Development Procedures and Guidelines

We welcome and encourage community development of PypeIt! All code contributors are expected to follow our Code of Conduct and these development guidelines.

Installing and working with your fork

If you plan to develop the PypeIt code, you should install the code from a fork of the main respository, as described below.

You may also need/want to create a fork of the PypeIt Development Suite! This process proceeds similarly to the main code repository, except that you do not need to pip install the dev-suite repository.

Setup a clean python environment

This is the same as described for a user installation; see Setup a clean python environment.

Fork the code

Except for a few maintainers, code development should be done in forks of the code base. To fork the code, go to GitHub and click the “Fork” button at the upper right. Do not change the name of the repository (PypeIt).

When you fork the code, you will be asked if you want to only copy the release branch (default). If you uncheck this box, you will get all of the current branches, which is almost certainly not something you want to do. See below for one way to add the develop branch to your repo.

Finally, you are strongly encouraged to add branch protection rules for both the release and develop branches in your fork (these rules are not inherited from the main repository).

Follow a similar process for creating a fork of the PypeIt Development Suite.

Local Install

To install from source, first create a local clone of your fork (replace {github_handle} with the GitHub handle used to create your fork):

git clone https://github.com/{github_handle}/PypeIt.git

This will create a PypeIt directory at the location the command above was executed.

To install the dev-suite, perform a similar operation (from your fork):

git clone https://github.com/{github_handle}/PypeIt-development-suite.git

Install the main PypeIt code, including its package dependencies, using pip (even if you’re in a conda environment):

cd PypeIt
pip install -e ".[dev]"

This (specifically the -e option) creates an “editable” installation, which means that any changes you make in the repository directory tree will take immediate effect the next time the code is imported. Including the [dev] set of optional dependencies ensures that all of the tools you need to test and build PypeIt are installed. (Note that you may or may not need the quotes above depending on your shell, and that you should avoid cutting and pasting these commands into a terminal window.)

You do not need to execute a similar installation for the dev-suite.

Connect the main repository to your fork

To ensure you are up-to-date with the main repository, you should add it as a remote:

% git remote -v
origin      https://github.com/{github_handle}/PypeIt.git (fetch)
origin      https://github.com/{github_handle}/PypeIt.git (push)
% git remote add upstream https://github.com/pypeit/PypeIt.git
% git remote -v
origin      https://github.com/{github_handle}/PypeIt.git (fetch)
origin      https://github.com/{github_handle}/PypeIt.git (push)
upstream    https://github.com/pypeit/PypeIt.git (fetch)
upstream    https://github.com/pypeit/PypeIt.git (push)

For the dev-suite:

% git remote -v
origin      https://github.com/{github_handle}/PypeIt-development-suite.git (fetch)
origin      https://github.com/{github_handle}/PypeIt-development-suite.git (push)
% git remote add upstream https://github.com/pypeit/PypeIt-development-suite.git
% git remote -v
origin      https://github.com/{github_handle}/PypeIt-development-suite.git (fetch)
origin      https://github.com/{github_handle}/PypeIt-development-suite.git (push)
upstream    https://github.com/pypeit/PypeIt-development-suite.git (fetch)
upstream    https://github.com/pypeit/PypeIt-development-suite.git (push)

Updating your fork

To update your fork so that it will recognize changes in the main repository, run:

% git fetch upstream

Do this often! Note, however, that this does not update the content of your fork to match the changes in the upstream repo.

Checkout a remote branch and add it to your fork

The most obvious application of this is for your first checkout of the develop branch into your fork. However, you can do this with any branch (and with any remote). The steps are (1) update your repo, (2) checkout the upstream branch, (3) push it to your fork (and change its remote tracking):

% git fetch upstream
% git checkout -b develop upstream/develop
% git push -u origin develop

Merging changes made to an upstream branch

The fetch command does not merge changes made to the upstream repo. You have to do that explicitly using either merge:

% git fetch upstream
% git checkout develop
% git merge upstream/develop
% git push

or rebase:

% git fetch upstream
% git checkout feature_branch
% git rebase upstream/develop
% git push --force

In the rebase example note two things:

  • This does not update your local develop branch because we were not on our local develop branch when we executed the rebase command. This only updates the feature_branch with the changes made to its original base branch, develop in this case.

  • Rebasing often requires forcing the push to your fork, using the --force option, because it alters the commit history. If you try pushing without the force argument, you will likely get a warning that your branch is out of date and you need to pull the origin branch. Do not do this. Pulling in your remote branch after rebasing will lead to a number of conflicts and, likely, lost work.

Collaborating on a branch

If you’re working with another developer (who has a different fork) on a single branch, you can add their fork as another remote and proceed similarly to how you work with the main repo:

% git remote add collab https://github.com/{collaborator}/PypeIt.git
% git remote -v
origin      https://github.com/{github_handle}/PypeIt.git (fetch)
origin      https://github.com/{github_handle}/PypeIt.git (push)
upstream    https://github.com/pypeit/PypeIt.git (fetch)
upstream    https://github.com/pypeit/PypeIt.git (push)
collab      https://github.com/{collaborator}/PypeIt.git (fetch)
collab      https://github.com/{collaborator}/PypeIt.git (push)

Then you can both work on a feature_branch while keeping your branches in sync:

% git fetch collab
% git checkout feature_branch
% git merge collab/feature_branch
% git push

When you’re done, one of you can issue the PR from one of your forks into the main repo. If you want to keep your remote list clean, you can remove the remote connection after finishing the collaborative work:

% git remote remove collab

Persistent and development branches

PypeIt maintains two persistent branches:

  • release: This is the primary stable version of the code. Modulo any very recent Hotfixes, this is closest to the most recently tagged and released version. Pull requests to this branch are only done before tagging a new release of the code or to perform critical bug hotfixes. The release schedule is discussed during our bi-weekly development meetings.

  • develop: This is the main development version of the code. It should be stable enough to use, but it may contain experimental, unsupported code that is work in progress.

When editing the code, please create a new branch stemming from the develop branch. You should also pull and merge in the most recent version of the release branch to make sure your new branch includes any very recent hotfixes. On the command line, you can do this as follows from your PypeIt directory:

# Fetch upstream changes
git fetch upstream
# Switch to your local release branch
git checkout release
# Update it
git merge upstream/release
# Push the updated branch to your fork
git push
# Switch to your local develop branch
git checkout develop
# Update it
git merge upstream/develop
# Push the updated branch to your fork
git push
# Create a new branch from your local develop branch
git checkout -b my_new_feature
# Make sure develop is up-to-date with release
git merge release
# Push the new branch to your fork
git push -u origin my_new_feature

Note

In terms of the merge with the release branch, beware that you may need to start a new release version doc that reflects the jump in the version number. This should only be necessary if your branch is the first one after a new tag is released. See Logging changes.

Development Principles and Communication

The main thing to keep in mind when developing for PypeIt is that its primary use is as an end-to-end reduction pipeline. This has a few implications:

  • By default, the execution of run_pypeit should continue either until a critical error is raised or the reduction is complete. No direct interaction with the code should be required at any point. PypeIt does have some interactive components, but these are executed only if specifically requested by command-line arguments or via separate scripts.

  • Any input needed from the user for your feature should be provided by User-level Parameters (preferred) or as a command-line argument.

  • When developing and debugging, you may need to interact with the code using IPython.embed; however, these instances should be removed before performing a pull request.

  • The success or failure of any given procedure must be assessed via automatically generated quality-assessment figures (preferred) or via scripts that interact with the primary output files.

  • See here for guidance on adding a new spectrograph to the list of spectroscopic data that PypeIt can reduce.

  • If your development includes adding a new executable script, see advice at Developing New PypeIt Scripts.

Feature development in PypeIt is unlikely to be fully independent of other development activities. Your feature will likely depend on or influence the outcome of other modules during the data-reduction process. This leads to a few important guidelines:

  • Make sure that your branch is always up-to-date with the develop and release branches. E.g.:

    git fetch upstream
git checkout release
git merge upstream/release
git checkout develop
git merge upstream/develop
git checkout my_new_feature
git merge release
git merge develop

  • Consider the effects of simultaneous development efforts on your work and vice versa. For example, if you’re working on a specific module of the code that depends on the result/datamodel of the wavelength-calibration module, you should communicate this and find out if someone else is developing that module and how/if they’re changing it. Depending on the scale of those changes, development priorities may need to be worked out to minimize merge conflicts and the need to immediately rework/refactor new code.

  • When you’re ready to, you can submit a PR at any time, but the core development team will need to discuss the merge order to ensure a smooth process.

Our primary means of communication for development is the PypeIt developers Slack and a biweekly telecon. Contact X Prochaska for Slack access and/or the relevant Zoom link.

Logging changes

It is important to log changes made to the code in a way that other developers and eventually users can interpret. In the past we have done this using the single CHANGES.rst file; however, we now have version specific change logs in the doc/releases directory. In terms of development guidelines:

  • Changes made to the code should be logged in the relevant development log. For example, all changes made after version 1.14.0 will be logged in a doc/release/1.14.1dev.rst file. If the relevant file doesn’t exist when you submit your PR, create it.

  • Changes are expected to fall under a small set of broad categories, like improvements to performance for specific instruments, minor bug fixes, or datamodel changes (see previous release docs for examples). When including your change, add it below the relevant heading; if no relevant heading exists, add a new one.

  • Hotfixes merged directly to the release branch should also be added to the relevant development log. I.e., these changes are not part of the released tag, even if they are in the “release” branch. Again, if the relevant file doesn’t exist when you perform the hotfix, create it in a way that it will get merged with the identical doc in the develop branch. See Hotfixes.

  • When tagging, the development log will be renamed to the new tag version, and a new file should be created for the next development phase. See Tagging Protocol.

Hotfixes

There may be bugs in the release version of the code that are not caught by the tests, but significantly impact some users. Fixing these issues leads to a patch release of the code, following this procedure:

  • Checkout the release version of the code.

  • Create a new branch from the release version (not the develop version).

  • Implement the hotfix.

  • Create a release doc that lists the hotfix. For example, if the current development doc is doc/release/1.14.1dev.rst: create the new file doc/release/1.14.1.rst, edit it to include a description of the hotfix, add it to the repo, and rename the existing development doc to indicate the version increment (doc/release/1.14.2dev.rst). Also update the doc/whatsnew.rst file to include the new release files.

  • Issue a PR and follow the Tagging Protocol. Following the example above, the new tag would be 1.14.1.

Testing

PypeIt performs extensive testing using the PypeIt Development Suite; follow that link for more details on executing the tests. Below, we describe how to add new tests.

Development Suite

To add new tests to the development suite

  1. Add the new data to shared Google Drive under RAW_DATA. The tests are organized into setup directories under a directory named for the instrument.

  2. Add a new PypeIt Reduction File specific to this data to the PypeIt Development Suite repo under pypeit_files. The file name must be lower case and named after the instrument and setup, for example: keck_deimos_1200g_m_7750.pypeit.

  3. If desired, add any files for pypeit_sensfunc, pypeit_flux_calib, pypeit_coadd_1dspec, pypeit_coadd_2dspec to the PypeIt Development Suite repo under sensfunc_files, fluxing_files, coadd1d_files, coadd2d_files, respectively.

  4. Edit the test_scripts/test_setups.py file in the PypeIt Development Suite to include the new setup among the tests to perform. Follow the instructions at the top of that file.

  5. Run the full development test suite to completion. Once all tests pass, the test_priority_file will be updated with the new test. This file tells the test scripts what order to run the tests in for optimum CPU utilization. Commit test_priority_list and any other files added to the dev-suite repository and submit a pull request.

The PypeIt Development Suite also contains unit tests that require use of data in the RAW_DATA directory and “vet” tests that are set of unit tests that require output files from PypeIt scripts. The former typically test simple functionality of the PypeIt code, whereas the latter (vet tests) check the results of the PypeIt scripts against the expected performance/result.

Unit Tests (GitHub CI)

Unit tests performed by GitHub continuous integration (CI) are located in the $PYPEIT_DIR/pypeit/tests directory. To run them, make sure you have pytest installed (this should be true if you followed the developer installation procedure) and then run, from your PypeIt directory:

pytest

If some tests fail, you can run an individual test, e.g. test_wvcalib.py with

pytest -s pypeit/tests/test_wvcalib.py

Note that the “-s” option allows you to insert interactive debugging commands into the test, here test_wvcalib.py, to help determine why the test is failing.

Warning

Running these tests may generate files that should be ignored. Please do not add these test files to the repository. We try to include clean-up as part of the tests, but these are not always caught.

Note also that the use of pytest requires the test dependencies to be installed. It is also possible, and often preferable, to run tests within their own isolated environments using tox. This provides the capability to easily run tests against different versions of the various dependencies, including different python versions. The available tox environments are defined in the tox.ini file and can be listed by running tox -a. To run tests against the default dependencies using the default python, do:

tox -e test

To specify a python version, do something like:

tox -e py312-test

To test against, for example, the main branch for astropy on GitHub, you can do:

cd $PYPEIT_DIR
tox -e py312-test-astropydev

Similar dev dependencies are configured for numpy, ginga, and linetools, as well.

Unit tests included in the main PypeIt repo should not require large data files. Some files are kept in the repo for this purpose (see the pypeit/data/tests directory), but they should be minimized to keep the size of the repository manageable (these test files are not included in the package distribution). In general, unit tests that require input data files should instead be added to the PypeIt Development Suite.

Workflow

A typical PypeIt development workflow is as follows:

  • Create a new branch stemming from the develop branch (Hotfixes should instead branch from release); see Persistent and development branches.

  • Develop and debug the feature

  • Run the unit tests, fix any failures, add new tests that test your new feature(s), and/or modify the tests to accommodate your new feature.

  • Run the Development Suite and fix any failures.

    Warning

    The PypeIt Development Suite is extensive and takes significant computing resources and time. The PypeIt development team consistently executes these tests using cloud computing. We recommend you ensure that your PypeIt branch successfully runs on either a specific instrument of interest or shane_kast_blue first, and then someone on the PypeIt development team can execute the tests in the cloud. From the top-level directory of the PypeIt Development Suite, you can run all tests for shane_kast_blue as follows, from the PypeIt-development-suite directory:

    ./pypeit_test all -i shane_kast_blue

  • Edit the relevant development log (e.g., doc/release/1.14.1dev.rst) to include your key developments (see Logging changes) and update the documentation. You can compile the docs using the update_docs script in the PypeIt directory (see below), which is just a simple convenience script for executing make clean ; make html in the doc directory.

    ./update_docs

    Any warnings in the sphinx build of the docs must be fixed (i.e., “warnings” should be considered the same as “errors” in this context). If you’re having difficulty getting the right sphinx/rst incantation, ping the documentation channel in the PypeIt Developers Slack. Also note that, even if no warnings are issued, it’s useful to check that the documentation formats as you expect. After building the docs, you can open the doc/_build/html/index.html file to view and navigate through the documentation in its entirety. Finally note that building the docs requires access to the RAW_DATA directory in the PypeIt Development Suite; the data are used to build some of the automatically generated content for the documentation.

  • Make sure all your edits are committed and pushed to your fork:

    git add -u
git commit -m 'final prep for PR'
git push

  • Submit a Pull Request (PR) from your fork to the main repository. Unless otherwise requested, all PRs should be submitted to the develop branch.

Note

The addition of new commits causes setuptools_scm to automatically increment the version based on the last tag that was pushed. This will be of the form {next_version}.dev{distance}+{scm letter}{revision hash}. See the setuptools_scm documentation for more details.

Pull Request Acceptance Requirements

Once you’ve submitted a pull request, two developers will review your PR and provide comments on the code. The minimum requirements for acceptance of a PR are as follows:

  • If your PR introduces a new instrument (see New Spectrograph) that PypeIt is to support for the long term, this instrument must be added to the PypeIt Development Suite. That means raw data should be added to the Google Drive and relevant tests should be added to the PypeIt-development-suite/pypeit_test script (via a PR to the PypeIt Development Suite repo) such that the new instrument is included in the list of instruments tested by the testing script (pypeit_test).

  • The CI tests run by GitHub (see the Checks tab of the PR) on the remote repository must pass.

  • You (or someone running the tests on your behalf) must post a successful report resulting from your execution of the PypeIt Development Suite, which should look something like this:

    ../_images/tests_success.png

    Example posting of successful tests.

    For Hotfixes, these tests can be circumvented at the discretion of the maintainers in the cases where the hotfix is obviously correct.

  • All new methods and classes must be at least minimally documented. “Minimally documented” means that each method has a docstring that gives at least:

    1. a one sentence description of the purpose of the method,

    2. a complete list of the required and optional arguments and their meaning,

    3. a description of the returned objects, if there are any.

    Documentation is expected to adhere to Sphinx syntax; i.e., the docstrings should be reStructuredText. We accept both Google-format docstrings and Numpy-format docstrings (preferred).

  • The docstrings for any changes to existing methods that were altered must have been modified so that they are up-to-date and accurate.

  • The documentation must be successfully recompiled, either using the update_docs scripts or but running make clean ; make html in the doc/ directory.

  • Spurious commented code used for debugging or testing is fine, but please let us know if you want it to be kept by adding a relevant comment, something like # TODO: Keep this around for now, at the beginning of the commented block. Otherwise, we’re likely to remove the commented code when we come across it.

  • “Unsupported code,” that is code that is experimental and still work in progress, should be minimized as much as is reasonable. The relevant code block should be clearly marked as experimental or WIP, and it should not be executed by the main PypeIt executable, run_pypeit.

  • At least two reviewers must accept the code.

Tagging Protocol

The core development team will regularly tag “release” versions of the repository. Tagging a release version of the code is triggered anytime the development branch of the code or a hotfix is merged into the release branch. Only a maintainer can tag the code.* The tagging process is as follows:

  • At biweekly PypeIt telecons or over the PypeIt developers Slack, the core development team will decide to merge the develop branch into release.

  • A branch is created off of develop (typically called staged) and then a PR is issued to merge staged into release. This release...staged PR must meet the same Pull Request Acceptance Requirements when merging new branches into develop. Code review is expected to be limited (because all code changes will have been reviewed before pulling into develop), but the result of the dev-suite tests must be shown and approved. The reason for creating the new branch, instead of a direct release...develop PR, is to allow for the following updates to staged before merging (develop is a protected branch and cannot be directly edited):

    • Fix any test failures. As necessary, an accompanying PypeIt Development Suite PR may be issued that includes test fixes required code changes. If no code changes are required, a PypeIt Development Suite PR should be issued that merges its develop branch directly into its main branch.

    • Make any final updates to the development log, and rename the log to the new tagged version (e.g., move 1.14.1dev.rst to either 1.14.1.rst or 1.15.0.rst). The doc/whatsnew.rst should also be updated to reflect the file name change.

    • Update the list of supported versions in the SECURITY.md file.

    • Update the documentation by executing cd doc ; make clean ; make html, add any updated files, and correct all errors/warnings.

  • Once the release branch and the PypeIt Development Suite main branch are updated, the dev-suite tests are re-run using these two branches. These tests must pass before tagging. Once they pass, the code is tagged as follows:

    # Create a tag of the form X.Y.Z (using 1.14.0 here as an example).
# The current autogenerated version is found in pypeit/version.py.
git checkout release
git pull
git tag 1.14.0

# Push the new tag
git push --tags

    Similarly, a matching tag is executed for the dev-suite code (these tags only exist for versions 1.15 and later).

  • The tag of the pypeit code-base (not the dev-suite) is released for pip installation.

    git checkout 1.14.0
# Make sure you have the most recent version of twine installed
pip install twine --upgrade
pip install build --upgrade
# Construct the pip distribution
python -m build --sdist --wheel .
# Test the upload
twine upload --repository pypeit-test dist/*
# Upload, this time it's for keeps
twine upload --repository pypeit dist/*

    For the uploading, you need a ~/.pypirc file that looks like this:

    [distutils]
index-servers =
    pypeit
    pypeit-test

[pypeit]
repository: https://upload.pypi.org/legacy/
username = pypeit
password = [ask for this]

[pypeit-test]
repository: https://test.pypi.org/legacy/
username = pypeit
password = [ask for this]

DOI

If we wish to generate a new DOI for the code, it is as simple as

This document was developed and mutually agreed upon by: Kyle Westfall, J. Xavier Prochaska, Joseph Hennawi.

Last Modified: 16 Apr 2025