Skip to content

README.md

Latest commit

 

History

History
102 lines (81 loc) · 4.57 KB

README.md

File metadata and controls

102 lines (81 loc) · 4.57 KB
Raw

yeastgem — Python interface to yeast-GEM

Python counterpart to the MATLAB code under ../. Builds on cobrapy and raven-toolbox — the latter hosts the generic GEM utilities (model diffing, SBO term assignment, condition / biomass / curation engines) that yeastgem configures with the yeast-specific data files under ../../data/.

See PORTING_PLAN.md for the porting history and UPSTREAM_CANDIDATES.md for the function-level upstream tracking.

Install (development)

pip install -e code/python/[dev]

The generic, organism-agnostic helpers live in raven-toolbox, which is resolved from PyPI via the raven-toolbox>=0.4.0 constraint in pyproject.toml.

Quick start

from yeastgem import read_yeast_model, commit_yeast_model

model = read_yeast_model()
print(model.optimize().objective_value)        # → ~0.088 / h on the default media

# Make some changes …
commit_yeast_model(model)                       # full release pipeline

yeastgem auto-locates the repo root via the package install path, the YEAST_GEM_PATH environment variable, or a legacy .env file — in that order. No additional setup needed for the common case.

API map

Area Module Highlights
I/O yeastgem.io read_yeast_model, commit_yeast_model (release pipeline: canonical state → SBML validity → aerobic + anaerobic growth → write .xml + ΔG CSVs → update README). write_yeast_model is a deprecated forwarding shim.
Comparison yeastgem.compare compare_models / ComparisonReport re-exported from raven_toolbox.comparison.diff_models. Use for cross-toolchain semantic-equality checks.
Conditions yeastgem.conditions apply(model, name) — minimal_Y6, anaerobic, glycine_nitrogen, nitrogen_limitation. Files under data/conditions/.
Biomass yeastgem.biomass sum_biomass, scale_biomass, rescale_pseudoreaction, set_gam, change_amino_acid_ratio. Configured from data/yeastgem/ids.yml.
Annotations yeastgem.missing_fields add_sbo_terms, load_delta_g, save_delta_g.
Model tests yeastgem.model_tests growth (Tobias 2013 chemostat R²), essential_genes (Stanford KO collection), anaerobic_flux_predictions, plot_anaerobic, find_duplicated_rxns.
Curation yeastgem.curation curate_mets_rxns_genes / ..._from_tsv — batch curation from data tables with the yeast s_/r_ id prefixes.

Layout

code/python/
  yeastgem/                # the package
    io.py                  # read_yeast_model + commit_yeast_model
    compare.py             # backwards-compat shim → raven_toolbox.comparison
    config.py              # YeastIDs loader (data/yeastgem/ids.yml)
    conditions.py          # apply(model, name)
    biomass.py             # sum_biomass / scale_biomass / set_gam / AA-ratio
    missing_fields.py      # add_sbo_terms, ΔG CSV persistence
    curation.py            # batch curation wrapper
    model_tests/           # Tier-3 benchmarks (growth, essential genes, …)
  tests/                   # pytest suite (65 tests across the package)
    reference/             # MATLAB-produced verification artefacts +
                           #   the runPhase*.m drivers
  pyproject.toml
  PORTING_PLAN.md
  UPSTREAM_CANDIDATES.md

Running the tests

cd code/python
pytest -q

Tests load the real model once per session (~2 min) and exercise every public function on it. ruff is the linter:

ruff check code/python

The CI workflow under .github/workflows/python.yml runs the same checks across Python 3.10 / 3.11 / 3.12, plus two cross-language parity gates (level-1 SBML round-trip vs the committed model, level-2 metric parity vs the committed reference values).

Where work happens

Code under yeastgem/ is only yeast-specific configuration and orchestration. Anything generic — model diff, condition application, biomass scaling, curation, annotation — lives in raven-toolbox. Functions tracked for future upstreaming are in UPSTREAM_CANDIDATES.md.