fast-forward cookiecutter, add mamba workaround

.cruft.json

@@ -1,6 +1,6 @@
 {
   "template": "https://github.com/Ouranosinc/cookiecutter-pypackage",
-  "commit": "b9dc57245a77dd3c465a444d4943884ee92157ea",
+  "commit": "1d9ee5f08d3e8e4f78a4aabb75e2ce4eff8750bf",
   "checkout": null,
   "context": {
     "cookiecutter": {

.github/dependabot.yml

@@ -1,13 +1,25 @@
+# Please see the documentation for all configuration options:
+# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
 version: 2
 updates:
   - package-ecosystem: github-actions
-    directory: /.github/workflows/
+    directory: /.github/workflows
     schedule:
       interval: monthly
-    open-pull-requests-limit: 10
+    groups:
+      actions:
+        patterns:
+          - "*"
 
   - package-ecosystem: pip
     directory: /
     schedule:
       interval: monthly
-    open-pull-requests-limit: 10
+    groups:
+      ci:
+        patterns:
+          - "CI/*"
+      python:
+        patterns:
+          - "pyproject.toml"

.github/workflows/main.yml

@@ -40,6 +40,7 @@ jobs:
         uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
         with:
           python-version: ${{ matrix.python-version }}
+          cache: "pip"
       - name: Install CI libraries
         run: |
           python -m pip install --require-hashes -r CI/requirements_ci.txt
@@ -48,16 +49,18 @@ jobs:
           python -m tox -e lint
 
   test-pypi:
-    name: Test with Python${{ matrix.python-version }} (tox)
+    name: Test with Python${{ matrix.python-version }} (tox, ${{ matrix.os }})
     needs: lint
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
     strategy:
       matrix:
+        os: [ 'ubuntu-latest' ]
         python-version:
           - "3.9"
           - "3.10"
           - "3.11"
           - "3.12"
+#          - "3.13"
     steps:
       - name: Harden Runner
         uses: step-security/harden-runner@5c7944e73c4c2a096b17a9cb74d65b6c2bbafbde # v2.9.1
@@ -69,13 +72,19 @@ jobs:
         uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
         with:
           python-version: ${{ matrix.python-version }}
+          cache: "pip"
       - name: Install GDAL
         run: |
           sudo apt-get update
           sudo apt-get install -y libgdal-dev
       - name: Install CI libraries
         run: |
           python -m pip install --require-hashes -r CI/requirements_ci.txt
+      - name: Environment Caching
+        uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4.0.2
+        with:
+          path: .tox
+          key: ${{ matrix.os }}-Python${{ matrix.python-version }}-${{ hashFiles('pyproject.toml', 'tox.ini') }}
       - name: Test with tox
         run: tox
         env:
@@ -85,11 +94,12 @@ jobs:
           COVERALLS_SERVICE_NAME: github
 
   test-conda:
-    name: Test with Python${{ matrix.python-version }} (Anaconda)
+    name: Test with Python${{ matrix.python-version }} (Anaconda, ${{ matrix.os }})
     needs: lint
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
     strategy:
       matrix:
+        os: [ 'ubuntu-latest' ]
         python-version:
           - "3.9"
           - "3.12"
@@ -110,6 +120,7 @@ jobs:
           environment-file: environment-dev.yml
           create-args: >-
             python=${{ matrix.python-version }}
+          micromamba-version: "1.5.10-0"  # pinned to avoid the breaking changes with mamba and micromamba (2.0.0).
       - name: Micromamba version
         run: |
           echo "micromamba $(micromamba --version)"
@@ -137,19 +148,13 @@ jobs:
       - test-pypi
       - test-conda
     runs-on: ubuntu-latest
-    container: python:3-slim
     steps:
-      - name: Checkout Repository
-        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
+      - name: Harden Runner
+        uses: step-security/harden-runner@5c7944e73c4c2a096b17a9cb74d65b6c2bbafbde # v2.9.1
         with:
-          sparse-checkout: |
-            CI/requirements_ci.txt
-      - name: Install CI libraries
-        run: |
-          python -m pip install --require-hashes -r CI/requirements_ci.txt
-      - name: Coveralls finished
-        run: |
-          python -m coveralls --finish
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          COVERALLS_SERVICE_NAME: github
+          disable-sudo: true
+          egress-policy: audit
+      - name: Coveralls Finished
+        uses: coverallsapp/github-action@643bc377ffa44ace6394b2b5d0d3950076de9f63 # v2.3.0
+        with:
+          parallel-finished: true

.pre-commit-config.yaml

@@ -59,7 +59,8 @@ repos:
     rev: v0.3.9
     hooks:
       - id: blackdoc
-        additional_dependencies: [ 'black==24.4.2' ]
+        additional_dependencies: [ 'black==24.8.0' ]
+      - id: blackdoc-autoupdate-black
   - repo: https://github.com/kynan/nbstripout
     rev: 0.7.1
     hooks:

docs/conf.py

@@ -67,10 +67,8 @@
 templates_path = ["_templates"]
 
 # The suffix(es) of source filenames.
-# You can specify multiple suffix as a list of string:
-#
-# source_suffix = ['.rst', '.md']
-source_suffix = [".rst"]
+# You can specify multiple suffix as a dictionary of suffix: filetype
+source_suffix = {'.rst': 'restructuredtext'}
 
 # The master toctree document.
 master_doc = "index"

pyproject.toml

@@ -30,6 +30,7 @@ classifiers = [
   "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
+  # "Programming Language :: Python :: 3.13",
   "Programming Language :: Python :: Implementation :: CPython"
 ]
 dynamic = ["description", "version"]
@@ -53,13 +54,13 @@ dependencies = [
 dev = [
   # Dev tools and testing
   "pip >=24.2.0",
-  "bump-my-version >=0.25.1",
+  "bump-my-version >=0.26.0",
   "watchdog >=4.0.0",
   "flake8 >=7.1.0",
   "flake8-alphabetize >=0.0.21",
   "flake8-rst-docstrings >=0.3.0",
   "flit >=3.9.0,<4.0",
-  "tox >=4.17.1",
+  "tox >=4.18.0",
   "coverage >=7.5.0",
   "coveralls >=4.0.1",
   "mypy",
@@ -107,7 +108,8 @@ target-version = [
   "py39",
   "py310",
   "py311",
-  "py312"
+  "py312",
+  "py313"
 ]
 
 [tool.bumpversion]
@@ -228,7 +230,7 @@ py_version = 39
 
 [tool.mypy]
 files = "."
-python_version = 3.9
+python_version = 3.8
 show_error_codes = true
 strict = true
 warn_no_return = true

tox.ini

@@ -1,8 +1,8 @@
 [tox]
-min_version = 4.17.1
+min_version = 4.18.0
 envlist =
     lint
-    py{39,310,311,312}
+    py{39,310,311,312,313}
     docs
     coveralls
 requires =
@@ -17,6 +17,7 @@ python =
     3.10 = py310-coveralls
     3.11 = py311-coveralls
     3.12 = py312-coveralls
+    3.13 = py313-coveralls
 
 [testenv:lint]
 skip_install = True