Merge pull request #923 from PMEAL/maint/hatch

- Migrated from bump2version to hatch for resolving version number #maint
- Refactored and updated Actions #maint
- Deprecated Python 3.8 and 3.9 #maint
- Added linter Action: ruff #maint
- Unified project config (pytest.ini, setup.cfg) files in pyproject.toml #maint
- Removed pyfastnoisesimd from dependencies as it no longer works on Python 3.9+ #maint

.github/workflows/bump-version-dev.yml

@@ -12,48 +12,31 @@ jobs:
     name: Bump version
     runs-on: ubuntu-latest
 
+    permissions:
+      contents: write
+
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: '3.10'
 
     - name: Set env variables
       run: |
-        # The next line is very important, otherwise the line after triggers
-        # git to track the permission change, which breaks bump2version API (needs clean git folder)
-        git config core.filemode false
-        chmod +x .github/workflows/utils.sh
-        echo "VERSION_FILE=porespy/__version__.py" >> $GITHUB_ENV
-        echo "SETUP_CFG_FILE=setup.cfg" >> $GITHUB_ENV
         echo "${{ github.event.head_commit.message }}"
 
     - name: Install dependencies
       run: |
-        pip install bump2version
+        pip install -e .[build]
 
-    - name: Bump version (build)
+    - name: Bump version (dev)
       run: |
-        source .github/workflows/utils.sh
-        bump_version build $VERSION_FILE
-        # Note that we don't want to create a new tag for "builds"
-
-    # - name: Commit files
-    #   run: |
-    #     REPOSITORY=${INPUT_REPOSITORY:-$GITHUB_REPOSITORY}
-    #     remote_repo="https://${GITHUB_ACTOR}:${{ secrets.PUSH_ACTION_TOKEN }}@github.com/${REPOSITORY}.git"
-
-    #     git config --local user.email "action@github.com"
-    #     git config --local user.name "GitHub Action"
-
-    #     # Commit version bump to dev ([no ci] to avoid infinite loop)
-    #     git commit -m "Bump version number (build) [no ci]" -a
-    #     git push "${remote_repo}" dev
+        hatch version dev
 
     - name: Commit files
-      uses: stefanzweifel/git-auto-commit-action@v4
+      uses: stefanzweifel/git-auto-commit-action@v5
       with:
-        commit_message: Bump version number (build part)
-        commit_author: Author <actions@github.com>
+        commit_message: Bump version number (dev segment)
+        commit_author: GitHub Actions <actions@github.com>

.github/workflows/bump-version.yml

@@ -11,53 +11,44 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
       with:
         persist-credentials: false  # otherwise, the token used is the GITHUB_TOKEN, instead of your personal token
         fetch-depth: 0              # otherwise, you will failed to push refs to dest repo
 
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
-        python-version: '3.8'
+        python-version: '3.10'
 
     - name: Set env variables
       run: |
-        # The next line is very important, otherwise the line after triggers
-        # git to track the permission change, which breaks bump2version API (needs clean git folder)
-        git config core.filemode false
-        chmod +x .github/workflows/utils.sh
-        echo "VERSION_FILE=porespy/__version__.py" >> $GITHUB_ENV
-        echo "SETUP_CFG_FILE=setup.cfg" >> $GITHUB_ENV
         echo "${{ github.event.head_commit.message }}"
 
     - name: Install dependencies
       run: |
-        pip install bump2version
+        pip install -e .[build]
 
     - name: Bump version (patch)
       if: contains(github.event.head_commit.message, '#patch')
       run: |
-        source .github/workflows/utils.sh
-        bump_version patch $VERSION_FILE
-        echo "TAG_NEW=v$(get_version $VERSION_FILE)" >> $GITHUB_ENV
+        hatch version patch
+        echo "TAG_NEW=v$(hatch version)" >> $GITHUB_ENV
 
     - name: Bump version (minor)
       if: contains(github.event.head_commit.message, '#minor')
       run: |
-        source .github/workflows/utils.sh
-        bump_version minor $VERSION_FILE
-        echo "TAG_NEW=v$(get_version $VERSION_FILE)" >> $GITHUB_ENV
+        hatch version minor
+        echo "TAG_NEW=v$(hatch version)" >> $GITHUB_ENV
 
     - name: Bump version (major)
       if: contains(github.event.head_commit.message, '#major')
       run: |
-        source .github/workflows/utils.sh
-        bump_version major $VERSION_FILE
-        echo "TAG_NEW=v$(get_version $VERSION_FILE)" >> $GITHUB_ENV
+        hatch version major
+        echo "TAG_NEW=v$(hatch version)" >> $GITHUB_ENV
 
     - name: Commit files
-      if:
+      if: |
         contains(github.event.head_commit.message, '#patch') ||
         contains(github.event.head_commit.message, '#minor') ||
         contains(github.event.head_commit.message, '#major')
@@ -68,7 +59,7 @@ jobs:
         git config --local user.email "action@github.com"
         git config --local user.name "GitHub Action"
 
-        # commit version bump to release
+        # Commit version bump to release
         git commit -m "Bump version number" -a
         git push "${remote_repo}" release
 
@@ -77,18 +68,14 @@ jobs:
       with:
         source_branch: "release"                          # If blank, default: triggered branch
         destination_branch: "dev"                         # If blank, default: master
-        pr_title: "Don't forget to merge release back into dev!"
+        pr_title: "Merge release -> dev to propagate version number bump"
         pr_body: "Changes made to the release branch (e.g. hotfixes), plus the version bump."
         pr_assignee: "jgostick,ma-sadeghi"                # Comma-separated list (no spaces)
         pr_label: "high priority"                         # Comma-separated list (no spaces)
         pr_draft: false                                   # Creates pull request as draft
         pr_allow_empty: true                              # Creates pull request even if there are no changes
         github_token: ${{ secrets.GITHUB_TOKEN }}
 
-    - name: Trim the 4th digit from the tag
-      run:
-        echo "TAG_NEW=${TAG_NEW%.dev?}" >> $GITHUB_ENV
-
     - name: Create new tag
       run: |
         REPOSITORY=${INPUT_REPOSITORY:-$GITHUB_REPOSITORY}

.github/workflows/cleanup-tags.yml

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     - name: Clean up tags
       run: |

.github/workflows/examples.yml

@@ -14,40 +14,39 @@ jobs:
       fail-fast: false
       max-parallel: 5
       matrix:
-        python-version: ['3.8']
+        python-version: ['3.10']
         operating-system: [ubuntu-latest]
         # Next line should be [1, 2, ..., max-parallel)
         test_group: [1, 2, 3, 4, 5]
 
     steps:
-      - uses: actions/checkout@v2
-      - uses: FedericoCarboni/setup-ffmpeg@v2
+      - uses: actions/checkout@v4
+      - uses: FedericoCarboni/setup-ffmpeg@v3
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
       - name: Cache pip
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
           # This path is specific to Ubuntu
           path: ~/.cache/pip
           # Look to see if there is a cache hit for the corresponding requirements file
-          key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}
+          key: ${{ runner.os }}-pip-${{ hashFiles('pyproject.toml') }}
           restore-keys: |
             ${{ runner.os }}-pip-
             ${{ runner.os }}-
 
       - name: Install dependencies (pip)
         run: |
-          pip install -r requirements.txt
-          pip install -r requirements/tests.txt
-          pip install -r requirements/examples.txt
+          pip install -e .[test,extras]
 
       - name: Running tests
         # Make sure to pass max-parallel to --splits
         run: |
-          pytest examples/ \
+          pytest \
+            -p no:python \
             --nbval-lax \
             --splits ${{ strategy.max-parallel}} \
             --group ${{ matrix.test_group }} \

.github/workflows/gh-pages.yml

@@ -15,28 +15,27 @@ jobs:
         shell: bash -l {0}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+      - name: Set up Python
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: '3.10'
 
       - name: Cache pip
         uses: actions/cache@v2
         with:
           # This path is specific to Ubuntu
           path: ~/.cache/pip
           # Look to see if there is a cache hit for the corresponding requirements file
-          key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}
+          key: ${{ runner.os }}-pip-${{ hashFiles('pyproject.toml') }}
           restore-keys: |
             ${{ runner.os }}-pip-
             ${{ runner.os }}-
 
       - name: Install dependencies (conda)
         run: |
-          pip install -r requirements.txt
-          pip install -r requirements/docs.txt
+          pip install -e .[docs,interactive]
 
       # Build the documentation
       - name: Build the documentation

.github/workflows/publish-to-pypi.yml

@@ -1,41 +1,32 @@
 name: Deploy to PyPI
 
 on:
+  workflow_dispatch:
   push:
     tags:
-      - '*'
+      - 'v*'
 
 jobs:
   deploy:
     name: Publish 🐍 📦 to PyPI
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
       with:
-        ref: release  # the production branch name (for proper version #)
+        ref: release
 
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
-        python-version: '3.8'
+        python-version: '3.10'
 
     - name: Set env variables
       run: |
         chmod +x .github/workflows/utils.sh
         source .github/workflows/utils.sh
-        VERSION_FILE=porespy/__version__.py
         echo "TAG=$(get_most_recent_tag)" >> $GITHUB_ENV
-        echo "VERSION=$(get_version $VERSION_FILE)" >> $GITHUB_ENV
-
-    - name: Set env variables (for tag mismatch)
-      run: |
-        echo "Tag: $TAG, Version: $VERSION"
-        if [ "${TAG//v}" = "${VERSION%.dev?}" ]; then
-            echo "TAG_MISMATCH=false" >> $GITHUB_ENV
-        else
-            echo "TAG_MISMATCH=true" >> $GITHUB_ENV
-        fi
+        echo "VERSION=$(hatch version)" >> $GITHUB_ENV
 
     - name: Install dependencies
       run: |
@@ -48,30 +39,9 @@ jobs:
       run: python setup.py sdist bdist_wheel
 
     - name: Publish distribution 📦 to PyPI
-      if: startsWith(github.event.ref, 'refs/tags') && contains(env.TAG_MISMATCH, 'false')
-      uses: pypa/gh-action-pypi-publish@master
+      if: startsWith(github.event.ref, 'refs/tags')
+      uses: pypa/gh-action-pypi-publish@release/v1
       with:
         user: __token__
         password: ${{ secrets.PYPI_TOKEN }}
-        skip_existing: true
-
-#    - name: Publish distribution 📦 to TestPyPI
-#      if: startsWith(github.event.ref, 'refs/tags') && contains(env.TAG_MISMATCH, 'false')
-#      uses: pypa/gh-action-pypi-publish@master
-#      with:
-#        user: __token__
-#        password: ${{ secrets.TESTPYPI_TOKEN }}
-#        repository_url: https://test.pypi.org/legacy/
-
-    # Not a good idea: if a non-conforming tag is push, e.g. random_tag, it
-    # first gets deleted by cleanup-tags.yml, and then publish-to-pypi.yml gets
-    # tricked and deletes the most recent tag! Ouch!
-
-    # - name: Delete tag if doesn't match with version
-    #   if: contains(env.TAG_MISMATCH, 'true')
-    #   run: |
-    #     git config --local user.email "action@github.com"
-    #     git config --local user.name "GitHub Action"
-    #     REPOSITORY=${INPUT_REPOSITORY:-$GITHUB_REPOSITORY}
-    #     remote_repo="https://${GITHUB_ACTOR}:${{ secrets.GITHUB_TOKEN }}@github.com/${REPOSITORY}.git"
-    #     git push "${remote_repo}" :refs/tags/$TAG
+        skip-existing: true

.github/workflows/release-notes.yml

@@ -12,26 +12,26 @@ jobs:
 
     steps:
       - name: Checkout code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
-            fetch-depth: 0  # to retrieve entire history of refs/tags
+            fetch-depth: 0  # Retrieve entire history of refs/tags
 
-      - name: Generate release notes
+      - name: get-recent-tag
         run: |
           git fetch --all --tags --force
           chmod +x .github/workflows/logger.sh
           chmod +x .github/workflows/utils.sh
           source .github/workflows/utils.sh
           bash .github/workflows/logger.sh
-          echo "TAG=$(get_most_recent_tag)" >> $GITHUB_ENV
+          echo "TAG=$(get_most_recent_tag)" >> $GITHUB_OUTPUT
 
       - name: Create GitHub release
-        uses: Roang-zero1/github-create-release-action@master
+        uses: Roang-zero1/github-create-release-action@v3
         with:
           version_regex: ^v[[:digit:]]+\.[[:digit:]]+\.[[:digit:]]+
           create_draft: true
-          created_tag: ${{ env.TAG }}
+          created_tag: ${{ steps.get-recent-tag.outputs.TAG }}
           update_existing: false
-          release_title: ${{ env.TAG }}
+          release_title: ${{ steps.get-recent-tag.outputs.TAG }}
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/ruff.yml

@@ -0,0 +1,10 @@
+name: Ruff
+
+on: pull_request
+
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: chartboost/ruff-action@v1