https://github.com/brsynth/rptools
Suite of tools that work on rpSBML format
https://github.com/brsynth/rptools
metabolic-engineering synbio synthetic-biology systems-biology
Last synced: 5 months ago
JSON representation
Suite of tools that work on rpSBML format
- Host: GitHub
- URL: https://github.com/brsynth/rptools
- Owner: brsynth
- License: mit
- Created: 2020-12-15T14:47:58.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2025-10-16T11:53:01.000Z (8 months ago)
- Last Synced: 2025-10-21T20:51:40.464Z (8 months ago)
- Topics: metabolic-engineering, synbio, synthetic-biology, systems-biology
- Language: HTML
- Size: 23 MB
- Stars: 7
- Watchers: 2
- Forks: 2
- Open Issues: 6
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
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README
# rpTools
[](https://anaconda.org/brsynth/rptools)
[](https://anaconda.org/brsynth/rptools)
rpTools are dedicated to work around rpSBML data structure. Tools are the following:
* rpCompletion: [README.md](rptools/rpcompletion/README.md)
* rpFBA: [README.md](rptools/rpfba/README.md)
* rpThermo: [README.md](rptools/rpthermo/README.md)
* rpExtractSink: [README.md](rptools/rpextractsink/README.md)
* rpLibs: [README.md](rptools/rplibs/README.md)
* rpScore: [README.md](rptools/rpscore/README.md)
* rpRank: [README.md](rptools/rprank/README.md)
* rpViz: [README.md](rptools/rpviz/README.md)
* rpReport: [README.md](rptools/rpreport/README.md)
## Install
```sh
[sudo] conda install -c conda-forge rptools
```
## Run
Please see tool documentation.
## Tests
Test can be run with the following commands:
### Natively
```bash
cd tests
pytest -v
```
## CI/CD
For further tests and development tools, a CI toolkit is provided in `ci` folder (see [ci/README.md](./ci/README.md)).
## For developers
### Development installation
After a git clone:
```sh
cd
conda env create -f environment.yaml -n
conda develop -n .
```
Warning: if you do not specify an environment name with `-n `,
then 'rptools-dev' will be used.
Test your installation with:
```sh
conda activate
python -m rptools
python -m rptools.rpcompletion -h
```
To uninstall:
```sh
conda deactivate
conda env remove -n
```
### Development installation (alternative using the ci toolkit)
After a git clone:
```sh
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.
```sh
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](./LICENSE) for details.