Absolute paths in test files and adapted test guide

hongzhonglu · May 1, 2017 · 6abdc77 · 6abdc77
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diff --git a/.github/guides/TESTGUIDE.md b/.github/guides/TESTGUIDE.md
@@ -72,11 +72,13 @@ A test template is readily available [here](https://github.com/opencobra/cobrato
 #### 2. Test initialization
 
 ````Matlab
+global CBTDIR
+
 % save the current path
 currentDir = pwd;
 
 % initialize the test
-cd(fileparts(which(mfilename)));
+cd(fileparts(which('fileName')));
 ````
 
 #### 3. Define the solver packages to be tested and the tolerance
@@ -93,7 +95,7 @@ solverPkgs = {'tomlab_cplex', 'glpk', 'gurobi6'};
 
 ```Matlab
 % load the model
-load('modelFile.mat', 'model');
+load([CBTDIR filesep 'test' filesep 'models' filesep 'testModel.mat'], 'model');
 load('testData_functionToBeTested.mat');
 ```
 

diff --git a/.github/guides/testTemplate.m b/.github/guides/testTemplate.m
@@ -7,6 +7,8 @@
 %     - <major change>: <your name> <date>
 %
 
+global CBTDIR
+
 % save the current path
 currentDir = pwd;
 
@@ -20,7 +22,7 @@
 solverPkgs = {'tomlab_cplex', 'glpk', 'gurobi6'};
 
 % load the model
-load('modelFile.mat', 'model');
+load([CBTDIR filesep 'test' filesep 'models' filesep 'testModel.mat'], 'model');
 load('testData_functionToBeTested.mat');
 
 %{

diff --git a/test/verifiedTests/testRBioNet/testGPR2Genes.m b/test/verifiedTests/testRBioNet/testGPR2Genes.m
@@ -8,6 +8,8 @@
 %     - Stefania Magnusdottir April 2017
 %
 
+global CBTDIR
+
 % save the current path
 currentDir = pwd;
 
@@ -16,7 +18,7 @@
 cd(fileDir);
 
 % load E. coli model
-load('ecoli_core_model.mat', 'model')
+load([CBTDIR filesep 'test' filesep 'models' filesep 'ecoli_core_model.mat'], 'model');
 
 % extract genes from grRules
 Genes = GPR2Genes(model.grRules);

diff --git a/test/verifiedTests/testRBioNet/testLegalRxnFormula.m b/test/verifiedTests/testRBioNet/testLegalRxnFormula.m
@@ -8,6 +8,8 @@
 %     - Stefania Magnusdottir April 2017
 %
 
+global CBTDIR
+
 % save the current path
 currentDir = pwd;
 
@@ -16,7 +18,7 @@
 cd(fileDir);
 
 % load E. coli model
-load('ecoli_core_model.mat', 'model')
+load([CBTDIR filesep 'test' filesep 'models' filesep 'ecoli_core_model.mat'], 'model');
 
 % check validity of reaction formulas
 formula = printRxnFormula(model, model.rxns(1));

diff --git a/test/verifiedTests/testRBioNet/testLoadReaction.m b/test/verifiedTests/testRBioNet/testLoadReaction.m
@@ -8,6 +8,8 @@
 %     - Stefania Magnusdottir April 2017
 %
 
+global CBTDIR
+
 % save the current path
 currentDir = pwd;
 
@@ -16,7 +18,7 @@
 cd(fileDir);
 
 % load E. coli model
-load('ecoli_core_model.mat', 'model')
+load([CBTDIR filesep 'test' filesep 'models' filesep 'ecoli_core_model.mat'], 'model');
 
 % load reaction and metabolite databases
 load([fileDir, filesep 'metab.mat'])

diff --git a/test/verifiedTests/testRBioNet/testModel2data.m b/test/verifiedTests/testRBioNet/testModel2data.m
@@ -8,6 +8,8 @@
 %     - Stefania Magnusdottir April 2017
 %
 
+global CBTDIR
+
 % save the current path
 currentDir = pwd;
 
@@ -22,7 +24,7 @@
 save([fileDir, filesep 'rBioNetSettingsDB.mat'], 'comp_path', 'met_path', 'rxn_path')
 
 % load E. coli model
-load('ecoli_core_model.mat', 'model');
+load([CBTDIR filesep 'test' filesep 'models' filesep 'ecoli_core_model.mat'], 'model');
 modelEcore = model;
 
 % model to data

diff --git a/test/verifiedTests/testRBioNet/testNeighborRxn2data.m b/test/verifiedTests/testRBioNet/testNeighborRxn2data.m
@@ -1,13 +1,15 @@
 % The COBRAToolbox: testNeighborRxn2data.m
 %
 % Purpose:
-%     - testNeighborRxn2data tests the functionality of neighborRxn2data in 
+%     - testNeighborRxn2data tests the functionality of neighborRxn2data in
 %       the rBioNet extension
 %
 % Authors:
 %     - Stefania Magnusdottir April 2017
 %
 
+global CBTDIR
+
 % save the current path
 currentDir = pwd;
 
@@ -16,7 +18,7 @@
 cd(fileDir);
 
 % load E. coli model
-load('ecoli_core_model.mat', 'model')
+load([CBTDIR filesep 'test' filesep 'models' filesep 'ecoli_core_model.mat'], 'model');
 
 % equires EC number field
 model.ecNumbers = cell(size(model.rxns));%requires EC number field