Merge pull request #358 from SysBioChalmers/develop

* fix: loadDatabases check for duplicate protIDs (#349) * fix: prevent NaN in light ecModels (#346) * fix: calculateFfactor if paxDB has taxID !4 chars (#347) * fix: runDLKcat if path has spaces (#352) * refactor: FSEOF (#356) * fix: FSEOF to 0.9 of teorethical max prod * refactor: switch force objetive to target * fix: remove unnecesary function * fix: update input arguments * fix: temporal solution k-score * refactor: FSEOF * feat: add gene essentiality to FSEOF * fix: file writing * feat: add cutoff based on quantile * feat: report target transport reactions * refactor: add cutoff for essentiality * fix: bug identifying gene essentiality * doc: move installations instructions to wiki (#357) * move installation instructions to wiki * GECKOInstaller checks for latest GECKO version * fix: prevent duplications in protein pseudometabolites * minor fixes * doc: update documentation * doc: swap gitter for GitHub Discussions * fix: correct link to upgrade instructions * fix: synchronize STEP numbers protocol and paper --------- Co-authored-by: Albert Tafur Rangel <[email protected]>
SysBioChalmers · Dec 2, 2023 · b1e31b7 · b1e31b7
2 parents b512ea3 + 074078c
commit b1e31b7
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diff --git a/GECKOInstaller.m b/GECKOInstaller.m
@@ -28,6 +28,7 @@
             end
             addpath(paths);
             savepath;
+            GECKOInstaller.checkGECKOversion;
         end
         function uninstall
             sourceDir = fileparts(which(mfilename));
@@ -59,6 +60,7 @@
             pathsLeft = splitPaths(1,okPaths);
             newPaths = char(join(pathsLeft, pathSep));
         end
+
         function checkRAVENversion(minmVer)
             try
                 currVer = checkInstallation('versionOnly');
@@ -81,6 +83,39 @@ function checkRAVENversion(minmVer)
             end
 
         end
+
+        function checkGECKOversion
+            sourceDir = fileparts(which(mfilename));
+            hasGit=isfolder(fullfile(sourceDir,'.git'));
+
+            if exist(fullfile(sourceDir,'version.txt'), 'file') == 2
+                currVer = fgetl(fopen(fullfile(sourceDir,'version.txt')));
+                fclose('all');
+                fprintf('GECKO version %s installed',currVer)
+                try
+                    newVer=strtrim(webread('https://raw.githubusercontent.com/SysBioChalmers/GECKO/main/version.txt'));
+                    newVerNum=str2double(strsplit(newVer,'.'));
+                    currVerNum=str2double(strsplit(currVer,'.'));
+                    for i=1:3
+                        if currVerNum(i)<newVerNum(i)
+                            fprintf(', newer version %s is available',newVer)
+                            if ~hasGit
+                                fprintf('\nRun git pull in your favourite git client to update GECKO\n');
+                            else
+                                fprintf('\nInstructions on how to upgrade <a href="https://github.com/SysBioChalmers/GECKO/wiki/Installation-and-upgrade#installation">here</a>\n');
+                            end
+                            break
+                        elseif i==3
+                            fprintf('\n');
+                        end
+                    end
+                catch
+                    fprintf('\n');
+                end
+            else
+                fprintf('GECKO installed, unknown version (cannot find version.txt)\n')
+            end
+        end
     end
 
     properties (Constant)

diff --git a/README.md b/README.md
@@ -1,72 +1,26 @@
 <img src="./GECKO.png" width="200px">
 
 ![Current version](https://badge.fury.io/gh/sysbiochalmers%2Fgecko.svg)
-[![Gitter](https://badges.gitter.im/SysBioChalmers/GECKO.svg)](https://gitter.im/SysBioChalmers/GECKO)
+[![GitHub Discussions](https://img.shields.io/github/discussions-search?query=repo%3Asysbiochalmers%2Fgecko&label=GitHub%20Discussions)](https://github.com/SysBioChalmers/GECKO/discussions)
 [![Zenodo](https://zenodo.org/badge/DOI/10.5281/zenodo.7699818.svg)](https://doi.org/10.5281/zenodo.7699818)
 
 ## About GECKO 3
 
 The **GECKO** toolbox enhances a **G**enome-scale model to account for **E**nzyme **C**onstraints, using **K**inetics and **O**mics. The resulting enzyme-constrained model (**ecModel**) can be used to perform simulations where enzyme allocation is either drawn from a total protein pool, or constrained by measured protein levels from proteomics data.
 
-💡 In the GECKO folder, `protocol.m` contains instructions on how to reconstruct and analyze an ecModel for _S. cerevisiae_. This demonstrates how many of GECKO's functions can be used.
 
-💡 In the [`GECKO/tutorials`](https://github.com/SysBioChalmers/GECKO/tree/main/tutorials) folder there are examples of how GECKO can be applied to GEMs, in either of its _full_ or _light_ forms. Each `protocol.m` contains instructions on how to reconstruct and analyze an ecModel, demonstrating how different fuctions in GECKO can be used. The source code documentation is also available
-[online](http://sysbiochalmers.github.io/GECKO/doc/).
+💡 In the [`GECKO/tutorials`](https://github.com/SysBioChalmers/GECKO/tree/main/tutorials) folder there are examples of how GECKO can be applied to GEMs, in either of its _full_ or _light_ forms. Each `protocol.m` contains instructions on how to reconstruct and analyze an ecModel, demonstrating how different fuctions in GECKO can be used. These two scripts complement the [protocols paper](#citation).
 
-_**Note:** Regarding code and model compatibility with earlier GECKO versions, see [Previous versions: GECKO 1 and 2](#previous-versions-gecko-1-and-2)_.
+_**Note:** Regarding code and model compatibility with earlier GECKO versions, see [Previous versions: GECKO 1 and 2](https://github.com/SysBioChalmers/GECKO/wiki/Previous-versions:-GECKO-1-and-2)_.
 
-### Citation
 
-- A GECKO 3 publication is currently under consideration, citation information will appear here in due course.
-- For GECKO release 2, please cite [Domenzain et al. (2022) doi:10.1038/s41467-022-31421-1](https://doi.org/10.1038/s41467-022-31421-1).
-- For GECKO release 1, please cite [Sánchez et al. (2017) doi:10.15252/msb.20167411](https://doi.org/10.15252/msb.20167411).
+## Documentation
+**Installation instructions** and other information is available in the **[Wiki](https://github.com/SysBioChalmers/GECKO/wiki)**. The source code documentation is also available 
+[online](http://sysbiochalmers.github.io/GECKO/doc/). Use [GitHub Discussions](https://github.com/SysBioChalmers/GECKO/discussions) for support, to ask questions or leave comments.
 
-### Getting started
+## Citation
 
-#### Required software
-
-- MATLAB version 2019b or later, no additional MathWorks toolboxes are required.
-- [RAVEN Toolbox](https://github.com/SysBioChalmers/RAVEN). The RAVEN Toolbox Wiki contains [installation instructions for both RAVEN](https://github.com/SysBioChalmers/RAVEN/wiki/Installation) and [Gurobi](https://github.com/SysBioChalmers/RAVEN/wiki/Installation#solvers). Briefly, RAVEN is either downloaded via `git clone`, as ZIP-archive from GitHub, or installed as a [MATLAB AddOn](https://se.mathworks.com/matlabcentral/fileexchange/112330-raven-toolbox). After finishing all installation instructions, the user should run installation checks in MATLAB with: `checkInstallation`.
-- [Gurobi Optimizer](https://www.gurobi.com/solutions/gurobi-optimizer/) is recommended for simulations (free academic license available). Alternatively, the open-source [GNU Linear Programming Kit](https://www.gnu.org/software/glpk/) (distributed with RAVEN) or SoPlex as part of the [SCIP Optimization Suite](https://scipopt.org/) can be used.
-- [Docker](https://www.docker.com/) for running DLKcat. Installation instructions are available at https://docs.docker.com/get-docker .
-
-#### Installation
-
-- The preferred way to download GECKO is via git clone:
-
-```
-git clone --depth=1 https://github.com/SysBioChalmers/GECKO
-```
-
-- Alternatively, [a ZIP-archive can be directly downloaded from GitHub](https://github.com/SysBioChalmers/GECKO/releases). The ZIP-archive should be extracted to a disk location where the user has read- and write-access rights.
-
-- After `git clone` or extracting the ZIP-archive, the user should navigate in MATLAB to the GECKO folder. GECKO can then be installed with the command that adds GECKO (sub-)folders to the MATLAB path::
-
-```
-  cd('C:\path\to\GECKO') % Modify to match GECKO folder and operating system
-  GECKOInstaller.install
-```
-
-- If desired, a removal command is available as::
-
-```
-  GECKOInstaller.uninstall
-```
-
-All set! 🚀
-
-## Previous versions: GECKO 1 and 2
-
-Due to significant refactoring of the code, GECKO version 3 is largely not backwards compatible with earlier GECKO versions.
-
-- Most notably, GECKO 3 ecModels have an `.ec` structure containing all enzyme and kcat information.
-- In addition, in GECKO 3 enzymes are incorporated in the S-matrix as MW/kcat, while in GECKO 1 and 2 this was 1/kcat (where the MW was instead considered in the protein exchange reactions).
-- GECKO 3 ecModels can be stored in YAML file format that retains all model content.
-- Most functions in GECKO 3 do not work on ecModels generated with GECKO versions 1 or 2.
-- ecModels generated in GECKO 3 do not work with functions from GECKO versions 1 or 2.
-- At this moment, there are no Python functions to work with GECKO 3 formatted ecModels.
-- The last GECKO 2 release (2.0.3) is available [here](https://github.com/SysBioChalmers/GECKO/releases/tag/v2.0.3).
-- The `gecko2` branch remains available for any potential fixes.
+- The GECKO 3 publication is in press at Nature Protocols. Once published, citation information will appear here.
 
 ## Contributing