resolve merge conflict when merging dev into sem view

.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/logger.sh

@@ -22,21 +22,23 @@ function filter_commits_by_label {
     temp=$(echo "${commits}" | grep -E --ignore-case "$exclude_labels")
     # Strip empty lines (that might include tabs, spaces, etc.)
     temp=$(echo "${temp}" | sed -r '/^\s*$/d')
-    # Make each line a bullet point by appending "- " to lines
-    temp=$(echo "${temp}" | sed -e 's/^/- /')
+    # Make each line a bullet point by appending "- " to lines if not already present
+    temp=$(echo "${temp}" | sed -e 's/^\(\s*\)\(\-\s\)\?/\1- /')
+    # Remove the specific tag at the end of each line
+    temp=$(echo "${temp}" | sed -r "s/\s$exclude_labels\b//g")
     echo "$temp"
 }
 
 function filter_commits_exclude_label {
     local temp
     local commits=$1            # fetch the first argument
     local exclude_labels=$2     # fetch the second argument
-    # Reverse filter commits by the given labels (i.e. exclude labels)
+    # Reverse filter commits by the given labels (i.e., exclude labels)
     temp=$(echo "$commits" | grep -v -E --ignore-case "$exclude_labels")
     # Strip empty lines (that might include tabs, spaces, etc.)
     temp=$(echo "${temp}" | sed -r '/^\s*$/d')
-    # Make each line a bullet point by appending "- " to lines
-    temp=$(echo "${temp}" | sed -e 's/^/- /')
+    # Make each line a bullet point by appending "- " to lines if not already present
+    temp=$(echo "${temp}" | sed -e 's/^\(\s*\)\(\-\s\)\?/\1- /')
     echo "$temp"
 }
 
@@ -53,9 +55,7 @@ function filter_commits_by_tag_interval {
 
 function append_to_entry_with_label {
     if [ "$(is_empty "$1")" == "false" ]; then
-        echo "### $3"   >> $2
-        echo "${1}"     >> $2
-        echo ""         >> $2
+        printf "### %s\n\n%s\n\n" "$3" "$1" >> $2
     fi
 }
 
@@ -93,7 +93,7 @@ if test -f CHANGELOG.md; then
 fi
 
 # Compile change log
-echo -e "## ${tag_new}\n" >> entry
+printf "## %s\n\n" "${tag_new}" >> entry
 append_to_entry_with_label "$features" entry ":rocket: New features"
 append_to_entry_with_label "$enhancements" entry ":cake: Enhancements"
 append_to_entry_with_label "$maintenance" entry ":wrench: Maintenace"
@@ -102,9 +102,9 @@ append_to_entry_with_label "$fixes" entry ":bug: Bugfixes"
 append_to_entry_with_label "$documentation" entry ":green_book: Documentation"
 append_to_entry_with_label "$uncategorized" entry ":question: Uncategorized"
 
-echo "$(<entry)"
+cat entry
 
 # Modify CHANGELOG.md to reflect new changes
-echo -e "# Change log\n" >> CHANGELOG.md
-echo "$(<entry)" >> CHANGELOG.md
+printf "# Change log\n\n" >> CHANGELOG.md
+cat entry >> CHANGELOG.md
 rm entry