Develop

.github/workflows/UpdateTutorialIndex.yml

@@ -1,59 +1,59 @@
-name: Extract HTML Info
+# name: Extract HTML Info
 
-on:
-  push:
-    branches: gh-pages
-    paths:
-    - '**.html'
+# on:
+#   push:
+#     branches: gh-pages
+#     paths:
+#     - '**.html'
 
-jobs:
-  extract-info:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout Repository
-        uses: actions/checkout@v2
-        with:
-          token: ${{ secrets.GITHUB_TOKEN }}
-          fetch-depth: 0
-          ref: gh-pages
+# jobs:
+#   extract-info:
+#     runs-on: ubuntu-latest
+#     steps:
+#       - name: Checkout Repository
+#         uses: actions/checkout@v2
+#         with:
+#           token: ${{ secrets.GITHUB_TOKEN }}
+#           fetch-depth: 0
+#           ref: gh-pages
 
-      - name: Check Commit Message
-        id: check_msg
-        run: |
-          commit_msg=$(git log --format=%B -n 1)
-          if [[ "$commit_msg" == "Sync files from source repo" ]]; then
-            echo "run_job=true" >> $GITHUB_OUTPUT
-          else
-            echo "run_job=false" >> $GITHUB_OUTPUT
-          fi
+#       - name: Check Commit Message
+#         id: check_msg
+#         run: |
+#           commit_msg=$(git log --format=%B -n 1)
+#           if [[ "$commit_msg" == "Sync files from source repo" ]]; then
+#             echo "run_job=true" >> $GITHUB_OUTPUT
+#           else
+#             echo "run_job=false" >> $GITHUB_OUTPUT
+#           fi
 
-      - name: Set up Python
-        uses: actions/setup-python@v2
-        if: steps.check_msg.outputs.run_job == 'true'
-        with:
-          python-version: '3.x'
+#       - name: Set up Python
+#         uses: actions/setup-python@v2
+#         if: steps.check_msg.outputs.run_job == 'true'
+#         with:
+#           python-version: '3.x'
 
-      - name: Install Dependencies
-        if: steps.check_msg.outputs.run_job == 'true'
-        run: |
-          python -m pip install --upgrade pip
-          pip install beautifulsoup4
+#       - name: Install Dependencies
+#         if: steps.check_msg.outputs.run_job == 'true'
+#         run: |
+#           python -m pip install --upgrade pip
+#           pip install beautifulsoup4
 
-      - name: Get Changed HTML Files and update the index.html file of tutorial
-        id: getfile
-        if: steps.check_msg.outputs.run_job == 'true'
-        run: |
-          changed_files=$(git diff --name-only HEAD~1 HEAD | grep '\.html' | tr '\n' ' ')
-          for file in $changed_files; do
-              echo "Processing: $file"
-              python ./stable/extract_info.py $file
-          done
+#       - name: Get Changed HTML Files and update the index.html file of tutorial
+#         id: getfile
+#         if: steps.check_msg.outputs.run_job == 'true'
+#         run: |
+#           changed_files=$(git diff --name-only HEAD~1 HEAD | grep '\.html' | tr '\n' ' ')
+#           for file in $changed_files; do
+#               echo "Processing: $file"
+#               python ./stable/extract_info.py $file
+#           done
 
-      - name: Commit and Push New File
-        if: steps.check_msg.outputs.run_job == 'true'
-        run: |
-          git config user.name "github-actions[bot]"
-          git config user.email "github-actions[bot]@users.noreply.github.com"
-          git add .
-          git commit -m "Update Tutorial (Automatic Workflow)" || echo "No changes to commit"
-          git push
+#       - name: Commit and Push New File
+#         if: steps.check_msg.outputs.run_job == 'true'
+#         run: |
+#           git config user.name "github-actions[bot]"
+#           git config user.email "github-actions[bot]@users.noreply.github.com"
+#           git add .
+#           git commit -m "Update Tutorial (Automatic Workflow)" || echo "No changes to commit"
+#           git push

deprecated/_testOptCardinality/testMinCardinalityConservationRelaxationVector.m

@@ -0,0 +1,81 @@
+% The COBRAToolbox: minCardinalityConservationRelaxationVector.m
+%
+% Purpose:
+%     - tests the functionality of checkStoichiometricConsistency and minCardinalityConservationRelaxationVector
+%
+% Authors:
+%     - Ronan Fleming 06/11/2025
+%     - Farid Zare    03/03/2025 enhanced formatting
+%
+
+% save the current path
+currentDir = pwd;
+
+% initialize the test
+fileDir = fileparts(which('testMinCardinalityConservationRelaxationVector'));
+cd(fileDir);
+
+solverPkgs = prepareTest('needsLP', true, 'excludeSolvers', {'ibm_cplex'});
+
+for k = 1:length(solverPkgs.LP)
+
+    % change the COBRA solver (LP)
+    solverOK = changeCobraSolver(solverPkgs.LP{k}, 'LP', 0);
+
+    if solverOK
+
+        fprintf('   Testing checkStoichiometricConsistency and minCardinalityConservationRelaxationVector using solver %s...\n', solverPkgs.LP{k})
+        model = getDistributedModel('Recon3DModel_301.mat');
+
+        printLevel=0;
+
+        model = findSExRxnInd(model,[],printLevel-1);
+
+        N = model.S(:,model.SIntRxnBool);
+
+        %Recon3DModel_301 is stoichiometrically consistent, so check should be
+        %positive
+        [isConsistent, m, model] = checkStoichiometricConsistency(model, printLevel);
+        assert(isConsistent==1)
+
+        [mlt,nlt]=size(N');
+        feasTol = getCobraSolverParams('LP', 'feasTol');
+        param.eta=feasTol*100;
+        param.checkConsistency=0;
+        param.epsilon=1e-4;
+        param.nonRelaxBool=false(mlt,1);
+        param.checkFeasibility = 0;
+        param.printLevel=printLevel;
+
+        %Recon3DModel_301 is stoichiometrically consistent, so no relaxations
+        %should be needed
+        [relaxRxnBool, solutionRelax] = minCardinalityConservationRelaxationVector(N,param);
+        assert(nnz(relaxRxnBool)==0);
+
+
+        [relaxRxnBool, solutionRelax] = minCardinalityConservationRelaxationVector(N);
+        assert(nnz(relaxRxnBool)==0);
+
+        if solutionRelax.stat==1
+            %conserved if relaxation is below epsilon
+            relaxRxnBool=abs(solutionRelax.x)>=param.eta;
+            if printLevel>1
+                fprintf('%g%s\n',norm(N(:,~relaxRxnBool)'*solutionRelax.z),' = ||N''*z|| (should be zero)')
+            end
+            if printLevel>1
+                fprintf('%s\n',[int2str(nnz(relaxRxnBool)) '/' int2str(length(relaxRxnBool)) ' reactions relaxed.'])
+            end
+        else
+            disp(solutionRelax)
+            error('solve for minimum cardinality of conservation relaxation vector failed')
+        end
+
+        assert(isConsistent & nnz(relaxRxnBool)==0);
+
+        % output a success message
+        fprintf('Done.\n');
+
+    end
+end
+% change the directory
+cd(currentDir)

deprecated/_testOptCardinality/testOptCardinality.m

@@ -0,0 +1,168 @@
+% The COBRAToolbox: testOptCardinality.m
+%
+% Purpose:
+%     - tests optimiseCardinality
+%
+% Authors:
+%     - CI integration: Laurent Heirendt March 2018
+%
+param = struct();
+param.printLevel=3;
+
+% save the current path
+currentDir = pwd;
+
+% initialize the test
+fileDir = fileparts(which('testOptCardinality'));
+cd(fileDir);
+
+solverPkgs = prepareTest('needsLP', true, 'excludeSolvers', {'ibm_cplex'});
+
+for k = 1:length(solverPkgs.LP)
+
+    % change the COBRA solver (LP)
+    solverOK = changeCobraSolver(solverPkgs.LP{k}, 'LP', 0);
+
+    if solverOK
+
+        fprintf('   Testing optimizeCardinality & optimizeWeightedCardinality using solver %s...', solverPkgs.LP{k})
+
+
+        if 1
+            filename='Recon2.0model.mat';
+            if exist('Recon2.0model.mat','file')==2
+                model = getDistributedModel(filename);
+                model.csense(1:size(model.S,1),1)='E';
+            else
+                modelFolder = getDistributedModelFolder('ecoli_core_model.mat');
+                % define the filename of the model
+                modelFile = [modelFolder filesep 'ecoli_core_model.mat'];
+                model = readCbModel(modelFile, 'modelName','model');
+            end
+        end
+
+        %paramaters
+        feasTol = getCobraSolverParams('LP', 'feasTol');
+        param.eta = feasTol*1e5;
+        if 0
+            param.nbMaxIteration = 1000;
+            param.zeta = 1e-6;
+            param.theta   = 0.5;    %parameter of capped l1 approximation
+            param.epsilon = 1e-3;
+        end
+
+        % DC programming for solving the cardinality optimization problem
+        % The `l0` norm is approximated by capped-`l1` function.
+        % :math:`min c'(x, y, z) + lambda_0*||k.*x||_0 - delta_0*||d.*y||_0
+        %                        + lambda_1*||x||_1 + delta_1*||y||_1`
+        % s.t. :math:`A*(x, y, z) <= b`
+        % :math:`l <= (x,y,z) <= u`
+        % :math:`x in R^p, y in R^q, z in R^r`
+
+        %problem structure
+        [mlt,nlt]=size(model.S);
+        cardProblem.r=1;%first reaction is the objective
+        p=20;%minimise first 20 reactions
+        q=nlt-p-cardProblem.r;%maximise remainder of reactions
+        cardProblem.p=p;%minimise
+        cardProblem.q=q;%maximise
+        cardProblem.c=zeros(nlt,1);
+        cardProblem.c(1)=-1;%maximise biomass reaction
+        cardProblem.A=[model.S(:,model.c~=0),model.S(:,model.c==0)];%stick the objective first
+        cardProblem.b=zeros(mlt,1);
+        cardProblem.lb=-10*ones(nlt,1);
+        cardProblem.lb(1)=1;
+        cardProblem.ub= 10*ones(nlt,1);
+        cardProblem.csense(1:mlt,1)='E';
+
+        if isfield(cardProblem,'lambda')
+            cardProblem=rmfield(cardProblem,'lambda');
+        end
+        if isfield(cardProblem,'delta')
+            cardProblem=rmfield(cardProblem,'delta');
+        end
+
+        cardProblem.lambda=0;
+        cardProblem.delta=1;
+
+        if 1
+            if 1
+                solution = optimizeCardinality(cardProblem,param);
+                boolx=solution.x>=param.eta;
+                booly=solution.y>=param.eta;
+                reactionDifference=nnz(booly)-nnz(boolx);
+                disp(reactionDifference)
+            else
+                try
+                    solution = optimizeCardinality(cardProblem,param);
+                    if solution.stat==1
+                        boolx=solution.x>=param.eta;
+                        booly=solution.y>=param.eta;
+                        reactionDifference=nnz(booly)-nnz(boolx);
+                        %disp(reactionDifference)
+                        assert(reactionDifference==19)
+                    else
+                        error('optimizeCardinality failed')
+                    end
+                catch ME
+                    error('optimizeCardinality failed')
+                    assert(length(ME.message) > 0)
+                end
+            end
+        end
+        %                   * .lambda_0 - trade-off parameter of `||x||_0`
+        %                   * .lambda_1 - trade-off parameter of `||x||_1`
+        %                   * .delta_0 - trade-off parameter of `||y||_0`
+        %                   * .delta_1 - trade-off parameter of `||y||_1`
+        %                   * .k - `p x 1` strictly positive weight vector of `x`
+        %                   * .d - `q x 1` strictly positive weight vector of `y`
+
+        if 1
+            cardProblem.k = rand(p,1);
+            cardProblem.d  = rand(q,1);
+
+            solution = optimizeCardinality(cardProblem, param);
+            printLevel=1;
+            if solution.stat==1
+                boolx=solution.x>=param.eta;
+                booly=solution.y>=param.eta;
+                reactionDifference=nnz(booly)-nnz(boolx);
+                %disp(reactionDifference)
+            else
+                clear
+                error('weighted optimizeCardinality failed')
+            end
+        else
+            try
+                if 1
+                    cardProblem.k = rand(p,1);
+                    cardProblem.d  = rand(q,1);
+                else
+                    cardProblem.k =[0.353261921655910;0.136198199554603;0.161199215283406;0.701598054693234;0.963104300338750;0.848915285870358;0.355696281562873;0.604026370901761;0.863208270875165;0.820516602129050];
+                    cardProblem.d = [0.856726006637269;0.479222295857706;0.693250365030223;0.184194690365269;0.160038122601110;0.994929983836258;0.0661195204254679;0.992606041060040;0.217668082980991;0.885563825134152;0.337216530505868;0.316453801160968;0.310462944504509;0.713112858468648;0.663679819631847;0.717971113445466;0.104640343889781;0.700479020824193;0.0805864297824039;0.891195523125197;0.693880161746020;0.436474899335492;0.656991109467124;0.948094246708429;0.771053864583346;0.883352985815948;0.342974266018114;0.312664798117314;0.507688818213242;0.512523050276335;0.581846823390724;0.302786199140526;0.240719695561023;0.716435558175071;0.769903255623647;0.791240133987633;0.730011734034978;0.0484591628058197;0.286317855807064;0.648463862349204;0.551974518354735;0.704768997987814;0.949221753797141;0.403674635085002;0.874755823584694;0.0673360092347605;0.803867257560051;0.337409460743523;0.775432615766947;0.0619856321579906;0.575368119807765;0.550765711061938;0.799440812589458;0.378435388052920;0.534250510907493;0.950082837953587;0.121105671067707;0.361260315188684;0.144154618911642;0.588725242952198;0.545911394577834;0.336007538977284;0.294563063293066;0.570170186151889];
+                end
+                solution = optimizeCardinality(cardProblem, param);
+                printLevel=1;
+                if solution.stat==1
+                    boolx=solution.x>=param.eta;
+                    booly=solution.y>=param.eta;
+                    reactionDifference=nnz(booly)-nnz(boolx);
+                    %disp(reactionDifference)
+                    assert(reactionDifference==19)
+                else
+                    clear
+                    error('weighted optimizeCardinality failed')
+                end
+
+            catch ME
+                error('weighted optimizeCardinality failed')
+                assert(length(ME.message) > 0)
+            end
+        end
+        % output a success message
+        fprintf('Done.\n');
+
+    end
+end
+% change the directory
+cd(currentDir)

deprecated/_testTopology/loop3b_neg_eq.ext

@@ -0,0 +1,17 @@
+
+*lrs:lrslib v.7.1 2021.6.2(64bit,lrslong.h,hybrid arithmetic)
+*Input taken from  /home/farid/cobratoolbox-develop/test/additionalTests/testTopology/loop3b_neg_eq.ine
+loop3b
+*Input linearity in row 3 is redundant--converted to inequality
+V-representation
+linearity 1  1
+begin
+***** 4 rational
+ 0 -1  1  1 
+ 1  0  0  0 
+end
+*Totals: vertices=1 rays=0 bases=1 integer_vertices=1  linearities=1 vertices+rays+linearities=2
+*Dictionary Cache: max size= 1 misses= 0/0   Tree Depth= 0
+*Overflow checking on lrslong arithmetic
+*lrs:lrslib v.7.1 2021.6.2(64bit,lrslong.h,hybrid arithmetic)
+*0.001u 0.000s 1920Kb 2 flts 0 swaps 640 blks-in 8 blks-out 

deprecated/_testTopology/loop3b_neg_eq.ine

@@ -0,0 +1,9 @@
+loop3b
+H-representation
+linearity 3 1 2 3
+begin
+3 4 integer
+0 1 0 1
+0 -1 -1 0
+0 0 1 -1
+end