From 314a73baed7b818ab6b61703e7fdf51e1ea2438b Mon Sep 17 00:00:00 2001 From: Zebedee Nicholls Date: Tue, 1 Oct 2024 14:18:28 +0200 Subject: [PATCH 1/8] Update repo structure --- .github/ISSUE_TEMPLATE/bug.md | 1 - .github/workflows/bump.yaml | 9 +- .github/workflows/ci.yaml | 43 +- .github/workflows/deploy.yaml | 4 + .github/workflows/install-pypi.yaml | 12 +- .gitignore | 24 +- .pre-commit-config.yaml | 14 +- .readthedocs.yaml | 5 +- Makefile | 41 +- README.md | 2 +- changelog/README.md | 32 +- docs/NAVIGATION.md | 21 + docs/changelog.md | 210 +- docs/gen_doc_stubs.py | 36 +- docs/installation.md | 9 +- environment-docs.yml | 173 +- mkdocs.yml | 91 +- pdm.lock | 1123 +- pixi.lock | 15139 ++++++++-------- pyproject.toml | 8 +- requirements.txt | 75 - scripts/changelog-to-release-template.py | 4 +- .../cvs/test_cv_loading_raw_integration.py | 6 +- tests/integration/test_cli_integration.py | 21 + 24 files changed, 8831 insertions(+), 8272 deletions(-) create mode 100644 docs/NAVIGATION.md delete mode 100644 requirements.txt create mode 100644 tests/integration/test_cli_integration.py diff --git a/.github/ISSUE_TEMPLATE/bug.md b/.github/ISSUE_TEMPLATE/bug.md index d43f7092..ebc36169 100644 --- a/.github/ISSUE_TEMPLATE/bug.md +++ b/.github/ISSUE_TEMPLATE/bug.md @@ -35,7 +35,6 @@ def test_bug_12(): - 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/workflows/bump.yaml b/.github/workflows/bump.yaml index 9b87b35f..fe16f052 100644 --- a/.github/workflows/bump.yaml +++ b/.github/workflows/bump.yaml @@ -5,7 +5,7 @@ on: inputs: bump_rule: type: choice - description: How to bump the project's version (see https://python-poetry.org/docs/cli/#version) + description: How to bump the project's version (see https://github.com/carstencodes/pdm-bump#usage) options: - no-pre-release # no micro because we always sit on a pre-release in main, @@ -41,7 +41,6 @@ jobs: run: | pdm self add pdm-bump - # Install the package and towncrier with pixi - uses: ./.github/actions/setup with: pixi-environments: "all-dev" @@ -72,15 +71,13 @@ jobs: # version as the tagged commit) BASE_VERSION=`sed -ne 's/^version = "\([0-9\.a]*\)"/\1/p' pyproject.toml` - # Bump (need two commands because of a bug in pdm-bump) - # See https://github.com/carstencodes/pdm-bump/issues/326 - pdm bump micro + # Bump to pre-release of next version pdm bump pre-release --pre alpha NEW_VERSION=`sed -ne 's/^version = "\([0-9\.a]*\)"/\1/p' pyproject.toml` echo "Bumping version $BASE_VERSION > $NEW_VERSION" - # Skip pre-commit to avoid pixi install throwing weird errors # Commit and push + # Skip pre-commit to avoid pixi install throwing weird errors git commit -n -a -m "bump(pre-release): version $BASE_VERSION > $NEW_VERSION" git push diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 4f4d219b..a0f10a55 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -17,7 +17,8 @@ jobs: with: pixi-environments: "all-dev" - name: mypy - run: MYPYPATH=stubs pixi run --frozen -e all-dev mypy src + run: | + MYPYPATH=stubs pixi run --frozen -e all-dev run mypy src docs: if: ${{ !github.event.pull_request.draft }} @@ -30,8 +31,17 @@ jobs: pixi-environments: "docs" - name: docs run: | - pixi run --frozen -e docs typer input4mips_validation.cli utils docs --output docs/cli/index.md --name input4mips-validation-cli + pixi run --frozen -e docs typer input4mips_validation.cli utils docs --output docs/cli/index.md --name input4mips-validation pixi run --frozen -e docs mkdocs build --strict + - uses: ./.github/actions/setup + with: + python-version: "3.11" + pdm-dependency-install-flags: "-G docs -G :all -G dev" + - uses: ./.github/actions/setup + with: + pixi-environments: "all-dev" + - name: docs-with-changelog + run: | # Check CHANGELOG will build too pixi run --frozen -e all-dev towncrier build --yes pixi run --frozen -e all-dev mkdocs build --strict @@ -47,8 +57,9 @@ jobs: runs-on: "${{ 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, + # 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: @@ -56,13 +67,22 @@ jobs: uses: actions/checkout@v4 - uses: ./.github/actions/setup with: + # When running the tests, install with all optional dependencies + # to get maximum test coverage. + # If we find that we're getting failures + # when people try to run without installing optional dependencies, + # we should add a CI step that runs the tests without optional dependencies too. + # We don't have that right now, because we're not sure this pain point exists. + # (Although pixi actually controls this, rather than the flags passed here.) pixi-environments: "test-${{ matrix.test-python-id }}" - name: Run tests run: | pixi run --frozen -e "test-${{ matrix.test-python-id }}" pytest -r a -v src tests --doctest-modules --cov=src --cov-report=term-missing --cov-report=xml - pixi run --frozen -e "test-${{ matrix.test-python-id }}" coverage report - - name: Upload coverage reports to Codecov - uses: codecov/codecov-action@v3 + pixi run --frozen -e "test-${{ matrix.test-python-id }}" coverage report + - name: Upload coverage reports to Codecov with GitHub Action + uses: codecov/codecov-action@v4.2.0 + env: + CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} imports-without-extras: strategy: @@ -104,6 +124,7 @@ jobs: uses: actions/checkout@v4 - name: Check locked install uses: prefix-dev/setup-pixi@v0.8.1 + - uses: ./.github/actions/setup with: locked: true @@ -116,13 +137,11 @@ jobs: # uses: actions/checkout@v4 # - uses: ./.github/actions/setup # with: - # python-version: "3.9" - # venv-id: "licence-check" - # poetry-dependency-install-flags: "--all-extras" + # pixi-environments: "all-dev" # - name: Check licences of dependencies # shell: bash # run: | # TEMP_FILE=$(mktemp) - # poetry export --without=tests --without=docs --without=dev > $TEMP_FILE - # poetry run liccheck -r $TEMP_FILE -R licence-check.txt + # pdm export --prod > $TEMP_FILE + # pixi run --frozen -e all-dev liccheck -r $TEMP_FILE -R licence-check.txt # cat licence-check.txt diff --git a/.github/workflows/deploy.yaml b/.github/workflows/deploy.yaml index 996a93db..3133d008 100644 --- a/.github/workflows/deploy.yaml +++ b/.github/workflows/deploy.yaml @@ -11,6 +11,10 @@ defaults: jobs: deploy-pypi: name: Deploy to PyPI + # Having an environment for deployment is strongly recommend by PyPI + # https://docs.pypi.org/trusted-publishers/adding-a-publisher/#github-actions + # You can comment this line out if you don't want it. + environment: deploy runs-on: ubuntu-latest permissions: # this permission is mandatory for trusted publishing with PyPI diff --git a/.github/workflows/install-pypi.yaml b/.github/workflows/install-pypi.yaml index 0c829f4d..cd18b5e0 100644 --- a/.github/workflows/install-pypi.yaml +++ b/.github/workflows/install-pypi.yaml @@ -63,11 +63,20 @@ jobs: if: matrix.os != 'windows-latest' run: | if grep -q "WARN" stderr.txt; then echo "Warnings in pip install output" && cat stderr.txt && exit 1; else exit 0; fi - - name: Get version + - name: Get version non-windows + if: matrix.os != 'windows-latest' run: | INSTALLED_VERSION=`python -c 'import input4mips_validation; print(f"v{input4mips_validation.__version__}")'` echo $INSTALLED_VERSION echo "INSTALLED_VERSION=$INSTALLED_VERSION" >> $GITHUB_ENV + - name: Get version windows + if: matrix.os == 'windows-latest' + run: | + chcp 65001 # use utf-8 + python -c 'import input4mips_validation; f = open("version.txt", "w"); f.write(f"INSTALLED_VERSION=v{input4mips_validation.__version__}"); f.close()' + echo "Showing version.txt" + type version.txt + type version.txt >> $env:GITHUB_ENV - name: Checkout repository uses: actions/checkout@v4 with: @@ -87,4 +96,5 @@ jobs: run: | export LD_LIBRARY_PATH="$HOME/udunits/lib/:$LD_LIBRARY_PATH" python -c 'import ctypes.util; print(ctypes.util.find_library("udunits2"))' + # Can't test coverage here because paths are different pytest tests -r a -vv -s diff --git a/.gitignore b/.gitignore index eb3a4fa1..82613a4a 100644 --- a/.gitignore +++ b/.gitignore @@ -1,35 +1,35 @@ -# Big test data. Not sure whether to add this or just store in a separate -# test data repo or something (or just download every time...) -tests/test-data/input4MIPs/CMIP6Plus/CMIP/PCMDI - # Default data download directory src/input4mips_validation/cvs_handling/input4MIPs/user_cvs src/input4mips_validation/cvs/user_cvs src/input4mips_validation/cvs/input4MIPs_CVs_* -# Auto-generated docs and helper files -docs/api -docs/cli +# Auto-generated docs stuff docs/how-to-guides/**/*.nc +# pixi stuff +.pixi + # Notebooks *.ipynb -# Lock file -poetry.lock +# Auto-generated docs and helper files +docs/api/* +!docs/api/.gitkeep +docs/cli/* +!docs/cli/.gitkeep # pdm stuff .pdm-python -# pixi stuff -.pixi - # Databases *.db # Jupyter cache .jupyter_cache +# IDE stuff +.idea/ + # Ruff cache .ruff_cache diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 123a6ddb..e3f0db5b 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -16,7 +16,7 @@ ci: # See https://pre-commit.com/hooks.html for more hooks repos: - repo: https://github.com/pre-commit/pre-commit-hooks - rev: 'v4.5.0' + rev: "v4.5.0" hooks: - id: check-added-large-files - id: check-ast @@ -40,7 +40,7 @@ repos: language: fail files: "\\.rej$" - repo: https://github.com/charliermarsh/ruff-pre-commit - rev: 'v0.1.8' + rev: "v0.1.8" hooks: - id: ruff args: [ --fix, --exit-non-zero-on-fix ] @@ -50,13 +50,11 @@ repos: hooks: # Check that the lock file is up to date. # We need the pdm lock file too - # so that we can build locked version of the package. + # so that we can build the locked version of the package. - id: pdm-lock-check - args: [ --dev, --group, ":all" ] - # Put a requirements.txt file in the repo too - - id: pdm-export - args: ['--prod', '-o', 'requirements.txt', '--without-hashes'] - # - id: pdm-sync # not used here because we manage environments with pixi + args: ["--dev", "-G", ":all", "--strategy", "inherit_metadata" ] + # No requirements exported because we use pixi + # and conda doesn't play nice with pip anyway. - repo: local hooks: # pixi doesn't have a lock/check command yet, diff --git a/.readthedocs.yaml b/.readthedocs.yaml index fc57e71b..200c2880 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -2,8 +2,6 @@ # 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 @@ -15,9 +13,8 @@ build: jobs: pre_build: - pip install --no-deps . - - typer input4mips_validation.cli utils docs --output docs/cli/index.md --name input4mips-validation-cli - - ls - input4mips-validation --help + - typer input4mips_validation.cli utils docs --output docs/cli/index.md --name input4mips-validation # Can add other checks in here if things blow up confusingly post_install: - mamba list diff --git a/Makefile b/Makefile index 25ee8bce..62ca4875 100644 --- a/Makefile +++ b/Makefile @@ -32,9 +32,9 @@ checks: ## run all the linting checks of the codebase 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 - pixi run -e all-dev ruff format src tests scripts - pixi run -e all-dev ruff check src tests scripts --fix - pixi run -e all-dev ruff format src tests scripts + pixi run -e all-dev ruff format src tests scripts docs + pixi run -e all-dev ruff check src tests scripts docs --fix + pixi run -e all-dev ruff format src tests scripts docs .PHONY: test @@ -42,20 +42,26 @@ test: ## run the tests pixi run -e all-dev 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 +# You must specify cov=src. +# 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. +# 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. + +docs/cli/index.md: src/input4mips_validation/cli/__init__.py ## auto-generate the typer app docs + pixi run -e all-dev typer input4mips_validation.cli utils docs --output docs/cli/index.md --name input4mips-validation .PHONY: docs docs: docs/cli/index.md ## build the docs pixi run -e all-dev mkdocs build -.PHONY: docs +.PHONY: docs-strict docs-strict: docs/cli/index.md ## build the docs strictly (e.g. raise an error on warnings, this most closely mirrors what we do in the CI) pixi run -e all-dev mkdocs build --strict @@ -63,24 +69,21 @@ docs-strict: docs/cli/index.md ## build the docs strictly (e.g. raise an error docs-serve: docs/cli/index.md ## serve the docs locally pixi run -e all-dev mkdocs serve -docs/cli/index.md: src/input4mips_validation/cli/__init__.py ## auto-generate the typer app docs - pixi run -e all-dev typer input4mips_validation.cli utils docs --output docs/cli/index.md --name input4mips-validation-cli - .PHONY: changelog-draft changelog-draft: ## compile a draft of the next changelog - pixi run -e all-dev towncrier build --draft + pixi run -e all-dev towncrier build --draft --version 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 - pdm export -o $(TEMP_FILE) --without=tests --without=docs --without=dev - pdm run liccheck -r $(TEMP_FILE) -R licence-check.txt - rm $(TEMP_FILE) + pdm export --without=tests --without=docs --without=dev > $(TEMP_FILE) + pixi run -e all-dev 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 pixi install -e all-dev pixi run -e all-dev pre-commit install # Make sure pdm lock file is up to date too - pdm lock --strategy=inherit_metadata --dev --group :all + pdm lock --dev --group :all --strategy inherit_metadata diff --git a/README.md b/README.md index ab2a7c20..869bdd31 100644 --- a/README.md +++ b/README.md @@ -184,7 +184,7 @@ Hence, you will also need to make sure that pdm is installed on your system although we found that installing with [pipx](https://pipx.pypa.io/stable/installation/) worked perfectly for us). -For all of work, we use our `Makefile`. +For all of our 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`. diff --git a/changelog/README.md b/changelog/README.md index 41ad1861..b050c182 100644 --- a/changelog/README.md +++ b/changelog/README.md @@ -1,11 +1,14 @@ # 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. +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 Input4MIPs-validation 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. +The CHANGELOG will be read by users, +so this description should be aimed to Input4MIPs validation users +instead of describing internal changes which are only relevant to developers. +Merge requests in combination with our git history +provide additional developer-centric information. Make sure to use phrases in the past tense and use punctuation, examples: @@ -27,15 +30,18 @@ Each file should have a name of the form `..md`, where `` is the m 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. +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. +`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 [mkdocs-autorefs cross-referencing](https://mkdocstrings.github.io/autorefs/) +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. +You can also run `towncrier build --draft --version draft` +to see the draft changelog that will be appended to the CHANGELOG on the next release. diff --git a/docs/NAVIGATION.md b/docs/NAVIGATION.md new file mode 100644 index 00000000..e9644f15 --- /dev/null +++ b/docs/NAVIGATION.md @@ -0,0 +1,21 @@ + +- [Home](index.md) +- [Installation](installation.md) +- [How-to guides](how-to-guides/index.md) + - [Do a basic calculation](how-to-guides/basic-calculation.md) + - [Run code in a notebook](how-to-guides/run-code-in-a-notebook.py) + - [How to write a single valid file](how-to-guides/how-to-write-a-single-valid-file.py) + - [How validate a single file](how-to-guides/how-to-validate-a-single-file.py) + - [How to write a single file in the DRS](how-to-guides/how-to-write-a-single-file-in-the-drs.py) + - [How to upload to an FTP server](how-to-guides/how-to-upload-to-ftp.py) + - [How to manage a database of file entries](how-to-guides/how-to-manage-a-database.py) +- [Tutorials](tutorials.md) +- [Further background](further-background/explanation.md) +- [Development](development.md) +- [Command-line interface](cli/index.md) +- [API reference](api/input4mips_validation/) +- [Changelog](changelog.md) diff --git a/docs/changelog.md b/docs/changelog.md index 7f41d311..c4e7a1a7 100644 --- a/docs/changelog.md +++ b/docs/changelog.md @@ -5,38 +5,40 @@ Versions follow [Semantic Versioning](https://semver.org/) (`.. -## input4mips-validation v0.13.0 (2024-09-30) +## Input4MIPs validation v0.13.0 (2024-09-30) ### 🆕 Features -- Add `--continue-on-error` flag to `input4mips-validation upload-ftp` ([#69](https://github.com/climate-resource/input4mips_validation/pulls/69)) -- Added validation of the tracking_id attribute, see [`input4mips_validation.validation.tracking_id.validate_tracking_id`][]. ([#70](https://github.com/climate-resource/input4mips_validation/pulls/70)) +- Add `--continue-on-error` flag to `input4mips-validation upload-ftp` ([#69](https://github.com/climate-resource/input4mips_validation/pull/69)) +- Added validation of the tracking_id attribute, see [`input4mips_validation.validation.tracking_id.validate_tracking_id`][]. ([#70](https://github.com/climate-resource/input4mips_validation/pull/70)) ### 🐛 Bug Fixes -- Fixed total failure of validation if an expected attribute wasn't in the file being validated. ([#70](https://github.com/climate-resource/input4mips_validation/pulls/70)) +- Fixed total failure of validation if an expected attribute wasn't in the file being validated. ([#70](https://github.com/climate-resource/input4mips_validation/pull/70)) ### 🔧 Trivial/Internal Changes -- [#67](https://github.com/climate-resource/input4mips_validation/pulls/67), [#68](https://github.com/climate-resource/input4mips_validation/pulls/68), [#69](https://github.com/climate-resource/input4mips_validation/pulls/69), [#71](https://github.com/climate-resource/input4mips_validation/pulls/71) +- [#67](https://github.com/climate-resource/input4mips_validation/pull/67), [#68](https://github.com/climate-resource/input4mips_validation/pull/68), [#69](https://github.com/climate-resource/input4mips_validation/pull/69), [#71](https://github.com/climate-resource/input4mips_validation/pull/71) -## input4mips-validation v0.12.0 (2024-08-29) +## Input4MIPs validation v0.12.0 (2024-08-29) ### 🗑️ Deprecations @@ -46,80 +48,80 @@ of rst and use slightly different categories. [`validate_ds_to_write_to_disk`][input4mips_validation.validation.datasets_to_write_to_disk.validate_ds_to_write_to_disk], [`validate_file`][input4mips_validation.validation.file.validate_file] and [`validate_tree`][input4mips_validation.validation.tree.validate_tree]. - See the docs for each function and deprecation warnings for recommended alternatives. ([#66](https://github.com/climate-resource/input4mips_validation/pulls/66)) + See the docs for each function and deprecation warnings for recommended alternatives. ([#66](https://github.com/climate-resource/input4mips_validation/pull/66)) ### 🆕 Features - Added the `--output-html` flag to `input4mips-validation validate-tree`. This allows you to output the results of the validation as HTML, - which provides easier exploration of the failures. ([#66](https://github.com/climate-resource/input4mips_validation/pulls/66)) + which provides easier exploration of the failures. ([#66](https://github.com/climate-resource/input4mips_validation/pull/66)) ### 📚 Improved Documentation - Improved documentation of our command-line interface, - particularly how to configure logging. ([#65](https://github.com/climate-resource/input4mips_validation/pulls/65)) + particularly how to configure logging. ([#65](https://github.com/climate-resource/input4mips_validation/pull/65)) ### 🔧 Trivial/Internal Changes -- [#65](https://github.com/climate-resource/input4mips_validation/pulls/65) +- [#65](https://github.com/climate-resource/input4mips_validation/pull/65) -## input4mips-validation v0.11.4 (2024-08-23) +## Input4MIPs validation v0.11.4 (2024-08-23) ### 🆕 Features -- Add "doi" to the list of fields tracked by our database entries. ([#64](https://github.com/climate-resource/input4mips_validation/pulls/64)) +- Add "doi" to the list of fields tracked by our database entries. ([#64](https://github.com/climate-resource/input4mips_validation/pull/64)) ### 🔧 Trivial/Internal Changes -- [#62](https://github.com/climate-resource/input4mips_validation/pulls/62) +- [#62](https://github.com/climate-resource/input4mips_validation/pull/62) -## input4mips-validation v0.11.3 (2024-08-06) +## Input4MIPs validation v0.11.3 (2024-08-06) ### 🎉 Improvements -- Made it explicit that [cftime](https://unidata.github.io/cftime/) and [typing-extensions](https://typing-extensions.readthedocs.io/en/latest/#) are required ([#59](https://github.com/climate-resource/input4mips_validation/pulls/59)) +- Made it explicit that [cftime](https://unidata.github.io/cftime/) and [typing-extensions](https://typing-extensions.readthedocs.io/en/latest/#) are required ([#59](https://github.com/climate-resource/input4mips_validation/pull/59)) ### 🐛 Bug Fixes -- Fixed up the writing of the `creation_time` attribute and datetime metadata inference to use the expected time format ([#60](https://github.com/climate-resource/input4mips_validation/pulls/60)) +- Fixed up the writing of the `creation_time` attribute and datetime metadata inference to use the expected time format ([#60](https://github.com/climate-resource/input4mips_validation/pull/60)) ### 🔧 Trivial/Internal Changes -- [#60](https://github.com/climate-resource/input4mips_validation/pulls/60) +- [#60](https://github.com/climate-resource/input4mips_validation/pull/60) -## input4mips-validation v0.11.2 (2024-08-05) +## Input4MIPs validation v0.11.2 (2024-08-05) ### 🔧 Trivial/Internal Changes -- [#57](https://github.com/climate-resource/input4mips_validation/pulls/57) +- [#57](https://github.com/climate-resource/input4mips_validation/pull/57) -## input4mips-validation v0.11.1 (2024-08-03) +## Input4MIPs validation v0.11.1 (2024-08-03) ### 🎉 Improvements - Added support for data without a time axis to [`from_data_producer_minimum_information`][input4mips_validation.dataset.Input4MIPsDataset.from_data_producer_minimum_information] - and [`from_data_producer_minimum_information_multiple_variable`][input4mips_validation.dataset.Input4MIPsDataset.from_data_producer_minimum_information_multiple_variable]. ([#56](https://github.com/climate-resource/input4mips_validation/pulls/56)) + and [`from_data_producer_minimum_information_multiple_variable`][input4mips_validation.dataset.Input4MIPsDataset.from_data_producer_minimum_information_multiple_variable]. ([#56](https://github.com/climate-resource/input4mips_validation/pull/56)) ### 🐛 Bug Fixes - Fixed the type hint for `datetime_end`, `datetime_start` and `time_range`. These fields will now serialise and de-serialise correctly. - Previously, if these fields were `None`, they were serialised and de-serialised as strings. ([#56](https://github.com/climate-resource/input4mips_validation/pulls/56)) + Previously, if these fields were `None`, they were serialised and de-serialised as strings. ([#56](https://github.com/climate-resource/input4mips_validation/pull/56)) ### 🔧 Trivial/Internal Changes -- [#56](https://github.com/climate-resource/input4mips_validation/pulls/56) +- [#56](https://github.com/climate-resource/input4mips_validation/pull/56) -## input4mips-validation v0.11.0 (2024-08-02) +## Input4MIPs validation v0.11.0 (2024-08-02) ### ⚠️ Breaking Changes @@ -131,13 +133,13 @@ of rst and use slightly different categories. - Changed the function signature of [`input4mips_validation.cvs.loading.load_cvs`][input4mips_validation.cvs.loading.load_cvs]. Now it simply expects the `cv_source` rather than requiring a [`RawCVLoader`][input4mips_validation.cvs.loading_raw.RawCVLoader] as input. - ([#55](https://github.com/climate-resource/input4mips_validation/pulls/55)) + ([#55](https://github.com/climate-resource/input4mips_validation/pull/55)) ### 🆕 Features - Added the ` --allow-cf-checker-warnings` flag to the `validate-file` and `validate-tree` commands. This allows the validation to pass, even if the CF-checker raises a warning. - This was added because the CF-checker's warnings are sometimes overly strict. ([#52](https://github.com/climate-resource/input4mips_validation/pulls/52)) + This was added because the CF-checker's warnings are sometimes overly strict. ([#52](https://github.com/climate-resource/input4mips_validation/pull/52)) - - Added `input4mips-validation db` command group for handling database creation and manipulation. This includes: @@ -152,7 +154,7 @@ of rst and use slightly different categories. We're not sure if this is a great solution. If you have another solution, PRs welcome! - ([#55](https://github.com/climate-resource/input4mips_validation/pulls/55)) + ([#55](https://github.com/climate-resource/input4mips_validation/pull/55)) ### 🎉 Improvements @@ -161,58 +163,58 @@ of rst and use slightly different categories. to clarify the different states of validation. - Parallelised [`create_db_file_entries`][input4mips_validation.database.creation.create_db_file_entries] - ([#55](https://github.com/climate-resource/input4mips_validation/pulls/55)) + ([#55](https://github.com/climate-resource/input4mips_validation/pull/55)) ### 🐛 Bug Fixes -- Fixed a missing f-string marker in `validate-tree`'s logging. ([#52](https://github.com/climate-resource/input4mips_validation/pulls/52)) +- Fixed a missing f-string marker in `validate-tree`'s logging. ([#52](https://github.com/climate-resource/input4mips_validation/pull/52)) - - Set `use_cftime=True` whenever we call `xr.open_dataset` to avoid spurious warnings - Only pass the directory to `extract_metadata_from_path` in [`DRS.validate_file_written_according_to_drs`][input4mips_validation.cvs.drs.DataReferenceSyntax.validate_file_written_according_to_drs]. This helps reduce the chance of incorrecetly parsing the metadata. - ([#55](https://github.com/climate-resource/input4mips_validation/pulls/55)) + ([#55](https://github.com/climate-resource/input4mips_validation/pull/55)) ### 📚 Improved Documentation -- Clarified the meaning of the `timestamp` and `version` fields in our database entries ([#54](https://github.com/climate-resource/input4mips_validation/pulls/54)) -- Added documentation for how to manage a database ([#55](https://github.com/climate-resource/input4mips_validation/pulls/55)) +- Clarified the meaning of the `timestamp` and `version` fields in our database entries ([#54](https://github.com/climate-resource/input4mips_validation/pull/54)) +- Added documentation for how to manage a database ([#55](https://github.com/climate-resource/input4mips_validation/pull/55)) ### 🔧 Trivial/Internal Changes -- [#55](https://github.com/climate-resource/input4mips_validation/pulls/55) +- [#55](https://github.com/climate-resource/input4mips_validation/pull/55) -## input4mips-validation v0.10.2 (2024-07-28) +## Input4MIPs validation v0.10.2 (2024-07-28) ### 🐛 Bug Fixes -- Make [loguru-config](https://github.com/erezinman/loguru-config) an optional dependency in `pyproject.toml` too ([#50](https://github.com/climate-resource/input4mips_validation/pulls/50)) +- Make [loguru-config](https://github.com/erezinman/loguru-config) an optional dependency in `pyproject.toml` too ([#50](https://github.com/climate-resource/input4mips_validation/pull/50)) ### 🔧 Trivial/Internal Changes -- [#50](https://github.com/climate-resource/input4mips_validation/pulls/50) +- [#50](https://github.com/climate-resource/input4mips_validation/pull/50) -## input4mips-validation v0.10.1 (2024-07-28) +## Input4MIPs validation v0.10.1 (2024-07-28) ### 🎉 Improvements -- Clarify handling of dry run in [`upload_ftp`][input4mips_validation.upload_ftp] ([#45](https://github.com/climate-resource/input4mips_validation/pulls/45)) +- Clarify handling of dry run in [`upload_ftp`][input4mips_validation.upload_ftp] ([#45](https://github.com/climate-resource/input4mips_validation/pull/45)) - [loguru-config](https://github.com/erezinman/loguru-config) is now an optional dependency. This makes it possible to install the package from conda without things exploding, as loguru-config is not available on conda. This may be changed in future, if loguru-config is released on conda - (relevant MR here: https://github.com/conda-forge/staged-recipes/pull/27110) ([#48](https://github.com/climate-resource/input4mips_validation/pulls/48)) + (relevant MR here: https://github.com/conda-forge/staged-recipes/pull/27110) ([#48](https://github.com/climate-resource/input4mips_validation/pull/48)) ### 🔧 Trivial/Internal Changes -- [#44](https://github.com/climate-resource/input4mips_validation/pulls/44), [#46](https://github.com/climate-resource/input4mips_validation/pulls/46), [#47](https://github.com/climate-resource/input4mips_validation/pulls/47), [#49](https://github.com/climate-resource/input4mips_validation/pulls/49) +- [#44](https://github.com/climate-resource/input4mips_validation/pull/44), [#46](https://github.com/climate-resource/input4mips_validation/pull/46), [#47](https://github.com/climate-resource/input4mips_validation/pull/47), [#49](https://github.com/climate-resource/input4mips_validation/pull/49) -## input4mips-validation v0.10.0 (2024-07-27) +## Input4MIPs validation v0.10.0 (2024-07-27) ### ⚠️ Breaking Changes @@ -220,7 +222,7 @@ of rst and use slightly different categories. - - Removed `--verbose` option from the `input4mips-validation` command - Moved logging to `input4mips_validation.logging` - ([#40](https://github.com/climate-resource/input4mips_validation/pulls/40)) + ([#40](https://github.com/climate-resource/input4mips_validation/pull/40)) ### 🆕 Features @@ -245,11 +247,11 @@ of rst and use slightly different categories. - Added [`DataReferenceSyntax.get_esgf_dataset_master_id`][input4mips_validation.cvs.drs.DataReferenceSyntax.get_esgf_dataset_master_id] - ([#40](https://github.com/climate-resource/input4mips_validation/pulls/40)) + ([#40](https://github.com/climate-resource/input4mips_validation/pull/40)) - - Added the `input4mips-validation upload-ftp` command - Added [`input4mips_validation.upload_ftp`][input4mips_validation.upload_ftp] - ([#43](https://github.com/climate-resource/input4mips_validation/pulls/43)) + ([#43](https://github.com/climate-resource/input4mips_validation/pull/43)) ### 🎉 Improvements @@ -276,7 +278,7 @@ of rst and use slightly different categories. - Made [commit `52841b0117474efd2705a083c21b3760531974f3`](https://raw.githubusercontent.com/PCMDI/input4MIPs_CVs/52841b0117474efd2705a083c21b3760531974f3/CVs/) a known registry for the raw CVs. - ([#40](https://github.com/climate-resource/input4mips_validation/pulls/40)) + ([#40](https://github.com/climate-resource/input4mips_validation/pull/40)) ### 🐛 Bug Fixes @@ -295,24 +297,24 @@ of rst and use slightly different categories. (i.e. the value from higher-priority sources is used) rather than an error being raised. - ([#40](https://github.com/climate-resource/input4mips_validation/pulls/40)) + ([#40](https://github.com/climate-resource/input4mips_validation/pull/40)) ### 📚 Improved Documentation -- Updated README so that the snippet comments don't show up ([#37](https://github.com/climate-resource/input4mips_validation/pulls/37)) +- Updated README so that the snippet comments don't show up ([#37](https://github.com/climate-resource/input4mips_validation/pull/37)) - - Added docs about project status to the README - Added docs about preparing a file in the how-to guides. How to upload will come in the next MR. - See ["How can I prepare my input4MIPs files for publication on ESGF?"](https://input4mips-validation.readthedocs.io/en/latest/how-to-guides/#how-can-i-prepare-my-input4mips-files-for-publication-on-esgf) - ([#40](https://github.com/climate-resource/input4mips_validation/pulls/40)) -- Added documentation about how to upload to an FTP server, and cross-linked these with the rest of the docs ([#43](https://github.com/climate-resource/input4mips_validation/pulls/43)) + ([#40](https://github.com/climate-resource/input4mips_validation/pull/40)) +- Added documentation about how to upload to an FTP server, and cross-linked these with the rest of the docs ([#43](https://github.com/climate-resource/input4mips_validation/pull/43)) ### 🔧 Trivial/Internal Changes -- [#40](https://github.com/climate-resource/input4mips_validation/pulls/40) +- [#40](https://github.com/climate-resource/input4mips_validation/pull/40) -## input4mips-validation v0.9.0 (2024-07-24) +## Input4MIPs validation v0.9.0 (2024-07-24) ### 🆕 Features @@ -327,7 +329,7 @@ of rst and use slightly different categories. - `input4mips-validation validate-tree --help` - `input4mips-validation create-db --help` - ([#36](https://github.com/climate-resource/input4mips_validation/pulls/36)) + ([#36](https://github.com/climate-resource/input4mips_validation/pull/36)) ### 📚 Improved Documentation @@ -335,22 +337,22 @@ of rst and use slightly different categories. [conda package](https://anaconda.org/conda-forge/input4mips-validation). - Generally cleaned up the docs - ([#36](https://github.com/climate-resource/input4mips_validation/pulls/36)) + ([#36](https://github.com/climate-resource/input4mips_validation/pull/36)) ### 🔧 Trivial/Internal Changes -- [#36](https://github.com/climate-resource/input4mips_validation/pulls/36) +- [#36](https://github.com/climate-resource/input4mips_validation/pull/36) -## input4mips-validation v0.8.1 (2024-07-22) +## Input4MIPs validation v0.8.1 (2024-07-22) ### 🔧 Trivial/Internal Changes -- [#34](https://github.com/climate-resource/input4mips_validation/pulls/34) +- [#34](https://github.com/climate-resource/input4mips_validation/pull/34) -## input4mips-validation v0.8.0 (2024-07-22) +## Input4MIPs validation v0.8.0 (2024-07-22) ### ⚠️ Breaking Changes @@ -365,20 +367,20 @@ of rst and use slightly different categories. - cleaned up the API to make clearer the different elements - changed dev tooling to supporting conda packages, because we needed iris - ([#31](https://github.com/climate-resource/input4mips_validation/pulls/31)) + ([#31](https://github.com/climate-resource/input4mips_validation/pull/31)) ### 📚 Improved Documentation -- Updated README badges ([#28](https://github.com/climate-resource/input4mips_validation/pulls/28)) -- Updated conda install workflow README badge ([#29](https://github.com/climate-resource/input4mips_validation/pulls/29)) -- Updated licence badge and tweaked badge layout ([#30](https://github.com/climate-resource/input4mips_validation/pulls/30)) +- Updated README badges ([#28](https://github.com/climate-resource/input4mips_validation/pull/28)) +- Updated conda install workflow README badge ([#29](https://github.com/climate-resource/input4mips_validation/pull/29)) +- Updated licence badge and tweaked badge layout ([#30](https://github.com/climate-resource/input4mips_validation/pull/30)) ### 🔧 Trivial/Internal Changes -- [#26](https://github.com/climate-resource/input4mips_validation/pulls/26), [#32](https://github.com/climate-resource/input4mips_validation/pulls/32), [#33](https://github.com/climate-resource/input4mips_validation/pulls/33) +- [#26](https://github.com/climate-resource/input4mips_validation/pull/26), [#32](https://github.com/climate-resource/input4mips_validation/pull/32), [#33](https://github.com/climate-resource/input4mips_validation/pull/33) -## input4mips-validation v0.7.0 (2024-07-19) +## Input4MIPs validation v0.7.0 (2024-07-19) ### Features @@ -387,49 +389,49 @@ of rst and use slightly different categories. The instructions in the README for installation from PyPI should now be valid. The instructions for installation from conda are still waiting on - https://github.com/conda-forge/staged-recipes/pull/26986. ([#25](https://github.com/climate-resource/input4mips_validation/pulls/25)) + https://github.com/conda-forge/staged-recipes/pull/26986. ([#25](https://github.com/climate-resource/input4mips_validation/pull/25)) ### Bug Fixes -- Fixed up version number, putting it back in line with PyPI ([#27](https://github.com/climate-resource/input4mips_validation/pulls/27)) +- Fixed up version number, putting it back in line with PyPI ([#27](https://github.com/climate-resource/input4mips_validation/pull/27)) ### Trivial/Internal Changes -- [#24](https://github.com/climate-resource/input4mips_validation/pulls/24) +- [#24](https://github.com/climate-resource/input4mips_validation/pull/24) -## input4mips-validation v0.5.2 (2024-07-19) +## Input4MIPs validation v0.5.2 (2024-07-19) ### Trivial/Internal Changes -- [#23](https://github.com/climate-resource/input4mips_validation/pulls/23) +- [#23](https://github.com/climate-resource/input4mips_validation/pull/23) -## input4mips-validation v0.5.1 (2024-07-19) +## Input4MIPs validation v0.5.1 (2024-07-19) ### Trivial/Internal Changes -- [#20](https://github.com/climate-resource/input4mips_validation/pulls/20), [#22](https://github.com/climate-resource/input4mips_validation/pulls/22) +- [#20](https://github.com/climate-resource/input4mips_validation/pull/20), [#22](https://github.com/climate-resource/input4mips_validation/pull/22) -## input4mips-validation v0.6.0 (2024-07-18) +## Input4MIPs validation v0.6.0 (2024-07-18) ### Breaking Changes - Re-named {py:attr}`input5mips_validation.cvs_handling.input4MIPs.activity_id.ActivityIDValues.url` to {py:attr}`input4mips_validation.cvs_handling.input4MIPs.activity_id.ActivityIDValues.URL` - i.e. "url" --> "URL" ([#17](https://github.com/climate-resource/input4mips_validation/pulls/17)) -- Loosened dependency pins ([#21](https://github.com/climate-resource/input4mips_validation/pulls/21)) + i.e. "url" --> "URL" ([#17](https://github.com/climate-resource/input4mips_validation/pull/17)) +- Loosened dependency pins ([#21](https://github.com/climate-resource/input4mips_validation/pull/21)) ### Features -- Added handling of the institution ID controlled vocabulary ([#16](https://github.com/climate-resource/input4mips_validation/pulls/16)) -- Added handling of the futher_info_url within the context of the controlled vocabulary ([#18](https://github.com/climate-resource/input4mips_validation/pulls/18)) +- Added handling of the institution ID controlled vocabulary ([#16](https://github.com/climate-resource/input4mips_validation/pull/16)) +- Added handling of the futher_info_url within the context of the controlled vocabulary ([#18](https://github.com/climate-resource/input4mips_validation/pull/18)) -## input4mips-validation v0.5.0 (2024-06-25) +## Input4MIPs validation v0.5.0 (2024-06-25) ### Breaking Changes @@ -439,10 +441,10 @@ of rst and use slightly different categories. The key module is still {py:mod}`input4mips_validation.dataset`. However, we now also have {py:mod}`input4mips_validation.cvs_handling`, which we use for sanely handling the CVs. - This package may be split out into a separate package in future. ([#15](https://github.com/climate-resource/input4mips_validation/pulls/15)) + This package may be split out into a separate package in future. ([#15](https://github.com/climate-resource/input4mips_validation/pull/15)) -## input4mips-validation v0.4.0 (2024-06-20) +## Input4MIPs validation v0.4.0 (2024-06-20) ### Bug Fixes @@ -450,42 +452,42 @@ of rst and use slightly different categories. - * Pinned input4MIPs CVs source files to avoid unexpected breaking changes * Pinned numpy < 2 to fix up install - ([#13](https://github.com/climate-resource/input4mips_validation/pulls/13)) + ([#13](https://github.com/climate-resource/input4mips_validation/pull/13)) -## input4mips-validation v0.3.4 (2024-05-24) +## Input4MIPs validation v0.3.4 (2024-05-24) ### Trivial/Internal Changes -- [#12](https://github.com/climate-resource/input4mips_validation/pulls/12) +- [#12](https://github.com/climate-resource/input4mips_validation/pull/12) -## input4mips-validation v0.3.3 (2024-05-23) +## Input4MIPs validation v0.3.3 (2024-05-23) ### Trivial/Internal Changes -- [#11](https://github.com/climate-resource/input4mips_validation/pulls/11) +- [#11](https://github.com/climate-resource/input4mips_validation/pull/11) -## input4mips-validation v0.3.2 (2024-05-22) +## Input4MIPs validation v0.3.2 (2024-05-22) ### Trivial/Internal Changes -- [#10](https://github.com/climate-resource/input4mips_validation/pulls/10) +- [#10](https://github.com/climate-resource/input4mips_validation/pull/10) -## input4mips-validation v0.3.1 (2024-04-23) +## Input4MIPs validation v0.3.1 (2024-04-23) ### Improvements -- Disabled grid validation while we wait to work out what it means ([#9](https://github.com/climate-resource/input4mips_validation/pulls/9)) +- Disabled grid validation while we wait to work out what it means ([#9](https://github.com/climate-resource/input4mips_validation/pull/9)) -## input4mips-validation v0.3.0 (2024-04-23) +## Input4MIPs validation v0.3.0 (2024-04-23) ### Breaking Changes @@ -494,46 +496,46 @@ of rst and use slightly different categories. This did not change the CLI, but it did include re-arranging a number of internal modules, - hence this is a breaking change. ([#7](https://github.com/climate-resource/input4mips_validation/pulls/7)) + hence this is a breaking change. ([#7](https://github.com/climate-resource/input4mips_validation/pull/7)) ### Features -- Add support for yearly time bounds to {py:func}`input4mips_validation.xarray_helpers.add_time_bounds` ([#6](https://github.com/climate-resource/input4mips_validation/pulls/6)) +- Add support for yearly time bounds to {py:func}`input4mips_validation.xarray_helpers.add_time_bounds` ([#6](https://github.com/climate-resource/input4mips_validation/pull/6)) ### Bug Fixes - Fixed {py:func}`input4mips_validation.controlled_vocabularies.inference.infer_frequency` so it can handle the switch from Julian to Gregorian calendars - (which affects the number of days in October 1582). ([#6](https://github.com/climate-resource/input4mips_validation/pulls/6)) + (which affects the number of days in October 1582). ([#6](https://github.com/climate-resource/input4mips_validation/pull/6)) ### Trivial/Internal Changes -- [#6](https://github.com/climate-resource/input4mips_validation/pulls/6), [#8](https://github.com/climate-resource/input4mips_validation/pulls/8) +- [#6](https://github.com/climate-resource/input4mips_validation/pull/6), [#8](https://github.com/climate-resource/input4mips_validation/pull/8) -## input4mips-validation v0.2.1 (2024-02-15) +## Input4MIPs validation v0.2.1 (2024-02-15) ### Bug Fixes -- Loosened dependencies ([#5](https://github.com/climate-resource/input4mips_validation/pulls/5)) +- Loosened dependencies ([#5](https://github.com/climate-resource/input4mips_validation/pull/5)) -## input4mips-validation v0.2.0 (2024-02-09) +## Input4MIPs validation v0.2.0 (2024-02-09) ### Features - Add structure required to support basic command-line interface. - The command-line interface provides the command `input4mips-validation validate-file`. ([#2](https://github.com/climate-resource/input4mips_validation/pulls/2)) + The command-line interface provides the command `input4mips-validation validate-file`. ([#2](https://github.com/climate-resource/input4mips_validation/pull/2)) ### Bug Fixes -- Added LICENCE to the project ([#3](https://github.com/climate-resource/input4mips_validation/pulls/3)) +- Added LICENCE to the project ([#3](https://github.com/climate-resource/input4mips_validation/pull/3)) -## input4mips-validation v0.1.1 (2024-02-06) +## Input4MIPs validation v0.1.1 (2024-02-06) No significant changes. diff --git a/docs/gen_doc_stubs.py b/docs/gen_doc_stubs.py index 13454f36..53bd1745 100644 --- a/docs/gen_doc_stubs.py +++ b/docs/gen_doc_stubs.py @@ -1,7 +1,8 @@ """ Generate virtual doc files for the mkdocs site. -This script can also be run directly to actually write out those files, as a preview. +This script can also be run directly to actually write out those files, +as a preview. All credit to the creators of: https://oprypin.github.io/mkdocs-gen-files/ @@ -21,15 +22,7 @@ ROOT_DIR = Path("api") PACKAGE_NAME_ROOT = "input4mips_validation" -TITLE_RENAMINGS = { - "cli": "CLI", - "io": "IO", - "cvs": "CVs", - "drs": "DRS", - "upload_ftp": "Upload FTP", - "datasets_to_write_to_disk": "Datasets to write to disk", - "input4mips_validation": "input4mips_validation", -} +nav = mkdocs_gen_files.Nav() @define @@ -56,16 +49,13 @@ def write_subpackage_pages(package: object) -> tuple[PackageInfo, ...]: return tuple(sub_packages) -def get_write_file(package_full_name: str, title: str) -> Path: +def get_write_file(package_full_name: str) -> Path: """Get directory in which to write the doc file""" write_dir = ROOT_DIR for sub_dir in package_full_name.split(".")[:-1]: - if sub_dir in TITLE_RENAMINGS: - write_dir = write_dir / TITLE_RENAMINGS[sub_dir] - else: - write_dir = write_dir / sub_dir + write_dir = write_dir / sub_dir - write_file = write_dir / title / "index.md" + write_file = write_dir / package_full_name.split(".")[-1] / "index.md" return write_file @@ -116,15 +106,15 @@ def write_module_page( sub_packages = None package_name = package_full_name.split(".")[-1] - try: - title = TITLE_RENAMINGS[package_name] - except KeyError: - title = package_name.title() - write_file = get_write_file(package_full_name, title) + write_file = get_write_file(package_full_name) + + nav[package_full_name.split(".")] = write_file.relative_to( + ROOT_DIR / PACKAGE_NAME_ROOT + ).as_posix() with mkdocs_gen_files.open(write_file, "w") as fh: - fh.write(f"# {title}\n") + fh.write(f"# {package_full_name}\n") if sub_packages: fh.write("\n") @@ -143,3 +133,5 @@ def write_module_page( write_module_page(PACKAGE_NAME_ROOT) +with mkdocs_gen_files.open(ROOT_DIR / PACKAGE_NAME_ROOT / "NAVIGATION.md", "w") as fh: + fh.writelines(nav.build_literate_nav()) diff --git a/docs/installation.md b/docs/installation.md index 0ffe72d1..e1ad8b0e 100644 --- a/docs/installation.md +++ b/docs/installation.md @@ -1,15 +1,16 @@ # Installation -There are a few different ways to install input4mips-validation. +There are a few different ways to install Input4MIPs validation. We provide these by use case below. As a short summary, if you: -- just want to use input4mips-validation for validation, +- just want to use Input4MIPs validation for validation, and nothing else, go to [installation as an application][as-an-application] -- want to use input4mips-validation's functionality +- want to use Input4MIPs validation's functionality as a library within another application, go to [installation as a library][as-a-library] -- want to develop input4mips-validation, go to [installation for developers][for-developers] +- want to develop Input4MIPs validation, + go to [installation for developers][for-developers] ## By use case diff --git a/environment-docs.yml b/environment-docs.yml index 6c1548fd..23034219 100644 --- a/environment-docs.yml +++ b/environment-docs.yml @@ -3,113 +3,118 @@ channels: dependencies: - pip=24.0 - blosc=1.21.6=hef167b5_0 -- brotli=1.1.0=hd590300_1 -- brotli-bin=1.1.0=hd590300_1 +- brotli=1.1.0=hb9d3cd8_2 +- brotli-bin=1.1.0=hb9d3cd8_2 - bzip2=1.0.8=h4bc722e_7 - c-ares=1.33.1=heb4867d_0 -- ca-certificates=2024.7.4=hbcca054_0 -- cartopy=0.23.0=py39hfc16268_1 -- certifi=2024.7.4=pyhd8ed1ab_0 -- cf-units=3.2.0=py39hd92a3bb_5 +- ca-certificates=2024.8.30=hbcca054_0 +- cartopy=0.23.0=py39h3b40f6f_2 +- certifi=2024.8.30=pyhd8ed1ab_0 +- cf-units=3.2.0=py39hf3d9206_6 - cfchecker=4.1.0=pyhd8ed1ab_0 -- cftime=1.6.4=py39hd92a3bb_0 +- cftime=1.6.4=py39hf3d9206_1 - cfunits=3.3.7=pyhd8ed1ab_0 - click=8.1.7=unix_pyh707e725_0 - cloudpickle=3.0.0=pyhd8ed1ab_0 -- contourpy=1.2.1=py39h7633fee_0 +- contourpy=1.3.0=py39h74842e3_2 - cycler=0.12.1=pyhd8ed1ab_0 - dask-core=2024.8.0=pyhd8ed1ab_0 -- fonttools=4.53.1=py39hcd6043d_0 +- fonttools=4.54.1=py39h8cd3c5a_0 - freetype=2.12.1=h267a509_2 -- fsspec=2024.6.1=pyhff2d567_0 +- fsspec=2024.9.0=pyhff2d567_0 - future=1.0.0=pyhd8ed1ab_0 -- geos=3.12.2=he02047a_1 +- geos=3.13.0=h5888daf_0 - hdf4=4.2.15=h2a13503_7 - hdf5=1.14.3=nompi_hdf9ad27_105 - icu=75.1=he02047a_0 -- importlib-metadata=8.4.0=pyha770c72_0 -- importlib-resources=6.4.4=pyhd8ed1ab_0 -- importlib_metadata=8.4.0=hd8ed1ab_0 -- importlib_resources=6.4.4=pyhd8ed1ab_0 +- importlib-metadata=8.5.0=pyha770c72_0 +- importlib-resources=6.4.5=pyhd8ed1ab_0 +- importlib_metadata=8.5.0=hd8ed1ab_0 +- importlib_resources=6.4.5=pyhd8ed1ab_0 - iris=3.8.1=pyha770c72_0 - jinja2=3.1.4=pyhd8ed1ab_0 -- kiwisolver=1.4.5=py39h7633fee_1 +- kiwisolver=1.4.7=py39h74842e3_0 - krb5=1.21.3=h659f571_0 - lcms2=2.16=hb7c19ff_0 -- ld_impl_linux-64=2.40=hf3520f5_7 +- ld_impl_linux-64=2.43=h712a8e2_1 - libaec=1.1.3=h59595ed_0 -- libblas=3.9.0=23_linux64_openblas -- libbrotlicommon=1.1.0=hd590300_1 -- libbrotlidec=1.1.0=hd590300_1 -- libbrotlienc=1.1.0=hd590300_1 -- libcblas=3.9.0=23_linux64_openblas -- libcurl=8.9.1=hdb1bdb2_0 +- libblas=3.9.0=24_linux64_openblas +- libbrotlicommon=1.1.0=hb9d3cd8_2 +- libbrotlidec=1.1.0=hb9d3cd8_2 +- libbrotlienc=1.1.0=hb9d3cd8_2 +- libcblas=3.9.0=24_linux64_openblas +- libcurl=8.10.1=hbbe4b11_0 - libdeflate=1.21=h4bc722e_0 - libev=4.33=hd590300_2 -- libexpat=2.6.2=h59595ed_0 -- libgcc-ng=14.1.0=h77fa898_0 -- libgfortran-ng=14.1.0=h69a702a_0 -- libgfortran5=14.1.0=hc5f4f2c_0 -- libgomp=14.1.0=h77fa898_0 +- libexpat=2.6.3=h5888daf_0 +- libgcc=14.1.0=h77fa898_1 +- libgcc-ng=14.1.0=h69a702a_1 +- libgfortran=14.1.0=h69a702a_1 +- libgfortran-ng=14.1.0=h69a702a_1 +- libgfortran5=14.1.0=hc5f4f2c_1 +- libgomp=14.1.0=h77fa898_1 - libiconv=1.17=hd590300_2 - libjpeg-turbo=3.0.0=hd590300_1 -- liblapack=3.9.0=23_linux64_openblas +- liblapack=3.9.0=24_linux64_openblas - libnetcdf=4.9.2=nompi_h135f659_114 - libnghttp2=1.58.0=h47da74e_1 - libnsl=2.0.1=hd590300_0 - libopenblas=0.3.27=pthreads_hac2b453_1 -- libpng=1.6.43=h2797004_0 -- libsqlite=3.46.0=hde9e2c9_0 +- libpng=1.6.44=hadc24fc_0 +- libsqlite=3.46.1=hadc24fc_0 - libssh2=1.11.0=h0841786_0 -- libstdcxx-ng=14.1.0=hc0a3c3a_0 -- libtiff=4.6.0=h46a8edc_4 +- libstdcxx=14.1.0=hc0a3c3a_1 +- libstdcxx-ng=14.1.0=h4852527_1 +- libtiff=4.7.0=h6565414_0 - libudunits2=2.2.28=h40f5838_3 - libuuid=2.38.1=h0b41bf4_0 - libwebp-base=1.4.0=hd590300_0 -- libxcb=1.16=hb9d3cd8_1 +- libxcb=1.17.0=h8a09558_0 - libxcrypt=4.4.36=hd590300_1 - libxml2=2.12.7=he7c6b58_4 -- libzip=1.10.1=h2629f0a_3 +- libzip=1.11.1=hf83b1b0_0 - libzlib=1.3.1=h4ab18f5_1 - lz4-c=1.9.4=hcb278e6_0 -- markupsafe=2.1.5=py39hd1e30aa_0 -- matplotlib-base=3.9.2=py39h0565ad7_0 +- markupsafe=2.1.5=py39h8cd3c5a_1 +- matplotlib-base=3.9.2=py39h16632d1_1 - ncurses=6.5=he02047a_1 -- netcdf4=1.7.1=nompi_py39hec96367_101 +- netcdf4=1.7.1=nompi_py39h9d02bfe_102 - numpy=1.26.4=py39h474f0d3_0 - openjpeg=2.5.2=h488ebb8_0 -- openssl=3.3.1=hb9d3cd8_3 +- openssl=3.3.2=hb9d3cd8_0 - packaging=24.1=pyhd8ed1ab_0 - partd=1.4.2=pyhd8ed1ab_0 -- pillow=10.4.0=py39h16a7006_0 -- proj=9.4.1=h54d7996_1 +- pillow=10.4.0=py39h648eaa6_1 +- proj=9.5.0=h12925eb_0 +- pthread-stubs=0.4=hb9d3cd8_1002 - pyparsing=3.1.4=pyhd8ed1ab_0 -- pyproj=3.6.1=py39hf8c1f24_8 -- python=3.9.19=h0755675_0_cpython +- pyproj=3.6.1=py39h306d449_10 +- python=3.9.20=h13acc7a_1_cpython - python-dateutil=2.9.0=pyhd8ed1ab_0 -- python-xxhash=3.5.0=py39hcd6043d_0 +- python-xxhash=3.5.0=py39h8cd3c5a_1 - python_abi=3.9=5_cp39 -- pyyaml=6.0.2=py39hcd6043d_0 +- pyyaml=6.0.2=py39h8cd3c5a_1 - qhull=2020.2=h434a139_5 - readline=8.2=h8228510_1 - scipy=1.13.1=py39haf93ffa_0 -- setuptools=72.2.0=pyhd8ed1ab_0 -- shapely=2.0.6=py39h1254fa4_0 +- setuptools=75.1.0=pyhd8ed1ab_0 +- shapely=2.0.6=py39hca88cd1_2 - snappy=1.2.1=ha2e4443_0 -- sqlite=3.46.0=h6d4b2fc_0 +- sqlite=3.46.1=h9eae976_0 - tk=8.6.13=noxft_h4845f30_101 - toolz=0.12.1=pyhd8ed1ab_0 -- tzdata=2024a=h0c530f3_0 +- tzdata=2024a=h8827d51_1 - udunits2=2.2.28=h40f5838_3 - unicodedata2=15.1.0=py39hd1e30aa_0 -- xorg-libxau=1.0.11=hd590300_0 +- xorg-libxau=1.0.11=hb9d3cd8_1 +- xorg-libxdmcp=1.1.3=hb9d3cd8_2 - xxhash=0.8.2=hd590300_0 -- zipp=3.20.0=pyhd8ed1ab_0 +- zipp=3.20.2=pyhd8ed1ab_0 - zlib=1.3.1=h4ab18f5_1 - zstd=1.5.6=ha6fb4c9_0 - pip: - alabaster==0.7.16 - - anyio==4.4.0 + - anyio==4.6.0 - appdirs==1.4.4 - argon2_cffi==23.1.0 - argon2_cffi_bindings==21.2.0 @@ -120,29 +125,29 @@ dependencies: - babel==2.16.0 - beautifulsoup4==4.12.3 - bleach==6.1.0 - - cattrs==23.2.3 + - cattrs==24.1.2 - cf_xarray==0.9.4 - - cffi==1.17.0 + - cffi==1.17.1 - charset_normalizer==3.3.2 - colorama==0.4.6 - comm==0.2.2 - - debugpy==1.8.5 + - debugpy==1.8.6 - decorator==5.1.1 - defusedxml==0.7.1 - docutils==0.21.2 - exceptiongroup==1.2.2 - - executing==2.0.1 + - executing==2.1.0 - fastjsonschema==2.20.0 - flexcache==0.3 - flexparser==0.3.1 - fqdn==1.5.1 - ghp_import==2.1.0 - - greenlet==3.0.3 - - griffe==1.2.0 + - greenlet==3.1.1 + - griffe==1.3.1 - h11==0.14.0 - httpcore==1.0.5 - - httpx==0.27.0 - - idna==3.8 + - httpx==0.27.2 + - idna==3.10 - imagesize==1.4.1 - ipykernel==6.29.5 - ipython==8.18.1 @@ -153,13 +158,13 @@ dependencies: - jsonschema==4.23.0 - jsonschema_specifications==2023.12.1 - jupyter_cache==1.0.0 - - jupyter_client==8.6.2 + - jupyter_client==8.6.3 - jupyter_core==5.7.2 - jupyter_events==0.10.0 - jupyter_lsp==2.2.5 - jupyter_server==2.14.2 - jupyter_server_terminals==0.5.3 - - jupyterlab==4.2.4 + - jupyterlab==4.2.5 - jupyterlab_pygments==0.3.0 - jupyterlab_server==2.27.3 - jupytext==1.16.4 @@ -167,22 +172,22 @@ dependencies: - Markdown==3.7 - markdown_it_py==3.0.0 - matplotlib_inline==0.1.7 - - mdit_py_plugins==0.4.1 + - mdit_py_plugins==0.4.2 - mdurl==0.1.2 - mergedeep==1.3.4 - mistune==3.0.2 - - mkdocs==1.6.0 - - mkdocs_autorefs==1.1.0 + - mkdocs==1.6.1 + - mkdocs_autorefs==1.2.0 - mkdocs_gen_files==0.5.0 - mkdocs_get_deps==0.2.0 - - mkdocs_jupyter==0.24.8 + - mkdocs_jupyter==0.25.0 - mkdocs_literate_nav==0.6.1 - - mkdocs_material==9.5.33 + - mkdocs_material==9.5.39 - mkdocs_material_extensions==1.3.1 - mkdocs_section_index==0.3.9 - - mkdocstrings==0.25.2 - - mkdocstrings_python==1.10.8 - - myst_nb==1.1.1 + - mkdocstrings==0.26.1 + - mkdocstrings_python==1.11.1 + - myst_nb==1.1.2 - myst_parser==3.0.1 - nbclient==0.10.0 - nbconvert==7.16.4 @@ -192,33 +197,33 @@ dependencies: - notebook_shim==0.2.4 - overrides==7.7.0 - paginate==0.5.7 - - pandas==2.2.2 + - pandas==2.2.3 - pandocfilters==1.5.1 - parso==0.8.4 - pathspec==0.12.1 - pexpect==4.9.0 - Pint==0.24.3 - pint_xarray==0.4 - - platformdirs==4.2.2 + - platformdirs==4.3.6 - pooch==1.8.2 - - prometheus_client==0.20.0 - - prompt_toolkit==3.0.47 + - prometheus_client==0.21.0 + - prompt_toolkit==3.0.48 - psutil==6.0.0 - ptyprocess==0.7.0 - pure_eval==0.2.3 - pycparser==2.22 - pygments==2.18.0 - - pymdown_extensions==10.9 + - pymdown_extensions==10.11.1 - python_json_logger==2.0.7 - - pytz==2024.1 + - pytz==2024.2 - pyyaml_env_tag==0.1 - pyzmq==26.2.0 - referencing==0.35.1 - - regex==2024.7.24 + - regex==2024.9.11 - requests==2.32.3 - rfc3339_validator==0.1.4 - rfc3986_validator==0.1.1 - - rich==13.7.1 + - rich==13.8.1 - rpds_py==0.20.0 - Send2Trash==1.8.3 - shellingham==1.5.4 @@ -232,7 +237,7 @@ dependencies: - sphinxcontrib_jsmath==1.0.1 - sphinxcontrib_qthelp==2.0.0 - sphinxcontrib_serializinghtml==2.0.0 - - SQLAlchemy==2.0.32 + - SQLAlchemy==2.0.35 - stack_data==0.6.3 - tabulate==0.9.0 - terminado==0.18.1 @@ -242,13 +247,13 @@ dependencies: - tqdm==4.66.5 - traitlets==5.14.3 - typer==0.12.5 - - types_python_dateutil==2.9.0.20240821 + - types_python_dateutil==2.9.0.20240906 - typing_extensions==4.12.2 - - tzdata==2024.1 + - tzdata==2024.2 - uri_template==1.3.0 - - urllib3==2.2.2 - - validators==0.33.0 - - watchdog==4.0.2 + - urllib3==2.2.3 + - validators==0.34.0 + - watchdog==5.0.3 - wcwidth==0.2.13 - webcolors==24.8.0 - webencodings==0.5.1 diff --git a/mkdocs.yml b/mkdocs.yml index f1809f1e..aec3f09d 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -50,72 +50,103 @@ extra_css: - stylesheets/style.css plugins: - # Required for auto-generating our documentation stubs, - # a bit like sphinx autodoc gen used to do + # https://mkdocstrings.github.io/autorefs/ + - autorefs + # Required for auto-generating our documentation stubs + # https://oprypin.github.io/mkdocs-gen-files/ - gen-files: scripts: - docs/gen_doc_stubs.py - - search - - autorefs + # Make the navigation easier to handle/auto-generate if we wish + # https://oprypin.github.io/mkdocs-literate-nav/ + - literate-nav: + nav_file: NAVIGATION.md + # Notebook support. + # Working out how to make this play with nb-exec would be nice, + # then it wouldn't run every time. + # See also: https://github.com/danielfrg/mkdocs-jupyter/issues/161 + # We could also get the nb-exec-table mentioned here: + # https://myst-nb.readthedocs.io/en/v0.12.2/use/execute.html + # One for another day. + - mkdocs-jupyter: + # Use filenames for titles + ignore_h1_titles: True + include: ["*.py"] + execute: true + # Toggle off for faster builds + # execute: false + allow_errors: false + # theme: dark + include_source: True + ignore: ["*.ipynb", "*.md", "docs/gen_doc_stubs.py"] + remove_tag_config: + remove_input_tags: + - remove_input + # Docstring generation - mkdocstrings: enable_inventory: true handlers: python: paths: [src] import: - - https://www.attrs.org/en/latest/objects.inv + # Cross-ref helpers (lots included here, remove what you don't want) + - https://www.attrs.org/en/stable/objects.inv - https://unidata.github.io/cftime/objects.inv - - https://ncdata.readthedocs.io/en/latest/objects.inv - - https://pint.readthedocs.io/en/latest/objects.inv + - https://ipython.readthedocs.io/en/stable/objects.inv + - https://loguru.readthedocs.io/en/latest/objects.inv + - https://matplotlib.org/stable/objects.inv + - https://ncdata.readthedocs.io/en/stable/objects.inv + - https://openscm-units.readthedocs.io/en/stable/objects.inv + - https://pandas.pydata.org/docs/objects.inv + - https://pint.readthedocs.io/en/stable/objects.inv - https://www.fatiando.org/pooch/latest/objects.inv - https://docs.python.org/3/objects.inv - - https://scitools-iris.readthedocs.io/en/latest/objects.inv - - https://validators.readthedocs.io/en/latest/objects.inv - - http://xarray.pydata.org/en/latest/objects.inv + - https://docs.scipy.org/doc/scipy/objects.inv + - https://scitools-iris.readthedocs.io/en/stable/objects.inv + - https://scmdata.readthedocs.io/en/stable/objects.inv + - https://validators.readthedocs.io/en/stable/objects.inv + - http://xarray.pydata.org/en/stable/objects.inv options: docstring_style: numpy show_root_heading: true show_source: true - # # Make the nav recursive - - literate-nav - # nav_file: SUMMARY.md + # https://squidfunk.github.io/mkdocs-material/plugins/search/ + - search # https://oprypin.github.io/mkdocs-section-index/ - # This won't work properly until we write a nav file too, job for another day - section-index - # Working out how to make this play with nb-exec would be nice, - # then it wouldn't run every time. - # We could also get the nb-exec-table mentioned here: - # https://myst-nb.readthedocs.io/en/v0.12.2/use/execute.html - # One for another day. - - mkdocs-jupyter: - execute: true - # execute: false - allow_errors: false - # theme: dark - include_source: True - ignore: ["*.ipynb", "docs/gen_doc_stubs.py"] - remove_tag_config: - remove_input_tags: - - remove_input markdown_extensions: + # https://squidfunk.github.io/mkdocs-material/setup/extensions/python-markdown/#attribute-lists - attr_list + # Allow admonitions, useful for deprecation warnings + # https://facelessuser.github.io/pymdown-extensions/extensions/blocks/plugins/admonition/ - pymdownx.blocks.admonition # Code highlighting handiness + # https://facelessuser.github.io/pymdown-extensions/extensions/highlight/ - pymdownx.highlight: anchor_linenums: true line_spans: __span pygments_lang_class: true + # https://facelessuser.github.io/pymdown-extensions/extensions/inlinehilite/ - pymdownx.inlinehilite + # Enable the use of snippets (e.g. taking snippets from README and putting them in docs) + # https://facelessuser.github.io/pymdown-extensions/extensions/snippets/ - pymdownx.snippets + # Support more complicated indents etc. + 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python >=3.8 license: MIT license_family: MIT purls: - - pkg:pypi/zipp?source=conda-forge-mapping - size: 20857 - timestamp: 1723591347715 + - pkg:pypi/zipp?source=hash-mapping + size: 21409 + timestamp: 1726248679175 - kind: conda name: zlib version: 1.3.1 diff --git a/pyproject.toml b/pyproject.toml index 80bfcf4d..95a072f8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -44,6 +44,10 @@ dev = [ "pandas-stubs>=2.2.2.240603", "tomli>=2.0.1", "types-tqdm>=4.66.0.20240417", + "liccheck>=0.9.2,<0.10", + # Required for liccheck + "setuptools>=70.0.0", + "pip>=24.2", ] docs = [ "mkdocs>=1.6.0", @@ -262,13 +266,13 @@ package = "input4mips_validation" package_dir = "src" filename = "docs/changelog.md" directory = "changelog/" -title_format = "## input4mips-validation {version} ({project_date})" +title_format = "## Input4MIPs validation {version} ({project_date})" underlines = [ "", "", "", ] -issue_format = "[#{issue}](https://github.com/climate-resource/input4mips_validation/pulls/{issue})" +issue_format = "[#{issue}](https://github.com/climate-resource/input4mips_validation/pull/{issue})" type = [ { directory = "breaking", name = "⚠️ Breaking Changes", showcontent = true }, { directory = "deprecation", name = "🗑️ Deprecations", showcontent = true }, diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 77ce7d98..00000000 --- a/requirements.txt +++ /dev/null @@ -1,75 +0,0 @@ -# This file is @generated by PDM. -# Please do not edit it manually. - -antlr4-python3-runtime==4.7.2 -appdirs==1.4.4 -attrs==24.2.0 -cartopy==0.23.0 -cattrs==24.1.0 -certifi==2024.7.4 -cf-units==3.2.0 -cf-xarray==0.9.4 -cfchecker==4.1.0 -cftime==1.6.4 -cfunits==3.3.7 -charset-normalizer==3.3.2 -click==8.1.7 -cloudpickle==3.0.0 -colorama==0.4.6 -contourpy==1.3.0 -cycler==0.12.1 -dask==2024.8.0 -dask[array]==2024.8.0 -exceptiongroup==1.2.2; python_version < "3.11" -flexcache==0.3 -flexparser==0.3.1 -fonttools==4.53.1 -fsspec==2024.6.1 -future==1.0.0 -idna==3.8 -importlib-metadata==8.4.0 -importlib-resources==6.4.4; python_version < "3.10" -jinja2==3.1.4 -kiwisolver==1.4.5 -locket==1.0.0 -loguru==0.7.2 -markdown-it-py==3.0.0 -markupsafe==2.1.5 -matplotlib==3.9.2 -mdurl==0.1.2 -ncdata==0.1.1 -netcdf4==1.7.1.post2 -numpy==1.26.4 -packaging==24.1 -pandas==2.2.2 -partd==1.4.2 -pillow==10.4.0 -pint==0.24.3 -pint-xarray==0.4 -platformdirs==4.2.2 -pooch==1.8.2 -pygments==2.18.0 -pyparsing==3.1.4 -pyproj==3.6.1 -pyshp==2.3.1 -python-dateutil==2.9.0.post0 -pytz==2024.1 -pyyaml==6.0.2 -requests==2.32.3 -rich==13.8.0 -scipy==1.13.1 -scitools-iris==3.8.1 -shapely==2.0.6 -shellingham==1.5.4 -six==1.16.0 -toolz==0.12.1 -tqdm==4.66.5 -typer==0.12.5 -typing-extensions==4.12.2 -tzdata==2024.1 -urllib3==2.2.2 -validators==0.33.0 -win32-setctime==1.1.0; sys_platform == "win32" -xarray==2024.7.0 -xxhash==3.5.0 -zipp==3.20.1 diff --git a/scripts/changelog-to-release-template.py b/scripts/changelog-to-release-template.py index efc0292e..002892c6 100644 --- a/scripts/changelog-to-release-template.py +++ b/scripts/changelog-to-release-template.py @@ -33,14 +33,14 @@ def main() -> None: continue if not grab_notes: - if line.startswith("## input4mips-validation"): + if line.startswith("## Input4MIPs validation"): grab_notes = True continue # We are grabbing notes now # If we've reached the next version's notes, break - if line.startswith("## input4mips-validation"): + if line.startswith("## Input4MIPs validation"): break latest_version_notes.append(line) diff --git a/tests/integration/cvs/test_cv_loading_raw_integration.py b/tests/integration/cvs/test_cv_loading_raw_integration.py index af8c58e0..564244e0 100644 --- a/tests/integration/cvs/test_cv_loading_raw_integration.py +++ b/tests/integration/cvs/test_cv_loading_raw_integration.py @@ -133,9 +133,9 @@ def test_get_raw_cvs_loader(input4mips_cv_source, force_download, exp): } if force_download is not None: - environ_patches[ - "INPUT4MIPS_VALIDATION_CV_SOURCE_force_download_DOWNLOAD" - ] = str(force_download) + environ_patches["INPUT4MIPS_VALIDATION_CV_SOURCE_FORCE_DOWNLOAD"] = str( + force_download + ) with patch.dict(os.environ, environ_patches): res = get_raw_cvs_loader() diff --git a/tests/integration/test_cli_integration.py b/tests/integration/test_cli_integration.py new file mode 100644 index 00000000..2279ff56 --- /dev/null +++ b/tests/integration/test_cli_integration.py @@ -0,0 +1,21 @@ +""" +Integration tests of the CLI +""" + +from __future__ import annotations + +from typer.testing import CliRunner + +import input4mips_validation +from input4mips_validation.cli import app + +runner = CliRunner() + + +def test_version(): + result = runner.invoke(app, ["--version"]) + + assert result.exit_code == 0, result.exc_info + assert ( + result.stdout == f"input4mips-validation {input4mips_validation.__version__}\n" + ) From b9d1bbef537701f3c201bc4623cac942282845bd Mon Sep 17 00:00:00 2001 From: Zebedee Nicholls Date: Tue, 1 Oct 2024 14:25:03 +0200 Subject: [PATCH 2/8] CHANGELOG --- changelog/72.trivial.md | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 changelog/72.trivial.md diff --git a/changelog/72.trivial.md b/changelog/72.trivial.md new file mode 100644 index 00000000..2bde7c6f --- /dev/null +++ b/changelog/72.trivial.md @@ -0,0 +1,9 @@ +Updated a number of internal set up bits and pieces, e.g.: + +- removing the mention of poetry from the bug issue template +- updating the CI workflows +- using an environment for deploying to PyPI +- updating the `Makefile` +- updating the docs to use a `NAVIGATION.md` file with literate-nav +- fixing all the pull request links in the CHANGELOG in the docs +- simplifying the auto-generated docs From 5f51885c78d3b9e8e9232d0af4456243acb44365 Mon Sep 17 00:00:00 2001 From: Zebedee Nicholls Date: Tue, 1 Oct 2024 14:25:09 +0200 Subject: [PATCH 3/8] Fix up workflow --- .github/workflows/ci.yaml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index a0f10a55..1e80d71b 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -33,10 +33,6 @@ jobs: run: | pixi run --frozen -e docs typer input4mips_validation.cli utils docs --output docs/cli/index.md --name input4mips-validation pixi run --frozen -e docs mkdocs build --strict - - uses: ./.github/actions/setup - with: - python-version: "3.11" - pdm-dependency-install-flags: "-G docs -G :all -G dev" - uses: ./.github/actions/setup with: pixi-environments: "all-dev" From 88ccc23c67c50b51de716f7bb2c7a78883f9ac85 Mon Sep 17 00:00:00 2001 From: Zebedee Nicholls Date: Tue, 1 Oct 2024 14:27:03 +0200 Subject: [PATCH 4/8] Fix up workflow again --- .github/workflows/ci.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 1e80d71b..421331d7 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -18,7 +18,7 @@ jobs: pixi-environments: "all-dev" - name: mypy run: | - MYPYPATH=stubs pixi run --frozen -e all-dev run mypy src + MYPYPATH=stubs pixi run --frozen -e all-dev mypy src docs: if: ${{ !github.event.pull_request.draft }} @@ -120,7 +120,6 @@ jobs: uses: actions/checkout@v4 - name: Check locked install uses: prefix-dev/setup-pixi@v0.8.1 - - uses: ./.github/actions/setup with: locked: true From e66baeb8ecc964ee4dbf460bca7e100c33000d08 Mon Sep 17 00:00:00 2001 From: Zebedee Nicholls Date: Tue, 1 Oct 2024 14:27:44 +0200 Subject: [PATCH 5/8] Fix up pre-commit config --- .pre-commit-config.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index e3f0db5b..e6938241 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -8,7 +8,6 @@ ci: skip: [ pixi-install, environment-docs, - pdm-export, pdm-lock-check, auto-generated-classes, ] From 46dd243d7dfaf0e8cdf1ca73300a1030f0ae00d9 Mon Sep 17 00:00:00 2001 From: Zebedee Nicholls Date: Tue, 1 Oct 2024 14:28:11 +0200 Subject: [PATCH 6/8] Update docs navigation --- docs/NAVIGATION.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/docs/NAVIGATION.md b/docs/NAVIGATION.md index e9644f15..21f17118 100644 --- a/docs/NAVIGATION.md +++ b/docs/NAVIGATION.md @@ -6,8 +6,6 @@ See https://oprypin.github.io/mkdocs-literate-nav/ - [Home](index.md) - [Installation](installation.md) - [How-to guides](how-to-guides/index.md) - - [Do a basic calculation](how-to-guides/basic-calculation.md) - - [Run code in a notebook](how-to-guides/run-code-in-a-notebook.py) - [How to write a single valid file](how-to-guides/how-to-write-a-single-valid-file.py) - [How validate a single file](how-to-guides/how-to-validate-a-single-file.py) - [How to write a single file in the DRS](how-to-guides/how-to-write-a-single-file-in-the-drs.py) From 31ee2af8ebfac1d6f032332e5ef8b6b6200f530e Mon Sep 17 00:00:00 2001 From: Zebedee Nicholls Date: Tue, 1 Oct 2024 16:23:35 +0200 Subject: [PATCH 7/8] Fix up docs --- docs/NAVIGATION.md | 2 +- docs/how-to-guides/index.md | 4 ++-- docs/index.md | 2 +- .../cli/common_arguments_and_options.py | 6 +++--- src/input4mips_validation/cvs/loading_raw.py | 2 +- src/input4mips_validation/logging.py | 2 +- 6 files changed, 9 insertions(+), 9 deletions(-) diff --git a/docs/NAVIGATION.md b/docs/NAVIGATION.md index 21f17118..94d55acb 100644 --- a/docs/NAVIGATION.md +++ b/docs/NAVIGATION.md @@ -12,7 +12,7 @@ See https://oprypin.github.io/mkdocs-literate-nav/ - [How to upload to an FTP server](how-to-guides/how-to-upload-to-ftp.py) - [How to manage a database of file entries](how-to-guides/how-to-manage-a-database.py) - [Tutorials](tutorials.md) -- [Further background](further-background/explanation.md) +- [Further background](explanation.md) - [Development](development.md) - [Command-line interface](cli/index.md) - [API reference](api/input4mips_validation/) diff --git a/docs/how-to-guides/index.md b/docs/how-to-guides/index.md index 8d00395a..ca45fcc2 100644 --- a/docs/how-to-guides/index.md +++ b/docs/how-to-guides/index.md @@ -63,11 +63,11 @@ As a result, here we provide a guide to configuring logging with input4MIPs vali We hope that, one day in the future, such a guide won't be needed because logging will be done in a consistent way across the Python ecosystem. -If you are using our [command-line interface][input4mips-validation-cli], +If you are using our [command-line interface](cli), you can specify every aspect of the logging, i.e. you have full control. Before you dive into this though, we provide much simpler options for basic logging control. -These are documented in [the command-line interface's docs][input4mips-validation-cli]. +These are documented in [the command-line interface's docs](cli). With that mentioned, back to complete logging control. Below is a sample `.yaml` logging configuration file. diff --git a/docs/index.md b/docs/index.md index 3a19b830..bd1570a5 100644 --- a/docs/index.md +++ b/docs/index.md @@ -8,5 +8,5 @@ Some other potential points of interest: - Installation instructions: [Installation][installation] - (How-to guides, just in case you missed it the first time: [How-to...][how-to-guides]) -- The command-line interface's documentation: [CLI][cli] +- The command-line interface's documentation: [CLI](cli) - The full API docs: [API reference][input4mips_validation] diff --git a/src/input4mips_validation/cli/common_arguments_and_options.py b/src/input4mips_validation/cli/common_arguments_and_options.py index afcc5679..cdcaf820 100644 --- a/src/input4mips_validation/cli/common_arguments_and_options.py +++ b/src/input4mips_validation/cli/common_arguments_and_options.py @@ -36,17 +36,17 @@ help=( "String identifying the source of the CVs. " "If not supplied, this is retrieved from the environment variable " - "``INPUT4MIPS_VALIDATION_CV_SOURCE``. " + "`INPUT4MIPS_VALIDATION_CV_SOURCE`. " "" "If this environment variable is also not set, " - "we raise a ``NotImplementedError``. " + "we raise a `NotImplementedError`. " "" "If this starts with 'gh:', we retrieve the data from PCMD's GitHub, " "using everything after the colon as the ID for the Git object to use " "(where the ID can be a branch name, a tag or a commit ID). " "" "Otherwise we simply return the path as provided and use the " - "[validators][https://validators.readthedocs.io/en/stable] " + "[validators](https://validators.readthedocs.io/en/stable) " "package to decide if the source points to a URL or not " "(i.e. whether we should look for the CVs locally " "or retrieve them from a URL)." diff --git a/src/input4mips_validation/cvs/loading_raw.py b/src/input4mips_validation/cvs/loading_raw.py index 11606ef2..133b29f0 100644 --- a/src/input4mips_validation/cvs/loading_raw.py +++ b/src/input4mips_validation/cvs/loading_raw.py @@ -239,7 +239,7 @@ def get_raw_cvs_loader( (where the ID can be a branch name, a tag or a commit ID). Otherwise we simply return the path as provided - and use the [validators][https://validators.readthedocs.io/en/stable] + and use the [validators](https://validators.readthedocs.io/en/stable) package to decide if the source points to a URL or not. force_download diff --git a/src/input4mips_validation/logging.py b/src/input4mips_validation/logging.py index 2580e390..25135fc4 100644 --- a/src/input4mips_validation/logging.py +++ b/src/input4mips_validation/logging.py @@ -142,7 +142,7 @@ def setup_logging( If a `dict`, passed to :meth:`loguru.logger.configure`. If not passed, :const:`DEFAULT_LOGGING_CONFIG` is used. Otherwise, we try and load this from disk using - [`loguru_config.LoguruConfig`][https://github.com/erezinman/loguru-config]. + [`loguru_config.LoguruConfig`](https://github.com/erezinman/loguru-config). This takes precedence over `log_level`. From 438671874eca15ebe78667604207e7f99dac2c3b Mon Sep 17 00:00:00 2001 From: Zebedee Nicholls Date: Tue, 1 Oct 2024 16:28:16 +0200 Subject: [PATCH 8/8] Fix up docs workflow --- .github/workflows/ci.yaml | 3 --- 1 file changed, 3 deletions(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 421331d7..0459d42e 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -33,9 +33,6 @@ jobs: run: | pixi run --frozen -e docs typer input4mips_validation.cli utils docs --output docs/cli/index.md --name input4mips-validation pixi run --frozen -e docs mkdocs build --strict - - uses: ./.github/actions/setup - with: - pixi-environments: "all-dev" - name: docs-with-changelog run: | # Check CHANGELOG will build too