Contributing guide#

Note

If you do not already have one, you will need to open a free account on github. You might also need to create an account on our Web site for API access. Please feel free to reaching out to us at avni@globalseismology.org.

Thanks for taking the time to contribute! AVNI is an open-source project sustained mostly by volunteer effort. We welcome contributions from anyone as long as they abide by our code of conduct.

There are several ways to contribute:

Use the software, and when you find bugs, tell us about them!
Fix bugs on your own.
Tell AVNI Forum about parts of the documentation that you find confusing or unclear.
Tell AVNI Forum about things you wish AVNI could do.
Answer questions on the AVNI Forum.
Fix mistakes or add notes in our function documentation strings.
Improve existing tutorials or write new ones.
Implement new features.

In order to report bugs, request new features, or ask about confusing documentation, it’s best to open a new issue on the AVNI Forum. You will get help fastest that way, and it helps keep our GitHub issues page focused on things that we know will require changes to our software (as opposed to problems that can be fixed in the user’s code). We may ultimately ask you to open an issue on the GitHub issues page too, but starting on the forum helps us keep things organized. For fastest results, be sure to include information about your operating system and AVNI version, and (if applicable) include a reproducible code sample that is as short as possible.

If you want to fix bugs, add new features, or improve our docstrings/tutorials/website, those kinds of contributions are made through our GitHub repository. The rest of this page explains how to set up your workflow to make contributing via GitHub seamless.

Overview of the contribution process#

Warning

Reminder: all contributors are expected to follow our code of conduct.

Changes to AVNI are typically made by forking the AVNI GitHub repository, making changes to your fork (usually by cloning it to your personal computer, making the changes locally, and then pushing the local changes up to your fork on GitHub), and finally creating a pull request to incorporate your changes back into the shared “upstream” version of the codebase.

In general you’ll be working with three different copies of the AVNI codebase: the official remote copy at globalseismology/avni (usually called upstream), your remote fork of the upstream repository (similar URL, but with your username in place of globalseismology, and usually called origin), and the local copy of the codebase on your computer. The typical contribution process is to:

synchronize your local copy with upstream
make changes to your local copy
push your changes to origin (your remote fork of the upstream)
submit a pull request from your fork into upstream

The sections Basic git commands and Regular daily git usage (below) describe this process in more detail.

Setting up your local development environment#

Configuring git#

Note

GitHub desktop is a GUI alternative to command line git that some users appreciate; it is available for Windows and MacOS.

To get set up for contributing, make sure you have git installed on your local computer:

On Linux, the command sudo apt install git is usually sufficient; see the official Linux instructions for more options.
On MacOS, download the .dmg installer; Atlassian also provides more detailed instructions and alternatives such as using MacPorts or Homebrew.
On Windows, download and install git for Windows. With Git BASH it provides its own shell that includes many Linux-equivalent command line programs that are useful for development.

Windows 10 also offers the Windows subsystem for Linux that offers similar functionality to git BASH, but has not been widely tested by AVNI developers yet and may still pose problems with graphical output (e.g. building the documentation)

Once git is installed, the only absolutely necessary configuration step is identifying yourself and your contact info:

$ git config --global user.name "Your Name"
$ git config --global user.email you@yourdomain.example.com

Make sure that the same email address is associated with your GitHub account and with your local git configuration. It is possible to associate multiple emails with a GitHub account, so if you initially set them up with different emails, you can add the local email to the GitHub account.

Sooner or later, git is going to ask you what text editor you want it to use when writing commit messages, so you might as well configure that now too:

$ git config --global core.editor vim    # or vim, or nano, or subl, or...

There are many other ways to customize git’s behavior; see configuring git for more information.

Forking the AVNI repository#

Once you have git installed and configured, and before creating your local copy of the codebase, go to the AVNI GitHub page and create a fork into your GitHub user account.

This will create a copy of the AVNI codebase inside your GitHub user account (this is called “your fork”). Changes you make to AVNI will eventually get “pushed” to your fork, and will be incorporated into the official version of AVNI (often called the “upstream version”) through a “pull request”. This process will be described in detail below; a summary of how that structure is set up is given here:

Creating the virtual environment#

Note

Supported Python environments

We strongly recommend the Anaconda or Miniconda environment managers for Python. Other setups are possible but are not officially supported by the AVNI development team; see discussion here. These instructions use conda where possible; experts may replace those lines with some combination of git and pip.

These instructions will set up a Python environment that is separated from your system-level Python and any other managed Python environments on your computer. This lets you switch between different versions of Python (AVNI version 0.1.0 requires Python version 3.7 or higher) and also switch between the stable and development versions of AVNI (so you can, for example, use the same computer to analyze your data with the stable release, and also work with the latest development version to fix bugs or add new features). Even if you’ve already followed the installation instructions for the stable version of AVNI, you should now repeat that process to create a new, separate environment for AVNI development (here we’ll give it the name avni-dev):

$ curl --remote-name https://raw.githubusercontent.com/globalseismology/avni/main/environment.yml
$ conda env create --file environment.yml --name avni-dev
$ conda activate avni-dev

Now you’ll have two AVNI environments: avni (or whatever custom name you used when installing the stable version of AVNI) and avni-dev that we just created. At this point avni-dev also has the stable version of AVNI (that’s what the environment.yml file installs), but we’re about to remove the stable version from avni-dev and replace it with the development version. To do that, we’ll clone the AVNI repository from your remote fork, and also connect the local copy to the upstream version of the codebase, so you can stay up-to-date with changes from other contributors. First, edit these two variables for your situation:

$ GITHUB_USERNAME="insert_your_actual_GitHub_username_here"
$ # pick where to put your local copy of AVNI development version:
$ INSTALL_LOCATION="/opt"

Note

On Windows, add set before the variable names (set GITHUB_USERNAME=..., etc.).

Then make a local clone of your remote fork (origin):

$ cd $INSTALL_LOCATION
$ git clone https://github.com/$GITHUB_USERNAME/avni.git

Finally, set up a link between your local clone and the official repository (upstream):

$ cd AVNI
$ git remote add upstream https://github.com/globalseismology/avni.git
$ git fetch --all

Now we’ll remove the stable version of AVNI and replace it with the development version (the clone we just created with git). Make sure you’re in the correct environment first (conda activate avni-dev), and then do:

$ cd $INSTALL_LOCATION/AVNI    # make sure we're in the right folder
$ conda remove --force avni  # the --force avoids dependency checking
$ pip install -e .

The command pip install -e . installs a python module into the current environment by creating a link to the source code directory (instead of copying the code to pip’s site_packages directory, which is what normally happens). This means that any edits you make to the AVNI source code will be reflected the next time you open a Python interpreter and import avni (the -e flag of pip stands for an “editable” installation).

Finally, we’ll add a few dependencies that are not needed for running AVNI, but are needed for locally running our test suite:

$ pip install -r requirements_testing.txt

And for building our documentation:

$ pip install -r requirements_doc.txt
$ conda install graphviz

Note

On Windows, if you installed graphviz using the conda command above but still get an error like this:

WARNING: dot command 'dot' cannot be run (needed for graphviz output),
check the graphviz_dot setting

try adding the graphviz folder to path:

$ PATH=$CONDA_PREFIX\\Library\\bin\\graphviz:$PATH

To build documentation, you will also require optipng:

On Linux, use the command sudo apt install optipng.
On MacOS, optipng can be installed using Homebrew.
On Windows, unzip optipng.exe from the optipng for Windows archive into the doc/ folder. This step is optional for Windows users.

You can also choose to install some optional linters for reStructuredText:

$ conda install -c conda-forge sphinx-autobuild doc8

Basic git commands#

Learning to work with git can take a long time, because it is a complex and powerful tool for managing versions of files across multiple users, each of whom have multiple copies of the codebase. We’ve already seen in the setup commands above a few of the basic git commands useful to an AVNI developer:

git clone <URL_OF_REMOTE_REPO> (make a local copy of a repository)
git remote add <NICKNAME_OF_REMOTE> <URL_OF_REMOTE_REPO> (connect a local copy to an additional remote)
git fetch --all (get the current state of connected remote repos)

Other commands that you will undoubtedly need relate to branches. Branches represent multiple copies of the codebase within a local clone or remote repo. Branches are typically used to experiment with new features while still keeping a clean, working copy of the original codebase that you can switch back to at any time. The default branch of any repo is called main, and it is recommended that you reserve the main branch to be that clean copy of the working upstream codebase. Therefore, if you want to add a new feature, you should first synchronize your local main branch with the upstream repository, then create a new branch based off of main and check it out so that any changes you make will exist on that new branch (instead of on main):

$ git checkout main            # switch to local main branch
$ git fetch upstream             # get the current state of the remote upstream repo
$ git merge upstream/main      # synchronize local main branch with remote upstream main branch
$ git checkout -b new-feature-x  # create local branch "new-feature-x" and check it out

Note

Alternative

You can save some typing by using git pull upstream/main to replace the fetch and merge lines above.

Now that you’re on a new branch, you can fix a bug or add a new feature, add a test, update the documentation, etc. When you’re done, it’s time to organize your changes into a series of commits. Commits are like snapshots of the repository — actually, more like a description of what has to change to get from the most recent snapshot to the current snapshot.

Git knows that people often work on multiple changes in multiple files all at once, but that ultimately they should separate those changes into sets of related changes that are grouped together based on common goals (so that it’s easier for their colleagues to understand and review the changes). For example, you might want to group all the code changes together in one commit, put new unit tests in another commit, and changes to the documentation in a third commit. Git makes this possible with something called the stage (or staging area). After you’ve made some changes to the codebase, you’ll have what git calls “unstaged changes”, which will show up with the status command:

$ git status    # see what state the local copy of the codebase is in

Those unstaged changes can be added to the stage one by one, by either adding a whole file’s worth of changes, or by adding only certain lines interactively:

$ git add avni/some_file.py      # add all the changes you made to this file
$ git add avni/some_new_file.py  # add a completely new file in its entirety
$ # enter interactive staging mode, to add only portions of a file:
$ git add -p avni/viz/some_other_file.py

Once you’ve collected all the related changes together on the stage, the git status command will now refer to them as “changes staged for commit”. You can commit them to the current branch with the commit command. If you just type git commit by itself, git will open the text editor you configured it to use so that you can write a commit message — a short description of the changes you’ve grouped together in this commit. You can bypass the text editor by passing a commit message on the command line with the -m flag. For example, if your first commit adds a new feature, your commit message might be:

$ git commit -m 'ENH: adds feature X to the Epochs class'

Once you’ve made the commit, the stage is now empty, and you can repeat the cycle, adding the unit tests and documentation changes:

$ git add avni/tests/some_testing_file.py
$ git commit -m 'add test of new feature X of the Epochs class'
$ git add -p avni/some_file.py avni/viz/some_other_file.py
$ git commit -m 'DOC: update Epochs and BaseEpochs docstrings'
$ git add tutorials/new_tutorial_file.py
$ git commit -m 'DOC: adds new tutorial about feature X'

When you’re done, it’s time to run the test suite to make sure your changes haven’t broken any existing functionality, and to make sure your new test covers the lines of code you’ve added (see Building the documentation, below). Once everything looks good, it’s time to push your changes to your fork:

$ # push local changes to remote branch origin/new-feature-x
$ # (this will create the remote branch if it doesn't already exist)
$ git push origin new-feature-x

Finally, go to the AVNI GitHub page, click on the pull requests tab, click the “new pull request” button, and choose “compare across forks” to select your new branch (new-feature-x) as the “head repository”. See the GitHub help page on creating a PR from a fork for more information about opening pull requests.

If any of the tests failed before you pushed your changes, try to fix them, then add and commit the changes that fixed the tests, and push to your fork. If you’re stuck and can’t figure out how to fix the tests, go ahead and push your commits to your fork anyway and open a pull request (as described above), then in the pull request you should describe how the tests are failing and ask for advice about how to fix them.

To learn more about git, check out the GitHub help website, the GitHub skills tutorial series, and the pro git book.

Regular daily git usage#

A typical workflow on a given workda involves the following steps in sequence on your local machine:

update your copy of the repository:
```
$ git pull
```
if you get conflicts when doing so (i.e. if local changes you have made conflict with changes made by others on the same line of the same file of the source code), a powerful way of resolving them is to type this: (meld needs to be installed on your system; if it is not, you can install it with apt-get install meld or similar):
```
$ git mergetool --tool=meld
```
make some changes to any file you want using your favorite editor (in the line below we use vi as an example):
```
$ vim some_file.f90
```
commit your changes locally, adding a very short message (one line) explaining what you have changed; it is recommended to do a git pull right before that in order to make sure that your local copy is up-to-date:
```
$ git pull ; git commit -a -m "Explain your commit"
```
if you get conflicts when committing your changes (i.e. if your changes conflict with changes made by others on the same line of the same file of the source code), a powerful way of resolving them is to type this: (meld needs to be installed on your system; if it is not, you can install it with yum install meld in Linux, download MacOS version from this webpage. ):
```
$ git mergetool --tool=meld
```
(optional) if you want to check what has changed (and thus what will be committed) before typing the git commit above, you can type one or both of these two commands:
```
$ git status -s
$ git diff
```
push your changes to your GitHub fork; it is recommended to do a git pull right before that in order to make sure that your local copy is up-to-date:
```
$ git pull ; git push
```
Create a pull-request to get your changes into the main repository (this is needed only once for each change; if you are fixing an existing change after receiving an error message from our BuildBot code-consistency checking system, you need the “git push” above again but you do NOT need to create a pull request a second time); it is recommended to do a git pull right before that in order to make sure that your local copy is up-to-date:
```
$ git pull ; git pull-request
```

Note (optional): It is not strictly necessary to create a pull request for every commit you make if you do not want to, you can safely submit pull requests after making a few commits instead if you prefer. However, it also does not hurt to do so.

Connecting to GitHub with SSH (optional)#

One easy way to speed up development is to reduce the number of times you have to type your password. SSH (secure shell) allows authentication with pre-shared key pairs. The private half of your key pair is kept secret on your computer, while the public half of your key pair is added to your GitHub account; when you connect to GitHub from your computer, the local git client checks the remote (public) key against your local (private) key, and grants access your account only if the keys fit. GitHub has several help pages that guide you through the process. As of the date of writing this document,

Once you have set up GitHub to use SSH authentication, you should change the addresses of your AVNI GitHub remotes, from https:// addresses to git@ addresses, so that git knows to connect via SSH instead of HTTPS. For example:

$ git remote -v  # show existing remote addresses
$ git remote set-url origin git@github.com:$GITHUB_USERNAME/avni.git
$ git remote set-url upstream git@github.com:globalseismology/avni.git

AVNI coding conventions#

General requirements#

All new functionality must be documented#

This includes thorough docstring descriptions for all public API changes, as well as how-to examples or longer tutorials for major contributions. Docstrings for private functions may be more sparse, but should usually not be omitted.

Avoid API changes when possible#

Changes to the public API (e.g., class/function/method names and signatures) should not be made lightly, as they can break existing user scripts. Bug fixes (when something isn’t doing what it says it will do) do not require a deprecation cycle.

Note that any new API elements should be added to the main reference; classes, functions, methods, and attributes cannot be cross-referenced unless they are included in the Python API Reference (doc/python_reference.rst).

Describe your changes in the changelog#

Include in your changeset a brief description of the change in the changelog (doc/changes/latest.inc; this can be skipped for very minor changes like correcting typos in the documentation).

There are different sections of the changelog for each release, and separate subsections for bugfixes, new features, and changes to the public API. Please be sure to add your entry to the appropriate subsection.

The styling and positioning of the entry depends on whether you are a first-time contributor or have been mentioned in the changelog before.

First-time contributors#

Welcome to AVNI! We’re very happy to have you here. And to ensure you get proper credit for your work, please add a changelog entry with the following pattern at the top of the respective subsection (bugs, enhancements, etc.):

Bugs
----

- Short description of the changes (:gh:`0000` by :newcontrib:`Firstname
  Lastname`)

- ...

where 0000 must be replaced with the respective GitHub pull request (PR) number, and Firstname Lastname must be replaced with your full name.

It is usually best to wait to add a line to the changelog until your PR is finalized, to avoid merge conflicts (since the changelog is updated with almost every PR).

Lastly, make sure that your name is included in the list of authors in doc/changes/names.inc, otherwise the documentation build will fail. To add an author name, append a line with the following pattern (note how the syntax is different from that used in the changelog):

.. _Your Name: https://www.your-website.com/

Many contributors opt to link to their GitHub profile that way. Have a look at the existing entries in the file to get some inspiration.

Recurring contributors#

The changelog entry should follow the following patterns:

- Short description of the changes from one contributor (:gh:`0000` by
  `Contributor Name`_)
- Short description of the changes from several contributors (:gh:`0000` by
  `Contributor Name`_, `Second Contributor`_, and `Third Contributor`_)

where 0000 must be replaced with the respective GitHub pull request (PR) number. Mind the Oxford comma in the case of multiple contributors.

Sometimes, changes that shall appear as a single changelog entry are spread out across multiple PRs. In this case, name all relevant PRs, separated by commas:

- Short description of the changes from one contributor in multiple PRs
  (:gh:`0000`, :gh:`1111` by `Contributor Name`_)
- Short description of the changes from several contributors in multiple PRs
  (:gh:`0000`, :gh:`1111` by `Contributor Name`_, `Second Contributor`_, and
  `Third Contributor`_)

Test locally before opening pull requests (PRs)#

AVNI uses continuous integration (CI) to ensure code quality and test across multiple installation targets. However, the CIs are often slower than testing locally, especially when other contributors also have open PRs (which is basically always the case). Therefore, do not rely on the CIs to catch bugs and style errors for you; run the tests locally instead before opening a new PR and before each time you push additional changes to an already-open PR.

Code style#

Adhere to standard Python style guidelines#

All contributions to AVNI are checked against style guidelines described in PEP 8. We also check for common coding errors (such as variables that are defined but never used). We allow very few exceptions to these guidelines, and use tools such as pep8, pyflakes, and flake8 to check code style automatically.

When modifying an existing file, try to maintain consistency with its original style. If the code you add looks drastically different from the original code, it may be difficult for readers to follow. Try to avoid this. Please give space for breathing by use 4 spaces instead of tabs:

Listing 1 good#

dx = 0.5 \* fac \* (a - b)

Listing 2 bad#

dx=1/2\ *fac*\ (a-b)

Use consistent variable naming#

Classes should be named using CamelCase. Functions and instances/variables should use snake_case (n_samples rather than nsamples). Avoid single-character variable names, unless inside a comprehension or generator.

We (mostly) follow NumPy style for docstrings#

In most cases you can look at existing AVNI docstrings to figure out how yours should be formatted. If you can’t find a relevant example, consult the Numpy docstring style guidelines for examples of more complicated formatting such as embedding example code, citing references, or including rendered mathematics.

Note that we diverge from the NumPy docstring standard in a few ways:

We use a module called sphinxcontrib-bibtex to render citations. Search our source code (git grep footcite and git grep footbibliography) to see examples of how to add in-text citations and formatted references to your docstrings, examples, or tutorials. The structured bibliographic data lives in doc/references.bib; please follow the existing key scheme when adding new references (e.g., Singleauthor2019, AuthoroneAuthortwo2020, FirstauthorEtAl2021a, FirstauthorEtAl2021b).
We don’t explicitly say “optional” for optional keyword parameters (because it’s clear from the function or method signature which parameters have default values).
For parameters that may take multiple types, we use pipe characters instead of the word “or”, like this: param_name : str | None.
We don’t always include a Raises or Warns section describing errors/warnings that might occur. Whenever we do, these are only for errors that are non-obvious or have a large chance of getting raised.

Other style guidance#

Guidelines for formatting in Fortran is provided in the Fortran Guidelines page.
Use single quotes whenever possible.
Prefer generators or comprehensions over filter(), map() and other functional idioms.
Use explicit functional constructors for builtin containers to improve readability (e.g., list(), dict(), set()).
Avoid nested functions or class methods if possible — use private functions instead.
Avoid *args and **kwargs in function/method signatures.

Code organization#

Importing#

Import modules in this order, preferably alphabetized within each subsection:

Python built-in (copy, functools, os, etc.)
NumPy (numpy as np) and, in test files, pytest (pytest)
AVNI imports (e.g., from .pick import pick_types)

When importing from other parts of AVNI, use relative imports in the main codebase and absolute imports in tests, tutorials, and how-to examples. Imports for matplotlib, scipy, and optional modules (sklearn, pandas, etc.) should be nested (i.e., within a function or method, not at the top of a file). This helps reduce import time and limit hard requirements for using AVNI.

Return types#

Methods should modify inplace and return self, functions should return copies (where applicable). Docstrings should always give an informative name for the return value, even if the function or method’s return value is never stored under that name in the code.

Building the documentation#

Important

Latest documentation should generally be written in MyST format, unless the use case requires more complicated use of the reStructuredText format. Conversion between the two formats can be done using pandoc: pandoc --from=rst --to=markdown --output=README.md README.rst

Our documentation (including docstrings in code files) is in two formats that are built using Sphinx:

reStructuredText format that is built using Sphinx-Gallery
MyST format, a rich and extensible flavour of Markdown format, that is built using myst_parser

The easiest way to ensure that your contributions to the documentation are properly formatted is to follow the style guidelines on this page, imitate existing documentation examples, refer to the Sphinx and Sphinx-Gallery reference materials when unsure how to format your contributions, and build the docs locally to confirm that everything looks correct before submitting the changes in a pull request.

You can build the documentation locally using GNU Make with doc/Makefile. From within the doc directory, you can test formatting and linking by running:

$ make html_dev-noplot

This will build the documentation except it will format (but not execute) the tutorial and example files. If you have created or modified an example or tutorial, you should instead run PATTERN=<REGEX_TO_SELECT_MY_TUTORIAL> make html_dev-pattern to render all the documentation and additionally execute just your example or tutorial (so you can make sure it runs successfully and generates the output / figures you expect).

Note

If you are using a Windows command shell, to use the pattern approach, use the following two lines:

> set PATTERN=<REGEX_TO_SELECT_MY_TUTORIAL> > make html_dev-pattern

If you are on Windows but using the git BASH shell, use the same two commands but replace set with export.

After either of these commands completes, make show will open the locally-rendered documentation site in your browser. If you see many warnings that seem unrelated to your contributions, it might be that your output folder for the documentation build contains old, now irrelevant, files. Running make clean will clean those up. Additional make recipes are available; run make help from the doc directory or consult the Sphinx-Gallery documentation for additional details.

GitHub workflow#

Nearly everyone in the community of AVNI contributors and maintainers is a working scientist, engineer, or student who contributes to AVNI in their spare time. For that reason, a set of best practices have been adopted to streamline the collaboration and review process. Most of these practices are common to many open-source software projects, so learning to follow them while working on AVNI will bear fruit when you contribute to other projects down the road. Here are the guidelines:

Search the GitHub issues page (both open and closed issues) in case someone else has already started work on the same bugfix or feature. If you don’t find anything, open a new issue to discuss changes with maintainers before starting work on your proposed changes.
Implement only one new feature or bugfix per pull request (PR). Occasionally it may make sense to fix a few related bugs at once, but this makes PRs harder to review and test, so check with AVNI maintainers first before doing this. Avoid purely cosmetic changes to the code; they make PRs harder to review.
It is usually better to make PRs from branches other than your main branch, so that you can use your main branch to easily get back to a working state of the code if needed (e.g., if you’re working on multiple changes at once, or need to pull in recent changes from someone else to get your new feature to work properly).
In most cases you should make PRs into the upstream’s main branch, unless you are specifically asked by a maintainer to PR into another branch (e.g., for backports or maintenance bugfixes to the current stable version).
Don’t forget to include in your PR a brief description of the change in the changelog (doc/whats_new.rst).
Our community uses the following commit tags and conventions:
- Work-in-progress PRs should be created as draft PRs and the PR title should begin with WIP.
- When you believe a PR is ready to be reviewed and merged, convert it from a draft PR to a normal PR, change its title to begin with MRG, and add a comment to the PR asking for reviews (changing the title does not automatically notify maintainers).
- PRs that only affect documentation should additionally be labelled DOC, bugfixes should be labelled FIX, and new features should be labelled ENH (for “enhancement”). STY is used for style changes (i.e., improving docstring consistency or formatting without changing its content).
- the following commit tags are used to interact with our continuous integration (CI) providers. Use them judiciously; do not skip tests simply because they are failing:
  - [skip actions] Skip our GitHub Actions, which test installation and execution on Linux and macOS systems.
  - [ci skip] is an alias for [skip actions][skip azp][skip circle]. Notice that [skip ci] is not a valid tag.
  - [circle full] triggers a “full” documentation build, i.e., all code in tutorials and how-to examples will be executed (instead of just nicely formatted) and the resulting output and figures will be rendered as part of the tutorial/example.