consolidate tests/test1 directory for NFsim

virtualcell · Jul 25, 2024 · 28c9532 · 28c9532
1 parent f2b1583
commit 28c9532
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Showing 5 changed files with 31 additions and 7 deletions.
diff --git a/NFsim_v1.11/CMakeLists.txt b/NFsim_v1.11/CMakeLists.txt
@@ -94,7 +94,7 @@ enable_testing()
 add_executable(${exe_target} ${SRC_FILES})
 target_link_libraries(${exe_target} vcommons vcellmessaging)
 
-add_test(NAME ${exe_target}_test1 COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/tests/test1.sh ${CMAKE_BINARY_DIR}/bin/${exe_target} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/tests)
+add_test(NAME ${exe_target}_test1 COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/tests/test1/test1.sh ${CMAKE_BINARY_DIR}/bin/${exe_target} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/tests/test1)
 
 install(TARGETS ${exe_target} RUNTIME DESTINATION ${OPTION_EXE_DIRECTORY})
 
diff --git a/NFsim_v1.11/tests/test1/SimID_273069657_0_.gdat.expected b/NFsim_v1.11/tests/test1/SimID_273069657_0_.gdat.expected
@@ -0,0 +1,12 @@
+#          time O0_MT0_tot_Count O0_MT1_tot_Count O0_MT2_tot_Count O0_MT3_tot_Count O0_MT4_tot_Count        s0_Count        s1_Count        s2_Count        s3_Count        s4_Count
+ 0.00000000e+00  6.02000000e+02  9.03000000e+02  1.20400000e+03  0.00000000e+00  0.00000000e+00  6.02000000e+02  9.03000000e+02  1.20400000e+03  0.00000000e+00  0.00000000e+00
+ 1.00000000e-01  5.37000000e+02  9.68000000e+02  1.13900000e+03  0.00000000e+00  0.00000000e+00  5.37000000e+02  9.68000000e+02  1.13900000e+03  0.00000000e+00  0.00000000e+00
+ 2.00000000e-01  5.24000000e+02  9.81000000e+02  1.12600000e+03  0.00000000e+00  0.00000000e+00  5.24000000e+02  9.81000000e+02  1.12600000e+03  0.00000000e+00  0.00000000e+00
+ 3.00000000e-01  5.23000000e+02  9.82000000e+02  1.12500000e+03  0.00000000e+00  0.00000000e+00  5.23000000e+02  9.82000000e+02  1.12500000e+03  0.00000000e+00  0.00000000e+00
+ 4.00000000e-01  5.30000000e+02  9.75000000e+02  1.13200000e+03  0.00000000e+00  0.00000000e+00  5.30000000e+02  9.75000000e+02  1.13200000e+03  0.00000000e+00  0.00000000e+00
+ 5.00000000e-01  5.23000000e+02  9.82000000e+02  1.12500000e+03  0.00000000e+00  0.00000000e+00  5.23000000e+02  9.82000000e+02  1.12500000e+03  0.00000000e+00  0.00000000e+00
+ 6.00000000e-01  5.21000000e+02  9.84000000e+02  1.12300000e+03  0.00000000e+00  0.00000000e+00  5.21000000e+02  9.84000000e+02  1.12300000e+03  0.00000000e+00  0.00000000e+00
+ 7.00000000e-01  5.20000000e+02  9.85000000e+02  1.12200000e+03  0.00000000e+00  0.00000000e+00  5.20000000e+02  9.85000000e+02  1.12200000e+03  0.00000000e+00  0.00000000e+00
+ 8.00000000e-01  5.13000000e+02  9.92000000e+02  1.11500000e+03  0.00000000e+00  0.00000000e+00  5.13000000e+02  9.92000000e+02  1.11500000e+03  0.00000000e+00  0.00000000e+00
+ 9.00000000e-01  5.13000000e+02  9.92000000e+02  1.11500000e+03  0.00000000e+00  0.00000000e+00  5.13000000e+02  9.92000000e+02  1.11500000e+03  0.00000000e+00  0.00000000e+00
+ 1.00000000e+00  5.33000000e+02  9.72000000e+02  1.13500000e+03  0.00000000e+00  0.00000000e+00  5.33000000e+02  9.72000000e+02  1.13500000e+03  0.00000000e+00  0.00000000e+00
diff --git a/.../tests/data/SimID_273069657_0_.nfsimInput → ...tests/test1/SimID_273069657_0_.nfsimInput b/.../tests/data/SimID_273069657_0_.nfsimInput → ...tests/test1/SimID_273069657_0_.nfsimInput
diff --git a/NFsim_v1.11/tests/test1/SimID_273069657_0_.species.expected b/NFsim_v1.11/tests/test1/SimID_273069657_0_.species.expected
@@ -0,0 +1,5 @@
+# nfsim generated species list for system: 'nameless'
+# warning! this feature is not yet fully tested! 
+MT0(AAA~c0,AAB~0)  532
+MT1(AAA~c0,AAB~0)  973
+MT2(AAA~c0,AAB~0)  1134
diff --git a/NFsim_v1.11/tests/test1.sh → NFsim_v1.11/tests/test1/test1.sh b/NFsim_v1.11/tests/test1.sh → NFsim_v1.11/tests/test1/test1.sh
@@ -1,12 +1,15 @@
 #!/bin/bash
 set -e
-set -x
 EXE=$1
-INPUT="data/SimID_273069657_0_.nfsimInput"
-OUTPUT="data/SimID_273069657_0_.gdat"
-EXPECTED_OUTPUT="data/SimID_273069657_0_.gdat.expected"
-SPECIES="data/SimID_273069657_0_.species"
-EXPECTED_SPECIES="data/SimID_273069657_0_.species.expected"
+
+# get the directory of this script
+TEST_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+
+INPUT="${TEST_DIR}/SimID_273069657_0_.nfsimInput"
+OUTPUT="${TEST_DIR}/SimID_273069657_0_.gdat"
+EXPECTED_OUTPUT="${TEST_DIR}/SimID_273069657_0_.gdat.expected"
+SPECIES="${TEST_DIR}/SimID_273069657_0_.species"
+EXPECTED_SPECIES="${TEST_DIR}/SimID_273069657_0_.species.expected"
 
 if [ ! -f $EXE ]; then
     echo "NFsim executable $EXE not found. Exiting..."
@@ -27,6 +30,7 @@ fi
 
 
 command="$EXE -seed 505790288 -vcell -xml $INPUT -o $OUTPUT -sim 1.0 -ss $SPECIES -oStep 20 -notf -utl 1000 -cb -pcmatch -tid 0"
+echo $command
 if ! $command; then
     echo "NFsim failed to run. Exiting..."
     exit 1
@@ -51,3 +55,6 @@ if ! diff $SPECIES $EXPECTED_SPECIES; then
     echo "Species file $SPECIES does not match expected species $EXPECTED_SPECIES. Exiting..."
     exit 1
 fi
+
+echo "NFsim solver complted and solution matched expected output. Exiting..."
+exit 0