Point repository, documentation and version-check links to CompMetEng

.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()`.
 

.github/issue_template.md

@@ -26,4 +26,4 @@ etc. etc.
 
 **I hereby confirm that I have:**
 <!-- Note: replace [ ] with [X] to check the box -->
-- [ ] 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).

.github/pull_request_template.md

@@ -11,4 +11,4 @@
 <!-- Chose ONE of the following two options
 and replace [ ] with [X] to check the box.-->
 - [ ] 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).

README.md

@@ -1,23 +1,23 @@
 <img src="./RAVEN.png" width="200px">
 
-[![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)
 
 ## About RAVEN
 
 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).

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('<a href="https://github.com/SysBioChalmers/RAVEN/wiki/Installation#upgrade-raven-after-easy-installation">here</a>\n');
+                            fprintf('<a href="https://raven-docs.readthedocs.io/en/latest/installation/raven.html#upgrade">here</a>\n');
                         case 2
                             printOrange(myStr('     Instructions on how to upgrade',40))
-                            fprintf('<a href="https://github.com/SysBioChalmers/RAVEN/wiki/Installation#upgrade-raven-after-medium-installation">here</a>\n');                            
+                            fprintf('<a href="https://raven-docs.readthedocs.io/en/latest/installation/raven.html#upgrade">here</a>\n');                            
                     end
                     break
                 elseif i==3

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

docs/v3_review.md

@@ -70,12 +70,12 @@ So the review does not repeat completed work. v3 already:
   as a new `UniProt` table column (§6.3).
 - 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).
 
 ---
 

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

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');

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');

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
 

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.
 

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.

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.

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

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