Contributing to NumCodecs¶
NumCodecs is a community maintained project. We welcome contributions in the form of bug reports, bug fixes, documentation, enhancement proposals and more. This page provides information on how best to contribute.
Asking for help¶
If you have a question about how to use NumCodecs, please post your question on StackOverflow using the “numcodecs” tag. If you don’t get a response within a day or two, feel free to raise a GitHub issue including a link to your StackOverflow question. We will try to respond to questions as quickly as possible, but please bear in mind that there may be periods where we have limited time to answer questions due to other commitments.
If you find a bug, please raise a GitHub issue. Please include the following items in a bug report:
A minimal, self-contained snippet of Python code reproducing the problem. You can format the code nicely using markdown, e.g.:
```python >>> import numcodecs >>> codec = numcodecs.Zlib(1) ... ```
Information about the version of NumCodecs, along with versions of dependencies and the Python interpreter, and installation information. The version of NumCodecs can be obtained from the
numcodecs.__version__property. Please also state how NumCodecs was installed, e.g., “installed via pip into a virtual environment”, or “installed using conda”. Information about other packages installed can be obtained by executing
pip list(if using pip to install packages) or
conda list(if using conda to install packages) from the operating system command prompt. The version of the Python interpreter can be obtained by running a Python interactive session, e.g.:
$ python Python 3.6.1 (default, Mar 22 2017, 06:17:05) [GCC 6.3.0 20170321] on linux
An explanation of why the current behaviour is wrong/not desired, and what you expect instead.
If you have an idea about a new feature or some other improvement to NumCodecs, please raise a GitHub issue first to discuss.
We very much welcome ideas and suggestions for how to improve NumCodecs, but please bear in mind that we are likely to be conservative in accepting proposals for new features. The reasons for this are that we would like to keep the NumCodecs code base lean and focused on a core set of functionalities, and available time for development, review and maintenance of new features is limited. But if you have a great idea, please don’t let that stop you posting it on GitHub, just please don’t be offended if we respond cautiously.
Contributing code and/or documentation¶
Forking the repository¶
The NumCodecs source code is hosted on GitHub at the following location:
You will need your own fork to work on the code. Go to the link above and hit the “Fork” button. Then clone your fork to your local machine:
$ git clone firstname.lastname@example.org:your-user-name/numcodecs.git $ cd numcodecs $ git remote add upstream email@example.com:zarr-developers/numcodecs.git
Creating a development environment¶
To work with the NumCodecs source code, it is recommended to set up a Python virtual environment and install all NumCodecs dependencies using the same versions as are used by the core developers and continuous integration services. Assuming you have a Python 3 interpreter already installed, and have also installed the virtualenv package, and you have cloned the NumCodecs source code and your current working directory is the root of the repository, you can do something like the following:
$ mkdir -p ~/pyenv/numcodecs-dev $ virtualenv --no-site-packages --python=/usr/bin/python3.9 ~/pyenv/numcodecs-dev $ source ~/pyenv/numcodecs-dev/bin/activate $ pip install -r requirements_dev.txt $ python setup.py build_ext --inplace
To verify that your development environment is working, you can run the unit tests:
$ pytest -v numcodecs
Creating a branch¶
Before you do any new work or submit a pull request, please open an issue on GitHub to report the bug or propose the feature you’d like to add.
It’s best to create a new, separate branch for each piece of work you want to do. E.g.:
git fetch upstream git checkout -b shiny-new-feature upsteam/master
This changes your working directory to the ‘shiny-new-feature’ branch. Keep any changes in this branch specific to one bug or feature so it is clear what the branch brings to NumCodecs.
To update this branch with latest code from NumCodecs, you can retrieve the changes from the master branch and perform a rebase:
git fetch upstream git rebase upstream/master
This will replay your commits on top of the latest NumCodecs git master. If this leads to merge conflicts, these need to be resolved before submitting a pull request. Alternatively, you can merge the changes in from upstream/master instead of rebasing, which can be simpler:
git fetch upstream git merge upstream/master
Again, any conflicts need to be resolved before submitting a pull request.
Running the test suite¶
NumCodecs includes a suite of unit tests, as well as doctests included in function and class docstrings. The simplest way to run the unit tests is to invoke:
$ pytest -v numcodecs
To also run the doctests within docstrings, run:
$ pytest -v --doctest-modules numcodecs
Tests can be run under different Python versions using tox. E.g. (assuming you have the corresponding Python interpreters installed on your system):
$ tox -e py36,py37,py38,py39
NumCodecs currently supports Python 6-3.9, so the above command must succeed before code can be accepted into the main code base. Note that only the py39 tox environment runs the doctests, i.e., doctests only need to succeed under Python 3.9.
All tests are automatically run via Travis (Linux) and AppVeyor (Windows) continuous integration services for every pull request. Tests must pass under both services before code can be accepted.
All code must conform to the PEP8 standard. Regarding line length, lines up to 100 characters are allowed, although please try to keep under 90 wherever possible. Conformance can be checked by running:
$ flake8 --max-line-length=100 numcodecs
This is automatically run when invoking
tox -e py39.
NumCodecs maintains 100% test coverage under the latest Python stable release (currently
Python 3.9). Both unit tests and docstring doctests are included when computing
tox -e py39 will automatically run the test suite with coverage
and produce a coverage report. This should be 100% before code can be accepted into the
main code base.
When submitting a pull request, coverage will also be collected across all supported Python versions via the Coveralls service, and will be reported back within the pull request. Coveralls coverage must also be 100% before code can be accepted.
Docstrings for user-facing classes and functions should follow the numpydoc standard, including sections for Parameters and Examples. All examples will be run as doctests under Python 3.9.
NumCodecs uses Sphinx for documentation, hosted on readthedocs.org. Documentation is
written in the RestructuredText markup language (.rst files) in the
The documentation consists both of prose and API documentation. All user-facing classes
and functions should be included in the API documentation. Any changes should also be
included in the release notes (
The documentation can be built by running:
$ tox -e docs
The resulting built documentation will be available in the
Development best practices, policies and procedures¶
The following information is mainly for core developers, but may also be of interest to contributors.
Merging pull requests¶
Pull requests submitted by an external contributor should be reviewed and approved by at least one core developers before being merged. Ideally, pull requests submitted by a core developer should be reviewed and approved by at least one other core developers before being merged.
Pull requests should not be merged until all CI checks have passed (Travis, AppVeyor, Coveralls) against code that has had the latest master merged in.
Compatibility and versioning policies¶
Because NumCodecs is a data encoding/decoding library, there are two types of compatibility to consider: API compatibility and data format compatibility.
All functions, classes and methods that are included in the API
documentation (files under
docs/api/*.rst) are considered as part of the NumCodecs
public API, except if they have been documented as an experimental feature, in which case they
are part of the experimental API.
Any change to the public API that does not break existing third party code importing NumCodecs, or cause third party code to behave in a different way, is a backwards-compatible API change. For example, adding a new function, class or method is usually a backwards-compatible change. However, removing a function, class or method; removing an argument to a function or method; adding a required argument to a function or method; or changing the behaviour of a function or method, are examples of backwards-incompatible API changes.
If a release contains no changes to the public API (e.g., contains only bug fixes or other maintenance work), then the micro version number should be incremented (e.g., 2.2.0 -> 2.2.1). If a release contains public API changes, but all changes are backwards-compatible, then the minor version number should be incremented (e.g., 2.2.1 -> 2.3.0). If a release contains any backwards-incompatible public API changes, the major version number should be incremented (e.g., 2.3.0 -> 3.0.0).
Backwards-incompatible changes to the experimental API can be included in a minor release, although this should be minimised if possible. I.e., it would be preferable to save up backwards-incompatible changes to the experimental API to be included in a major release, and to stabilise those features at the same time (i.e., move from experimental to public API), rather than frequently tinkering with the experimental API in minor releases.
Data format compatibility¶
Each codec class in NumCodecs exposes a
codec_id attribute, which is an identifier for the
format of the encoded data produced by that codec. Thus it is valid for two or more codec
classes to expose the same value for the
codec_id attribute if the format of the encoded data
is identical. The
codec_id is intended to provide a basis for achieving and managing
interoperability between versions of the NumCodecs package, as well as between NumCodecs and other
software libraries that aim to provide compatible codec implementations. Currently there is no
formal specification of the encoded data format corresponding to each
codec_id, so the codec
classes provided in the NumCodecs package should be taken as the reference implementation for a
There must be a one-to-one mapping from
codec_id values to encoded data formats, and that
mapping must not change once the first implementation of a
codec_id has been published within a
NumCodecs release. If a change is proposed to the encoded data format for a particular type of
codec, then this must be implemented in NumCodecs via a new codec class exposing a new
Note that the NumCodecs test suite includes a data fixture and tests to try and ensure that
data format compatibility is not accidentally broken. See the
test_backwards_compatibility() functions in test modules for each codec for examples.
When to make a release¶
Ideally, any bug fixes that don’t change the public API should be released as soon as possible. It is fine for a micro release to contain only a single bug fix.
When to make a minor release is at the discretion of the core developers. There are no hard-and-fast rules, e.g., it is fine to make a minor release to make a single new feature available; equally, it is fine to make a minor release that includes a number of changes.
Major releases obviously need to be given careful consideration, and should be done as infrequently as possible, as they will break existing code and/or affect data compatibility in some way.
Checkout and update the master branch:
$ git checkout master $ git pull
Verify all tests pass on all supported Python versions, and docs build:
Tag the version (where “X.X.X” stands for the version number, e.g., “2.2.0”):
$ version=X.X.X $ git tag -a v$version -m v$version $ git push --tags
This will trigger a GitHub Action which will build the source distribution as well as wheels for all major platforms.