The latest stable release of TPOT is on the master branch, whereas the latest version of TPOT in development is on the development branch. Make sure you are looking at and working on the correct branch if you're looking to contribute code.
In terms of directory structure:
- All of TPOT's code sources are in the
- The documentation sources are in the
- Images in the documentation are in the
- Tutorials for TPOT are in the
- Unit tests for TPOT are in the
Make sure to familiarize yourself with the project layout before making any major contributions, and especially make sure to send all code changes to the
How to contribute
The preferred way to contribute to TPOT is to fork the main repository on GitHub:
Fork the project repository: click on the 'Fork' button near the top of the page. This creates a copy of the code under your account on the GitHub server.
Clone this copy to your local disk:
$ git clone firstname.lastname@example.org:YourUsername/tpot.git $ cd tpot
Create a branch to hold your changes:
$ git checkout -b my-contribution
Make sure your local environment is setup correctly for development. Installation instructions are almost identical to the user instructions except that TPOT should not be installed. If you have TPOT installed on your computer then make sure you are using a virtual environment that does not have TPOT installed. Furthermore, you should make sure you have installed the
nosepackage into your development environment so that you can test changes locally.
$ conda install nose
Start making changes on your newly created branch, remembering to never work on the
masterbranch! Work on this copy on your computer using Git to do the version control.
Once some changes are saved locally, you can use your tweaked version of TPOT by navigating to the project's base directory and running TPOT directly from the command line:
$ python -m tpot.driver
or by running script that imports and uses the TPOT module with code similar to
from tpot import TPOTClassifier
To check your changes haven't broken any existing tests and to check new tests you've added pass run the following (note, you must have the
nosepackage installed within your dev environment for this to work):
$ nosetests -s -v
When you're done editing and local testing, run:
$ git add modified_files $ git commit
to record your changes in Git, then push them to GitHub with:
$ git push -u origin my-contribution
Finally, go to the web page of your fork of the TPOT repo, and click 'Pull Request' (PR) to send your changes to the maintainers for review. Make sure that you send your PR to the
development branch, as the
master branch is reserved for the latest stable release. This will start the CI server to check all the project's unit tests run and send an email to the maintainers.
(If any of the above seems like magic to you, then look up the Git documentation on the web.)
Before submitting your pull request
Before you submit a pull request for your contribution, please work through this checklist to make sure that you have done everything necessary so we can efficiently review and accept your changes.
If your contribution changes TPOT in any way:
Update the documentation so all of your changes are reflected there.
Update the README if anything there has changed.
If your contribution involves any code changes:
Update the project unit tests to test your code changes.
Make sure that your code is properly commented with docstrings and comments explaining your rationale behind non-obvious coding practices.
If your code affected any of the pipeline operators, make sure that the corresponding export functionality reflects those changes.
If your contribution requires a new library dependency:
Double-check that the new dependency is easy to install via
pipor Anaconda and supports both Python 2 and 3. If the dependency requires a complicated installation, then we most likely won't merge your changes because we want to keep TPOT easy to install.
Add the required version of the library to .travis.yml
Add a line to pip install the library to .travis_install.sh
Add a line to print the version of the library to .travis_install.sh
Similarly add a line to print the version of the library to .travis_test.sh
Updating the documentation
We use mkdocs to manage our project documentation. This allows us to write the documentation in Markdown and compile them to HTML as needed. Below are a couple useful commands to know when updating the documentation. Make sure that you are running these commands in the base directory of the TPOT project.
mkdocs serve: Hosts of a local version of the documentation that you can access at the provided URL. The local version will update automatically as you save changes to the documentation.
mkdocs build --clean: Creates a fresh build of the documentation in HTML in the
docsdirectory. Always run this before pushing the documentation to GitHub.
After submitting your pull request
After submitting your pull request, Travis-CI will automatically run unit tests on your changes and make sure that your updated code builds and runs on Python 2 and 3. We also use services that automatically check code quality and test coverage.
Check back shortly after submitting your pull request to make sure that your code passes these checks. If any of the checks come back with a red X, then do your best to address the errors.