edkerk · Oct 17, 2026 · Oct 17, 2026
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -86,12 +86,12 @@ jobs:
       - uses: actions/checkout@v5
       # RAVEN is GPL and this package is MIT, so its files are never vendored
       # here -- the cross-language checks read them from a checkout instead.
-      # develop3 is the branch raven-docs documents and raven-toolbox tracks.
+      # develop is the RAVEN branch raven-docs documents and raven-toolbox tracks.
       - name: Check out MATLAB RAVEN
         uses: actions/checkout@v5
         with:
-          repository: SysBioChalmers/RAVEN
-          ref: develop3
+          repository: CompMetEng/RAVEN
+          ref: develop
           path: .raven
       - uses: actions/setup-python@v6
         with:

diff --git a/.github/workflows/parity-nightly.yml b/.github/workflows/parity-nightly.yml
@@ -33,7 +33,7 @@ jobs:
     name: genome-scale parity
     # Forks do not have the secrets, and a scheduled run there would fail every
     # night for no reason.
-    if: github.repository == 'SysBioChalmers/raven-toolbox'
+    if: github.repository == 'CompMetEng/raven-toolbox'
     runs-on: ubuntu-latest
     # Measured against the classic INIT MILP this job used to check (now
     # ftINIT's run_ftinit, bounded to time_limit=600s -- see
@@ -51,8 +51,8 @@ jobs:
       - name: Check out MATLAB RAVEN
         uses: actions/checkout@v5
         with:
-          repository: SysBioChalmers/RAVEN
-          ref: develop3
+          repository: CompMetEng/RAVEN
+          ref: develop
           path: .raven
 
       - uses: actions/setup-python@v6

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -115,7 +115,7 @@ jobs:
     # Trusted Publishing: PyPI verifies this workflow's OIDC identity, so no
     # long-lived token is stored in the repo. Requires a one-time publisher on
     # PyPI for raven-toolbox with:
-    #   owner: SysBioChalmers   repo: raven-toolbox
+    #   owner: CompMetEng       repo: raven-toolbox
     #   workflow: release.yml   environment: pypi
     environment: pypi
     permissions:

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,8 +1,8 @@
 # Changelog
 
 Milestones in the raven-toolbox port. For function-level status see
-[docs/raven_migration.md](https://github.com/SysBioChalmers/raven-toolbox/blob/develop/docs/reference/migration.md); for open work see
-[docs/todo.md](https://github.com/SysBioChalmers/raven-toolbox/blob/develop/docs/reference/todo.md).
+[docs/raven_migration.md](https://github.com/CompMetEng/raven-toolbox/blob/develop/docs/reference/migration.md); for open work see
+[docs/todo.md](https://github.com/CompMetEng/raven-toolbox/blob/develop/docs/reference/todo.md).
 
 ## 3.0.0b1 — 2026-09-07
 

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -49,7 +49,7 @@ automatically; that side is documented in
 
 Publishing the results, and the versioning model behind the releases, is a shared
 convention rather than a raven-toolbox concern, and is documented in
-[raven-gecko-parity](https://github.com/SysBioChalmers/raven-gecko-parity/blob/develop/docs/publishing_artefacts.md).
+[raven-gecko-parity](https://github.com/CompMetEng/raven-gecko-parity/blob/develop/docs/publishing_artefacts.md).
 
 ## Rebuilding the KEGG artefacts
 

diff --git a/IMPROVEMENTS.md b/IMPROVEMENTS.md
@@ -5,7 +5,7 @@ made smarter/faster, or where a logical gap in RAVEN's feature set is worth fill
 change — with enough detail that it can **also be back-ported to MATLAB RAVEN** later.
 
 > **Implemented improvements** — and the ones worth carrying upstream into MATLAB RAVEN — now live
-> in [matlab_raven_backports.md](https://github.com/SysBioChalmers/raven-toolbox/blob/develop/docs/reference/matlab_raven_backports.md),
+> in [matlab_raven_backports.md](https://github.com/CompMetEng/raven-toolbox/blob/develop/docs/reference/matlab_raven_backports.md),
 > the MATLAB ↔ raven-toolbox **differences** record (both directions: improvements to back-port, and
 > functionality MATLAB has that raven-toolbox deliberately doesn't). **This file** keeps only the
 > design decisions behind what was ported *differently* or *not at all*, and the improvements still
@@ -92,7 +92,7 @@ several places — and ask before re-adding (see process note: argue pros/cons f
 ### removeReactions — not ported (orphan cleanup kept coupled)
 
 `remove_metabolites` / `remove_genes` are ported
-([manipulation/remove.py](https://github.com/SysBioChalmers/raven-toolbox/blob/develop/src/raven_toolbox/manipulation/remove.py)).
+([manipulation/remove.py](https://github.com/CompMetEng/raven-toolbox/blob/develop/src/raven_toolbox/manipulation/remove.py)).
 `removeReactions` was **not** ported: with orphan cleanup kept coupled (decision: don't separate
 metabolites from genes), it is identical to `cobra.Model.remove_reactions(remove_orphans=...)`.
 Separable orphan-met vs orphan-gene cleanup (**R1**, ❌ rejected) was considered then dropped — keep
@@ -127,7 +127,7 @@ OR-of-AND-complex (DNF) form (`findPotentialErrors`). **Decision (raven-toolbox)
 only.** cobra auto-normalizes a GPR on assignment (`"(G1 AND G2)  OR  G3"` is stored as
 `"(G1 and G2) or G3"`), so the normalization half is redundant. The non-DNF lint has no cobra
 equivalent and was ported as `find_non_dnf_grrules`/`is_dnf`
-([utils/gpr.py](https://github.com/SysBioChalmers/raven-toolbox/blob/develop/src/raven_toolbox/utils/gpr.py)).
+([utils/gpr.py](https://github.com/CompMetEng/raven-toolbox/blob/develop/src/raven_toolbox/utils/gpr.py)).
 
 ### readYAMLmodel — no separate legacy parser needed
 

diff --git a/README.md b/README.md
@@ -1,12 +1,12 @@
 # raven-toolbox
 
-[![CI](https://github.com/SysBioChalmers/raven-toolbox/actions/workflows/ci.yml/badge.svg)](https://github.com/SysBioChalmers/raven-toolbox/actions/workflows/ci.yml)
+[![CI](https://github.com/CompMetEng/raven-toolbox/actions/workflows/ci.yml/badge.svg)](https://github.com/CompMetEng/raven-toolbox/actions/workflows/ci.yml)
 [![PyPI](https://img.shields.io/pypi/v/raven-toolbox.svg)](https://pypi.org/project/raven-toolbox/)
 
 **Reconstruction, Analysis and Visualisation of Metabolic Networks — in Python.**
 
 `raven-toolbox` is the Python counterpart of the
-[RAVEN Toolbox](https://github.com/SysBioChalmers/RAVEN) (MATLAB). It builds on
+[RAVEN Toolbox](https://github.com/CompMetEng/RAVEN) (MATLAB). It builds on
 [**cobrapy**](https://github.com/opencobra/cobrapy) for everything cobrapy already does
 well — simulation, standard analyses, SBML I/O, model manipulation — and adds the
 functionality that is unique to RAVEN:
@@ -41,7 +41,7 @@ COBRA ecosystem.
 ## Status
 
 **raven-toolbox 3.0.0b1** is out — the first beta toward 3.0, tracking the upcoming MATLAB
-RAVEN 3.0 beta ([release notes](https://github.com/SysBioChalmers/raven-toolbox/releases/tag/v3.0.0b1),
+RAVEN 3.0 beta ([release notes](https://github.com/CompMetEng/raven-toolbox/releases/tag/v3.0.0b1),
 [changelog](CHANGELOG.md)). It has been validated against MATLAB RAVEN on **Human-GEM** (5 Hart2015
 cell-line models, Jaccard 0.975–0.980 — see
 [the Human-GEM validation study](https://github.com/edkerk/raven-docs/blob/main/docs/parameter-tuning/studies/humangem-validation.md)
@@ -75,7 +75,7 @@ pip install --pre raven-toolbox
 To work against the unreleased code on `develop` instead, install from git:
 
 ```bash
-git clone https://github.com/SysBioChalmers/raven-toolbox
+git clone https://github.com/CompMetEng/raven-toolbox
 cd raven-toolbox
 pip install -e ".[dev]"
 ```
@@ -123,12 +123,12 @@ site is generated from the docstrings here at build time, so a docstring edit
 reaches the site without anything being copied across. Contributor and maintainer
 notes are in [CONTRIBUTING.md](CONTRIBUTING.md); the roadmap, the backlog and the
 MATLAB parity record are in
-[raven-gecko-parity](https://github.com/SysBioChalmers/raven-gecko-parity).
+[raven-gecko-parity](https://github.com/CompMetEng/raven-gecko-parity).
 
 ## Relationship to MATLAB RAVEN
 
 `raven-toolbox` is an independent Python reimplementation of the
-[RAVEN Toolbox](https://github.com/SysBioChalmers/RAVEN), released under the permissive
+[RAVEN Toolbox](https://github.com/CompMetEng/RAVEN), released under the permissive
 **MIT** license. If you use it in scientific work, please cite the RAVEN 2 paper:
 
 > Wang H, Marcišauskas S, Sánchez BJ, Domenzain I, Hermansson D, Agren R, Nielsen J,

diff --git a/data/manifest.schema.json b/data/manifest.schema.json
@@ -1,6 +1,6 @@
 {
   "$schema": "https://json-schema.org/draft/2020-12/schema",
-  "$id": "https://github.com/SysBioChalmers/raven-toolbox/manifest.schema.json",
+  "$id": "https://github.com/CompMetEng/raven-toolbox/manifest.schema.json",
   "title": "RAVEN data/binary manifest",
   "description": "Language-agnostic registry of downloadable raven-toolbox / RAVEN data artefacts and external binary bundles. Consumed by the Python resolvers (raven_toolbox.data / raven_toolbox.binaries) and by MATLAB RAVEN. Every file carries a SHA256 so consumers verify integrity after download.",
   "type": "object",

diff --git a/pyproject.toml b/pyproject.toml
@@ -61,10 +61,10 @@ excel = [
 raven-toolbox-binaries = "raven_toolbox.binaries_cli:main"
 
 [project.urls]
-Homepage = "https://github.com/SysBioChalmers/raven-toolbox"
-Source = "https://github.com/SysBioChalmers/raven-toolbox"
-Issues = "https://github.com/SysBioChalmers/raven-toolbox/issues"
-"RAVEN MATLAB" = "https://github.com/SysBioChalmers/RAVEN"
+Homepage = "https://github.com/CompMetEng/raven-toolbox"
+Source = "https://github.com/CompMetEng/raven-toolbox"
+Issues = "https://github.com/CompMetEng/raven-toolbox/issues"
+"RAVEN MATLAB" = "https://github.com/CompMetEng/RAVEN"
 
 [tool.hatch.build.targets.wheel]
 packages = ["src/raven_toolbox"]

diff --git a/scripts/README.md b/scripts/README.md
@@ -4,23 +4,23 @@ Release-time tooling. Not part of the installed package — run them from a chec
 with raven-toolbox installed (`pip install -e .`). End users never need these.
 
 The full publish workflow (build → upload → manifest → sync) is documented in
-[artefact_hosting.md](https://github.com/SysBioChalmers/raven-gecko-parity/blob/main/docs/artefact_hosting.md)
+[artefact_hosting.md](https://github.com/CompMetEng/raven-gecko-parity/blob/develop/docs/artefact_hosting.md)
 (raven-gecko-parity).
 
 The localisation/DeepLoc benchmark scripts (`benchmark_deeploc*.py`,
 `compare_predictlocalization.py`, `benchmark_certified_*.py`, `benchmark_vs_carvefungi.py`,
 `build_carvefungi_yeast_model.py`, `compare_localization_sources.py`,
 `extract_compartment_structure.py`, `finetune_localization_yeast.py`,
 `benchmark_replicate_yeast_gem.py`) expect their input/output data under `data/deeploc/`,
-which lives in [raven-gecko-parity](https://github.com/SysBioChalmers/raven-gecko-parity/tree/develop/data/deeploc) —
+which lives in [raven-gecko-parity](https://github.com/CompMetEng/raven-gecko-parity/tree/develop/data/deeploc) —
 fetch it there first. The write-ups that use these scripts are in
-[raven-gecko-parity/docs/localization/](https://github.com/SysBioChalmers/raven-gecko-parity/tree/develop/docs/localization).
+[raven-gecko-parity/docs/localization/](https://github.com/CompMetEng/raven-gecko-parity/tree/develop/docs/localization).
 
 ## `build_binary_bundles.py`
 
 Build the per-platform binary ZIPs (BLAST+/DIAMOND/HMMER) from RAVEN's vetted
 `software/` binaries (pinned commits) into `dist/binaries/`, with checksums and
-provenance. See [maintaining_binaries.md](https://github.com/SysBioChalmers/raven-gecko-parity/blob/main/docs/maintaining_binaries.md)
+provenance. See [maintaining_binaries.md](https://github.com/CompMetEng/raven-gecko-parity/blob/develop/docs/maintaining_binaries.md)
 (raven-gecko-parity).
 
 ```bash
@@ -43,7 +43,7 @@ python scripts/publish_to_raven_data.py --dry-run release --tag manifest-v1 data
 Build the publishable KEGG artefact set from an arranged KEGG dump (see
 `download_kegg_dump`): the gzipped-YAML reference model, the gzipped-TSV tables,
 and (with `--hmms`) the per-domain pressed HMM libraries. Output is laid out ready
-to upload as release assets. See [maintaining_kegg_data.md](https://github.com/SysBioChalmers/raven-gecko-parity/blob/main/docs/maintaining_kegg_data.md)
+to upload as release assets. See [maintaining_kegg_data.md](https://github.com/CompMetEng/raven-gecko-parity/blob/develop/docs/maintaining_kegg_data.md)
 (raven-gecko-parity).
 
 ```bash

diff --git a/src/raven_toolbox/analysis/differential_sampling.py b/src/raven_toolbox/analysis/differential_sampling.py
@@ -10,7 +10,7 @@
 changed, or they moved in opposite directions.
 
 ``analyzeSampling.m`` calls ``getFluxZ.m`` directly and cannot be usefully
-ported without it (SysBioChalmers/raven-gecko-parity#41), so both are ported
+ported without it (CompMetEng/raven-gecko-parity#41), so both are ported
 together here.
 
 Sample orientation is *samples × reactions* (rows are samples, columns are

diff --git a/src/raven_toolbox/binaries.py b/src/raven_toolbox/binaries.py
@@ -8,7 +8,7 @@
       →  FileNotFoundError with install guidance
 
 So a pre-installed/conda binary always wins; the bundled ZIP is the zero-setup
-fallback. See https://github.com/SysBioChalmers/raven-gecko-parity/blob/main/docs/maintaining_binaries.md
+fallback. See https://github.com/CompMetEng/raven-gecko-parity/blob/develop/docs/maintaining_binaries.md
 for how the release ZIPs and the registry are produced and updated.
 """
 from __future__ import annotations
@@ -26,7 +26,7 @@
 # Keyed by *bundle*; one bundle can provide several executables (e.g. "blast" ->
 # blastp + makeblastdb). Baked snapshot of data/manifest.json's `binaries` block —
 # regenerate from the manifest with `python scripts/make_registry_snippet.py sync`
-# (never hand-edit). See https://github.com/SysBioChalmers/raven-gecko-parity/blob/main/docs/maintaining_binaries.md.
+# (never hand-edit). See https://github.com/CompMetEng/raven-gecko-parity/blob/develop/docs/maintaining_binaries.md.
 #   bundle -> {version, provides:[exe...], platforms:{"<os>-<arch>": {url, sha256}}}
 _REGISTRY: dict = {
     "blast": {

diff --git a/src/raven_toolbox/binaries_cli.py b/src/raven_toolbox/binaries_cli.py
@@ -13,7 +13,7 @@
 unless ``--force-download`` is given. Tools with no bundle for this OS/arch
 (e.g. MAFFT/CD-HIT on native Windows) are reported as unavailable with a
 conda/WSL2 hint — see
-https://github.com/SysBioChalmers/raven-gecko-parity/blob/main/docs/maintaining_binaries.md.
+https://github.com/CompMetEng/raven-gecko-parity/blob/develop/docs/maintaining_binaries.md.
 """
 from __future__ import annotations
 
@@ -82,7 +82,7 @@ def main(argv: list[str] | None = None) -> int:
             f"{', '.join(r.executable for r in unavailable)}.\n"
             "Install them via conda (`conda install -c bioconda <tool>`) or, on "
             "native Windows for HMMER/MAFFT/CD-HIT, run inside WSL2 (see "
-            "https://github.com/SysBioChalmers/raven-gecko-parity/blob/main/docs/maintaining_binaries.md)."
+            "https://github.com/CompMetEng/raven-gecko-parity/blob/develop/docs/maintaining_binaries.md)."
         )
     if errors:
         print(f"\n{len(errors)} download(s) failed:")

diff --git a/src/raven_toolbox/confidence.py b/src/raven_toolbox/confidence.py
@@ -31,7 +31,7 @@
 "non-growth associated maintenance reaction", and a name regex must never silence a chemistry check.
 
 The design and the measured yeast-GEM distributions are in the `confidence tracking study
-<https://github.com/SysBioChalmers/raven-gecko-parity/blob/develop/docs/localization/confidence_tracking.md>`_ on raven-gecko-parity; the
+<https://github.com/CompMetEng/raven-gecko-parity/blob/develop/docs/localization/confidence_tracking.md>`_ on raven-gecko-parity; the
 facet set above is closed. Wire it in by calling :func:`score_localization_confidence` on an
 :class:`~raven_toolbox.localization.AssignmentProposal`, :func:`score_equation_confidence` and
 :func:`score_gene_association_confidence` on any model, and :func:`mark_curated` when a curator firmly

diff --git a/src/raven_toolbox/localization/certify.py b/src/raven_toolbox/localization/certify.py
@@ -25,7 +25,7 @@
 that cannot grow is never reported as if it could.
 
 See the `compartment-assignment redesign
-<https://github.com/SysBioChalmers/raven-gecko-parity/blob/develop/docs/localization/localization_redesign.md>`_ on raven-gecko-parity for the design rationale.
+<https://github.com/CompMetEng/raven-gecko-parity/blob/develop/docs/localization/localization_redesign.md>`_ on raven-gecko-parity for the design rationale.
 """
 from __future__ import annotations
 
@@ -473,7 +473,7 @@ def _enrich_multilocalization(model, proposal, scores, sc, conditions, default_c
 
     The scalable, ghost-free replacement for the in-MILP ``aF``/``aR`` machinery (see
     `multi-localisation design
-    <https://github.com/SysBioChalmers/raven-gecko-parity/blob/develop/docs/localization/multi_localization_design.md>`_): propose, for each placed reaction, a second
+    <https://github.com/CompMetEng/raven-gecko-parity/blob/develop/docs/localization/multi_localization_design.md>`_): propose, for each placed reaction, a second
     compartment its gene has DeepLoc evidence for (score ``>= threshold``); materialise every candidate
     as a duplicate; then keep only those a **loopless FVA** shows can carry flux ``>= eps`` in a
     biomass-supporting solution. A dead duplicate (which would harvest a compartment's score for free)
@@ -581,7 +581,7 @@ def assign_compartments(
     Placement is decided by a flux-free score MILP, and functionality is a separate,
     materialised-FBA-verified repair (see the module docstring and
     the `compartment-assignment redesign
-    <https://github.com/SysBioChalmers/raven-gecko-parity/blob/develop/docs/localization/localization_redesign.md>`_ on raven-gecko-parity). Notable parameters:
+    <https://github.com/CompMetEng/raven-gecko-parity/blob/develop/docs/localization/localization_redesign.md>`_ on raven-gecko-parity). Notable parameters:
 
     ``transport_cost``
         Accepted for signature compatibility but **not used**: the placement master is flux-free and

diff --git a/src/raven_toolbox/localization/curation.py b/src/raven_toolbox/localization/curation.py
@@ -5,7 +5,7 @@
 thousands of calls and review only the highest-value few percent. It is a post-processor — no new solve
 except an optional gated essentiality FBA — combining several cheap signals that each flag a *distinct*
 way a placement can be wrong. See the `curation-priority signals study
-<https://github.com/SysBioChalmers/raven-gecko-parity/blob/develop/docs/localization/curation_priority_signals.md>`_ on raven-gecko-parity for the full catalogue;
+<https://github.com/CompMetEng/raven-gecko-parity/blob/develop/docs/localization/curation_priority_signals.md>`_ on raven-gecko-parity for the full catalogue;
 this ships the recommended first composite:
 
 * **override** — the reaction was placed *against* its gene's top DeepLoc compartment, and that top

diff --git a/src/raven_toolbox/localization/scores.py b/src/raven_toolbox/localization/scores.py
@@ -184,7 +184,7 @@ def load_deeploc(path: str | Path, *,
     compartment ids (post-``compartment_map``). **Only the mitochondrial split (`m`/`mm`) is supported
     by the evidence** (matrix-vs-membrane AUC ~0.92); DeepLoc does *not* separate ER lumen from
     membrane, so do not add `er`/`erm`. See the `DeepLoc yeast-GEM benchmark
-    <https://github.com/SysBioChalmers/raven-gecko-parity/blob/develop/docs/localization/deeploc_yeast_benchmark.md>`_ on raven-gecko-parity.
+    <https://github.com/CompMetEng/raven-gecko-parity/blob/develop/docs/localization/deeploc_yeast_benchmark.md>`_ on raven-gecko-parity.
 
     ``keep_raw_confidence=True`` attaches the per-gene *pre-normalisation* top probability to
     :attr:`LocalizationScores.raw_confidence` (normalisation otherwise forces every top to 1.0). It
@@ -195,7 +195,7 @@ def load_deeploc(path: str | Path, *,
     a 0.40 one), so leaving them un-normalised lets a downstream assignment weight confident genes
     more heavily; the default ``True`` preserves the RAVEN ``parseScores`` convention and keeps
     multi-source scales comparable. See the `DeepLoc normalisation benchmark
-    <https://github.com/SysBioChalmers/raven-gecko-parity/blob/develop/docs/localization/deeploc_normalisation_benchmark.md>`_ on raven-gecko-parity.
+    <https://github.com/CompMetEng/raven-gecko-parity/blob/develop/docs/localization/deeploc_normalisation_benchmark.md>`_ on raven-gecko-parity.
     """
     raw = pd.read_csv(path)
     wide = _wide_mapped(raw, id_column=None, compartment_map=compartment_map, source=str(path))

diff --git a/src/raven_toolbox/localization/transport_evidence.py b/src/raven_toolbox/localization/transport_evidence.py
@@ -18,7 +18,7 @@
 :func:`annotate_transporters` takes a pre-computed table instead. Substrate matching is *coarse-first*
 (family → coarse class), with a finer per-substrate ChEBI layer available via ``ontology``. See
 the `evidence-aware transport scoring design
-<https://github.com/SysBioChalmers/raven-gecko-parity/blob/develop/docs/localization/transport_evidence_scoring.md>`_ on raven-gecko-parity for the full design.
+<https://github.com/CompMetEng/raven-gecko-parity/blob/develop/docs/localization/transport_evidence_scoring.md>`_ on raven-gecko-parity for the full design.
 """
 from __future__ import annotations