biosimulations / biosimulations-bigg

Command-line program and scheduled GitHub action for publishing the BiGG model repository to BioSimulations

BioSimulations-BiGG

BioSimulations-BiGG provides a command-line application for publishing the BiGG model repository of flux balance models to the BioSimulations repository for simulation projects.

This command-line program is run weekly by the GitHub action in this repository.

Installation

Requirements

• Python >= 3.7
• pip

Install latest revision from GitHub

pip install git+https://github.com/biosimulations/biosimulations-bigg.git#biosimulations-bigg

API documentation

API documentation is available here.

License

This package is released under the MIT license. BiGG is licensed under the BiGG License.

Development team

This package was developed by the Karr Lab at the Icahn School of Medicine at Mount Sinai in New York and the Center for Reproducible Biomedical Modeling. BiGG was developed by the Systems Biology Research Group at the University of California, San Diego with assistance from the contributors listed here.

Contributing to BioSimulations-BiGG

We enthusiastically welcome contributions to BioSimulations-BiGG! Please see the guide to contributing and the developer's code of conduct.

Acknowledgements

This work was supported by National Institutes of Health award P41EB023912.

Questions and comments

Please contact the BioSimulations Team with any questions or comments about this package. Please contact the BiGG Team with any questions or comments about BiGG.

biosimulations-bigg's Issues

Use Gurobi

• Add optional gurobi requirement which requires biosimulators_cobra[gurobi]
• Add installation of this requirement to GitHub action
• Map Gurobi secrets to environment variables in GitHub action:

   env:
       GRB_WLSACCESSID: ${{ secrets.GRB_WLSACCESSID }}
       GRB_WLSSECRET: ${{ secrets.GRB_WLSSECRET }}
       GRB_LICENSEID: ${{ secrets.GRB_LICENSEID }}

Enable submission to BioSimulations

Remove the --dry-run option from the GitHub action.

Can be done once BioSimulations is ready.

Dependency Dashboard

This issue lists Renovate updates and detected dependencies. Read the Dependency Dashboard docs to learn more.

Open

These updates have all been created already. Click a checkbox below to force a retry/rebase of any.

• Update actions/cache action to v4
• Update actions/checkout action to v4
• Update actions/setup-python action to v5
• Update codecov/codecov-action action to v4
• Click on this checkbox to rebase all open PRs at once

Detected dependencies

github-actions

.github/workflows/ci.yml

• actions/checkout v2
• actions/setup-python v2
• actions/cache v2
• codecov/codecov-action v2
• actions/checkout v2
• actions/setup-python v2
• actions/cache v2
• actions/create-release v1

.github/workflows/publish-runs-to-biosimulations.yml

• actions/checkout v2
• actions/setup-python v2
• actions/cache v2

.github/workflows/submit-runs-to-runbiosimulations-and-publish.yml

• actions/checkout v2
• actions/setup-python v2
• actions/cache v2

.github/workflows/verify-publication-to-biosimulations.yml

• actions/checkout v2
• actions/setup-python v2
• actions/cache v2

pip_requirements

docs-src/requirements.txt

• sphinx >= 1.8

requirements.txt

• biosimulators_utils >= 0.1.152

---

• Check this box to trigger a request for Renovate to run again on this repository

Enable pyomexmeta processing of models

Can be done once sys-bio/libOmexMeta#136 is addressed.

Use Gurobi in GitHub actions

Our license permits Gurobi use, but only inside containers.

• Switch CI and import workflows to run in Docker images
• Add installation of Gurobi (pip install . --> pip install .[all])

Fix actions

Noticed by @bilalshaikh42. The actions are expecting this package to be in a different location. I think this just requires installing this package with the editable option (-e).

Change CI workflow to use Google S3 bucket rather than UConn

Reuse Escher maps with other models

Escher maps have only been created for a few models. But many of those maps can substantially be reused with other models. For example, the E. coli maps for the Orth model can substantially be used with older models. The Escher software supports such reuse, and so does BioSimulations.

One (minor) limitation is that alternative models don't make predictions for each mapped reaction. In that case, some edges in maps wouldn't be painted with flux predictions. Instead, they would be colored grey. The grey would indicate mapped reactions that are beyond the scope of the model.

• Build YAML file with maps to be re-used for each model
• Read YAML file into COMBINE archive construction

Add genome assemblies to metadata

Change intermediate data files to output relative rather than absolute paths

When running the package with the command biosimulations-bigg publish --update-simulation-runs --update-combine-archives , I get the following error suggesting a filepath is hardocded somewhere

Traceback (most recent call last):
  File "/home/bilal/env/python/biosimbigg/bin/biosimulations-bigg", line 33, in <module>
    sys.exit(load_entry_point('biosimulations-bigg', 'console_scripts', 'biosimulations-bigg')())
  File "/home/bilal/Projects/work/biosimulations-bigg/biosimulations_bigg/__main__.py", line 290, in main
    app.run()
  File "/home/bilal/env/python/biosimbigg/lib/python3.8/site-packages/cement/core/foundation.py", line 916, in run
    return_val = self.controller._dispatch()
  File "/home/bilal/env/python/biosimbigg/lib/python3.8/site-packages/cement/ext/ext_argparse.py", line 810, in _dispatch
    return func()
  File "/home/bilal/Projects/work/biosimulations-bigg/biosimulations_bigg/__main__.py", line 119, in _default
    import_models(config)
  File "/home/bilal/Projects/work/biosimulations-bigg/biosimulations_bigg/core.py", line 628, in import_models
    build_combine_archive_for_model(model_filename, project_filename, extra_contents=extra_contents)
  File "/home/bilal/Projects/work/biosimulations-bigg/biosimulations_bigg/core.py", line 403, in build_combine_archive_for_model
    shutil.copyfile(local_path, os.path.join(archive_dirname, extra_content.location))
  File "/usr/lib/python3.8/shutil.py", line 264, in copyfile
    with open(src, 'rb') as fsrc, open(dst, 'wb') as fdst:
FileNotFoundError: [Errno 2] No such file or directory: '/home/jonrkarr/Documents/biosimulations-bigg/biosimulations_bigg/./source/thumbnails/PMC3032673/PMC3032673/1752-0509-5-8-2.jpg'