ci(actions): upgrade to ubuntu 24.04 and Python 3.12 (#465)

.github/workflows/ci.yml

@@ -10,7 +10,7 @@ on: [push, pull_request]
 
 jobs:
   lint-commitlint:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     steps:
       - name: Checkout
         uses: actions/checkout@v4
@@ -33,10 +33,10 @@ jobs:
       - name: Check commit message compliance of the pull request
         if: github.event_name == 'pull_request'
         run: |
-          ./run-tests.sh --check-commitlint ${{ github.event.pull_request.head.sha }}~${{ github.event.pull_request.commits }} ${{ github.event.pull_request.head.sha }} ${{ github.event.pull_request.number }}
+          ./run-tests.sh --check-commitlint ${{ github.event.pull_request.base.sha }} ${{ github.event.pull_request.head.sha }} ${{ github.event.pull_request.number }}
 
   lint-shellcheck:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     steps:
       - name: Checkout
         uses: actions/checkout@v4
@@ -47,79 +47,79 @@ jobs:
           ./run-tests.sh --check-shellcheck
 
   lint-black:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     steps:
       - name: Checkout
         uses: actions/checkout@v4
 
       - name: Setup Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.8"
+          python-version: "3.12"
 
       - name: Check Python code formatting
         run: |
           pip install black
           ./run-tests.sh --check-black
 
   lint-flake8:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     steps:
       - name: Checkout
         uses: actions/checkout@v4
 
       - name: Setup Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.8"
+          python-version: "3.12"
 
       - name: Check compliance with pep8, pyflakes and circular complexity
         run: |
           pip install flake8
           ./run-tests.sh --check-flake8
 
   lint-pydocstyle:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     steps:
       - name: Checkout
         uses: actions/checkout@v4
 
       - name: Setup Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.8"
+          python-version: "3.12"
 
       - name: Check compliance with Python docstring conventions
         run: |
           pip install pydocstyle
           ./run-tests.sh --check-pydocstyle
 
   lint-check-manifest:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     steps:
       - name: Checkout
         uses: actions/checkout@v4
 
       - name: Setup Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.8"
+          python-version: "3.12"
 
       - name: Check Python manifest completeness
         run: |
           pip install check-manifest
           ./run-tests.sh --check-manifest
 
   docs-sphinx:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     steps:
       - name: Checkout
         uses: actions/checkout@v4
 
       - name: Setup Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.8"
+          python-version: "3.12"
 
       - name: Install system dependencies
         run: |
@@ -140,7 +140,7 @@ jobs:
         run: ./run-tests.sh --check-sphinx
 
   python-tests:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     strategy:
       matrix:
         python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
@@ -168,7 +168,7 @@ jobs:
         run: ./run-tests.sh --check-pytest
 
       - name: Codecov Coverage
-        if: matrix.python-version == '3.8'
+        if: matrix.python-version == '3.12'
         uses: codecov/codecov-action@v4
         with:
           token: ${{ secrets.CODECOV_TOKEN }}

.readthedocs.yaml

@@ -7,9 +7,9 @@
 version: 2
 
 build:
-  os: ubuntu-22.04
+  os: ubuntu-24.04
   tools:
-    python: "3.8"
+    python: "3.12"
 
 sphinx:
   configuration: docs/conf.py

run-tests.sh

@@ -16,15 +16,28 @@ check_commitlint () {
     npx commitlint --from="$from" --to="$to"
     found=0
     while IFS= read -r line; do
-        if echo "$line" | grep -qP "\(\#$pr\)$"; then
-            true
-        elif echo "$line" | grep -qP "^chore\(.*\): release"; then
-            true
-        else
-            echo "✖   Headline does not end by '(#$pr)' PR number: $line"
+        commit_hash=$(echo "$line" | cut -d ' ' -f 1)
+        commit_title=$(echo "$line" | cut -d ' ' -f 2-)
+        commit_number_of_parents=$(git rev-list --parents "$commit_hash" -n1 | awk '{print NF-1}')
+        # (i) skip checking release commits generated by Release Please
+        if [ "$commit_number_of_parents" -le 1 ] && echo "$commit_title" | grep -qP "^chore\(.*\): release"; then
+            continue
+        fi
+        # (ii) check presence of PR number
+        if ! echo "$commit_title" | grep -qP "\(\#$pr\)$"; then
+            echo "✖   Headline does not end by '(#$pr)' PR number: $commit_title"
             found=1
         fi
-    done < <(git log "$from..$to" --format="%s")
+        # (iii) check absence of merge commits in feature branches
+        if [ "$commit_number_of_parents" -gt 1 ]; then
+            if echo "$commit_title" | grep -qP "^chore\(.*\): merge "; then
+                break  # skip checking maint-to-master merge commits
+            else
+                echo "✖   Merge commits are not allowed in feature branches: $commit_title"
+                found=1
+            fi
+        fi
+    done < <(git log "$from..$to" --format="%H %s")
     if [ $found -gt 0 ]; then
         exit 1
     fi

setup.py

@@ -38,11 +38,15 @@
     ],
     "cwl": ["cwltool==3.1.20210628163208"],
     "snakemake": [
-        "snakemake==7.32.4",
+        # install patched version of snakemake v7 that works with Python 3.12
+        # see https://github.com/snakemake/snakemake/issues/2480
+        # see https://github.com/snakemake/snakemake/issues/2648
+        # see https://github.com/snakemake/snakemake/issues/2657
+        "snakemake @ git+https://github.com/mdonadoni/snakemake.git@cea31624976989ad0645eb2e1751260d32259506",  # branch `7.32.4-python3.12`
         "pulp>=2.7.0,<2.8.0",
     ],
     "snakemake-reports": [
-        "snakemake[reports]==7.32.4",
+        "snakemake[reports] @ git+https://github.com/mdonadoni/snakemake.git@cea31624976989ad0645eb2e1751260d32259506",  # branch `7.32.4-python3.12`
         "pulp>=2.7.0,<2.8.0",
     ],
 }