Overhaul PyDesigner Code 2

.github/workflows/publish.yml

@@ -0,0 +1,75 @@
+name: Build and Publish
+
+on:
+  push:
+    branches:
+      - master
+    tags:
+        - "**"
+
+jobs:
+
+  python:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        id: checkout
+        uses: actions/checkout@v4
+        with:
+          token: ${{ secrets.GH_BRIDGE_PAT }}
+      - name: Build and publish to PyPI
+        id: publish
+        uses: JRubics/[email protected]
+        with:
+          python_version: 3.12
+          pypi_token: ${{ secrets.PYPI }}
+          poetry_install_options: --without dev
+
+  docker:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        id: checkout
+        uses: actions/checkout@v3
+        with:
+          token: ${{ secrets.GH_BRIDGE_PAT }}
+
+      - name: Fetch version
+        id: version
+        uses: SebRollen/[email protected]
+        with:
+          file: 'pyproject.toml'
+          field: 'tool.poetry.version'
+
+      - name: Setup QEMU
+        id: qemu
+        uses: docker/setup-qemu-action@v3
+
+      - name: Setup Docker Buildx
+        id: buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Login to Docker Hub
+        id: login
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Login to GitHub Container Registry
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.repository_owner }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Build and push
+        id: docker_build_push
+        uses: docker/build-push-action@v5
+        with:
+          push: true
+          tags: |
+            dmri/neurodock:latest
+            dmri/neurodock:${{ steps.version.outputs.value }}
+            ghcr.io/muscbridge/PyDesigner:latest
+            ghcr.io/muscbridge/PyDesigner:${{ steps.version.outputs.value }}

.github/workflows/pydesigner_ci.yml

@@ -3,26 +3,140 @@ name: CI
 on:
   pull_request:
   push:
-    branches: [main]
+    branches: master
+    tags:
+      - "**"
+permissions:
+  checks: write
+  pull-requests: write
 
-
 jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
     - name: Checkout
+      id: checkout
       uses: actions/checkout@v3
+      with:
+        token: ${{ secrets.GH_BRIDGE_PAT }}
+
     - name: Set up Python
-      uses: actions/setup-python@v3
+      id: setup-python
+      uses: actions/setup-python@v5
+      with:
+        python-version: 3.12
+        architecture: 'x64'
+
     - name: Run Pre-Commit
+      id: pre-commit
       uses: pre-commit/[email protected]
+      continue-on-error: true
       with:
-        pre-commit_version: latest
-        python_version: 3.8
-        system: true 
-    # - name: Auto-commit changed files
-    #   uses: stefanzweifel/git-auto-commit-action@v5
-    #   with:
-    #     commit_message: "Pre-commit fixes"
-
-
+        extra_args: --all-files
+
+    - name: Auto-commit changed files
+      id: git-auto-commit
+      uses: stefanzweifel/git-auto-commit-action@v5
+      with:
+        commit_message: "Pre-commit autofix"
+
+    - name: Return pre-commit response
+      if: steps.pre-commit.outcome == 'failure'
+      run: exit 1
+
+  pytest:
+    needs: pre-commit
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        id: checkout
+        uses: actions/checkout@v4
+        with:
+          token: ${{ secrets.GH_BRIDGE_PAT }}
+
+      - name: Login to Docker Hub
+        id: login
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Build Docker image
+        run: docker build -t pydesigner-test -f tests/Dockerfile .
+
+      - name: Run tests in Docker container
+        run: docker run --name pydesigner-test-container pydesigner-test
+
+      - name: Copy test results
+        if: always()
+        run: docker cp pydesigner-test-container:/test_results/ ./test_results
+
+      - name: Upload test results
+        uses: actions/upload-artifact@v4
+        if: always()
+        with:
+          name: test-results
+          path: ./test_results/results.xml
+
+      - name: Upload coverage report
+        if: always()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-report
+          path: ./test_results/coverage.xml
+
+      - name: Clean up
+        run: |
+          docker container rm pydesigner-test-container
+          docker image rm pydesigner-test
+
+  summary-reports:
+    needs: pytest
+    if: always()
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        id: checkout
+        uses: actions/checkout@v4
+        with:
+          token: ${{ secrets.GH_BRIDGE_PAT }}
+
+      - name: Download test results
+        uses: actions/download-artifact@v4
+        with:
+          name: test-results
+          path: ./test_results
+
+      - name: Download coverage report
+        uses: actions/download-artifact@v4
+        with:
+          name: coverage-report
+          path: ./test_results
+
+      - name: Code coverage summary report
+        uses: irongut/[email protected]
+        with:
+          filename: ./test_results/coverage.xml
+          badge: true
+          fail_below_min: true
+          format: markdown
+          hide_branch_rate: false
+          hide_complexity: true
+          indicators: true
+          output: both
+          thresholds: '10 50'
+
+      - name: Publish Coverage PR Comment
+        uses: marocchino/sticky-pull-request-comment@v2
+        with:
+          recreate: true
+          path: code-coverage-results.md
+
+      - name: Output Coverage to Job Summary
+        run: cat code-coverage-results.md >> $GITHUB_STEP_SUMMARY
+
+      - name: Publish Test Results
+        uses: EnricoMi/publish-unit-test-result-action@v2
+        with:
+          files: |
+            test_results/results.xml

.gitignore

@@ -1,4 +1,5 @@
 # Folders to ignore
+.coverage*
 .idea/
 __pycache__/
 .ipynb_checkpoints/
@@ -13,6 +14,8 @@ docs/html/
 docs/doctrees/
 
 # Files to ignore
-.DS_Store
+**.DS_Store
+**._.
+**._./
 designer/._DESIGNER.py
 .nii

.pre-commit-config.yaml

@@ -1,13 +1,13 @@
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: 'v4.5.0'
+    rev: 'v5.0.0'
     hooks:
     - id: check-yaml
     - id: end-of-file-fixer
     - id: trailing-whitespace
 
 - repo: https://github.com/python-jsonschema/check-jsonschema
-  rev: '0.27.0'
+  rev: '0.33.0'
   hooks:
     - id: check-readthedocs
 
@@ -18,20 +18,20 @@ repos:
       args: ['--html-dir', 'docs/html', '--source-dir', 'docs/source']
       language_version: python3
 
-- repo: https://github.com/psf/black
-  rev: '23.9.1'
-  hooks:
-    - id: black
-
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: 'v0.1.0'
+  rev: 'v0.11.7'
   hooks:
     - id: ruff
-      args: [--fix, --exit-non-zero-on-fix]
+      args: [--config, pyproject.toml, --fix, --exit-non-zero-on-fix]
+    - id: ruff-format
 
 - repo: https://github.com/python-poetry/poetry
-  rev: '1.6.0'
+  rev: '1.8.0'
   hooks:
+    - id: poetry-lock
+      args: ["--no-update"]
     - id: poetry-check
-    # - id: poetry-lock
     - id: poetry-export
+      args: ["--without-hashes", "-f", "requirements.txt", "-o", "requirements.txt"]
+    - id: poetry-export
+      args: ["--without-hashes", "--only", "dev", "-f", "requirements.txt", "-o", "requirements-dev.txt"]