Refresh this CPG repo template

.github/workflows/lint.yaml

@@ -1,5 +1,10 @@
-name: Lint
-on: [push]
+name: Run pre-commit hooks
+on:
+  # Running on pull-requests and new pushes to main
+  pull_request:
+  push:
+    branches:
+      - main
 
 jobs:
   lint:
@@ -11,12 +16,14 @@ jobs:
     steps:
     - uses: actions/checkout@v4
 
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
-        python-version: '3.10'
+        python-version: '3.11'
+        cache: 'pip'
+        cache-dependency-path: pyproject.toml
 
     - name: Install packages
-      run: pip install -r requirements-dev.txt
+      run: pip install .[dev]
 
     - name: Install pre-commit hooks
       run: pre-commit install --install-hooks

.github/workflows/test.yaml

@@ -0,0 +1,28 @@
+name: Test
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - uses: actions/setup-python@v5
+      with:
+        python-version: '3.11'
+        cache: 'pip'
+        cache-dependency-path: pyproject.toml
+
+    - name: Install packages
+      run: pip install .[test]
+
+    - name: Run tests
+      run: pytest test

.gitignore

@@ -7,6 +7,7 @@ __pycache__/
 
 # local irrelevant files
 .idea
+.vscode
 .DS_Store
 
 # C extensions

.pre-commit-config.yaml

@@ -1,6 +1,8 @@
+default_language_version:
+  python: python3.11
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v6.0.0
     hooks:
       - id: check-yaml
         exclude: '\.*conda/.*'
@@ -13,35 +15,19 @@ repos:
       - id: debug-statements
       - id: check-added-large-files
 
-  - repo: https://github.com/igorshubovych/markdownlint-cli
-    rev: v0.38.0
-    hooks:
-      - id: markdownlint
-
   - repo: https://github.com/populationgenomics/pre-commits
     rev: "v0.1.3"
     hooks:
       - id: cpg-id-checker
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    # Ruff version.
-    rev: v0.6.2
+    rev: v0.15.12
     hooks:
       - id: ruff
-        args: ["--fix"]
       - id: ruff-format
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.8.0
+    rev: v1.20.2
     hooks:
       - id: mypy
-        args:
-          [
-            --pretty,
-            --show-error-codes,
-            --no-strict-optional,
-            --ignore-missing-imports,
-            --install-types,
-            --non-interactive,
-          ]
-        additional_dependencies: [types-PyYAML==6.0.4, types-toml]
+        args: [--pretty, --show-error-codes, --install-types, --non-interactive]

README.md

@@ -1,6 +1,25 @@
 # CPG Python Template
 
-Template repository based on the [CPG team-docs](https://github.com/populationgenomics/team-docs/blob/main/new_repository.md) content.
+General-purpose template for CPG Python repositories. Provides project structure, linting, type checking, testing, and CI out of the box. Works as a scripts-only repo (just linting, no installation) or as an installable package — see the comments at the top of `pyproject.toml`.
 
-This contains python and markdown linting configuration, and a github linting action.
-Before making a new repository based on this template, it may be worth auditing the versions of linting tools and GitHub Actions listed in _.pre-commit-config.yaml_ and _.github/workflows_.
+## What's included
+
+- `pyproject.toml` with hatchling build, ruff linting, mypy, pytest config
+- `.pre-commit-config.yaml` with ruff, mypy, and CPG ID checker hooks
+- GitHub Actions for linting and testing
+- `src/` layout with placeholder package
+- `test/` directory with pytest
+
+## Quick start
+
+1. Create a new repo from this template
+2. Rename `package_name` in `src/`, `pyproject.toml`, and hatch build config
+3. Update the project name, description, and repository URL in `pyproject.toml`
+4. Add your dependencies to `pyproject.toml`
+5. Install: `pip install .[dev]`
+6. Run linting: `pre-commit run --all-files`
+7. Run tests: `pytest test`
+
+## For cpg-flow workflows
+
+If you're building a cpg-flow pipeline, use the [cpg-flow-pipeline-template](https://github.com/populationgenomics/cpg-flow-pipeline-template) instead. It extends this template with stages, jobs, scripts, Docker builds, and Artifact Registry CI.

pull_request_template.md

@@ -0,0 +1,14 @@
+# Purpose
+
+  - < The reason for this PR >
+
+## Proposed Changes
+
+  -
+  -
+
+## Checklist
+
+- [ ] Related GitHub Issue created
+- [ ] Tests covering new change
+- [ ] Linting checks pass

pyproject.toml

@@ -1,22 +1,73 @@
+# This template supports two use cases:
+#   1. Scripts repo — linting/formatting only, no installation required.
+#      Remove the [build-system], [tool.hatch.*], and [project] sections;
+#      keep everything from [tool.ruff] onward.
+#   2. Installable package — the default. Uses src/ layout with hatchling.
+#      Replace "package_name" with your package name in [project], [tool.hatch.*],
+#      and the src/ directory.
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/package_name"]
+
+[tool.hatch.build.targets.wheel.sources]
+"src" = ""
+
+[project]
+# TODO: replace with your project name
+name = "package_name"
+# TODO: replace with your project description
+description = "TODO: project description"
+readme = "README.md"
+requires-python = ">=3.10"
+version = "0.1.0"
+license = { file = "LICENSE" }
+classifiers = [
+    "Environment :: Console",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Natural Language :: English",
+    "Operating System :: Unix",
+    "Programming Language :: Python",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+dependencies = []
+
+[project.optional-dependencies]
+dev = ["pre-commit", "pytest", "bump-my-version"]
+test = ["pytest"]
+
+[project.urls]
+# TODO: replace with your project repository URL
+Repository = "https://github.com/populationgenomics/package_name"
+
+
+[tool.pytest.ini_options]
+testpaths = ["test"]
+
 [tool.ruff]
 line-length = 120
 
 [tool.ruff.format]
 quote-style = "single"
 
 [tool.ruff.lint]
-# ignore pydocstyle, flake8-boolean-trap (FBT)
-select = ["A", "B", "C",  "E", "F", "G", "I", "N", "Q", "S", "W", "ANN", "ARG", "BLE", "COM", "DJ", "DTZ", "ERA", "EXE", "ICN", "ISC", "NPY", "PD", "PGH", "PIE", "PL", "PT", "PYI", "RET", "RSE", "RUF", "SIM", "SLF", "TCH", "TID", "UP", "YTT"]
+select = ["A", "B", "C", "E", "F", "G", "I", "N", "Q", "S", "W", "ANN", "ARG", "BLE", "COM", "DJ", "DTZ", "ERA", "EXE", "ICN", "ISC", "NPY", "PD", "PGH", "PIE", "PL", "PT", "PYI", "RET", "RSE", "RUF", "SIM", "SLF", "TCH", "TID", "UP", "YTT"]
 
-fixable = ["A", "B", "C", "D", "E", "F", "G", "I", "N", "Q", "S", "T", "W", "ANN", "ARG", "BLE", "COM", "DJ", "DTZ", "ERA", "EXE", "FBT", "ICN", "ISC", "NPY", "PD", "PGH", "PIE", "PL", "PT", "PYI", "RET", "RSE", "RUF", "SIM", "SLF", "TCH", "TID", "UP", "YTT"]
+fixable = ["ALL"]
 
 ignore = [
-    "ANN101",  # Missing type annotation for self in method
+    "ANN001",  # Missing type annotation for function argument
     "ANN201",  # Missing return type annotation for public function
-    "ANN401",  # Dynamically typed expressions (typing.Any) are disallowed in `**kwargs`
+    "ANN204",  # Missing type annotation for special method __init__
+    "ANN401",  # Dynamically typed expressions (typing.Any) are disallowed
+    "COM812",  # Trailing comma prohibited
     "G004",    # Logging statement uses f-string
-    "PLW0603", # Using the global statement to update `<VAR>` is discouraged
-    "PT018",   # Assertion should be broken down into multiple parts
+    "PLR0913", # Too many arguments in function definition
+    "PLR2004", # Magic value used in comparison
     "Q000",    # Single quotes found but double quotes preferred
     "S101",    # Use of assert detected
 ]
@@ -26,15 +77,7 @@ section-order = ["future", "standard-library", "third-party", "hail", "cpg", "fi
 
 [tool.ruff.lint.isort.sections]
 hail = ["hail", "hailtop"]
+cpg = ["cpg_flow", "cpg_utils", "cpg_infra", "metamist", "analysis_runner"]
 
-# Adjust these for each repository, e.g., removing those that should be
-# local rather than CPG. Also fill in extend_skip below if there are any
-# subdirectories that should be ignored.
-cpg = [
-    "analysis_runner",
-    "cpg_infra",
-    "cpg_utils",
-    "cpg_workflows",
-    "gnomad",
-    "metamist",
-]
+[tool.mypy]
+ignore_missing_imports = true

src/package_name/__init__.py

@@ -0,0 +1 @@
+# TODO: put something here

test/test_placeholder.py

@@ -0,0 +1,5 @@
+# TODO: put something here
+
+
+def test_placeholder():
+    assert True