WIP: template refresh

.gitignore

@@ -1,24 +1 @@
-# PyCharm
-.idea
-
-# Python compiled & optimized files
-*.pyc
-*.pyo
-
-# MyPy Cache directory
-.mypy_cache
-
-# for develop installs
-*.egg-info
-
-# local dirs
-envs
-environments
-.conda
-conda-env-builder
-
-# snakemake
-.snakemake
-
-# VSCode dir
-.vscode
+.DS_Store

LICENSE

@@ -1,6 +1,6 @@
 The MIT License
 
-Copyright (c) 2022 Fulcrum Genomics LLC
+Copyright (c) 2025 Fulcrum Genomics LLC
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -1,84 +1,37 @@
-[![build](https://github.com/fulcrumgenomics/python-snakemake-skeleton/actions/workflows/pythonpackage.yml/badge.svg)](https://github.com/fulcrumgenomics/python-snakemake-skeleton/actions/workflows/pythonpackage.yml)
-[![License](https://img.shields.io/badge/license-MIT-blue.svg)](https://github.com/fulcrumgenomics/fgbio/blob/main/LICENSE)
-[![Language](https://img.shields.io/badge/python-3.6.10-brightgreen)](https://www.python.org/downloads/release/python-3610/)
+# Snakemake Project Template
 
-A skeleton repository for Snakemake pipepline(s) and a python command-line toolkit.
+This repository provides a template for a Fulcrum Genomics [Snakemake](https://snakemake.readthedocs.io/en/stable/) project with optional supporting [Python toolkit](https://github.com/fulcrumgenomics/python-template).
 
-## Why this repo?
-
-This the starting point for [Fulcrum Genomics][fulcrum-genomics-link] projects that contain Snakemake pipelines
-and a python toolkit.
-
-This repo contains the following, in no particular order:
-
-- a hello world snakefile in `src/snakemake/hello_world.smk`
-  - this uses the `onerror` directive to better display rule errors, in particular the last file
-    lines of the rule's log
-- a python toolkit (`client-tools`) in `src/python/pyclient`
-  - uses `defopt` for arg parsing
-  - has custom logging in `core/logging.py`
-  - has utility methods to support the above `onerror` snakemake directive in `pipeline/snakemake_utils.py`
-  - has a unit test to ensure the above snakefile is runnable and generally executes the expected rules in `tests/test_hello_world.py`.
-    This also includes a utility method to support running and verifying snakemake in `tests/util.py`
-  - supports multiple sub-commands in `tools/__main__.py` with some nice logging when a tool fails
-  - a little hello world tool in `tools/hello_world.py`
-
-## Modifying this repo for a new client
-
-This repo is a skeleton for Snakemake pipelines and a Python toolkit.
-
-- [ ] Modify `setup.py`
-- [ ] update `conda-requirements-minimal.txt` with minimal requirements for the `client-tools` toolkit
-- [ ] update `conda-requirements-test.txt` with minimal requirements for the `client-tools` unit testing
-- [ ] update `pip-requirements.txt` with minimal requirements for the `client-tools` (prefer conda)
-- [ ] update `src/python/pyclient` source code (search for terms: `PYCLIENT`, `pyclient`, `client-tools`
-
-## Install client-tools
-
-- [Install conda][conda-link]
-
-
-- Create the `pyclient` conda environment
+## Creating a Snakemake Project
 
+Install [`cookiecutter`](https://cookiecutter.readthedocs.io/en/stable/) and run a command like:
 
 ```console
-mamba create -n pyclient \
-  --override-channels -y \
-  -c bioconda -c conda-forge -c defaults \
-  --file conda-requirements-minimal.txt \
-  --file conda-requirements-test.txt
-```
-
-- Activate the `pyclient` conda environment
-
-```bash
-conda activate pyclient
+❯ cookiecutter [email protected]:fulcrumgenomics/python-snakemake-template.git --output-dir ~/git/
+  [1/5] Repository name for your project (e.g. 'myworkflow'): myworkflow
+  [2/5] Describe your project with a period-terminated sentence (...):
+  [3/5] Your GitHub handle (e.g. @example):
+  [4/5] GitHub organization to host your project (fulcrumgenomics):
+  [5/5] License. If 'MIT (Open Source) is selected', a LICENSE file will be generated.
+    1 - Proprietary (no license)
+    2 - MIT (Open Source)
+    Choose from [1/2] (1):
 ```
 
-- Install all non-conda dependencies via pip
+You will have a Git-initialized Snakemake project at the following location:
 
-```bash
-pip install -r pip-requirements.txt
-```
-
-- Install `pyclient` (in developer mode)
-
-```bash
-python setup.py develop
-```
-
-- Validate the install via the help message
-
-```bash
-client-tools -h
-```
-
-- Validate the snakemake install
-
-```bash
-snakemake --snakefile src/snakemake/hello_world.smk -j 1
+```console
+❯ > tree -a myworkflow 
+myworkflow
+├── .git # contents omitted for brevity
+├── .github
+│   └── CODEOWNERS
+├── .gitignore
+├── README.md
+├── config
+│   ├── config.yml
+│   └── config_schema.yml
+├── environment.yml
+└── workflow
+    └── myworkflow.smk
 ```
-
-[fulcrum-genomics-link]: https://www.fulcrumgenomics.com
-[conda-link]: https://docs.conda.io/projects/conda/en/latest/user-guide/install/
-

cookiecutter.json

@@ -0,0 +1,15 @@
+{
+    "project_slug": null,
+    "project_short_description": "...",
+    "your_github_handle": null,
+    "project_org": "fulcrumgenomics",
+    "license": ["Proprietary (no license)", "MIT (Open Source)"],
+    "__license": "{{ cookiecutter.license.split(' ')|first }}",
+    "__prompts__": {
+        "project_slug": "Repository name for your project (e.g. 'myworkflow')",
+        "project_short_description": "Describe your project with a period-terminated sentence",
+        "your_github_handle": "Your GitHub handle (e.g. @example)",
+        "project_org": "GitHub organization to host your project",
+        "license": "License. If 'MIT (Open Source) is selected', a LICENSE file will be generated."
+    }
+}

hooks/post_gen_project.py

@@ -0,0 +1,8 @@
+import subprocess
+
+# Projects need an initialized Git repository
+subprocess.call(["rm", "-rf", ".git/"])
+subprocess.call(["git", "init"])
+subprocess.call(["git", "remote", "add", "origin", "[email protected]:{{cookiecutter.project_org}}/{{cookiecutter.project_slug}}.git"])
+subprocess.call(["git", "add", "-A"])
+subprocess.call(["git", "commit", "-m", "First commit"])

hooks/pre_gen_project.py

@@ -0,0 +1,14 @@
+import re
+import sys
+
+
+GITHUB_HANDLE_REGEX = re.compile(r'^\@[a-z\d][_a-zA-Z\d]+$')
+"""Regex for valid GitHub handle with the `@` symbol prepended."""
+
+if not GITHUB_HANDLE_REGEX.match("{{cookiecutter.your_github_handle}}"):
+    print("ERROR: {{cookiecutter.your_github_handle}} is not a GitHub handle!")
+    print("ERROR: GitHub handles must start with an `@` character.")
+    print("ERROR: GitHub handles must not have an underscore after the `@` character.")
+    print("ERROR: GitHub handles must have more than one character after the `@`.")
+    print("ERROR: GitHub handles must only contain ASCII letters, numbers, and underscores.")
+    sys.exit(1)