Merge branch 'develop' into fix/exprotModel

.gitattributes

@@ -1,7 +1,11 @@
 # Ensure that EOL characters are properly converted for all files
 *	text=auto
 # Use MATLAB style diff
-*.m	text diff=matlab
+*.m text diff=matlab
+# Mark as binary to prevent EOL changes. Also no need to track 
+mafft.bat  binary
+mafft/  binary
+mafft binary
 # Files/folders that should not be included when downloading repo as ZIP
 .gitattributes	export-ignore
 .gitignore	export-ignore

.github/issue_template.md

@@ -0,0 +1,29 @@
+### Description of the issue:
+<!-- Try to be as clear as possible, e.g.
+- Is there a functionality missing?
+- Did an existing function fail?
+- What is the exact error message, and other output that you got?
+- What have you tried yourself to fix it? -->
+
+#### Reproducing this issue:
+<!-- If applicable, please attach the problematic code. -->
+```matlab
+INSERT CODE HERE
+```
+
+#### System information
+<!-- Please report the complete output from checkInstallation, for instance:
+ > Installing from location             C:\Work\GitHub\RAVEN
+ > Checking RAVEN release               2.8.6
+   > You are running the latest RAVEN release
+ > Checking MATLAB release              2023b
+ > Checking system architecture         win64
+ > Set RAVEN in MATLAB path             Pass
+ > Save MATLAB path                     Pass
+
+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).

.github/pull_request_template.md

@@ -0,0 +1,14 @@
+### Main improvements in this PR:
+<!-- Pointwise mention what changes were made in what function. Examples: 
+- Fixes:
+  - `functionName` failed to do action X
+- Documentation:
+  - Updated all documentation 
+- Features:
+  - Introduced option to do function Y (issue #12345) -->
+
+#### Instructions on merging this PR:
+<!-- 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 with a *merge commit*.

.github/workflows/commentsFromTests.md

@@ -0,0 +1,7 @@
+This PR has been [automatically tested with GH Actions](https://github.com/SysBioChalmers/RAVEN/actions/runs/{GH_ACTION_RUN}). Here is the output of the tests:
+
+<pre>
+{TEST_RESULTS}
+</pre>
+
+> _Note: In the case of multiple test runs, this post will be edited._

.github/workflows/tests.yml

@@ -0,0 +1,29 @@
+name: Tests
+
+on: [pull_request]
+
+jobs:
+  matlab-tests:
+    runs-on: self-hosted
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Run tests
+        id: matlab-test
+        run: |
+          TEST_RESULTS=$(/usr/local/bin/matlab -nodisplay -nosplash -nodesktop -r "warning('off', 'MATLAB:rmpath:DirNotFound'); rmpath(genpath('/home/m/ecModels-dependencies/RAVEN')); rmpath(genpath('/home/m/actions-runner')); addpath(genpath('.')); checkInstallation; cd('testing/unit_tests'); runtests(struct2table(dir('*.m')).name); exit;" | awk 'NR>13 && !/^(___|===|---)/')
+          PARSED_RESULTS="${TEST_RESULTS//'%'/'%25'}"
+          PARSED_RESULTS="${PARSED_RESULTS//$'\n'/'<br>'}"
+          PARSED_RESULTS="${PARSED_RESULTS//$'\r'/'<br>'}"
+          echo "results=$PARSED_RESULTS" >> $GITHUB_OUTPUT
+
+      - name: Post comment
+        uses: NejcZdovc/comment-pr@v2
+        with:
+          file: "commentsFromTests.md"
+        env:
+          GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
+          TEST_RESULTS: ${{steps.matlab-test.outputs.results}}
+          GH_ACTION_RUN: ${{github.run_id}}

.gitignore

@@ -40,4 +40,11 @@ Temporary Items
 #external/kegg/keggRxns.mat
 external/kegg/keggModel.mat
 #software
+software/scip/
+!.keep
 #doc
+
+# IDE stuff #
+################
+.idea/
+*.iml

INIT/INITStepDesc.m

@@ -0,0 +1,75 @@
+classdef INITStepDesc
+% Describes a step in the ftINIT algorithm. A cell array of objects of this
+% class is used as input to ftINIT to specify how the algorithm should be run.
+   properties
+      PosRevOff
+      AllowMetSecr
+      HowToUsePrevResults %'ignore', 'exclude', 'essential'
+      RxnsToIgnoreMask %Specifies reactions to leave outside the problem in
+                       %the MILP.
+                       % [b1,b2,b3,b4,b5,b6,b7,b8], bx is either 0 or 1, 
+                       % where 1 means that the group is excluded.
+                       % b1 - Exchange rxns
+                       % b2 - Import rxns without GPRs (from s into the cell)
+                       % b3 - Simple transport reactions without GPRs (moves one metabolite between compartments)
+                       % b4 - Advanced transport reactions without GPRs (moves metabolites between compartments, more complex function such as antiporter)
+                       % b5 - Spontaneous reactions
+                       % b6 - Reactions in the s compartment without GPRs
+                       % b7 - Customly specified rxns (sent in when generating prepData)
+                       % b8 - All rxns without GPRs
+
+      MetsToIgnore % Structure describing mets that can be removed from the model
+                   % before running ftINIT, such as water etc.
+                   % .simpleMets
+                   %      .mets        Names of metabolites to remove
+                   %      .compsToKeep Compartments for which metabolites should be kept.
+      MILPParams %Cell array of MILPparams - dictates how many iterations that will be run in this step.
+                 %Typically, MIPGap and TimeLimit is specified
+      AbsMIPGaps %If the objective is close to zero, a percentage of that is very small. 
+                 %Therefore, also set an absolut value for this (typically 10 or 20). 
+                 %For practical reasons, the first number is not used
+   end
+   methods
+      function obj = INITStepDesc(posRevOff_, AllowMetSecr_, howToUsePrevResults_, rxnsToIgnoreMask_, metsToIgnore_, MILPParams_, absMIPGaps_)
+         if nargin > 0
+            obj.PosRevOff = posRevOff_;
+         else
+            obj.PosRevOff = false;
+         end
+         if nargin > 1
+            obj.AllowMetSecr = AllowMetSecr_;
+         else
+            obj.AllowMetSecr = false;
+         end
+         if nargin > 2
+            obj.HowToUsePrevResults = howToUsePrevResults_;
+         else
+            obj.HowToUsePrevResults = 'essential';
+         end
+         if nargin > 3
+            obj.RxnsToIgnoreMask = rxnsToIgnoreMask_;
+         else
+            obj.RxnsToIgnoreMask = [1;0;0;0;0;0;0;0];
+         end
+         if nargin > 4
+            obj.MetsToIgnore = metsToIgnore_;
+         else
+            obj.MetsToIgnore = [1;0;0;0;0;0;0;0];
+         end
+         if nargin > 5
+            obj.MILPParams = MILPParams_;
+         else
+            params = struct();
+            params.TimeLimit = 5000;
+            params.MIPGap = 0.0004;            
+            obj.MILPParams = {params};
+         end
+
+         if nargin > 6
+            obj.AbsMIPGaps = absMIPGaps_;
+         else
+            obj.AbsMIPGaps = 10;            
+         end
+      end
+   end
+end