equilibrator-pathway-core

Max-min driving force (MDF) and enzyme cost minimization (ECM) for fully specified pathway models, with no compound database.

This is the lower layer of equilibrator-pathway. It analyses model SBtab files that already carry everything the optimisation needs -- stoichiometry, concentration bounds, fluxes and standard Gibbs energies -- and it never predicts or looks anything up. That is what lets it install in a few megabytes of Python on top of numpy, including in the browser via Pyodide.

Units

Everything here works on plain floats in one canonical set of units -- M, kJ/mol, K, 1/s, Da -- documented in equilibrator_pathway_core.constants. Units are attached at the boundary, by equilibrator-pathway's pint adapter or by the browser client's string parser.

Staying small

Importing this package must not pull in the equilibrator database stack. That is tested directly, in a fresh interpreter, by tests/test_isolation.py, which fails if equilibrator_api, equilibrator_cache, component_contribution, sqlalchemy, pint or matplotlib appear in sys.modules. A dependency added to pyproject.toml without the code that needs it is equally unwelcome.

Status

In place:

Both equilibrator-pathway and the browser client run MDF and ECM through this package; the browser also reads models (model.load_model), edits their Configuration (configuration.py) and writes reports with it.

The SBtab modules use sbtabpy directly, and need sbtabpy 1.1.1 or later. 1.1.0 was the first release with no required dependencies (earlier ones declared pandas, pyarrow, python-libsbml and openpyxl, which its parser never imports); 1.1.1 added the dictionary rows, attribute defaults and pandas-free SBtabTable.from_rows that replaced the core's own adapter module. tests/test_isolation.py still forbids all four: nothing installs them by default now, but the test is what guarantees the core never imports them, and so stays loadable in the browser.

The extraction plan is in enzyme-cost-minimization-webapp/CORE_EXTRACTION_PLAN.txt. Correctness is held to the golden results frozen in that repository (tests/golden/), which record what equilibrator-pathway and the browser port each produced while they were still independent implementations. After the move, both consumers reproduce every one of those 482 numbers bit for bit, not merely within the checker's 1e-6 tolerance.

Where the two replaced copies disagreed, see the docstring of ecm.py for which behaviour was kept and why. In short: the port's get_volumes (the server's zeroed the last metabolite when a model had no water), and working versions of get_fluxes and is_feasible, which raised on every call in equilibrator-pathway without any test noticing.

PYTHONPATH=src pytest tests/