Merge branch 'develop'

.github/actions/install_eitprocessing/action.yml

@@ -45,5 +45,5 @@ runs:
         key: ${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }}-[${{ inputs.dependencies }}]
     - name: Install eitprocessing with [${{ inputs.dependencies }}] dependencies
       if: steps.cache-python-env.outputs.cache-hit != 'true'
-      run: python3 -m pip install -e ".[${{ inputs.dependencies }}]"
+      run: python3 -m pip install ".[${{ inputs.dependencies }}]"
       shell: bash

.github/workflows/cffconvert.yml

@@ -1,4 +1,4 @@
-name: Citation file
+name: Citation File
 
 on:
   push:

.github/workflows/lint.yml

@@ -1,4 +1,4 @@
-name: Linting
+name: Lint
 
 on:
   push:

.github/workflows/release_github.yml

@@ -4,154 +4,208 @@ on:
   workflow_dispatch:
     inputs:
       version_level:
-        description: "Semantic version level increase."
+        description: Semantic version level increase
         required: true
         type: choice
+        default: patch
         options:
           - patch
           - minor
           - major
 
 permissions:
   contents: write
-  pull-requests: write
   packages: read
+  statuses: read
+  checks: read
+  pull-requests: write
+  actions: read
+  repository-projects: read
+
+env:
+  GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  GH_PAGER: cat
 
 jobs:
+  checks:
+    name: Check requirements
+    runs-on: ubuntu-latest
+    steps:
+      - name: Fail if main branch was selected
+        if: ${{ github.ref_name == 'main' }}
+        run: |
+          echo "Cannot release from main branch, please select valid release branch."
+          exit 1
+
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Check if PR exists
+        run: gh pr view ${{ github.ref_name }}
+
+      - name: Check if PR base is main
+        run: gh pr view ${{ github.ref_name }} --json baseRefName -q 'if .baseRefName == "main" then "PR base is main" else error("PR base is not main") end'
+
+      - name: Check if PR is mergeable
+        run: gh pr view ${{ github.ref_name }} --json mergeable -q 'if .mergeable == "MERGEABLE" then "PR is mergeable" else error("PR is not mergeable") end'
+
+      - name: Check whether PR checks pass(ed)
+        # note that this assumed there are checks to be passed; this fails if there are no checks, which is no
+        # relevant to this repo
+        run: |
+          gh pr checks ${{ github.ref_name }} --watch --fail-fast
+          gh pr checks ${{ github.ref_name }} --json state -q 'if . | length == 0 then "No checks found." elif map(.state == "SUCCESS") | all then "All checks passed" else error("Not all checks passed") end'
+
   test_python_releases:
+    needs: checks
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
-      matrix: 
+      matrix:
         os: ["ubuntu-latest"]
         python-version: ["3.10", "3.11", "3.12", "3.13"]
     name: Build for ${{ matrix.python-version }}, ${{ matrix.os }}
-    env: 
+    env:
       EIT_PROCESSING_TEST_DATA: ${{ github.workspace }}/../eitprocessing_data/
     steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/install_eitprocessing
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Install eitprocessing
+        uses: ./.github/actions/install_eitprocessing
         with:
           dependencies: testing
           extract-data: true
           python-version: ${{ matrix.python-version }}
           token: ${{ secrets.GITHUB_TOKEN }}
           data-directory: ${{ env.EIT_PROCESSING_TEST_DATA }}
+
       - name: Run pytest
         run: pytest -v
-      - name: Install eitprocessing with dev dependencies
+
+      - name: Install additional dependencies for building
         run: python3 -m pip install --upgrade ".[publishing]"
+
       - name: Build eitprocessing
         run: python3 -m build
-
 
-  github_release:
+  merge_and_bump:
+    name: Merge the changes into main and bump the version
     needs: test_python_releases
-    runs-on: "ubuntu-latest"
-    defaults:
-      run:
-        shell: bash -l {0}
-
+    runs-on: ubuntu-latest
+    outputs:
+      new-version: ${{ steps.bump.outputs.current-version }}
+    env:
+      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - name: Fail if main branch was selected
-        if: ${{ github.ref_name == 'main' }}
-        run: |
-          echo "Cannot release from main branch, please select valid release branch."
-          exit 1
-
       - name: Checkout repository
         uses: actions/checkout@v4
         with:
-          token: ${{ secrets.GH_PAT }}
           ref: main
           fetch-depth: 0
+          token: ${{ secrets.GH_PAT }}
 
       - name: Configure git
         run: |
-          git config user.email "actions@github.com"
+          git config user.email "${GITHUB_ACTOR_ID}+${GITHUB_ACTOR}@users.noreply.github.com"
           git config user.name "GitHub Actions"
-          git pull
+          git config -l
 
-      - name: Merge changes into main
+      - name: Merge branch into main
         run: |
           git switch main
-          git branch ${{ github.ref_name }} origin/${{ github.ref_name }} 
-          git merge ${{ github.ref_name }} --no-ff --no-commit
-          git commit --no-edit
+          git branch -f ${{ github.ref_name }} origin/${{ github.ref_name }}
+          git merge ${{ github.ref_name }} --no-ff --no-edit
+
+      - name: Install Python
+        uses: actions/[email protected]
+        with:
+          python-version: "3.12"
 
-      - name: Bump version
+      - name: Install bump-my-version
+        shell: bash
+        run: |
+          python3 -m pip install pyproject-deplister
+          pyproject-deplister --extra dev --path pyproject.toml | grep bump-my-version | sed 's/ //g' | xargs -I{} python3 -m pip install "{}"
+
+      - name: Pass Inputs to Shell
         id: bump
+        shell: bash
+        run: |
+          echo "previous-version=$(bump-my-version show current_version)" >> $GITHUB_OUTPUT
+          bump-my-version bump ${{ inputs.version_level }} --commit --tag
+          ([[ $? -gt 0 ]] && echo "bumped=false" || echo "bumped=true") >> $GITHUB_OUTPUT
+          echo "current-version=$(bump-my-version show current_version)" >> $GITHUB_OUTPUT
+
+      - name: Fail if bumping failes
+        if: steps.bump.outputs.bumped == 'false'
+        run: |
+          echo "Bumping failed."
+          git reset --hard HEAD^
+          exit 1
+
+      - name: Check new version number
+        if: steps.bump.outputs.bumped == 'true'
+        run: |
+          echo "Version was bumped from ${{ steps.bump.outputs.previous-version }} to ${{ steps.bump.outputs.current-version }}!"
+
+      - name: Merge main into develop
+        run: |
+          git checkout develop
+          git merge main --no-ff --no-edit || { echo "Can't merge changes to develop. Manually merge PR and create GitHub release."; exit 1; }
+
+      - name: Push changes to develop
+        uses: ad-m/github-push-action@master
+        with:
+          github_token: ${{ secrets.GH_PAT }}
+          branch: develop
+          force_with_lease: true
+
+      - name: Checkout main
         run: |
-          echo "-- install bump-my-version"
-          python3 -m pip install bump-my-version
-          echo "-- bump the version"
-          bump-my-version bump ${{ github.event.inputs.version_level }} --commit --tag
-          echo "-- push bumped version"
-          echo "RELEASE_TAG=$(git describe --tags --abbrev=0)" >> $GITHUB_OUTPUT
-          git push --tags -f
-          git push
+          git checkout main
+
+      - name: Push changes to main
+        uses: ad-m/github-push-action@master
+        with:
+          github_token: ${{ secrets.GH_PAT }}
+          branch: main
+          force_with_lease: true
+
+  github_release:
+    name: Create a draft GitHub release
+    needs: merge_and_bump
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          ref: main
 
       - name: Create GitHub Release
         id: create_release
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
-          gh release create ${{ steps.bump.outputs.RELEASE_TAG }} \
-              --title="Release ${{ steps.bump.outputs.RELEASE_TAG }}" \
+          gh release create v${{ needs.merge_and_bump.outputs.new-version }} \
+              --title="Release v${{ needs.merge_and_bump.outputs.new-version }}" \
               --generate-notes \
               --draft
 
-      - name: Validate CITATION.cff
-        id: validate_cff
-        env:
-          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-        uses: dieghernan/cff-validator@v3
-
-  tidy_workspace:
-    # only run if action above succeeds
+  remove_branch:
+    name: Remove PR branch
     needs: github_release
-    runs-on: "ubuntu-latest"
-    defaults:
-      run:
-        shell: bash -l {0}
-
+    if: ${{ github.ref_name != 'develop' }}
+    runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4
         with:
-          token: ${{ secrets.GH_PAT }}
+          ref: develop
           fetch-depth: 0
 
-      - name: Configure git
-        run: |
-          git config user.email "[email protected]"
-          git config user.name "GitHub Actions"
-          git pull
-
-      - name: Close PR
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: |
-          echo "-- searching for associated PR"
-          pr_number=$(gh pr list --head ${{ github.ref_name }} --json number --jq '.[0].number')
-          if [ -n "$pr_number" ]; then
-            echo "-- closing PR #$pr_number"
-            gh pr close $pr_number
-          else
-            echo "-- no open pull request found for branch $branch_name"
-          fi
-
-      - name: Merge updates into develop
-        run: |
-          git switch develop
-          git merge --no-ff origin/main
-          git push
-
-      - name: Delete release branch other than main or develop
-        run: |
-          if [[ ${{ github.ref_name }} != "main" && ${{ github.ref_name }} != "develop" ]]; then
-            echo "-- deleting branch '${{ github.ref_name }}'"
-            git push origin -d ${{ github.ref_name }}
-          else
-            echo "-- branch '${{ github.ref_name }}' will not be deleted from remote"
-          fi
+      - name: Remove PR branch
+        uses: dawidd6/action-delete-branch@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          branches: ${{ github.ref_name }}

.github/workflows/test_build_documentation.yml

@@ -1,4 +1,4 @@
-name: Test build documentation
+name: Documentation
 
 on:
   push:

.github/workflows/testing.yml

@@ -1,4 +1,4 @@
-name: Run tests
+name: Build and Test
 
 on:
   push:

.gitignore

@@ -39,3 +39,5 @@ venv3
 
 /site/
 uv.lock
+
+worktrees

.prettierignore

@@ -0,0 +1 @@
+docs/*

.vscode/settings.json

@@ -26,6 +26,7 @@
   "rewrap.wrappingColumn": 120,
   "rewrap.autoWrap.enabled": true,
   "editor.formatOnSave": true,
+  "files.trimTrailingWhitespace": true,
   "editor.defaultFormatter": "esbenp.prettier-vscode",
   "[ignore]": {
     "editor.defaultFormatter": "foxundermoon.shell-format"

README.dev.md

@@ -128,7 +128,7 @@ We use [prettier](https://prettier.io/) for formatting most other files. If you
 
 ## Making a release
 
-### Automated release workflow:
+### Automated release workflow
 
 0. **IMP0RTANT:** [Create a PR](#creating-a-pr) for the release branch (usually `develop`) and make sure that all checks pass!
    - if everything goes well, this PR will automatically be closed after the draft release is created.
@@ -152,7 +152,7 @@ We use [prettier](https://prettier.io/) for formatting most other files. If you
 8. Click green "Publish Release" button to convert the draft to a published release on GitHub.
    - This will automatically trigger [another GitHub workflow](https://github.com/EIT-ALIVE/eitprocessing/actions/workflows/release.yml) that will take care of publishing the package on PyPi.
 
-#### Updating the token:
+#### Updating the token
 
 NOTE: the current token (associated to @DaniBodor) allowing to bypass branch protection will expire on June 20th, 2025. To update the token do the following:
 
@@ -164,7 +164,7 @@ NOTE: the current token (associated to @DaniBodor) allowing to bypass branch pro
 5. Navigate to the [secrets settings](https://github.com/EIT-ALIVE/eitprocessing/settings/secrets/actions).
 6. Edit the `GH_PAT` key giving your access token as the new value.
 
-### Manually create a release:
+### Manually create a release
 
 0. Make sure you have all required developers tools installed `pip install -e .'[dev]'`.
 1. Create a `release` branch from `main` and merge the changes into this branch.