Drop setuptools, use flit (#519)

### What kind of change does this PR introduce? * Drops `setuptools` build backend for `flit`. * Moves the `requirements_upstream.txt` file to CI folder. * Removes the obsolete `Manifest.in`. ### Does this PR introduce a breaking change? Yes. `setuptools` is no longer used to build the package. Build requirements are much simpler. ### Other information: [`flit`](https://flit.pypa.io/en/stable/) is the backend used by the cookiecutter and most Ouranos projects. It is much simpler in its configuration and design. We don't compile `xscen` nor do we manage dependencies using lock files (like `poetry` does).
Ouranosinc · Feb 6, 2025 · e5223b6 · e5223b6
2 parents fc049a2 + c9f9f36
commit e5223b6
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diff --git a/.cruft.json b/.cruft.json
@@ -1,6 +1,6 @@
 {
   "template": "https://github.com/Ouranosinc/cookiecutter-pypackage",
-  "commit": "36ea29394390254407194bd37315d9e3e9238585",
+  "commit": "2b31b0f76a180ad93e5a49fe5744306fefb48c9c",
   "checkout": null,
   "context": {
     "cookiecutter": {
@@ -24,7 +24,7 @@
       "generated_with_cruft": "y",
       "__gh_slug": "https://github.com/Ouranosinc/xscen",
       "_template": "https://github.com/Ouranosinc/cookiecutter-pypackage",
-      "_commit": "36ea29394390254407194bd37315d9e3e9238585"
+      "_commit": "2b31b0f76a180ad93e5a49fe5744306fefb48c9c"
     }
   },
   "directory": null

diff --git a/.github/workflows/bump-version.yml b/.github/workflows/bump-version.yml
@@ -47,7 +47,7 @@ jobs:
       actions: read
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@c95a14d0e5bab51a9f56296a4eb0e416910cd350 # v2.10.3
+        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
         with:
           disable-sudo: true
           egress-policy: block
@@ -68,7 +68,7 @@ jobs:
           token: ${{ steps.token_generator.outputs.token }}
           persist-credentials: false
       - name: Set up Python3
-        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5.3.0
+        uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5.4.0
         with:
           python-version: "3.x"
       - name: Import GPG Key

diff --git a/.github/workflows/cache-cleaner.yml b/.github/workflows/cache-cleaner.yml
@@ -16,7 +16,7 @@ jobs:
       actions: write
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@c95a14d0e5bab51a9f56296a4eb0e416910cd350 # v2.10.3
+        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
         with:
           disable-sudo: true
           egress-policy: block

diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml
@@ -53,7 +53,7 @@ jobs:
         # your codebase is analyzed, see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/codeql-code-scanning-for-compiled-languages
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@c95a14d0e5bab51a9f56296a4eb0e416910cd350 # v2.10.3
+        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
         with:
           disable-sudo: true
           egress-policy: audit

diff --git a/.github/workflows/dependency-review.yml b/.github/workflows/dependency-review.yml
@@ -17,7 +17,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@c95a14d0e5bab51a9f56296a4eb0e416910cd350 # v2.10.3
+        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
         with:
           disable-sudo: true
           egress-policy: block

diff --git a/.github/workflows/first-pull-request.yml b/.github/workflows/first-pull-request.yml
@@ -16,7 +16,7 @@ jobs:
       pull-requests: write
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@c95a14d0e5bab51a9f56296a4eb0e416910cd350 # v2.10.3
+        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
         with:
           disable-sudo: true
           egress-policy: block

diff --git a/.github/workflows/label.yml b/.github/workflows/label.yml
@@ -22,7 +22,7 @@ jobs:
       pull-requests: write
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@c95a14d0e5bab51a9f56296a4eb0e416910cd350 # v2.10.3
+        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
         with:
           disable-sudo: true
           egress-policy: block

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -30,7 +30,7 @@ jobs:
           - "3.x"
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@c95a14d0e5bab51a9f56296a4eb0e416910cd350 # v2.10.3
+        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
         with:
           disable-sudo: true
           egress-policy: block
@@ -43,13 +43,19 @@ jobs:
         with:
           persist-credentials: false
       - name: Setup Python${{ matrix.python-version }}
-        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5.3.0
+        uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5.4.0
         with:
           python-version: ${{ matrix.python-version }}
           cache: pip
       - name: Install CI libraries
         run: |
           python -m pip install --require-hashes -r CI/requirements_ci.txt
+      - name: Environment Caching
+        uses: actions/cache@1bd1e32a3bdc45362d1e726936510720a7c30a57 # v4.2.0
+        with:
+          path: |
+            .tox
+          key: ${{ hashFiles('pyproject.toml', 'tox.ini') }}-lint
       - name: Run linting suite
         run: |
           python -m tox -e lint
@@ -72,7 +78,7 @@ jobs:
         shell: bash -l {0}
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@c95a14d0e5bab51a9f56296a4eb0e416910cd350 # v2.10.3
+        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
         with:
           egress-policy: audit
       - name: Checkout Repository
@@ -83,12 +89,13 @@ jobs:
         uses: mamba-org/setup-micromamba@0dea6379afdaffa5d528b3d1dabc45da37f443fc # v2.0.4
         with:
           cache-downloads: true
+          cache-environment: true
           environment-name: xscen-pypi
           create-args: >-
             esmf=${{ env.esmf-version }}
             python=${{ matrix.python-version }}
-            tox>=4.17.1
-            tox-gh>=1.3.2
+            tox>=4.24.1
+            tox-gh>=1.5.0
       - name: Environment Caching
         uses: actions/cache@1bd1e32a3bdc45362d1e726936510720a7c30a57 # v4.2.0
         with:
@@ -141,7 +148,7 @@ jobs:
         shell: bash -l {0}
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@c95a14d0e5bab51a9f56296a4eb0e416910cd350 # v2.10.3
+        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
         with:
           egress-policy: audit
       - name: Checkout Repository
@@ -152,7 +159,7 @@ jobs:
         uses: mamba-org/setup-micromamba@0dea6379afdaffa5d528b3d1dabc45da37f443fc # v2.0.4
         with:
           cache-downloads: true
-          cache-environment: false  # FIXME: No environment caching until issues with micromamba 2.0.0 are resolved.
+          cache-environment: true
           environment-file: environment-dev.yml
           create-args: >-
             python=${{ matrix.python-version }}
@@ -183,7 +190,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@c95a14d0e5bab51a9f56296a4eb0e416910cd350 # v2.10.3
+        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
         with:
           disable-sudo: true
           egress-policy: audit

diff --git a/.github/workflows/publish-pypi.yml b/.github/workflows/publish-pypi.yml
@@ -18,7 +18,7 @@ jobs:
       id-token: write
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@c95a14d0e5bab51a9f56296a4eb0e416910cd350 # v2.10.3
+        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
         with:
           disable-sudo: true
           egress-policy: block
@@ -34,7 +34,7 @@ jobs:
         with:
           persist-credentials: false
       - name: Set up Python3
-        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5.3.0
+        uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5.4.0
         with:
           python-version: "3.x"
       - name: Install CI libraries
@@ -44,4 +44,4 @@ jobs:
         run: |
           python -m build --sdist --wheel
       - name: Publish distribution 📦 to PyPI
-        uses: pypa/gh-action-pypi-publish@67339c736fd9354cd4f8cb0b744f2b82a74b5c70 # v1.12.3
+        uses: pypa/gh-action-pypi-publish@76f52bc884231f62b9a034ebfe128415bbaabdfc # v1.12.4
diff --git a/.github/workflows/scorecard.yml b/.github/workflows/scorecard.yml
@@ -31,7 +31,7 @@ jobs:
       id-token: write
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@c95a14d0e5bab51a9f56296a4eb0e416910cd350 # v2.10.3
+        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
         with:
           disable-sudo: true
           egress-policy: block

diff --git a/.github/workflows/tag-testpypi.yml b/.github/workflows/tag-testpypi.yml
@@ -17,7 +17,7 @@ jobs:
       contents: write
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@c95a14d0e5bab51a9f56296a4eb0e416910cd350 # v2.10.3
+        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
         with:
           disable-sudo: true
           egress-policy: block
@@ -48,7 +48,7 @@ jobs:
       id-token: write
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@c95a14d0e5bab51a9f56296a4eb0e416910cd350 # v2.10.3
+        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
         with:
           disable-sudo: true
           egress-policy: audit
@@ -64,7 +64,7 @@ jobs:
         with:
           persist-credentials: false
       - name: Set up Python3
-        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5.3.0
+        uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5.4.0
         with:
           python-version: "3.x"
       - name: Install CI libraries
@@ -74,7 +74,7 @@ jobs:
         run: |
           python -m build --sdist --wheel
       - name: Publish distribution 📦 to Test PyPI
-        uses: pypa/gh-action-pypi-publish@67339c736fd9354cd4f8cb0b744f2b82a74b5c70 # v1.12.3
+        uses: pypa/gh-action-pypi-publish@76f52bc884231f62b9a034ebfe128415bbaabdfc # v1.12.4
         with:
           repository-url: https://test.pypi.org/legacy/
           skip-existing: true
diff --git a/.github/workflows/upstream.yml b/.github/workflows/upstream.yml
@@ -40,7 +40,7 @@ jobs:
         shell: bash -l {0}
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@c95a14d0e5bab51a9f56296a4eb0e416910cd350 # v2.10.3
+        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
         with:
           egress-policy: audit
       - name: Checkout Repository

diff --git a/.github/workflows/workflow-warning.yml b/.github/workflows/workflow-warning.yml
@@ -25,7 +25,7 @@ jobs:
       pull-requests: write
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@c95a14d0e5bab51a9f56296a4eb0e416910cd350 # v2.10.3
+        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
         with:
           disable-sudo: true
           egress-policy: block

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -21,31 +21,39 @@ repos:
       - id: check-toml
       - id: check-yaml
         args: [ '--allow-multiple-documents' ]
+  - repo: https://github.com/pappasam/toml-sort
+    rev: v0.24.2
+    hooks:
+      - id: toml-sort-fix
+  - repo: https://github.com/adrienverge/yamllint.git
+    rev: v1.35.1
+    hooks:
+      - id: yamllint
+        args: [ '--config-file=.yamllint.yaml' ]
   - repo: https://github.com/pre-commit/pygrep-hooks
     rev: v1.10.0
     hooks:
       - id: python-check-blanket-noqa
+      - id: python-check-blanket-type-ignore
       - id: python-no-eval
         exclude: biasadjust.py
       - id: python-no-log-warn
       - id: python-use-type-annotations
+      - id: rst-directive-colons
       - id: rst-inline-touching-normal
-  - repo: https://github.com/pappasam/toml-sort
-    rev: v0.24.2
-    hooks:
-      - id: toml-sort-fix
+      - id: text-unicode-replacement-char
   - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 24.10.0
+    rev: 25.1.0
     hooks:
       - id: black
         exclude: ^docs/
   - repo: https://github.com/pycqa/isort
-    rev: 5.13.2
+    rev: 6.0.0
     hooks:
       - id: isort
         exclude: ^docs/
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.6
+    rev: v0.9.0
     hooks:
       - id: ruff
         args: [ '--fix', '--show-fixes' ]
@@ -68,14 +76,15 @@ repos:
     rev: v0.3.9
     hooks:
       - id: blackdoc
-        additional_dependencies: [ 'black==24.10.0' ]
+        additional_dependencies: [ 'black==25.1.0' ]
         exclude: config.py
       - id: blackdoc-autoupdate-black
-  - repo: https://github.com/adrienverge/yamllint.git
-    rev: v1.35.1
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.3.0
     hooks:
-      - id: yamllint
-        args: [ '--config-file=.yamllint.yaml' ]
+      - id: codespell
+        additional_dependencies: [ 'tomli' ]
+        args: [ '--toml=pyproject.toml' ]
 #  - repo: https://github.com/numpy/numpydoc
 #    rev: v1.8.0
 #    hooks:
@@ -86,12 +95,12 @@ repos:
     hooks:
       - id: nbqa-pyupgrade
         args: [ '--py310-plus' ]
-        additional_dependencies: [ 'pyupgrade==3.17.0' ]
+        additional_dependencies: [ 'pyupgrade==3.19.1' ]
       - id: nbqa-black
         args: [ '--target-version=py310' ]
-        additional_dependencies: [ 'black==24.10.0' ]
+        additional_dependencies: [ 'black==25.1.0' ]
       - id: nbqa-isort
-        additional_dependencies: [ 'isort==5.13.2' ]
+        additional_dependencies: [ 'isort==6.0.0' ]
   - repo: https://github.com/kynan/nbstripout
     rev: 0.8.1
     hooks:

diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -5,9 +5,9 @@ sphinx:
   fail_on_warning: true
 
 build:
-  os: ubuntu-22.04
+  os: "ubuntu-24.04"
   tools:
-    python: "mambaforge-22.9"
+    python: "mambaforge-23.11"
   jobs:
     post_create_environment:
       - make translate

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -2,6 +2,25 @@
 Changelog
 =========
 
+v0.12.0 (unreleased)
+--------------------
+Contributors to this version: Trevor James Smith (:user:`Zeitsperre`).
+
+Breaking changes
+^^^^^^^^^^^^^^^^
+* `xscen` now uses `flit` as its build-engine and no longer uses `setuptools`, `setuptools-scm`, or `wheel`. (:pull:`519`).
+
+Bug fixes
+^^^^^^^^^
+* Docstrings and documentation have been updated to remove several small grammatical errors. (:pull:`527`).
+
+Internal changes
+^^^^^^^^^^^^^^^^
+* Updated the cookiecutter template to the latest commit. (:pull:`527`):
+    * Updated versions of many GitHub Actions and Python dependencies.
+    * Removed `coveralls` from the CI dependencies.
+    * Added `pre-commit` hooks for `vulture` (dead code) and `codespell` (typos).
+
 v0.11.0 (2025-01-23)
 --------------------
 Contributors to this version: Gabriel Rondeau-Genesse (:user:`RondeauG`), Juliette Lavoie (:user:`juliettelavoie`), Trevor James Smith (:user:`Zeitsperre`).
@@ -433,7 +452,7 @@ New features and enhancements
 * New 'cos-lat' averaging in `spatial_mean`. (:issue:`94`, :pull:`125`).
 * Support for computing anomalies in `compute_deltas`.  (:pull:`165`).
 * Add function `diagnostics.measures_improvement_2d`. (:pull:`167`).
-* Add function ``regrid.create_bounds_rotated_pole`` and automatic use in ``regrid_dataset`` and ``spatial_mean``. This is temporary, while we wait for a functionning method in ``cf_xarray``. (:pull:`174`, :issue:`96`).
+* Add function ``regrid.create_bounds_rotated_pole`` and automatic use in ``regrid_dataset`` and ``spatial_mean``. This is temporary, while we wait for a functioning method in ``cf_xarray``. (:pull:`174`, :issue:`96`).
 * Add ``spatial`` submodule with functions ``creep_weights`` and ``creep_fill`` for filling NaNs using neighbours. (:pull:`174`).
 * Allow passing ``GeoDataFrame`` instances in ``spatial_mean``'s ``region`` argument, not only geospatial file paths. (:pull:`174`).
 * Allow searching for periods in `catalog.search`. (:issue:`123`, :pull:`170`).
@@ -549,7 +568,7 @@ New features and enhancements
 * In extract_dataset, add option ``ensure_correct_time`` to ensure the time coordinate matches the expected freq. Ex: monthly values given on the 15th day are moved to the 1st, as expected when asking for "MS". (:issue: `53`).
 * In regrid_dataset: (:pull:`68`).
     * Allow passing skipna to the regridder kwargs.
-    * Do not fail for any grid mapping problem, includin if a grid_mapping attribute mentions a variable that doesn't exist.
+    * Do not fail for any grid mapping problem, including if a grid_mapping attribute mentions a variable that doesn't exist.
 * Default email sent to the local user. (:pull:`68`).
 * Special accelerated pathway for parsing catalogs with all dates within the datetime64[ns] range. (:pull:`75`).
 * New functions ``reduce_ensemble`` and ``build_reduction_data`` to support kkz and kmeans clustering. (:issue:`4`, :pull:`63`).