Contributing#
This document describes how to contribute to the development of this software.
Contribution Workflow#
Create an Issue#
Before starting please search for and review the existing issues (both
open and closed) and pull requests to see if anyone has reported the
bug or requested the feature already or work is in progress. If nothing exists then you should create a new
issue using one of the templates provided.
Cloning the repository#
If you wish to make changes yourself you will have to fork the repository to your own account and then clone that if you are not a member of AFM-SPM Organisation. If you are a member then you can clone the repository and make contributions directly.
# Member of AFM-SPM Organisation
git clone git@github.com:AFM-SPM/TopoStats.git
# Non-member of AFM-SPM cloning fork
git clone git@github.com:<YOUR_GITHUB_USERNAME>/TopoStats.git
Install Additional Dependencies#
If you are going to contribute you should install the additional dependencies for undertaking such work. There are three
groups of additional dependencies, dev, docs and tests and you should install all three using pip as shown below.
cd TopoStats
pip install ".[dev,docs,tests]"
Creating a branch#
Typically you will now create a branch to
work on the issue you wish to address. It is not compulsory but we try to use a consistent nomenclature for branches
that shows who has worked on the branch, the issue it pertains to and a short description of the work. To which end you
will see branches with the form <GITHUB_USERNAME>/<GITHUB_ISSUE>-<DESCRIPTION>. Some examples are shown below…
| Branch | User | Issue | Description |
|---|---|---|---|
ns-rse/259-contributing |
ns-rse |
259 | contributing short for the issue subject Add contributing section to documentation. |
SylviaWhittle/204-nanometre-scaling |
SylviaWhittle |
204 | nanometre-scaling short for the issue subject Colour scale in nanometers not pixels. |
How you create a branch depends on how you use Git, some use the integration provided by their IDE, others dedicated clients such as GitKraken and some may use the command line interface. These instructions use the later but you are of course free to use your chosen method of managing Git and GitHub.
In this example we branch from dev and create a new branch called ns-rse/000-fix-an-issue.
# Ensure you are up-to-date on the main branch
git checkout main
git pull
# Create and checkout a branch in one step
git checkout -b ns-rse/000-fix-an-issue
# Create and checkout a branch in two steps
git branch dev ns-rse/000-fix-an-issue
git checkout ns-rse/000-fix-an-issue
You can now start working on your issue and making regular commits, but please bear in mind the following section on Coding Standards.
Coding Standards#
To make the codebase easier to maintain we ask that you follow the guidelines below on coding style, linting, typing, documentation and testing.
Coding Style/Linting#
Using a consistent coding style has many benefits (see Linting : What is all the fluff about?). For this project we aim to adhere to PEP8 - the style Guide for Python Code and do so using the formatting linters black and ruff. Ruff implements the checks made by Flake8, isort and pydocstyle and has some overlap with both Black and Pylint.
We also like to ensure the code passes pylint which helps identify code duplication
and reduces some of the code smells that we are all prone to
making. A .pylintrc is included in the repository. Currently this isn’t strictly applied but it is planned for part of
the CI/CD pipeline and so we would be grateful if you could lint your code before making Pull Requests.
Many popular IDEs such as VSCode, PyCharm, Spyder and Emacs all have support for integrating these linters into your workflow such that when you save a file the linting/formatting is automatically applied.
Pre-commit#
pre-commit is a powerful and useful tool that runs hooks on your code prior to making commits. For a more detailed exposition see pre-commit : Protecting your future self.
The repository includes pre-commit as a development dependency as well as a .pre-commit-config.yaml. To use these
locally install pre-commit in your virtual environment and then install the configuration and all the configured hooks
(NB this will download specific virtual environments that pre-commit uses when running hooks so the first time
this is run may take a little while).
pip install ".[dev]"
pre-commit install --install-hooks
Currently there are hooks to remove trailing whitespace, check YAML configuration files and a few other common checks as
well as hooks for black and ruff. If these fail then you will not be able to make a commit until they are
fixed. The black hook will automatically format failed files so you can simply git add those and try committing
straight away. flake8 does not correct files automatically so the errors will need manually correcting.
If you do not enable and resolve issues reported by pre-commit locally before making a pull request you will find the
pre-commit.ci GitHub Action will fail, preventing your Pull Request from being merged. You
can shorten the feedback loop and speed up the resolution of errors by enabling pre-commit locally and resolving
issues before making your commits.
Typing#
Whilst Python is a dynamically typed language (that is the type of an object is determined dynamically) the use of Type Hints is strongly encouraged as it makes reading and understanding the code considerably easier for contributors. For more on Type Hints see PEP483 and PEP484
Documentation#
All classes, methods and functions should have Numpy Docstrings
defining their functionality, parameters and return values and pylint will note and report the absence of docstrings
by way of the missing-function-docstring condition.
Further, when new methods are incorporated into the package that introduce changes to the configuration they should be documented under Parameter Configuration. pre-commit has the markdownlint-cli2 hook enabled to lint all Markdown files and will where possible automatically fix things, but some issues need resolving manually.
Testing#
New features should have unit-tests written and included under the tests/ directory to ensure the functions work as
expected. The pytest framework is used for running tests along with a number of
plugins (pytest-regtest for regression testing;
pytest-mpl for testing generated Matplotlib images).
Configuration#
As described in Parameter Configuration options are primarily passed to TopoStats via a
YAML configuration file. When introducing new features that require configuration options you will
have to ensure that the default configuration file (topostats/default.yaml) is updated to include your options.
Further the topostats.validation.validate.config() function, which checks a valid configuration file with all necessary
fields has been passed when invoking run_topostats, will also need updating to include new options in the Schema against
which validation of configuration files is made.
IDE Configuration#
Linters such as black, flake8 and pylint can be configured to work with your IDE so that say Black and/or
formatting is applied on saving a file or the code is analysed with pylint on saving and errors reported. Setting up
and configuring IDEs to work in this manner is beyond the scope of this document but some links to articles on how to do
so are provided.