Scientists often do the same bad stuff. Automate giving feedback during peer review for Python packages.
Goals:
- Given a GitHub repository, automate finding common issues such as
- No setup.py/setup.cfg/pyproject.toml
- No zenodo archive linked from the README
- Non-standard code layout (
src/or bust) - Files contain hard-coded file paths
- No documentation (search README for link to readthedocs)
- Package name doesn't match github repository name
- No reproducible installation instructions (i.e., does the README contain
pip) - Uses conda for installation
- Code does not have consistent style (i.e., there's no configuration for
black) pyromadoesn't pass 10/10- missing
LICENSEfile - missing
CITATION.cfffile
- Automate sending issues to the repository instructing how to do these things
- Use deterministic titles for all issues to avoid duplicates / make idempotent
- Create and edit "epic" issue that links others
Example Reviews:
Want to collaborate? What do you expect out of Python packages? Let me know in the comments. I envision this being sort of modular so people can contribute their own checks.
Desired interface:
Run on the command line with:
$ autoreviewer https://github.com/rs-costa/sbml2hyb
There's a submodule autoreviewer.jcheminf that has utilities for scraping the paper list
from the Journal of Cheminformatics, getting their ePub files,
extracting GitHub references from the availability statements, running autoreview on each,
then making the following summary with python -m autoreviewer.jcheminf.
The most recent release can be installed from PyPI with:
$ pip install autoreviewerThe most recent code and data can be installed directly from GitHub with:
$ pip install git+https://github.com/cthoyt/autoreviewer.gitYou'll also need to make sure pandoc is installed.
The best way to do this is brew install pandoc on macOS.
Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See CONTRIBUTING.md for more information on getting involved.
The code in this package is licensed under the MIT License.
This package was created with @audreyfeldroy's cookiecutter package using @cthoyt's cookiecutter-snekpack template.
See developer instructions
The final section of the README is for if you want to get involved by making a code contribution.
To install in development mode, use the following:
$ git clone git+https://github.com/cthoyt/autoreviewer.git
$ cd autoreviewer
$ pip install -e .After cloning the repository and installing tox with pip install tox, the unit tests in the tests/ folder can be
run reproducibly with:
$ toxAdditionally, these tests are automatically re-run with each commit in a GitHub Action.
The documentation can be built locally using the following:
$ git clone git+https://github.com/cthoyt/autoreviewer.git
$ cd autoreviewer
$ tox -e docs
$ open docs/build/html/index.htmlThe documentation automatically installs the package as well as the docs
extra specified in the setup.cfg. sphinx plugins
like texext can be added there. Additionally, they need to be added to the
extensions list in docs/source/conf.py.
After installing the package in development mode and installing
tox with pip install tox, the commands for making a new release are contained within the finish environment
in tox.ini. Run the following from the shell:
$ tox -e finishThis script does the following:
- Uses Bump2Version to switch the version number in the
setup.cfg,src/autoreviewer/version.py, anddocs/source/conf.pyto not have the-devsuffix - Packages the code in both a tar archive and a wheel using
build - Uploads to PyPI using
twine. Be sure to have a.pypircfile configured to avoid the need for manual input at this step - Push to GitHub. You'll need to make a release going with the commit where the version was bumped.
- Bump the version to the next patch. If you made big changes and want to bump the version by minor, you can
use
tox -e bumpversion minorafter.