Contributing#
Welcome to fhirpack
contributor’s guide.
This document focuses on getting any potential contributor familiarized with the development processes, but other kinds of contributions are also appreciated.
If you are new to using git or have never collaborated in a project previously, please have a look at contribution-guide.org. Other resources are also listed in the excellent guide created by FreeCodeCamp[1].
Please notice, all users and contributors are expected to be open, considerate, reasonable, and respectful. When in doubt, Python Software Foundation’s Code of Conduct is a good reference in terms of behavior guidelines.
Issue Reports#
If you experience bugs or general issues with fhirpack
, please have a
look on the issue
tracker. If you
don’t see anything useful there, please feel free to fire an issue
report.
NOTE: Please don’t forget to include the closed issues in your search. Sometimes a solution was already reported, and the problem is considered
New issue reports should include information about your programming environment (e.g., operating system, Python version) and steps to reproduce the problem. Please try also to simplify the reproduction steps to a very minimal example that still illustrates the problem you are facing. By removing other factors, you help us to identify the root cause of the issue.
Documentation Improvements#
You can help improve fhirpack
docs by making them more readable and
coherent, or by adding missing information and correcting mistakes.
fhirpack
documentation uses
Sphinx as its main
documentation compiler. This means that the docs are kept in the same
repository as the project code, and that any documentation update is
done in the same way was a code contribution.
When working on documentation changes in your local machine, you can
compile them using tox
:
tox -e docs
and use Python’s built-in web server for a preview in your web browser
(http://localhost:8000
):
python3 -m http.server --directory 'docs/_build/html'
Code Contributions#
fhirpack
is build around the PACK
class which uses a custom subclass of
pandas.DataFrame
, called Frame
, as the main underlying
datastructure. Upon connecting to a server, the workflow follows the ETL
principle. In general, methods that extract FHIR resources can be found
inside the extraction
directory. These methods expect a list of
either fhirpy
resources, fhirpy
references or FHIR-ID strings as
input. Alternatively, the methods can operate on a Frame
object
according to the
mixin
pattern. In this case, no other input is expected. All extraction
methods return Frame
objects which can be used by the Transformer for
data manipulation or Loader for uploading.
You can use Jupyter, JupyterLab or VSCode’s Jupyter Plugin to use and
improve usage.py
and minimal.py
. However, keep in mind to not upload
notebook outputs as they bloat the files and are irrelevant to the
reader. To prevent that, execute:
echo -e '[filter "strip-notebook-output"]\n\tclean = jupyter nbconvert \
--ClearOutputPreprocessor.enabled=True --to=notebook --stdin --stdout --log-level=ERROR' \
>> .git/config
within the repository. That line defines a clean for Jupyter notebooks
that git can then use for all *.ipynb
.
Submit an issue#
Before you work on any non-trivial code contribution it’s best to first create a report in the issue tracker to start a discussion on the subject. This often provides additional considerations and avoids unnecessary work.
Create an environment#
Before you start coding, we recommend creating an isolated virtual
environment
to avoid any problems with your installed Python packages. This can
easily be done via either virtualenv
:
virtualenv <PATH TO VENV>
source <PATH TO VENV>/bin/activate
or Miniconda:
conda create -n fhirpack python=3.9.6 six virtualenv pytest pytest-cov
conda activate fhirpack
or Pipenv:
pipenv install fhirpack
pipenv
Clone the repository#
Create an user account on GitLab if you do not already have one.
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 GitLab.
Clone this repository to your local disk from GitLab with:
git clone https://gitlab.com/fhirpack/main.git
or from GitHub with:
git clone https://github.com/fhirpack/main.git
You should run:
pip install -U pip setuptools -e .
to be able to import the package under development in the Python REPL.
Verify you can run tests and build
fhirpack
:tox -e; tox -e build; tox -e clean
Dependencies#
This projetc relies on the followin python packages.
Implement your changes#
Create a branch to hold your changes:
git checkout -b my-feature
and start making changes. Never work on the main branch!
Start your work on this branch. Don’t forget to add docstrings to new functions, modules and classes, especially if they are part of public APIs.
Test your Improvements:
pytest -s --use-running-containers --docker-compose-no-build --pyargs fhirpack tests tox
Add yourself to the list of contributors in
AUTHORS.rst
.When you’re done editing, do:
git add <MODIFIED FILES> git commit
to record your changes in git.
NOTE: Don’t forget to add unit tests and documentation in case your contribution adds an additional feature and is not just a bugfix. Moreover, writing a descriptive commit message is highly recommended.
Please check that your changes don’t break any unit tests with:
tox
(after having installed
tox
withpip install tox
orpipx
).You can also use
tox
to run several other pre-configured tasks in the repository. Trytox -av
to see a list of the available checks.
Submit your contribution#
If everything works fine, push your local branch to GitLab with:
git push -u origin my-feature
Go to the web page of your fork and click “Create merge request” to send your changes for review.
Troubleshooting#
The following tips can be used when facing problems to build or test the package:
Make sure to fetch all the tags from the upstream repository. The command
git describe --abbrev=0 --tags
should return the version you are expecting. If you are trying to run CI scripts in a fork repository, make sure to push all the tags. You can also try to remove all the egg files or the complete egg folder, i.e.,.eggs
, as well as the*.egg-info
folders in thesrc
folder or potentially in the root of your project.Sometimes
tox
misses out when new dependencies are added, especially tosetup.cfg
anddocs/requirements.txt
. If you find any problems with missing dependencies when running a command withtox
, try to recreate thetox
environment using the-r
flag. For example, instead of:tox -e docs
Try running:
tox -r -e docs
Make sure to have a reliable
tox
installation that uses the correct Python version (3.9). When in doubt you can run:tox --version # OR which tox
If you have trouble and are seeing weird errors upon running
tox
, you can also try to create a dedicated virtual environment with atox
binary freshly installed. For example:virtualenv .venv source .venv/bin/activate .venv/bin/pip install tox .venv/bin/tox -e all
Pytest can drop you in an interactive session in the case an error occurs. In order to do that you need to pass a
--pdb
option (for example by runningtox -- -k <NAME OF THE FALLING TEST> --pdb
). You can also setup breakpoints manually instead of using the--pdb
option.
Maintainer tasks#
Releases#
If you are part of the group of maintainers and have correct user
permissions on PyPI, the following steps can be
used to release a new version for fhirpack
:
Make sure all unit tests are successful.
Tag the current commit on the main branch with a release tag, e.g.,
v1.2.3
.Push the new tag to the upstream repository, e.g.,
git push upstream v1.2.3
Clean up the
dist
andbuild
folders withtox -e clean
(orrm -rf dist build
) to avoid confusion with old builds and Sphinx docs.Run
tox -e build
and check that the files indist
have the correct version (no.dirty
or git hash) according to the git tag. Also check the sizes of the distributions, if they are too big (e.g., > 500KB), unwanted clutter may have been accidentally included.Run
tox -e publish -- --repository pypi
and check that everything was uploaded to PyPI correctly.