Tidy up codebase v2

.github/workflows/ci.yml

@@ -8,9 +8,7 @@ on:
     paths:
       - 'src/**'
       - 'tests/**'
-      - 'requirements*.txt'
       - 'setup.py'
-      - 'setup.cfg'
       - 'pyproject.toml'
       - 'MANIFEST.in'
       - '.pre-commit-config.yaml'
@@ -23,9 +21,7 @@ on:
     paths:
       - 'src/**'
       - 'tests/**'
-      - 'requirements*.txt'
       - 'setup.py'
-      - 'setup.cfg'
       - 'pyproject.toml'
       - 'MANIFEST.in'
       - '.pre-commit-config.yaml'
@@ -62,20 +58,17 @@ jobs:
           key: >-
             ${{ env.CACHE_VERSION}}-${{ runner.os }}-base-venv-${{
             steps.python.outputs.python-version }}-${{
-            hashFiles('requirements.txt') }}-${{
-            hashFiles('requirements_test.txt') }}
+            hashFiles('pyproject.toml') }}
           restore-keys: |
-            ${{ env.CACHE_VERSION}}-${{ runner.os }}-base-venv-${{ steps.python.outputs.python-version }}-${{ hashFiles('requirements.txt') }}-${{ hashFiles('requirements_test.txt') }}-
-            ${{ env.CACHE_VERSION}}-${{ runner.os }}-base-venv-${{ steps.python.outputs.python-version }}-${{ hashFiles('requirements.txt') }}
             ${{ env.CACHE_VERSION}}-${{ runner.os }}-base-venv-${{ steps.python.outputs.python-version }}-
       - name: Create Python virtual environment
         if: steps.cache-venv.outputs.cache-hit != 'true'
         run: |
           sudo apt-get update && sudo apt-get install -y libxml2-dev libxslt1-dev python3-dev build-essential
           python -m venv venv
           . venv/bin/activate
-          pip install -U "pip<20.3" setuptools
-          pip install -r requirements.txt -r requirements_test.txt
+          pip install -U pip setuptools
+          pip install -e ".[dev]"
       - name: Restore pre-commit environment from cache
         id: cache-precommit
         uses: actions/cache@v4
@@ -111,8 +104,7 @@ jobs:
           key: >-
             ${{ env.CACHE_VERSION}}-${{ runner.os }}-base-venv-${{
             steps.python.outputs.python-version }}-${{
-            hashFiles('requirements.txt') }}-${{
-            hashFiles('requirements_test.txt') }}
+            hashFiles('pyproject.toml') }}
       - name: Fail job if Python cache restore failed
         if: steps.cache-venv.outputs.cache-hit != 'true'
         run: |
@@ -135,50 +127,6 @@ jobs:
           . venv/bin/activate
           pre-commit run --hook-stage manual bandit --all-files --show-diff-on-failure
 
-  lint-black:
-    name: Check black
-    runs-on: ubuntu-latest
-    needs: prepare-base
-    steps:
-      - name: Check out code from GitHub
-        uses: actions/checkout@v5
-      - name: Set up Python ${{ env.DEFAULT_PYTHON }}
-        uses: actions/setup-python@v5
-        id: python
-        with:
-          python-version: ${{ env.DEFAULT_PYTHON }}
-      - name: Restore base Python virtual environment
-        id: cache-venv
-        uses: actions/cache@v4
-        with:
-          path: venv
-          key: >-
-            ${{ env.CACHE_VERSION}}-${{ runner.os }}-base-venv-${{
-            steps.python.outputs.python-version }}-${{
-            hashFiles('requirements.txt') }}-${{
-            hashFiles('requirements_test.txt') }}
-      - name: Fail job if Python cache restore failed
-        if: steps.cache-venv.outputs.cache-hit != 'true'
-        run: |
-          echo "Failed to restore Python virtual environment from cache"
-          exit 1
-      - name: Restore pre-commit environment from cache
-        id: cache-precommit
-        uses: actions/cache@v4
-        with:
-          path: ${{ env.PRE_COMMIT_HOME }}
-          key: |
-            ${{ env.CACHE_VERSION}}-${{ runner.os }}-pre-commit-${{ hashFiles('.pre-commit-config.yaml') }}
-      - name: Fail job if cache restore failed
-        if: steps.cache-venv.outputs.cache-hit != 'true'
-        run: |
-          echo "Failed to restore Python virtual environment from cache"
-          exit 1
-      - name: Run black
-        run: |
-          . venv/bin/activate
-          pre-commit run --hook-stage manual black --all-files --show-diff-on-failure
-
   lint-codespell:
     name: Check codespell
     runs-on: ubuntu-latest
@@ -199,8 +147,7 @@ jobs:
           key: >-
             ${{ env.CACHE_VERSION}}-${{ runner.os }}-base-venv-${{
             steps.python.outputs.python-version }}-${{
-            hashFiles('requirements.txt') }}-${{
-            hashFiles('requirements_test.txt') }}
+            hashFiles('pyproject.toml') }}
       - name: Fail job if Python cache restore failed
         if: steps.cache-venv.outputs.cache-hit != 'true'
         run: |
@@ -246,8 +193,7 @@ jobs:
           key: >-
             ${{ env.CACHE_VERSION}}-${{ runner.os }}-base-venv-${{
             steps.python.outputs.python-version }}-${{
-            hashFiles('requirements.txt') }}-${{
-            hashFiles('requirements_test.txt') }}
+            hashFiles('pyproject.toml') }}
       - name: Fail job if Python cache restore failed
         if: steps.cache-venv.outputs.cache-hit != 'true'
         run: |
@@ -273,8 +219,8 @@ jobs:
           . venv/bin/activate
           pre-commit run --hook-stage manual check-executables-have-shebangs --all-files
 
-  lint-flake8:
-    name: Check flake8
+  lint-json:
+    name: Check JSON
     runs-on: ubuntu-latest
     needs: prepare-base
     steps:
@@ -293,8 +239,7 @@ jobs:
           key: >-
             ${{ env.CACHE_VERSION}}-${{ runner.os }}-base-venv-${{
             steps.python.outputs.python-version }}-${{
-            hashFiles('requirements.txt') }}-${{
-            hashFiles('requirements_test.txt') }}
+            hashFiles('pyproject.toml') }}
       - name: Fail job if Python cache restore failed
         if: steps.cache-venv.outputs.cache-hit != 'true'
         run: |
@@ -312,16 +257,16 @@ jobs:
         run: |
           echo "Failed to restore Python virtual environment from cache"
           exit 1
-      - name: Register flake8 problem matcher
+      - name: Register check-json problem matcher
         run: |
-          echo "::add-matcher::.github/workflows/matchers/flake8.json"
-      - name: Run flake8
+          echo "::add-matcher::.github/workflows/matchers/check-json.json"
+      - name: Run check-json
         run: |
           . venv/bin/activate
-          pre-commit run --hook-stage manual flake8 --all-files
+          pre-commit run --hook-stage manual check-json --all-files
 
-  lint-isort:
-    name: Check isort
+  lint-pyupgrade:
+    name: Check pyupgrade
     runs-on: ubuntu-latest
     needs: prepare-base
     steps:
@@ -340,8 +285,7 @@ jobs:
           key: >-
             ${{ env.CACHE_VERSION}}-${{ runner.os }}-base-venv-${{
             steps.python.outputs.python-version }}-${{
-            hashFiles('requirements.txt') }}-${{
-            hashFiles('requirements_test.txt') }}
+            hashFiles('pyproject.toml') }}
       - name: Fail job if Python cache restore failed
         if: steps.cache-venv.outputs.cache-hit != 'true'
         run: |
@@ -359,13 +303,13 @@ jobs:
         run: |
           echo "Failed to restore Python virtual environment from cache"
           exit 1
-      - name: Run isort
+      - name: Run pyupgrade
         run: |
           . venv/bin/activate
-          pre-commit run --hook-stage manual isort --all-files --show-diff-on-failure
+          pre-commit run --hook-stage manual pyupgrade --all-files --show-diff-on-failure
 
-  lint-json:
-    name: Check JSON
+  lint-ruff:
+    name: Check ruff
     runs-on: ubuntu-latest
     needs: prepare-base
     steps:
@@ -384,8 +328,7 @@ jobs:
           key: >-
             ${{ env.CACHE_VERSION}}-${{ runner.os }}-base-venv-${{
             steps.python.outputs.python-version }}-${{
-            hashFiles('requirements.txt') }}-${{
-            hashFiles('requirements_test.txt') }}
+            hashFiles('pyproject.toml') }}
       - name: Fail job if Python cache restore failed
         if: steps.cache-venv.outputs.cache-hit != 'true'
         run: |
@@ -403,57 +346,14 @@ jobs:
         run: |
           echo "Failed to restore Python virtual environment from cache"
           exit 1
-      - name: Register check-json problem matcher
-        run: |
-          echo "::add-matcher::.github/workflows/matchers/check-json.json"
-      - name: Run check-json
+      - name: Run ruff
         run: |
           . venv/bin/activate
-          pre-commit run --hook-stage manual check-json --all-files
-
-  lint-pyupgrade:
-    name: Check pyupgrade
-    runs-on: ubuntu-latest
-    needs: prepare-base
-    steps:
-      - name: Check out code from GitHub
-        uses: actions/checkout@v5
-      - name: Set up Python ${{ env.DEFAULT_PYTHON }}
-        uses: actions/setup-python@v5
-        id: python
-        with:
-          python-version: ${{ env.DEFAULT_PYTHON }}
-      - name: Restore base Python virtual environment
-        id: cache-venv
-        uses: actions/cache@v4
-        with:
-          path: venv
-          key: >-
-            ${{ env.CACHE_VERSION}}-${{ runner.os }}-base-venv-${{
-            steps.python.outputs.python-version }}-${{
-            hashFiles('requirements.txt') }}-${{
-            hashFiles('requirements_test.txt') }}
-      - name: Fail job if Python cache restore failed
-        if: steps.cache-venv.outputs.cache-hit != 'true'
-        run: |
-          echo "Failed to restore Python virtual environment from cache"
-          exit 1
-      - name: Restore pre-commit environment from cache
-        id: cache-precommit
-        uses: actions/cache@v4
-        with:
-          path: ${{ env.PRE_COMMIT_HOME }}
-          key: |
-            ${{ env.CACHE_VERSION}}-${{ runner.os }}-pre-commit-${{ hashFiles('.pre-commit-config.yaml') }}
-      - name: Fail job if cache restore failed
-        if: steps.cache-venv.outputs.cache-hit != 'true'
-        run: |
-          echo "Failed to restore Python virtual environment from cache"
-          exit 1
-      - name: Run pyupgrade
+          pre-commit run ruff --all-files --show-diff-on-failure
+      - name: Run ruff-format
         run: |
           . venv/bin/activate
-          pre-commit run --hook-stage manual pyupgrade --all-files --show-diff-on-failure
+          pre-commit run ruff-format --all-files --show-diff-on-failure
 
   lint-yaml:
     name: Check YAML
@@ -475,8 +375,7 @@ jobs:
           key: >-
             ${{ env.CACHE_VERSION}}-${{ runner.os }}-base-venv-${{
             steps.python.outputs.python-version }}-${{
-            hashFiles('requirements.txt') }}-${{
-            hashFiles('requirements_test.txt') }}
+            hashFiles('pyproject.toml') }}
       - name: Fail job if Python cache restore failed
         if: steps.cache-venv.outputs.cache-hit != 'true'
         run: |
@@ -516,4 +415,4 @@ jobs:
           pip install pylint
       - name: Analysing the code with pylint
         run: |
-          python -m pylint --fail-under=10 `find -regextype egrep -regex '(.*.py)$'`
+          python -m pylint --fail-under=10 `find -regextype egrep -regex '(.*.py)$' -not -path './graphify-out/*'`

.github/workflows/dev-release-pr.yml

@@ -30,18 +30,18 @@ jobs:
             echo "PR #$existing already open; skipping version bump."
           fi
 
-      - name: Bump patch version in setup.py
+      - name: Bump patch version in pyproject.toml
         if: steps.check.outputs.existing == ''
         run: |
           python - <<'PY'
           import re, pathlib
-          p = pathlib.Path("setup.py")
+          p = pathlib.Path("pyproject.toml")
           s = p.read_text()
-          m = re.search(r'version="(\d+)\.(\d+)\.(\d+)"', s)
+          m = re.search(r'^version\s*=\s*"(\d+)\.(\d+)\.(\d+)"', s, re.MULTILINE)
           if not m:
-              raise SystemExit("version not found")
+              raise SystemExit("version not found in pyproject.toml")
           maj, mnr, pat = map(int, m.groups())
-          new = f'version="{maj}.{mnr}.{pat+1}"'
+          new = f'version = "{maj}.{mnr}.{pat+1}"'
           p.write_text(s[:m.start()] + new + s[m.end():])
           print("Bumped to", new)
           PY
@@ -51,7 +51,7 @@ jobs:
         run: |
           git config user.name  "github-actions[bot]"
           git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
-          git add setup.py
+          git add pyproject.toml
           if ! git diff --cached --quiet; then
             git commit -m "chore: bump version [skip ci]"
             git push

.github/workflows/release-on-master.yml

@@ -15,10 +15,10 @@ jobs:
         with:
           fetch-depth: 0
 
-      - name: Read version from setup.py
+      - name: Read version from pyproject.toml
         id: version
         run: |
-          v=$(python -c "import re; print(re.search(r'version=\"([^\"]+)\"', open('setup.py').read()).group(1))")
+          v=$(python -c "import re; m=re.search(r'^version\s*=\s*\"([^\"]+)\"', open('pyproject.toml').read(), re.MULTILINE); print(m.group(1))")
           echo "version=$v" >> "$GITHUB_OUTPUT"
           echo "tag=v$v" >> "$GITHUB_OUTPUT"