Merge pull request #25 from Ouranosinc/modernize

Modernize library
Ouranosinc · Sep 18, 2024 · d6d46ef · d6d46ef
2 parents 8046090 + b80d3c4
commit d6d46ef
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Showing 25 changed files with 318 additions and 3,116 deletions.
diff --git a/.flake8 b/.flake8
@@ -0,0 +1,13 @@
+[flake8]
+exclude =
+	.eggs,
+	.git,
+	build,
+	docs,
+	tests
+ignore =
+	C,
+	D,
+	E,
+	F,
+	W503
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -9,8 +9,16 @@ updates:
     directory: /
     schedule:
       interval: monthly
+    groups:
+      actions:
+        patterns:
+          - "*"
 
   - package-ecosystem: pip
     directory: /
     schedule:
       interval: monthly
+    groups:
+      python:
+        patterns:
+          - "*"
diff --git a/.github/workflows/cache-cleaner.yml b/.github/workflows/cache-cleaner.yml
@@ -0,0 +1,50 @@
+# Example taken from https://docs.github.com/en/actions/using-workflows/caching-dependencies-to-speed-up-workflows#managing-caches
+name: Cleanup Caches on Pull Request Merge
+on:
+  pull_request:
+    types:
+      - closed
+
+permissions:  # added using https://github.com/step-security/secure-repo
+  contents: read
+
+jobs:
+  cleanup:
+    name: Cleanup
+    runs-on: ubuntu-latest
+    permissions:
+      actions: write
+    steps:
+      - name: Harden Runner
+        uses: step-security/harden-runner@5c7944e73c4c2a096b17a9cb74d65b6c2bbafbde # v2.9.1
+        with:
+          disable-sudo: true
+          egress-policy: block
+          allowed-endpoints: >
+            api.github.com:443
+            github.com:443
+            objects.githubusercontent.com:443
+
+      - name: Checkout Repository
+        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
+
+      - name: Cleanup
+        run: |
+          gh extension install actions/gh-actions-cache
+
+          REPO=${{ github.repository }}
+          BRANCH="refs/pull/${{ github.event.pull_request.number }}/merge"
+
+          echo "Fetching list of cache key"
+          cacheKeysForPR=$(gh actions-cache list -R $REPO -B $BRANCH -L 100 | cut -f 1 )
+
+          ## Setting this to not fail the workflow while deleting cache keys.
+          set +e
+          echo "Deleting caches..."
+          for cacheKey in $cacheKeysForPR
+          do
+              gh actions-cache delete $cacheKey -R $REPO -B $BRANCH --confirm
+          done
+          echo "Done"
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -9,7 +9,7 @@ on:
       - README.rst
       - setup.cfg
       - setup.py
-      - lmoments3/__init__.py
+      - src/lmoments3/__init__.py
   pull_request:
 
 concurrency:
@@ -18,7 +18,8 @@ concurrency:
   cancel-in-progress: ${{ github.ref != 'refs/heads/main' }}
 
 jobs:
-  black:
+  lint:
+    name: Linting Suite
     runs-on: ubuntu-latest
     steps:
       - name: Harden Runner
@@ -28,24 +29,21 @@ jobs:
           egress-policy: audit
       - name: Checkout Repository
         uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
-      - name: Set up Python${{ matrix.python-version }}
+      - name: Set up Python3
         uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
         with:
-          python-version: "3.8"
-      - name: Install black
-        run: |
-          pip install black>=24.8.0
-      - name: Run linting suite
-        run: |
-          black --check lmoments3
+          python-version: "3.x"
+          cache: "pip"
+      - name: Run pre-commit hooks
+        uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1
 
   test:
     name: Pip with Python${{ matrix.python-version }}
-    needs: black
+    needs: lint
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12", "3.13.0-rc.1"]
     steps:
       - name: Harden Runner
         uses: step-security/harden-runner@5c7944e73c4c2a096b17a9cb74d65b6c2bbafbde # v2.9.1
@@ -58,9 +56,10 @@ jobs:
         uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
         with:
           python-version: ${{ matrix.python-version }}
+          cache: "pip"
       - name: Install lmoments3
         run: |
-          pip install -e .
+          python -m pip install --editable .
       - name: Test
         run: |
-          python -m unittest discover -v
+          python -m unittest discover src/lmoments3 -v
diff --git a/.github/workflows/publish-pypi.yml b/.github/workflows/publish-pypi.yml
@@ -32,9 +32,9 @@ jobs:
           python-version: "3.x"
       - name: Install packaging libraries
         run: |
-          pip install build>=1.0 wheel>=0.42.0
+          python -m pip install --require-hashes -r CI/requirements_ci.txt
       - name: Build a binary wheel and a source tarball
         run: |
           python -m build --sdist --wheel .
       - name: Publish distribution 📦 to PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
+        uses: pypa/gh-action-pypi-publish@0ab0b79471669eb3a4d647e625009c62f9f3b241 # v1.10.1
diff --git a/.github/workflows/tag-testpypi.yml b/.github/workflows/tag-testpypi.yml
@@ -27,12 +27,12 @@ jobs:
           python-version: "3.x"
       - name: Install packaging libraries
         run: |
-          pip install build>=1.0 wheel>=0.42.0
+          python -m pip install --require-hashes -r CI/requirements_ci.txt
       - name: Build a binary wheel and a source tarball
         run: |
           python -m build --sdist --wheel .
       - name: Publish distribution 📦 to Test PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
+        uses: pypa/gh-action-pypi-publish@0ab0b79471669eb3a4d647e625009c62f9f3b241 # v1.10.1
         with:
           repository_url: https://test.pypi.org/legacy/
           skip_existing: true
diff --git a/.gitignore b/.gitignore
@@ -22,6 +22,9 @@ var/
 .installed.cfg
 *.egg
 
+# setuptools-scm
+src/lmoments3/_version.py
+
 # PyInstaller
 #  Usually these files are written by a python script from a template
 #  before PyInstaller builds the exe, so as to inject date/other infos into it.

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -11,7 +11,6 @@ repos:
     rev: v4.6.0
     hooks:
       - id: trailing-whitespace
-        exclude: setup.cfg
       - id: end-of-file-fixer
       - id: debug-statements
       - id: check-toml
@@ -27,30 +26,40 @@ repos:
       - id: yamllint
         args: [ '--config-file=.yamllint.yaml' ]
         exclude: conda-recipe/meta.yaml
-  - repo: https://github.com/psf/black
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.10.0
+    hooks:
+      - id: python-no-eval
+      - id: python-no-log-warn
+#      - id: rst-backticks
+      - id: rst-directive-colons
+      - id: rst-inline-touching-normal
+  - repo: https://github.com/psf/black-pre-commit-mirror
     rev: 24.8.0
     hooks:
       - id: black
   - repo: https://github.com/pycqa/flake8
     rev: 7.1.1
     hooks:
       - id: flake8
-        args: [ '--config=setup.cfg' ]
-  - repo: https://github.com/PyCQA/isort
-    rev: 5.13.2
+        args: [ '--config=.flake8' ]
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.5.7
+    hooks:
+      - id: ruff
+        args: [ '--fix', '--show-fixes' ]
+#      - id: ruff-format
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.4
     hooks:
-      - id: isort
-        args: [ '--settings-file=pyproject.toml' ]
-#  - repo: https://github.com/pycqa/pydocstyle
-#    rev: 6.3.0
-#    hooks:
-#      - id: pydocstyle
-#        args: ['--config=setup.cfg']
+      - id: codespell
+        additional_dependencies: [ 'tomli' ]
   - repo: https://github.com/keewis/blackdoc
     rev: v0.3.9
     hooks:
       - id: blackdoc
         additional_dependencies: [ 'black==24.8.0' ]
+      - id: blackdoc-autoupdate-black
   - repo: meta
     hooks:
       - id: check-hooks-apply

diff --git a/CI/requirements_ci.in b/CI/requirements_ci.in
@@ -0,0 +1,2 @@
+build==1.2.2
+wheel==0.44.0
diff --git a/CI/requirements_ci.txt b/CI/requirements_ci.txt
@@ -0,0 +1,34 @@
+#
+# This file is autogenerated by pip-compile with Python 3.8
+# by the following command:
+#
+#    pip-compile --generate-hashes --output-file=CI/requirements_ci.txt CI/requirements_ci.in
+#
+build==1.2.2 \
+    --hash=sha256:119b2fb462adef986483438377a13b2f42064a2a3a4161f24a0cca698a07ac8c \
+    --hash=sha256:277ccc71619d98afdd841a0e96ac9fe1593b823af481d3b0cea748e8894e0613
+    # via -r CI/requirements_ci.in
+importlib-metadata==8.4.0 \
+    --hash=sha256:66f342cc6ac9818fc6ff340576acd24d65ba0b3efabb2b4ac08b598965a4a2f1 \
+    --hash=sha256:9a547d3bc3608b025f93d403fdd1aae741c24fbb8314df4b155675742ce303c5
+    # via build
+packaging==24.1 \
+    --hash=sha256:026ed72c8ed3fcce5bf8950572258698927fd1dbda10a5e981cdf0ac37f4f002 \
+    --hash=sha256:5b8f2217dbdbd2f7f384c41c628544e6d52f2d0f53c6d0c3ea61aa5d1d7ff124
+    # via build
+pyproject-hooks==1.1.0 \
+    --hash=sha256:4b37730834edbd6bd37f26ece6b44802fb1c1ee2ece0e54ddff8bfc06db86965 \
+    --hash=sha256:7ceeefe9aec63a1064c18d939bdc3adf2d8aa1988a510afec15151578b232aa2
+    # via build
+tomli==2.0.1 \
+    --hash=sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc \
+    --hash=sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f
+    # via build
+wheel==0.44.0 \
+    --hash=sha256:2376a90c98cc337d18623527a97c31797bd02bad0033d41547043a1cbfbe448f \
+    --hash=sha256:a29c3f2817e95ab89aa4660681ad547c0e9547f20e75b0562fe7723c9a2a9d49
+    # via -r CI/requirements_ci.in
+zipp==3.20.1 \
+    --hash=sha256:9960cd8967c8f85a56f920d5d507274e74f9ff813a0ab8889a5b5be2daf44064 \
+    --hash=sha256:c22b14cc4763c5a5b04134207736c107db42e9d3ef2d9779d465f5f1bcba572b
+    # via importlib-metadata
diff --git a/conda-build.ps1 b/conda-build.ps1
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -1,14 +1,14 @@
 import os
 import sys
 from datetime import date
+from importlib.metadata import version as get_version
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 os.chdir("../..")  # Versioneer requires us to work from the root of the project
 
 sys.path.insert(0, os.getcwd())
-import versioneer  # noqa: E402
 
 # -- General configuration ------------------------------------------------
 
@@ -43,7 +43,7 @@
     "William Asquith, "
     "J. R. M. Hosking"
 )
-release = versioneer.get_version()
+release = get_version("lmoments3")
 version = ".".join(release.split(".")[:2])
 
 # The language for content autogenerated by Sphinx. Refer to documentation

diff --git a/docs/source/usage.rst b/docs/source/usage.rst
@@ -122,7 +122,7 @@ Example:  Calculate the Negative Log Likelihood of a Gamma distribution with par
 Other statistical methods
 -------------------------
 
-The :mod:`lmoments3.stats` module provides some additional statistical parametes to evaluate fitting of data to
+The :mod:`lmoments3.stats` module provides some additional statistical parameters to evaluate fitting of data to
 distribution function.
 
 :func:`AIC(data, distr_name, distr_paras)`

diff --git a/environment.yml b/environment.yml
@@ -2,14 +2,17 @@ name: lmoments3
 channels:
  - conda-forge
 dependencies:
- - python >=3.9,<3.13
+ - python >=3.9,<3.14
  - numpy
  - scipy
  - black >=24.8.0
  - blackdoc >=0.3.9
  - python-build >=1.0
  - flake8 >=7.0.0
  - pydocstyle >=6.3.0
+ - ruff >=0.5.7
+ - setuptools
+ - setuptools-scm >=8.0
  - sphinx >=6.0.0
  - sphinx-rtd-theme >=1.0
  - wheel >=0.42.0