From fa745f069d43df6ec132e31ee39fe00961e63400 Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Sat, 17 Oct 2026 07:08:20 +0200 Subject: [PATCH] Point repository, documentation and version-check links to CompMetEng --- .github/CONTRIBUTING.md | 2 +- .github/issue_template.md | 2 +- .github/pull_request_template.md | 2 +- README.md | 14 +++++++------- checkRaven.m | 8 ++++---- conversion/standardizeModelFieldOrder.m | 2 +- docs/v3_review.md | 4 ++-- tutorial/tutorial1.m | 2 +- tutorial/tutorial2.m | 2 +- tutorial/tutorial2_solutions.m | 2 +- tutorial/tutorial3.m | 2 +- tutorial/tutorial3_solutions.m | 2 +- tutorial/tutorial4.m | 2 +- tutorial/tutorial4_solutions.m | 2 +- tutorial/tutorial5.m | 2 +- tutorial/tutorial7.m | 2 +- 16 files changed, 26 insertions(+), 26 deletions(-) diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 308c1f82..8cdcf209 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -41,7 +41,7 @@ A more detailed explanation or comments can be left in the commit description. * A merge with the mainbranch invokes a new release (see [versioning](#versioning)). ### Versioning -RAVEN Toolbox follows [semantic versioning](https://semver.org/). After each successful Pull Request (PR) to `main`, the `version.txt` file should be updated in a separate PR. When this PR is merged, a new [release](https://github.com/SysBioChalmers/RAVEN/releases) should be specified, with a list detailing the most significant changes since the previous release. +RAVEN Toolbox follows [semantic versioning](https://semver.org/). After each successful Pull Request (PR) to `main`, the `version.txt` file should be updated in a separate PR. When this PR is merged, a new [release](https://github.com/CompMetEng/RAVEN/releases) should be specified, with a list detailing the most significant changes since the previous release. Ensure that the documentation is also updated (in `devel`) before creating a PR to `main`. It can be updated by running `updateDocumentation()`. diff --git a/.github/issue_template.md b/.github/issue_template.md index d31135e1..48b4ee61 100644 --- a/.github/issue_template.md +++ b/.github/issue_template.md @@ -26,4 +26,4 @@ etc. etc. **I hereby confirm that I have:** -- [ ] Checked that a similar issue does not [already exist](https://github.com/SysBioChalmers/RAVEN/issues?q=is%3Aissue) or is already [discussed](https://github.com/SysBioChalmers/RAVEN/discussions). +- [ ] Checked that a similar issue does not [already exist](https://github.com/CompMetEng/RAVEN/issues?q=is%3Aissue) or is already [discussed](https://github.com/CompMetEng/RAVEN/discussions). diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md index 35742302..c04f8144 100644 --- a/.github/pull_request_template.md +++ b/.github/pull_request_template.md @@ -11,4 +11,4 @@ - [ ] This PR has `develop` as target branch, and will be resolved with a *squash-merge*. -- [ ] This PR has `main` as target branch, and will be resolved as descriped [here](https://github.com/SysBioChalmers/RAVEN/wiki/Development-policy#make-a-new-release). +- [ ] This PR has `main` as target branch, and will be resolved as described [here](https://github.com/CompMetEng/RAVEN/blob/develop/.github/CONTRIBUTING.md#versioning). diff --git a/README.md b/README.md index 26e597fd..fe1385cf 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ -[![Current release](https://img.shields.io/github/release/SysBioChalmers/RAVEN/all.svg)](https://GitHub.com/SysBioChalmers/RAVEN/releases/) -[![GitHub Discussions](https://img.shields.io/github/discussions-search?query=repo%3Asysbiochalmers%2raven&label=GitHub%20Discussions)](https://github.com/SysBioChalmers/RAVEN/discussions) +[![Current release](https://img.shields.io/github/release/CompMetEng/RAVEN/all.svg)](https://github.com/CompMetEng/RAVEN/releases/) +[![GitHub Discussions](https://img.shields.io/github/discussions-search?query=repo%3ACompMetEng%2FRAVEN&label=GitHub%20Discussions)](https://github.com/CompMetEng/RAVEN/discussions) [![Zenodo](https://zenodo.org/badge/DOI/10.5281/zenodo.3689518.svg)](https://doi.org/10.5281/zenodo.3689518) [![MATLAB File Exchange](https://www.mathworks.com/matlabcentral/images/matlab-file-exchange.svg)](https://se.mathworks.com/matlabcentral/fileexchange/112330-raven-toolbox) @@ -9,15 +9,15 @@ The **RAVEN** (Reconstruction, Analysis and Visualization of Metabolic Networks) Toolbox is a software suite for MATLAB that allows for semi-automated reconstruction of genome-scale models (GEMs). It makes use of published models and/or the KEGG database, coupled with extensive gap-filling and quality control features. The software suite also contains methods for visualizing simulation results and omics data, as well as a range of methods for performing simulations and analyzing the results. The software is a useful tool for system-wide data analysis in a metabolic context and for streamlined reconstruction of metabolic networks based on protein homology. -The latest stable release is **RAVEN 2.11.3**, on the `main` branch. +The latest stable release is **RAVEN 2.11.4**, maintained in [SysBioChalmers/RAVEN](https://github.com/SysBioChalmers/RAVEN). -> **This `develop3` branch is where RAVEN 3 is under active development**, with the upcoming **3.0.0b1** beta as its first release, targeting a final **3.0.0**. RAVEN 3 is a deliberate breaking release: the codebase has been reorganized into functional folders, optional function arguments can now be passed positionally, by name, or both, external binaries and KEGG reference data are fetched on demand instead of bundled in the repository, several MATLAB toolbox dependencies were dropped, and a number of low-value or duplicate functions were removed alongside new capabilities. Until 3.0.0 is tagged, this branch can still change. See the [migration guide](#documentation) for the full list of changes for users upgrading from RAVEN 2. +> **This repository is where RAVEN 3 is under active development**, with the upcoming **3.0.0b1** beta as its first release, targeting a final **3.0.0**. RAVEN 3 is a deliberate breaking release: the codebase has been reorganized into functional folders, optional function arguments can now be passed positionally, by name, or both, external binaries and KEGG reference data are fetched on demand instead of bundled in the repository, several MATLAB toolbox dependencies were dropped, and a number of low-value or duplicate functions were removed alongside new capabilities. Until 3.0.0 is tagged, the code can still change. See the [migration guide](#documentation) for the full list of changes for users upgrading from RAVEN 2. For context-specific model extraction, use `ftINIT`; `getINITModel` and `runINIT` are the original tINIT implementation, kept for reproducing models built with it. ## Documentation -The information about downloading, installing and developing RAVEN is included in the [Wiki](https://github.com/SysBioChalmers/RAVEN/wiki). The source code documentation is also available [online](http://sysbiochalmers.github.io/RAVEN/doc/). +Installation instructions, a user guide and the API reference are published at [raven-docs](https://raven-docs.readthedocs.io/en/latest/). Full user documentation, including a migration guide for users upgrading from RAVEN 2 to RAVEN 3, is published at [raven-docs](https://raven-docs.readthedocs.io/en/latest/). @@ -34,8 +34,8 @@ If you use ftINIT in your scientific work, please cite: For crediting supporting work, please cite doi:[10.1002/msb.145122](http://msb.embopress.org/content/10/3/721) (`tInit`); doi:[10.1371/journal.pcbi.1000859](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000859) (`randomsampling`). For crediting RAVEN 1, cite doi:[10.1371/journal.pcbi.1002980](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002980). For more details, see [wiki#cite-us](https://github.com/SysBioChalmers/RAVEN/wiki#cite-us). ## Contact Us -Use [GitHub Discussions](https://github.com/SysBioChalmers/RAVEN/discussions) for support, to ask questions or leave comments. +Use [GitHub Discussions](https://github.com/CompMetEng/RAVEN/discussions) for support, to ask questions or leave comments. ## Contributing -Contributions are always welcome! Please read the [Contributor guidelines](https://github.com/SysBioChalmers/RAVEN/blob/main/.github/CONTRIBUTING.md) to get started. RAVEN 2.x maintenance happens on the `develop` branch; RAVEN 3 development happens on `develop3`. +Contributions are always welcome! Please read the [Contributor guidelines](https://github.com/CompMetEng/RAVEN/blob/develop/.github/CONTRIBUTING.md) to get started. RAVEN 3 development happens on the `develop` branch of this repository; RAVEN 2.x is maintained in [SysBioChalmers/RAVEN](https://github.com/SysBioChalmers/RAVEN). diff --git a/checkRaven.m b/checkRaven.m index aa462a86..e65111b8 100755 --- a/checkRaven.m +++ b/checkRaven.m @@ -28,7 +28,7 @@ % 1: as MATLAB Add-On % 2: neither of the above, direct download of ZIP file % This matches the installations mentioned in the wiki: -% https://github.com/SysBioChalmers/RAVEN/wiki/Installation +% https://raven-docs.readthedocs.io/en/latest/installation/raven.html % 0 = advanced / 1 = easy / 2 = medium % % Usage: [currVer, installType] = checkRaven(developMode) @@ -82,7 +82,7 @@ if ~versionOnly fprintf([currVer '\n']); try - newVer=strtrim(webread('https://raw.githubusercontent.com/SysBioChalmers/RAVEN/main/version.txt')); + newVer=strtrim(webread('https://raw.githubusercontent.com/CompMetEng/RAVEN/main/version.txt')); newVerNum=str2double(strsplit(newVer,'.')); currVerNum=str2double(strsplit(currVer,'.')); for i=1:3 @@ -95,10 +95,10 @@ printOrange(' to get the latest RAVEN release\n'); case 1 printOrange(myStr(' Instructions on how to upgrade',40)) - fprintf('here\n'); + fprintf('here\n'); case 2 printOrange(myStr(' Instructions on how to upgrade',40)) - fprintf('here\n'); + fprintf('here\n'); end break elseif i==3 diff --git a/conversion/standardizeModelFieldOrder.m b/conversion/standardizeModelFieldOrder.m index b81441f1..c0b63639 100755 --- a/conversion/standardizeModelFieldOrder.m +++ b/conversion/standardizeModelFieldOrder.m @@ -2,7 +2,7 @@ % standardizeModelFieldOrder Order RAVEN model structure fields. % % Orders fields of a RAVEN model structure as specified at -% https://github.com/SysBioChalmers/RAVEN/wiki/RAVEN-Model-Structure +% https://raven-docs.readthedocs.io/en/latest/guide/model-structure.html % % The model fields themselves are not changed, only the order is modified. % For changing model fields between RAVEN and COBRA format, use diff --git a/docs/v3_review.md b/docs/v3_review.md index 691c4568..82d9a4e0 100644 --- a/docs/v3_review.md +++ b/docs/v3_review.md @@ -70,12 +70,12 @@ So the review does not repeat completed work. v3 already: as a new `UniProt` table column (ยง6.3). - Removed `followFluxes` (SysBioChalmers/RAVEN#725): a strict subset of `printFluxes`'s cutoff filtering plus `followChanged`'s single-reference-flux comparison, with nothing of - its own (SysBioChalmers/raven-gecko-parity#46). + its own (CompMetEng/raven-gecko-parity#46). - Removed `exportToTabDelimited` and the `exportToExcelFormat` bare-path fallback that called it (SysBioChalmers/RAVEN#727): the fallback silently switched output format depending on whether `fileName` looked like a path, contradicting `exportToExcelFormat`'s own error message ("only xlsx format is supported" as of RAVEN 1.9) whenever a full filename *was* - given (SysBioChalmers/raven-gecko-parity#55). + given (CompMetEng/raven-gecko-parity#55). --- diff --git a/tutorial/tutorial1.m b/tutorial/tutorial1.m index 3d748cd5..abcc7db7 100755 --- a/tutorial/tutorial1.m +++ b/tutorial/tutorial1.m @@ -9,7 +9,7 @@ % this tutorial. The model is provided as the SBML file % "iAL1006 v1.00.xml". % See Tutorial 1 on the RAVEN wiki for more details: -% https://github.com/SysBioChalmers/RAVEN/wiki/Tutorials +% https://raven-docs.readthedocs.io/en/latest/tutorials/ %Import the model from SBML. This function performs a number of checks %regarding the model structure (such as for incorrectly written equations diff --git a/tutorial/tutorial2.m b/tutorial/tutorial2.m index 5df2143e..77bf8acf 100755 --- a/tutorial/tutorial2.m +++ b/tutorial/tutorial2.m @@ -4,7 +4,7 @@ % stoichiometric modelling. It is shown how to build a simple model from % scratch, set parameters and perform simple simulations. % See Tutorial 2 on the RAVEN wiki for more details: -% https://github.com/SysBioChalmers/RAVEN/wiki/Tutorials +% https://raven-docs.readthedocs.io/en/latest/tutorials/ %Import the model into a RAVEN model structure smallModel=importModel('empty.xml'); diff --git a/tutorial/tutorial2_solutions.m b/tutorial/tutorial2_solutions.m index 4038575f..a9ea35a4 100755 --- a/tutorial/tutorial2_solutions.m +++ b/tutorial/tutorial2_solutions.m @@ -1,7 +1,7 @@ % tutorial2_solutions % This script contains the solutions for Tutorial 2, see Tutorial 2 on % the RAVEN wiki for more details: -% https://github.com/SysBioChalmers/RAVEN/wiki/Tutorials +% https://raven-docs.readthedocs.io/en/latest/tutorials/ %Import the model into a RAVEN model structure smallModel=readYAMLmodel('small.yml'); diff --git a/tutorial/tutorial3.m b/tutorial/tutorial3.m index 399ed42b..85637f3b 100755 --- a/tutorial/tutorial3.m +++ b/tutorial/tutorial3.m @@ -4,7 +4,7 @@ % data. A simplified model of yeast metabolism is used in this approach % as an example. % See Tutorial 3 on the RAVEN wiki for more details: -% https://github.com/SysBioChalmers/RAVEN/wiki/Tutorials +% https://raven-docs.readthedocs.io/en/latest/tutorials/ % % It is assumed that the user has already completed Tutorial 2 diff --git a/tutorial/tutorial3_solutions.m b/tutorial/tutorial3_solutions.m index 1451360b..5e2f5e7a 100755 --- a/tutorial/tutorial3_solutions.m +++ b/tutorial/tutorial3_solutions.m @@ -1,7 +1,7 @@ % tutorial3_solutions % This script contains the solutions for Tutorial 3, see Tutorial 3 on % the RAVEN wiki for more details: -% https://github.com/SysBioChalmers/RAVEN/wiki/Tutorials +% https://raven-docs.readthedocs.io/en/latest/tutorials/ % All the parameters are set in this script, rather than modifying the % Excel model file. diff --git a/tutorial/tutorial4.m b/tutorial/tutorial4.m index 8f00ba88..20b29dcb 100755 --- a/tutorial/tutorial4.m +++ b/tutorial/tutorial4.m @@ -1,7 +1,7 @@ % tutorial4 % This script contains the list of functions necessary for running % Tutorial 4, see Tutorial 4 on the RAVEN wiki for more details: -% https://github.com/SysBioChalmers/RAVEN/wiki/Tutorials +% https://raven-docs.readthedocs.io/en/latest/tutorials/ % Several key stages may be missing, try to fill these gaps before % checking the solutions in tutorial4_solutions. It is assumed that the % user is somewhat familiar with linear programming. diff --git a/tutorial/tutorial4_solutions.m b/tutorial/tutorial4_solutions.m index 19db2a2c..55b4d00f 100755 --- a/tutorial/tutorial4_solutions.m +++ b/tutorial/tutorial4_solutions.m @@ -1,7 +1,7 @@ % tutorial4_solutions % This script contains the solutions for Tutorial 4, see Tutorial 4 on % the RAVEN wiki for more details: -% https://github.com/SysBioChalmers/RAVEN/wiki/Tutorials +% https://raven-docs.readthedocs.io/en/latest/tutorials/ % % NOTE: Many of these changes are easier to do in the Excel sheet. They % are done here in code just to avoid having several model files. diff --git a/tutorial/tutorial5.m b/tutorial/tutorial5.m index 8764181d..5f1a985d 100755 --- a/tutorial/tutorial5.m +++ b/tutorial/tutorial5.m @@ -6,7 +6,7 @@ % purpose is to serve as a scaffold to reconstruct a GEM for any % organism. % This refers to Tutorial 5 on the RAVEN wiki: -% https://github.com/SysBioChalmers/RAVEN/wiki/Tutorials +% https://raven-docs.readthedocs.io/en/latest/tutorials/ % % Start by downloading trained Hidden Markov Models for eukaryotes. This can % be done automatically or manually from the RAVEN Wiki in its GitHub diff --git a/tutorial/tutorial7.m b/tutorial/tutorial7.m index 77cfad99..9a3f02f4 100644 --- a/tutorial/tutorial7.m +++ b/tutorial/tutorial7.m @@ -6,7 +6,7 @@ % measured values (with one component left to absorb whatever is left, % so the total stays at 1 g/gDW), and setGAM to apply a % growth-associated maintenance value. See Tutorial 7 on the RAVEN wiki -% for more details: https://github.com/SysBioChalmers/RAVEN/wiki/Tutorials +% for more details: https://raven-docs.readthedocs.io/en/latest/tutorials/ % % A small hand-built model is used instead of a real GEM, so the % pseudoreaction layout is visible in full below. Real GEMs lay this out