Contributing#

Thank you for considering contributing to MACPie!

Reporting issues#

Include the following information in your post:

  • Describe what you expected to happen.

  • Describe what actually happened. Include the full traceback if there was an exception.

  • List your Python and MACPie versions. If possible, check if this issue is already fixed in the latest releases or the latest code in the repository.

  • If possible, include a minimal reproducible example to help us identify the issue. This also helps check that the issue is not with your own code.

  • Email the above to albert.lee2@ucsf.edu

Submitting patches#

Include the following in your patch:

  • Include tests if your patch adds or changes code. Make sure the test fails without your patch.

  • Update any relevant docs pages and docstrings. Docs pages and docstrings should be wrapped at 72 characters.

  • Add an entry in CHANGES.rst. Use the same style as other entries. Also include .. versionchanged:: inline changelogs in relevant docstrings.

First time setup#

  • Download and install the latest version of git.

  • Configure git with your username and email.

    $ git config --global user.name 'your name'
    $ git config --global user.email 'your email'
    
  • Make sure you have a GitHub account.

  • Fork MACPie to your GitHub account by clicking the Fork button.

  • Clone the main repository locally.

    $ git clone https://github.com/UCSFMemoryAndAging/macpie
    $ cd macpie
    
  • Add your fork as a remote to push your work to. Replace {username} with your username. This names the remote “fork”, the default remote is “origin”.

    git remote add fork https://github.com/{username}/macpie
    
  • Create a virtualenv.

    $ python3 -m venv env
    $ . env/bin/activate
    
  • Upgrade pip and setuptools.

    $ python -m pip install --upgrade pip setuptools
    
  • Install MACPie in editable mode with development dependencies.

    $ pip install -e . -r requirements/dev.txt
    

    If you want to start with all dependencies:

    • At the prompt:

      $ pip install -e .[all] -r requirements/dev.txt
      
    • Or if you are using zsh shell, note that square brackets are used for globbing / pattern matching, so you’ll need to quote the argument like so:

      $ pip install -e '.[all]' -r requirements/dev.txt
      

Start coding#

  • Create a branch to identify the issue you would like to work on. If you’re submitting a bug or documentation fix, branch off of the latest “.x” branch.

    $ git fetch origin
    $ git checkout -b your-branch-name origin/0.2.x
    

    If you’re submitting a feature addition or change, branch off of the “master” branch.

    $ git fetch origin
    $ git checkout -b your-branch-name origin/master
    
  • Using your favorite editor, make your changes, committing as you go.

  • Include tests that cover any code changes you make. Make sure the test fails without your patch. Run the tests as described below.

  • Push your commits to your fork on GitHub and create a pull request. Link to the issue being addressed with fixes #123 in the pull request.

    $ git push --set-upstream fork your-branch-name
    

Running basic test suite#

Run the basic test suite with pytest.

$ pytest --runslow

This runs the tests for the current environment, which is usually sufficient. The --runslow flag tell pytest to run any tests marked as slow.

Running full test suite#

The full test suite takes a long time to run because it tests multiple combinations of Python and dependencies. You need to have Python 3.8, 3.9, and 3.10 installed to run all of the environments. Then run:

$ tox
# or "tox -r" to force recreation of virtual environments

If you aren’t already set up to install multiple version of Python, I recommend using pyenv.

  • Install pyenv

  • Update list of available versions.

    $ pyenv update
    
  • List available versions to install.

    $ pyenv install -l
    
  • Install the Python versions you want to test

    $ pyenv install 3.8.13
    $ pyenv install 3.9.13
    $ pyenv install 3.10.4
    
  • In your local repo root:

    $ pyenv local 3.8.13 3.9.13 3.10.4
    

    This will set local application-specific Python version(s) (in order of preference) by writing the version name(s) to a .python-version file in the current directory.

    Now you can execute the full test suite with tox.

    $ tox
    

    When you’re done and/or want to unset the local version:

    $ pyenv local --unset
    

Other useful pyenv commands:

$ # list versions
$ pyenv versions
$
$ # set the global Python version
$ pyenv global 3.6.12
$
$ # set application-specific version by creating a .python-version file in current dir.
$ # sets the pyverison for current dir and subdirs
$ pyenv local 3.8.5
$
$ # set shell-specific Python version
$ pyenv shell 3.8-dev

Read more about tox.

Running test coverage#

Generating a report of lines that do not have test coverage can indicate where to start contributing. Run pytest using coverage and generate a report.

$ pip install coverage
$ coverage run -m pytest --runslow
$ coverage html

Open htmlcov/index.html in your browser to explore the report.

Read more about coverage.

Building the docs#

Build the docs in the docs directory using Sphinx.

$ cd docs
$ make html

Open _build/html/index.html in your browser to view the docs.

Read more about Sphinx.

Upgrading dependencies#

To upgrade dependencies, we use pip tools.

  • Update all packages for dev

    $ pip-compile --upgrade --output-file requirements/dev.txt requirements/dev.in
    
  • Update all packages for tests

    $ pip-compile --upgrade --output-file requirements/tests.txt requirements/tests.in
    
  • Update all packages for docs

    $ pip-compile --upgrade --output-file requirements/doc.txt requirements/doc.in
    
  • Then to proceed with development, install the upgraded dev dependencies

    $ pip install -r requirements/dev.txt
    

Uploading new version to PyPI#

  • Create a git tag for the new version

    $ git tag -a v0.5.0 -m "release: v0.5.0"
    
  • Push tag to remote

    $ git push origin v0.5.0
    
  • Create distribution archives

    $ python setup.py sdist bdist_wheel
    
  • Upload distribution files to PyPI via twine (pip install twine if needed)

    $ python3 -m twine upload dist/macpie-0.5.0*
    
  • In github, perform the following:

    1. Click on Releases

    2. Click on Draft a new release

    3. Choose the proper tag

    4. Release title: v0.5.0

    5. Describe this release: Refer to the [changelog](https://macpie.readthedocs.io/en/latest/changelog/) for details.