rpTools

rpTools are dedicated to work around rpSBML data structure. Tools are the following:

• rpCompletion: README.md
• rpFBA: README.md
• rpThermo: README.md
• rpExtractSink: README.md
• rpLibs: README.md
• rpScore: README.md
• rpRank: README.md
• rpViz: README.md
• rpReport: README.md

Install

[sudo] conda install -c conda-forge rptools

Run

Please see tool documentation.

Tests

Test can be run with the following commands:

Natively

cd tests
pytest -v

CI/CD

For further tests and development tools, a CI toolkit is provided in ci folder (see ci/README.md).

For developers

Development installation

After a git clone:

cd <repository>
conda env create -f environment.yaml -n <dev_env>
conda develop -n <dev_env> .

Warning: if you do not specify an environment name with -n <dev_env>, then 'rptools-dev' will be used.

Test your installation with:

conda activate <dev_env>
python -m rptools
python -m rptools.rpcompletion -h

To uninstall:

conda deactivate
conda env remove -n <dev_env>

Development installation (alternative using the ci toolkit)

After a git clone:

git clone https://github.com/breakthewall/cicd-toolkit.git
cd cicd-toolkit
make test
cd ..
conda develop -n rptools_test .

This will create a rptools_test environnement that can be activated to further develop / debug rptools.

conda activate rptools_test
python -m rptools
python -m rptools.rpcompletion -h

Authors

• Melchior du Lac
• Joan Hérisson
• Thomas Duigou

Licence

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