Contributing to OGGM
On this page
Contributing to OGGM#
All contributions, bug reports, bug fixes, documentation improvements, enhancements and ideas are welcome! OGGM is still in an early development phase, so most things are not written in stone and can probably be enhanced/corrected/ameliorated by anyone!
You can report issues or discuss OGGM on the issue tracker.
Copyright note: this page is a shorter version of the excellent pandas documentation.
Working with the code#
Before you contribute, you will need to learn how to work with GitHub and the OGGM code base.
Version control, Git, and GitHub#
Some great resources for learning Git:
the GitHub help pages.
Getting started with Git#
GitHub has instructions for installing git, setting up your SSH key, and configuring git. All these steps need to be completed before you can work seamlessly between your local repository and GitHub.
You will need your own fork to work on the code. Go to the OGGM project
page and hit the
Fork button. You will
want to clone your fork to your machine:
git clone email@example.com:your-GitHub-username/oggm.git oggm-yourname cd oggm-yourname git remote add upstream https://github.com/OGGM/oggm.git
This creates the directory oggm-yourname and connects your repository to the upstream (main project) oggm repository (with the your-GitHub-username the user name of your GitHub account).
Creating a branch#
You want your master branch to reflect only production-ready code, so create a feature branch for making your changes. For example:
git branch shiny-new-feature git checkout shiny-new-feature
The above can be simplified to:
git checkout -b shiny-new-feature
This changes your working directory to the shiny-new-feature branch. Try to keep any changes in this branch specific to one bug or feature. You can have many shiny-new-features and switch in between them using the git checkout command.
To update this branch, you need to retrieve the changes from the master branch:
git fetch upstream git rebase upstream/master
This will replay your commits on top of the latest oggm git master. If this
leads to merge conflicts, you must resolve these before submitting your pull
request. If you have uncommitted changes, you will need to
stash them prior
to updating. This will effectively store your changes and they can be reapplied
Creating a development environment#
An easy way to create an OGGM development environment is explained in Installing OGGM.
Contributing to the code base#
OGGM uses the PEP8 standard. There are several tools to ensure you abide by this standard, and some Integrated Development Environment (IDE, for example PyCharm) will warn you if you don’t follow PEP8.
Test-driven development/code writing#
OGGM is serious about testing and strongly encourages contributors to embrace test-driven development (TDD). Like many packages, OGGM uses the pytest testing system and the convenient extensions in numpy.testing.
All tests should go into the
tests subdirectory of OGGM.
This folder contains many current examples of tests, and we suggest looking to
these for inspiration.
Running the test suite#
The tests can then be run directly inside your Git clone by typing:
Running the tests will take several minutes. If everything worked fine, you should see something like:
==== test session starts ==== platform linux -- Python 3.4.3, pytest-3.0.5, py-1.4.31, pluggy-0.4.0 rootdir: plugins: collected 92 items oggm/tests/test_graphics.py .............. oggm/tests/test_models.py .........s....sssssssssssssssss oggm/tests/test_prepro.py ...s................s.s... oggm/tests/test_utils.py ...sss..ss.sssss. oggm/tests/test_workflow.py ssss ===== 57 passed, 35 skipped in 102.50 seconds ====
You can safely ignore deprecation warnings and other
Dynamic Link Library (DLL) messages as long as
the tests end with
Often it is worth running only a subset of tests first around your changes before running the entire suite. This is done using one of the following constructs:
pytest oggm/tests/[test-module].py pytest oggm/tests/[test-module].py:[TestClass] pytest oggm/tests/[test-module].py:[TestClass].[test_method]
Contributing to the documentation#
Contributing to the documentation is of huge value. Something as simple as rewriting small passages for clarity is a simple but effective way to contribute.
About the documentation#
The documentation is written in reStructuredText, which is almost like writing in plain English, and built using Sphinx. The Sphinx documentation has an excellent introduction to reST. Review the Sphinx docs to perform more complex changes to the documentation as well.
Some other important things to know about the docs:
The OGGM documentation consists of two parts: the docstrings in the code itself and the docs in this folder
The docstrings should provide a clear explanation of the usage of individual functions (currently this is not the case everywhere, unfortunately), while the
oggm/docs/folder consists of tutorial-like overviews per topic together with some other information (what’s new, installation, etc).
The docstrings follow the Numpy Docstring Standard, which is used widely in the Scientific Python community. This standard specifies the format of the different sections of the docstring. See this document for a detailed explanation, or look at some of the existing functions to extend it in a similar manner.
Some pages make use of the ipython directive sphinx extension. This directive lets you put code in the documentation which will be run during the doc build.
How to build the documentation#
There are some extra requirements to build the docs: you will need to
If you have a conda environment named
oggm_env, you can install the extra
mamba install -c conda-forge sphinx ipython numpydoc sphinx-book-theme pip install sphinx-togglebutton
If you don’t have an oggm installation yet, download (or clone) the latest version
of the oggm repository.
From the repository’s root folder, activate conda if necessary and then,
from your base environment, run
mamba env create -f docs/environment.yml
conda env create -f docs/environment.yml). To activate the environment,
conda activate oggm_docs.
Building the documentation#
So how do you build the docs? Navigate to your local
oggm/docs/ directory in the console and run:
Then you can find the HTML output in the folder
The first time you build the docs, it will take quite a while because it has to run all the code examples and build all the generated docstring pages. In subsequent evocations, sphinx will try to only build the pages that have been modified.
If you want to do a full clean build, do:
make clean make html
Open the following file in a web browser to see the full documentation you just built:
If you performed some changes in the documentation or even created new pages/sections (the
you’ll have the satisfaction of seeing your new and improved documentation!
Contributing your changes#
Committing your code#
Keep style fixes to a separate commit to make your pull request more readable.
Once you’ve made changes, you can see them by typing:
If you have created a new file, it is not being tracked by git. Add it by typing:
git add path/to/file-to-be-added.py
Doing ‘git status’ again should give something like:
# On branch shiny-new-feature # # modified: /relative/path/to/file-you-added.py #
Finally, commit your changes to your local repository with an explanatory message:
git commit -a -m 'added shiny feature'
You can make as many commits as you want before submitting your changes to OGGM, but it is a good idea to keep your commits organised.
Pushing your changes#
When you want your changes to appear publicly on your GitHub page, push your forked feature branch’s commits:
git push origin shiny-new-feature
origin is the default name given to your remote repository on GitHub.
You can see the remote repositories:
git remote -v
If you added the upstream repository as described above you will see something like:
origin firstname.lastname@example.org:yourname/oggm.git (fetch) origin email@example.com:yourname/oggm.git (push) upstream git://github.com/OGGM/oggm.git (fetch) upstream git://github.com/OGGM/oggm.git (push)
Now your code is on GitHub, but it is not yet a part of the OGGM project. For that to happen, a pull request needs to be submitted on GitHub.
Review your code#
When you’re ready to ask for a code review, file a pull request. Before you do, once again make sure that you have followed all the guidelines outlined in this document regarding code style, tests, and documentation. You should also double check your branch changes against the branch it was based on:
Navigate to your repository on GitHub –
Click on the
Comparebutton for your feature branch
comparebranches, if necessary. This will be
Finally, make the pull request#
If everything looks good, you are ready to make a pull request. A pull request is how code from a local repository becomes available to the GitHub community and can be looked at and eventually merged into the master version. This pull request and its associated changes will eventually be committed to the master branch and available in the next release. To submit a pull request:
Navigate to your repository on GitHub
Click on the
You can then click on
Files Changedto make sure everything looks okay one last time
Write a description of your changes in the
Send Pull Request.
This request then goes to the repository maintainers, and they will review the code. If you need to make more changes, you can make them in your branch, push them to GitHub, and the pull request will be automatically updated. Pushing them to GitHub again is done by:
git push -f origin shiny-new-feature
This will automatically update your pull request with the latest code.
Delete your merged branch (optional)#
Once your feature branch is accepted into upstream, you’ll probably want to get rid of the branch. First, merge upstream master into your branch so git knows it is safe to delete your branch:
git fetch upstream git checkout master git merge upstream/master
Then you can just do:
git branch -d shiny-new-feature
Make sure you use a lower-case
-d, or else git won’t warn you if your feature
branch has not actually been merged.
The branch will still exist on GitHub, so to delete it there do:
git push origin --delete shiny-new-feature