https://github.com/brsynth/rptools
Suite of tools that work on rpSBML format
Science Score: 36.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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✓Committers with academic emails
1 of 8 committers (12.5%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (10.1%) to scientific vocabulary
Keywords
Repository
Suite of tools that work on rpSBML format
Basic Info
- Host: GitHub
- Owner: brsynth
- License: mit
- Language: HTML
- Default Branch: master
- Size: 23 MB
Statistics
- Stars: 7
- Watchers: 2
- Forks: 2
- Open Issues: 5
- Releases: 27
Topics
Metadata Files
README.md
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
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).
For developers
Development installation
After a git clone:
sh
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:
sh
conda activate <dev_env>
python -m rptools
python -m rptools.rpcompletion -h
To uninstall:
sh
conda deactivate
conda env remove -n <dev_env>
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 for details.
Owner
- Name: BioRetroSynth
- Login: brsynth
- Kind: organization
- Website: http://www.jfaulon.com
- Repositories: 33
- Profile: https://github.com/brsynth
Our group is interested in synthetic biology and systems metabolic engineering in whole-cell and cell-free systems.
GitHub Events
Total
- Push event: 7
- Pull request event: 2
- Create event: 1
Last Year
- Push event: 7
- Pull request event: 2
- Create event: 1
Committers
Last synced: almost 3 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| breakthewall | j****n@u****r | 576 |
| Guillaume Gricourt | g****i@g****m | 25 |
| oTelle | o****e@g****m | 24 |
| Thomas Duigou | t****u@i****r | 14 |
| niraito | 7****o@u****m | 2 |
| kbazi-kabbaj | k****k@l****r | 2 |
| otelle | o****e@i****r | 2 |
| Guillaume Gricourt | g****t@i****r | 1 |
Committer Domains (Top 20 + Academic)
Packages
- Total packages: 1
- Total downloads: unknown
- Total dependent packages: 2
- Total dependent repositories: 4
- Total versions: 13
conda-forge.org: rptools
- Homepage: https://github.com/brsynth/rptools
- License: MIT
-
Latest release: 6.0.1
published over 3 years ago
Rankings
Dependencies
- actions/checkout v2 composite
- docker://continuumio/miniconda3 * composite
- actions/checkout v3 composite
- actions/create-release v1 composite
- actions/download-artifact v3 composite
- actions/upload-artifact v3 composite
- ad-m/github-push-action master composite
- conda-incubator/setup-miniconda v2 composite
- mathieudutour/github-tag-action v5.6 composite
- ruby/setup-ruby v1 composite
- actions/checkout v3 composite
- conda-incubator/setup-miniconda v2 composite