README.md

CI toolkit

This Continuous Integration toolkit provides tools to build and publish Conda packages. It is also possible to run fast tests in order to debug code.

Requirements

Packages

• conda
• make

Files

This CI toolkit is designed to provide full development chain for a conda package. Thus, some files and folders are required in the package's root directory:

• <package_name>/ folder which contains package source code
• tests/ folder which contains test source code
• recipe/ folder with:
  • meta.yaml: recipe file
  • conda_build_config.yaml: variants file for conda-build process
  • conda_build_env.yaml: environment file for conda-build processes
  • conda_channels.txt: file with channels needed to install the current package (one channel per line)

Requirements can be provided by a docker container by running the following commands (at package root folder):

docker run -it --rm -v $PWD:$PWD -w $PWD continuumio/miniconda3 bash
conda update --all -y
conda install -y make
cd ci

Conda workflow

Build

The building stage of conda package can be performed by:

make conda-build [variants=<variants>]

Equivalent to conda build --build-only. Only run the build, without any post processing or testing. For tests, please see section about Test stage.

If variants option is set according to --variants conda-build option format, then this stage is performed all combinations of variants, otherwise combinations are deducted from recipe/conda_build_config.yaml file.

Also, recipe/conda_build_config.yaml file can be edited to target specific variant(s).

Test

The testing stage of conda package can be performed by:

make conda-test [env=<conda_env_name>]

Equivalent to conda build --test.

If env option is set, then the conda-build --test command will run inside env conda environment. By default, env is set to <package_name>_build.

Convert

The converting stage of conda package can be performed by:

make conda-convert [env=<conda_env_name>]

Equivalent to conda convert, the conversion is performed for all plaforms (linux-64, osx-64 and win-64).

If env option is set, then the conda convert command will run inside env conda environment. By default, env is set to <package_name>_build.

Publish

The publishing stage of conda package can be performed by:

make conda-publish [env=<conda_env_name>]

Equivalent to anaconda upload.

If env option is set, then the anaconda upload command will run inside env conda environment. By default, env is set to <package_name>_build.

Credentials have to be stored in ci/.secrets file with the following syntax:

ANACONDA_USER=<username>
ANACONDA_TOKEN=<token>

Development tools

Conda workflow is heavy and long to perform. For development or debugging purposes, fast testing process is possible by:

make test [env=<conda_env_name>] args=[PATH_1, PATH_2...]

Equivalent to pytest, this stage is achieved within a conda environment. Then, PATH_1, PATH2... are paths to folders or filenames, just like in pytest command.

If env option is set then this stage is performed in <conda_env_name> (default: test) conda environment.

For environment automatic building, tests can be processed within conda environment:

make test-inconda [env=<conda_env_name>]  args=[PATH_1, PATH_2...]

Run in interactive mode

To run the code in a debug process, it can be done with the following commands at the root of the repository:

conda activate {PACKAGE}_test

Run from command-line

python -m {PACKAGE} --help

Run from Python command-line

python
from brs_libs import rpSBML

Workflows

The user will find into workflows/ folder, several workflows for different CI/CD platform. These worfklows have to be copied into the right folder. For instance, GitHub needs to find workflows into .github/workflows to trigger actions.

Authors

• Joan Hérisson

Acknowledgments

• Thomas Duigou

Licence

CI toolkit is released under the MIT licence. See the LICENCE file for details.