diff --git a/.copier-answers.yml b/.copier-answers.yml new file mode 100644 index 0000000..c3152ec --- /dev/null +++ b/.copier-answers.yml @@ -0,0 +1,17 @@ +# Changes here will be overwritten by Copier; NEVER EDIT MANUALLY +_commit: v0.6.1 +_src_path: ../../repos/copier-core-python-repository +email: zebedee.nicholls@climate-energy-college.org +initial_setup: true +name: Zebedee Nicholls +notebook_dependencies: true +pandas_doctests: false +plot_dependencies: false +project_description_short: Implementations of the two layer radiative forcing driven + models by [Held et al.](https://journals.ametsoc.org/doi/full/10.1175/2009JCLI3466.1) + and [Geoffroy et al.](https://journals.ametsoc.org/doi/pdf/10.1175/JCLI-D-12-00195.1) +project_name_human: OpenSCM Two Layer Model +project_name_pip: openscm-twolayermodel +project_name_python: openscm_twolayermodel +project_url: https://github.com/openscm/openscm-twolayermodel +track_lock_file: true diff --git a/.github/ISSUE_TEMPLATE/bug.md b/.github/ISSUE_TEMPLATE/bug.md new file mode 100644 index 0000000..d43f709 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/bug.md @@ -0,0 +1,41 @@ +--- +name: Bug report +about: Report a bug +title: '' +labels: bug +assignees: '' + +--- + +## Describe the bug + + +## Failing Test + + +## Expected behavior + + +## Screenshots + + +## System + + + - OS: [e.g. Windows, Linux, macOS] + - Python version [e.g. Python 3.11] + - Please also upload your `poetry.lock` file (first run `poetry lock` to make sure the lock file is up-to-date) + +## Additional context + diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md deleted file mode 100644 index 745f695..0000000 --- a/.github/ISSUE_TEMPLATE/bug_report.md +++ /dev/null @@ -1,30 +0,0 @@ ---- -name: Bug Report -about: Write a report to help us improve - ---- - -**Describe the bug** - -A clear and concise description of what the bug is, in particular: - -- What did you do? -- What actually happened? -- What did you expect to happen? - -**Failing Test** - -Please put code (ideally in the form of a unit test) which fails below - -**Screenshots** - -If applicable, add screenshots to help explain your problem. - -**System (please complete the following information):** - - - OS: [e.g. Windows, Linux, macOS] - - Python and openscm commit/version [e.g. Python 3.6] - -**Additional context** - -Add any other context about the problem here. diff --git a/.github/ISSUE_TEMPLATE/default.md b/.github/ISSUE_TEMPLATE/default.md new file mode 100644 index 0000000..8b7025e --- /dev/null +++ b/.github/ISSUE_TEMPLATE/default.md @@ -0,0 +1,21 @@ +--- +name: Default +about: Report an issue or problem +title: '' +labels: triage +assignees: '' + +--- + +## The problem + + +## Definition of "done" + + +## Additional context + diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md index be69a0b..f297ebb 100644 --- a/.github/ISSUE_TEMPLATE/feature_request.md +++ b/.github/ISSUE_TEMPLATE/feature_request.md @@ -1,21 +1,32 @@ --- name: Feature Request -about: Suggest an idea for this project +about: Request a feature or suggest an idea for this project +title: '' +labels: feature +assignees: '' --- -**Is your feature request related to a problem? Please describe.** +## The motivation -A clear and concise description of what the problem is. E.g. It's annoying that I always have to [...] + -**Describe the solution you'd like** +## The proposed solution -A clear and concise description of the solution you would like to see. + -A clear and concise description of any alternative solutions or features you've considered. +## Alternatives -**Additional context** + + +## Additional context + + diff --git a/.github/actions/setup/action.yml b/.github/actions/setup/action.yml new file mode 100644 index 0000000..62e2d74 --- /dev/null +++ b/.github/actions/setup/action.yml @@ -0,0 +1,63 @@ +name: "Setup Python and Poetry" +description: "setup Python and Poetry with caches" + +inputs: + os: + description: "Operating system to use" + required: false + default: "ubuntu-latest" + 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: Install poetry + shell: bash + run: | + pipx install poetry + which poetry + poetry --version # Check poetry installation + + - name: Set up Python ${{ inputs.python-version }} + id: setup-python + uses: actions/setup-python@v5 + with: + python-version: ${{ inputs.python-version }} + cache: poetry + - name: Set Poetry environment + shell: bash + run: | + # This line used to be needed, but seems to have been + # sorted with newer poetry versions. We can still check whether + # the right version of python is used by looking at the output of + # `poetry run which python` below and whether the right version + # of python is used in the tests (or whatever step is being done) + # poetry env use "python${{ inputs.python-version }}" + poetry config virtualenvs.create true + poetry config virtualenvs.in-project true + - name: Install dependencies + if: ${{ (inputs.run-poetry-install == 'true') && (steps.setup-python.outputs.cache-hit != 'true') }} + shell: bash + run: | + poetry install --no-interaction --no-root ${{ inputs.poetry-dependency-install-flags }} + # Now run same command but let the package install too + - name: Install package + # To ensure that the package is always installed, this step is run even if the cache was hit + if: ${{ inputs.run-poetry-install == 'true' }} + shell: bash + run: | + poetry install --no-interaction ${{ inputs.poetry-dependency-install-flags }} + poetry run python --version # Check python version just in case diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md index 8b4cea6..7ff7065 100644 --- a/.github/pull_request_template.md +++ b/.github/pull_request_template.md @@ -1,6 +1,9 @@ - +## Description + +## Checklist + +Please confirm that this pull request has done the following: - [ ] Tests added -- [ ] Documentation added -- [ ] Example added (in the documentation, to an existing notebook, or in a new notebook) -- [ ] Description in ``CHANGELOG.rst`` added (single line such as: ``(`#XX `_) Added feature which does something``) +- [ ] Documentation added (where applicable) +- [ ] Changelog item added to `changelog/` diff --git a/.github/release_template.md b/.github/release_template.md new file mode 100644 index 0000000..c07018c --- /dev/null +++ b/.github/release_template.md @@ -0,0 +1,7 @@ +## Announcements + +* Announcement 1 + +## Changes + +* Change 1 diff --git a/.github/workflows/bump.yaml b/.github/workflows/bump.yaml new file mode 100644 index 0000000..8052e18 --- /dev/null +++ b/.github/workflows/bump.yaml @@ -0,0 +1,67 @@ +name: Bump version + +on: + workflow_dispatch: + inputs: + bump_rule: + type: choice + description: How to bump the project's version (see https://python-poetry.org/docs/cli/#version) + options: + - patch + - minor + - major + - prepatch + - preminor + - premajor + - prerelease + required: true + +jobs: + bump_version: + name: "Bump version and create changelog" + if: "!startsWith(github.event.head_commit.message, 'bump:')" + runs-on: ubuntu-latest + env: + CI_COMMIT_EMAIL: "ci-runner@openscm-twolayermodel.invalid" + steps: + - name: Check out repository + uses: actions/checkout@v3 + with: + fetch-depth: 0 + token: "${{ 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: | + git config --global user.name "$GITHUB_ACTOR" + git config --global user.email "$CI_COMMIT_EMAIL" + + # Bump + BASE_VERSION=`poetry version -s` + NEW_VERSION=`poetry version -s ${{ github.event.inputs.bump_rule }}` + echo "Bumping version $BASE_VERSION > $NEW_VERSION" + poetry run towncrier build --yes --version v$NEW_VERSION + git commit -a -m "bump: version $BASE_VERSION -> $NEW_VERSION" + git tag v$NEW_VERSION + + # Bump to alpha (so that future commits do not have the same + # version as the tagged commit) + BASE_VERSION=`poetry version -s` + NEW_VERSION=`poetry version -s prerelease` + echo "Bumping version $BASE_VERSION > $NEW_VERSION" + git commit -a -m "bump(pre-release): version $BASE_VERSION > $NEW_VERSION" + git push && git push --tags diff --git a/.github/workflows/ci-cd-workflow.yml b/.github/workflows/ci-cd-workflow.yml deleted file mode 100644 index 39a2d30..0000000 --- a/.github/workflows/ci-cd-workflow.yml +++ /dev/null @@ -1,152 +0,0 @@ -name: OpenSCM Two Layer Model CI-CD -on: push - -jobs: - linting-and-docs: - - runs-on: ubuntu-latest - strategy: - matrix: - python-version: [3.7] - - steps: - - name: Checkout repository - uses: actions/checkout@v2 - - name: Setup python - uses: actions/setup-python@v1 - with: - python-version: ${{ matrix.python-version }} - - name: Install dev dependencies - run: | - pip install --upgrade pip wheel - pip install -e .[dev] - - name: Formatting and linters - # TODO: add `pylint src` back in - run: | - black --check src tests setup.py --exclude openscm_twolayermodel/_version.py - isort --check-only --quiet --recursive src tests setup.py - pydocstyle src - bandit -c .bandit.yml -r openscm_twolayermodel - flake8 src tests setup.py - - name: Install pandoc - uses: r-lib/actions/setup-pandoc@v1 - with: - pandoc-version: '2.11' - - name: Build docs - # treat warnings as errors (-W)... - # ...but not when being nitpicky (-n) - run: | - sphinx-build -M html docs/source docs/build -qW - sphinx-build -M html docs/source docs/build -Eqn -b coverage - if [[ -s docs/build/html/python.txt ]] - then - echo - echo \"Error: Documentation missing:\" - echo - cat docs/build/html/python.txt - exit 1 - fi - - build: - runs-on: ubuntu-latest - strategy: - matrix: - python-version: [3.6, 3.7, 3.8, 3.9] - - steps: - - name: Checkout repository - uses: actions/checkout@v2 - - name: Setup python - uses: actions/setup-python@v1 - with: - python-version: ${{ matrix.python-version }} - - name: Install test dependencies - run: | - pip install --upgrade pip wheel - pip install -e .[tests] - - name: Test with pytest - env: - MIN_COVERAGE: 95 - run: | - pytest tests -r a --cov=openscm_twolayermodel --cov-report=xml - if ! coverage report --fail-under=${MIN_COVERAGE} --show-missing - then - echo - echo "Error: Test coverage has to be at least ${MIN_COVERAGE}" - exit 1 - fi - - name: Upload coverage to Codecov - if: startsWith(runner.os, 'Linux') && matrix.python-version == 3.7 - uses: codecov/codecov-action@v1 - with: - file: ./coverage.xml - - test-notebooks: - runs-on: ubuntu-latest - strategy: - matrix: - python-version: [3.6, 3.7, 3.8, 3.9] - - steps: - - name: Checkout repository - uses: actions/checkout@v2 - - name: Setup python - uses: actions/setup-python@v1 - with: - python-version: ${{ matrix.python-version }} - - name: Install notebook dependencies - run: | - pip install --upgrade pip wheel - pip install -e .[tests,notebooks] - - name: Test notebooks with nbval - run: | - pytest docs/source/usage -r a --nbval-lax --sanitize-with tests/notebook-tests.cfg --no-cov - - name: Test notebooks strictly - if: matrix.python-version == 3.7 - run: | - pytest docs/source/usage -r a --nbval --sanitize-with tests/notebook-tests.cfg --no-cov - - readme-requirements-up-to-date: - runs-on: ubuntu-latest - strategy: - matrix: - python-version: [3.7] - - steps: - - name: Checkout repository - uses: actions/checkout@v2 - - name: Setup python - uses: actions/setup-python@v1 - with: - python-version: ${{ matrix.python-version }} - - name: Check README is up-to-date with setup.py - run: | - python scripts/check_requirements_in_readme.py - - deploy-pypi: - needs: [build,linting-and-docs,readme-requirements-up-to-date,test-notebooks] - if: startsWith(github.ref, 'refs/tags/v') - - runs-on: ubuntu-latest - strategy: - matrix: - python-version: [3.7] - - steps: - - name: Checkout repository - uses: actions/checkout@v2 - - name: Setup python - uses: actions/setup-python@v1 - with: - python-version: ${{ matrix.python-version }} - - name: Install dependencies - run: | - pip install --upgrade pip wheel - pip install -e .[dev] - - name: Create package - run: python setup.py sdist bdist_wheel --universal - - name: Publish package to PyPI - uses: pypa/gh-action-pypi-publish@master - with: - user: __token__ - password: ${{ secrets.pypi_password }} diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml new file mode 100644 index 0000000..a43bf99 --- /dev/null +++ b/.github/workflows/ci.yaml @@ -0,0 +1,127 @@ +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: + os: "ubuntu-latest" + 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: ${{ !github.event.pull_request.draft }} + runs-on: ubuntu-latest + steps: + - name: Check out repository + uses: actions/checkout@v3 + - uses: ./.github/actions/setup + with: + os: "ubuntu-latest" + python-version: "3.9" + venv-id: "docs" + poetry-dependency-install-flags: "--all-extras --only 'main,docs'" + - name: docs + # Disable warning as error on build because something weird happens + # with how pint has set things up. In future, add the `-W` flag back + # in here. + # (see https://github.com/hgrecco/pint/blob/fc1aeba21823092007adc62fae96596e15aa0127/pint/registry.py#L109) + # and how autodoc-typehints tries to then handle the types + # (see https://github.com/tox-dev/sphinx-autodoc-typehints/issues/186) + run: poetry run sphinx-build --keep-going -T -b html docs/source docs/build + + tests: + strategy: + fail-fast: false + matrix: + os: [ "ubuntu-latest" ] + python-version: [ "3.9", "3.10", "3.11" ] + runs-on: "${{ matrix.os }}" + defaults: + run: + # This might be needed for Windows and doesn't seem to affect unix-based systems + # so we include it. If you have better proof of whether this is needed or not, + # feel free to update. + shell: bash + steps: + - name: Check out repository + uses: actions/checkout@v3 + - uses: ./.github/actions/setup + with: + os: "${{ matrix.os }}" + python-version: "${{ 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-${{ runner.os }}" + run-poetry-install: false + poetry-dependency-install-flags: "not used" + - name: Build package + run: | + poetry build --no-interaction + - name: Check build + run: | + tar -tvf dist/openscm_twolayermodel-*.tar.gz --wildcards '*openscm_twolayermodel/py.typed' + + check-dependency-licences: + runs-on: ubuntu-latest + steps: + - name: Check out repository + uses: actions/checkout@v3 + - uses: ./.github/actions/setup + with: + python-version: "3.9" + venv-id: "licence-check" + poetry-dependency-install-flags: "--all-extras" + - name: Check licences of dependencies + shell: bash + run: | + TEMP_FILE=$(mktemp) + poetry export --without=tests --without=docs --without=dev > $TEMP_FILE + poetry run liccheck -r $TEMP_FILE -R licence-check.txt + cat licence-check.txt diff --git a/.github/workflows/deploy.yaml b/.github/workflows/deploy.yaml new file mode 100644 index 0000000..2b8e1aa --- /dev/null +++ b/.github/workflows/deploy.yaml @@ -0,0 +1,33 @@ +name: Deploy + +on: + release: + types: [published] + +defaults: + run: + shell: bash + +jobs: + deploy-pypi: + name: Deploy to PyPI + runs-on: ubuntu-latest + steps: + - name: Check out repository + uses: actions/checkout@v3 + with: + fetch-depth: 0 + - uses: ./.github/actions/setup + with: + python-version: "3.9" + venv-id: "deploy" + poetry-dependency-install-flags: "--all-extras" + - name: Run tests + run: | + poetry run pytest -r a src tests --doctest-modules + - name: Publish to PyPI + env: + PYPI_TOKEN: "${{ secrets.PYPI_TOKEN }}" + run: | + poetry config pypi-token.pypi $PYPI_TOKEN + poetry publish --build --no-interaction diff --git a/.github/workflows/install.yaml b/.github/workflows/install.yaml new file mode 100644 index 0000000..72cf6c9 --- /dev/null +++ b/.github/workflows/install.yaml @@ -0,0 +1,60 @@ +name: Test installation + +on: + workflow_dispatch: + schedule: + # * is a special character in YAML so you have to quote this string + - cron: '0 0 * * 3' + +jobs: + test-pypi-install: + name: Test PyPI install (${{ matrix.python-version }}, ${{ matrix.os }}) + runs-on: "${{ 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 openscm-twolayermodel + - name: Checkout repository + uses: actions/checkout@v3 + - name: Test installation + run: | + which python + python scripts/test-install.py + + test-micromamba-installation: + name: Test (micro)mamba install (${{ matrix.python-version }}, ${{ matrix.os }}) + runs-on: "${{ matrix.os }}" + strategy: + fail-fast: false + matrix: + os: ["ubuntu-latest", "macos-latest", "windows-latest"] + python-version: [ "3.9", "3.10", "3.11" ] + + steps: + - name: Setup (micro)mamba and install package + uses: mamba-org/setup-micromamba@v1 + with: + environment-name: test-mamba-install + create-args: >- + python=${{ matrix.python-version }} + -c conda-forge + openscm-twolayermodel + init-shell: bash + - name: Checkout repository + uses: actions/checkout@v3 + - name: Test installation + shell: bash -leo pipefail {0} + run: | + which python + python scripts/test-install.py diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml new file mode 100644 index 0000000..21b7ff6 --- /dev/null +++ b/.github/workflows/release.yaml @@ -0,0 +1,46 @@ +name: Release + +on: + push: + tags: ['v*'] + +defaults: + run: + shell: bash + +jobs: + draft-release: + name: Create draft release + runs-on: ubuntu-latest + steps: + - name: Check out repository + uses: actions/checkout@v3 + with: + fetch-depth: 0 + - uses: ./.github/actions/setup + with: + python-version: "3.9" + venv-id: "release" + poetry-dependency-install-flags: "--all-extras" + - name: Add version to environment + run: | + PROJECT_VERSION=$(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 $(git describe --tags --abbrev=0 HEAD^)..HEAD --pretty='format:* %h %s' --no-merges >> ".github/release_template.md" + - name: Create Release Draft + uses: softprops/action-gh-release@v1 + with: + body_path: ".github/release_template.md" + token: "${{ secrets.PERSONAL_ACCESS_TOKEN }}" + draft: true + files: | + dist/openscm_twolayermodel-${{ env.PROJECT_VERSION }}-py3-none-any.whl + dist/openscm_twolayermodel-${{ env.PROJECT_VERSION }}.tar.gz diff --git a/.github/workflows/test-conda-install.yml b/.github/workflows/test-conda-install.yml deleted file mode 100644 index 3931b00..0000000 --- a/.github/workflows/test-conda-install.yml +++ /dev/null @@ -1,35 +0,0 @@ -name: Test conda install -on: - schedule: - # * is a special character in YAML so you have to quote this string - - cron: '0 * * * 3' - -jobs: - test-installation: - name: Test conda install (${{ matrix.python-version }}, ${{ matrix.os }}) - runs-on: ${{ matrix.os }} - strategy: - matrix: - os: ["ubuntu-latest", "macos-latest", "windows-latest"] - python-version: [3.7, 3.8, 3.9] - - steps: - - name: Setup conda - uses: conda-incubator/setup-miniconda@v2.0.1 - with: - auto-update-conda: true - python-version: ${{ matrix.python-version }} - activate-environment: test - - name: Conda info - shell: bash -l {0} - run: conda info - - name: Install package - shell: bash -l {0} - run: conda install -c conda-forge openscm-twolayermodel - - name: Checkout repository - uses: actions/checkout@v2 - - name: Test installation - shell: bash -l {0} - run: | - which python - python scripts/test_install.py diff --git a/.github/workflows/test-pypi-install.yml b/.github/workflows/test-pypi-install.yml deleted file mode 100644 index 0483dc5..0000000 --- a/.github/workflows/test-pypi-install.yml +++ /dev/null @@ -1,32 +0,0 @@ -name: Test PyPI install -on: - schedule: - # * is a special character in YAML so you have to quote this string - - cron: '0 * * * 3' - -jobs: - test-installation: - name: Test PyPI install (${{ matrix.python-version }}, ${{ matrix.os }}) - runs-on: ${{ matrix.os }} - strategy: - matrix: - os: ["ubuntu-latest", "macos-latest", "windows-latest"] - python-version: [3.6, 3.7, 3.8, 3.9] - - steps: - - name: Setup python - uses: actions/setup-python@v1 - with: - python-version: ${{ matrix.python-version }} - - name: Install package - # install basic first, then install pre-releases afterwards so we don't - # pick up pre-releases of dependencies (e.g. pandas) - run: | - pip install --upgrade pip - pip install openscm-twolayermodel - pip install openscm-twolayermodel --pre - - name: Checkout repository - uses: actions/checkout@v2 - - name: Test installation - run: | - python scripts/test_install.py diff --git a/.gitignore b/.gitignore index bd3e08d..c9c571a 100644 --- a/.gitignore +++ b/.gitignore @@ -1,6 +1,21 @@ # paper paper.pdf +# Notebooks +*.ipynb + +# Databases +*.db + +# Jupyter cache +.jupyter_cache + +# Ruff cache +.ruff_cache + +# Licence check +licence-check.txt + # Byte-compiled / optimized / DLL files __pycache__/ *.py[cod] @@ -23,6 +38,8 @@ parts/ sdist/ var/ wheels/ +pip-wheel-metadata/ +share/python-wheels/ *.egg-info/ .installed.cfg *.egg @@ -41,12 +58,14 @@ 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/ @@ -58,6 +77,7 @@ coverage.xml *.log local_settings.py db.sqlite3 +db.sqlite3-journal # Flask stuff: instance/ @@ -75,11 +95,26 @@ target/ # Jupyter Notebook .ipynb_checkpoints +# IPython +profile_default/ +ipython_config.py + # pyenv .python-version -# celery beat schedule file +# 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 @@ -87,14 +122,11 @@ celerybeat-schedule # Environments .env .venv -.venv3 env/ venv/ -venv3/ ENV/ env.bak/ venv.bak/ -venv3.bak/ # Spyder project settings .spyderproject @@ -108,6 +140,11 @@ venv3.bak/ # mypy .mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ -# DS_Store +# Mac stuff *.DS_Store diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..2e3e88b --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,42 @@ +# 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: 'v4.5.0' + 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: 'v0.1.8' + hooks: + - id: ruff + args: [ --fix, --exit-non-zero-on-fix ] + - id: ruff-format + - repo: https://github.com/python-poetry/poetry + rev: '1.7.0' + hooks: + - id: poetry-check diff --git a/.readthedocs.yaml b/.readthedocs.yaml new file mode 100644 index 0000000..9543d49 --- /dev/null +++ b/.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 diff --git a/LICENSE b/LICENCE similarity index 100% rename from LICENSE rename to LICENCE diff --git a/Makefile b/Makefile index e6e4f2f..b8011be 100644 --- a/Makefile +++ b/Makefile @@ -1,133 +1,76 @@ -.DEFAULT_GOAL := help - -VENV_DIR ?= venv -TESTS_DIR=$(PWD)/tests +# Makefile to help automate key steps -NOTEBOOKS_DIR=./docs/source/usage -NOTEBOOKS_SANITIZE_FILE=$(TESTS_DIR)/notebook-tests.cfg +.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) + match = re.match(r'^([\$$\(\)a-zA-Z_-]+):.*?## (.*)$$', line) if match: target, help = match.groups() - print("%-20s %s" % (target, help)) + print("%-30s %s" % (target, help)) endef export PRINT_HELP_PYSCRIPT -.PHONY: help -help: - @python -c "$$PRINT_HELP_PYSCRIPT" < $(MAKEFILE_LIST) - -checks: $(VENV_DIR) ## run all the checks - @echo "=== bandit ==="; $(VENV_DIR)/bin/bandit -c .bandit.yml -r openscm_twolayermodel || echo "--- bandit failed ---" >&2; \ - echo "\n\n=== black ==="; $(VENV_DIR)/bin/black --check src tests setup.py docs/source/conf.py scripts/*.py --exclude openscm_twolayermodel/_version.py || echo "--- black failed ---" >&2; \ - echo "\n\n=== flake8 ==="; $(VENV_DIR)/bin/flake8 src tests setup.py || echo "--- flake8 failed ---" >&2; \ - echo "\n\n=== isort ==="; $(VENV_DIR)/bin/isort --check-only --quiet --recursive src tests setup.py || echo "--- isort failed ---" >&2; \ - echo "\n\n=== pydocstyle ==="; $(VENV_DIR)/bin/pydocstyle src || echo "--- pydocstyle failed ---" >&2; \ - echo "\n\n=== pylint ==="; $(VENV_DIR)/bin/pylint src || echo "--- pylint failed ---" >&2; \ - echo "\n\n=== notebook tests ==="; $(VENV_DIR)/bin/pytest $(NOTEBOOKS_DIR)k -r a --nbval --sanitize-with tests/notebook-tests.cfg || echo "--- notebook tests failed ---" >&2; \ - echo "\n\n=== tests ==="; $(VENV_DIR)/bin/pytest tests -r a --cov=openscm_twolayermodel --cov-report='' \ - && $(VENV_DIR)/bin/coverage report --fail-under=95 || echo "--- tests failed ---" >&2; \ - echo - -.PHONY: format -format: ## re-format files - make isort - make black - -.PHONY: format-notebooks -format-notebooks: $(VENV_DIR) ## format the notebooks - @status=$$(git status --porcelain $(NOTEBOOKS_DIR)); \ - if test "x$${status}" = x; then \ - $(VENV_DIR)/bin/black-nb $(NOTEBOOKS_DIR); \ - else \ - echo Not trying any formatting. Working directory is dirty ... >&2; \ - fi; - -.PHONY: black -black: $(VENV_DIR) ## apply black formatter to source and tests - @status=$$(git status --porcelain src tests docs scripts); \ - if test "x$${status}" = x; then \ - $(VENV_DIR)/bin/black --exclude _version.py setup.py src tests docs/source/conf.py scripts/*.py; \ - else \ - echo Not trying any formatting. Working directory is dirty ... >&2; \ - fi; - -.PHONY: isort -isort: $(VENV_DIR) ## format the code - @status=$$(git status --porcelain src tests); \ - if test "x$${status}" = x; then \ - $(VENV_DIR)/bin/isort --recursive src tests setup.py; \ - else \ - echo Not trying any formatting. Working directory is dirty ... >&2; \ - fi; - -docs: $(VENV_DIR) ## build the docs - $(VENV_DIR)/bin/sphinx-build -M html docs/source docs/build - -test: $(VENV_DIR) ## run the full testsuite - $(VENV_DIR)/bin/pytest --cov -rfsxEX --cov-report term-missing - -test-notebooks: $(VENV_DIR) ## test the notebooks - $(VENV_DIR)/bin/pytest ${NOTEBOOKS_DIR} -r a --nbval --sanitize-with tests/notebook-tests.cfg -test-install: $(VENV_DIR) ## test whether installing in a fresh venv works - $(eval TEMPVENV := $(shell mktemp -d)) - python3 -m venv $(TEMPVENV) - $(TEMPVENV)/bin/pip install pip wheel --upgrade - $(TEMPVENV)/bin/pip install wheel 'setuptools>=41.2' - $(TEMPVENV)/bin/pip install . - $(TEMPVENV)/bin/python scripts/test_install.py - -test-testpypi-install: $(VENV_DIR) ## test whether installing from test PyPI works - $(eval TEMPVENV := $(shell mktemp -d)) - python3 -m venv $(TEMPVENV) - $(TEMPVENV)/bin/pip install pip wheel --upgrade - $(TEMPVENV)/bin/pip install wheel 'setuptools>=41.2' - # Install dependencies not on testpypi registry - $(TEMPVENV)/bin/pip install pandas - # Install pymagicc without dependencies. - $(TEMPVENV)/bin/pip install \ - -i https://testpypi.python.org/pypi openscm-twolayermodel \ - --no-dependencies --pre - $(TEMPVENV)/bin/python -c "import sys; sys.path.remove(''); import openscm_twolayermodel; print(openscm_twolayermodel.__version__)" - -test-pypi-install: $(VENV_DIR) ## test whether installing from PyPI works - $(eval TEMPVENV := $(shell mktemp -d)) - python3 -m venv $(TEMPVENV) - $(TEMPVENV)/bin/pip install pip wheel --upgrade - $(TEMPVENV)/bin/pip install wheel 'setuptools>=41.2' - $(TEMPVENV)/bin/pip install openscm-twolayermodel --pre - $(TEMPVENV)/bin/python scripts/test_install.py - -virtual-environment: ## update venv, create a new venv if it doesn't exist - make $(VENV_DIR) - -$(VENV_DIR): setup.py - [ -d $(VENV_DIR) ] || python3 -m venv $(VENV_DIR) - - $(VENV_DIR)/bin/pip install --upgrade pip wheel - $(VENV_DIR)/bin/pip install -e ".[dev]" - $(VENV_DIR)/bin/jupyter nbextension enable --py widgetsnbextension - - touch $(VENV_DIR) - -paper.pdf: paper.md paper.bib latex.template - pandoc --filter pandoc-citeproc --bibliography paper.bib paper.md \ - --from markdown+grid_tables \ - --template latex.template -o paper.pdf \ - --pdf-engine=xelatex - -clean: - rm paper.pdf - - -first-venv: ## create a new virtual environment for the very first repo setup - python3 -m venv $(VENV_DIR) - - $(VENV_DIR)/bin/pip install --upgrade pip wheel - $(VENV_DIR)/bin/pip install versioneer - # don't touch here as we don't want this venv to persist anyway +.PHONY: help +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: ruff-fixes +ruff-fixes: ## fix the code using ruff + # format before and after checking so that the formatted stuff is checked and + # the fixed stuff is formatted + poetry run ruff format src tests scripts docs/source/conf.py docs/source/notebooks/*.py + poetry run ruff src tests scripts docs/source/conf.py docs/source/notebooks/*.py --fix + poetry run ruff format src tests scripts docs/source/conf.py docs/source/notebooks/*.py + + +.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 diff --git a/README.md b/README.md new file mode 100644 index 0000000..72a61ef --- /dev/null +++ b/README.md @@ -0,0 +1,82 @@ +# OpenSCM Two Layer Model + + + + + +Implementations of the two layer radiative forcing driven models by [Held et al.](https://journals.ametsoc.org/doi/full/10.1175/2009JCLI3466.1) and [Geoffroy et al.](https://journals.ametsoc.org/doi/pdf/10.1175/JCLI-D-12-00195.1) + + + +[![CI](https://github.com/openscm/openscm-twolayermodel/actions/workflows/ci.yaml/badge.svg?branch=main)](https://github.com/openscm/openscm-twolayermodel/actions/workflows/ci.yaml) +[![Coverage](https://codecov.io/gh/openscm/openscm-twolayermodel/branch/main/graph/badge.svg)](https://codecov.io/gh/openscm/openscm-twolayermodel) +[![Docs](https://readthedocs.org/projects/openscm-twolayermodel/badge/?version=latest)](https://openscm-twolayermodel.readthedocs.io) + +**PyPI :** +[![PyPI](https://img.shields.io/pypi/v/openscm-twolayermodel.svg)](https://pypi.org/project/openscm-twolayermodel/) +[![PyPI: Supported Python versions](https://img.shields.io/pypi/pyversions/openscm-twolayermodel.svg)](https://pypi.org/project/openscm-twolayermodel/) +[![PyPI install](https://github.com/openscm/openscm-twolayermodel/actions/workflows/install.yaml/badge.svg?branch=main)](https://github.com/openscm/openscm-twolayermodel/actions/workflows/install.yaml) + +**Other info :** +[![Licence](https://img.shields.io/github/license/openscm/openscm-twolayermodel.svg)](https://github.com/openscm/openscm-twolayermodel/blob/main/LICENCE) +[![Last Commit](https://img.shields.io/github/last-commit/openscm/openscm-twolayermodel.svg)](https://github.com/openscm/openscm-twolayermodel/commits/main) +[![Contributors](https://img.shields.io/github/contributors/openscm/openscm-twolayermodel.svg)](https://github.com/openscm/openscm-twolayermodel/graphs/contributors) + + + + +Full documentation can be found at: +[openscm-twolayermodel.readthedocs.io](https://openscm-twolayermodel.readthedocs.io/en/latest/). +We recommend reading the docs there because the internal documentation links +don't render correctly on GitHub's viewer. + +## Installation + + + +OpenSCM Two Layer Model can be installed with pip, mamba or conda: + +```bash +pip install openscm-twolayermodel +mamba install -c conda-forge openscm-twolayermodel +conda install -c conda-forge openscm-twolayermodel +``` + +Additional dependencies can be installed using + +```bash +# To add notebook dependencies +pip install openscm-twolayermodel[notebooks] + +# 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) +``` + + + +### For developers + + + +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](https://github.com/openscm/openscm-twolayermodel/issues). + +For the rest of our developer docs, please see [](development-reference). + + diff --git a/TODO.md b/TODO.md new file mode 100644 index 0000000..a34dd79 --- /dev/null +++ b/TODO.md @@ -0,0 +1,6 @@ +- flip to using pyproject.toml, remove setup.cfg and setup.py and versioneer +- fix up docs (switch everything to markdown, get build going again) +- fix up checks +- check that nothing important got lost from the Makefile or CI +- fix up CHANGELOG +- get CI passing again diff --git a/changelog/README.md b/changelog/README.md new file mode 100644 index 0000000..b45b02f --- /dev/null +++ b/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 OpenSCM Two Layer Model 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 `..md`, where `` is the merge request number, and `` 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. diff --git a/docs/make.bat b/docs/make.bat index 6247f7e..747ffb7 100644 --- a/docs/make.bat +++ b/docs/make.bat @@ -10,8 +10,6 @@ if "%SPHINXBUILD%" == "" ( set SOURCEDIR=source set BUILDDIR=build -if "%1" == "" goto help - %SPHINXBUILD% >NUL 2>NUL if errorlevel 9009 ( echo. @@ -21,10 +19,12 @@ if errorlevel 9009 ( echo.may add the Sphinx directory to PATH. echo. echo.If you don't have Sphinx installed, grab it from - echo.http://sphinx-doc.org/ + echo.https://www.sphinx-doc.org/ exit /b 1 ) +if "%1" == "" goto help + %SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% goto end diff --git a/docs/source/_templates/.gitkeep b/docs/source/_templates/.gitkeep new file mode 100644 index 0000000..e69de29 diff --git a/docs/source/api/openscm_twolayermodel.base.rst b/docs/source/api/openscm_twolayermodel.base.rst new file mode 100644 index 0000000..4db0639 --- /dev/null +++ b/docs/source/api/openscm_twolayermodel.base.rst @@ -0,0 +1,21 @@ +openscm\_twolayermodel.base +~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +.. automodule:: openscm_twolayermodel.base + +.. currentmodule:: openscm_twolayermodel.base + + + +Model +===== + +.. autoclass:: Model + :members: + + +TwoLayerVariant +=============== + +.. autoclass:: TwoLayerVariant + :members: diff --git a/docs/source/api/openscm_twolayermodel.constants.rst b/docs/source/api/openscm_twolayermodel.constants.rst new file mode 100644 index 0000000..5a3b450 --- /dev/null +++ b/docs/source/api/openscm_twolayermodel.constants.rst @@ -0,0 +1,19 @@ +openscm\_twolayermodel.constants +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +.. automodule:: openscm_twolayermodel.constants + +.. currentmodule:: openscm_twolayermodel.constants + + + +DENSITY\_WATER +============== + +.. autodata:: DENSITY_WATER + + +HEAT\_CAPACITY\_WATER +===================== + +.. autodata:: HEAT_CAPACITY_WATER diff --git a/docs/source/api/openscm_twolayermodel.errors.rst b/docs/source/api/openscm_twolayermodel.errors.rst new file mode 100644 index 0000000..7536b20 --- /dev/null +++ b/docs/source/api/openscm_twolayermodel.errors.rst @@ -0,0 +1,21 @@ +openscm\_twolayermodel.errors +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +.. automodule:: openscm_twolayermodel.errors + +.. currentmodule:: openscm_twolayermodel.errors + + + +UnitError +========= + +.. autoclass:: UnitError + :members: + + +ModelStateError +=============== + +.. autoclass:: ModelStateError + :members: diff --git a/docs/source/api/openscm_twolayermodel.impulse_response_model.rst b/docs/source/api/openscm_twolayermodel.impulse_response_model.rst new file mode 100644 index 0000000..abec912 --- /dev/null +++ b/docs/source/api/openscm_twolayermodel.impulse_response_model.rst @@ -0,0 +1,14 @@ +openscm\_twolayermodel.impulse\_response\_model +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +.. automodule:: openscm_twolayermodel.impulse_response_model + +.. currentmodule:: openscm_twolayermodel.impulse_response_model + + + +ImpulseResponseModel +==================== + +.. autoclass:: ImpulseResponseModel + :members: diff --git a/docs/source/api/openscm_twolayermodel.rst b/docs/source/api/openscm_twolayermodel.rst new file mode 100644 index 0000000..b6974c1 --- /dev/null +++ b/docs/source/api/openscm_twolayermodel.rst @@ -0,0 +1,18 @@ +API Reference +~~~~~~~~~~~~~ + +.. automodule:: openscm_twolayermodel + +.. currentmodule:: openscm_twolayermodel + + +.. autosummary:: + :toctree: ./ + + openscm_twolayermodel.base + openscm_twolayermodel.constants + openscm_twolayermodel.errors + openscm_twolayermodel.impulse_response_model + openscm_twolayermodel.testing + openscm_twolayermodel.two_layer_model + openscm_twolayermodel.utils diff --git a/docs/source/api/openscm_twolayermodel.testing.rst b/docs/source/api/openscm_twolayermodel.testing.rst new file mode 100644 index 0000000..30d2a9d --- /dev/null +++ b/docs/source/api/openscm_twolayermodel.testing.rst @@ -0,0 +1,35 @@ +openscm\_twolayermodel.testing +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +.. automodule:: openscm_twolayermodel.testing + +.. currentmodule:: openscm_twolayermodel.testing + + + +ModelTester +=========== + +.. autoclass:: ModelTester + :members: + + +TwoLayerVariantTester +===================== + +.. autoclass:: TwoLayerVariantTester + :members: + + +ModelIntegrationTester +====================== + +.. autoclass:: ModelIntegrationTester + :members: + + +TwoLayerVariantIntegrationTester +================================ + +.. autoclass:: TwoLayerVariantIntegrationTester + :members: diff --git a/docs/source/api/openscm_twolayermodel.two_layer_model.rst b/docs/source/api/openscm_twolayermodel.two_layer_model.rst new file mode 100644 index 0000000..3a0890b --- /dev/null +++ b/docs/source/api/openscm_twolayermodel.two_layer_model.rst @@ -0,0 +1,14 @@ +openscm\_twolayermodel.two\_layer\_model +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +.. automodule:: openscm_twolayermodel.two_layer_model + +.. currentmodule:: openscm_twolayermodel.two_layer_model + + + +TwoLayerModel +============= + +.. autoclass:: TwoLayerModel + :members: diff --git a/docs/source/api/openscm_twolayermodel.utils.rst b/docs/source/api/openscm_twolayermodel.utils.rst new file mode 100644 index 0000000..19fca80 --- /dev/null +++ b/docs/source/api/openscm_twolayermodel.utils.rst @@ -0,0 +1,13 @@ +openscm\_twolayermodel.utils +~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +.. automodule:: openscm_twolayermodel.utils + +.. currentmodule:: openscm_twolayermodel.utils + + + +convert\_lambda\_to\_ecs +======================== + +.. autofunction:: convert_lambda_to_ecs diff --git a/docs/source/changelog.md b/docs/source/changelog.md new file mode 100644 index 0000000..ce40395 --- /dev/null +++ b/docs/source/changelog.md @@ -0,0 +1,20 @@ +# Changelog + +Versions follow [Semantic Versioning](https://semver.org/) (`..`). + +Backward incompatible (breaking) changes will only be introduced in major versions +with advance notice in the **Deprecations** section of releases. + + + + + diff --git a/docs/source/conf.py b/docs/source/conf.py index e34f014..f984c52 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -1,243 +1,176 @@ -# Configuration file for the Sphinx documentation builder. -# -# This file only contains a selection of the most common options. For a full -# list see the documentation: -# https://www.sphinx-doc.org/en/master/usage/configuration.html - -# -- Path setup -------------------------------------------------------------- +""" +Configuration file for the Sphinx documentation builder. -import os -import sys +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 -sys.path.append(os.path.dirname(os.path.dirname(__file__))) -sys.path.append( - os.path.join(os.path.dirname(__file__), "../../src/openscm_twolayermodel") -) -from _version import get_versions # isort:skip # append path before +from sphinxcontrib_autodocgen import AutoDocGen +import openscm_twolayermodel # -- Project information ----------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information project = "OpenSCM Two Layer Model" -authors = ", ".join(["Chris Smith", "Zeb Nicholls"]) -copyright_year = "2020" -copyright = "{}, {}".format(copyright_year, authors) -author = authors - -# The short X.Y version -version = get_versions()["version"].split("+")[0] -# The full version, including alpha/beta/rc tags -release = get_versions()["version"] - +# put the authors in their own variable, so they can be reused later +authors = ", ".join(["Zebedee Nicholls"]) +# 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 -# Add any Sphinx extension module names here, as strings. They can be -# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom -# ones. extensions = [ + # create documentation automatically from source code + # https://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html "sphinx.ext.autodoc", - "sphinx.ext.coverage", + # 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", - "sphinx.ext.napoleon", # pass numpy style docstrings - "nbsphinx", - "sphinx.ext.mathjax", + # add source code to docs + "sphinx.ext.viewcode", + # add copy code button to code examples "sphinx_copybutton", + # math support + "sphinx.ext.mathjax", ] -autodoc_default_options = { - "inherited-members": None, - "members": None, - # "private-members": False, - "show-inheritance": None, - "undoc-members": None, -} -# Add any paths that contain templates here, relative to this directory. +# 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"] - -# The suffix(es) of source filenames. -# You can specify multiple suffix as a list of string: -# -# source_suffix = ['.rst', '.md'] -source_suffix = ".rst" - -# The master toctree document. -master_doc = "index" - -# The language for content autogenerated by Sphinx. Refer to documentation -# for a list of supported languages. -# -# This is also used if you do content translation via gettext catalogs. -# Usually you set "language" from the command line for these cases. -language = "en" - -# List of patterns, relative to source directory, that match files and -# directories to ignore when looking for source files. -# This pattern also affects html_static_path and html_extra_path. -exclude_patterns = ["build", "**.ipynb_checkpoints"] - -# The name of the Pygments (syntax highlighting) style to use. -pygments_style = "sphinx" - -# -- Options for HTML output ------------------------------------------------- - -# The theme to use for HTML and HTML Help pages. See the documentation for -# a list of builtin themes. -# -html_theme = "sphinx_rtd_theme" - -# Add any paths that contain custom static files (such as style sheets) here, -# relative to this directory. They are copied after the builtin static files, -# so a file named "default.css" will overwrite the builtin "default.css". -html_static_path = ["_static"] - -# Custom sidebar templates, must be a dictionary that maps document names -# to template names. -# -# The default sidebars (for documents that don't match any pattern) are -# defined by theme itself. Builtin themes are using these templates by -# default: ``['localtoc.html', 'relations.html', 'sourcelink.html', -# 'searchbox.html']``. -# -# html_sidebars = {} - -html_context = { - "display_github": False, - "github_user": "openscm", - "github_repo": "openscm-twolayermodel", - "github_version": "master", - "conf_py_path": "/docs/source", -} - -# -- Options for HTMLHelp output --------------------------------------------- - -# Output file base name for HTML help builder. -htmlhelp_basename = "openscmtwolayermodeldoc" - - -# -- Options for LaTeX output ------------------------------------------------ - -latex_elements = { - # The paper size ('letterpaper' or 'a4paper'). - # - # 'papersize': 'letterpaper', - # The font size ('10pt', '11pt' or '12pt'). - # - # 'pointsize': '10pt', - # Additional stuff for the LaTeX preamble. - # - # 'preamble': '', - # Latex figure (float) alignment - # - # 'figure_align': 'htbp', +# 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, } -# Grouping the document tree into LaTeX files. List of tuples -# (source start file, target name, title, -# author, documentclass [howto, manual, or own class]). -latex_documents = [ - ( - master_doc, - "openscm-twolayermodel.tex", - "OpenSCM Two Layer Model Documentation", - author, - "manual", - ) +# autosummary with autodocgen +# make sure autosummary doesn't interfere +autosummary_generate = True +autosummary_generate_overwrite = False + +autodocgen_config = [ + { + "modules": [openscm_twolayermodel], + "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 == "openscm_twolayermodel" + else modulename, + } ] +# monkey patch to remove leading newlines +generate_module_rst_orig = AutoDocGen.generate_module_rst -# -- Options for manual page output ------------------------------------------ -# One entry per manual page. List of tuples -# (source start file, name, description, authors, manual section). -man_pages = [ - ( - master_doc, - "openscm-twolayermodel", - "OpenSCM Two Layer Model Documentation", - [author], - 1, - ) -] - - -# -- Options for Texinfo output ---------------------------------------------- - -# Grouping the document tree into Texinfo files. List of tuples -# (source start file, target name, title, author, -# dir menu entry, description, category) -texinfo_documents = [ - ( - master_doc, - "openscm-twolayermodel", - "OpenSCM Two Layer Model Documentation", - author, - "openscm-twolayermodel", - ( - "Implementations of the two layer radiative forcing driven models by " - "`Held et al. `_ " - "and `Geoffroy et al. `_" - ), - "Miscellaneous", - ) -] +@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" -# -- Options for Epub output ------------------------------------------------- + return out -# Bibliographic Dublin Core info. -epub_title = project -# The unique identifier of the text. This can be a ISBN number -# or the project homepage. -# -# epub_identifier = '' +AutoDocGen.generate_module_rst = _generate_module_rst_new -# A unique identification for the text. -# -# epub_uid = '' - -# A list of files that should not be packed into the epub file. -epub_exclude_files = ["search.html"] - - -# -- Extension configuration ------------------------------------------------- +# 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"}]} -## cov +# -- Options for HTML output ------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output -coverage_write_headline = False # do not write headlines. +# Pick your theme for html output, we typically use the read the docs theme +html_theme = "sphinx_book_theme" +html_static_path = ["_static"] +html_theme_options = { + "repository_url": "https://github.com/openscm/openscm-twolayermodel", + "repository_branch": "main", + "path_to_docs": "docs/source", + "use_repository_button": True, + "use_issues_button": True, + "use_edit_page_button": True, +} -## nbsphinx -nbsphinx_execute = "always" +# 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) -# -- Options for intersphinx extension --------------------------------------- -# Example configuration for intersphinx: refer to the Python standard library. +# 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), - # "pint": ("https://pint.readthedocs.io/en/latest", None), # no full API doc here, unfortunately + "xarray": ("http://xarray.pydata.org/en/stable", None), + "pint": ( + "https://pint.readthedocs.io/en/latest", + None, + ), } -napoleon_google_docstring = False -napoleon_numpy_docstring = True -set_type_checking_flag = False - -# -- Options for todo extension ---------------------------------------------- - -# If true, `todo` and `todoList` produce output, else they produce nothing. -todo_include_todos = True - -# # -- Logos ------------------------------------------------------------------- - -# html_logo = "_static/logo_200px_wide.png" -# latex_logo = "_static/logo.png" - - -# -- Misc configuration ------------------------------------------------- - -rst_epilog = """ -.. |CO2| replace:: CO\ :sub:`2`\ -""" diff --git a/docs/source/development.md b/docs/source/development.md new file mode 100644 index 0000000..215940e --- /dev/null +++ b/docs/source/development.md @@ -0,0 +1,83 @@ +(development-reference)= +# Development + +Notes for developers. If you want to get involved, please do! +We welcome all kinds of contributions, for example: + +- docs fixes/clarifications +- bug reports +- bug fixes +- feature requests +- pull requests +- tutorials + +## Workflows + + + +We don't mind whether you use a branching or forking workflow. +However, please only push to your own branches, +pushing to other people's branches is often a recipe for disaster, +is never required in our experience +so is best avoided. + +Try and keep your merge requests as small as possible +(focus on one thing if you can). +This makes life much easier for reviewers +which allows contributions to be accepted at a faster rate. + +## 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: [bump workflow](https://github.com/openscm/openscm-twolayermodel/actions/workflows/bump.yaml)). + A valid "bump_rule" (see [poetry's docs](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: + [project releases](https://github.com/openscm/openscm-twolayermodel/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 +[openscm-twolayermodel.readthedocs.io](https://openscm-twolayermodel.readthedocs.io/en/latest/). diff --git a/docs/source/index.md b/docs/source/index.md new file mode 100644 index 0000000..de664bd --- /dev/null +++ b/docs/source/index.md @@ -0,0 +1,42 @@ +% OpenSCM Two Layer Model 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. + +# OpenSCM Two Layer Model + +```{include} ../../README.md +:start-after: +:end-before: +``` + +## Installation + +```{include} ../../README.md +:start-after: +:end-before: +``` + +### For developers + +```{include} ../../README.md +:start-after: +:end-before: +``` + +```{toctree} +:caption: Contents +:maxdepth: 2 +notebooks +development +api/openscm_twolayermodel +changelog +``` + +Index +----- + +- :ref:`genindex` +- :ref:`modindex` +- :ref:`search` diff --git a/docs/source/notebooks.md b/docs/source/notebooks.md new file mode 100644 index 0000000..3a3c027 --- /dev/null +++ b/docs/source/notebooks.md @@ -0,0 +1,21 @@ +(notebooks-reference)= +# Notebooks + +Here we provide various examples of how to use OpenSCM Two Layer Model. +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} +``` diff --git a/docs/source/notebooks/basic-demo.py b/docs/source/notebooks/basic-demo.py new file mode 100644 index 0000000..a7f5fab --- /dev/null +++ b/docs/source/notebooks/basic-demo.py @@ -0,0 +1,26 @@ +# --- +# 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 OpenSCM Two Layer Model. + +# %% +import openscm_twolayermodel + +# %% +print( + f"You are using openscm_twolayermodel version {openscm_twolayermodel.__version__}" +) diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 0000000..de5a2bd --- /dev/null +++ b/poetry.lock @@ -0,0 +1,3574 @@ +# This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand. + +[[package]] +name = "accessible-pygments" +version = "0.0.4" +description = "A collection of accessible pygments styles" +category = "dev" +optional = false +python-versions = "*" +files = [ + {file = "accessible-pygments-0.0.4.tar.gz", hash = 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"sha256:a105f02791082c888ebe2622090beaff2e7b68571488d62fe6afdab35b4b717f"}, +] + +[package.dependencies] +numpy = ">=1.23" +packaging = ">=22" +pandas = ">=1.5" + +[package.extras] +accel = ["bottleneck", "flox", "numbagg", "opt-einsum", "scipy"] +complete = ["xarray[accel,dev,io,parallel,viz]"] +dev = ["hypothesis", "pre-commit", "pytest", "pytest-cov", "pytest-env", "pytest-timeout", "pytest-xdist", "ruff", "xarray[complete]"] +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" +category = "main" +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] +notebooks = ["notebook", "tqdm"] + +[metadata] +lock-version = "2.0" +python-versions = "^3.9" +content-hash = "903f61f37b7566303eb63c6a3986c80e15fbdda4ca14b4fd8e01c90dcf309901" diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..a47c85d --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,214 @@ +[tool.poetry] +name = "openscm-twolayermodel" +version = "0.1.0" +description = "Implementations of the two layer radiative forcing driven models by [Held et al.](https://journals.ametsoc.org/doi/full/10.1175/2009JCLI3466.1) and [Geoffroy et al.](https://journals.ametsoc.org/doi/pdf/10.1175/JCLI-D-12-00195.1)" +authors = ["Zebedee Nicholls "] +readme = "README.md" +packages = [{include = "openscm_twolayermodel", from = "src"}] +license = "TBD" +include = ["LICENCE"] # poetry uses US English so assumes it will be spelt LICENSE + +[tool.poetry.dependencies] +python = "^3.9" +notebook = { version = "^6.5.3", optional = true } +numpy = "^1.26.4" +openscm-units = "^0.5.4" +scmdata = "^0.17.0" +tqdm = { version = "^4.66.2", optional = true } + +[tool.poetry.extras] +notebooks = ["notebook", "tqdm"] + +[tool.poetry.group.tests.dependencies] +pytest = "^7.3.1" +scipy = "^1.12.0" + +[tool.poetry.group.docs.dependencies] +myst-nb = "^0.17.0" +sphinx-book-theme = "^1.1.0" +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" +mypy = "^1.2.0" +ruff = "^0.1.8" +pre-commit = "^3.3.1" +towncrier = "^23.6.0" +liccheck = "^0.9.1" + +[build-system] +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", +] + +[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 +] +line-length = 88 + +[tool.ruff.format] +docstring-code-format = true + +[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 = "openscm_twolayermodel" +package_dir = "src" +filename = "docs/source/changelog.md" +directory = "changelog/" +title_format = "## openscm-twolayermodel {version} ({project_date})" +underlines = ["", "", ""] +issue_format = "[#{issue}](https://github.com/openscm/openscm-twolayermodel/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", +] diff --git a/scripts/test-install.py b/scripts/test-install.py new file mode 100644 index 0000000..53eba71 --- /dev/null +++ b/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 openscm_twolayermodel + + +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("openscm_twolayermodel") +print(openscm_twolayermodel.__version__) diff --git a/src/openscm_twolayermodel/__init__.py b/src/openscm_twolayermodel/__init__.py index 4d96ac0..4ff4a32 100644 --- a/src/openscm_twolayermodel/__init__.py +++ b/src/openscm_twolayermodel/__init__.py @@ -1,12 +1,9 @@ """ -OpenSCM Two Layer Model, implementations of the two layer radiative forcing driven models by `Held et al. `_ and `Geoffroy et al. `_. - -See README and docs for more info. +Implementations of the two layer radiative forcing driven models by [Held et al.](https://journals.ametsoc.org/doi/full/10.1175/2009JCLI3466.1) and [Geoffroy et al.](https://journals.ametsoc.org/doi/pdf/10.1175/JCLI-D-12-00195.1) """ +import importlib.metadata -from ._version import get_versions -from .impulse_response_model import ImpulseResponseModel # noqa -from .two_layer_model import TwoLayerModel # noqa +__version__ = importlib.metadata.version("openscm_twolayermodel") -__version__ = get_versions()["version"] -del get_versions +from .impulse_response_model import ImpulseResponseModel # noqa: F401 +from .two_layer_model import TwoLayerModel # noqa: F401 diff --git a/src/openscm_twolayermodel/base.py b/src/openscm_twolayermodel/base.py index ea817ed..7cbe010 100644 --- a/src/openscm_twolayermodel/base.py +++ b/src/openscm_twolayermodel/base.py @@ -7,14 +7,18 @@ import pandas as pd import pint import pint.errors -import tqdm.autonotebook as tqdman from openscm_units import unit_registry as ur from scmdata.run import ScmRun from .constants import DENSITY_WATER, HEAT_CAPACITY_WATER from .errors import UnitError -# pylint: disable=invalid-name +try: + import tqdm.autonotebook as tqdman + + HAS_TQDM = True +except ImportError: + HAS_TQDM = False class Model(ABC): @@ -29,12 +33,12 @@ class Model(ABC): @staticmethod def _assert_is_pint_quantity_with_units(quantity, name, model_units): if not isinstance(quantity, pint.Quantity): - raise TypeError("{} must be a pint.Quantity".format(name)) + raise TypeError(f"{name} must be a pint.Quantity") try: quantity.to(model_units) except pint.errors.DimensionalityError as exc: - raise UnitError("Wrong units for `{}`".format(name)) from exc + raise UnitError(f"Wrong units for `{name}`") from exc @abstractmethod def set_drivers(self, *args, **kwargs): @@ -111,9 +115,7 @@ def erf(self, val): self._erf = val self._erf_mag = val.to(self._erf_unit).magnitude - def set_drivers( - self, erf - ): # pylint: disable=arguments-differ # hmm need to think about this + def set_drivers(self, erf): # pylint: disable=arguments-differ # hmm need to think about this """ Set drivers for a model run @@ -144,8 +146,8 @@ def _ensure_scenarios_are_scmrun(scenarios): @staticmethod def _create_ts(base, unit, variable, values): out = base.copy() - out.index = out.index.set_levels([unit], "unit") - out.index = out.index.set_levels([variable], "variable") + out.index = out.index.set_levels(levels=[unit], level="unit") + out.index = out.index.set_levels(levels=[variable], level="variable") out.iloc[:, :] = values return out @@ -173,7 +175,10 @@ def _select_timestep(driver): ) def run_scenarios( # pylint:disable=too-many-locals - self, scenarios, driver_var="Effective Radiative Forcing", progress=True, + self, + scenarios, + driver_var="Effective Radiative Forcing", + progress=True, ): """ Run scenarios. @@ -209,15 +214,13 @@ def run_scenarios( # pylint:disable=too-many-locals driver = self._ensure_scenarios_are_scmrun(scenarios) save_paras_meta = { - "{} ({})".format(k, getattr(self, k).units): getattr(self, k).magnitude + f"{k} ({getattr(self, k).units})": getattr(self, k).magnitude for k in self._save_paras } driver = driver.filter(variable=driver_var, region="World") if np.equal(driver.shape[0], 0): - raise ValueError( - "No World data available for driver_var `{}`".format(driver_var) - ) + raise ValueError(f"No World data available for driver_var `{driver_var}`") driver["climate_model"] = self._name for k, v in save_paras_meta.items(): @@ -229,12 +232,16 @@ def run_scenarios( # pylint:disable=too-many-locals run_store = list() driver_ts = driver.timeseries() - for i, (label, row) in tqdman.tqdm( - enumerate(driver_ts.iterrows()), - desc="scenarios", - leave=False, - disable=not (progress), - ): + iterator = enumerate(driver_ts.iterrows()) + if HAS_TQDM: + iterator = tqdman.tqdm( + iterator, + desc="scenarios", + leave=False, + disable=not (progress), + ) + + for i, (label, row) in iterator: meta = dict(zip(driver_ts.index.names, label)) row_no_nan = row.dropna() @@ -283,15 +290,15 @@ def _calculate_geoffroy_helper_parameters( # pylint:disable=too-many-locals b_pt2 = (eta) / (C_D) b = b_pt1 + b_pt2 b_star = b_pt1 - b_pt2 - delta = b ** 2 - (4 * lambda0 * eta) / (C * C_D) + delta = b**2 - (4 * lambda0 * eta) / (C * C_D) taucoeff = C * C_D / (2 * lambda0 * eta) - tau1 = taucoeff * (b - delta ** 0.5) - tau2 = taucoeff * (b + delta ** 0.5) + tau1 = taucoeff * (b - delta**0.5) + tau2 = taucoeff * (b + delta**0.5) phicoeff = C / (2 * efficacy * eta) - phi1 = phicoeff * (b_star - delta ** 0.5) - phi2 = phicoeff * (b_star + delta ** 0.5) + phi1 = phicoeff * (b_star - delta**0.5) + phi2 = phicoeff * (b_star + delta**0.5) adenom = C * (phi2 - phi1) a1 = tau1 * phi2 * lambda0 / adenom diff --git a/src/openscm_twolayermodel/py.typed b/src/openscm_twolayermodel/py.typed new file mode 100644 index 0000000..e69de29 diff --git a/src/openscm_twolayermodel/testing.py b/src/openscm_twolayermodel/testing.py new file mode 100644 index 0000000..bdd0dc5 --- /dev/null +++ b/src/openscm_twolayermodel/testing.py @@ -0,0 +1,179 @@ +import re +from abc import ABC, abstractmethod +from unittest.mock import MagicMock + +import numpy as np +import pint.errors +import pytest +from openscm_units import unit_registry as ur +from scmdata import ScmRun + +from openscm_twolayermodel.errors import ModelStateError, UnitError + + +class ModelTester(ABC): + tmodel = None + + parameters = None + + @abstractmethod + def test_init(self): + """ + Test the model initialises as intended + """ + pass + + def test_init_no_units(self): + """ + Test error thrown if the model is initiliased with a unitless + quantity + """ + for parameter in self.parameters.keys(): + error_msg = f"{parameter} must be a pint.Quantity" + with pytest.raises(TypeError, match=error_msg): + self.tmodel(**{parameter: 34.3}) + + @abstractmethod + def test_init_wrong_units(self): + """ + Test error thrown if the model is initiliased with wrong units + for a quantity + """ + # e.g. + for parameter, value in self.parameters.items(): + error_msg = f"{parameter} units must be {value.units}" + with pytest.raises(TypeError, match=error_msg): + self.tmodel(**{parameter: 34.3 * ur("kg")}) + + def test_run(self): + test = self.tmodel() + test.step = MagicMock() + test.run() + + test.step.assert_called() + + +class TwoLayerVariantTester(ModelTester): + def test_init_wrong_units(self): + helper = self.tmodel() + + for parameter in self.parameters.keys(): + tinp = 34.3 * ur("kg") + default = getattr(helper, parameter) + + try: + tinp.to(default.units) + except pint.errors.DimensionalityError: + pass + + error_msg = re.escape(f"Wrong units for `{parameter}`") + with pytest.raises(UnitError, match=error_msg): + self.tmodel(**{parameter: tinp}) + + def test_set_erf(self, check_equal_pint): + terf = np.array([0, 1, 2]) * ur("W/m^2") + + res = self.tmodel() + res.erf = terf + + check_equal_pint(res.erf, terf) + + def test_set_erf_unitless_error(self, check_equal_pint): + terf = np.array([0, 1, 2]) + + res = self.tmodel() + with pytest.raises(TypeError, match="erf must be a pint.Quantity"): + res.erf = terf + + def test_reset_not_set_error(self): + error_msg = "The model's drivers have not been set yet, call :meth:`self.set_drivers` first." + with pytest.raises(ModelStateError, match=error_msg): + self.tmodel().reset() + + +class ModelIntegrationTester(ABC): + tmodel = None + + @abstractmethod + def test_run_scenarios_single(self): + """ + Test the model can run a single scenario correctly + """ + pass + + @abstractmethod + def test_run_scenarios_multiple(self): + """ + Test the model can run multiple scenarios correctly + """ + pass + + +class TwoLayerVariantIntegrationTester(ModelIntegrationTester): + tinp = ScmRun( + data=np.linspace(0, 4, 101), + index=np.linspace(1750, 1850, 101).astype(int), + columns={ + "scenario": "test_scenario", + "model": "unspecified", + "climate_model": "junk input", + "variable": "Effective Radiative Forcing", + "unit": "W/m^2", + "region": "World", + }, + ) + + def test_run_unit_handling(self, check_scmruns_allclose): + inp = self.tinp.copy() + + model = self.tmodel() + + res = model.run_scenarios(inp) + + # scmdata bug + # inp.convert_unit("kW/m^2") blows up + inp_other_unit = inp.copy() + inp_other_unit *= 10**-3 + inp_other_unit["unit"] = "kW/m^2" + res_other_unit = model.run_scenarios(inp_other_unit) + + assert res.get_unique_meta("climate_model", no_duplicates=True) == model._name + + check_scmruns_allclose( + res.filter(variable="Effective Radiative Forcing", keep=False), + res_other_unit.filter(variable="Effective Radiative Forcing", keep=False), + ) + + def test_run_wrong_units(self): + inp = self.tinp.copy() + inp["unit"] = "W" + + model = self.tmodel() + + with pytest.raises(UnitError): + model.run_scenarios(inp) + + def test_run_wrong_region(self): + inp = self.tinp.copy() + inp["region"] = "World|R5LAM" + + model = self.tmodel() + + error_msg = ( + "No World data available for driver_var `Effective Radiative Forcing`" + ) + + with pytest.raises(ValueError, match=error_msg): + model.run_scenarios(inp) + + def test_run_wrong_driver(self): + inp = self.tinp.copy() + + model = self.tmodel() + + error_msg = ( + "No World data available for driver_var `Effective Radiative Forcing|CO2`" + ) + + with pytest.raises(ValueError, match=error_msg): + model.run_scenarios(inp, driver_var="Effective Radiative Forcing|CO2") diff --git a/stubs/.gitkeep b/stubs/.gitkeep new file mode 100644 index 0000000..e69de29 diff --git a/tests/integration/.gitkeep b/tests/integration/.gitkeep new file mode 100644 index 0000000..e69de29 diff --git a/tests/integration/test_impulse_response_integration.py b/tests/integration/test_impulse_response_integration.py index f79dd0a..8b2eeae 100644 --- a/tests/integration/test_impulse_response_integration.py +++ b/tests/integration/test_impulse_response_integration.py @@ -3,13 +3,12 @@ import pytest from openscm_units import unit_registry as ur from scmdata import ScmRun -from test_model_integration_base import TwoLayerVariantIntegrationTester from openscm_twolayermodel import ImpulseResponseModel +from openscm_twolayermodel.testing import TwoLayerVariantIntegrationTester class TestTwoLayerModel(TwoLayerVariantIntegrationTester): - tmodel = ImpulseResponseModel def test_run_scenarios_single(self): @@ -147,7 +146,10 @@ def test_run_scenarios_multiple(self): @pytest.mark.parametrize( "driver_var", - ("Effective Radiative Forcing", "Effective Radiative Forcing|CO2",), + ( + "Effective Radiative Forcing", + "Effective Radiative Forcing|CO2", + ), ) def test_run_scenarios_multiple_drive_var(self, driver_var): ts1_erf = np.linspace(0, 4, 101) diff --git a/tests/integration/test_model_integration_base.py b/tests/integration/test_model_integration_base.py deleted file mode 100644 index a4024bb..0000000 --- a/tests/integration/test_model_integration_base.py +++ /dev/null @@ -1,96 +0,0 @@ -from abc import ABC, abstractmethod - -import numpy as np -import pytest -from scmdata import ScmRun - -from openscm_twolayermodel.errors import UnitError - - -class ModelIntegrationTester(ABC): - tmodel = None - - @abstractmethod - def test_run_scenarios_single(self): - """ - Test the model can run a single scenario correctly - """ - pass - - @abstractmethod - def test_run_scenarios_multiple(self): - """ - Test the model can run multiple scenarios correctly - """ - pass - - -class TwoLayerVariantIntegrationTester(ModelIntegrationTester): - - tinp = ScmRun( - data=np.linspace(0, 4, 101), - index=np.linspace(1750, 1850, 101).astype(int), - columns={ - "scenario": "test_scenario", - "model": "unspecified", - "climate_model": "junk input", - "variable": "Effective Radiative Forcing", - "unit": "W/m^2", - "region": "World", - }, - ) - - def test_run_unit_handling(self, check_scmruns_allclose): - inp = self.tinp.copy() - - model = self.tmodel() - - res = model.run_scenarios(inp) - - # scmdata bug - # inp.convert_unit("kW/m^2") blows up - inp_other_unit = inp.copy() - inp_other_unit *= 10 ** -3 - inp_other_unit["unit"] = "kW/m^2" - res_other_unit = model.run_scenarios(inp_other_unit) - - assert res.get_unique_meta("climate_model", no_duplicates=True) == model._name - - check_scmruns_allclose( - res.filter(variable="Effective Radiative Forcing", keep=False), - res_other_unit.filter(variable="Effective Radiative Forcing", keep=False), - ) - - def test_run_wrong_units(self): - inp = self.tinp.copy() - inp["unit"] = "W" - - model = self.tmodel() - - with pytest.raises(UnitError): - model.run_scenarios(inp) - - def test_run_wrong_region(self): - inp = self.tinp.copy() - inp["region"] = "World|R5LAM" - - model = self.tmodel() - - error_msg = ( - "No World data available for driver_var `Effective Radiative Forcing`" - ) - - with pytest.raises(ValueError, match=error_msg): - model.run_scenarios(inp) - - def test_run_wrong_driver(self): - inp = self.tinp.copy() - - model = self.tmodel() - - error_msg = ( - "No World data available for driver_var `Effective Radiative Forcing|CO2`" - ) - - with pytest.raises(ValueError, match=error_msg): - model.run_scenarios(inp, driver_var="Effective Radiative Forcing|CO2") diff --git a/tests/integration/test_twolayer_integration.py b/tests/integration/test_twolayer_integration.py index 7784202..aaa932b 100644 --- a/tests/integration/test_twolayer_integration.py +++ b/tests/integration/test_twolayer_integration.py @@ -3,13 +3,12 @@ import pytest from openscm_units import unit_registry as ur from scmdata import ScmRun -from test_model_integration_base import TwoLayerVariantIntegrationTester from openscm_twolayermodel import TwoLayerModel +from openscm_twolayermodel.testing import TwoLayerVariantIntegrationTester class TestTwoLayerModel(TwoLayerVariantIntegrationTester): - tmodel = TwoLayerModel def test_run_scenarios_single(self): @@ -125,7 +124,10 @@ def test_run_scenarios_multiple(self): @pytest.mark.parametrize( "driver_var", - ("Effective Radiative Forcing", "Effective Radiative Forcing|CO2",), + ( + "Effective Radiative Forcing", + "Effective Radiative Forcing|CO2", + ), ) def test_run_scenarios_multiple_drive_var(self, driver_var): ts1_erf = np.linspace(0, 4, 101) diff --git a/tests/regression/.gitkeep b/tests/regression/.gitkeep new file mode 100644 index 0000000..e69de29 diff --git a/tests/test-data/.gitkeep b/tests/test-data/.gitkeep new file mode 100644 index 0000000..e69de29 diff --git a/tests/unit/.gitkeep b/tests/unit/.gitkeep new file mode 100644 index 0000000..e69de29 diff --git a/tests/unit/test_impulse_response_unit.py b/tests/unit/test_impulse_response_unit.py index 6ea0879..8bee3cb 100644 --- a/tests/unit/test_impulse_response_unit.py +++ b/tests/unit/test_impulse_response_unit.py @@ -2,11 +2,11 @@ import numpy.testing as npt import pytest from openscm_units import unit_registry as ur -from test_model_base import TwoLayerVariantTester from openscm_twolayermodel import ImpulseResponseModel, TwoLayerModel from openscm_twolayermodel.base import _calculate_geoffroy_helper_parameters from openscm_twolayermodel.constants import DENSITY_WATER, HEAT_CAPACITY_WATER +from openscm_twolayermodel.testing import TwoLayerVariantTester class TestImpulseResponseModel(TwoLayerVariantTester): @@ -34,7 +34,7 @@ def test_init(self): res = self.tmodel(**init_kwargs) for k, v in init_kwargs.items(): - assert getattr(res, k) == v, "{} not set properly".format(k) + assert getattr(res, k) == v, f"{k} not set properly" assert np.isnan(res.erf) assert np.isnan(res._temp1_mag) @@ -42,7 +42,10 @@ def test_init(self): assert np.isnan(res._rndt_mag) def test_init_backwards_timescales_error(self): - init_kwargs = dict(d1=250.0 * ur("yr"), d2=3 * ur("yr"),) + init_kwargs = dict( + d1=250.0 * ur("yr"), + d2=3 * ur("yr"), + ) error_msg = "The short-timescale must be d1" with pytest.raises(ValueError, match=error_msg): @@ -133,7 +136,8 @@ def test_calculate_next_rndt(self, check_same_unit): ), ) check_same_unit( - self.tmodel._erf_unit, efficacy_term.units, + self.tmodel._erf_unit, + efficacy_term.units, ) def test_step(self): @@ -241,7 +245,13 @@ def test_get_two_layer_model_parameters(self, check_equal_pint): td2 = 300.0 * ur("yr") tefficacy = 1.2 * ur("dimensionless") - start_paras = dict(d1=td1, d2=td2, q1=tq1, q2=tq2, efficacy=tefficacy,) + start_paras = dict( + d1=td1, + d2=td2, + q1=tq1, + q2=tq2, + efficacy=tefficacy, + ) mod_instance = self.tmodel(**start_paras) diff --git a/tests/unit/test_misc.py b/tests/unit/test_misc.py deleted file mode 100644 index ba27735..0000000 --- a/tests/unit/test_misc.py +++ /dev/null @@ -1,39 +0,0 @@ -import warnings - -import numpy as np -import pytest -from conftest import assert_pint_equal, assert_same_unit -from openscm_units import unit_registry - - -def test_pint_array_comparison(): - a = np.array([0, 2]) * unit_registry("GtC") - b = np.array([0, 2]) * unit_registry("MtC") - - # no error but does raise warning about stripping units - with warnings.catch_warnings(record=True): - np.testing.assert_allclose(a, b) - - # actually gives an error as we want - with pytest.raises(AssertionError): - assert_pint_equal(a, b) - - -@pytest.mark.parametrize( - "unit_1,unit_2,error", - (("g", "kg", True), ("W", "J/yr", True), ("W", "J/s", False),), -) -@pytest.mark.parametrize("unit_1_type", (str, "pint_unit")) -@pytest.mark.parametrize("unit_2_type", (str, "pint_unit")) -def test_assert_same_unit(unit_1, unit_2, error, unit_1_type, unit_2_type): - if unit_1_type == "pint_unit": - unit_1 = unit_registry(unit_1) - - if unit_2_type == "pint_unit": - unit_2 = unit_registry(unit_2) - - if error: - with pytest.raises(AssertionError): - assert_same_unit(unit_1, unit_2) - else: - assert_same_unit(unit_1, unit_2) diff --git a/tests/unit/test_model_base.py b/tests/unit/test_model_base.py deleted file mode 100644 index b178433..0000000 --- a/tests/unit/test_model_base.py +++ /dev/null @@ -1,90 +0,0 @@ -import re -from abc import ABC, abstractmethod -from unittest.mock import MagicMock - -import numpy as np -import pint.errors -import pytest -from openscm_units import unit_registry as ur - -from openscm_twolayermodel.errors import ModelStateError, UnitError - - -class ModelTester(ABC): - tmodel = None - - parameters = None - - @abstractmethod - def test_init(self): - """ - Test the model initialises as intended - """ - pass - - def test_init_no_units(self): - """ - Test error thrown if the model is initiliased with a unitless - quantity - """ - for parameter in self.parameters.keys(): - error_msg = "{} must be a pint.Quantity".format(parameter) - with pytest.raises(TypeError, match=error_msg): - self.tmodel(**{parameter: 34.3}) - - @abstractmethod - def test_init_wrong_units(self): - """ - Test error thrown if the model is initiliased with wrong units - for a quantity - """ - # e.g. - for parameter, value in self.parameters.items(): - error_msg = "{} units must be {}".format(parameter, value.units) - with pytest.raises(TypeError, match=error_msg): - self.tmodel(**{parameter: 34.3 * ur("kg")}) - - def test_run(self): - test = self.tmodel() - test.step = MagicMock() - test.run() - - test.step.assert_called() - - -class TwoLayerVariantTester(ModelTester): - def test_init_wrong_units(self): - helper = self.tmodel() - - for parameter in self.parameters.keys(): - tinp = 34.3 * ur("kg") - default = getattr(helper, parameter) - - try: - tinp.to(default.units) - except pint.errors.DimensionalityError: - pass - - error_msg = re.escape("Wrong units for `{}`".format(parameter)) - with pytest.raises(UnitError, match=error_msg): - self.tmodel(**{parameter: tinp}) - - def test_set_erf(self, check_equal_pint): - terf = np.array([0, 1, 2]) * ur("W/m^2") - - res = self.tmodel() - res.erf = terf - - check_equal_pint(res.erf, terf) - - def test_set_erf_unitless_error(self, check_equal_pint): - terf = np.array([0, 1, 2]) - - res = self.tmodel() - with pytest.raises(TypeError, match="erf must be a pint.Quantity"): - res.erf = terf - - def test_reset_not_set_error(self): - error_msg = "The model's drivers have not been set yet, call :meth:`self.set_drivers` first." - with pytest.raises(ModelStateError, match=error_msg): - self.tmodel().reset() diff --git a/tests/unit/test_two_layer_model_unit.py b/tests/unit/test_two_layer_model_unit.py index 22d4160..2f20f71 100644 --- a/tests/unit/test_two_layer_model_unit.py +++ b/tests/unit/test_two_layer_model_unit.py @@ -4,11 +4,11 @@ import numpy.testing as npt import pytest from openscm_units import unit_registry as ur -from test_model_base import TwoLayerVariantTester from openscm_twolayermodel import TwoLayerModel from openscm_twolayermodel.base import _calculate_geoffroy_helper_parameters from openscm_twolayermodel.constants import DENSITY_WATER, HEAT_CAPACITY_WATER +from openscm_twolayermodel.testing import TwoLayerVariantTester class TestTwoLayerModel(TwoLayerVariantTester): @@ -38,7 +38,7 @@ def test_init(self): res = self.tmodel(**init_kwargs) for k, v in init_kwargs.items(): - assert getattr(res, k) == v, "{} not set properly".format(k) + assert getattr(res, k) == v, f"{k} not set properly" assert np.isnan(res.erf) assert np.isnan(res._temp_upper_mag) @@ -60,7 +60,10 @@ def test_heat_capacity_upper(self, check_equal_pint): def test_heat_capacity_upper_no_setter(self): model = self.tmodel() - with pytest.raises(AttributeError, match="can't set attribute"): + error_msg = ( + "property 'heat_capacity_upper' of 'TwoLayerModel' object has no setter" + ) + with pytest.raises(AttributeError, match=error_msg): model.heat_capacity_upper = 4 def test_heat_capacity_lower(self, check_equal_pint): @@ -78,7 +81,10 @@ def test_heat_capacity_lower(self, check_equal_pint): def test_heat_capacity_lower_no_setter(self): model = self.tmodel() - with pytest.raises(AttributeError, match="can't set attribute"): + error_msg = ( + "property 'heat_capacity_lower' of 'TwoLayerModel' object has no setter" + ) + with pytest.raises(AttributeError, match=error_msg): model.heat_capacity_lower = 4 def test_calculate_next_temp_upper(self, check_same_unit): @@ -90,7 +96,7 @@ def test_calculate_next_temp_upper(self, check_same_unit): ta = 0.02 tefficacy = 0.9 teta = 0.78 - theat_capacity_upper = 10 ** 10 + theat_capacity_upper = 10**10 res = self.tmodel._calculate_next_temp_upper( tdelta_t, @@ -163,7 +169,7 @@ def test_calculate_next_temp_lower(self, check_same_unit): ttemp_upper = 0.1 ttemp_lower = 0.2 teta = 0.78 - theat_capacity_lower = 10 ** 8 + theat_capacity_lower = 10**8 res = self.tmodel._calculate_next_temp_lower( tdelta_t, ttemp_lower, ttemp_upper, teta, theat_capacity_lower @@ -177,7 +183,8 @@ def test_calculate_next_temp_lower(self, check_same_unit): # check internal units make sense check_same_unit( - self.tmodel._temp_upper_unit, self.tmodel._temp_lower_unit, + self.tmodel._temp_upper_unit, + self.tmodel._temp_lower_unit, ) check_same_unit( self.tmodel._temp_lower_unit, @@ -198,8 +205,8 @@ def test_calculate_next_rndt(self, check_same_unit): ttemp_lower_t = 0.2 ttemp_upper_t_prev = 0.09 ttemp_lower_t_prev = 0.18 - theat_capacity_upper = 10 ** 10 - theat_capacity_lower = 10 ** 8 + theat_capacity_upper = 10**10 + theat_capacity_lower = 10**8 res = self.tmodel._calculate_next_rndt( tdelta_t, @@ -220,7 +227,8 @@ def test_calculate_next_rndt(self, check_same_unit): # check internal units make sense check_same_unit( - self.tmodel._temp_upper_unit, self.tmodel._temp_lower_unit, + self.tmodel._temp_upper_unit, + self.tmodel._temp_lower_unit, ) check_same_unit( ( @@ -377,12 +385,12 @@ def test_get_impulse_response_parameters(self, check_equal_pint): b = (tlambda0 + tefficacy * teta) / C + teta / C_D b_star = (tlambda0 + tefficacy * teta) / C - teta / C_D - delta = b ** 2 - 4 * tlambda0 * teta / (C * C_D) + delta = b**2 - 4 * tlambda0 * teta / (C * C_D) - tau1 = C * C_D / (2 * tlambda0 * teta) * (b - delta ** 0.5) - tau2 = C * C_D / (2 * tlambda0 * teta) * (b + delta ** 0.5) - phi1 = C / (2 * tefficacy * teta) * (b_star - delta ** 0.5) - phi2 = C / (2 * tefficacy * teta) * (b_star + delta ** 0.5) + tau1 = C * C_D / (2 * tlambda0 * teta) * (b - delta**0.5) + tau2 = C * C_D / (2 * tlambda0 * teta) * (b + delta**0.5) + phi1 = C / (2 * tefficacy * teta) * (b_star - delta**0.5) + phi2 = C / (2 * tefficacy * teta) * (b_star + delta**0.5) expected = { "q1": tau1 * phi2 / (C * (phi2 - phi1)), @@ -405,8 +413,7 @@ def test_get_impulse_response_parameters_non_zero_a_raises(self): ta = 0.1 * ur("W/m^2/delta_degC^2") error_msg = re.escape( - "Cannot calculate impulse response parameters with " - "non-zero a={}".format(ta) + "Cannot calculate impulse response parameters with " f"non-zero a={ta}" ) with pytest.raises(ValueError, match=error_msg): self.tmodel(a=ta).get_impulse_response_parameters() @@ -426,12 +433,12 @@ def test_calculate_geoffroy_helper_parameters(check_equal_pint): b = (tlambda0 + tefficacy * teta) / C + teta / C_D b_star = (tlambda0 + tefficacy * teta) / C - teta / C_D - delta = b ** 2 - 4 * tlambda0 * teta / (C * C_D) + delta = b**2 - 4 * tlambda0 * teta / (C * C_D) - tau1 = C * C_D / (2 * tlambda0 * teta) * (b - delta ** 0.5) - tau2 = C * C_D / (2 * tlambda0 * teta) * (b + delta ** 0.5) - phi1 = C / (2 * tefficacy * teta) * (b_star - delta ** 0.5) - phi2 = C / (2 * tefficacy * teta) * (b_star + delta ** 0.5) + tau1 = C * C_D / (2 * tlambda0 * teta) * (b - delta**0.5) + tau2 = C * C_D / (2 * tlambda0 * teta) * (b + delta**0.5) + phi1 = C / (2 * tefficacy * teta) * (b_star - delta**0.5) + phi2 = C / (2 * tefficacy * teta) * (b_star + delta**0.5) a1 = phi2 * tau1 * tlambda0 / (C * (phi2 - phi1)) a2 = -phi1 * tau2 * tlambda0 / (C * (phi2 - phi1))