Note
This document assumes some familiarity with contributing to open source scientific Python projects using GitHub pull requests.
If you are a first-time contributor:
You'll need to install GraphViz on your local computer, if you haven't already. For OS-specific installation instructions, refer to INSTALL.txt.
Go to https://github.com/pygraphviz/pygraphviz and click the "fork" button to create your own copy of the project.
Clone the project to your local computer:
git clone [email protected]:your-username/pygraphviz.git
Navigate to the folder pygraphviz and add the upstream repository:
git remote add upstream [email protected]:pygraphviz/pygraphviz.git
Now, you have remote repositories named:
upstream, which refers to thepygraphvizrepositoryorigin, which refers to your personal fork
Next, you need to set up your build environment. Here are instructions using
venv:venv(pip based)# Create a virtualenv named ``pygraphviz-dev`` that lives in the directory of # the same name python -m venv pygraphviz-dev # Activate it source pygraphviz-dev/bin/activate # Install main development and runtime dependencies of pygraphviz pip install -r requirements/test.txt -r requirements/developer.txt # # Build and install pygraphviz from source pip install -e . # Test your installation PYTHONPATH=. pytest pygraphviz
Finally, we recommend you use a pre-commit hook, which runs black when you type
git commit:pre-commit install
Develop your contribution:
Pull the latest changes from upstream:
git checkout main git pull upstream main
Create a branch for the feature you want to work on. Since the branch name will appear in the merge message, use a sensible name such as 'bugfix-for-issue-1480':
git checkout -b bugfix-for-issue-1480
Commit locally as you progress (
git addandgit commit)
Test your contribution:
Run the test suite locally (see Testing for details):
PYTHONPATH=. pytest pygraphviz
Running the tests locally before submitting a pull request helps catch problems early and reduces the load on the continuous integration system.
Submit your contribution:
Push your changes back to your fork on GitHub:
git push origin bugfix-for-issue-1480
Go to GitHub. The new branch will show up with a green Pull Request button---click it.
If you want, post on the mailing list to explain your changes or to ask for review.
Review process:
- Every Pull Request (PR) update triggers a set of continuous integration services that check that the code is up to standards and passes all our tests. These checks must pass before your PR can be merged. If one of the checks fails, you can find out why by clicking on the "failed" icon (red cross) and inspecting the build and test log.
- Reviewers (the other developers and interested community members) will write inline and/or general comments on your PR to help you improve its implementation, documentation, and style. Every single developer working on the project has their code reviewed, and we've come to see it as friendly conversation from which we all learn and the overall code quality benefits. Therefore, please don't let the review discourage you from contributing: its only aim is to improve the quality of project, not to criticize (we are, after all, very grateful for the time you're donating!).
- To update your PR, make your changes on your local repository and commit. As soon as those changes are pushed up (to the same branch as before) the PR will update automatically.
Note
If the PR closes an issue, make sure that GitHub knows to automatically close the issue when the PR is merged. For example, if the PR closes issue number 1480, you could use the phrase "Fixes #1480" in the PR description or commit message.
To reviewers: make sure the merge message also has a brief description of the change(s).
If GitHub indicates that the branch of your Pull Request can no longer be merged automatically, merge the main branch into yours:
git fetch upstream main git merge upstream/main
If any conflicts occur, they need to be fixed before continuing. See which files are in conflict using:
git status
Which displays a message like:
Unmerged paths: (use "git add <file>..." to mark resolution) both modified: file_with_conflict.txt
Inside the conflicted file, you'll find sections like these:
<<<<<<< HEAD The way the text looks in your branch ======= The way the text looks in the main branch >>>>>>> main
Choose one version of the text that should be kept, and delete the rest:
The way the text looks in your branch
Now, add the fixed file:
git add file_with_conflict.txt
Once you've fixed all merge conflicts, do:
git commit
Note
Advanced Git users may want to rebase instead of merge, but we squash and merge PRs either way.
- All code should have tests.
- All code should be documented, to the same standard as NumPy and SciPy.
- All changes are reviewed. Ask on the mailing list if you get no response to your pull request.
To run all tests:
$ PYTHONPATH=. pytest pygraphviz
Or tests from a specific file:
$ PYTHONPATH=. pytest pygraphviz/tests/test_readwrite.py
Use --doctest-modules to run doctests.
For example, run all tests and all doctests using:
$ PYTHONPATH=. pytest --doctest-modules pygraphviz
Tests for a module should ideally cover all code in that module, i.e., statement coverage should be at 100%.
To measure the test coverage, run:
$ PYTHONPATH=. pytest --cov=pygraphviz pygraphviz
This will print a report with one line for each file in pygraphviz, detailing the test coverage:
Name Stmts Miss Cover -------------------------------------------- pygraphviz/__init__.py 12 4 67% pygraphviz/agraph.py 1022 196 81% pygraphviz/graphviz.py 179 42 77% pygraphviz/scraper.py 26 18 31% pygraphviz/testing.py 16 0 100% -------------------------------------------- TOTAL 1255 260 79%
If you're new to testing, see existing test files for examples of things to do. Don't let the tests keep you from submitting your contribution! If you're not sure how to do this or are having trouble, submit your pull request anyway. We will help you create the tests and sort out any kind of problem during code review.
The gallery examples are managed by
sphinx-gallery.
The source files for the example gallery are .py scripts in examples/ that
generate one or more figures. They are executed automatically by sphinx-gallery when the
documentation is built. The output is gathered and assembled into the gallery.
You can add a new plot by placing a new .py file in one of the directories inside the
examples directory of the repository. See the other examples to get an idea for the
format.
Note
Gallery examples should start with plot_, e.g. plot_new_example.py
General guidelines for making a good gallery plot:
- Examples should highlight a single feature/command.
- Try to make the example as simple as possible.
- Data needed by examples should be included in the same directory and the example script.
- Add comments to explain things are aren't obvious from reading the code.
- Describe the feature that you're showcasing and link to other relevant parts of the documentation.
pygraphviz uses SWIG to generate wrappers around the graphviz C code.
Any modifications to C source code should be made in the SWIG wrapper file,
graphviz.i, not graphviz_wrap.c as this file is auto-generated by
SWIG and any manual changes will be overwritten.
The wrappers can be generated with: swig -python pygraphviz/graphviz.i.
This requires SWIG to be installed.
Note
The wrappers must be generated from the top-level directory, i.e.
swig -python pygraphviz/graphviz.i
Attempting to regenerate the wrappers from another directory will result in broken builds.
Please report bugs on GitHub.