diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index 7485677..fdccce0 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -1,4 +1,4 @@ -name: Tests +name: Template on: push: @@ -6,7 +6,7 @@ on: 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: @@ -14,18 +14,25 @@ concurrency: 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: ${{ runner.temp }}/my-analysis + run: pixi run pre-commit run --all-files diff --git a/.gitignore b/.gitignore index fa3cbba..d6d1d50 100644 --- a/.gitignore +++ b/.gitignore @@ -1,182 +1,7 @@ -# Byte-compiled / optimized / DLL files __pycache__/ -*.py[cod] -*$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//.../_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/ diff --git a/CLAUDE.md b/CLAUDE.md deleted file mode 100644 index 5a69517..0000000 --- a/CLAUDE.md +++ /dev/null @@ -1,3 +0,0 @@ -# Analysis Template Agent Entry Point - -@AGENTS.md diff --git a/README.md b/README.md index dc650eb..0148a6f 100644 --- a/README.md +++ b/README.md @@ -1,295 +1,47 @@ -# 🧬 Analysis Template +# 🧬 analysis_template -A notebook-first template for single-cell/spatial analysis projects. Uses [pixi](https://pixi.sh) for environment management. +A [cruft](https://cruft.github.io/cruft/) template for notebook-first single-cell and spatial analysis +repos, managed with [pixi](https://pixi.sh). Humans work in notebooks; coding agents follow the +[analysis-workflow](https://github.com/quadbio/analysis-workflow) plugin, which every generated repo enables. -> If you're building a reusable Python library, use the [scverse cookiecutter](https://github.com/scverse/cookiecutter-scverse) instead. +> Building a reusable Python library? Use the [scverse cookiecutter](https://github.com/scverse/cookiecutter-scverse) instead. ---- - -## πŸš€ Getting Started - -**You've initialized a new repo from this templateβ€”great!** Follow these steps to set up your project. - -### Step 1: Install pixi - -*Skip this if you already have pixi installed.* - -```bash -# macOS / Linux -curl -fsSL https://pixi.sh/install.sh | bash - -# Or with Homebrew (macOS) -brew install pixi -``` - -Restart your terminal after installation. See [pixi installation docs](https://pixi.sh/latest/#installation) for Windows and other options. - -### Step 1b: Install GitHub CLI (optional) - -*Recommended if you're working on a remote server and need to authenticate with GitHub.* - -```bash -# macOS -brew install gh - -# Linux (no sudo required) -curl -sS https://webi.sh/gh | sh -``` - -Then authenticate: `gh auth login`. See [GitHub CLI installation docs](https://github.com/cli/cli#installation) for more options. - -### Step 2: Clone your repo locally - -```bash -git clone -cd -``` - -The URL depends on your authentication method: -- **HTTPS**: `https://github.com/owner/repo.git` -- **SSH**: `git@github.com:owner/repo.git` -- **GitHub CLI**: `gh repo clone owner/repo` - -### Step 3: Customize the template - -The template ships with a placeholder package name (`myanalysis`) and project -name (`analysis-template`). Rename them in one shot with the included script -(stdlib-only, so run it with plain `python` *before* installing the env): - -```bash -python scripts/rename_package.py myproject -# or set the Jupyter kernel display name explicitly: -python scripts/rename_package.py myproject --display-name "My Project" -``` - -This renames `src/myanalysis/` β†’ `src/myproject/` and updates every reference in -`pyproject.toml`, `pixi.toml` (package + workspace + kernel name), `tests/`, and -the notebooks under `analysis/`. - -Then finish by hand: - -| File | What to change | -|------|----------------| -| `pixi.toml` | Update `[workspace]` `description` and `authors` | -| `README.md` | Replace with your own project documentation (Step 6 / later) | - -> Doing it manually instead? The placeholder `myanalysis` appears in -> `pyproject.toml`, the `src/myanalysis/` folder name, `pixi.toml` -> (`[pypi-dependencies]`), `tests/test_basic.py`, and the demo notebook; the -> project name `analysis-template` and the kernel `display-name` live in the -> `pixi.toml` `[tasks]` `install-kernel` command. The script handles all of them. - -### Step 4: Set up the environment - -```bash -pixi install # create environment from pixi.toml -pixi run install-hooks # pre-commit hooks -pixi run install-kernel # register Jupyter kernel -``` - -> **Notebook outputs are committed.** They are the record of what a notebook actually -> produced, and GitHub renders them. Keep them small: clear a notebook by hand before -> committing if it carries a huge embedded image or an accidental dump. - -πŸ’‘ **Tip**: Use `pixi shell` to enter the environment interactivelyβ€”then you can run commands directly without the `pixi run` prefix. - -### Step 5: Verify your setup - -```bash -pixi run test # should pass (tests your package imports correctly) -pixi run lab # opens Jupyter Lab -``` - -In Jupyter Lab, check that your kernel appears (look for the name you set in `pixi.toml`). - -### Step 6: Make your first commit - -```bash -git add -A -git commit -m "Initial project setup" -git push -``` - -πŸ’‘ Pre-commit hooks will run and may reformat some files. If so, just `git add -A && git commit -m "Initial project setup"` again. - -πŸŽ‰ **You're ready to start analyzing!** - ---- - -## πŸ“Š Start Your Analysis - -- **Demo notebook**: Check out `analysis/ML-2026-01-27_demo_scRNA_workflow.ipynb` for a complete scRNA-seq workflow example using scanpy's PBMC 3k dataset. -- **New notebooks**: Copy `analysis/XX-2026-01-27_sample_notebook.ipynb` as a starting point. Follow the naming convention: `[INITIALS]-[YYYY]-[MM]-[DD]_description.ipynb`. -- **Add your data**: Create folders under `data/` and register paths in `src//_constants.py`. -- **Replace this README** with your project documentation once you're set up. - ---- - -## πŸ€– Working with coding agents - -Agents follow [`AGENTS.md`](AGENTS.md) and the -[analysis-workflow](https://github.com/quadbio/analysis-workflow) Claude Code plugin (a skill plus -guard hooks) that this repo enables. Install the plugin once per machine: +## Create a project ```bash -claude plugin marketplace add quadbio/claude-plugins -claude plugin install analysis-workflow@quadbio +uvx cruft create https://github.com/quadbio/analysis_template +cd my-analysis +git init -b main # before pixi install: the package takes its version from git +pixi install +pixi run install-hooks +pixi run test +git add -A && git commit -m "Create from analysis_template" ``` ---- +You're prompted for the repository name, the package name (derived from it), a description, and your +name and e-mail. Then push it, e.g. `gh repo create /my-analysis --private --source . --push`. The +generated `README.md` takes it from there. -## β˜• Daily Workflow +## Update a project ```bash -cd your-project -pixi shell # activate environment -jupyter lab # work in notebooks, or start via jupyter-hub -# ... do your analysis ... -exit # leave pixi shell when done -``` - -Or run commands directly without entering the shell: - -```bash -pixi run lab # start Jupyter Lab -pixi run python script.py # run a script -``` - ---- - -## πŸ“š Reference - -
-πŸ“¦ What is pixi? - -[Pixi](https://pixi.sh) is a modern package manager that handles both **conda** and **PyPI** packages in one tool: - -- πŸ”’ Creates **isolated environments** per project -- πŸ”€ Installs from **conda-forge AND PyPI** together -- πŸ“Œ Locks exact versions for **reproducibility** (`pixi.lock`) -- πŸ’» Works **cross-platform** (macOS, Linux, Windows) - -**You don't need conda or pip installed** β€” pixi handles everything! - -
- -
-βž• Adding packages - -All dependencies live in `pixi.toml`. To add a new package: - -```bash -# From conda-forge (preferred for scientific packages) -pixi add numpy -pixi add "scanpy>=1.10" - -# From PyPI (when not on conda-forge) -pixi add --pypi some-package -``` - -Or edit `pixi.toml` directly and run `pixi install`. - -πŸ’‘ **Tip**: Prefer PyPI packages when available β€” mixing conda and pip can cause dependency conflicts. - -πŸ‘‰ See [pixi documentation](https://pixi.sh/latest/) for more details. - -
- -
-πŸ““ Data and notebook conventions - -- **Notebook naming**: `[INITIALS]-[YYYY]-[MM]-[DD]_description.ipynb` -- **Data layout** (one folder per dataset, gitignored): - - `data//raw/` β€” bytes as they arrived; never written by analysis - - `data//resources/` β€” curated inputs that are not data: gene lists, marker tables - - `data//processed/` β€” objects code loads to do new work, as AnnData `.zarr` - - `data//results/` β€” a notebook's own outputs, file names prefixed with the notebook's stem -- **Figures**: `figures//` -- **Import paths** via the local package: - -```python -from yourpackage import FilePaths -``` - -
- -
-πŸ”§ Pre-commit & code quality - -This template uses **pre-commit hooks** to automatically check your code before each commit: - -| Tool | What it does | -|------|--------------| -| [Ruff](https://docs.astral.sh/ruff/) | Lints and formats Python code + notebooks | -| [Biome](https://biomejs.dev/) | Formats JSON/JSONC files | -| [pyproject-fmt](https://github.com/tox-dev/pyproject-fmt) | Formats `pyproject.toml` | - -Hooks run automatically on `git commit`. To run manually: - -```bash -pre-commit run --all-files -``` - -πŸ’‘ If a check reformats your code, just `git add` the changes and commit again. - -
- -
-πŸ–₯️ GPU notes - -The **default** environment is CPU-only on every platform (on macOS, PyTorch -still uses MPS automatically). This is what `pixi install` and CI use. - -GPU acceleration lives in a separate **`gpu`** environment that you opt into -explicitly on a Linux/CUDA machine (e.g. ETH Euler): - -```bash -pixi install -e gpu # CUDA 12 build of JAX + rapids-singlecell -pixi run -e gpu install-kernel # register a kernel for the gpu env -pixi shell -e gpu # or activate it interactively -``` - -| Environment | PyTorch | JAX | rapids-singlecell | -|-------------|---------|-----|-------------------| -| `default` (all platforms) | βœ… (MPS on macOS) | CPU | ❌ | -| `gpu` (Linux + NVIDIA only) | βœ… CUDA | βœ… CUDA 12 | βœ… | - -> Keeping the GPU stack out of the default environment means CI and CPU-only -> machines don't try to resolve unusable CUDA wheels. See -> [rapids-singlecell](https://rapids-singlecell.readthedocs.io/). - -
- -
-πŸ”‘ Secrets & environment variables - -Store API keys and other secrets in a `.env` file at the repo root. It is -**gitignored** and must never be committed. - -```bash -cp .env.example .env # then fill in your real values -``` - -`.env.example` (tracked, placeholder values only) documents which variables the -project expects. Load them in a notebook or script with, e.g., -[python-dotenv](https://github.com/theskumar/python-dotenv): - -```python -from dotenv import load_dotenv -load_dotenv() +uvx cruft check # is this project behind the template? +uvx cruft update # apply the template's changes since the last update ``` -If you ever paste a real key into a tracked file, rotate it immediately in the -provider's dashboard β€” git history is hard to scrub. +Resolve conflicts and any `*.rej` files by hand; pre-commit refuses to commit either. `README.md`, +`analysis/`, `data/`, `src/` and `tests/` belong to the project once created, and updates leave them alone +(`[tool.cruft] skip` in its `pyproject.toml`). -
+A repo created before this template used cruft starts receiving updates with +`uvx cruft link https://github.com/quadbio/analysis_template`. -
-πŸ–§ Cluster usage +## Develop the template -For cluster usage (e.g., ETH Euler): +Everything a project gets lives under `{{cookiecutter.project_name}}/`; `cookiecutter.json` holds the prompts. +`uvx cookiecutter . --no-input -o ` renders your working tree (`cruft create` renders the last commit). +CI creates a project on every pull request and runs its tests and pre-commit. -- πŸ“š General docs: https://docs.hpc.ethz.ch/ -- πŸš€ Notebooks via JupyterHub: https://jupyter.euler.hpc.ethz.ch/hub/ +## License -
+[BSD 3-Clause](LICENSE). diff --git a/cookiecutter.json b/cookiecutter.json new file mode 100644 index 0000000..e09e33d --- /dev/null +++ b/cookiecutter.json @@ -0,0 +1,15 @@ +{ + "project_name": "my-analysis", + "package_name": "{{ cookiecutter.project_name | lower | replace('-', '_') }}", + "project_description": "Single-cell analysis project", + "author_full_name": "Your Name", + "author_email": "yourname@example.com", + "_copy_without_render": [".github/workflows/*.yaml"], + "__prompts__": { + "project_name": "Repository name, e.g. my-analysis", + "package_name": "Python import name of the local package", + "project_description": "One-line description", + "author_full_name": "Your full name", + "author_email": "Your e-mail address" + } +} diff --git a/hooks/pre_gen_project.py b/hooks/pre_gen_project.py new file mode 100644 index 0000000..381f094 --- /dev/null +++ b/hooks/pre_gen_project.py @@ -0,0 +1,23 @@ +"""Refuse answers that would render into a broken project.""" + +import keyword +import sys + +PACKAGE_NAME = "{{ cookiecutter.package_name }}" +# Rendered into TOML strings, which these characters would break. +TOML_VALUES = { + "project_description": r"""{{ cookiecutter.project_description }}""", + "author_full_name": r"""{{ cookiecutter.author_full_name }}""", + "author_email": r"""{{ cookiecutter.author_email }}""", +} + +# An identifier, and with `_` as `-` a valid distribution name: ASCII, letter first, letter or digit last. +if ( + not PACKAGE_NAME.isidentifier() + or keyword.iskeyword(PACKAGE_NAME) + or not (PACKAGE_NAME.isascii() and PACKAGE_NAME[0].isalpha() and PACKAGE_NAME[-1].isalnum()) +): + sys.exit(f"ERROR: package_name {PACKAGE_NAME!r} must be an ASCII identifier starting with a letter and ending with a letter or digit.") +for key, value in TOML_VALUES.items(): + if '"' in value or "\\" in value: + sys.exit(f"ERROR: {key} may not contain double quotes or backslashes.") diff --git a/pixi.lock b/pixi.lock deleted file mode 100644 index 4918c67..0000000 --- a/pixi.lock +++ /dev/null @@ -1,12247 +0,0 @@ -version: 6 -environments: - default: - channels: - - url: https://conda.anaconda.org/conda-forge/ - indexes: - - https://pypi.org/simple - options: - pypi-prerelease-mode: if-necessary-or-explicit - packages: - linux-64: - - conda: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2 - - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2 - - conda: https://conda.anaconda.org/conda-forge/noarch/_python_abi3_support-1.0-hd8ed1ab_2.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/attr-2.5.2-h39aace5_0.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.34.6-hb03c661_0.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.1.4-hbd8a1cb_0.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/cpython-3.12.12-py312hd8ed1ab_2.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/fftw-3.3.10-mpi_openmpi_h76e6d66_11.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/geos-3.14.1-h480dda7_0.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/hdf5-1.14.6-mpi_openmpi_h106f004_5.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/hypre-2.32.0-mpi_openmpi_h398ea61_1.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/icu-78.2-h33c6efd_0.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.3-hb9d3cd8_0.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.3-h659f571_0.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.45-default_hbd61a6d_105.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/libaec-1.1.5-h088129d_0.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/libamd-3.3.3-h456b2da_7100101.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/libblas-3.11.0-7_hc00574d_netlib.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/libbtf-2.3.2-hf02c80a_7100101.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/libcamd-3.3.3-hf02c80a_7100101.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/libcap-2.77-h3ff7636_0.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.11.0-7_h8e06fc2_netlib.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/libccolamd-3.3.4-hf02c80a_7100101.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/libcholmod-5.3.1-h9cf07ce_7100101.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/libcolamd-3.3.4-hf02c80a_7100101.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.18.0-h4e3cde8_0.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20250104-pl5321h7949ede_0.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/libevent-2.1.12-hf998b51_1.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.7.3-hecca717_0.conda - 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Run it once, right after cloning your new repo from the template and *before* -``pixi install`` (it uses only the standard library, so plain ``python`` works): - - python scripts/rename_package.py myproject - # or, with an explicit Jupyter display name: - python scripts/rename_package.py myproject --display-name "My Project" - -(Also available as ``pixi run rename`` once the environment is installed.) - -``PACKAGE`` must be a valid Python identifier (letters, digits, underscores; -not starting with a digit), e.g. ``myproject`` or ``pbmc_atlas``. The project -slug used for the pixi workspace and the Jupyter kernel is derived from it by -turning underscores into hyphens (``pbmc_atlas`` -> ``pbmc-atlas``). - -The script is intentionally dependency-free (stdlib only) so it runs before the -environment is installed. It does NOT touch README.md (you're meant to replace -that with your own project docs) or .env.example. -""" - -from __future__ import annotations - -import argparse -import re -import sys -from pathlib import Path - -OLD_PACKAGE = "myanalysis" -OLD_PROJECT = "analysis-template" -OLD_DISPLAY = "Analysis Template (Pixi)" - -REPO_ROOT = Path(__file__).resolve().parents[1] - -# Files in which to replace the package name (whole-word) and project slug. -TARGET_FILES = [ - "pyproject.toml", - "pixi.toml", - "tests/test_basic.py", -] -# Notebooks are scanned dynamically so new ones are picked up too. -NOTEBOOK_GLOB = "analysis/*.ipynb" - - -def _fail(msg: str) -> None: - sys.exit(f"error: {msg}") - - -def replace_in_file(path: Path, replacements: list[tuple[str, str]]) -> bool: - """Apply (pattern, repl) regex substitutions to a file. Returns True if changed.""" - if not path.exists(): - return False - original = path.read_text() - text = original - for pattern, repl in replacements: - text = re.sub(pattern, repl, text) - if text != original: - path.write_text(text) - return True - return False - - -def main() -> None: - parser = argparse.ArgumentParser(description="Rename the template package/project in place.") - parser.add_argument("package", help="New package import name (valid Python identifier, e.g. 'myproject').") - parser.add_argument( - "--display-name", - default=None, - help="Jupyter kernel display name (default: derived from the package name).", - ) - args = parser.parse_args() - - new_package = args.package - if not new_package.isidentifier(): - _fail(f"{new_package!r} is not a valid Python identifier (use letters, digits, underscores).") - if new_package == OLD_PACKAGE: - _fail(f"the new name equals the placeholder {OLD_PACKAGE!r}; nothing to do.") - - new_project = new_package.replace("_", "-") - new_display = args.display_name or f"{new_package.replace('_', ' ').title()} (Pixi)" - - src_old = REPO_ROOT / "src" / OLD_PACKAGE - src_new = REPO_ROOT / "src" / new_package - if not src_old.is_dir(): - _fail( - f"{src_old.relative_to(REPO_ROOT)} not found. The template may already be renamed " - "(this script is meant to run once on a fresh clone)." - ) - if src_new.exists(): - _fail(f"{src_new.relative_to(REPO_ROOT)} already exists; refusing to overwrite.") - - # Whole-word replacements so we never touch substrings of other identifiers. - replacements = [ - (rf"\b{re.escape(OLD_PACKAGE)}\b", new_package), - (re.escape(OLD_PROJECT), new_project), - (re.escape(OLD_DISPLAY), new_display), - ] - - changed: list[str] = [] - for rel in TARGET_FILES: - if replace_in_file(REPO_ROOT / rel, replacements): - changed.append(rel) - # The package's own sources (e.g. `version("myanalysis")` in __init__.py) β€” - # process these before renaming the directory, while the old path is valid. - for py in sorted(src_old.rglob("*.py")): - if replace_in_file(py, replacements): - changed.append(str(py.relative_to(REPO_ROOT))) - for nb in sorted(REPO_ROOT.glob(NOTEBOOK_GLOB)): - if replace_in_file(nb, replacements): - changed.append(str(nb.relative_to(REPO_ROOT))) - - # Rename the package directory last, after its references are updated. - src_old.rename(src_new) - changed.append(f"src/{OLD_PACKAGE}/ -> src/{new_package}/") - - print(f"Renamed package '{OLD_PACKAGE}' -> '{new_package}'") - print(f"Project/kernel slug '{OLD_PROJECT}' -> '{new_project}'") - print(f"Kernel display name -> '{new_display}'") - print("\nChanged:") - for c in changed: - print(f" - {c}") - print( - "\nNext steps:\n" - " 1. Review the diff (git diff / git status).\n" - " 2. Update the [workspace] description and authors in pixi.toml.\n" - " 3. Replace README.md with your own project docs.\n" - " 4. pixi install && pixi run install-hooks && pixi run install-kernel\n" - " 5. pixi run test" - ) - - -if __name__ == "__main__": - main() diff --git a/.claude/settings.json b/{{cookiecutter.project_name}}/.claude/settings.json similarity index 100% rename from .claude/settings.json rename to {{cookiecutter.project_name}}/.claude/settings.json diff --git a/.editorconfig b/{{cookiecutter.project_name}}/.editorconfig similarity index 100% rename from .editorconfig rename to {{cookiecutter.project_name}}/.editorconfig diff --git a/.env.example b/{{cookiecutter.project_name}}/.env.example similarity index 100% rename from .env.example rename to {{cookiecutter.project_name}}/.env.example diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/{{cookiecutter.project_name}}/.github/ISSUE_TEMPLATE/bug_report.md similarity index 100% rename from .github/ISSUE_TEMPLATE/bug_report.md rename to {{cookiecutter.project_name}}/.github/ISSUE_TEMPLATE/bug_report.md diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/{{cookiecutter.project_name}}/.github/ISSUE_TEMPLATE/feature_request.md similarity index 100% rename from .github/ISSUE_TEMPLATE/feature_request.md rename to {{cookiecutter.project_name}}/.github/ISSUE_TEMPLATE/feature_request.md diff --git a/.github/copilot-instructions.md b/{{cookiecutter.project_name}}/.github/copilot-instructions.md similarity index 100% rename from .github/copilot-instructions.md rename to {{cookiecutter.project_name}}/.github/copilot-instructions.md diff --git a/.github/pull_request_template.md b/{{cookiecutter.project_name}}/.github/pull_request_template.md similarity index 100% rename from .github/pull_request_template.md rename to {{cookiecutter.project_name}}/.github/pull_request_template.md diff --git a/.github/workflows/lint.yaml b/{{cookiecutter.project_name}}/.github/workflows/lint.yaml similarity index 100% rename from .github/workflows/lint.yaml rename to {{cookiecutter.project_name}}/.github/workflows/lint.yaml diff --git a/{{cookiecutter.project_name}}/.github/workflows/test.yaml b/{{cookiecutter.project_name}}/.github/workflows/test.yaml new file mode 100644 index 0000000..7485677 --- /dev/null +++ b/{{cookiecutter.project_name}}/.github/workflows/test.yaml @@ -0,0 +1,31 @@ +name: Tests + +on: + push: + branches: [main] + pull_request: + branches: [main] + schedule: + # Run weekly on Mondays at 6:00 UTC + - cron: "0 6 * * 1" + +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + +jobs: + test: + name: Run pytest + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + with: + filter: blob:none + fetch-depth: 0 + - uses: prefix-dev/setup-pixi@v0.8.0 + with: + pixi-version: v0.60.0 + cache: true + frozen: true + - name: Run tests + run: pixi run test diff --git a/{{cookiecutter.project_name}}/.gitignore b/{{cookiecutter.project_name}}/.gitignore new file mode 100644 index 0000000..e0645da --- /dev/null +++ b/{{cookiecutter.project_name}}/.gitignore @@ -0,0 +1,183 @@ +# 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//.../_vN/): the untracked half of a task, anchored to the main checkout. +**/figures/* +!/figures/.gitkeep +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 +**.DS_Store + +# R stuff +*.Rhistory + +.vscode/* +.github/prompts/* + +# Claude Code local files (personal settings + local agent worktrees) +.claude/settings.local.json +.claude/worktrees/ diff --git a/.pre-commit-config.yaml b/{{cookiecutter.project_name}}/.pre-commit-config.yaml similarity index 76% rename from .pre-commit-config.yaml rename to {{cookiecutter.project_name}}/.pre-commit-config.yaml index e7868e5..2e25aec 100644 --- a/.pre-commit-config.yaml +++ b/{{cookiecutter.project_name}}/.pre-commit-config.yaml @@ -10,6 +10,7 @@ repos: rev: v2.2.3 hooks: - id: biome-format + exclude: ^\.cruft\.json$ # written by cruft in its own format - repo: https://github.com/tox-dev/pyproject-fmt rev: v2.6.0 hooks: @@ -33,3 +34,10 @@ repos: - id: trailing-whitespace - id: check-case-conflict - id: check-merge-conflict + - repo: local + hooks: + - id: forbid-rej + name: no *.rej files left by cruft update + entry: resolve the conflict by hand, then delete the .rej file + language: fail + files: \.rej$ diff --git a/AGENTS.md b/{{cookiecutter.project_name}}/AGENTS.md similarity index 96% rename from AGENTS.md rename to {{cookiecutter.project_name}}/AGENTS.md index 17c1d5e..0759c3e 100644 --- a/AGENTS.md +++ b/{{cookiecutter.project_name}}/AGENTS.md @@ -19,7 +19,7 @@ environment specifics, companion code packages. Rules the plugin owns are not re - **Paths**: every dataset path hangs off `FilePaths` in `src//_constants.py`: ```python -from myanalysis import FilePaths +from {{ cookiecutter.package_name }} import FilePaths FilePaths.EXAMPLE_DATASET / "processed" / "adata.zarr" ``` diff --git a/{{cookiecutter.project_name}}/CLAUDE.md b/{{cookiecutter.project_name}}/CLAUDE.md new file mode 100644 index 0000000..b06ba47 --- /dev/null +++ b/{{cookiecutter.project_name}}/CLAUDE.md @@ -0,0 +1,3 @@ +# {{ cookiecutter.project_name }} agent entry point + +@AGENTS.md diff --git a/{{cookiecutter.project_name}}/LICENSE b/{{cookiecutter.project_name}}/LICENSE new file mode 100644 index 0000000..7ee6ffe --- /dev/null +++ b/{{cookiecutter.project_name}}/LICENSE @@ -0,0 +1,28 @@ +BSD 3-Clause License + +Copyright (c) 2024, QuaDBio Lab + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + +1. Redistributions of source code must retain the above copyright notice, this + list of conditions and the following disclaimer. + +2. Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + +3. Neither the name of the copyright holder nor the names of its + contributors may be used to endorse or promote products derived from + this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/{{cookiecutter.project_name}}/README.md b/{{cookiecutter.project_name}}/README.md new file mode 100644 index 0000000..beddc01 --- /dev/null +++ b/{{cookiecutter.project_name}}/README.md @@ -0,0 +1,253 @@ +# 🧬 {{ cookiecutter.project_name }} + +{{ cookiecutter.project_description }} + + + +--- + +## πŸš€ Getting Started + +### Step 1: Install pixi + +*Skip this if you already have pixi installed.* + +```bash +# macOS / Linux +curl -fsSL https://pixi.sh/install.sh | bash + +# Or with Homebrew (macOS) +brew install pixi +``` + +Restart your terminal after installation. See [pixi installation docs](https://pixi.sh/latest/#installation) for Windows and other options. + +### Step 1b: Install GitHub CLI (optional) + +*Recommended if you're working on a remote server and need to authenticate with GitHub.* + +```bash +# macOS +brew install gh + +# Linux (no sudo required) +curl -sS https://webi.sh/gh | sh +``` + +Then authenticate: `gh auth login`. See [GitHub CLI installation docs](https://github.com/cli/cli#installation) for more options. + +### Step 2: Clone the repo + +```bash +git clone +cd {{ cookiecutter.project_name }} +``` + +The URL depends on your authentication method: +- **HTTPS**: `https://github.com/owner/repo.git` +- **SSH**: `git@github.com:owner/repo.git` +- **GitHub CLI**: `gh repo clone owner/repo` + +### Step 3: Set up the environment + +```bash +pixi install # create environment from pixi.toml +pixi run install-hooks # pre-commit hooks +pixi run install-kernel # register Jupyter kernel +``` + +> **Notebook outputs are committed.** They are the record of what a notebook actually +> produced, and GitHub renders them. Keep them small: clear a notebook by hand before +> committing if it carries a huge embedded image or an accidental dump. + +πŸ’‘ **Tip**: Use `pixi shell` to enter the environment interactivelyβ€”then you can run commands directly without the `pixi run` prefix. + +### Step 4: Verify your setup + +```bash +pixi run test # should pass (tests your package imports correctly) +pixi run lab # opens Jupyter Lab +``` + +In Jupyter Lab, check that your kernel appears (look for `{{ cookiecutter.project_name }} (pixi)`). + +πŸŽ‰ **You're ready to start analyzing!** + +--- + +## πŸ“Š Start Your Analysis + +- **Demo notebook**: Check out `analysis/ML-2026-01-27_demo_scRNA_workflow.ipynb` for a complete scRNA-seq workflow example using scanpy's PBMC 3k dataset. +- **New notebooks**: Copy `analysis/XX-2026-01-27_sample_notebook.ipynb` as a starting point. Follow the naming convention: `[INITIALS]-[YYYY]-[MM]-[DD]_description.ipynb`. +- **Add your data**: Create folders under `data/` and register paths in `src/{{ cookiecutter.package_name }}/_constants.py`. + +--- + +## πŸ€– Working with coding agents + +Agents follow [`AGENTS.md`](AGENTS.md) and the +[analysis-workflow](https://github.com/quadbio/analysis-workflow) Claude Code plugin (a skill plus +guard hooks) that this repo enables. Install the plugin once per machine: + +```bash +claude plugin marketplace add quadbio/claude-plugins +claude plugin install analysis-workflow@quadbio +``` + +--- + +## β˜• Daily Workflow + +```bash +cd {{ cookiecutter.project_name }} +pixi shell # activate environment +jupyter lab # work in notebooks, or start via jupyter-hub +# ... do your analysis ... +exit # leave pixi shell when done +``` + +Or run commands directly without entering the shell: + +```bash +pixi run lab # start Jupyter Lab +pixi run python script.py # run a script +``` + +--- + +## πŸ“š Reference + +
+πŸ“¦ What is pixi? + +[Pixi](https://pixi.sh) is a modern package manager that handles both **conda** and **PyPI** packages in one tool: + +- πŸ”’ Creates **isolated environments** per project +- πŸ”€ Installs from **conda-forge AND PyPI** together +- πŸ“Œ Locks exact versions for **reproducibility** (`pixi.lock`) +- πŸ’» Works **cross-platform** (macOS, Linux, Windows) + +**You don't need conda or pip installed** β€” pixi handles everything! + +
+ +
+βž• Adding packages + +All dependencies live in `pixi.toml`. To add a new package: + +```bash +# From conda-forge (preferred for scientific packages) +pixi add numpy +pixi add "scanpy>=1.10" + +# From PyPI (when not on conda-forge) +pixi add --pypi some-package +``` + +Or edit `pixi.toml` directly and run `pixi install`. + +πŸ’‘ **Tip**: Prefer PyPI packages when available β€” mixing conda and pip can cause dependency conflicts. + +πŸ‘‰ See [pixi documentation](https://pixi.sh/latest/) for more details. + +
+ +
+πŸ““ Data and notebook conventions + +- **Notebook naming**: `[INITIALS]-[YYYY]-[MM]-[DD]_description.ipynb` +- **Data layout** (one folder per dataset, gitignored): + - `data//raw/` β€” bytes as they arrived; never written by analysis + - `data//resources/` β€” curated inputs that are not data: gene lists, marker tables + - `data//processed/` β€” objects code loads to do new work, as AnnData `.zarr` + - `data//results/` β€” a notebook's own outputs, file names prefixed with the notebook's stem +- **Figures**: `figures//` +- **Import paths** via the local package: + +```python +from {{ cookiecutter.package_name }} import FilePaths +``` + +
+ +
+πŸ”§ Pre-commit & code quality + +This repo uses **pre-commit hooks** to automatically check your code before each commit: + +| Tool | What it does | +|------|--------------| +| [Ruff](https://docs.astral.sh/ruff/) | Lints and formats Python code + notebooks | +| [Biome](https://biomejs.dev/) | Formats JSON/JSONC files | +| [pyproject-fmt](https://github.com/tox-dev/pyproject-fmt) | Formats `pyproject.toml` | + +Hooks run automatically on `git commit`. To run manually: + +```bash +pre-commit run --all-files +``` + +πŸ’‘ If a check reformats your code, just `git add` the changes and commit again. + +
+ +
+πŸ–₯️ GPU notes + +The **default** environment is CPU-only on every platform (on macOS, PyTorch +still uses MPS automatically). This is what `pixi install` and CI use. + +GPU acceleration lives in a separate **`gpu`** environment that you opt into +explicitly on a Linux/CUDA machine (e.g. ETH Euler): + +```bash +pixi install -e gpu # CUDA 12 build of JAX + rapids-singlecell +pixi run -e gpu install-kernel # register a kernel for the gpu env +pixi shell -e gpu # or activate it interactively +``` + +| Environment | PyTorch | JAX | rapids-singlecell | +|-------------|---------|-----|-------------------| +| `default` (all platforms) | βœ… (MPS on macOS) | CPU | ❌ | +| `gpu` (Linux + NVIDIA only) | βœ… CUDA | βœ… CUDA 12 | βœ… | + +> Keeping the GPU stack out of the default environment means CI and CPU-only +> machines don't try to resolve unusable CUDA wheels. See +> [rapids-singlecell](https://rapids-singlecell.readthedocs.io/). + +
+ +
+πŸ”‘ Secrets & environment variables + +Store API keys and other secrets in a `.env` file at the repo root. It is +**gitignored** and must never be committed. + +```bash +cp .env.example .env # then fill in your real values +``` + +`.env.example` (tracked, placeholder values only) documents which variables the +project expects. Load them in a notebook or script with, e.g., +[python-dotenv](https://github.com/theskumar/python-dotenv): + +```python +from dotenv import load_dotenv +load_dotenv() +``` + +If you ever paste a real key into a tracked file, rotate it immediately in the +provider's dashboard β€” git history is hard to scrub. + +
+ +
+πŸ–§ Cluster usage + +For cluster usage (e.g., ETH Euler): + +- πŸ“š General docs: https://docs.hpc.ethz.ch/ +- πŸš€ Notebooks via JupyterHub: https://jupyter.euler.hpc.ethz.ch/hub/ + +
diff --git a/REVIEW_GUIDE.md b/{{cookiecutter.project_name}}/REVIEW_GUIDE.md similarity index 100% rename from REVIEW_GUIDE.md rename to {{cookiecutter.project_name}}/REVIEW_GUIDE.md diff --git a/analysis/ML-2026-01-27_demo_scRNA_workflow.ipynb b/{{cookiecutter.project_name}}/analysis/ML-2026-01-27_demo_scRNA_workflow.ipynb similarity index 96% rename from analysis/ML-2026-01-27_demo_scRNA_workflow.ipynb rename to {{cookiecutter.project_name}}/analysis/ML-2026-01-27_demo_scRNA_workflow.ipynb index 9d57fa1..b7e5af6 100644 --- a/analysis/ML-2026-01-27_demo_scRNA_workflow.ipynb +++ b/{{cookiecutter.project_name}}/analysis/ML-2026-01-27_demo_scRNA_workflow.ipynb @@ -73,8 +73,8 @@ "import matplotlib.pyplot as plt\n", "import scanpy as sc\n", "\n", - "# Local analysis package β€” edit these functions in src/myanalysis/\n", - "from myanalysis import FilePaths, qc_violin\n", + "# Local analysis package β€” edit these functions in src/{{ cookiecutter.package_name }}/\n", + "from {{ cookiecutter.package_name }} import FilePaths, qc_violin\n", "\n", "warnings.filterwarnings(\"ignore\", category=FutureWarning)" ] @@ -110,7 +110,7 @@ "source": [ "### Function definitions\n", "\n", - "Any utility functions specific to this notebook go here. For reusable functions, add them to `src/myanalysis/`." + "Any utility functions specific to this notebook go here. For reusable functions, add them to `src/{{ cookiecutter.package_name }}/`." ] }, { @@ -182,7 +182,7 @@ "outputs": [], "source": [ "# Use our custom plotting function from the local package!\n", - "# πŸ’‘ TIP: Edit src/myanalysis/plotting.py locally, then run again, autoreload will update automatically!\n", + "# πŸ’‘ TIP: Edit src/{{ cookiecutter.package_name }}/plotting.py locally, then run again, autoreload will update automatically!\n", "fig = qc_violin(adata, figsize=(12, 3))\n", "plt.show()" ] @@ -555,9 +555,9 @@ ], "metadata": { "kernelspec": { - "display_name": "Analysis Template (Pixi)", + "display_name": "{{ cookiecutter.project_name }} (pixi)", "language": "python", - "name": "analysis-template" + "name": "{{ cookiecutter.project_name }}" }, "language_info": { "codemirror_mode": { diff --git a/analysis/XX-2026-01-27_sample_notebook.ipynb b/{{cookiecutter.project_name}}/analysis/XX-2026-01-27_sample_notebook.ipynb similarity index 98% rename from analysis/XX-2026-01-27_sample_notebook.ipynb rename to {{cookiecutter.project_name}}/analysis/XX-2026-01-27_sample_notebook.ipynb index ff4165c..3de5c38 100644 --- a/analysis/XX-2026-01-27_sample_notebook.ipynb +++ b/{{cookiecutter.project_name}}/analysis/XX-2026-01-27_sample_notebook.ipynb @@ -77,7 +77,7 @@ "source": [ "import scanpy as sc\n", "\n", - "from myanalysis import FilePaths" + "from {{ cookiecutter.package_name }} import FilePaths" ] }, { diff --git a/biome.jsonc b/{{cookiecutter.project_name}}/biome.jsonc similarity index 100% rename from biome.jsonc rename to {{cookiecutter.project_name}}/biome.jsonc diff --git a/data/example_dataset/README.md b/{{cookiecutter.project_name}}/data/example_dataset/README.md similarity index 100% rename from data/example_dataset/README.md rename to {{cookiecutter.project_name}}/data/example_dataset/README.md diff --git a/data/example_dataset/processed/.gitkeep b/{{cookiecutter.project_name}}/data/example_dataset/processed/.gitkeep similarity index 100% rename from data/example_dataset/processed/.gitkeep rename to {{cookiecutter.project_name}}/data/example_dataset/processed/.gitkeep diff --git a/data/example_dataset/raw/.gitkeep b/{{cookiecutter.project_name}}/data/example_dataset/raw/.gitkeep similarity index 100% rename from data/example_dataset/raw/.gitkeep rename to {{cookiecutter.project_name}}/data/example_dataset/raw/.gitkeep diff --git a/data/example_dataset/resources/.gitkeep b/{{cookiecutter.project_name}}/data/example_dataset/resources/.gitkeep similarity index 100% rename from data/example_dataset/resources/.gitkeep rename to {{cookiecutter.project_name}}/data/example_dataset/resources/.gitkeep diff --git a/data/example_dataset/results/.gitkeep b/{{cookiecutter.project_name}}/data/example_dataset/results/.gitkeep similarity index 100% rename from data/example_dataset/results/.gitkeep rename to {{cookiecutter.project_name}}/data/example_dataset/results/.gitkeep diff --git a/figures/.gitkeep b/{{cookiecutter.project_name}}/figures/.gitkeep similarity index 100% rename from figures/.gitkeep rename to {{cookiecutter.project_name}}/figures/.gitkeep diff --git a/pixi.toml b/{{cookiecutter.project_name}}/pixi.toml similarity index 82% rename from pixi.toml rename to {{cookiecutter.project_name}}/pixi.toml index c72eeba..2b0927b 100644 --- a/pixi.toml +++ b/{{cookiecutter.project_name}}/pixi.toml @@ -1,16 +1,15 @@ [workspace] -name = "analysis-template" +name = "{{ cookiecutter.project_name }}" version = "0.1.0" -description = "Template for single-cell/spatial analysis projects (pixi-managed)" -authors = ["Your Name "] +description = "{{ cookiecutter.project_description }}" +authors = ["{{ cookiecutter.author_full_name }} <{{ cookiecutter.author_email }}>"] channels = ["conda-forge"] platforms = ["osx-arm64", "linux-64"] [tasks] lab = "jupyter lab" test = "pytest" -rename = { cmd = "python scripts/rename_package.py", description = "Rename the placeholder package/project (run once on a fresh clone; see scripts/rename_package.py)" } -install-kernel = "python -m ipykernel install --user --name=analysis-template --display-name='Analysis Template (Pixi)'" +install-kernel = "python -m ipykernel install --user --name={{ cookiecutter.project_name }} --display-name='{{ cookiecutter.project_name }} (pixi)'" install-hooks = { cmd = "pre-commit install --install-hooks", description = "Install pre-commit hooks (run once per clone)" } [dependencies] @@ -58,7 +57,7 @@ pytest = "*" session-info2 = "*" # Local editable package for path helpers -myanalysis = { path = ".", editable = true } +{{ cookiecutter.package_name | replace('_', '-') }} = { path = ".", editable = true } # Task paths and additive write-back for agent-run tasks (README: "Working with coding agents") analysis-workflow = { git = "https://github.com/quadbio/analysis-workflow", tag = "v0.1.0" } igraph = ">=1.0.0, <2" diff --git a/pyproject.toml b/{{cookiecutter.project_name}}/pyproject.toml similarity index 92% rename from pyproject.toml rename to {{cookiecutter.project_name}}/pyproject.toml index c535440..aafc6fb 100644 --- a/pyproject.toml +++ b/{{cookiecutter.project_name}}/pyproject.toml @@ -3,9 +3,9 @@ build-backend = "hatchling.build" requires = [ "hatch-vcs", "hatchling" ] [project] -name = "myanalysis" +name = "{{ cookiecutter.package_name | replace('_', '-') }}" # Minimal metadata - project info lives in pixi.toml -# Only the package name matters here (must match src/NAME/ directory) +# Only the name matters here: with `-` read as `_`, it must match the src/NAME/ directory readme = "README.md" license = { file = "LICENSE" } requires-python = ">=3.12" @@ -87,3 +87,7 @@ xfail_strict = true addopts = [ "--import-mode=importlib", # allow using test files with same name ] + +[tool.cruft] +# Project-owned after creation: `cruft update` leaves these alone. +skip = [ "README.md", "analysis", "data", "src", "tests" ] diff --git a/src/myanalysis/__init__.py b/{{cookiecutter.project_name}}/src/{{cookiecutter.package_name}}/__init__.py similarity index 71% rename from src/myanalysis/__init__.py rename to {{cookiecutter.project_name}}/src/{{cookiecutter.package_name}}/__init__.py index 9b44508..27a4830 100644 --- a/src/myanalysis/__init__.py +++ b/{{cookiecutter.project_name}}/src/{{cookiecutter.package_name}}/__init__.py @@ -4,4 +4,4 @@ from .plotting import qc_violin __all__ = ["FilePaths", "qc_violin"] -__version__ = version("myanalysis") +__version__ = version("{{ cookiecutter.package_name }}") diff --git a/src/myanalysis/_constants.py b/{{cookiecutter.project_name}}/src/{{cookiecutter.package_name}}/_constants.py similarity index 100% rename from src/myanalysis/_constants.py rename to {{cookiecutter.project_name}}/src/{{cookiecutter.package_name}}/_constants.py diff --git a/src/myanalysis/plotting.py b/{{cookiecutter.project_name}}/src/{{cookiecutter.package_name}}/plotting.py similarity index 100% rename from src/myanalysis/plotting.py rename to {{cookiecutter.project_name}}/src/{{cookiecutter.package_name}}/plotting.py diff --git a/tests/test_basic.py b/{{cookiecutter.project_name}}/tests/test_basic.py similarity index 86% rename from tests/test_basic.py rename to {{cookiecutter.project_name}}/tests/test_basic.py index 9e6ae0e..9ea4fdb 100644 --- a/tests/test_basic.py +++ b/{{cookiecutter.project_name}}/tests/test_basic.py @@ -4,15 +4,15 @@ import pytest from matplotlib.figure import Figure -import myanalysis -from myanalysis import FilePaths, qc_violin +import {{ cookiecutter.package_name }} +from {{ cookiecutter.package_name }} import FilePaths, qc_violin # Headless backend so plotting works in CI. matplotlib.use("Agg") def test_package_has_version(): - assert myanalysis.__version__ is not None + assert {{ cookiecutter.package_name }}.__version__ is not None def test_filepaths():