Adopt pyproject.toml standard, fast-forward cookiecutter

.cruft.json

@@ -1,6 +1,6 @@
 {
   "template": "https://github.com/Ouranosinc/cookiecutter-pypackage",
-  "commit": "240a2c784f89cb1e2c5952869413c5582e590345",
+  "commit": "844fb9600b45d5d51d6e88dfdc4acdf88aa09bac",
   "checkout": null,
   "context": {
     "cookiecutter": {
@@ -9,11 +9,12 @@
       "github_username": "TC-FF",
       "project_name": "xHydro",
       "project_slug": "xhydro",
-      "project_short_description": "Hydrological analysis library built with xarray",
+      "project_short_description": "Hydrological analysis library built with xarray.",
       "pypi_username": "TC-FF",
       "version": "0.2.4",
       "use_pytest": "y",
       "use_black": "y",
+      "use_conda": "y",
       "add_pyup_badge": "n",
       "make_docs": "y",
       "command_line_interface": "No command-line interface",

.flake8

@@ -0,0 +1,30 @@
+[flake8]
+exclude =
+	.eggs,
+	.git,
+	build,
+	docs,
+	tests
+ignore =
+	AZ100,
+	AZ200,
+	AZ300,
+	C,
+	D,
+	E,
+	F,
+	W503
+per-file-ignores =
+rst-roles =
+	doc,
+	mod,
+	py:attr,
+	py:attribute,
+	py:class,
+	py:const,
+	py:data,
+	py:func,
+	py:meth,
+	py:mod,
+	py:obj,
+	py:ref

.github/workflows/actions-versions-updater.yml

@@ -0,0 +1,24 @@
+name: GitHub Actions Version Updater
+
+on:
+  schedule:
+    # 12:00 AM on the first of every month
+    - cron:  '0 0 1 * *'
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4.1.1
+        with:
+          # This requires a personal access token with the privileges to push directly to `main`
+          token: ${{ secrets.WORKFLOW_TOKEN }}
+          persist-credentials: true
+      - name: Run GitHub Actions Version Updater
+        uses: saadmk11/github-actions-version-updater@v0.8.1
+        with:
+          token: ${{ secrets.WORKFLOW_TOKEN }}
+          committer_email: 'bumpversion[bot]@ouranos.ca'
+          committer_username: 'update-github-actions[bot]'
+          pull_request_title: '[bot] Update GitHub Action Versions'

.github/workflows/bump-version.yml

@@ -49,9 +49,9 @@ jobs:
         run: echo "current_version=$(grep -E '__version__'  xhydro/__init__.py | cut -d ' ' -f3)"
       - name: Bump Patch Version
         run: |
-          pip install bump2version
+          pip install bump-my-version
           echo "Bumping version"
-          bump2version patch
+          bump-my-version bump --tag patch
           echo "new_version=$(grep -E '__version__'  xhydro/__init__.py | cut -d ' ' -f3)"
       - name: Push Changes
         uses: ad-m/github-push-action@master

.github/workflows/main.yml

@@ -5,100 +5,92 @@ on:
     branches:
       - main
     paths-ignore:
-      - HISTORY.rst
-      - MANIFEST.in
+      - CHANGES.rst
       - README.rst
       - setup.cfg
-      - setup.py
+      - pyproject.toml
       - xhydro/__init__.py
   pull_request:
 
 jobs:
-  black:
-    name: Black (Python${{ matrix.python-version }})
+  lint:
+    name: Lint (Python${{ matrix.python-version }})
     runs-on: ubuntu-latest
     strategy:
       matrix:
         python-version:
-          - "3.9"
+          - "3.x"
     steps:
       - name: Cancel previous runs
         uses: styfle/cancel-workflow-action@0.11.0
         with:
           access_token: ${{ secrets.GITHUB_TOKEN }}
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python${{ matrix.python-version }}
         uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install tox
-        run: pip install tox
+        run: |
+          python -m pip install tox
       - name: Run linting suite
-        run: tox -e black
+        run: |
+          python -m tox -e lint
 
-  test:
-    name: Test with Python${{ matrix.python-version }}
-    needs: black
+  test-conda:
+    name: Test with Python${{ matrix.python-version }} (Anaconda)
+    needs: lint
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        include:
-          - python-version: "3.9"
-#            tox-build: "py39"
-          - python-version: "3.10"
-#            tox-build: "py310"
-          - python-version: "3.11"
-#            tox-build: "py311"
+        python-version: ["3.9", "3.10", "3.11"]
     defaults:
       run:
         shell: bash -l {0}
     steps:
-      - uses: actions/checkout@v3
-      - name: Setup Conda (Micromamba) with Python ${{ matrix.python-version }}
+      - uses: actions/checkout@v4
+      - name: Setup Conda (Micromamba) with Python${{ matrix.python-version }}
         uses: mamba-org/setup-micromamba@v1
         with:
           cache-downloads: true
-          environment-file: environment.yml
+          environment-file: environment-dev.yml
           create-args: >-
-            coveralls
             mamba
             python=${{ matrix.python-version }}
-            pytest
-            pytest-cov
       - name: Conda and Mamba versions
         run: |
           mamba --version
           echo "micromamba $(micromamba --version)"
       - name: Install xhydro
         run: |
-          pip install --editable .
+          python -m pip install --no-deps .
       - name: Check versions
         run: |
           conda list
-          pip check || true
+          python -m pip check || true
       - name: Test with pytest
         run: |
-          pytest --cov xhydro
+          python -m pytest --cov xhydro
       - name: Report coverage
         run: |
-          coveralls
+          python -m coveralls
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          COVERALLS_FLAG_NAME: run-Python${{ matrix.python-version }}
+          COVERALLS_FLAG_NAME: run-Python${{ matrix.python-version }}-conda
           COVERALLS_PARALLEL: true
           COVERALLS_SERVICE_NAME: github
 
   finish:
     needs:
-      - test
+      - test-conda
     runs-on: ubuntu-latest
     container: python:3-slim
     steps:
       - name: Coveralls Finished
         run: |
-          pip install --upgrade coveralls
-          coveralls --finish
+          python -m pip install --upgrade coveralls
+          python -m coveralls --finish
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           COVERALLS_SERVICE_NAME: github

.github/workflows/publish-pypi.yml

@@ -8,9 +8,10 @@ on:
 jobs:
   build-n-publish-pypi:
     name: Build and publish Python 🐍 distributions 📦 to PyPI
-    environment: production
     runs-on: ubuntu-latest
+    environment: production
     permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
       id-token: write
     steps:
       - uses: actions/checkout@v4
@@ -20,9 +21,9 @@ jobs:
           python-version: "3.9"
       - name: Install packaging libraries
         run: |
-          pip install setuptools wheel
+          python -m pip install flit
       - name: Build a binary wheel and a source tarball
         run: |
-          python setup.py sdist bdist_wheel
+          python -m flit build
       - name: Publish distribution 📦 to PyPI
         uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/tag-testpypi.yml

@@ -3,14 +3,33 @@ name: Publish Python 🐍 distributions 📦 to TestPyPI
 on:
   push:
     tags:
-      - 'v*.*.*'
+      - 'v*.*' # Push events to matching v*, i.e. v1.0, v20.15.10
 
 jobs:
-  build-n-publish-testpypi:
+  release:
+    name: Create Release from tag
+    runs-on: ubuntu-latest
+    if: startsWith(github.ref, 'refs/tags/v') && endsWith(github.ref, '.0')
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+      - name: Create Release
+        uses: softprops/action-gh-release@v1
+        env:
+          # This token is provided by Actions, you do not need to create your own token
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          tag_name: ${{ github.ref }}
+          name: Release ${{ github.ref }}
+          draft: true
+          prerelease: false
+
+  deploy-testpypi:
     name: Build and publish Python 🐍 distributions 📦 to TestPyPI
-    environment: staging
     runs-on: ubuntu-latest
+    environment: staging
     permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
       id-token: write
     steps:
       - uses: actions/checkout@v4
@@ -20,10 +39,10 @@ jobs:
           python-version: "3.9"
       - name: Install packaging libraries
         run: |
-          pip install setuptools wheel
+          python -m pip install flit
       - name: Build a binary wheel and a source tarball
         run: |
-          python setup.py sdist bdist_wheel
+          python -m flit build
       - name: Publish distribution 📦 to Test PyPI
         uses: pypa/gh-action-pypi-publish@release/v1
         with:

.pre-commit-config.yaml

@@ -11,15 +11,19 @@ repos:
     rev: v4.5.0
     hooks:
       - id: trailing-whitespace
-        exclude: setup.cfg
       - id: end-of-file-fixer
       - id: debug-statements
       - id: check-json
+      - id: check-toml
       - id: pretty-format-json
         args: [ '--autofix', '--no-ensure-ascii', '--no-sort-keys' ]
         # exclude: .ipynb
       - id: check-yaml
         args: [ '--allow-multiple-documents' ]
+  - repo: https://github.com/pappasam/toml-sort
+    rev: v0.23.1
+    hooks:
+      - id: toml-sort-fix
   - repo: https://github.com/pre-commit/pygrep-hooks
     rev: v1.10.0
     hooks:
@@ -28,39 +32,31 @@ repos:
     rev: 23.11.0
     hooks:
       - id: black
-        args: [ '--target-version=py39' ]
-        exclude: ^docs/
-  - repo: https://github.com/pycqa/flake8
-    rev: 6.1.0
-    hooks:
-      - id: flake8
-        additional_dependencies: [ 'flake8-rst-docstrings' ]
-        args: ['--config=setup.cfg']
   - repo: https://github.com/PyCQA/isort
     rev: 5.12.0
     hooks:
       - id: isort
-        args: ['--settings-file=setup.cfg']
         exclude: ^docs/
-  - repo: https://github.com/PyCQA/pydocstyle
-    rev: 6.3.0
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.4
     hooks:
-      - id: pydocstyle
-        args: [ '--config=setup.cfg' ]
+      - id: ruff
+  - repo: https://github.com/pycqa/flake8
+    rev: 6.0.0
+    hooks:
+      - id: flake8
+        additional_dependencies: [ 'flake8-alphabetize', 'flake8-rst-docstrings' ]
+        args: [ '--config=.flake8' ]
   - repo: https://github.com/keewis/blackdoc
     rev: v0.3.9
     hooks:
       - id: blackdoc
-        additional_dependencies: [ 'black==23.10.1' ]
+        additional_dependencies: [ 'black==23.11.0' ]
   - repo: https://github.com/adrienverge/yamllint.git
     rev: v1.33.0
     hooks:
       - id: yamllint
         args: ['--config-file', '.yamllint.yaml']
-  - repo: https://github.com/mgedmin/check-manifest
-    rev: "0.49"
-    hooks:
-      - id: check-manifest
   - repo: https://github.com/python-jsonschema/check-jsonschema
     rev: 0.27.1
     hooks:

.readthedocs.yml

@@ -16,6 +16,8 @@ build:
     python: "mambaforge-22.9"
   jobs:
     post_create_environment:
+      # FIXME: this is a workaround for xdatasets until the `xagg-no-xesmf-deps` issue is addressed
+      - pip install xdatasets
       - pip install . --no-deps
     pre_build:
       - sphinx-apidoc -o docs/apidoc --private --module-first xhydro