From 656264d1361f9b81e9ded4fb82e9de29b532275a Mon Sep 17 00:00:00 2001 From: Will Dampier Date: Thu, 23 Apr 2026 16:48:22 -0400 Subject: [PATCH 1/3] pep8ing --- outerspace/cli/commands/pipeline.py | 120 +++++++++++++------- tests/test_cli/test_functional_iterative.py | 2 + tests/test_cli/test_functional_pipeline.py | 2 + 3 files changed, 86 insertions(+), 38 deletions(-) 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/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) From 98782a27926d232926b0876527cbd7ab33e461b7 Mon Sep 17 00:00:00 2001 From: Will Dampier Date: Thu, 23 Apr 2026 16:49:00 -0400 Subject: [PATCH 2/3] docs setup --- .readthedocs.yaml | 18 +++++++++++++++ README.md | 27 ++++++++++++++++++++++ docs/index.md | 22 ++++++++++++++++++ mkdocs.yml | 58 +++++++++++++++++++++++++++++++++++++++++++++++ 4 files changed, 125 insertions(+) create mode 100644 .readthedocs.yaml create mode 100644 docs/index.md create mode 100644 mkdocs.yml 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/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/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 From 91c14d3851dc7195a4ca89d318e719f2b4627ceb Mon Sep 17 00:00:00 2001 From: Will Dampier Date: Thu, 23 Apr 2026 16:53:31 -0400 Subject: [PATCH 3/3] config updates --- .github/workflows/ci.yml | 42 +++ .github/workflows/publish.yml | 32 ++ .pre-commit-config.yaml | 7 + LICENSE | 674 ++++++++++++++++++++++++++++++++++ makefile | 28 +- pyproject.toml | 91 ++++- tox.ini | 39 ++ 7 files changed, 897 insertions(+), 16 deletions(-) create mode 100644 .github/workflows/ci.yml create mode 100644 .github/workflows/publish.yml create mode 100644 .pre-commit-config.yaml create mode 100644 LICENSE create mode 100644 tox.ini 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/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. By contrast, +the GNU General Public License is intended to guarantee your freedom to +share and change all versions of a program--to make sure it remains free +software for all its users. We, the Free Software Foundation, use the +GNU General Public License for most of our software; it applies also to +any other work released this way by its authors. You can apply it to +your programs, too. + + When we speak of free software, we are referring to freedom, not +price. Our General Public Licenses are designed to make sure that you +have the freedom to distribute copies of free software (and charge for +them if you wish), that you receive source code or can get it if you +want it, that you can change the software or use pieces of it in new +free programs, and that you know you can do these things. + + To protect your rights, we need to prevent others from denying you +these rights or asking you to surrender the rights. Therefore, you have +certain responsibilities if you distribute copies of the software, or if +you modify it: responsibilities to respect the freedom of others. + + For example, if you distribute copies of such a program, whether +gratis or for a fee, you must pass on to the recipients the same +freedoms that you received. You must make sure that they, too, receive +or can get the source code. And you must show them these terms so they +know their rights. + + Developers that use the GNU GPL protect your rights with two steps: +(1) assert copyright on the software, and (2) offer you this License +giving you legal permission to copy, distribute and/or modify it. + + For the developers' and authors' protection, the GPL clearly explains +that there is no warranty for this free software. For both users' and +authors' sake, the GPL requires that modified versions be marked as +changed, so that their problems will not be attributed erroneously to +authors of previous versions. + + Some devices are designed to deny users access to install or run +modified versions of the software inside them, although the manufacturer +can do so. This is fundamentally incompatible with the aim of +protecting users' freedom to change the software. The systematic +pattern of such abuse occurs in the area of products for individuals to +use, which is precisely where it is most unacceptable. Therefore, we +have designed this version of the GPL to prohibit the practice for those +products. If such problems arise substantially in other domains, we +stand ready to extend this provision to those domains in future versions +of the GPL, as needed to protect the freedom of users. + + Finally, every program is threatened constantly by software patents. +States should not allow patents to restrict development and use of +software on general-purpose computers, but in those that do, we wish to +avoid the special danger that patents applied to a free program could +make it effectively proprietary. To prevent this, the GPL assures that +patents cannot be used to render the program non-free. + + The precise terms and conditions for copying, distribution and +modification follow. + + TERMS AND CONDITIONS + + 0. Definitions. + + "This License" refers to version 3 of the GNU General Public License. + + "Copyright" also means copyright-like laws that apply to other kinds of +works, such as semiconductor masks. + + "The Program" refers to any copyrightable work licensed under this +License. Each licensee is addressed as "you". "Licensees" and +"recipients" may be individuals or organizations. + + To "modify" a work means to copy from or adapt all or part of the work +in a fashion requiring copyright permission, other than the making of an +exact copy. The resulting work is called a "modified version" of the +earlier work or a work "based on" the earlier work. + + A "covered work" means either the unmodified Program or a work based +on the Program. + + To "propagate" a work means to do anything with it that, without +permission, would make you directly or secondarily liable for +infringement under applicable copyright law, except executing it on a +computer or modifying a private copy. Propagation includes copying, +distribution (with or without modification), making available to the +public, and in some countries other activities as well. + + To "convey" a work means any kind of propagation that enables other +parties to make or receive copies. Mere interaction with a user through +a computer network, with no transfer of a copy, is not conveying. + + An interactive user interface displays "Appropriate Legal Notices" +to the extent that it includes a convenient and prominently visible +feature that (1) displays an appropriate copyright notice, and (2) +tells the user that there is no warranty for the work (except to the +extent that warranties are provided), that licensees may convey the +work under this License, and how to view a copy of this License. If +the interface presents a list of user commands or options, such as a +menu, a prominent item in the list meets this criterion. + + 1. Source Code. + + The "source code" for a work means the preferred form of the work +for making modifications to it. "Object code" means any non-source +form of a work. + + A "Standard Interface" means an interface that either is an official +standard defined by a recognized standards body, or, in the case of +interfaces specified for a particular programming language, one that +is widely used among developers working in that language. + + The "System Libraries" of an executable work include anything, other +than the work as a whole, that (a) is included in the normal form of +packaging a Major Component, but which is not part of that Major +Component, and (b) serves only to enable use of the work with that +Major Component, or to implement a Standard Interface for which an +implementation is available to the public in source code form. A +"Major Component", in this context, means a major essential component +(kernel, window system, and so on) of the specific operating system +(if any) on which the executable work runs, or a compiler used to +produce the work, or an object code interpreter used to run it. + + The "Corresponding Source" for a work in object code form means all +the source code needed to generate, install, and (for an executable +work) run the object code and to modify the work, including scripts to +control those activities. However, it does not include the work's +System Libraries, or general-purpose tools or generally available free +programs which are used unmodified in performing those activities but +which are not part of the work. For example, Corresponding Source +includes interface definition files associated with source files for +the work, and the source code for shared libraries and dynamically +linked subprograms that the work is specifically designed to require, +such as by intimate data communication or control flow between those +subprograms and other parts of the work. + + The Corresponding Source need not include anything that users +can regenerate automatically from other parts of the Corresponding +Source. + + The Corresponding Source for a work in source code form is that +same work. + + 2. Basic Permissions. + + All rights granted under this License are granted for the term of +copyright on the Program, and are irrevocable provided the stated +conditions are met. This License explicitly affirms your unlimited +permission to run the unmodified Program. The output from running a +covered work is covered by this License only if the output, given its +content, constitutes a covered work. This License acknowledges your +rights of fair use or other equivalent, as provided by copyright law. + + You may make, run and propagate covered works that you do not +convey, without conditions so long as your license otherwise remains +in force. You may convey covered works to others for the sole purpose +of having them make modifications exclusively for you, or provide you +with facilities for running those works, provided that you comply with +the terms of this License in conveying all material for which you do +not control copyright. Those thus making or running the covered works +for you must do so exclusively on your behalf, under your direction +and control, on terms that prohibit them from making any copies of +your copyrighted material outside their relationship with you. + + Conveying under any other circumstances is permitted solely under +the conditions stated below. Sublicensing is not allowed; section 10 +makes it unnecessary. + + 3. Protecting Users' Legal Rights From Anti-Circumvention Law. + + No covered work shall be deemed part of an effective technological +measure under any applicable law fulfilling obligations under article +11 of the WIPO copyright treaty adopted on 20 December 1996, or +similar laws prohibiting or restricting circumvention of such +measures. + + When you convey a covered work, you waive any legal power to forbid +circumvention of technological measures to the extent such circumvention +is effected by exercising rights under this License with respect to +the covered work, and you disclaim any intention to limit operation or +modification of the work as a means of enforcing, against the work's +users, your or third parties' legal rights to forbid circumvention of +technological measures. + + 4. Conveying Verbatim Copies. + + You may convey verbatim copies of the Program's source code as you +receive it, in any medium, provided that you conspicuously and +appropriately publish on each copy an appropriate copyright notice; +keep intact all notices stating that this License and any +non-permissive terms added in accord with section 7 apply to the code; +keep intact all notices of the absence of any warranty; and give all +recipients a copy of this License along with the Program. + + You may charge any price or no price for each copy that you convey, +and you may offer support or warranty protection for a fee. + + 5. Conveying Modified Source Versions. + + You may convey a work based on the Program, or the modifications to +produce it from the Program, in the form of source code under the +terms of section 4, provided that you also meet all of these conditions: + + a) The work must carry prominent notices stating that you modified + it, and giving a relevant date. + + b) The work must carry prominent notices stating that it is + released under this License and any conditions added under section + 7. This requirement modifies the requirement in section 4 to + "keep intact all notices". + + c) You must license the entire work, as a whole, under this + License to anyone who comes into possession of a copy. This + License will therefore apply, along with any applicable section 7 + additional terms, to the whole of the work, and all its parts, + regardless of how they are packaged. This License gives no + permission to license the work in any other way, but it does not + invalidate such permission if you have separately received it. + + d) If the work has interactive user interfaces, each must display + Appropriate Legal Notices; however, if the Program has interactive + interfaces that do not display Appropriate Legal Notices, your + work need not make them do so. + + A compilation of a covered work with other separate and independent +works, which are not by their nature extensions of the covered work, +and which are not combined with it such as to form a larger program, +in or on a volume of a storage or distribution medium, is called an +"aggregate" if the compilation and its resulting copyright are not +used to limit the access or legal rights of the compilation's users +beyond what the individual works permit. Inclusion of a covered work +in an aggregate does not cause this License to apply to the other +parts of the aggregate. + + 6. Conveying Non-Source Forms. + + You may convey a covered work in object code form under the terms +of sections 4 and 5, provided that you also convey the +machine-readable Corresponding Source under the terms of this License, +in one of these ways: + + a) Convey the object code in, or embodied in, a physical product + (including a physical distribution medium), accompanied by the + Corresponding Source fixed on a durable physical medium + customarily used for software interchange. + + b) Convey the object code in, or embodied in, a physical product + (including a physical distribution medium), accompanied by a + written offer, valid for at least three years and valid for as + long as you offer spare parts or customer support for that product + model, to give anyone who possesses the object code either (1) a + copy of the Corresponding Source for all the software in the + product that is covered by this License, on a durable physical + medium customarily used for software interchange, for a price no + more than your reasonable cost of physically performing this + conveying of source, or (2) access to copy the + Corresponding Source from a network server at no charge. + + c) Convey individual copies of the object code with a copy of the + written offer to provide the Corresponding Source. This + alternative is allowed only occasionally and noncommercially, and + only if you received the object code with such an offer, in accord + with subsection 6b. + + d) Convey the object code by offering access from a designated + place (gratis or for a charge), and offer equivalent access to the + Corresponding Source in the same way through the same place at no + further charge. You need not require recipients to copy the + Corresponding Source along with the object code. If the place to + copy the object code is a network server, the Corresponding Source + may be on a different server (operated by you or a third party) + that supports equivalent copying facilities, provided you maintain + clear directions next to the object code saying where to find the + Corresponding Source. Regardless of what server hosts the + Corresponding Source, you remain obligated to ensure that it is + available for as long as needed to satisfy these requirements. + + e) Convey the object code using peer-to-peer transmission, provided + you inform other peers where the object code and Corresponding + Source of the work are being offered to the general public at no + charge under subsection 6d. + + A separable portion of the object code, whose source code is excluded +from the Corresponding Source as a System Library, need not be +included in conveying the object code work. + + A "User Product" is either (1) a "consumer product", which means any +tangible personal property which is normally used for personal, family, +or household purposes, or (2) anything designed or sold for incorporation +into a dwelling. In determining whether a product is a consumer product, +doubtful cases shall be resolved in favor of coverage. For a particular +product received by a particular user, "normally used" refers to a +typical or common use of that class of product, regardless of the status +of the particular user or of the way in which the particular user +actually uses, or expects or is expected to use, the product. A product +is a consumer product regardless of whether the product has substantial +commercial, industrial or non-consumer uses, unless such uses represent +the only significant mode of use of the product. + + "Installation Information" for a User Product means any methods, +procedures, authorization keys, or other information required to install +and execute modified versions of a covered work in that User Product from +a modified version of its Corresponding Source. The information must +suffice to ensure that the continued functioning of the modified object +code is in no case prevented or interfered with solely because +modification has been made. + + If you convey an object code work under this section in, or with, or +specifically for use in, a User Product, and the conveying occurs as +part of a transaction in which the right of possession and use of the +User Product is transferred to the recipient in perpetuity or for a +fixed term (regardless of how the transaction is characterized), the +Corresponding Source conveyed under this section must be accompanied +by the Installation Information. But this requirement does not apply +if neither you nor any third party retains the ability to install +modified object code on the User Product (for example, the work has +been installed in ROM). + + The requirement to provide Installation Information does not include a +requirement to continue to provide support service, warranty, or updates +for a work that has been modified or installed by the recipient, or for +the User Product in which it has been modified or installed. Access to a +network may be denied when the modification itself materially and +adversely affects the operation of the network or violates the rules and +protocols for communication across the network. + + Corresponding Source conveyed, and Installation Information provided, +in accord with this section must be in a format that is publicly +documented (and with an implementation available to the public in +source code form), and must require no special password or key for +unpacking, reading or copying. + + 7. Additional Terms. + + "Additional permissions" are terms that supplement the terms of this +License by making exceptions from one or more of its conditions. +Additional permissions that are applicable to the entire Program shall +be treated as though they were included in this License, to the extent +that they are valid under applicable law. If additional permissions +apply only to part of the Program, that part may be used separately +under those permissions, but the entire Program remains governed by +this License without regard to the additional permissions. + + When you convey a copy of a covered work, you may at your option +remove any additional permissions from that copy, or from any part of +it. (Additional permissions may be written to require their own +removal in certain cases when you modify the work.) You may place +additional permissions on material, added by you to a covered work, +for which you have or can give appropriate copyright permission. + + Notwithstanding any other provision of this License, for material you +add to a covered work, you may (if authorized by the copyright holders of +that material) supplement the terms of this License with terms: + + a) Disclaiming warranty or limiting liability differently from the + terms of sections 15 and 16 of this License; or + + b) Requiring preservation of specified reasonable legal notices or + author attributions in that material or in the Appropriate Legal + Notices displayed by works containing it; or + + c) Prohibiting misrepresentation of the origin of that material, or + requiring that modified versions of such material be marked in + reasonable ways as different from the original version; or + + d) Limiting the use for publicity purposes of names of licensors or + authors of the material; or + + e) Declining to grant rights under trademark law for use of some + trade names, trademarks, or service marks; or + + f) Requiring indemnification of licensors and authors of that + material by anyone who conveys the material (or modified versions of + it) with contractual assumptions of liability to the recipient, for + any liability that these contractual assumptions directly impose on + those licensors and authors. + + All other non-permissive additional terms are considered "further +restrictions" within the meaning of section 10. If the Program as you +received it, or any part of it, contains a notice stating that it is +governed by this License along with a term that is a further +restriction, you may remove that term. If a license document contains +a further restriction but permits relicensing or conveying under this +License, you may add to a covered work material governed by the terms +of that license document, provided that the further restriction does +not survive such relicensing or conveying. + + If you add terms to a covered work in accord with this section, you +must place, in the relevant source files, a statement of the +additional terms that apply to those files, or a notice indicating +where to find the applicable terms. + + Additional terms, permissive or non-permissive, may be stated in the +form of a separately written license, or stated as exceptions; +the above requirements apply either way. + + 8. Termination. + + You may not propagate or modify a covered work except as expressly +provided under this License. Any attempt otherwise to propagate or +modify it is void, and will automatically terminate your rights under +this License (including any patent licenses granted under the third +paragraph of section 11). + + However, if you cease all violation of this License, then your +license from a particular copyright holder is reinstated (a) +provisionally, unless and until the copyright holder explicitly and +finally terminates your license, and (b) permanently, if the copyright +holder fails to notify you of the violation by some reasonable means +prior to 60 days after the cessation. + + Moreover, your license from a particular copyright holder is +reinstated permanently if the copyright holder notifies you of the +violation by some reasonable means, this is the first time you have +received notice of violation of this License (for any work) from that +copyright holder, and you cure the violation prior to 30 days after +your receipt of the notice. + + Termination of your rights under this section does not terminate the +licenses of parties who have received copies or rights from you under +this License. If your rights have been terminated and not permanently +reinstated, you do not qualify to receive new licenses for the same +material under section 10. + + 9. Acceptance Not Required for Having Copies. + + You are not required to accept this License in order to receive or +run a copy of the Program. Ancillary propagation of a covered work +occurring solely as a consequence of using peer-to-peer transmission +to receive a copy likewise does not require acceptance. However, +nothing other than this License grants you permission to propagate or +modify any covered work. These actions infringe copyright if you do +not accept this License. Therefore, by modifying or propagating a +covered work, you indicate your acceptance of this License to do so. + + 10. Automatic Licensing of Downstream Recipients. + + Each time you convey a covered work, the recipient automatically +receives a license from the original licensors, to run, modify and +propagate that work, subject to this License. You are not responsible +for enforcing compliance by third parties with this License. + + An "entity transaction" is a transaction transferring control of an +organization, or substantially all assets of one, or subdividing an +organization, or merging organizations. If propagation of a covered +work results from an entity transaction, each party to that +transaction who receives a copy of the work also receives whatever +licenses to the work the party's predecessor in interest had or could +give under the previous paragraph, plus a right to possession of the +Corresponding Source of the work from the predecessor in interest, if +the predecessor has it or can get it with reasonable efforts. + + You may not impose any further restrictions on the exercise of the +rights granted or affirmed under this License. For example, you may +not impose a license fee, royalty, or other charge for exercise of +rights granted under this License, and you may not initiate litigation +(including a cross-claim or counterclaim in a lawsuit) alleging that +any patent claim is infringed by making, using, selling, offering for +sale, or importing the Program or any portion of it. + + 11. Patents. + + A "contributor" is a copyright holder who authorizes use under this +License of the Program or a work on which the Program is based. The +work thus licensed is called the contributor's "contributor version". + + A contributor's "essential patent claims" are all patent claims +owned or controlled by the contributor, whether already acquired or +hereafter acquired, that would be infringed by some manner, permitted +by this License, of making, using, or selling its contributor version, +but do not include claims that would be infringed only as a +consequence of further modification of the contributor version. For +purposes of this definition, "control" includes the right to grant +patent sublicenses in a manner consistent with the requirements of +this License. + + Each contributor grants you a non-exclusive, worldwide, royalty-free +patent license under the contributor's essential patent claims, to +make, use, sell, offer for sale, import and otherwise run, modify and +propagate the contents of its contributor version. + + In the following three paragraphs, a "patent license" is any express +agreement or commitment, however denominated, not to enforce a patent +(such as an express permission to practice a patent or covenant not to +sue for patent infringement). To "grant" such a patent license to a +party means to make such an agreement or commitment not to enforce a +patent against the party. + + If you convey a covered work, knowingly relying on a patent license, +and the Corresponding Source of the work is not available for anyone +to copy, free of charge and under the terms of this License, through a +publicly available network server or other readily accessible means, +then you must either (1) cause the Corresponding Source to be so +available, or (2) arrange to deprive yourself of the benefit of the +patent license for this particular work, or (3) arrange, in a manner +consistent with the requirements of this License, to extend the patent +license to downstream recipients. "Knowingly relying" means you have +actual knowledge that, but for the patent license, your conveying the +covered work in a country, or your recipient's use of the covered work +in a country, would infringe one or more identifiable patents in that +country that you have reason to believe are valid. + + If, pursuant to or in connection with a single transaction or +arrangement, you convey, or propagate by procuring conveyance of, a +covered work, and grant a patent license to some of the parties +receiving the covered work authorizing them to use, propagate, modify +or convey a specific copy of the covered work, then the patent license +you grant is automatically extended to all recipients of the covered +work and works based on it. + + A patent license is "discriminatory" if it does not include within +the scope of its coverage, prohibits the exercise of, or is +conditioned on the non-exercise of one or more of the rights that are +specifically granted under this License. You may not convey a covered +work if you are a party to an arrangement with a third party that is +in the business of distributing software, under which you make payment +to the third party based on the extent of your activity of conveying +the work, and under which the third party grants, to any of the +parties who would receive the covered work from you, a discriminatory +patent license (a) in connection with copies of the covered work +conveyed by you (or copies made from those copies), or (b) primarily +for and in connection with specific products or compilations that +contain the covered work, unless you entered into that arrangement, +or that patent license was granted, prior to 28 March 2007. + + Nothing in this License shall be construed as excluding or limiting +any implied license or other defenses to infringement that may +otherwise be available to you under applicable patent law. + + 12. No Surrender of Others' Freedom. + + If conditions are imposed on you (whether by court order, agreement or +otherwise) that contradict the conditions of this License, they do not +excuse you from the conditions of this License. If you cannot convey a +covered work so as to satisfy simultaneously your obligations under this +License and any other pertinent obligations, then as a consequence you may +not convey it at all. For example, if you agree to terms that obligate you +to collect a royalty for further conveying from those to whom you convey +the Program, the only way you could satisfy both those terms and this +License would be to refrain entirely from conveying the Program. + + 13. Use with the GNU Affero General Public License. + + Notwithstanding any other provision of this License, you have +permission to link or combine any covered work with a work licensed +under version 3 of the GNU Affero General Public License into a single +combined work, and to convey the resulting work. The terms of this +License will continue to apply to the part which is the covered work, +but the special requirements of the GNU Affero General Public License, +section 13, concerning interaction through a network will apply to the +combination as such. + + 14. Revised Versions of this License. + + The Free Software Foundation may publish revised and/or new versions of +the GNU General Public License from time to time. Such new versions will +be similar in spirit to the present version, but may differ in detail to +address new problems or concerns. + + Each version is given a distinguishing version number. If the +Program specifies that a certain numbered version of the GNU General +Public License "or any later version" applies to it, you have the +option of following the terms and conditions either of that numbered +version or of any later version published by the Free Software +Foundation. If the Program does not specify a version number of the +GNU General Public License, you may choose any version ever published +by the Free Software Foundation. + + If the Program specifies that a proxy can decide which future +versions of the GNU General Public License can be used, that proxy's +public statement of acceptance of a version permanently authorizes you +to choose that version for the Program. + + Later license versions may give you additional or different +permissions. However, no additional obligations are imposed on any +author or copyright holder as a result of your choosing to follow a +later version. + + 15. Disclaimer of Warranty. + + THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY +APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT +HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY +OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, +THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM +IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF +ALL NECESSARY SERVICING, REPAIR OR CORRECTION. + + 16. Limitation of Liability. + + IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING +WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS +THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY +GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE +USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF +DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD +PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), +EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF +SUCH DAMAGES. + + 17. 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/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/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/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