diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml new file mode 100644 index 0000000..3794586 --- /dev/null +++ b/.github/workflows/ci.yml @@ -0,0 +1,42 @@ +name: CI + +on: + push: + branches: [main, master] + pull_request: + branches: [main, master] + +concurrency: + group: ci-${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + +jobs: + ruff: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - uses: actions/setup-python@v5 + with: + python-version: "3.12" + cache: pip + - name: Install tox + run: pip install --upgrade pip tox + - name: Ruff + run: tox -e ruff + + test: + runs-on: ubuntu-latest + strategy: + fail-fast: false + matrix: + python-version: ["3.9", "3.10", "3.11", "3.12"] + steps: + - uses: actions/checkout@v4 + - uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python-version }} + cache: pip + - name: Install tox + run: pip install --upgrade pip tox + - name: Unit tests + run: tox -e py diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml new file mode 100644 index 0000000..9fd8bb6 --- /dev/null +++ b/.github/workflows/publish.yml @@ -0,0 +1,32 @@ +# Upload to PyPI when a GitHub Release is published or a version tag is pushed. +# Configure "pending" trusted publishing on PyPI for this repository before first use. + +name: Publish to PyPI + +on: + release: + types: [published] + push: + tags: ["v*"] + +permissions: + contents: read + id-token: write + +jobs: + publish: + runs-on: ubuntu-latest + environment: + name: pypi + url: https://pypi.org/p/outerspace + steps: + - uses: actions/checkout@v4 + - uses: actions/setup-python@v5 + with: + python-version: "3.12" + - name: Install build + run: pip install --upgrade pip build + - name: Build wheel and sdist + run: python -m build + - name: Publish to PyPI + uses: pypa/gh-action-pypi-publish@release/v1 diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..cde4b24 --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,7 @@ +repos: + - repo: https://github.com/astral-sh/ruff-pre-commit + rev: v0.8.4 + hooks: + - id: ruff + args: [--fix, --exit-non-zero-on-fix] + - id: ruff-format diff --git a/.readthedocs.yaml b/.readthedocs.yaml new file mode 100644 index 0000000..234d445 --- /dev/null +++ b/.readthedocs.yaml @@ -0,0 +1,18 @@ +# Read the Docs build configuration +# See https://docs.readthedocs.io/en/stable/config-file/v2.html + +version: 2 + +build: + os: ubuntu-24.04 + tools: + python: "3.12" + +python: + install: + - method: pip + path: . + extra_requirements: [docs] + +mkdocs: + configuration: mkdocs.yml diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..f288702 --- /dev/null +++ b/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + + END OF TERMS AND CONDITIONS + + How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these terms. + + To do so, attach the following notices to the program. It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/README.md b/README.md index 22728f1..046699d 100644 --- a/README.md +++ b/README.md @@ -68,4 +68,31 @@ For more detailed instructions, including how to run individual commands and per For running your tasks in parallel or on a cluster consider using our Snakemake [wrappers](wrappers.md). +## Development + +The repository expects a **conda environment** in this clone’s `venv` directory (for example +`/home/jupyter-will/repos/outerspace/venv`). Create or refresh it, then use that interpreter +for all tooling: + +```bash +# One-time: create env and install with dev + pipeline extras +make venv +# or: conda create -y -p ./venv python=3.12 && ./venv/bin/pip install -e ".[dev,pipeline]" + +# Run tools via the env (from repo root) +./venv/bin/python -m tox -e py # fast unit tests (default) +./venv/bin/python -m tox -e ruff # lint + format check +./venv/bin/python -m tox -e functional # long integration/functional tests (optional) + +# Or with conda run (same env) +conda run -p /home/jupyter-will/repos/outerspace/venv python -m tox -e py +``` + +Shorter: `make test` and `make ruff` use `$(CURDIR)/venv` automatically. Install +[pre-commit](https://pre-commit.com/) hooks with `pre-commit install` after the dev extra is installed. + +**Documentation (MkDocs):** `pip install -e ".[docs]" && mkdocs serve` (or `tox -e docs`). + +- **User guide (Read the Docs):** [https://outerspace.readthedocs.io/](https://outerspace.readthedocs.io/) (enable the project in RTD when ready). + Copyright (C) 2025, SCB, DVK PhD, RB, WND PhD. All rights reserved. diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 0000000..d99891a --- /dev/null +++ b/docs/index.md @@ -0,0 +1,22 @@ +# OuterSpace + +Outerspace is a collection of tools for analyzing pooled CRISPR screens, viral barcode population studies, and other applications that require extraction and counting of variable regions in pooled amplicons. + +**Quick links** + +- [User guide: biological applications](usage.md) +- [Commands](commands.md) +- [Configuration](config.md) +- [Walkthrough](walkthrough.md) +- [CLI API](cli_api.md) +- [Snakemake](snakemake.md) +- [Statistics](stats.md) +- [Regex design](regex_explainer.md) +- [Collapse steps](collapse_steps.md) +- [Tutorials](tutorials/siv-barcoding/README.md) + +The project [README on GitHub](https://github.com/DamLabResources/outerspace) has installation and quick start. + +## Copyright + +See the [LICENSE](https://github.com/DamLabResources/outerspace/blob/main/LICENSE) file in the repository. diff --git a/makefile b/makefile index 494f036..95b7cc2 100644 --- a/makefile +++ b/makefile @@ -1,3 +1,8 @@ +# Conda environment for this clone (e.g. /home/.../outerspace/venv) +VENV := $(abspath $(dir $(lastword $(MAKEFILE_LIST)))/venv) +PY := $(VENV)/bin/python +PIP := $(VENV)/bin/pip + DIR_RB_READS := /data/share/nonn-lab/rachel-test-crispr/reads P1 := $(DIR_RB_READS)/409-4_S1_L001_R1_001.fastq.gz P2 := $(DIR_RB_READS)/409-4_S1_L001_R2_001.fastq.gz @@ -5,17 +10,19 @@ P2 := $(DIR_RB_READS)/409-4_S1_L001_R2_001.fastq.gz run: bin/main.py $(P1) $(P2) +# Default: unit tests only (see pyproject.toml / tox.ini) test: - pytest + $(PY) -m tox -e py + +ruff: + $(PY) -m tox -e ruff -black: - black outerspace - black tests +format-check: ruff venv: - # Create a new conda environment in the venv directory - conda create -p ./venv python=3.12 pytest - conda run -p ./venv pip install . + conda create -y -p $(VENV) python=3.12 + $(PIP) install -e ".[dev,pipeline]" + $(VENV)/bin/pre-commit install files: @ls $(P1) @@ -52,10 +59,9 @@ clobber: RB: findseq rb.cfg -1 reads_sample/409-4_S1_L002_R1_001.fastq.gz -2 reads_sample/409-4_S1_L002_R2_001.fastq.gz -o 409-4_S1_L002_R1_R2_output.csv -# Running coverage on pytest test scripts -# Do this first- then report below +# Unit-test coverage (same selection as `make test` / tox -e py) coverage: - coverage run -m pytest tests/test_*.py + $(PY) -m coverage run -m pytest report: - coverage report -m + $(PY) -m coverage report -m diff --git a/mkdocs.yml b/mkdocs.yml new file mode 100644 index 0000000..68a69c3 --- /dev/null +++ b/mkdocs.yml @@ -0,0 +1,58 @@ +site_name: OuterSpace +site_url: https://outerspace.readthedocs.io/ +site_description: Tools for CRISPR screens, viral barcoding, and amplicon extraction +site_author: Dam Lab +repo_url: https://github.com/DamLabResources/outerspace +repo_name: DamLabResources/outerspace +edit_uri: edit/main/docs/ + +theme: + name: material + palette: + - media: "(prefers-color-scheme: light)" + scheme: default + primary: indigo + toggle: + icon: material/brightness-7 + name: Switch to dark mode + - media: "(prefers-color-scheme: dark)" + scheme: slate + primary: indigo + toggle: + icon: material/brightness-4 + name: Switch to light mode + features: + - content.action.edit + - navigation.expand + - navigation.sections + - search.suggest + - search.highlight + - toc.integrate + +plugins: + - search + +markdown_extensions: + - admonition + - tables + - toc: + permalink: true + - pymdownx.superfences + +nav: + - Home: index.md + - Usage: usage.md + - Commands: commands.md + - Configuration: config.md + - Walkthrough: walkthrough.md + - "CLI API": cli_api.md + - Snakemake: snakemake.md + - Statistics: stats.md + - "Regex explainer": regex_explainer.md + - "Collapse steps": collapse_steps.md + - Tutorials: + - "SIV barcoding": tutorials/siv-barcoding/README.md + - "CRISPR screen": tutorials/crispr-screen/README.md + - "Pipeline (cluster)": tutorials/pipeline/README.md + +strict: true diff --git a/outerspace/cli/commands/pipeline.py b/outerspace/cli/commands/pipeline.py index 56393d5..7061f51 100644 --- a/outerspace/cli/commands/pipeline.py +++ b/outerspace/cli/commands/pipeline.py @@ -5,10 +5,13 @@ and workflow execution with comprehensive error handling. """ +from __future__ import annotations + import logging import os import shlex import sys +from dataclasses import fields from pathlib import Path try: # Python 3.9+ @@ -19,38 +22,76 @@ resource_files = None # type: ignore as_file = None # type: ignore _HAS_FILES_API = False -from typing import Any, Dict, List, Optional +from types import SimpleNamespace +from typing import Any, Dict, List, Optional, TYPE_CHECKING from argparse import ArgumentParser -import pulp import yaml -from snakemake.api import SnakemakeApi -from snakemake.resources import DefaultResources -from snakemake.settings.types import ( - ConfigSettings, - DAGSettings, - DeploymentSettings, - ExecutionSettings, - OutputSettings, - RemoteExecutionSettings, - ResourceSettings, - SchedulingSettings, - StorageSettings, - WorkflowSettings, -) - from outerspace.cli.commands.base import BaseCommand +if TYPE_CHECKING: + from snakemake.resources import DefaultResources + # Set up logging logger = logging.getLogger(__name__) __copyright__ = "Copyright (C) 2025, SC Barrera, R Berman, Drs DVK & WND. All Rights Reserved." __author__ = "WND" -# Monkey patch pulp.list_solvers if it doesn't exist -if not hasattr(pulp, "list_solvers"): - pulp.list_solvers = pulp.listSolvers +_PIPELINE_HELP = ( + "Install the pipeline extra: pip install 'outerspace[pipeline]' " + "(requires Snakemake and its dependencies)." +) + + +def _load_pipeline_backends() -> SimpleNamespace: + """Import Snakemake and pulp on demand (optional [pipeline] extra).""" + try: + import pulp + except ImportError as e: # pragma: no cover - env without extras + raise ImportError( + f"pulp is required for the pipeline command. {_PIPELINE_HELP}" + ) from e + if not hasattr(pulp, "list_solvers"): + pulp.list_solvers = pulp.listSolvers + try: + from snakemake.api import SnakemakeApi + from snakemake.resources import DefaultResources + from snakemake.settings.types import ( + ConfigSettings, + DAGSettings, + DeploymentSettings, + ExecutionSettings, + OutputSettings, + RemoteExecutionSettings, + ResourceSettings, + SchedulingSettings, + StorageSettings, + WorkflowSettings, + ) + from snakemake_interface_executor_plugins.registry import ExecutorPluginRegistry + except ImportError as e: # pragma: no cover - env without extras + raise ImportError( + f"snakemake is required for the pipeline command. {_PIPELINE_HELP}" + ) from e + + return SimpleNamespace( + pulp=pulp, + SnakemakeApi=SnakemakeApi, + DefaultResources=DefaultResources, + ConfigSettings=ConfigSettings, + DAGSettings=DAGSettings, + DeploymentSettings=DeploymentSettings, + ExecutionSettings=ExecutionSettings, + OutputSettings=OutputSettings, + RemoteExecutionSettings=RemoteExecutionSettings, + ResourceSettings=ResourceSettings, + SchedulingSettings=SchedulingSettings, + StorageSettings=StorageSettings, + WorkflowSettings=WorkflowSettings, + ExecutorPluginRegistry=ExecutorPluginRegistry, + ) class PipelineCommand(BaseCommand): @@ -405,13 +446,17 @@ def _load_profile_config(self, profile_path: Path) -> Dict[str, Any]: logger.warning(f"No config file found in profile directory: {profile_path}") return {} - def _parse_default_resources(self, profile_config: Dict[str, Any]) -> Optional[DefaultResources]: + def _parse_default_resources( + self, profile_config: Dict[str, Any], backends: SimpleNamespace + ) -> Optional[DefaultResources]: """Parse default resources from profile configuration. Parameters ---------- profile_config : Dict[str, Any] Profile configuration dictionary + backends : SimpleNamespace + Lazy-loaded snakemake / pulp module objects Returns ------- @@ -442,7 +487,7 @@ def _parse_default_resources(self, profile_config: Dict[str, Any]) -> Optional[D return None try: - default_resources = DefaultResources(args=default_resources_list) + default_resources = backends.DefaultResources(args=default_resources_list) logger.info(f"Loaded default resources from profile: {default_resources_list}") return default_resources except Exception as e: @@ -485,6 +530,8 @@ def _execute_snakemake( logger.info(f"Additional arguments: {snakemake_args}") try: + b = _load_pipeline_backends() + # Ensure .snakemake directory exists for logs and metadata snakemake_dir = Path(".snakemake") snakemake_dir.mkdir(exist_ok=True) @@ -521,7 +568,7 @@ def _execute_snakemake( logger.info(f"Using executor from profile: {executor}") # Parse default resources from profile - default_resources = self._parse_default_resources(profile_config) + default_resources = self._parse_default_resources(profile_config, b) # Configure resource settings based on executor type # For local/dryrun: use cores @@ -546,28 +593,28 @@ def _execute_snakemake( logger.info(f"Default resources: {default_resources.args}") # Create output settings (use defaults for now) - output_settings = OutputSettings() + output_settings = b.OutputSettings() # Execute with the new API logger.info("Starting Snakemake workflow execution") - with SnakemakeApi(output_settings) as snakemake_api: + with b.SnakemakeApi(output_settings) as snakemake_api: # Create workflow with explicit workdir (defaults to current directory) workflow_api = snakemake_api.workflow( - resource_settings=ResourceSettings(**resource_kwargs), - config_settings=ConfigSettings( + resource_settings=b.ResourceSettings(**resource_kwargs), + config_settings=b.ConfigSettings( config=config_dict, configfiles=[Path(self.args.snakemake_config)], ), - storage_settings=StorageSettings(), - workflow_settings=WorkflowSettings(), - deployment_settings=DeploymentSettings(), + storage_settings=b.StorageSettings(), + workflow_settings=b.WorkflowSettings(), + deployment_settings=b.DeploymentSettings(), snakefile=snakefile_path, workdir=Path.cwd(), # Explicitly set working directory ) # Create DAG dag_api = workflow_api.dag( - dag_settings=DAGSettings(), + dag_settings=b.DAGSettings(), ) # Get executor-specific settings @@ -575,10 +622,7 @@ def _execute_snakemake( executor_settings = None if executor not in ["local", "dryrun", "touch"]: try: - from snakemake_interface_executor_plugins.registry import ExecutorPluginRegistry - from dataclasses import fields - - executor_plugin = ExecutorPluginRegistry().get_plugin(executor) + executor_plugin = b.ExecutorPluginRegistry().get_plugin(executor) # Create args object with all required attributes set to None/defaults # The plugin will use defaults for any None values @@ -616,9 +660,9 @@ def __init__(self): # Execute workflow dag_api.execute_workflow( executor=executor, - execution_settings=ExecutionSettings(), - remote_execution_settings=RemoteExecutionSettings(), - scheduling_settings=SchedulingSettings(), + execution_settings=b.ExecutionSettings(), + remote_execution_settings=b.RemoteExecutionSettings(), + scheduling_settings=b.SchedulingSettings(), executor_settings=executor_settings, ) diff --git a/pyproject.toml b/pyproject.toml index 127f911..0695a3d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,7 +7,7 @@ name = "outerspace" version = "0.0a1" description = "A code to extract sequences from fastq files when the surrounding sequence is known" readme = "README.md" -requires-python = ">=3.8" +requires-python = ">=3.9" license = {text = "GPL-3.0-or-later"} authors = [ {name = "SB, DVK, REB, WD", email = "wnd22@drexel.edu"} @@ -19,13 +19,38 @@ dependencies = [ "regex", "umi_tools", "pyyaml", - "snakemake>=9.12", - "pulp>=2.3.1,<3.3", "numpy>=2", "pandas>=2", "pyspoa" ] +[project.optional-dependencies] +pipeline = [ + "snakemake>=9.12", + "pulp>=2.3.1,<3.3", +] +dev = [ + "pytest>=7", + "pytest-cov", + "coverage[toml]", + "tox>=4", + "ruff>=0.4", + "pre-commit", + "build", + "twine", +] +docs = [ + "mkdocs>=1.5", + "mkdocs-material>=9", + "pymdown-extensions", +] + +[project.urls] +Homepage = "https://github.com/DamLabResources/outerspace" +Repository = "https://github.com/DamLabResources/outerspace" +Documentation = "https://outerspace.readthedocs.io/en/latest/" +"Bug Tracker" = "https://github.com/DamLabResources/outerspace/issues" + [project.scripts] outerspace = "outerspace.cli:main" @@ -36,7 +61,7 @@ packages = [ "outerspace.cli.commands", "outerspace.cli.utils", "outerspace.stats" -] +] [tool.setuptools.data-files] "outerspace/workflow" = [ @@ -66,4 +91,60 @@ packages = [ "workflow/wrappers/stats/wrapper.py", "workflow/wrappers/stats/environment.yaml", "workflow/wrappers/stats/README.md" -] \ No newline at end of file +] + +[tool.pytest.ini_options] +minversion = "7.0" +testpaths = ["tests"] +# Default: fast unit tests. Use `tox -e functional` or override addopts to run integration/functional. +addopts = [ + "-ra", + "--strict-markers", + "-m", "not integration and not functional", +] +markers = [ + "integration: end-to-end integration tests (Snakemake; opt-in via tox -e functional)", + "functional: long-running pipeline/CLI functional tests (opt-in via tox -e functional)", +] + +[tool.coverage.run] +source = ["outerspace"] +branch = true +parallel = true + +[tool.coverage.report] +show_missing = true +skip_covered = false +omit = [ + "*/tests/*", + "*/test_*.py", +] + +[tool.coverage.paths] +source = ["outerspace"] + +[tool.ruff] +target-version = "py39" +line-length = 100 +src = ["outerspace", "tests"] +exclude = [ + "build", + "venv", + ".tox", + "docs", +] + +[tool.ruff.lint] +select = [ + "E", # pycodestyle + "F", # Pyflakes + "I", # isort + "UP", # pyupgrade + "B", # bugbear +] +ignore = [ + "B008", # function call in default argument — common in CLI +] + +[tool.ruff.lint.isort] +known-first-party = ["outerspace"] diff --git a/tests/test_cli/test_functional_iterative.py b/tests/test_cli/test_functional_iterative.py index 1b0faad..4b214c7 100644 --- a/tests/test_cli/test_functional_iterative.py +++ b/tests/test_cli/test_functional_iterative.py @@ -7,6 +7,8 @@ import pytest from outerspace.cli.main import Cli +pytestmark = pytest.mark.functional + def test_full_workflow(temp_workspace): """Test the full workflow from example.sh""" diff --git a/tests/test_cli/test_functional_pipeline.py b/tests/test_cli/test_functional_pipeline.py index 90b5bc2..7dfb0d1 100644 --- a/tests/test_cli/test_functional_pipeline.py +++ b/tests/test_cli/test_functional_pipeline.py @@ -10,6 +10,8 @@ from outerspace.cli.main import Cli from outerspace.cli.logging_config import setup_logging +pytestmark = pytest.mark.functional + # Set up logging logger = setup_logging(level=logging.DEBUG) diff --git a/tox.ini b/tox.ini new file mode 100644 index 0000000..c0181d5 --- /dev/null +++ b/tox.ini @@ -0,0 +1,39 @@ +[tox] +envlist = ruff, py +isolated_build = true +minversion = 4.0 + +[testenv:py] +description = Unit and fast tests (excludes integration and functional markers) +usedevelop = true +package = wheel +extras = dev +passenv = CI, GITHUB_* +setenv = COVERAGE_FILE = {toxworkdir}/.coverage.{envname} +commands = + python -m pytest {posargs:} + +[testenv:functional] +description = Long-running integration/functional tests (installs [pipeline] extra) +usedevelop = true +package = wheel +extras = dev, pipeline +passenv = CI, GITHUB_* +setenv = COVERAGE_FILE = {toxworkdir}/.coverage.{envname} +# Override default addopts that exclude these markers (see pyproject.toml). +commands = python -m pytest {posargs:} -m "integration or functional" --override-ini "addopts=-ra --strict-markers" + +[testenv:docs] +description = Build the MkDocs site +usedevelop = true +extras = docs +commands = + mkdocs build --strict + +[testenv:ruff] +description = Ruff lint and format check +skip_install = true +deps = ruff>=0.4 +commands = + ruff check outerspace tests + ruff format --check outerspace tests