Turn the template into a cruft template

.github/workflows/test.yaml

@@ -1,31 +1,38 @@
-name: Tests
+name: Template
 
 on:
   push:
     branches: [main]
   pull_request:
     branches: [main]
   schedule:
-    # Run weekly on Mondays at 6:00 UTC
+    # Weekly, to catch upstream releases that break a freshly created project
     - cron: "0 6 * * 1"
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
 jobs:
-  test:
-    name: Run pytest
+  generate:
+    name: Create a project and run its checks
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-        with:
-          filter: blob:none
-          fetch-depth: 0
+      - uses: astral-sh/setup-uv@v6
+      - name: Create a project with the default answers
+        run: uvx cruft create . --no-input --output-dir "$RUNNER_TEMP"
+      - name: Put it under git, as the README's create steps do
+        working-directory: ${{ runner.temp }}/my-analysis
+        run: git init -q -b main && git add -A
       - uses: prefix-dev/setup-pixi@v0.8.0
         with:
           pixi-version: v0.60.0
-          cache: true
-          frozen: true
+          manifest-path: ${{ runner.temp }}/my-analysis/pixi.toml
+          cache: false
       - name: Run tests
+        working-directory: ${{ runner.temp }}/my-analysis
         run: pixi run test
+      - name: Run pre-commit
+        working-directory: ${{ runner.temp }}/my-analysis
+        run: pixi run pre-commit run --all-files

.gitignore

@@ -1,182 +1,7 @@
-# Byte-compiled / optimized / DLL files
 __pycache__/
-*.py[cod]
-*$py.class
-
-# C extensions
-*.so
-
-# Distribution / packaging
-.Python
-build/
-develop-eggs/
-dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-wheels/
-pip-wheel-metadata/
-share/python-wheels/
-*.egg-info/
-.installed.cfg
-*.egg
-MANIFEST
-
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
-
-# Unit test / coverage reports
-htmlcov/
-.tox/
-.nox/
-.coverage
-.coverage.*
-.cache
-nosetests.xml
-coverage.xml
-*.cover
-*.py,cover
-.hypothesis/
-.pytest_cache/
-
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
-local_settings.py
-db.sqlite3
-db.sqlite3-journal
-
-# Flask stuff:
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
-
-# Sphinx documentation
-docs/_build/
-
-# PyBuilder
-target/
-
-# Jupyter Notebook
-.ipynb_checkpoints
-
-# IPython
-profile_default/
-ipython_config.py
-
-# pyenv
-.python-version
-
-# pipenv
-#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
-#   However, in case of collaboration, if having platform-specific dependencies or dependencies
-#   having no cross-platform support, pipenv may install dependencies that don't work, or not
-#   install all needed dependencies.
-#Pipfile.lock
-
-# PEP 582; used by e.g. github.com/David-OConnor/pyflow
-__pypackages__/
-
-# Celery stuff
-celerybeat-schedule
-celerybeat.pid
-
-# SageMath parsed files
-*.sage.py
-
-# Environments
-.env
-.venv
-env/
-venv/
-ENV/
-env.bak/
-venv.bak/
-.pixi/
-
-# Spyder project settings
-.spyderproject
-.spyproject
-
-# Rope project settings
-.ropeproject
-
-# mkdocs documentation
-/site
-
-# mypy
-.mypy_cache/
-.dmypy.json
-dmypy.json
-
-# Pyre type checker
-.pyre/
-
-# patterns to prevent data and figures from being uploaded
-*.csv
-*.pickle
-*.h5ad
-*.RData
-*.loom
-*.pdf
-*.eps
-*.png
-*.jpg
-*.jpeg
-*.svg
-*.mtx
-*.txt
-*.rds
-*.npz
-*.h5
-*.txt.gz
-*.gmt
-*.gmx
-
-*.zarr
-
-# Data never enters git; only its READMEs and placeholders do.
-data/**
-!data/**/
-!data/**/README.md
-!data/**/.gitkeep
-
-# Directories to ignore. Unanchored, so they also match inside every analysis task directory
-# (analysis/<topic>/.../<name>_vN/): the untracked half of a task, anchored to the main checkout.
-figures/
-outputs/
-logs/
-
-# A task's results/ (small evidence tables) is tracked even though *.csv / *.txt are ignored above.
-!analysis/**/results/**/*.csv
-!analysis/**/results/**/*.txt
-
-# OS specifics
+.ruff_cache/
 **.DS_Store
 
-# R stuff
-*.Rhistory
-
-.vscode/*
-.github/prompts/*
-
 # Claude Code local files (personal settings + local agent worktrees)
 .claude/settings.local.json
 .claude/worktrees/