Testing Recipes Locally

Queue times on Azure DevOps may sometimes make it more convenient and faster to work on complex packages locally. There are several ways to do so, each with their own caveats.

Using bioconda-utils

Whether on a CI node or locally, Bioconda packages are built and tested using bioconda-utils. You can install bioconda-utils locally by creating a new conda environment:

# You can use "conda create" here instead, if you don't have mamba installed
mamba create -n bioconda -c conda-forge -c bioconda bioconda-utils

conda activate bioconda

# optional linting
bioconda-utils lint --git-range master

# build and test
bioconda-utils build --docker --mulled-test --git-range master

The above commands do the following:

  • Creates a new environment with bioconda-utils.

  • Activates the new environment. You can later just start at conda activate bioconda

  • Run bioconda-utils in the new environment:

    • The lint command will run the lint checks on your recipes

    • The build command will run the build pipeline

Note

  • You can select recipes to lint/build using --git-range master, which which will select those recipes that have been changed between your master and your branch. Or you can specify recipes directly using --packages mypackage1 mypackage2.

  • The --docker flag instructs bioconda-utils to execute the build within a docker container. On MacOS, this will do a Linux build in addition to the local MacOS build.

  • The --mulled-test flag instructs bioconda-utils to repeat the recipes test in a clean, freshly created docker container to ensure that the package does not depend on anything that happens to be included in the build container.

  • Make sure you have bioconda and conda-forge channels explicitly added to your environment or your .condarc. It is not sufficient to have those channels specified in .mambarc.

If you do not have access to Docker, you can still run the basic test by omitting the --docker and --mulled-test options.

Using the “Debug” Method

Todo

  • Explain how to use conda debug for difficult recipes.

  • Explain how to create patch series.