{"id":16748996,"url":"https://github.com/cthoyt/autoreviewer","last_synced_at":"2025-03-21T22:31:59.135Z","repository":{"id":77808239,"uuid":"527751025","full_name":"cthoyt/autoreviewer","owner":"cthoyt","description":"👁️‍🗨️ Scientists often do the same bad stuff. Automate giving feedback during peer review.","archived":false,"fork":false,"pushed_at":"2024-09-23T08:17:19.000Z","size":455,"stargazers_count":27,"open_issues_count":6,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-03-18T05:51:11.316Z","etag":null,"topics":["metascience","peer-review","reproducibility"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/cthoyt.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":".github/CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":".github/CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2022-08-22T22:27:07.000Z","updated_at":"2025-02-13T07:02:29.000Z","dependencies_parsed_at":"2024-06-11T21:40:40.921Z","dependency_job_id":"5eb72ab7-f557-45e0-9fa4-43dc56d1901d","html_url":"https://github.com/cthoyt/autoreviewer","commit_stats":null,"previous_names":[],"tags_count":5,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cthoyt%2Fautoreviewer","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cthoyt%2Fautoreviewer/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cthoyt%2Fautoreviewer/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cthoyt%2Fautoreviewer/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/cthoyt","download_url":"https://codeload.github.com/cthoyt/autoreviewer/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":244880385,"owners_count":20525507,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["metascience","peer-review","reproducibility"],"created_at":"2024-10-13T02:23:33.517Z","updated_at":"2025-03-21T22:31:58.559Z","avatar_url":"https://github.com/cthoyt.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003ch1 align=\"center\"\u003e\n  AutoReviewer\n\u003c/h1\u003e\n\n\u003cp align=\"center\"\u003e\n    \u003ca href=\"https://github.com/cthoyt/autoreviewer/actions?query=workflow%3ATests\"\u003e\n        \u003cimg alt=\"Tests\" src=\"https://github.com/cthoyt/autoreviewer/workflows/Tests/badge.svg\" /\u003e\n    \u003c/a\u003e\n    \u003ca href=\"https://pypi.org/project/autoreviewer\"\u003e\n        \u003cimg alt=\"PyPI\" src=\"https://img.shields.io/pypi/v/autoreviewer\" /\u003e\n    \u003c/a\u003e\n    \u003ca href=\"https://pypi.org/project/autoreviewer\"\u003e\n        \u003cimg alt=\"PyPI - Python Version\" src=\"https://img.shields.io/pypi/pyversions/autoreviewer\" /\u003e\n    \u003c/a\u003e\n    \u003ca href=\"https://github.com/cthoyt/autoreviewer/blob/main/LICENSE\"\u003e\n        \u003cimg alt=\"PyPI - License\" src=\"https://img.shields.io/pypi/l/autoreviewer\" /\u003e\n    \u003c/a\u003e\n    \u003ca href='https://autoreviewer.readthedocs.io/en/latest/?badge=latest'\u003e\n        \u003cimg src='https://readthedocs.org/projects/autoreviewer/badge/?version=latest' alt='Documentation Status' /\u003e\n    \u003c/a\u003e\n    \u003ca href=\"https://codecov.io/gh/cthoyt/autoreviewer/branch/main\"\u003e\n        \u003cimg src=\"https://codecov.io/gh/cthoyt/autoreviewer/branch/main/graph/badge.svg\" alt=\"Codecov status\" /\u003e\n    \u003c/a\u003e  \n    \u003ca href=\"https://github.com/cthoyt/cookiecutter-python-package\"\u003e\n        \u003cimg alt=\"Cookiecutter template from @cthoyt\" src=\"https://img.shields.io/badge/Cookiecutter-snekpack-blue\" /\u003e \n    \u003c/a\u003e\n    \u003ca href='https://github.com/psf/black'\u003e\n        \u003cimg src='https://img.shields.io/badge/code%20style-black-000000.svg' alt='Code style: black' /\u003e\n    \u003c/a\u003e\n    \u003ca href=\"https://github.com/cthoyt/autoreviewer/blob/main/.github/CODE_OF_CONDUCT.md\"\u003e\n        \u003cimg src=\"https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg\" alt=\"Contributor Covenant\"/\u003e\n    \u003c/a\u003e\n\u003c/p\u003e\n\nScientists often do the same bad stuff. Automate giving feedback during peer review for Python packages.\n\nGoals:\n\n1. Given a GitHub repository, automate finding common issues such as\n    - No setup.py/setup.cfg/pyproject.toml\n    - No zenodo archive linked from the README\n    - Non-standard code layout (`src/` or bust)\n    - Files contain hard-coded file paths\n    - No documentation (search README for link to readthedocs)\n    - Package name doesn't match github repository name\n    - No reproducible installation instructions (i.e., does the README contain `pip`)\n    - Uses conda for installation\n    - Code does not have consistent style (i.e., there's no configuration for `black`)\n    - `pyroma` doesn't pass 10/10\n    - missing `LICENSE` file\n    - missing `CITATION.cff` file\n2. Automate sending issues to the repository instructing how to do these things\n    - Use deterministic titles for all issues to avoid duplicates / make idempotent\n    - Create and edit \"epic\" issue that links others\n\nExample Reviews:\n\n- https://github.com/fanavarro/lexical-analysis-obo-foundry/issues/4\n- https://github.com/krishnanlab/PecanPy/issues/12\n- https://github.com/huihui1126/drugSim-pathway/issues/14\n\nWant to collaborate? What do you expect out of Python packages? Let me know in the comments. I envision this being sort\nof modular so people can contribute their own checks.\n\nDesired interface:\n\nRun on the command line with:\n\n```shell\n$ autoreviewer https://github.com/rs-costa/sbml2hyb\n```\n\n## J. Chem. Inf. Analysis\n\n![](/src/autoreviewer/jcheminf/jcheminf_summary.png)\n\nThere's a submodule `autoreviewer.jcheminf` that has utilities for scraping the paper list\nfrom the Journal of Cheminformatics, getting their ePub files,\nextracting GitHub references from the availability statements, running autoreview on each,\nthen making the following summary with `python -m autoreviewer.jcheminf`.\n\n## 🚀 Installation\n\nThe most recent release can be installed from\n[PyPI](https://pypi.org/project/autoreviewer/) with:\n\n```bash\n$ pip install autoreviewer\n```\n\nThe most recent code and data can be installed directly from GitHub with:\n\n```bash\n$ pip install git+https://github.com/cthoyt/autoreviewer.git\n```\n\nYou'll also need to make sure [`pandoc`](https://pandoc.org/) is installed.\nThe best way to do this is `brew install pandoc` on macOS.\n\n## 👐 Contributing\n\nContributions, whether filing an issue, making a pull request, or forking, are appreciated. See\n[CONTRIBUTING.md](https://github.com/cthoyt/autoreviewer/blob/master/.github/CONTRIBUTING.md) for more information on\ngetting involved.\n\n## 👋 Attribution\n\n### ⚖️ License\n\nThe code in this package is licensed under the MIT License.\n\n### 🍪 Cookiecutter\n\nThis package was created with [@audreyfeldroy](https://github.com/audreyfeldroy)'s\n[cookiecutter](https://github.com/cookiecutter/cookiecutter) package using [@cthoyt](https://github.com/cthoyt)'s\n[cookiecutter-snekpack](https://github.com/cthoyt/cookiecutter-snekpack) template.\n\n## 🛠️ For Developers\n\n\u003cdetails\u003e\n  \u003csummary\u003eSee developer instructions\u003c/summary\u003e\n\n\nThe final section of the README is for if you want to get involved by making a code contribution.\n\n### Development Installation\n\nTo install in development mode, use the following:\n\n```bash\n$ git clone git+https://github.com/cthoyt/autoreviewer.git\n$ cd autoreviewer\n$ pip install -e .\n```\n\n### 🥼 Testing\n\nAfter cloning the repository and installing `tox` with `pip install tox`, the unit tests in the `tests/` folder can be\nrun reproducibly with:\n\n```shell\n$ tox\n```\n\nAdditionally, these tests are automatically re-run with each commit in\na [GitHub Action](https://github.com/cthoyt/autoreviewer/actions?query=workflow%3ATests).\n\n### 📖 Building the Documentation\n\nThe documentation can be built locally using the following:\n\n```shell\n$ git clone git+https://github.com/cthoyt/autoreviewer.git\n$ cd autoreviewer\n$ tox -e docs\n$ open docs/build/html/index.html\n``` \n\nThe documentation automatically installs the package as well as the `docs`\nextra specified in the [`setup.cfg`](setup.cfg). `sphinx` plugins\nlike `texext` can be added there. Additionally, they need to be added to the\n`extensions` list in [`docs/source/conf.py`](docs/source/conf.py).\n\n### 📦 Making a Release\n\nAfter installing the package in development mode and installing\n`tox` with `pip install tox`, the commands for making a new release are contained within the `finish` environment\nin `tox.ini`. Run the following from the shell:\n\n```shell\n$ tox -e finish\n```\n\nThis script does the following:\n\n1. Uses [Bump2Version](https://github.com/c4urself/bump2version) to switch the version number in the `setup.cfg`,\n   `src/autoreviewer/version.py`, and [`docs/source/conf.py`](docs/source/conf.py) to not have the `-dev` suffix\n2. Packages the code in both a tar archive and a wheel using [`build`](https://github.com/pypa/build)\n3. Uploads to PyPI using [`twine`](https://github.com/pypa/twine). Be sure to have a `.pypirc` file configured to avoid\n   the need for manual input at this\n   step\n4. Push to GitHub. You'll need to make a release going with the commit where the version was bumped.\n5. Bump the version to the next patch. If you made big changes and want to bump the version by minor, you can\n   use `tox -e bumpversion minor` after.\n\n\u003c/details\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcthoyt%2Fautoreviewer","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcthoyt%2Fautoreviewer","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcthoyt%2Fautoreviewer/lists"}