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jbreue16jbreue16
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Rename test reference data files consistently (#405)
1 parent 26756ce commit d386d67

19 files changed

+27
-27
lines changed

‎test/Crystallization.cpp‎

Lines changed: 22 additions & 22 deletions
Original file line numberDiff line numberDiff line change
@@ -31,7 +31,7 @@ const char* getTestDirectory();
3131
*/
3232
TEST_CASE("Crystallization in a CSTR with initial distribution and growth", "[Crystallization],[PBM],[Simulation],[Reference],[CI]")
3333
{
34-
const std::string& modelFilePath = std::string("/data/configuration_cry_CSTR_PBM_growth_benchmark1.json");
34+
const std::string& modelFilePath = std::string("/data/model_cry_CSTR_PBM_growth_benchmark1.json");
3535
const std::string& refFilePath = std::string("/data/ref_cry_CSTR_PBM_growth_benchmark1.h5");
3636
const std::vector<double> absTol = { 1e-10 };
3737
const std::vector<double> relTol = { 1e-10 };
@@ -42,7 +42,7 @@ TEST_CASE("Crystallization in a CSTR with initial distribution and growth", "[Cr
4242

4343
TEST_CASE("Crystallization in a CSTR with initial distribution and size-dependent growth", "[Crystallization],[PBM],[Simulation],[Reference],[CI]")
4444
{
45-
const std::string& modelFilePath = std::string("/data/configuration_cry_CSTR_PBM_growthSizeDep_benchmark1.json");
45+
const std::string& modelFilePath = std::string("/data/model_cry_CSTR_PBM_growthSizeDep_benchmark1.json");
4646
const std::string& refFilePath = std::string("/data/ref_cry_CSTR_PBM_growthSizeDep_benchmark1.h5");
4747
const std::vector<double> absTol = { 1e-10 };
4848
const std::vector<double> relTol = { 1e-10 };
@@ -53,7 +53,7 @@ TEST_CASE("Crystallization in a CSTR with initial distribution and size-dependen
5353

5454
TEST_CASE("Crystallization in a CSTR with primary nucleation and growth", "[Crystallization],[PBM],[Simulation],[Reference],[CI]")
5555
{
56-
const std::string& modelFilePath = std::string("/data/configuration_cry_CSTR_PBM_primaryNucleationAndGrowth_benchmark1.json");
56+
const std::string& modelFilePath = std::string("/data/model_cry_CSTR_PBM_primaryNucleationAndGrowth_benchmark1.json");
5757
const std::string& refFilePath = std::string("/data/ref_cry_CSTR_PBM_primaryNucleationAndGrowth_benchmark1.h5");
5858
const std::vector<double> absTol = { 1e-10 };
5959
const std::vector<double> relTol = { 1e-10 };
@@ -64,7 +64,7 @@ TEST_CASE("Crystallization in a CSTR with primary nucleation and growth", "[Crys
6464

6565
TEST_CASE("Crystallization in a CSTR with primary nucleation, growth and growth rate dispersion", "[Crystallization],[PBM],[Simulation],[Reference],[CI]")
6666
{
67-
const std::string& modelFilePath = std::string("/data/configuration_cry_CSTR_PBM_primaryNucleationGrowthGrowthRateDispersion_benchmark1.json");
67+
const std::string& modelFilePath = std::string("/data/model_cry_CSTR_PBM_primaryNucleationGrowthGrowthRateDispersion_benchmark1.json");
6868
const std::string& refFilePath = std::string("/data/ref_cry_CSTR_PBM_primaryNucleationGrowthGrowthRateDispersion_benchmark1.h5");
6969
const std::vector<double> absTol = { 1e-10 };
7070
const std::vector<double> relTol = { 1e-10 };
@@ -75,7 +75,7 @@ TEST_CASE("Crystallization in a CSTR with primary nucleation, growth and growth
7575

7676
TEST_CASE("Crystallization in a CSTR with primary and secondary nucleation and growth", "[Crystallization],[PBM],[Simulation],[Reference],[CI]")
7777
{
78-
const std::string& modelFilePath = std::string("/data/configuration_cry_CSTR_PBM_primarySecondaryNucleationAndGrowth_benchmark1.json");
78+
const std::string& modelFilePath = std::string("/data/model_cry_CSTR_PBM_primarySecondaryNucleationAndGrowth_benchmark1.json");
7979
const std::string& refFilePath = std::string("/data/ref_cry_CSTR_PBM_primarySecondaryNucleationAndGrowth_benchmark1.h5");
8080
const std::vector<double> absTol = { 5e+6 };
8181
const std::vector<double> relTol = { 1e-6 };
@@ -86,7 +86,7 @@ TEST_CASE("Crystallization in a CSTR with primary and secondary nucleation and g
8686

8787
TEST_CASE("Crystallization in a DPFR/LRM with primary and secondary nucleation and growth", "[CrysToFix0],[Crystallization],[PBM],[Simulation],[Reference],[CI]")
8888
{
89-
const std::string& modelFilePath = std::string("/data/configuration_cry_DPFR_PBM_primarySecondaryNucleationGrowth_benchmark1.json");
89+
const std::string& modelFilePath = std::string("/data/model_cry_DPFR_PBM_primarySecondaryNucleationGrowth_benchmark1.json");
9090
const std::string& refFilePath = std::string("/data/ref_cry_DPFR_PBM_primarySecondaryNucleationGrowth_benchmark1.h5");
9191
const std::vector<double> absTol = { 2e+8 };
9292
const std::vector<double> relTol = { 5e-6 };
@@ -98,7 +98,7 @@ TEST_CASE("Crystallization in a DPFR/LRM with primary and secondary nucleation a
9898
TEST_CASE("Crystallization Jacobian verification for a CSTR with initial distribution and growth", "[Crystallization],[PBM],[UnitOp],[Jacobian],[CI]")
9999
{
100100
// read json model setup file
101-
const std::string& modelFileRelPath = std::string("/data/configuration_cry_CSTR_PBM_growth_benchmark1.json");
101+
const std::string& modelFileRelPath = std::string("/data/model_cry_CSTR_PBM_growth_benchmark1.json");
102102
const std::string setupFile = std::string(getTestDirectory()) + modelFileRelPath;
103103
cadet::JsonParameterProvider pp_setup(cadet::JsonParameterProvider::fromFile(setupFile));
104104

@@ -116,7 +116,7 @@ TEST_CASE("Crystallization Jacobian verification for a CSTR with initial distrib
116116
TEST_CASE("Crystallization Jacobian verification for a CSTR with initial distribution and size-dependent growth", "[Crystallization],[PBM],[UnitOp],[Jacobian],[CI]")
117117
{
118118
// read json model setup file
119-
const std::string& modelFileRelPath = std::string("/data/configuration_cry_CSTR_PBM_growthSizeDep_benchmark1.json");
119+
const std::string& modelFileRelPath = std::string("/data/model_cry_CSTR_PBM_growthSizeDep_benchmark1.json");
120120
const std::string setupFile = std::string(getTestDirectory()) + modelFileRelPath;
121121
cadet::JsonParameterProvider pp_setup(cadet::JsonParameterProvider::fromFile(setupFile));
122122

@@ -134,7 +134,7 @@ TEST_CASE("Crystallization Jacobian verification for a CSTR with initial distrib
134134
TEST_CASE("Crystallization Jacobian verification for a CSTR with primary nucleation and growth", "[Crystallization],[PBM],[UnitOp],[Jacobian],[CI]")
135135
{
136136
// read json model setup file
137-
const std::string& modelFileRelPath = std::string("/data/configuration_cry_CSTR_PBM_primaryNucleationAndGrowth_benchmark1.json");
137+
const std::string& modelFileRelPath = std::string("/data/model_cry_CSTR_PBM_primaryNucleationAndGrowth_benchmark1.json");
138138
const std::string setupFile = std::string(getTestDirectory()) + modelFileRelPath;
139139
cadet::JsonParameterProvider pp_setup(cadet::JsonParameterProvider::fromFile(setupFile));
140140

@@ -152,7 +152,7 @@ TEST_CASE("Crystallization Jacobian verification for a CSTR with primary nucleat
152152
TEST_CASE("Crystallization Jacobian verification for a CSTR with primary nucleation, growth and growth rate dispersion", "[Crystallization],[PBM],[UnitOp],[Jacobian],[CI]")
153153
{
154154
// read json model setup file
155-
const std::string& modelFileRelPath = std::string("/data/configuration_cry_CSTR_PBM_primaryNucleationGrowthGrowthRateDispersion_benchmark1.json");
155+
const std::string& modelFileRelPath = std::string("/data/model_cry_CSTR_PBM_primaryNucleationGrowthGrowthRateDispersion_benchmark1.json");
156156
const std::string setupFile = std::string(getTestDirectory()) + modelFileRelPath;
157157
cadet::JsonParameterProvider pp_setup(cadet::JsonParameterProvider::fromFile(setupFile));
158158

@@ -170,7 +170,7 @@ TEST_CASE("Crystallization Jacobian verification for a CSTR with primary nucleat
170170
TEST_CASE("Crystallization Jacobian verification for a CSTR with primary and secondary nucleation and growth", "[Crystallization],[PBM],[UnitOp],[Jacobian],[CI]")
171171
{
172172
// read json model setup file
173-
const std::string& modelFileRelPath = std::string("/data/configuration_cry_CSTR_PBM_primarySecondaryNucleationAndGrowth_benchmark1.json");
173+
const std::string& modelFileRelPath = std::string("/data/model_cry_CSTR_PBM_primarySecondaryNucleationAndGrowth_benchmark1.json");
174174
const std::string setupFile = std::string(getTestDirectory()) + modelFileRelPath;
175175
cadet::JsonParameterProvider pp_setup(cadet::JsonParameterProvider::fromFile(setupFile));
176176

@@ -188,7 +188,7 @@ TEST_CASE("Crystallization Jacobian verification for a CSTR with primary and sec
188188
TEST_CASE("Crystallization Jacobian verification for a DPFR/LRM with primary and secondary nucleation and growth", "[Crystallization1],[UnitOp],[Jacobian],[CI]")
189189
{
190190
// read json model setup file
191-
const std::string& modelFileRelPath = std::string("/data/configuration_cry_DPFR_PBM_primarySecondaryNucleationGrowth_benchmark1.json");
191+
const std::string& modelFileRelPath = std::string("/data/model_cry_DPFR_PBM_primarySecondaryNucleationGrowth_benchmark1.json");
192192
const std::string setupFile = std::string(getTestDirectory()) + modelFileRelPath;
193193
cadet::JsonParameterProvider pp_setup(cadet::JsonParameterProvider::fromFile(setupFile));
194194

@@ -207,7 +207,7 @@ TEST_CASE("Crystallization Jacobian verification for a DPFR/LRM with primary and
207207
*/
208208
TEST_CASE("Crystallization Aggregation in a CSTR", "[Crystallization],[Aggregation],[Simulation],[Reference],[CI]")
209209
{
210-
const std::string& modelFilePath = std::string("/data/configuration_cry_CSTR_aggregation_benchmark1.json");
210+
const std::string& modelFilePath = std::string("/data/model_cry_CSTR_aggregation_benchmark1.json");
211211
const std::string& refFilePath = std::string("/data/ref_cry_CSTR_aggregation_benchmark1.h5");
212212
const std::vector<double> absTol = { 1e-10 };
213213
const std::vector<double> relTol = { 1e-10 };
@@ -219,7 +219,7 @@ TEST_CASE("Crystallization Aggregation in a CSTR", "[Crystallization],[Aggregati
219219
TEST_CASE("Crystallization Jacobian verification for Aggregation in a CSTR", "[Crystallization],[Aggregation],[UnitOp],[Jacobian],[CI]")
220220
{
221221
// read json model setup file
222-
const std::string& modelFileRelPath = std::string("/data/configuration_cry_CSTR_aggregation_benchmark1.json");
222+
const std::string& modelFileRelPath = std::string("/data/model_cry_CSTR_aggregation_benchmark1.json");
223223
const std::string setupFile = std::string(getTestDirectory()) + modelFileRelPath;
224224
cadet::JsonParameterProvider pp_setup(cadet::JsonParameterProvider::fromFile(setupFile));
225225

@@ -237,7 +237,7 @@ TEST_CASE("Crystallization Jacobian verification for Aggregation in a CSTR", "[C
237237
*/
238238
TEST_CASE("Crystallization Fragmentation in a CSTR", "[Crystallization],[Fragmentation],[Simulation],[Reference],[CI]")
239239
{
240-
const std::string& modelFilePath = std::string("/data/configuration_cry_CSTR_fragmentation_benchmark1.json");
240+
const std::string& modelFilePath = std::string("/data/model_cry_CSTR_fragmentation_benchmark1.json");
241241
const std::string& refFilePath = std::string("/data/ref_cry_CSTR_fragmentation_benchmark1.h5");
242242
const std::vector<double> absTol = { 1e-7 };
243243
const std::vector<double> relTol = { 1e-7 };
@@ -249,7 +249,7 @@ TEST_CASE("Crystallization Fragmentation in a CSTR", "[Crystallization],[Fragmen
249249
TEST_CASE("Crystallization Jacobian verification for Fragmentation in a CSTR", "[Crystallization],[Fragmentation],[UnitOp],[Jacobian],[CI]")
250250
{
251251
// read json model setup file
252-
const std::string& modelFileRelPath = std::string("/data/configuration_cry_CSTR_fragmentation_benchmark1.json");
252+
const std::string& modelFileRelPath = std::string("/data/model_cry_CSTR_fragmentation_benchmark1.json");
253253
const std::string setupFile = std::string(getTestDirectory()) + modelFileRelPath;
254254
cadet::JsonParameterProvider pp_setup(cadet::JsonParameterProvider::fromFile(setupFile));
255255

@@ -267,7 +267,7 @@ TEST_CASE("Crystallization Jacobian verification for Fragmentation in a CSTR", "
267267
*/
268268
TEST_CASE("Crystallization combined Aggregation and Fragmentation in a CSTR", "[Crystallization],[AggFrag],[Simulation],[Reference],[CI]")
269269
{
270-
const std::string& modelFilePath = std::string("/data/configuration_cry_CSTR_aggFrag_benchmark1.json");
270+
const std::string& modelFilePath = std::string("/data/model_cry_CSTR_aggFrag_benchmark1.json");
271271
const std::string& refFilePath = std::string("/data/ref_cry_CSTR_aggFrag_benchmark1.h5");
272272
const std::vector<double> absTol = { 1e-8 };
273273
const std::vector<double> relTol = { 1e-8 };
@@ -279,7 +279,7 @@ TEST_CASE("Crystallization combined Aggregation and Fragmentation in a CSTR", "[
279279
TEST_CASE("Crystallization Jacobian verification for combined Aggregation and Fragmentation in a CSTR", "[Crystallization],[AggFrag],[UnitOp],[Jacobian],[CI]")
280280
{
281281
// read json model setup file
282-
const std::string& modelFileRelPath = std::string("/data/configuration_cry_CSTR_aggFrag_benchmark1.json");
282+
const std::string& modelFileRelPath = std::string("/data/model_cry_CSTR_aggFrag_benchmark1.json");
283283
const std::string setupFile = std::string(getTestDirectory()) + modelFileRelPath;
284284
cadet::JsonParameterProvider pp_setup(cadet::JsonParameterProvider::fromFile(setupFile));
285285

@@ -297,7 +297,7 @@ TEST_CASE("Crystallization Jacobian verification for combined Aggregation and Fr
297297
*/
298298
TEST_CASE("Crystallization combined PBM, Aggregation and Fragmentation in a CSTR", "[Crystallization],[PBMAggFrag],[Simulation],[Reference],[CI]")
299299
{
300-
const std::string& modelFilePath = std::string("/data/configuration_cry_CSTR_PBM_Agg_Frag_benchmark1.json");
300+
const std::string& modelFilePath = std::string("/data/model_cry_CSTR_PBM_Agg_Frag_benchmark1.json");
301301
const std::string& refFilePath = std::string("/data/ref_cry_CSTR_PBM_Agg_Frag_benchmark1.h5");
302302
const std::vector<double> absTol = { 2e-7 };
303303
const std::vector<double> relTol = { 8e-1 };
@@ -309,7 +309,7 @@ TEST_CASE("Crystallization combined PBM, Aggregation and Fragmentation in a CSTR
309309
TEST_CASE("Crystallization Jacobian verification for combined PBM, Aggregation and Fragmentation in a CSTR", "[Crystallization],[PBMAggFrag],[UnitOp],[Jacobian],[CI]")
310310
{
311311
// read json model setup file
312-
const std::string& modelFileRelPath = std::string("/data/configuration_cry_CSTR_PBM_Agg_Frag_benchmark1.json");
312+
const std::string& modelFileRelPath = std::string("/data/model_cry_CSTR_PBM_Agg_Frag_benchmark1.json");
313313
const std::string setupFile = std::string(getTestDirectory()) + modelFileRelPath;
314314
cadet::JsonParameterProvider pp_setup(cadet::JsonParameterProvider::fromFile(setupFile));
315315

@@ -327,7 +327,7 @@ TEST_CASE("Crystallization Jacobian verification for combined PBM, Aggregation a
327327
*/
328328
TEST_CASE("Crystallization combined PBM and Aggregation in a DPFR", "[Crystallization],[DPFR_PBMAgg],[Simulation],[Reference],[CI]")
329329
{
330-
const std::string& modelFilePath = std::string("/data/configuration_cry_DPFR_PBM_aggregation_benchmark1.json");
330+
const std::string& modelFilePath = std::string("/data/model_cry_DPFR_PBM_aggregation_benchmark1.json");
331331
const std::string& refFilePath = std::string("/data/ref_cry_DPFR_PBM_aggregation_benchmark1.h5");
332332
const std::vector<double> absTol = { 1E+10 }; // we need to define a (high) tolerances as the numerical values in this test are extremely high, values of up to xE+27
333333
const std::vector<double> relTol = { 1E-12 };
@@ -339,7 +339,7 @@ TEST_CASE("Crystallization combined PBM and Aggregation in a DPFR", "[Crystalliz
339339
TEST_CASE("Crystallization Jacobian verification for combined PBM and Aggregation in a DPFR", "[Crystallization],[DPFR_PBMAgg],[UnitOp],[Jacobian],[CI]")
340340
{
341341
// read json model setup file
342-
const std::string& modelFileRelPath = std::string("/data/configuration_cry_DPFR_PBM_aggregation_benchmark1.json");
342+
const std::string& modelFileRelPath = std::string("/data/model_cry_DPFR_PBM_aggregation_benchmark1.json");
343343
const std::string setupFile = std::string(getTestDirectory()) + modelFileRelPath;
344344
cadet::JsonParameterProvider pp_setup(cadet::JsonParameterProvider::fromFile(setupFile));
345345

‎test/ReactionModels.cpp‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -80,8 +80,8 @@ TEST_CASE("MassActionLaw kinetic analytic Jacobian vs AD", "[MassActionLaw],[Rea
8080

8181
TEST_CASE("MichaelisMenten kinetic and specific mass action law micro-kinetics yield same result", "[MichaelisMenten],[ReactionModel],[Simulation],[CI]")
8282
{
83-
const std::string& configFilePath1 = std::string("/data/configuration_CSTR_MichaelisMenten_benchmark1.json");
84-
const std::string& configFilePath2 = std::string("/data/configuration_CSTR_MicroKineticsSMA_benchmark1.json");
83+
const std::string& configFilePath1 = std::string("/data/model_CSTR_MichaelisMenten_benchmark1.json");
84+
const std::string& configFilePath2 = std::string("/data/model_CSTR_MicroKineticsSMA_benchmark1.json");
8585

8686
const double absTol = 1e-12;
8787
const double relTol = 5e-4;
@@ -91,8 +91,8 @@ TEST_CASE("MichaelisMenten kinetic and specific mass action law micro-kinetics y
9191

9292
TEST_CASE("MichaelisMenten kinetic with two inhibitors and specific mass action law micro-kinetics yield same result", "[MichaelisMenten],[ReactionModel],[Simulation],[Reference],[CI]")
9393
{
94-
const std::string& configFilePath1 = std::string("/data/configuration_CSTR_MichaelisMenten_twoInhib_benchmark1.json");
95-
const std::string& configFilePath2 = std::string("/data/configuration_CSTR_MicroKineticsSMA_twoInhib_benchmark1.json");
94+
const std::string& configFilePath1 = std::string("/data/model_CSTR_MichaelisMenten_twoInhib_benchmark1.json");
95+
const std::string& configFilePath2 = std::string("/data/model_CSTR_MicroKineticsSMA_twoInhib_benchmark1.json");
9696

9797
const double absTol = 1e-3;
9898
const double relTol = 5e-4;
@@ -102,7 +102,7 @@ TEST_CASE("MichaelisMenten kinetic with two inhibitors and specific mass action
102102

103103
TEST_CASE("MichaelisMenten kinetic and numerical reference with Crank-Nicolson yield same result", "[MichaelisMenten],[ReactionModel],[Simulation],[Reference],[CI]")
104104
{
105-
const std::string& configFileRelPath = std::string("/data/configuration_CSTR_MichaelisMenten_benchmark2.json");
105+
const std::string& configFileRelPath = std::string("/data/model_CSTR_MichaelisMenten_benchmark2.json");
106106
const std::string& refFileRelPath = std::string("/data/ref_CSTR_MichaelisMenten_benchmark2.h5");
107107

108108
const double absTol = 1e-3;

test/data/configuration_CSTR_MichaelisMenten_benchmark1.json renamed to test/data/model_CSTR_MichaelisMenten_benchmark1.json

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test/data/configuration_CSTR_MichaelisMenten_benchmark2.json renamed to test/data/model_CSTR_MichaelisMenten_benchmark2.json

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test/data/configuration_CSTR_MichaelisMenten_twoInhib_benchmark1.json renamed to test/data/model_CSTR_MichaelisMenten_twoInhib_benchmark1.json

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test/data/configuration_CSTR_MicroKineticsSMA_benchmark1.json renamed to test/data/model_CSTR_MicroKineticsSMA_benchmark1.json

File renamed without changes.

test/data/configuration_CSTR_MicroKineticsSMA_twoInhib_benchmark1.json renamed to test/data/model_CSTR_MicroKineticsSMA_twoInhib_benchmark1.json

File renamed without changes.

test/data/configuration_cry_CSTR_PBM_Agg_Frag_benchmark1.json renamed to test/data/model_cry_CSTR_PBM_Agg_Frag_benchmark1.json

File renamed without changes.

test/data/configuration_cry_CSTR_PBM_growthSizeDep_benchmark1.json renamed to test/data/model_cry_CSTR_PBM_growthSizeDep_benchmark1.json

File renamed without changes.

test/data/configuration_cry_CSTR_PBM_growth_benchmark1.json renamed to test/data/model_cry_CSTR_PBM_growth_benchmark1.json

File renamed without changes.

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