From f01cd36872df875fb5187c7da6531331927f933e Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Sat, 17 Oct 2026 07:22:31 +0200 Subject: [PATCH 1/2] Build from CompMetEng/RAVEN and point repository links to CompMetEng --- .gitmodules | 6 +++--- RAVEN | 2 +- README.md | 8 ++++---- docs/conf.py | 4 ++-- docs/guide/combining.md | 2 +- docs/index.md | 16 ++++++++-------- docs/installation/data-and-binaries.md | 2 +- docs/installation/python.md | 2 +- docs/installation/raven.md | 19 ++++++++----------- .../studies/init-param-calibration.md | 2 +- .../studies/kegg-hmm-cutoff-calibration.md | 2 +- .../sampling-convergence-calibration.md | 2 +- docs/protocol/materials.md | 4 ++-- docs/raven3-migration.md | 2 +- docs/tuned-parameters.md | 2 +- docs/tutorials/index.md | 2 +- docs/yaml-format.md | 4 ++-- mkdocs.yml | 4 ++-- 18 files changed, 41 insertions(+), 44 deletions(-) diff --git a/.gitmodules b/.gitmodules index efac870..a7be996 100644 --- a/.gitmodules +++ b/.gitmodules @@ -1,11 +1,11 @@ [submodule "RAVEN"] path = RAVEN - url = https://github.com/SysBioChalmers/RAVEN.git - branch = develop3 + url = https://github.com/CompMetEng/RAVEN.git + branch = develop shallow = true [submodule "raven-toolbox"] path = raven-toolbox - url = https://github.com/SysBioChalmers/raven-toolbox.git + url = https://github.com/CompMetEng/raven-toolbox.git branch = develop shallow = true [submodule "hanpo-GEM"] diff --git a/RAVEN b/RAVEN index 00bbd23..1366b44 160000 --- a/RAVEN +++ b/RAVEN @@ -1 +1 @@ -Subproject commit 00bbd234d53defeca469e2856aae6b91181cd56e +Subproject commit 1366b4410f4f8d790a12ca9cc8896d67fe126ef4 diff --git a/README.md b/README.md index fb04475..5269f0e 100644 --- a/README.md +++ b/README.md @@ -15,10 +15,10 @@ The site combines: - a complete, worked **GEM reconstruction protocol** (the *Hansenula polymorpha* `hanpo-GEM` example). -The source repositories are tracked as git submodules pinned to their `main` -branches: [`RAVEN`](https://github.com/SysBioChalmers/RAVEN), -[`raven-toolbox`](https://github.com/SysBioChalmers/raven-toolbox) and -[`hanpo-GEM`](https://github.com/SysBioChalmers/hanpo-GEM). +The source repositories are tracked as git submodules that follow the branches +set in `.gitmodules`: [`RAVEN`](https://github.com/CompMetEng/RAVEN) and +[`raven-toolbox`](https://github.com/CompMetEng/raven-toolbox) at `develop`, and +[`hanpo-GEM`](https://github.com/SysBioChalmers/hanpo-GEM) at `main`. ## Building locally diff --git a/docs/conf.py b/docs/conf.py index eac4147..f977dfe 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -60,13 +60,13 @@ "icon_links": [ { "name": "RAVEN (MATLAB) on GitHub", - "url": "https://github.com/SysBioChalmers/RAVEN", + "url": "https://github.com/CompMetEng/RAVEN", "icon": "fa-brands fa-github", "type": "fontawesome", }, { "name": "raven-toolbox (Python) on GitHub", - "url": "https://github.com/SysBioChalmers/raven-toolbox", + "url": "https://github.com/CompMetEng/raven-toolbox", "icon": "fa-brands fa-github", "type": "fontawesome", }, diff --git a/docs/guide/combining.md b/docs/guide/combining.md index 91a03e1..3af3a37 100644 --- a/docs/guide/combining.md +++ b/docs/guide/combining.md @@ -285,7 +285,7 @@ information and should go; an **exchange** had a single metabolite all along (`=> glucose`) and must be kept. raven-toolbox used to delete those too, along with the objective, taking this model from growth `0.1222` to `0.0000` with no error and no warning. Fixed in -[raven-toolbox#96](https://github.com/SysBioChalmers/raven-toolbox/pull/96); +[raven-toolbox#96](https://github.com/CompMetEng/raven-toolbox/pull/96); if a flattened model comes back with no boundary reactions, update raven-toolbox. ::: diff --git a/docs/index.md b/docs/index.md index 278391b..2ea1d79 100644 --- a/docs/index.md +++ b/docs/index.md @@ -27,14 +27,14 @@ Then run `checkRaven` to verify. :::{tab-item} Python (git) ```bash -git clone --depth=1 https://github.com/SysBioChalmers/raven-toolbox.git +git clone --depth=1 https://github.com/CompMetEng/raven-toolbox.git pip install -e raven-toolbox/ ``` ::: :::{tab-item} MATLAB (git) ```bash -git clone --depth=1 https://github.com/SysBioChalmers/RAVEN.git +git clone --depth=1 https://github.com/CompMetEng/RAVEN.git ``` Add the folder to the MATLAB path, then run `checkRaven` to verify. @@ -171,20 +171,20 @@ RAVEN paper and the GEM reconstruction protocol. ## Source code RAVEN is publicly available under the GPLv3 license at -[SysBioChalmers/RAVEN](https://github.com/SysBioChalmers/RAVEN){.github}, +[CompMetEng/RAVEN](https://github.com/CompMetEng/RAVEN){.github}, archived at [https://doi.org/10.5281/zenodo.3689518](https://doi.org/10.5281/zenodo.3689518). raven-toolbox, the Python port, is under the MIT license at -[SysBioChalmers/raven-toolbox](https://github.com/SysBioChalmers/raven-toolbox){.github}. +[CompMetEng/raven-toolbox](https://github.com/CompMetEng/raven-toolbox){.github}. ## Issues and discussions Report a bug or request a feature on the tracker for the toolbox it concerns: -[RAVEN issues](https://github.com/SysBioChalmers/RAVEN/issues){.github} for the -MATLAB toolbox, [raven-toolbox issues](https://github.com/SysBioChalmers/raven-toolbox/issues){.github} +[RAVEN issues](https://github.com/CompMetEng/RAVEN/issues){.github} for the +MATLAB toolbox, [raven-toolbox issues](https://github.com/CompMetEng/raven-toolbox/issues){.github} for the Python package. For questions and general discussion, use -[RAVEN discussions](https://github.com/SysBioChalmers/RAVEN/discussions){.github} -or [raven-toolbox discussions](https://github.com/SysBioChalmers/raven-toolbox/discussions){.github}. +[RAVEN discussions](https://github.com/CompMetEng/RAVEN/discussions){.github} +or [raven-toolbox discussions](https://github.com/CompMetEng/raven-toolbox/discussions){.github}. ```{toctree} :hidden: diff --git a/docs/installation/data-and-binaries.md b/docs/installation/data-and-binaries.md index 26d5adf..e5b010b 100644 --- a/docs/installation/data-and-binaries.md +++ b/docs/installation/data-and-binaries.md @@ -6,7 +6,7 @@ fetched on first use from a shared, checksummed release and cached locally. This page covers what is fetched, where it is kept, and how to override each step. Both toolboxes read from the same -[`raven-data`](https://github.com/SysBioChalmers/raven-data) repository, so the +[`toolbox-assets`](https://github.com/CompMetEng/toolbox-assets) repository, so the files RAVEN downloads and the files raven-toolbox downloads are the same files. ## What gets downloaded diff --git a/docs/installation/python.md b/docs/installation/python.md index e655412..d869c28 100644 --- a/docs/installation/python.md +++ b/docs/installation/python.md @@ -40,7 +40,7 @@ pip install raven-toolbox For the latest unreleased code or to contribute: ```bash -git clone https://github.com/SysBioChalmers/raven-toolbox.git +git clone https://github.com/CompMetEng/raven-toolbox.git cd raven-toolbox pip install -e . ``` diff --git a/docs/installation/raven.md b/docs/installation/raven.md index eaad891..38cd66f 100644 --- a/docs/installation/raven.md +++ b/docs/installation/raven.md @@ -1,9 +1,7 @@ # RAVEN (MATLAB) The RAVEN Toolbox runs in MATLAB and works completely independently; it does -not require the COBRA Toolbox, although it can interoperate with it. The -canonical reference is the -[RAVEN installation wiki](https://github.com/SysBioChalmers/RAVEN/wiki/Installation). +not require the COBRA Toolbox, although it can interoperate with it. ## Requirements @@ -103,12 +101,12 @@ If MATLAB does not pick up the toolbox after step 2, run :::{tab-item} {octicon}`download;1em` Release download Good for offline or managed environments. **The -[RAVEN releases page](https://github.com/SysBioChalmers/RAVEN/releases) +[RAVEN releases page](https://github.com/CompMetEng/RAVEN/releases) itself only lists stable releases**; 3.0.0b1 is a git tag with no packaged release, so download it directly instead: 1. Download - [the 3.0.0b1 archive](https://github.com/SysBioChalmers/RAVEN/archive/refs/tags/3.0.0b1.zip) + [the 3.0.0b1 archive](https://github.com/CompMetEng/RAVEN/archive/refs/tags/3.0.0b1.zip) directly (this works without git). 2. Extract it to a location of your choice. 3. In MATLAB, add the RAVEN folder to the path (`pathtool`), then @@ -117,11 +115,11 @@ release, so download it directly instead: :::{tab-item} {octicon}`git-branch;1em` Clone with git Clones the repository, then checks out the `3.0.0b1` tag specifically: a -plain `git clone` alone tracks the `main` branch (stable RAVEN 2), not this -site's pre-release. +plain `git clone` alone tracks the `develop` branch, which can contain changes +made after this site's pre-release. ```bash -git clone --depth=1 https://github.com/SysBioChalmers/RAVEN.git +git clone --depth=1 https://github.com/CompMetEng/RAVEN.git cd RAVEN git fetch --depth=1 origin tag 3.0.0b1 git checkout 3.0.0b1 @@ -253,6 +251,5 @@ Then delete the cloned RAVEN folder from disk. ## Getting help -For installation problems, consult the -[RAVEN wiki](https://github.com/SysBioChalmers/RAVEN/wiki/Installation) or -open an issue on [GitHub](https://github.com/SysBioChalmers/RAVEN/issues). +For installation problems, open an issue on +[GitHub](https://github.com/CompMetEng/RAVEN/issues). diff --git a/docs/parameter-tuning/studies/init-param-calibration.md b/docs/parameter-tuning/studies/init-param-calibration.md index beac8d2..10296d0 100644 --- a/docs/parameter-tuning/studies/init-param-calibration.md +++ b/docs/parameter-tuning/studies/init-param-calibration.md @@ -200,7 +200,7 @@ nothing to reconcile, but the values rest on convention rather than evidence. ## 4. Cross-solver portability See [init-solver-benchmark.md](init-solver-benchmark.md) for the genome-scale -solver comparison (Gurobi/HiGHS/GLPK) and [tests/test_init_solvers.py](https://github.com/SysBioChalmers/raven-toolbox/blob/develop/tests/test_init_solvers.py) +solver comparison (Gurobi/HiGHS/GLPK) and [tests/test_init_solvers.py](https://github.com/CompMetEng/raven-toolbox/blob/develop/tests/test_init_solvers.py) for CI parameterised over installed MILP backends. Summary: at genome scale only Gurobi is viable today; HiGHS fails on an upstream optlang `hybrid_interface.clone()` bug; GLPK ignores `configuration.timeout` on MIP and ran 1 h+ without converging. Toy-scale diff --git a/docs/parameter-tuning/studies/kegg-hmm-cutoff-calibration.md b/docs/parameter-tuning/studies/kegg-hmm-cutoff-calibration.md index 10c2e65..d69ab5d 100644 --- a/docs/parameter-tuning/studies/kegg-hmm-cutoff-calibration.md +++ b/docs/parameter-tuning/studies/kegg-hmm-cutoff-calibration.md @@ -29,7 +29,7 @@ in three steps: recall = |pred ∩ truth| / |truth|, F1. Reaction-level: `rxn_rec` = fraction of the organism's true reactions recovered (KO→reaction via `ko_reaction`); `rxn_novel` = predicted reactions **not** in the annotation set. -- Reproduce with [`scripts/analyze_hmm_cutoffs.py`](https://github.com/SysBioChalmers/raven-toolbox/blob/develop/scripts/analyze_hmm_cutoffs.py). +- Reproduce with [`scripts/analyze_hmm_cutoffs.py`](https://github.com/CompMetEng/raven-toolbox/blob/develop/scripts/analyze_hmm_cutoffs.py). ### Important caveat diff --git a/docs/parameter-tuning/studies/sampling-convergence-calibration.md b/docs/parameter-tuning/studies/sampling-convergence-calibration.md index 9e5e8cb..0fcc7f9 100644 --- a/docs/parameter-tuning/studies/sampling-convergence-calibration.md +++ b/docs/parameter-tuning/studies/sampling-convergence-calibration.md @@ -44,7 +44,7 @@ convergence threshold) or > 1.01 (the stricter one used in published MCMC work) flags a reaction whose distribution still depends on where its chain started. -* Driver: [`scripts/analyze_sampling_convergence.py`](https://github.com/SysBioChalmers/raven-toolbox/blob/docs/parameter-defaults/scripts/analyze_sampling_convergence.py) +* Driver: [`scripts/analyze_sampling_convergence.py`](https://github.com/CompMetEng/raven-toolbox/blob/docs/parameter-defaults/scripts/analyze_sampling_convergence.py) * Settings matched to the existing single-chain study for direct comparison: `n_samples=300`, `thinning=100`, `warmup=1000` (cobrapy/RAVEN defaults). * `n_chains=4`, run in parallel via `ProcessPoolExecutor` (one process per diff --git a/docs/protocol/materials.md b/docs/protocol/materials.md index 8f68e2d..947b33a 100644 --- a/docs/protocol/materials.md +++ b/docs/protocol/materials.md @@ -9,7 +9,7 @@ Most of it is open source or available under an academic license. | Software | Dependency | Source | |---|---|---| | MATLAB | License | | -| RAVEN | libSBML, solver | | +| RAVEN | libSBML, solver | | | COBRA | MATLAB | | | Gurobi | License | | | libSBML | MATLAB | | @@ -78,5 +78,5 @@ successful run looks like. If `checkRaven` reports that importing SBML format **failed**, uninstall MATLAB's **Text Analytics Toolbox**, which conflicts with RAVEN's Excel parser. For support, see the -[RAVEN issues](https://github.com/SysBioChalmers/RAVEN/issues) page. +[RAVEN issues](https://github.com/CompMetEng/RAVEN/issues) page. ::: diff --git a/docs/raven3-migration.md b/docs/raven3-migration.md index bc1fb28..c737a94 100644 --- a/docs/raven3-migration.md +++ b/docs/raven3-migration.md @@ -28,7 +28,7 @@ RAVEN 3 is a deliberate breaking release: the codebase was reorganized, a large number of low-value or duplicate functions were removed, several external dependencies were dropped, and the calling convention for optional function arguments changed almost everywhere. None of this was accidental; see the -project's [v3 development review](https://github.com/SysBioChalmers/RAVEN/blob/develop3/docs/v3_review.md) +project's [v3 development review](https://github.com/CompMetEng/RAVEN/blob/develop/docs/v3_review.md) for the rationale, but it means that **most non-trivial RAVEN 2 scripts need to be checked**, even though the core reconstruction and analysis behavior is mostly the same. diff --git a/docs/tuned-parameters.md b/docs/tuned-parameters.md index ea900e2..ce69de9 100644 --- a/docs/tuned-parameters.md +++ b/docs/tuned-parameters.md @@ -175,7 +175,7 @@ still changing. **Full detail:** the measurements behind these values (the yeast-GEM benchmark, the head-to-head against MATLAB's `predictLocalization`, the predictor benchmarks across four organisms, and the design documents) are in -[raven-gecko-parity](https://github.com/SysBioChalmers/raven-gecko-parity/tree/develop/docs/localization), +[raven-gecko-parity](https://github.com/CompMetEng/raven-gecko-parity/tree/develop/docs/localization), with the rest of the work in progress on this method. ## Model manipulation diff --git a/docs/tutorials/index.md b/docs/tutorials/index.md index 1c32655..c8f5390 100644 --- a/docs/tutorials/index.md +++ b/docs/tutorials/index.md @@ -10,7 +10,7 @@ the exercises themselves are otherwise unchanged. They use the **MATLAB** toolbox and build up from running a simulation on an existing model to reconstructing a genome-scale model from sequence data. The scripts and all the data files they use live in the -[`tutorial/`](https://github.com/SysBioChalmers/RAVEN/tree/main/tutorial) +[`tutorial/`](https://github.com/CompMetEng/RAVEN/tree/develop/tutorial) folder of the RAVEN repository. | # | Tutorial | What you learn | diff --git a/docs/yaml-format.md b/docs/yaml-format.md index db12aa4..96705cf 100644 --- a/docs/yaml-format.md +++ b/docs/yaml-format.md @@ -4,7 +4,7 @@ This document describes the YAML format produced and consumed by - **cobrapy** ([`cobra.io.{load,save}_yaml_model`](https://github.com/opencobra/cobrapy)) - **raven-toolbox** (`raven_toolbox.io.yaml.{read,write}_yaml_model`, see [API](api/index.md)) -- **RAVEN MATLAB** (`readYAMLmodel.m` / `writeYAMLmodel.m` in the [RAVEN repo](https://github.com/SysBioChalmers/RAVEN/tree/develop3/io)) +- **RAVEN MATLAB** (`readYAMLmodel.m` / `writeYAMLmodel.m` in the [RAVEN repo](https://github.com/CompMetEng/RAVEN/tree/develop/io)) The same file can be round-tripped through any of the three. cobrapy is the canonical core; raven-toolbox and RAVEN MATLAB add namespaced extensions (RAVEN curation fields, MIRIAM cross-refs already covered by cobrapy's `annotation`, and the GECKO `ec-*` sections) without disturbing the cobra-known shape. @@ -296,7 +296,7 @@ In a double-quoted string, only `\` and `"` are escaped. Other characters (inclu "Full" = every field read back into its canonical position on the model object; "core" = cobrapy-known fields, RAVEN extensions ignored or kept on the object as attribute fall-through (`reaction.eccodes` etc., not re-emitted on save). A round-trip through cobrapy is therefore **lossy for RAVEN extensions**: only the core fields survive `cobrapy.load → cobrapy.save`. Round-trips through raven-toolbox or RAVEN MATLAB are lossless. -Neither writer reproduces cobrapy's own `ruamel`-default layout byte-for-byte (indentation, quoting style, line folding); RAVEN and raven-toolbox instead share a layout with each other, close to cobrapy's structural shape but not identical to it. See [raven-gecko-parity's reconciliation record](https://github.com/SysBioChalmers/raven-gecko-parity/blob/develop/docs/yaml-reconciliation.md) for why, and for the one scenario (`yaml_roundtrip_smallyeast`) that continuously checks the two writers agree. +Neither writer reproduces cobrapy's own `ruamel`-default layout byte-for-byte (indentation, quoting style, line folding); RAVEN and raven-toolbox instead share a layout with each other, close to cobrapy's structural shape but not identical to it. See [raven-gecko-parity's reconciliation record](https://github.com/CompMetEng/raven-gecko-parity/blob/develop/docs/yaml-reconciliation.md) for why, and for the one scenario (`yaml_roundtrip_smallyeast`) that continuously checks the two writers agree. --- diff --git a/mkdocs.yml b/mkdocs.yml index 1eeb880..f5cbd95 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -4,8 +4,8 @@ site_description: >- Toolbox (MATLAB) and raven-toolbox, documented side by side. site_author: Wang, Marcisauskas, Sanchez, Domenzain, Hermansson, Agren, Nielsen, Kerkhoven et al. site_url: https://raven-docs.readthedocs.io/en/latest/ -repo_url: https://github.com/SysBioChalmers/RAVEN -repo_name: SysBioChalmers/RAVEN +repo_url: https://github.com/CompMetEng/RAVEN +repo_name: CompMetEng/RAVEN edit_uri: "" # Build-time hooks that keep the site resilient to structural changes in the From 4a3fca1e5d828ecd2dc2d180cf50ead18152d32f Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Sat, 17 Oct 2026 07:30:44 +0200 Subject: [PATCH 2/2] Name CompMetEng as the copyright holder in the site footer --- docs/conf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/conf.py b/docs/conf.py index f977dfe..a8df462 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -10,7 +10,7 @@ from __future__ import annotations project = "RAVEN" -copyright = "SysBioChalmers" +copyright = "CompMetEng" author = "Wang, Marcisauskas, Sanchez, Domenzain, Hermansson, Agren, Nielsen, Kerkhoven et al." extensions = [