Contributing¶

Contributions are welcome, and they are greatly appreciated! Every little bit helps, and credit will always be given.

You can contribute in many ways:

Types of Contributions¶

Report Bugs¶

Report bugs at https://github.com/cloudbopper/anamod/issues.

If you are reporting a bug, please include:

Your operating system name and version.
Any details about your local setup that might be helpful in troubleshooting.
Detailed steps to reproduce the bug.

Fix Bugs¶

Look through the GitHub issues for bugs. Anything tagged with “bug” and “help wanted” is open to whoever wants to implement it.

Implement Features¶

Look through the GitHub issues for features. Anything tagged with “enhancement” and “help wanted” is open to whoever wants to implement it.

Write Documentation¶

anamod could always use more documentation, whether as part of the official anamod docs, in docstrings, or even on the web in blog posts, articles, and such.

Submit Feedback¶

The best way to send feedback is to file an issue at https://github.com/cloudbopper/anamod/issues.

If you are proposing a feature:

Explain in detail how it would work.
Keep the scope as narrow as possible, to make it easier to implement.

Get Started!¶

Ready to contribute? Here’s how to set up anamod for local development.

Fork the anamod repo on GitHub.

Clone your fork locally:

git clone git@github.com:your_name_here/anamod.git

Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development:
```
mkvirtualenv -p python3 anamod
cd anamod/
pip install -r requirements_dev.txt -r requirements.txt
```
Create a branch for local development:
```
git checkout -b name-of-your-bugfix-or-feature
```
Now you can make your changes locally.
When you’re done making changes, check that your changes pass the pylint/flake8 and the tests for all python versions:
```
tox
```
You may use pyenv to install and test with multiple python versions.

While testing with a specific python version, you may invoke the tests as follows:
```
pytest tests
```
To profile the code, add the –profile-svg flag (by default, the profiling results are saved in the ‘prof’ directory):
```
pytest --profile-svg tests
```
If the change affects the distributed (HTCondor) implementation, you should also run condor tests in an environment that supports condor with a shared filesystem (these tests are disabled by default):
```
pytest --basetemp=condor_test_outputs tests/condor_tests
```
When writing new tests, corresponding tests and gold (expected) files for condor may be generated automatically using the following script:
```
python -m anamod.gen_condor_tests
```
If regression tests fail because the new data is correct, you can use the –force-regen flag to update the gold file (see pytest-regressions):
```
pytest --force-regen
```
Note: Most regression tests perform two comparisons - the output p-values and the FDR output, so the tests must be run with the –force-regen flag twice to update both the gold files.

Condor gold files may be overwritten using –force-regen as well, or simply copied over by running:
```
python -m tests.gen_condor_tests -overwrite_golds
```

Commit your changes and push your branch to GitHub:

git add .
git commit -m "Your detailed description of your changes."
git push origin name-of-your-bugfix-or-feature

Submit a pull request through the GitHub website.

Pull Request Guidelines¶

Before you submit a pull request, check that it meets these guidelines:

The pull request should include tests.
If the pull request adds functionality, the docs should be updated. Put your new functionality into a function with a docstring, and add the feature to the list in README.rst.
The pull request should work for Python 3.5, 3.6, 3.7 and 3.8. Check https://travis-ci.com/cloudbopper/anamod/pull_requests and make sure that the tests pass for all supported Python versions.

Tips¶

To run all tests:

make test

To run a subset of tests:

pytest tests/test_anamod.py  # Only run tests from specific file
pytest -k test_simulation_interactions tests/test_anamod.py  # Only run specific test from given file

To run debugger within pytest:

pytest --trace  # Drop to PDB at the start of a test
pytest --pdb  # Drop to PDB on failures

To generate interactive coverage report:

make coverage

To profile the code:

make profile

To run linters:

make lint

Deploying¶

A reminder for the maintainers on how to deploy. Make sure all your changes are committed (including an entry in changelog.rst). Then run:

bumpversion patch # possible: major / minor / patch
git push
git push --tags

Travis will then deploy to PyPI if tests pass.