Development

Development Flow

To manage new features, bug-fix and release we use Git-Flow. External contributions can be submitted through Github Pull Requests.

For maintainers: - The master branch is used for production (i.e., features ready for the public to use). - The develop branch is used to merge intermediate features during before releasing to the master branch. - All feature/$FEATURE_NAME branches are used to develop each intermediate feature (many can be used in parallel).

For other developers, it is better to use Github Pull Requests so that the submitted code can be reviewed by maintainers of the repository. The first, step is to fork the github repository (i.e., do not forget to “synchronise” your fork regularly with the main repository), then develop new features the develop branch and once completed or well advanced submit it to the main repository develop branch.

Developer Installation

The installation of the development dependencies (e.g., code formatting, linter, documentation) uses the [dev] marker. It is also important to install the pre-commit environment before starting to develop to run static code-checks (e.g., syntax and format) before each commit. In addition, before cloning the repository from Github git-lfs needs to be installed (see more on Installing Git Large File System).

Git Large File System (LFS) is used to store all files which are necessary and not quickly retrievable such as figures derived from tutorials or data for testing.

$ git clone -b develop git@github.com:deephyper/deephyper.git
$ cd deephyper/

$ # Generic installation
$ pip install -e ".[default,dev]"

$ # MacOS (arm64) installation
$ conda env create -f install/environment.dev.macOS.arm64.yml

$ pre-commit install

Warning

When installing the develop branch of DeepHyper the published documentation may be outdated. In case of trouble, do not hesitate to contact the maintainers of the repository on Slack or Github.

Note

More details about DeepHyper’s optional modules can be found in the Install DeepHyper with pip section.

Code Formatting (Black)

The code needs to be formatted with Black which should be installed through the pre-commit. For a manual usage it can be installed with pip install black. Then to check the diff you can do the following from the root of the repository:

$ black --diff --check $(git ls-files '*.py')

And to apply the formatting you can do from the same location:

$ black $(git ls-files '*.py')

Note

It is important to note that files not yet added to the git tree will not be processed by the previous commands.

Linter (Flake8)

The linter used is Flake8. The linter can be launched with:

$ flake8 deephyper/

To ignore a specific linter directive the `` # noqa: F541`` can be used.

The list of Flake8 rules can be found here.

The configuration of flake8 is located in the at `deephyper/setup.cfg under the [flake8] section.