Update cookiecutter, restructure library (#126)

### What kind of change does this PR introduce? * Updates the cookiecutter to the latest commit. * The `ruff` linter has been adjusted to render the `flake8-alphabetize` dependency redundant (and removed). * Several `noqa` and `fixme` statements have been added to pass additional linting checks for now. ### Does this PR introduce a breaking change? Yes. * The structure of the package is slightly modified from a flat layout to a src layout. (https://packaging.python.org/en/latest/discussions/src-layout-vs-flat-layout/) * `CHANGES.rst` is now `CHANGELOG.rst`. (https://keepachangelog.com/en/1.1.0/#frequently-asked-questions) * Bumping a release version will trigger changes in the `CHANGELOG.rst` file. (Ouranosinc/cookiecutter-pypackage#41) ### Other information: ~This does not yet integrate changes from Ouranosinc/cookiecutter-pypackage#50 (but it should before merging)~ We should perform a release after this and then see about proposing the package to `conda-forge`!
hydrologie · Jul 4, 2024 · 3d46287 · 3d46287
2 parents a7d276b + c5cfe0d
commit 3d46287
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diff --git a/.cruft.json b/.cruft.json
@@ -1,12 +1,12 @@
 {
   "template": "https://github.com/Ouranosinc/cookiecutter-pypackage",
-  "commit": "f391bbd6ee14ab2478c64a1f78b74bd9903cae81",
+  "commit": "3b3598ae9524e7eb495bcba91093fac3369e753a",
   "checkout": null,
   "context": {
     "cookiecutter": {
       "full_name": "Sebastien Langlois",
       "email": "[email protected]",
-      "github_username": "sebastienlanglois",
+      "github_username": "hydrologie",
       "project_name": "xdatasets",
       "project_slug": "xdatasets",
       "project_short_description": "Easy access to Earth observation datasets with xarray.",
@@ -22,6 +22,7 @@
       "create_author_file": "y",
       "open_source_license": "MIT license",
       "generated_with_cruft": "y",
+      "__gh_slug": "https://github.com/hydrologie/xdatasets",
       "_template": "https://github.com/Ouranosinc/cookiecutter-pypackage"
     }
   },

diff --git a/.flake8 b/.flake8
@@ -6,9 +6,6 @@ exclude =
 	docs,
 	tests
 ignore =
-	AZ100,
-	AZ200,
-	AZ300,
 	C,
 	D,
 	E,

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -5,7 +5,7 @@
   - This PR fixes #xyz
 - [ ] (If applicable) Documentation has been added / updated (for bug fixes / features).
 - [ ] (If applicable) Tests have been added.
-- [ ] CHANGES.rst has been updated (with summary of main changes).
+- [ ] CHANGELOG.rst has been updated (with summary of main changes).
   - [ ] Link to issue (:issue:`number`) and pull request (:pull:`number`) has been added.
 
 ### What kind of change does this PR introduce?

diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -1,15 +1,13 @@
 version: 2
 updates:
   - package-ecosystem: github-actions
-    directory: /
+    directory: /.github/workflows/
     schedule:
-      interval: daily
-      time: '12:00'
+      interval: monthly
     open-pull-requests-limit: 10
 
   - package-ecosystem: pip
     directory: /
     schedule:
-      interval: daily
-      time: '12:00'
+      interval: monthly
     open-pull-requests-limit: 10
diff --git a/.github/workflows/bump-version.yml b/.github/workflows/bump-version.yml
@@ -19,7 +19,7 @@ on:
       - .pre-commit-config.yaml
       - .yamllint.yaml
       - AUTHORS.rst
-      - CHANGES.rst
+      - CHANGELOG.rst
       - CONTRIBUTING.rst
       - docs/notebooks/**.ipynb
       - docs/*.py
@@ -51,10 +51,13 @@ jobs:
             files.pythonhosted.org:443
             github.com:443
             pypi.org:443
-      - uses: actions/[email protected]
+      - name: Checkout Repository (no persist-credentials)
+        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
         with:
           persist-credentials: false
-      - uses: actions/[email protected]
+          fetch-depth: 0
+      - name: Set up Python3
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5.1.0
         with:
           python-version: "3.x"
       - name: Config Commit Bot
@@ -68,7 +71,7 @@ jobs:
       - name: Current Version
         run: |
           bump-my-version show current_version
-          CURRENT_VERSION="$(grep -E '__version__' xdatasets/__init__.py | cut -d ' ' -f3)"
+          CURRENT_VERSION="$(grep -E '__version__' src/xdatasets/__init__.py | cut -d ' ' -f3)"
           echo "CURRENT_VERSION=${CURRENT_VERSION}" >> $GITHUB_ENV
       - name: Conditional Bump Version
         run: |
@@ -81,7 +84,7 @@ jobs:
           fi
           bump-my-version show-bump
       - name: Push Changes
-        uses: ad-m/[email protected]
+        uses: ad-m/github-push-action@d91a481090679876dfc4178fef17f286781251df # v0.8.0
         with:
           force: false
           github_token: ${{ secrets.BUMP_VERSION_TOKEN }}

diff --git a/.github/workflows/cache-cleaner.yml b/.github/workflows/cache-cleaner.yml
@@ -25,7 +25,8 @@ jobs:
             github.com:443
             objects.githubusercontent.com:443
 
-      - uses: actions/[email protected]
+      - name: Checkout Repository
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4.1.4
 
       - name: Cleanup
         run: |

diff --git a/.github/workflows/dependency-review.yml b/.github/workflows/dependency-review.yml
@@ -25,8 +25,8 @@ jobs:
             api.github.com:443
             github.com:443
 
-      - name: 'Checkout Repository'
+      - name: Checkout Repository
         uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
 
-      - name: 'Dependency Review'
-        uses: actions/dependency-review-action@0659a74c94536054bfa5aeb92241f70d680cc78e
+      - name: Dependency Review
+        uses: actions/dependency-review-action@0c155c5e8556a497adf53f2c18edabf945ed8e70 # v4.3.2
diff --git a/.github/workflows/first-pull-request.yml b/.github/workflows/first-pull-request.yml
@@ -24,7 +24,8 @@ jobs:
           allowed-endpoints: >
             api.github.com:443
 
-      - uses: actions/[email protected]
+      - name: Verify Pull Request Opener
+        uses: actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea # v7.0.1
         with:
           script: |
             // Get a list of all issues created by the PR opener

diff --git a/.github/workflows/label.yml b/.github/workflows/label.yml
@@ -32,6 +32,7 @@ jobs:
           allowed-endpoints: >
             api.github.com:443
 
-      - uses: actions/[email protected]
+      - name: Label Pull Request
+        uses: actions/labeler@8558fd74291d67161a8a78ce36a881fa63b766a9 # v5.0.0
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -6,7 +6,7 @@ on:
       - main
     paths-ignore:
       - .cruft.json
-      - CHANGES.rst
+      - CHANGELOG.rst
       - README.rst
       - pyproject.toml
       - tests/test_xdatasets.py
@@ -30,9 +30,14 @@ jobs:
         python-version:
           - "3.x"
     steps:
-      - uses: actions/[email protected]
+      - name: Harden Runner
+        uses: step-security/harden-runner@a4aa98b93cab29d9b1101a6143fb8bce00e2eac4 # v2.7.1
+        with:
+          egress-policy: audit
+      - name: Checkout Repository
+        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
       - name: Set up Python${{ matrix.python-version }}
-        uses: actions/[email protected]
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5.1.0
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install tox
@@ -62,7 +67,12 @@ jobs:
           - tox-env: "py312"
             python-version: "3.12"
     steps:
-      - uses: actions/[email protected]
+      - name: Harden Runner
+        uses: step-security/harden-runner@17d0e2bd7d51742c71671bd19fa12bdc9d40a3d6 # v2.8.1
+        with:
+          egress-policy: audit
+      - name: Checkout Repository
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4.1.4
       - name: Install NetCDF
         run: |
           sudo apt-get -y update
@@ -75,7 +85,7 @@ jobs:
           cache: true
           version: ${{ env.ESMF_VERSION }}
       - name: Set up Python${{ matrix.python-version }}
-        uses: actions/[email protected]
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5.1.0
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install tox
@@ -102,9 +112,14 @@ jobs:
       run:
         shell: bash -l {0}
     steps:
-      - uses: actions/[email protected]
+      - name: Harden Runner
+        uses: step-security/harden-runner@17d0e2bd7d51742c71671bd19fa12bdc9d40a3d6 # v2.8.1
+        with:
+          egress-policy: audit
+      - name: Checkout Repository
+        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
       - name: Setup Conda (Micromamba) with Python${{ matrix.python-version }}
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@422500192359a097648154e8db4e39bdb6c6eed7 # v1.8.1
         with:
           cache-downloads: true
           environment-file: environment-dev.yml
@@ -123,7 +138,7 @@ jobs:
       - name: Test with pytest
         run: |
           python -m pytest --cov xdatasets
-      - name: Report coverage
+      - name: Report Coverage
         run: |
           python -m pip install coveralls
           python -m coveralls
@@ -140,10 +155,6 @@ jobs:
     runs-on: ubuntu-latest
     container: python:3-slim
     steps:
-      - name: Harden Runner
-        uses: step-security/harden-runner@17d0e2bd7d51742c71671bd19fa12bdc9d40a3d6 # v2.8.1
-        with:
-          egress-policy: audit
       - name: Coveralls Finished
         run: |
           python -m pip install --upgrade coveralls

diff --git a/.github/workflows/publish-pypi.yml b/.github/workflows/publish-pypi.yml
@@ -27,9 +27,10 @@ jobs:
             github.com:443
             pypi.org:443
             upload.pypi.org:443
-      - uses: actions/[email protected]
+      - name: Checkout Repository
+        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
       - name: Set up Python3
-        uses: actions/[email protected]
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5.1.0
         with:
           python-version: "3.x"
       - name: Install packaging libraries
@@ -39,4 +40,4 @@ jobs:
         run: |
           python -m flit build
       - name: Publish distribution 📦 to PyPI
-        uses: pypa/[email protected]
+        uses: pypa/gh-action-pypi-publish@ec4db0b4ddc65acdf4bff5fa45ac92d78b56bdf0 # v1.9.0
diff --git a/.github/workflows/scorecard.yml b/.github/workflows/scorecard.yml
@@ -46,12 +46,13 @@ jobs:
             tuf-repo-cdn.sigstore.dev:443
             www.bestpractices.dev:443
 
-      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332
+      - name: Checkout Repository
+        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
         with:
           persist-credentials: false
 
-      - name: Run analysis
-        uses: ossf/scorecard-action@dc50aa9510b46c811795eb24b2f1ba02a914e534
+      - name: Run Analysis
+        uses: ossf/scorecard-action@dc50aa9510b46c811795eb24b2f1ba02a914e534 # v2.3.3
         with:
           results_file: results.sarif
           results_format: sarif
@@ -70,8 +71,8 @@ jobs:
 
       # Upload the results as artifacts (optional). Commenting out will disable uploads of run results in SARIF
       # format to the repository Actions tab.
-      - name: Upload artifact
-        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808
+      - name: Upload Artifact
+        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4.3.3
         with:
           name: SARIF file
           path: results.sarif

diff --git a/.github/workflows/tag-testpypi.yml b/.github/workflows/tag-testpypi.yml
@@ -20,10 +20,10 @@ jobs:
         uses: step-security/harden-runner@17d0e2bd7d51742c71671bd19fa12bdc9d40a3d6 # v2.8.1
         with:
           egress-policy: audit
-      - name: Checkout code
-        uses: actions/[email protected]
+      - name: Checkout Repository
+        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
       - name: Create Release
-        uses: softprops/action-gh-release@v2
+        uses: softprops/action-gh-release@69320dbe05506a9a39fc8ae11030b214ec2d1f87 # 2.0.5
         env:
           # This token is provided by Actions, you do not need to create your own token
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -51,9 +51,10 @@ jobs:
             github.com:443
             pypi.org:443
             test.pypi.org:443
-      - uses: actions/[email protected]
+      - name: Checkout Repository
+        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
       - name: Set up Python3
-        uses: actions/[email protected]
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5.1.0
         with:
           python-version: "3.x"
       - name: Install packaging libraries
@@ -63,7 +64,7 @@ jobs:
         run: |
           python -m flit build
       - name: Publish distribution 📦 to Test PyPI
-        uses: pypa/[email protected]
+        uses: pypa/gh-action-pypi-publish@ec4db0b4ddc65acdf4bff5fa45ac92d78b56bdf0 # v1.9.0
         with:
           repository-url: https://test.pypi.org/legacy/
           skip-existing: true
diff --git a/.github/workflows/workflow-warning.yml b/.github/workflows/workflow-warning.yml
@@ -32,15 +32,15 @@ jobs:
           egress-policy: block
           allowed-endpoints: >
             api.github.com:443
-      - name: Find comment
+      - name: Find Comment
         uses: peter-evans/find-comment@3eae4d37986fb5a8592848f6a574fdf654e61f9e # v3.1.0
         id: fc
         with:
           issue-number: ${{ github.event.pull_request.number }}
           comment-author: 'github-actions[bot]'
           body-includes: |
             This Pull Request modifies GitHub workflows and is coming from a fork.
-      - name: Create comment
+      - name: Create Comment
         if: |
           (steps.fc.outputs.comment-id == '') &&
           (!contains(github.event.pull_request.labels.*.name, 'approved')) &&
@@ -54,7 +54,7 @@ jobs:
             > This Pull Request modifies GitHub Workflows and is coming from a fork.
             **It is very important for the reviewer to ensure that the workflow changes are appropriate.**
           edit-mode: replace
-      - name: Update comment
+      - name: Update Comment
         if: |
           contains(github.event.pull_request.labels.*.name, 'approved')
         uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4.0.0

diff --git a/.gitignore b/.gitignore
@@ -100,6 +100,9 @@ target/
 # Jupyter Notebook
 .ipynb_checkpoints
 
+# Dask worker cache
+dask-worker-space/
+
 # IPython
 profile_default/
 ipython_config.py

diff --git a/.nojekyll b/.nojekyll
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -44,11 +44,13 @@ repos:
     rev: v0.5.0
     hooks:
       - id: ruff
+        args: [ '--fix' ]
+      # - id: ruff-format
   - repo: https://github.com/pycqa/flake8
     rev: 7.1.0
     hooks:
       - id: flake8
-        additional_dependencies: [ 'flake8-alphabetize', 'flake8-rst-docstrings' ]
+        additional_dependencies: [ 'flake8-rst-docstrings' ]
         args: ['--config=.flake8']
   - repo: https://github.com/nbQA-dev/nbQA
     rev: 1.8.5
@@ -64,7 +66,7 @@ repos:
     rev: v0.3.9
     hooks:
       - id: blackdoc
-        additional_dependencies: [ 'black==24.4.0' ]
+        additional_dependencies: [ 'black==24.4.2' ]
   - repo: https://github.com/kynan/nbstripout
     rev: 0.7.1
     hooks:
@@ -94,6 +96,6 @@ ci:
     autofix_prs: true
     autoupdate_branch: ''
     autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
-    autoupdate_schedule: quarterly
+    autoupdate_schedule: monthly
     skip: []
     submodules: false
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -16,7 +16,7 @@ build:
     python: "mambaforge-22.9"
   jobs:
     pre_build:
-      - sphinx-apidoc -o docs/apidoc --private --module-first xdatasets
+      - sphinx-apidoc -o docs/apidoc --private --module-first src/xdatasets
 #      - sphinx-build -M gettext docs docs/_build
 
 conda:
-Original file line number
+Diff line change
@@ Expand Up / @@ -6,9 +6,6 @@ exclude = @@
     	docs,
     	tests
     ignore =
-    	AZ100,
-    	AZ200,
-    	AZ300,
     	C,
     	D,
     	E,
@@ Expand Down @@