From a79bc2d4ded3466aad1252f496f5e3702884eaaa Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Sat, 17 Oct 2026 07:14:34 +0200 Subject: [PATCH] Point repository, documentation and RAVEN data links to CompMetEng --- README.md | 8 ++++---- docs/internal/raven_inventory.md | 2 +- docs/migrating_from_gecko_matlab.md | 4 ++-- docs/raven_integration.md | 2 +- docs/yaml_format.md | 2 +- pyproject.toml | 10 +++++----- src/geckopy/databases/phyl_dist.py | 2 +- tests/test_gecko_matlab_parity.py | 2 +- 8 files changed, 16 insertions(+), 16 deletions(-) diff --git a/README.md b/README.md index e6e67f4..b65b10c 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # geckopy -[![tests](https://github.com/SysBioChalmers/geckopy/actions/workflows/test.yml/badge.svg)](https://github.com/SysBioChalmers/geckopy/actions/workflows/test.yml) +[![tests](https://github.com/CompMetEng/geckopy/actions/workflows/test.yml/badge.svg)](https://github.com/CompMetEng/geckopy/actions/workflows/test.yml) Enzyme-constrained genome-scale metabolic modelling in Python. @@ -11,7 +11,7 @@ Enzyme-constrained genome-scale metabolic modelling in Python. > the place to actually learn or look things up. > **Disambiguation.** This is a new, from-scratch port of the -> [GECKO Toolbox](https://github.com/SysBioChalmers/GECKO) (MATLAB). It is unrelated to +> [GECKO Toolbox](https://github.com/CompMetEng/GECKO) (MATLAB). It is unrelated to > the earlier and separate `geckopy` Python package > ([on PyPI as release 2.0.2 and earlier](https://pypi.org/project/geckopy/2.0.2/)) > described in Carrasco Muriel, Long & Sonnenschein, *Microbiology Spectrum* @@ -26,7 +26,7 @@ each enzyme has a finite capacity (its kcat) and a finite supply (the cell's total protein budget). An *ec*Model (enzyme-constrained model) adds those limits to the network. -geckopy is a Python port of the [GECKO Toolbox](https://github.com/SysBioChalmers/GECKO) +geckopy is a Python port of the [GECKO Toolbox](https://github.com/CompMetEng/GECKO) (MATLAB). It builds on [cobrapy](https://github.com/opencobra/cobrapy) for the standard modelling layer, then layers GECKO's enzyme-constraint machinery on top: it fetches kcat values from BRENDA, predicts them with DLKcat, tunes @@ -40,7 +40,7 @@ curations, and integrates proteomics measurements. ## Install -geckopy depends on [raven-toolbox](https://github.com/SysBioChalmers/raven-toolbox) +geckopy depends on [raven-toolbox](https://github.com/CompMetEng/raven-toolbox) (the Python port of the RAVEN Toolbox). Both are currently pre-releases on PyPI, so a plain `pip install geckopy` will install the wrong version — `--pre` is required: diff --git a/docs/internal/raven_inventory.md b/docs/internal/raven_inventory.md index 133cb83..332df16 100644 --- a/docs/internal/raven_inventory.md +++ b/docs/internal/raven_inventory.md @@ -1,7 +1,7 @@ # RAVEN function inventory GECKO MATLAB is built on top of -[RAVEN](https://github.com/SysBioChalmers/RAVEN), a MATLAB toolkit +[RAVEN](https://github.com/CompMetEng/RAVEN), a MATLAB toolkit for genome-scale metabolic modelling. RAVEN handles all the low-level work: parsing SBML files, editing reactions and metabolites, solving FBAs, manipulating gene-protein-reaction diff --git a/docs/migrating_from_gecko_matlab.md b/docs/migrating_from_gecko_matlab.md index 28fbaca..6074819 100644 --- a/docs/migrating_from_gecko_matlab.md +++ b/docs/migrating_from_gecko_matlab.md @@ -14,7 +14,7 @@ them require you to change your model files. > (forward-direction protein reactions, several bug fixes, a reformatted > BRENDA snapshot, the REST-based OpenKineticsPredictor flow) that > geckopy also follows — see -> [GECKO3_to_GECKO4.md](https://github.com/SysBioChalmers/GECKO/blob/main/GECKO3_to_GECKO4.md) +> [GECKO 3 to GECKO 4](https://gecko-docs.readthedocs.io/en/latest/gecko3-to-gecko4.html) > for the full list. Throughout this guide, individual functions that > are affected by those 3→4 changes carry a **`[3→4]`** marker; that > marker is geckopy's signal that the function's behaviour or schema @@ -475,7 +475,7 @@ for the MATLAB-side items the port surfaced. - MATLAB-side bugs and rough edges the port found are tracked in [future_improvements.md](future_improvements.md). - For the GECKO 3→4 changes as they apply on the MATLAB side, see - [GECKO3_to_GECKO4.md](https://github.com/SysBioChalmers/GECKO/blob/main/GECKO3_to_GECKO4.md) + [GECKO 3 to GECKO 4](https://gecko-docs.readthedocs.io/en/latest/gecko3-to-gecko4.html) in the GECKO repository. - For the YAML schema (shared with MATLAB GECKO 4 / RAVEN), see [yaml_format.md](yaml_format.md). diff --git a/docs/raven_integration.md b/docs/raven_integration.md index c278b13..970ad8f 100644 --- a/docs/raven_integration.md +++ b/docs/raven_integration.md @@ -1,6 +1,6 @@ # raven-toolbox integration -geckopy depends on [raven-toolbox](https://github.com/SysBioChalmers/raven-toolbox), +geckopy depends on [raven-toolbox](https://github.com/CompMetEng/raven-toolbox), the Python port of the RAVEN Toolbox. raven-toolbox owns the generic model-manipulation primitives and the YAML I/O (including the GECKO ec-model substructure); geckopy keeps the enzyme-constraint *algorithms* diff --git a/docs/yaml_format.md b/docs/yaml_format.md index 9fe8c86..283c58a 100644 --- a/docs/yaml_format.md +++ b/docs/yaml_format.md @@ -12,7 +12,7 @@ cobra doesn't model: kcat values, the enzyme list (MW, sequence, concentration), and the reaction-enzyme coupling matrix. geckopy delegates the I/O to -[raven-toolbox](https://github.com/SysBioChalmers/raven-toolbox), which +[raven-toolbox](https://github.com/CompMetEng/raven-toolbox), which calls cobrapy for the cobra-shaped portion and parses the GECKO `ec-rxns` / `ec-enzymes` / `gecko_light` sections into a typed `EcData` substructure attached as `model.ec`. That means: diff --git a/pyproject.toml b/pyproject.toml index 13b7526..e4e65eb 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -68,11 +68,11 @@ evotune = [ ] [project.urls] -Homepage = "https://github.com/SysBioChalmers/geckopy" -Source = "https://github.com/SysBioChalmers/geckopy" -Issues = "https://github.com/SysBioChalmers/geckopy/issues" -"GECKO MATLAB" = "https://github.com/SysBioChalmers/GECKO" -"raven-toolbox" = "https://github.com/SysBioChalmers/raven-toolbox" +Homepage = "https://github.com/CompMetEng/geckopy" +Source = "https://github.com/CompMetEng/geckopy" +Issues = "https://github.com/CompMetEng/geckopy/issues" +"GECKO MATLAB" = "https://github.com/CompMetEng/GECKO" +"raven-toolbox" = "https://github.com/CompMetEng/raven-toolbox" [project.scripts] geckopy = "geckopy.cli:main" diff --git a/src/geckopy/databases/phyl_dist.py b/src/geckopy/databases/phyl_dist.py index 36991a0..126ec0b 100644 --- a/src/geckopy/databases/phyl_dist.py +++ b/src/geckopy/databases/phyl_dist.py @@ -20,7 +20,7 @@ # keggPhylDist.mat as distributed with RAVEN, pinned to a release tag so # the download is reproducible. KEGG_PHYL_DIST_URL = ( - "https://raw.githubusercontent.com/SysBioChalmers/RAVEN/3.0.0b1/" + "https://raw.githubusercontent.com/CompMetEng/RAVEN/3.0.0b1/" "reconstruction/kegg/keggPhylDist.mat" ) _TIMEOUT_SECONDS = 120 diff --git a/tests/test_gecko_matlab_parity.py b/tests/test_gecko_matlab_parity.py index f1a2cf7..1145759 100644 --- a/tests/test_gecko_matlab_parity.py +++ b/tests/test_gecko_matlab_parity.py @@ -25,7 +25,7 @@ Parity on ecTestGEM does not prove parity on yeast-GEM; it proves the core functions agree on every behaviour MATLAB itself pins down. Whole-GEM parity needs MATLAB in the loop (see - ``SysBioChalmers/raven-gecko-parity``). + ``CompMetEng/raven-gecko-parity``). - Stages that need the network (UniProt/KEGG/ComplexPortal downloads, DLKcat inference) are out of scope here, exactly as in MATLAB's suite, which also runs them off stored files.