as_posix()} --countries={countries} "\
     #      f"--submission_year={submission_year}"
@@ -443,11 +451,10 @@ def get_input_and_output_files_for_country(
         submission_year: int,
         submission_date: Optional[str]=None,
         verbose: Optional[bool]=True,
-) -> Dict[str, Union[List, str]]:
+) -> dict[str, Union[list, str]]:
     """
     Get input and output files for a given country
     """
-
     country_info = {}
 
     if country in custom_country_mapping:
@@ -463,7 +470,7 @@ def get_input_and_output_files_for_country(
     print(f"Determining input and output files for {country}")
     if submission_date is None:
         if verbose:
-            print(f"No submission date given, find latest date.")
+            print("No submission date given, find latest date.")
         submission_date = get_latest_date_for_country(country_code, submission_year)
     else:
         if verbose:
@@ -488,7 +495,7 @@ def get_input_and_output_files_for_country(
                               f"v{submission_date}. Are they already submitted and included in the "
                               f"repository?")
     elif verbose:
-        print(f"Found the following input_files:")
+        print("Found the following input_files:")
         for file in input_files:
             print(file.name)
         print("")
@@ -504,7 +511,7 @@ def get_input_and_output_files_for_country(
                                     f"_{submission_date}.{suffix}" for suffix
                     in ['yaml', 'csv', 'nc']]
     if verbose:
-        print(f"The following files are considered as output_files:")
+        print("The following files are considered as output_files:")
         for file in output_files:
             print(file)
         print("")
@@ -551,4 +558,4 @@ def submission_has_been_read(
             print(f"No read data available for {country_code}, "
                   f"CRF{submission_year}, version {submission_date}. ")
 
-    return has_been_read
+    return has_been_read

UNFCCC_GHG_data/UNFCCC_CRF_reader/util.py → src/unfccc_ghg_data/unfccc_crf_reader/util.py

@@ -13,4 +13,4 @@ all_crf_countries = [
 ]
 
 class NoCRFFilesError(Exception):
-    pass
+    pass

src/unfccc_ghg_data/unfccc_di_reader/__init__.py

@@ -0,0 +1,36 @@
+# submodule to read data from UNFCCC DI API using the unfccc_di_api package
+
+#import unfccc_di_api
+from .unfccc_di_reader_core import (
+    convert_DI_data_to_pm2_if,
+    convert_DI_IF_data_to_pm2,
+    read_UNFCCC_DI_for_country,
+    read_UNFCCC_DI_for_country_group,
+)
+from .unfccc_di_reader_datalad import (
+    process_DI_for_country_datalad,
+    process_DI_for_country_group_datalad,
+    read_DI_for_country_datalad,
+    read_DI_for_country_group_datalad,
+)
+from .unfccc_di_reader_helper import determine_filename
+from .unfccc_di_reader_proc import (
+    process_and_save_UNFCCC_DI_for_country,
+    process_UNFCCC_DI_for_country,
+    process_UNFCCC_DI_for_country_group,
+)
+
+__all__ = [
+    "read_UNFCCC_DI_for_country",
+    "convert_DI_data_to_pm2_if",
+    "convert_DI_IF_data_to_pm2",
+    "read_UNFCCC_DI_for_country_group",
+    "process_UNFCCC_DI_for_country",
+    "process_and_save_UNFCCC_DI_for_country",
+    "process_UNFCCC_DI_for_country_group",
+    "process_DI_for_country_group_datalad",
+    "read_DI_for_country_datalad",
+    "process_DI_for_country_datalad",
+    "read_DI_for_country_group_datalad",
+    "determine_filename",
+]

UNFCCC_GHG_data/UNFCCC_DI_reader/process_UNFCCC_DI_for_country.py → src/unfccc_ghg_data/unfccc_di_reader/process_unfccc_di_for_country.py

@@ -4,9 +4,8 @@ function such that it can be called from datalad
 """
 
 import argparse
-from UNFCCC_GHG_data.UNFCCC_DI_reader import \
-    process_and_save_UNFCCC_DI_for_country
 
+from unfccc_ghg_data.UNFCCC_DI_reader import process_and_save_UNFCCC_DI_for_country
 
 parser = argparse.ArgumentParser()
 parser.add_argument('--country', help='Country code')

UNFCCC_GHG_data/UNFCCC_DI_reader/process_UNFCCC_DI_for_country_datalad.py → src/unfccc_ghg_data/unfccc_di_reader/process_unfccc_di_for_country_datalad.py

@@ -4,10 +4,10 @@ from doit in the current setup where doit runs on system python and
 not in the venv.
 """
 
-from UNFCCC_GHG_data.UNFCCC_DI_reader import \
-    process_DI_for_country_datalad
 import argparse
 
+from unfccc_ghg_data.UNFCCC_DI_reader import process_DI_for_country_datalad
+
 parser = argparse.ArgumentParser()
 parser.add_argument('--country', help='Country name or code')
 parser.add_argument('--date', help='String with date to read and process. If not '
@@ -19,4 +19,4 @@ date_str = args.date
 if date_str == "None":
     date_str = None
 
-process_DI_for_country_datalad(country, date_str=date_str)
+process_DI_for_country_datalad(country, date_str=date_str)

UNFCCC_GHG_data/UNFCCC_DI_reader/process_UNFCCC_DI_for_country_group.py → src/unfccc_ghg_data/unfccc_di_reader/process_unfccc_di_for_country_group.py

@@ -4,9 +4,8 @@ function such that it can be called from datalad
 """
 
 import argparse
-from UNFCCC_GHG_data.UNFCCC_DI_reader import \
-    process_UNFCCC_DI_for_country_group
 
+from unfccc_ghg_data.UNFCCC_DI_reader import process_UNFCCC_DI_for_country_group
 
 parser = argparse.ArgumentParser()
 parser.add_argument('--annexI', help='read for AnnexI countries (default is for '

UNFCCC_GHG_data/UNFCCC_DI_reader/process_UNFCCC_DI_for_country_group_datalad.py → src/unfccc_ghg_data/unfccc_di_reader/process_unfccc_di_for_country_group_datalad.py

@@ -4,10 +4,10 @@ from doit in the current setup where doit runs on system python and
 not in the venv.
 """
 
-from UNFCCC_GHG_data.UNFCCC_DI_reader import \
-    process_DI_for_country_group_datalad
 import argparse
 
+from unfccc_ghg_data.UNFCCC_DI_reader import process_DI_for_country_group_datalad
+
 parser = argparse.ArgumentParser()
 parser.add_argument('--annexI', help='read for AnnexI countries (default is for '
                                      'non-AnnexI)', action='store_true')

UNFCCC_GHG_data/UNFCCC_DI_reader/read_UNFCCC_DI_for_country.py → src/unfccc_ghg_data/unfccc_di_reader/read_unfccc_di_for_country.py

@@ -4,9 +4,8 @@ function such that it can be called from datalad
 """
 
 import argparse
-from UNFCCC_GHG_data.UNFCCC_DI_reader.UNFCCC_DI_reader_core import \
-    read_UNFCCC_DI_for_country
 
+from unfccc_ghg_data.UNFCCC_DI_reader.UNFCCC_DI_reader_core import read_UNFCCC_DI_for_country
 
 parser = argparse.ArgumentParser()
 parser.add_argument('--country', help='Country code')

UNFCCC_GHG_data/UNFCCC_DI_reader/read_UNFCCC_DI_for_country_datalad.py → src/unfccc_ghg_data/unfccc_di_reader/read_unfccc_di_for_country_datalad.py

@@ -4,14 +4,14 @@ from doit in the current setup where doit runs on system python and
 not in the venv.
 """
 
-from UNFCCC_GHG_data.UNFCCC_DI_reader import \
-    read_DI_for_country_datalad
 import argparse
 
+from unfccc_ghg_data.UNFCCC_DI_reader import read_DI_for_country_datalad
+
 parser = argparse.ArgumentParser()
 parser.add_argument('--country', help='Country name or code')
 
 args = parser.parse_args()
 country = args.country
 
-read_DI_for_country_datalad(country)
+read_DI_for_country_datalad(country)

UNFCCC_GHG_data/UNFCCC_DI_reader/read_UNFCCC_DI_for_country_group.py → src/unfccc_ghg_data/unfccc_di_reader/read_unfccc_di_for_country_group.py

@@ -4,9 +4,8 @@ function such that it can be called from datalad
 """
 
 import argparse
-from UNFCCC_GHG_data.UNFCCC_DI_reader import \
-    read_UNFCCC_DI_for_country_group
 
+from unfccc_ghg_data.UNFCCC_DI_reader import read_UNFCCC_DI_for_country_group
 
 parser = argparse.ArgumentParser()
 parser.add_argument('--annexI', help='read for AnnexI countries (default is for '

UNFCCC_GHG_data/UNFCCC_DI_reader/read_UNFCCC_DI_for_country_group_datalad.py → src/unfccc_ghg_data/unfccc_di_reader/read_unfccc_di_for_country_group_datalad.py

@@ -4,10 +4,10 @@ from doit in the current setup where doit runs on system python and
 not in the venv.
 """
 
-from UNFCCC_GHG_data.UNFCCC_DI_reader import \
-    read_DI_for_country_group_datalad
 import argparse
 
+from unfccc_ghg_data.UNFCCC_DI_reader import read_DI_for_country_group_datalad
+
 parser = argparse.ArgumentParser()
 parser.add_argument('--annexI', help='read for AnnexI countries (default is for '
                                      'non-AnnexI)', action='store_true')

UNFCCC_GHG_data/UNFCCC_DI_reader/UNFCCC_DI_reader_core.py → src/unfccc_ghg_data/unfccc_di_reader/unfccc_di_reader_core.py

@@ -1,29 +1,28 @@
-import primap2 as pm2
-import unfccc_di_api
-import pandas as pd
-import pycountry
-import itertools
 import copy
-import xarray as xr
-
-from datetime import date
-from typing import Optional, Dict
+import itertools
 from copy import deepcopy
+from datetime import date
+from typing import Optional
 
-from .UNFCCC_DI_reader_config import di_to_pm2if_template_nai
-from .UNFCCC_DI_reader_config import di_to_pm2if_template_ai
-from .UNFCCC_DI_reader_config import di_query_filters
-
-from .UNFCCC_DI_reader_config import cat_code_regexp
-from .util import NoDIDataError, nAI_countries, AI_countries
-from .util import DI_date_format
+import pandas as pd
+import primap2 as pm2
+import pycountry
+import unfccc_di_api
+import xarray as xr
 
-from .UNFCCC_DI_reader_io import save_DI_dataset, save_DI_country_data
+from .unfccc_di_reader_config import (
+    cat_code_regexp,
+    di_query_filters,
+    di_to_pm2if_template_ai,
+    di_to_pm2if_template_nai,
+)
+from .unfccc_di_reader_io import save_DI_country_data, save_DI_dataset
+from .util import AI_countries, DI_date_format, nAI_countries
 
 
 def read_UNFCCC_DI_for_country(
         country_code: str,
-        category_groups: Optional[Dict]=None,
+        category_groups: Optional[dict]=None,
         read_subsectors: bool=False,
         save_data: Optional[bool]=True,
         date_str: Optional[str]=None,
@@ -36,7 +35,6 @@ def read_UNFCCC_DI_for_country(
     reads data for a country from the UNFCCC DI interface and saves to native and
     interchange format
     """
-
     # read the data
     if use_zenodo:
         data_df = read_UNFCCC_DI_for_country_df_zenodo(
@@ -81,7 +79,7 @@ def read_UNFCCC_DI_for_country(
 
 def read_UNFCCC_DI_for_country_df(
         country_code: str,
-        category_groups: Optional[Dict]=None,
+        category_groups: Optional[dict]=None,
         read_subsectors: bool=False,
         debug: Optional[bool]=False,
 )->pd.DataFrame:
@@ -193,7 +191,7 @@ def read_UNFCCC_DI_for_country_df(
                     node_codes = node_codes + (
                         [sub_node.identifier for sub_node in sub_nodes])
                 else:
-                    node_codes = node_codes + [node.identifier]
+                    node_codes = [*node_codes, node.identifier]
             if debug:
                 print(f"Found node_codes: {node_codes}")
             # add category node_codes to query
@@ -254,7 +252,7 @@ def read_UNFCCC_DI_for_country_df(
 
 def read_UNFCCC_DI_for_country_df_zenodo(
         country_code: str,
-        category_groups: Optional[Dict]=None,
+        category_groups: Optional[dict]=None,
         read_subsectors: bool=False,
         debug: Optional[bool]=False,
 )->pd.DataFrame:
@@ -338,7 +336,6 @@ def convert_DI_data_to_pm2_if(
     TODO: consider moving the specification template into this function and just use the config parameter
     to overwrite certain parameters (makes sense if function is used in a broader context
     """
-
     print("Convert data to PRIMAP2 interchange format")
 
     # create a copy of the data to avoid data altering the original data
@@ -373,7 +370,7 @@ def convert_DI_data_to_pm2_if(
 
     # set the scenario to today's date if not given explicitly
     if date_str == "country":
-        pm2if_specifications["coords_defaults"]["scenario"] = f"DIrolling"
+        pm2if_specifications["coords_defaults"]["scenario"] = "DIrolling"
     elif date_str is None:
         today = date.today()
         date_str = today.strftime(DI_date_format)
@@ -434,7 +431,8 @@ def convert_DI_data_to_pm2_if(
         data_temp["category_copy"] = data_temp["category"]
 
     # replace category name and code by just the code
-    repl = lambda m: m.group('code')
+    def repl(m):
+        return m.group("code")
     data_temp["category"] = data_temp["category"].str.replace(cat_code_regexp, repl,
                                                               regex=True)
 
@@ -473,7 +471,6 @@ def read_UNFCCC_DI_for_country_group(
     The function reads all data in one go using datalad run. as the output data file
     names are unknown beforehand datalad run uses explicit=false
     '''
-
     today = date.today()
     date_str = today.strftime(DI_date_format)
 

UNFCCC_GHG_data/UNFCCC_DI_reader/UNFCCC_DI_reader_datalad.py → src/unfccc_ghg_data/unfccc_di_reader/unfccc_di_reader_datalad.py

@@ -1,12 +1,15 @@
 from datetime import date
-from typing import Union, Optional
+from typing import Optional, Union
+
 import datalad.api
 from datalad.support.exceptions import IncompleteResultsError
-from UNFCCC_GHG_data.helper import root_path, code_path
 
-from .UNFCCC_DI_reader_helper import get_input_and_output_files_for_country_DI
+from unfccc_ghg_data.helper import code_path, root_path
+
+from .unfccc_di_reader_helper import get_input_and_output_files_for_country_DI
 from .util import DI_date_format
 
+
 ## datalad and pydoit interface functions
 def read_DI_for_country_datalad(
         country: str,
@@ -16,13 +19,13 @@ def read_DI_for_country_datalad(
     and output files and using datalad run to trigger the data reading
 
     Parameters
+    ----------
     __________
 
     country: str
         country name or ISO 3-letter country code
 
     """
-
     # get date to determine output filename
     today = date.today()
     date_str = today.strftime(DI_date_format)
@@ -34,10 +37,10 @@ def read_DI_for_country_datalad(
     print(f"Attempting to read DI data for {country_info['name']}.")
     print("#"*80)
     print("")
-    print(f"Using the UNFCCC_DI_reader")
+    print("Using the unfccc_di_reader")
     print("")
-    print(f"Run the script using datalad run via the python api")
-    script = code_path / "UNFCCC_DI_reader" / "read_UNFCCC_DI_for_country.py"
+    print("Run the script using datalad run via the python api")
+    script = code_path / "unfccc_di_reader" / "read_unfccc_di_for_country.py"
     script = script.relative_to(root_path)
 
     cmd = f"./venv/bin/python3 {script.as_posix()} --country={country_info['code']} " \
@@ -68,6 +71,7 @@ def process_DI_for_country_datalad(
     and output files and using datalad run to trigger the data processing
 
     Parameters
+    ----------
     __________
 
     country: str
@@ -76,7 +80,6 @@ def process_DI_for_country_datalad(
         Date of the data to be processed in the format %Y-%m-%d (e.g. 2023-01-30). If
         no date is given the last data read will be processed.
     """
-
     # get all the info for the country
     country_info = get_input_and_output_files_for_country_DI(country, date_str,
                                                              raw=True, verbose=True)
@@ -84,10 +87,10 @@ def process_DI_for_country_datalad(
     print(f"Attempting to process DI data for {country_info['name']}.")
     print("#"*80)
     print("")
-    print(f"Using the UNFCCC_DI_reader")
+    print("Using the unfccc_di_reader")
     print("")
-    print(f"Run the script using datalad run via the python api")
-    script = code_path / "UNFCCC_DI_reader" / "process_UNFCCC_DI_for_country.py"
+    print("Run the script using datalad run via the python api")
+    script = code_path / "unfccc_di_reader" / "process_unfccc_di_for_country.py"
     script = script.relative_to(root_path)
 
     cmd = f"./venv/bin/python3 {script.as_posix()} --country={country_info['code']} " \
@@ -117,6 +120,7 @@ def read_DI_for_country_group_datalad(
     and output files and using datalad run to trigger the data processing
 
     Parameters
+    ----------
     __________
 
     country: str
@@ -125,7 +129,6 @@ def read_DI_for_country_group_datalad(
         Date of the data to be processed in the format %Y-%m-%d (e.g. 2023-01-30). If
         no date is given the last data read will be processed.
     """
-
     if annexI:
         country_group = "AnnexI"
     else:
@@ -134,15 +137,15 @@ def read_DI_for_country_group_datalad(
     print(f"Attempting to read DI data for {country_group}.")
     print("#"*80)
     print("")
-    print(f"Using the UNFCCC_DI_reader")
+    print("Using the unfccc_di_reader")
     print("")
-    print(f"Run the script using datalad run via the python api")
-    script = code_path / "UNFCCC_DI_reader" / "read_UNFCCC_DI_for_country_group.py"
+    print("Run the script using datalad run via the python api")
+    script = code_path / "unfccc_di_reader" / "read_unfccc_di_for_country_group.py"
     script = script.relative_to(root_path)
 
     cmd = f"./venv/bin/python3 {script.as_posix()} "
     if annexI:
-        cmd = cmd + f" --annexI"
+        cmd = cmd + " --annexI"
 
     try:
         datalad.api.run(
@@ -170,6 +173,7 @@ def process_DI_for_country_group_datalad(
     and output files and using datalad run to trigger the data processing
 
     Parameters
+    ----------
     __________
 
     annexI: bool (default False)
@@ -179,7 +183,6 @@ def process_DI_for_country_group_datalad(
         Date of the data to be processed in the format %Y-%m-%d (e.g. 2023-01-30). If
         no date is given the last data read will be processed.
     """
-
     if annexI:
         country_group = "AnnexI"
     else:
@@ -188,15 +191,15 @@ def process_DI_for_country_group_datalad(
     print(f"Attempting to process DI data for {country_group}.")
     print("#"*80)
     print("")
-    print(f"Using the UNFCCC_DI_reader")
+    print("Using the unfccc_di_reader")
     print("")
-    print(f"Run the script using datalad run via the python api")
-    script = code_path / "UNFCCC_DI_reader" / "process_UNFCCC_DI_for_country_group.py"
+    print("Run the script using datalad run via the python api")
+    script = code_path / "unfccc_di_reader" / "process_unfccc_di_for_country_group.py"
     script = script.relative_to(root_path)
 
     cmd = f"./venv/bin/python3 {script.as_posix()} "
     if annexI:
-        cmd = cmd + f" --annexI"
+        cmd = cmd + " --annexI"
     if date_str is not None:
         cmd = cmd + f" --date_str={date_str}"
     else:
@@ -216,4 +219,4 @@ def process_DI_for_country_group_datalad(
         print(f"IncompleteResultsError occurred when running {cmd}: {IRE}")
     except Exception as ex:
         print(f"Exception occurred when running {cmd}")
-        print(ex.message)
+        print(ex.message)

UNFCCC_GHG_data/UNFCCC_DI_reader/UNFCCC_DI_reader_helper.py → src/unfccc_ghg_data/unfccc_di_reader/unfccc_di_reader_helper.py

@@ -1,14 +1,20 @@
 import json
 import re
-from typing import Optional, Dict, List, Union
-from pathlib import Path
 from datetime import date
-from UNFCCC_GHG_data.UNFCCC_CRF_reader.UNFCCC_CRF_reader_core import find_latest_date
-from .util import regex_date, DI_date_format
-from UNFCCC_GHG_data.helper import custom_country_mapping
-from UNFCCC_GHG_data.helper import get_country_code, get_country_name
-from UNFCCC_GHG_data.helper import extracted_data_path_UNFCCC, root_path, code_path
-from UNFCCC_GHG_data.helper import dataset_path_UNFCCC
+from pathlib import Path
+from typing import Optional, Union
+
+from unfccc_ghg_data.helper import (
+    custom_country_mapping,
+    dataset_path_UNFCCC,
+    extracted_data_path_UNFCCC,
+    get_country_code,
+    get_country_name,
+    root_path,
+)
+from unfccc_ghg_data.UNFCCC_CRF_reader.UNFCCC_CRF_reader_core import find_latest_date
+
+from .util import DI_date_format, regex_date
 
 
 ## helper functions
@@ -21,7 +27,6 @@ def determine_filename(
     """
     Determine the filename for a dataset from given country code and date string.
 
-
     Parameters
     ----------
     country_code: str
@@ -33,13 +38,13 @@ def determine_filename(
     hash: str
 
     Returns
+    -------
     _______
         pathlib Path object for the file name (without suffix)
 
     """
-
     # get the country folder
-    with open(extracted_data_path_UNFCCC / "folder_mapping.json", "r") as mapping_file:
+    with open(extracted_data_path_UNFCCC / "folder_mapping.json") as mapping_file:
         folder_mapping = json.load(mapping_file)
 
     if country_code in folder_mapping:
@@ -98,10 +103,10 @@ def determine_dataset_filename(
     hash: str
 
     Returns
+    -------
     _______
         pathlib Path object for the file name (without suffix)
     """
-
     # get the country folder
     if annexI:
         current_dataset_path = dataset_path_UNFCCC / "DI_AnnexI"
@@ -127,11 +132,10 @@ def get_input_and_output_files_for_country_DI(
         date_str: str,
         raw: bool,
         verbose: Optional[bool]=True,
-) -> Dict[str, Union[List, str]]:
+) -> dict[str, Union[list, str]]:
     """
     Get input and output files for a given country
     """
-
     country_info = {}
 
     if country in custom_country_mapping:
@@ -175,7 +179,7 @@ def get_input_and_output_files_for_country_DI(
                         suffix in ['yaml', 'csv', 'nc']]
 
         if verbose:
-            print(f"The following files are considered as input_files:")
+            print("The following files are considered as input_files:")
             for file in input_files:
                 print(file)
             print("")
@@ -186,7 +190,7 @@ def get_input_and_output_files_for_country_DI(
                     suffix in ['yaml', 'csv', 'nc']]
 
     if verbose:
-        print(f"The following files are considered as output_files:")
+        print("The following files are considered as output_files:")
         for file in output_files:
             print(file)
         print("")
@@ -202,19 +206,18 @@ def get_input_and_output_files_for_country_DI(
 def get_present_hashes_for_country_DI(
         country_code: str,
         raw: bool,
-) -> List:
+) -> list:
     '''
     Get the hashes of outputs
     '''
-
     regex_hash = r"_([a-f0-9]*)_"
     if raw:
-        regex_hash = regex_hash + "raw_hash\.nc"
+        regex_hash = regex_hash + "raw_hash\\.nc"
     else:
-        regex_hash = regex_hash + "hash\.nc"
+        regex_hash = regex_hash + "hash\\.nc"
 
     # get the country folder
-    with open(extracted_data_path_UNFCCC / "folder_mapping.json", "r") as mapping_file:
+    with open(extracted_data_path_UNFCCC / "folder_mapping.json") as mapping_file:
         folder_mapping = json.load(mapping_file)
 
     if country_code in folder_mapping:
@@ -252,7 +255,6 @@ def find_latest_DI_data(
     '''
     Find the path to the nc file with the latest DI data for a given country
     '''
-
     if raw:
         regex = f"{country_code}_DI_{regex_date}" + r"_raw\.nc"
     else:
@@ -260,7 +262,7 @@ def find_latest_DI_data(
         #regex = f"{country_code}_DI_{regex_date}" + r"\.nc"
 
     # get the country folder
-    with open(extracted_data_path_UNFCCC / "folder_mapping.json", "r") as mapping_file:
+    with open(extracted_data_path_UNFCCC / "folder_mapping.json") as mapping_file:
         folder_mapping = json.load(mapping_file)
 
     if country_code in folder_mapping:

UNFCCC_GHG_data/UNFCCC_DI_reader/UNFCCC_DI_reader_io.py → src/unfccc_ghg_data/unfccc_di_reader/unfccc_di_reader_io.py

@@ -2,9 +2,10 @@ import primap2 as pm2
 import xarray as xr
 from dask.base import tokenize
 
-from UNFCCC_GHG_data.helper import root_path
+from unfccc_ghg_data.helper import root_path
+
+from .unfccc_di_reader_helper import determine_dataset_filename, determine_filename
 
-from .UNFCCC_DI_reader_helper import determine_filename, determine_dataset_filename
 
 def save_DI_country_data(
         data_pm2: xr.Dataset,
@@ -14,7 +15,6 @@ def save_DI_country_data(
     save primap2 and IF data to country folder
     can be used for raw and processed data but for a single country only
     '''
-
     # preparations
     data_if = data_pm2.pr.to_interchange_format()
 
@@ -88,7 +88,6 @@ def save_DI_dataset(
     save primap2 and IF data to dataset folder
     can be used for raw and processed data but not to save to country folders
     '''
-
     # preparations
     data_if = data_pm2.pr.to_interchange_format()
     if annexI:
@@ -149,4 +148,4 @@ def save_DI_dataset(
         file_hash = filename_hash.name + suffix
         if file_date.exists():
             file_date.unlink()
-        file_date.symlink_to(file_hash)
+        file_date.symlink_to(file_hash)

UNFCCC_GHG_data/UNFCCC_DI_reader/UNFCCC_DI_reader_proc.py → src/unfccc_ghg_data/unfccc_di_reader/unfccc_di_reader_proc.py

@@ -1,21 +1,16 @@
-import primap2 as pm2
-import unfccc_di_api
-import numpy as np
-import xarray as xr
 import re
 from datetime import date
-from typing import Optional, Dict, List, Union
+from typing import Optional, Union
 
-from .UNFCCC_DI_reader_config import di_processing_info
-from .UNFCCC_DI_reader_config import cat_conversion
-from .util import NoDIDataError, nAI_countries
-from .util import DI_date_format
+import primap2 as pm2
+import xarray as xr
 
-from UNFCCC_GHG_data.helper import process_data_for_country, gas_baskets
-from .UNFCCC_DI_reader_helper import find_latest_DI_data
-from .UNFCCC_DI_reader_helper import determine_filename
+from unfccc_ghg_data.helper import gas_baskets, process_data_for_country
 
-from .UNFCCC_DI_reader_io import save_DI_dataset, save_DI_country_data
+from .unfccc_di_reader_config import cat_conversion, di_processing_info
+from .unfccc_di_reader_helper import determine_filename, find_latest_DI_data
+from .unfccc_di_reader_io import save_DI_country_data, save_DI_dataset
+from .util import DI_date_format, nAI_countries
 
 
 def process_and_save_UNFCCC_DI_for_country(
@@ -25,7 +20,6 @@ def process_and_save_UNFCCC_DI_for_country(
     """
     process data and save them to disk using default parameters
     """
-
     # get latest dataset if no date given
     if date_str is None:
         # get the latest date
@@ -82,19 +76,19 @@ def process_and_save_UNFCCC_DI_for_country(
 
 def process_UNFCCC_DI_for_country(
         data_country: xr.Dataset,
-        entities_to_ignore: List[str],
-        gas_baskets: Dict[str, List[str]],
-        filter_dims: Optional[Dict[str, List[str]]] = None,
-        category_conversion: Dict[str, Dict] = None,
-        sectors_out: List[str] = None,
-        processing_info_country: Dict = None,
+        entities_to_ignore: list[str],
+        gas_baskets: dict[str, list[str]],
+        filter_dims: Optional[dict[str, list[str]]] = None,
+        category_conversion: dict[str, dict] = None,
+        sectors_out: list[str] = None,
+        processing_info_country: dict = None,
 ) -> xr.Dataset:
     """
-        Process data from DI interface (where necessary).
-        * Downscaling including subtraction of time series
-        * country specific sector aggregation
-        * Conversion to IPCC2006 categories
-        * general sector and gas basket aggregation (in new categories)
+    Process data from DI interface (where necessary).
+    * Downscaling including subtraction of time series
+    * country specific sector aggregation
+    * Conversion to IPCC2006 categories
+    * general sector and gas basket aggregation (in new categories)
     """
     # get country
     countries = list(data_country.coords[data_country.attrs['area']].values)
@@ -167,6 +161,7 @@ def process_UNFCCC_DI_for_country_group(
     This function processes DI data for all countries in a group (annexI or non-AnnexI)
 
     Parameters
+    ----------
     __________
 
     annexI: bool (default False)
@@ -205,7 +200,7 @@ def process_UNFCCC_DI_for_country_group(
             data_country = data_country.assign_coords({"scenario (Access_Date)": [
                 f"DI{date_str_today}"]})
             scen_dim = data_country.attrs["scen"]
-            data_country.attrs["scen"] = f"scenario (Process_Date)"
+            data_country.attrs["scen"] = "scenario (Process_Date)"
             data_country = data_country.rename({scen_dim: data_country.attrs["scen"]})
 
             if data_all is None:

UNFCCC_GHG_data/UNFCCC_DI_reader/util.py → src/unfccc_ghg_data/unfccc_di_reader/util.py

@@ -1,13 +1,13 @@
-import unfccc_di_api
 import pandas as pd
-from UNFCCC_GHG_data.helper import code_path
+
+from unfccc_ghg_data.helper import code_path
 
 #reader = unfccc_di_api.UNFCCCApiReader()
 #nAI_countries = list(reader.non_annex_one_reader.parties["code"])
-nAI_countries = list(pd.read_csv(code_path / 'UNFCCC_DI_reader' /
+nAI_countries = list(pd.read_csv(code_path / 'unfccc_di_reader' /
                                  'DI_NAI_parties.conf')["code"])
 #AI_countries = list(reader.annex_one_reader.parties["code"])
-AI_countries = list(pd.read_csv(code_path / 'UNFCCC_DI_reader' /
+AI_countries = list(pd.read_csv(code_path / 'unfccc_di_reader' /
                                 'DI_AI_parties.conf')["code"])
 
 DI_date_format = '%Y-%m-%d'

UNFCCC_GHG_data/UNFCCC_downloader/__init__.py → src/unfccc_ghg_data/unfccc_downloader/__init__.py

@@ -2,4 +2,4 @@ from .unfccc_submission_info import get_unfccc_submission_info
 
 __all__ = [
     "get_unfccc_submission_info",
-]
+]

UNFCCC_GHG_data/UNFCCC_downloader/download_annexI.py → src/unfccc_ghg_data/unfccc_downloader/download_annexI.py

@@ -1,17 +1,18 @@
 import argparse
-import pandas as pd
-import requests
+import os
 import shutil
 import time
-import os
 import zipfile
 from datetime import date
+from pathlib import Path
+from random import randrange
+
+import pandas as pd
+import requests
 from selenium.webdriver import Firefox
 from selenium.webdriver.firefox.options import Options
-from random import randrange
-from pathlib import Path
 
-from UNFCCC_GHG_data.helper import root_path, downloaded_data_path_UNFCCC
+from unfccc_ghg_data.helper import downloaded_data_path_UNFCCC, root_path
 
 ###############
 #
@@ -60,7 +61,7 @@ if int(year) == 2019:
     )
 elif int(year) in range(2020,2023):
     url = (
-        "https://unfccc.int/ghg-inventories-annex-i-parties/{}".format(year)
+        f"https://unfccc.int/ghg-inventories-annex-i-parties/{year}"
     )
 elif int(year) >= 2023:
     url = (
@@ -132,7 +133,7 @@ for idx, submission in items.iterrows():
         if Path(local_filename).stat().st_size in error_file_sizes:
             # found the error page. delete file
             os.remove(local_filename)
-    
+
     # now we have removed error pages, so a present file should not be overwritten
     if (not local_filename.exists()) and (not local_filename.is_symlink()):
         i = 0  # reset counter
@@ -140,7 +141,7 @@ for idx, submission in items.iterrows():
             # for i = 0 and i = 5 try to get a new session ID
             if i == 1 or i == 5:
                 driver = Firefox(options=options)
-    
+
                 # visit the main data page once to create cookies
                 driver.get(url)
                 time.sleep(20)
@@ -154,15 +155,15 @@ for idx, submission in items.iterrows():
             r = requests.get(url, stream=True, cookies=cookies)
             with open(str(local_filename), 'wb') as f:
                 shutil.copyfileobj(r.raw, f)
-            
+
             # check file size. if 210 or 212 bytes it's the error page
             if Path(local_filename).stat().st_size in error_file_sizes:
                 # found the error page. delete file
                 os.remove(local_filename)
-            
+
             # sleep a bit to avoid running into captchas
             time.sleep(randrange(5, 15))
-            
+
         if local_filename.exists():
             new_downloaded.append(submission)
             print(f"Download => {local_filename.relative_to(root_path)}")

UNFCCC_GHG_data/UNFCCC_downloader/download_ndc.py → src/unfccc_ghg_data/unfccc_downloader/download_ndc.py

@@ -1,13 +1,15 @@
-import pandas as pd
-import requests
-import shutil
-import time
 import os
 import re
+import shutil
+import time
 from datetime import date
-from random import randrange
-from UNFCCC_GHG_data.helper import downloaded_data_path_UNFCCC
 from pathlib import Path
+from random import randrange
+
+import pandas as pd
+import requests
+
+from unfccc_ghg_data.helper import downloaded_data_path_UNFCCC
 
 """
 based on download_bur from national-inventory-submissions
@@ -73,7 +75,7 @@ for idx, submission in submissions.iterrows():
         if Path(local_filename_underscore).stat().st_size in error_file_sizes:
             # found the error page. delete file
             os.remove(local_filename_underscore)
-    
+
     # now we have to remove error pages, so a present file should not be overwritten
     if (not local_filename_underscore.exists()) \
             and (not local_filename_underscore.is_symlink()):
@@ -83,15 +85,15 @@ for idx, submission in submissions.iterrows():
             r = requests.get(url, stream=True)
             with open(str(local_filename_underscore), 'wb') as f:
                 shutil.copyfileobj(r.raw, f)
-            
+
             # check file size. if 210 or 212 bytes it's the error page
             if Path(local_filename_underscore).stat().st_size in error_file_sizes:
                 # found the error page. delete file
                 os.remove(local_filename_underscore)
-            
+
             # sleep a bit to avoid running into captchas
             time.sleep(randrange(5, 15))
-            
+
         if local_filename_underscore.exists():
             new_downloaded.append(submission)
             print("Download => downloaded_data/UNFCCC/" + country + "/" +
@@ -105,4 +107,4 @@ for idx, submission in submissions.iterrows():
 
 
 df = pd.DataFrame(new_downloaded)
-df.to_csv(downloaded_data_path_UNFCCC / "00_new_downloads_ndc-{}.csv".format(date.today()), index=False)
+df.to_csv(downloaded_data_path_UNFCCC / f"00_new_downloads_ndc-{date.today()}.csv", index=False)

UNFCCC_GHG_data/UNFCCC_downloader/download_non-annexI.py → src/unfccc_ghg_data/unfccc_downloader/download_non-annexI.py

@@ -1,15 +1,17 @@
 import argparse
-import pandas as pd
-import requests
+import os
 import shutil
 import time
-import os
 from datetime import date
+from pathlib import Path
+from random import randrange
+
+import pandas as pd
+import requests
 from selenium.webdriver import Firefox
 from selenium.webdriver.firefox.options import Options
-from random import randrange
-from pathlib import Path
-from UNFCCC_GHG_data.helper import root_path, downloaded_data_path_UNFCCC
+
+from unfccc_ghg_data.helper import downloaded_data_path_UNFCCC, root_path
 
 ###############
 #
@@ -94,7 +96,7 @@ for idx, submission in submissions.iterrows():
         if Path(local_filename).stat().st_size in error_file_sizes:
             # found the error page. delete file
             os.remove(local_filename)
-    
+
     # now we have removed error pages, so a present file should not be overwritten
     if (not local_filename.exists()) and (not local_filename.is_symlink()):
         i = 0  # reset counter
@@ -102,7 +104,7 @@ for idx, submission in submissions.iterrows():
             # for i = 0 and i = 5 try to get a new session ID
             if i == 1 or i == 5:
                 driver = Firefox(options=options)
-    
+
                 # visit the main data page once to create cookies
                 driver.get(url)
                 time.sleep(20)
@@ -116,15 +118,15 @@ for idx, submission in submissions.iterrows():
             r = requests.get(url, stream=True, cookies=cookies)
             with open(str(local_filename), 'wb') as f:
                 shutil.copyfileobj(r.raw, f)
-            
+
             # check file size. if 210 or 212 bytes it's the error page
             if Path(local_filename).stat().st_size in error_file_sizes:
                 # found the error page. delete file
                 os.remove(local_filename)
-            
+
             # sleep a bit to avoid running into captchas
             time.sleep(randrange(5, 15))
-            
+
         if local_filename.exists():
             new_downloaded.append(submission)
             print(f"Download => {local_filename.relative_to(root_path)}")

UNFCCC_GHG_data/UNFCCC_downloader/fetch_submissions_annexI.py → src/unfccc_ghg_data/unfccc_downloader/fetch_submissions_annexI.py

@@ -8,7 +8,7 @@ from selenium.webdriver import Firefox
 from selenium.webdriver.firefox.options import Options
 from random import randrange
 from unfccc_submission_info import get_unfccc_submission_info
-from UNFCCC_GHG_data.helper import downloaded_data_path_UNFCCC
+from unfccc_ghg_data.helper import downloaded_data_path_UNFCCC
 
 max_tries = 10
 

UNFCCC_GHG_data/UNFCCC_downloader/fetch_submissions_bur.py → src/unfccc_ghg_data/unfccc_downloader/fetch_submissions_bur.py

@@ -1,20 +1,21 @@
 #import requests
-import time
-import pandas as pd
 import re
-
+import time
 from pathlib import Path
+from random import randrange
+
+import pandas as pd
 from bs4 import BeautifulSoup
 from selenium.webdriver import Firefox
 from selenium.webdriver.firefox.options import Options
-from random import randrange
 from unfccc_submission_info import get_unfccc_submission_info
-from UNFCCC_GHG_data.helper import downloaded_data_path_UNFCCC
+
+from unfccc_ghg_data.helper import downloaded_data_path_UNFCCC
 
 """
 Download UNFCCC Biennial Update Report submissions
 from Non-Annex I Parties and create list of submissions as CSV file
-Based on `process_bur` from national-inventory-submissions 
+Based on `process_bur` from national-inventory-submissions
 (https://github.com/openclimatedata/national-inventory-submisions)
 """
 

UNFCCC_GHG_data/UNFCCC_downloader/fetch_submissions_nc.py → src/unfccc_ghg_data/unfccc_downloader/fetch_submissions_nc.py

@@ -1,21 +1,21 @@
 #import requests
-import time
-import pandas as pd
 import re
-
+import time
 from pathlib import Path
+from random import randrange
+
+import pandas as pd
 from bs4 import BeautifulSoup
 from selenium.webdriver import Firefox
 from selenium.webdriver.firefox.options import Options
-from random import randrange
-from UNFCCC_GHG_data.UNFCCC_downloader import \
-    get_unfccc_submission_info
-from UNFCCC_GHG_data.helper import downloaded_data_path_UNFCCC
+
+from unfccc_ghg_data.helper import downloaded_data_path_UNFCCC
+from unfccc_ghg_data.UNFCCC_downloader import get_unfccc_submission_info
 
 """
 Download UNFCCC Biennial Update Report submissions
 from Non-Annex I Parties and create list of submissions as CSV file
-Based on `process_bur` from national-inventory-submissions 
+Based on `process_bur` from national-inventory-submissions
 (https://github.com/openclimatedata/national-inventory-submisions)
 """
 

UNFCCC_GHG_data/UNFCCC_downloader/unfccc_submission_info.py → src/unfccc_ghg_data/unfccc_downloader/unfccc_submission_info.py

@@ -1,11 +1,11 @@
 # helper functions to gather submission info from UNFCCC website
-import time
 import re
+import time
 from random import randrange
-from typing import Dict, List
-from selenium.webdriver import Firefox
-from selenium.common.exceptions import WebDriverException
+
 from bs4 import BeautifulSoup
+from selenium.common.exceptions import WebDriverException
+from selenium.webdriver import Firefox
 
 
 def get_unfccc_submission_info(
@@ -13,7 +13,7 @@ def get_unfccc_submission_info(
         driver: Firefox,
         max_tries: int=10,
 
-) -> List[Dict[str,str]]:
+) -> list[dict[str,str]]:
     info = []
     pattern = re.compile(r"BUR ?\d")
     pattern_NC = re.compile(r"NC ?\d")
@@ -53,7 +53,7 @@ def get_unfccc_submission_info(
             subtree = html.find_all(
                 class_="field field--name-field-document-country field--type-termstore-entity-reference field--label-inline")
             country = subtree[0].find(class_="field--item").contents[0]
-        except (AttributeError, IndexError) as e:
+        except (AttributeError, IndexError):
             # author as backup for country
             subtree = html.find_all(class_="field--name-field-document-ca")
             country = subtree[0].find(class_="field--item").contents[0]

UNFCCC_GHG_data/UNFCCC_reader/Argentina/read_ARG_BUR4_from_pdf.py → src/unfccc_ghg_data/unfccc_reader/Argentina/read_ARG_BUR4_from_pdf.py

@@ -2,13 +2,13 @@
 # Data is read from the xlsx file
 
 import sys
+
 import camelot
 import primap2 as pm2
 from primap2.pm2io._conversion import convert_ipcc_code_primap_to_primap2
-from UNFCCC_GHG_data.helper import downloaded_data_path, extracted_data_path, \
-    process_data_for_country
-from UNFCCC_GHG_data.UNFCCC_DI_reader.UNFCCC_DI_reader_config import gas_baskets
 
+from unfccc_ghg_data.helper import downloaded_data_path, extracted_data_path, process_data_for_country
+from unfccc_ghg_data.unfccc_di_reader.unfccc_di_reader_config import gas_baskets
 
 # ###
 # configuration
@@ -83,7 +83,7 @@ cat_codes_manual = {  # conversion to PRIMAP1 format
     'S/N': 'MMULTIOP',
 }
 
-cat_code_regexp = r'(?P<UNFCCC_GHG_data>^[A-Z0-9]{1,8}).*'
+cat_code_regexp = r'(?P<code>^[A-Z0-9]{1,8}).*'
 
 time_format = "%Y"
 
@@ -216,7 +216,7 @@ for page in pages_to_read:
     if page in range(232, 235):
         df_current.iloc[
             metadata["entity"][0], metadata["entity"][1]] = "KYOTOGHG (SARGWP100)"
-    # drop all rows where the index cols (category UNFCCC_GHG_data and name) are both NaN
+    # drop all rows where the index cols (category code and name) are both NaN
     # as without one of them there is no category information
     df_current.dropna(axis=0, how='all', subset=index_cols, inplace=True)
     # set index. necessary for the stack operation in the conversion to long format
@@ -250,7 +250,8 @@ for page in pages_to_read:
 
     df_current["category"] = df_current["category"].replace(cat_codes_manual)
     # then the regex replacements
-    repl = lambda m: convert_ipcc_code_primap_to_primap2('IPC' + m.group('UNFCCC_GHG_data'))
+    def repl(m):
+        return convert_ipcc_code_primap_to_primap2('IPC' + m.group('code'))
     df_current["category"] = df_current["category"].str.replace(cat_code_regexp, repl,
                                                                 regex=True)
 
@@ -308,8 +309,7 @@ for page in pages_to_read_fgases:
         dict(zip(df_current.columns, list(df_current.loc[idx_header[0]]))), axis=1)
     df_current = df_current.drop(idx_header)
 
-    # drop all rows where the index cols (category UNFCCC_GHG_data and name) are both NaN
-    # as without one of them there is no category information
+    # drop all rows where the index cols (category code
     df_current.dropna(axis=0, how='all', subset=index_cols_fgases, inplace=True)
     # set index. necessary for the stack operation in the conversion to long format
     # df_current = df_current.set_index(index_cols)
@@ -347,7 +347,8 @@ for page in pages_to_read_fgases:
 
     df_current["category"] = df_current["category"].replace(cat_codes_manual)
     # then the regex repalcements
-    repl = lambda m: convert_ipcc_code_primap_to_primap2('IPC' + m.group('UNFCCC_GHG_data'))
+    def repl(m):
+        return convert_ipcc_code_primap_to_primap2('IPC' + m.group('code'))
     df_current["category"] = df_current["category"].str.replace(cat_code_regexp, repl,
                                                                 regex=True)
 

UNFCCC_GHG_data/UNFCCC_reader/Chile/config_CHL_BUR4.py → src/unfccc_ghg_data/unfccc_reader/Chile/config_chl_bur4.py

@@ -42,8 +42,8 @@ filter_remove_IPCC2006 = {
             '3.G.1', '3.G.2',
             # additional subsector levels of 4.A.1 (3.A.1.a Forest land remaining forest land)
             '4.A.1.a', '4.A.1.a.i', '4.A.1.a.i.1', '4.A.1.a.i.1.a', '4.A.1.a.i.1.b', '4.A.1.a.i.1.c',
-            '4.A.1.a.i.1.d', '4.A.1.a.i.1.e', '4.A.1.a.i.1.f', '4.A.1.a.i.1.g', '4.A.1.a.i.1.h', 
-            '4.A.1.a.i.1.i', '4.A.1.a.i.1.j', '4.A.1.a.i.1.k', '4.A.1.a.i.1.l', '4.A.1.a.i.2', 
+            '4.A.1.a.i.1.d', '4.A.1.a.i.1.e', '4.A.1.a.i.1.f', '4.A.1.a.i.1.g', '4.A.1.a.i.1.h',
+            '4.A.1.a.i.1.i', '4.A.1.a.i.1.j', '4.A.1.a.i.1.k', '4.A.1.a.i.1.l', '4.A.1.a.i.2',
             '4.A.1.a.i.2.a', '4.A.1.a.i.2.b', '4.A.1.a.i.2.c', '4.A.1.a.i.2.d', '4.A.1.a.i.2.e',
             '4.A.1.a.i.2.f', '4.A.1.a.i.2.g', '4.A.1.a.i.2.h', '4.A.1.a.i.2.i', '4.A.1.a.i.2.j',
             '4.A.1.a.i.2.k', '4.A.1.a.i.2.l', '4.A.1.a.i.3', '4.A.1.a.i.3.a', '4.A.1.a.i.3.b',
@@ -90,7 +90,7 @@ cat_mapping = { # categories not listed here have the same UNFCCC_GHG_data as in
     '3.B.4.e': '3.A.2.i',
     '3.B.5': '3.C.6',
     '3.C': '3.C.7',
-    '3.D.1': '3.C.4', 
+    '3.D.1': '3.C.4',
     '3.D.2': '3.C.5',
     '3.D.2.a': '3.C.5.a', # not in climate_categories
     '3.D.2.b': '3.C.5.b', # not in climate_categories
@@ -166,10 +166,10 @@ cat_mapping = { # categories not listed here have the same UNFCCC_GHG_data as in
 # comments
 # '2.F.1.a.': included in '2.F.1.a.3', # not in climate categories
 # '2.F.1.b.': included in '2.F.1.a.2', # not in climate categories
-# '2.F.1.c.': included in '2.F.1.a.1', # not in climate categories 
+# '2.F.1.c.': included in '2.F.1.a.1', # not in climate categories
 # '2.F.1.d.': included in 2.F.1.a (transport refigeration)
 # '2.F.1.e.', includeded in 2.F.1.a (stationary air conditioning)
-# '2.F.1.f.': 2.F.1.b, (mobile air conditioning) 
+# '2.F.1.f.': 2.F.1.b, (mobile air conditioning)
 #    '3.A.4.f.': included in '3.A.1.j',
 # '3.A.4.g.': included in '3.A.1.j',
 # '3.A.4.g.i.',
@@ -183,4 +183,4 @@ aggregate_cats = {
     '3.C': {'sources': ['3.C.1', '3.C.2', '3.C.3', '3.C.4', '3.C.5', '3.C.6', '3.C.7', '3.C.8'], 'name': 'Aggregate sources and non-CO2 emissions sources on land'},
     '3.D': {'sources': ['3.D.1', '3.D.2'], 'name': 'Other'},
     '3': {'sources': ['3.A', '3.B', '3.C', '3.D'], 'name': 'AFOLU'},
-}
+}

UNFCCC_GHG_data/UNFCCC_reader/Chile/read_CHL_BUR4_from_xlsx.py → src/unfccc_ghg_data/unfccc_reader/Chile/read_CHL_BUR4_from_xlsx.py

@@ -3,13 +3,13 @@
 
 import os
 import sys
+
 import pandas as pd
 import primap2 as pm2
+from config_chl_bur4 import aggregate_cats, cat_mapping, filter_remove_IPCC2006
+from primap2.pm2io._data_reading import filter_data, matches_time_format
 
-from config_CHL_BUR4 import cat_mapping, filter_remove_IPCC2006, aggregate_cats
-from UNFCCC_GHG_data.helper import downloaded_data_path, extracted_data_path
-from primap2.pm2io._data_reading import matches_time_format
-from primap2.pm2io._data_reading import filter_data
+from unfccc_ghg_data.helper import downloaded_data_path, extracted_data_path
 
 # ###
 # configuration
@@ -47,7 +47,7 @@ unit_info = {
 }
 cols_to_drop = ['Unnamed: 14', 'Unnamed: 16', 'Código IPCC.1',
                 'Categorías de fuente y sumidero de gases de efecto invernadero.1']
-# columns for category UNFCCC_GHG_data and original category name
+# columns for category code and original category name
 index_cols = ['Código IPCC', 'Categorías de fuente y sumidero de gases de efecto invernadero']
 
 # operations on long format DF
@@ -164,7 +164,7 @@ for year in years_to_read:
     df_current = pd.read_excel(input_folder / inventory_file, sheet_name=str(year), skiprows=2, nrows=442, engine="openpyxl")
     # drop the columns which are empty and repetition of the metadata for the second block
     df_current.drop(cols_to_drop, axis=1, inplace=True)
-    # drop all rows where the index cols (category UNFCCC_GHG_data and name) are both NaN
+    # drop all rows where the index cols (category code and name) are both NaN
     # as without one of them there is no category information
     df_current.dropna(axis=0, how='all', subset=index_cols, inplace=True)
     # set multi-index. necessary for the stack operation in the conversion to long format

UNFCCC_GHG_data/UNFCCC_reader/Chile/read_CHL_BUR5_from_xlsx.py → src/unfccc_ghg_data/unfccc_reader/Chile/read_CHL_BUR5_from_xlsx.py

@@ -3,13 +3,13 @@
 
 import os
 import sys
+
 import pandas as pd
 import primap2 as pm2
+from config_chl_bur4 import aggregate_cats, cat_mapping, filter_remove_IPCC2006
+from primap2.pm2io._data_reading import filter_data, matches_time_format
 
-from config_CHL_BUR4 import cat_mapping, filter_remove_IPCC2006, aggregate_cats
-from UNFCCC_GHG_data.helper import downloaded_data_path, extracted_data_path
-from primap2.pm2io._data_reading import matches_time_format
-from primap2.pm2io._data_reading import filter_data
+from unfccc_ghg_data.helper import downloaded_data_path, extracted_data_path
 
 # ###
 # configuration
@@ -48,7 +48,7 @@ unit_info = {
 }
 cols_to_drop = ['Unnamed: 14', 'Unnamed: 16', 'Código IPCC.1',
                 'Categorías de fuente y sumidero de gases de efecto invernadero.1']
-# columns for category UNFCCC_GHG_data and original category name
+# columns for category code and original category name
 index_cols = ['Código IPCC', 'Categorías de fuente y sumidero de gases de efecto invernadero']
 
 # operations on long format DF
@@ -165,7 +165,7 @@ for year in years_to_read:
     df_current = pd.read_excel(input_folder / inventory_file, sheet_name=str(year), skiprows=2, nrows=442, engine="openpyxl")
     # drop the columns which are empty and repetition of the metadata for the second block
     df_current.drop(cols_to_drop, axis=1, inplace=True)
-    # drop all rows where the index cols (category UNFCCC_GHG_data and name) are both NaN
+    # drop all rows where the index cols (category code and name) are both NaN
     # as without one of them there is no category information
     df_current.dropna(axis=0, how='all', subset=index_cols, inplace=True)
     # set multi-index. necessary for the stack operation in the conversion to long format

UNFCCC_GHG_data/UNFCCC_reader/Colombia/read_COL_BUR3_from_xlsx.py → src/unfccc_ghg_data/unfccc_reader/Colombia/read_COL_BUR3_from_xlsx.py

@@ -5,7 +5,8 @@
 import pandas as pd
 import primap2 as pm2
 from primap2.pm2io._data_reading import matches_time_format
-from UNFCCC_GHG_data.helper import downloaded_data_path, extracted_data_path
+
+from unfccc_ghg_data.helper import downloaded_data_path, extracted_data_path
 
 # TODO: add fgases, sector summing (proc version)
 
@@ -207,7 +208,7 @@ data_if = pm2.pm2io.convert_long_dataframe_if(
 
 
 # combine CO2 emissions and absorptions
-data_CO2 = data_if[data_if[f"entity"].isin([
+data_CO2 = data_if[data_if["entity"].isin([
     'CO2 Absorptions', 'CO2 Emissions'])]
 
 time_format = '%Y'
@@ -246,4 +247,4 @@ if not output_folder.exists():
 pm2.pm2io.write_interchange_format(output_folder / (output_filename + coords_terminologies["category"]), data_if)
 
 encoding = {var: compression for var in data_pm2.data_vars}
-data_pm2.pr.to_netcdf(output_folder / (output_filename + coords_terminologies["category"] + ".nc"), encoding=encoding)
+data_pm2.pr.to_netcdf(output_folder / (output_filename + coords_terminologies["category"] + ".nc"), encoding=encoding)

UNFCCC_GHG_data/UNFCCC_reader/Indonesia/read_IDN_BUR3_from_pdf.py → src/unfccc_ghg_data/unfccc_reader/Indonesia/read_IDN_BUR3_from_pdf.py

@@ -2,12 +2,13 @@
 # Data is read from pdf
 # only the 2019 inventory is read as the BUR refers to BUR2 for earlier years
 
-import pandas as pd
-import primap2 as pm2
 import camelot
 import numpy as np
+import pandas as pd
+import primap2 as pm2
 from primap2.pm2io._data_reading import matches_time_format
-from UNFCCC_GHG_data.helper import downloaded_data_path, extracted_data_path
+
+from unfccc_ghg_data.helper import downloaded_data_path, extracted_data_path
 
 # ###
 # configuration
@@ -31,7 +32,7 @@ year = 2019
 entity_row = 0
 unit_row = 1
 index_cols = "Categories"
-# special header as category UNFCCC_GHG_data and name in one column
+# special header as category code and name in one column
 header_long = ["orig_cat_name", "entity", "unit", "time", "data"]
 
 
@@ -195,7 +196,8 @@ df_all["category"] = df_all["orig_cat_name"]
 # first the manual replacements
 df_all["category"] = df_all["category"].replace(cat_codes_manual)
 # then the regex replacements
-repl = lambda m: m.group('code')
+def repl(m):
+    return m.group('code')
 df_all["category"] = df_all["category"].str.replace(cat_code_regexp, repl, regex=True)
 df_all = df_all.reset_index(drop=True)
 

UNFCCC_GHG_data/UNFCCC_reader/Israel/config_ISR_BUR2.py → src/unfccc_ghg_data/unfccc_reader/Israel/config_isr_bur2.py

@@ -1,5 +1,6 @@
 #### configuration for trend tables
 import locale
+
 gwp_to_use = 'SARGWP100'
 terminology_proc = 'IPCC2006_PRIMAP'
 # bunkers [0,1] need different specs
@@ -432,4 +433,4 @@ def is_int(input: str) -> bool:
         locale.atoi(input)
         return True
     except:
-        return False
+        return False

UNFCCC_GHG_data/UNFCCC_reader/Israel/read_ISR_BUR2_from_pdf.py → src/unfccc_ghg_data/unfccc_reader/Israel/read_ISR_BUR2_from_pdf.py

@@ -2,21 +2,34 @@
 
 # TODO: bunkers trend tables not read because of special format
 
-from UNFCCC_GHG_data.helper import process_data_for_country, GWP_factors
-from UNFCCC_GHG_data.helper import downloaded_data_path, extracted_data_path
+import locale
+
 import camelot
-import primap2 as pm2
 import pandas as pd
-import locale
+import primap2 as pm2
 
 # configuration import
-from config_ISR_BUR2 import trend_table_def, gwp_to_use
-from config_ISR_BUR2 import inv_tab_conf, inv_table_def
-from config_ISR_BUR2 import coords_cols, coords_terminologies, coords_defaults, \
-    coords_value_mapping, filter_remove, filter_keep, meta_data
-from config_ISR_BUR2 import cat_conversion, sectors_to_save, downscaling, \
-    cats_to_agg, gas_baskets, terminology_proc
-from config_ISR_BUR2 import is_int, basket_copy
+from config_isr_bur2 import (
+    basket_copy,
+    cat_conversion,
+    cats_to_agg,
+    coords_cols,
+    coords_defaults,
+    coords_terminologies,
+    coords_value_mapping,
+    downscaling,
+    filter_remove,
+    gas_baskets,
+    inv_tab_conf,
+    inv_table_def,
+    is_int,
+    meta_data,
+    sectors_to_save,
+    terminology_proc,
+    trend_table_def,
+)
+
+from unfccc_ghg_data.helper import downloaded_data_path, extracted_data_path, process_data_for_country
 
 ### genral configuration
 input_folder = downloaded_data_path / 'UNFCCC' / 'Israel' / 'BUR2'
@@ -298,4 +311,4 @@ pm2.pm2io.write_interchange_format(
 encoding = {var: compression for var in data_proc_pm2.data_vars}
 data_proc_pm2.pr.to_netcdf(
     output_folder / (output_filename + terminology_proc + ".nc"),
-    encoding=encoding)
+    encoding=encoding)

UNFCCC_GHG_data/UNFCCC_reader/Malaysia/config_MYS_BUR3.py → src/unfccc_ghg_data/unfccc_reader/Malaysia/config_mys_bur3.py

@@ -1,4 +1,3 @@
-import pandas as pd
 gwp_to_use = "AR4GWP100"
 
 
@@ -673,4 +672,4 @@ gas_baskets = {
     'KYOTOGHG (AR4GWP100)': ['CO2', 'CH4', 'N2O', 'FGASES (AR4GWP100)'],
     'KYOTOGHG (AR5GWP100)': ['CO2', 'CH4', 'N2O', 'FGASES (AR5GWP100)'],
     'KYOTOGHG (AR6GWP100)': ['CO2', 'CH4', 'N2O', 'FGASES (AR6GWP100)'],
-}
+}