Update image and packages

.github/workflows/build.yaml

@@ -9,6 +9,7 @@ on:
 
 jobs:
   push-to-ghcr-and-gar:
+    name: Build docker image and publish to GHCR and GAR
     runs-on: ubuntu-22.04
 
     permissions:

.github/workflows/ci.yaml

@@ -7,7 +7,57 @@ on:
     branches: [main]
 
 jobs:
+  check-version:
+    name: Ensure version has been bumped
+    runs-on: ubuntu-22.04
+    if: github.event_name == 'pull_request' # Only run on PRs
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Install Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+
+      - name: Install toml package
+        run: pip install toml
+
+      - name: Check version
+        run: |
+          # Read current version from PR branch
+          CURRENT_VERSION=$(python -c "import toml; print(toml.load('pyproject.toml')['project']['version'])")
+          echo "Current version: $CURRENT_VERSION"
+
+          # Checkout main branch to compare
+          git fetch origin main
+          git checkout origin/main
+
+          # Read version from main branch
+          MAIN_VERSION=$(python -c "import toml; print(toml.load('pyproject.toml')['project']['version'])")
+          echo "Main version: $MAIN_VERSION"
+
+          # Checkout back to PR branch
+          git checkout -
+
+          # Compare versions
+          if [ "$CURRENT_VERSION" = "$MAIN_VERSION" ]; then
+            echo "Error: Version has not been bumped from $MAIN_VERSION"
+            exit 1
+          fi
+
+          # Check if new version already exists as a tag
+          if git rev-parse "v$CURRENT_VERSION" >/dev/null 2>&1; then
+            echo "Error: Version v$CURRENT_VERSION already exists as a tag"
+            exit 1
+          fi
+
+          echo "Version v$CURRENT_VERSION is new and has been bumped from v$MAIN_VERSION"
+
   test:
+    name: Run tests
     runs-on: ubuntu-22.04
 
     steps:
@@ -31,6 +81,7 @@ jobs:
         run: uv run pytest
 
   lint:
+    name: Check code style
     runs-on: ubuntu-22.04
 
     steps:

Dockerfile

@@ -5,7 +5,7 @@
 #
 # docker run -v /path/to/credentials.json:/app/credentials.json -e GOOGLE_APPLICATION_CREDENTIALS=/app/credentials.json pis -s so
 
-FROM python:3.12.8-alpine3.21
+FROM python:3.13.1-alpine3.21
 COPY --from=ghcr.io/astral-sh/uv:latest /uv /bin/uv
 
 ADD . /app

pyproject.toml

@@ -1,9 +1,9 @@
 [project]
 name = "PIS"
-version = "24.7.3"
-description = "Open Target's Pipeline Input Stage Application"
+version = "25.0.0-rc.1"
+description = "Open Targets Pipeline Input Stage application"
 readme = "README.md"
-requires-python = ">=3.12"
+requires-python = ">=3.13"
 authors = [{ name = "Open Targets core team", email = "devs@opentargets.net" }]
 license = { text = "Apache-2.0" }
 dependencies = [
@@ -21,10 +21,12 @@ dependencies = [
 [tool.uv]
 override-dependencies = ["urllib3>=2.2.0"]
 
+[dependency-groups]
+dev = ["ruff==0.8.5", "deptry==0.21.2"]
+
 [project.optional-dependencies]
-dev = ["ruff==0.8.4", "deptry==0.21.2"]
 test = [
-  "coverage==7.6.9",
+  "coverage==7.6.10",
   "freezegun==1.5.1",
   "pytest==8.3.4",
   "pytest-mock==3.14.0",
@@ -69,6 +71,9 @@ target-version = 'py312'
 line-length = 120
 preview = true
 
+[tool.ruff.format]
+quote-style = 'single'
+
 [tool.ruff.lint]
 select = [
   'E',      # pycodestyle
@@ -173,14 +178,6 @@ extend-safe-fixes = [
   'PERF102', # ^ likewise
 ]
 
-[tool.ruff.format]
-quote-style = 'single'
-
-[tool.ruff.lint.per-file-ignores]
-'**/*_test.py' = ['S108', 'S602', 'D']
-'**/__init__.py' = ['F401']
-'**/tasks/*.py' = ['D102']
-
 [tool.ruff.lint.flake8-quotes]
 inline-quotes = 'single'
 multiline-quotes = 'double'
@@ -194,6 +191,11 @@ parametrize-names-type = 'tuple'
 parametrize-values-type = 'list'
 parametrize-values-row-type = 'tuple'
 
+[tool.ruff.lint.per-file-ignores]
+'**/*_test.py' = ['S108', 'S602', 'D']
+'**/__init__.py' = ['F401']
+'**/tasks/*.py' = ['D102']
+
 [tool.ruff.lint.pydocstyle]
 convention = "google"
 ignore-decorators = ["pis.tasks.report", "pis.manifest.task_reporter.report"]