mibiscreen developer documentation

Development install

```shell

Create a virtual environment, e.g. with

python -m venv env

activate virtual environment

source env/bin/activate

make sure to have a recent version of pip and setuptools

python -m pip install --upgrade pip setuptools

(from the project root directory)

install mibiscreen as an editable package

python -m pip install --no-cache-dir --editable .

install development dependencies

python -m pip install --no-cache-dir --editable .[dev] ```

Afterwards check that the install directory is present in the PATH environment variable.

Running the tests

There are two ways to run tests.

The first way requires an activated virtual environment with the development tools installed:

shell pytest -v

The second is to use tox, which can be installed separately (e.g. with pip install tox), i.e. not necessarily inside the virtual environment you use for installing mibiscreen, but then builds the necessary virtual environments itself by simply running:

shell tox

Testing with tox allows for keeping the testing environment separate from your development environment. The development environment will typically accumulate (old) packages during development that interfere with testing; this problem is avoided by testing with tox.

Test coverage

In addition to just running the tests to see if they pass, they can be used for coverage statistics, i.e. to determine how much of the package's code is actually executed during tests. In an activated virtual environment with the development tools installed, inside the package directory, run:

shell coverage run

This runs tests and stores the result in a .coverage file. To see the results on the command line, run

shell coverage report

coverage can also generate output in HTML and other formats; see coverage help for more information.

Running linters locally

For linting and sorting imports we will use ruff. Running the linters requires an activated virtual environment with the development tools installed.

```shell

linter

ruff check .

linter with automatic fixing

ruff check . --fix ```

To fix readability of your code style you can use yapf.

You can enable automatic linting with ruff on commit by enabling the git hook from .githooks/pre-commit, like so:

shell git config --local core.hooksPath .githooks

Testing docs locally

To build the documentation locally, first make sure mkdocs and its dependencies are installed: shell python -m pip install .[doc]

Then you can build the documentation and serve it locally with shell mkdocs serve

This will return a URL (e.g. http://127.0.0.1:8000/mibiscreen/) where the docs site can be viewed.

Versioning

Bumping the version across all files is done with bump-my-version, e.g.

shell bump-my-version bump major # bumps from e.g. 0.3.2 to 1.0.0 bump-my-version bump minor # bumps from e.g. 0.3.2 to 0.4.0 bump-my-version bump patch # bumps from e.g. 0.3.2 to 0.3.3

Making a release

To create a release you need write permission on the repository.

This section describes how to make a release:

1. preparation
2. making a release on GitHub

(1/2) Preparation

1. Checkout the main branch locally
2. Verify that the information (especially the author list) in CITATION.cff is correct.
3. Make sure the version has been updated.
4. Run the unit tests with pytest -v
5. Make sure the docs build and look good

(2/2) GitHub

When all is well, navigate to the releases on GitHub.

1. Press draft a new release button
2. Select the "Choose a tag" drop down and write out the new version (e.g. v1.3.2)
3. Press "Generate release notes" to automatically fill the title (with the version number) and generate a description (the changelog from the merge pull requests)
4. Press the Publish release button

This will create the release on github and automatically trigger:

1. The .github/workflows/publish.yml workflow which will build the package and publish it on PyPI
2. The Zenodo-Github integration into making a snapshot of your repository and sticking a DOI on it and adding the new version to the main Zenodo entry for your software at 10.5281/zenodo.10878799