Point repository, documentation and RAVEN data links to CompMetEng

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:

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

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).

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*

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:

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"

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

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.