def testNoArgs(self):
with capture_stderr(main, []) as output:
self.assertTrue(
"WARNING: Problems reading file: Could not read file" in
output)
with capture_stdout(main, []) as output:
self.assertTrue("optional arguments" in output)
def testDefInp(self):
try:
with capture_stdout(main, ["-f", DEF_INPUT]) as output:
self.assertTrue(GOOD_OUT in output)
self.assertFalse(diff_lines(CSV_OUT, GOOD_CSV_OUT))
finally:
silent_remove(CSV_OUT, disable=DISABLE_REMOVE)
def testMultFileToPDBXYZ(self):
# When checking output, ignore differences in version and time
try:
test_input = ["-c", MULT_2PDB_INI]
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stdout(main, test_input) as output:
self.assertTrue(
'"tests/test_data/cp2k_proc/glu_2.5_1.0.out",-283.341542,"False","False"'
in output)
self.assertTrue(
'"tests/test_data/cp2k_proc/glu_2.5_1.05-1.out",-283.526959,"True","True"'
in output)
diffs = diff_lines(GLU_PDB_OUT, GOOD_GLU_PDB_OUT)
diffs1 = diff_lines(GLU_PDB_OUT2, GOOD_GLU_PDB_OUT2)
for diff_list in [diffs, diffs1]:
self.assertEqual(len(diff_list), 2)
self.assertTrue("Created on " in diff_list[0])
self.assertFalse(diff_lines(GLU_XYZ_OUT, GOOD_GLU_XYZ_OUT))
finally:
silent_remove(GLU_PDB_OUT, disable=DISABLE_REMOVE)
silent_remove(GLU_PDB_OUT1, disable=DISABLE_REMOVE)
silent_remove(GLU_PDB_OUT2, disable=DISABLE_REMOVE)
silent_remove(GLU_XYZ_OUT, disable=DISABLE_REMOVE)
silent_remove(GLU_XYZ_OUT1, disable=DISABLE_REMOVE)
silent_remove(GLU_XYZ_OUT2, disable=DISABLE_REMOVE)
def testDefInp(self):
try:
with capture_stdout(main, ["-f", DEF_INPUT, "-c", DEF_INI]) as output:
self.assertTrue("Keeping 2 of 4 rows based on filtering criteria" in output)
self.assertFalse(diff_lines(CSV_OUT, GOOD_CSV_OUT))
finally:
silent_remove(CSV_OUT)
def testMissingFileList(self):
test_input = ["-l", " "]
with capture_stdout(main, test_input) as output:
self.assertTrue("show this help message" in output)
with capture_stderr(main, test_input) as output:
self.assertTrue(
"Specified file listing cp2k force files missing" in output)
def testNoIni(self):
test_input = []
with capture_stdout(main, test_input) as output:
self.assertTrue("optional arguments:" in output)
with capture_stderr(main, test_input) as output:
self.assertTrue(
"Problems reading file: Could not read file" in output)
def testMaxTimestepsCalcHIJ(self):
try:
with capture_stdout(main, ["-c", HIJ_INI]) as output:
self.assertTrue("Reached the maximum timesteps" in output)
self.assertFalse(diff_lines(HIJ_OUT, GOOD_HIJ_OUT))
finally:
silent_remove(HIJ_OUT, disable=DISABLE_REMOVE)
def testNoSuchOption(self):
# main(["-@", DEF_OUT])
with capture_stderr(main, ["-@", DEF_OUT]) as output:
self.assertTrue("unrecognized argument" in output)
self.assertTrue(DEF_OUT in output)
with capture_stdout(main, ["-@", DEF_OUT]) as output:
self.assertTrue("optional arguments" in output)
def testMaxTimestepsCalcHIJ(self):
try:
with capture_stdout(main, ["-c", HIJ_INI]) as output:
self.assertTrue("Reached the maximum timesteps" in output)
self.assertFalse(diff_lines(HIJ_OUT, GOOD_HIJ_OUT))
finally:
silent_remove(HIJ_OUT, disable=DISABLE_REMOVE)
def testDefInp(self):
try:
with capture_stdout(main, ["-f", DEF_INPUT]) as output:
self.assertTrue(GOOD_OUT in output)
self.assertFalse(diff_lines(CSV_OUT, GOOD_CSV_OUT))
finally:
silent_remove(CSV_OUT, disable=DISABLE_REMOVE)
def testCheckCharge(self):
try:
with capture_stdout(main, ["-c", CHECK_CHARGE_INI]) as output:
self.assertFalse("total charge" in output)
finally:
silent_remove(VMD_OUT)
silent_remove(WATER_OUT)
def testHelp(self):
test_input = ['-h']
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertFalse(output)
with capture_stdout(main, test_input) as output:
self.assertTrue("optional arguments" in output)
def testHelp(self):
test_input = ['-h']
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertFalse(output)
with capture_stdout(main, test_input) as output:
self.assertTrue("optional arguments" in output)
def testNoArgs(self):
test_input = []
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue("Could not read file" in output)
with capture_stdout(main, test_input) as output:
self.assertTrue("optional arguments" in output)
def testDefInpWithBuffer(self):
try:
with capture_stdout(main, ["-f", DEF_INPUT, "-b", "6"]) as output:
self.assertTrue('Max plus 6.0 buffer:'
' 17.891000 21.605000 24.314000' in output)
self.assertFalse(diff_lines(CSV_OUT, GOOD_CSV_BUFFER_OUT))
finally:
silent_remove(CSV_OUT, disable=DISABLE_REMOVE)
def testNoArgs(self):
test_input = []
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue("Could not read file" in output)
with capture_stdout(main, test_input) as output:
self.assertTrue("optional arguments" in output)
def testMissingConfig(self):
test_input = ["-c", INCOMP_INI_PATH]
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue("Missing config val" in output)
with capture_stdout(main, test_input) as output:
self.assertTrue("optional arguments" in output)
def testReorderAtoms(self):
try:
with capture_stdout(main, ["-c", DEF_INI]) as output:
for message in WATER_OUT_OF_ORDER_MESSAGES:
self.assertFalse(message in output)
self.assertFalse(diff_lines(DEF_OUT, GOOD_OUT))
finally:
silent_remove(DEF_OUT)
def testNoIni(self):
test_input = []
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stdout(main, test_input) as output:
self.assertTrue("usage:" in output)
with capture_stderr(main, test_input) as output:
self.assertTrue("Problems reading file: Could not read file" in output)
def testDefInpWithBuffer(self):
try:
with capture_stdout(main, ["-f", DEF_INPUT, "-b", "6"]) as output:
self.assertTrue('Max plus 6.0 buffer:'
' 17.891000 21.605000 24.314000' in output)
self.assertFalse(diff_lines(CSV_OUT, GOOD_CSV_BUFFER_OUT))
finally:
silent_remove(CSV_OUT, disable=DISABLE_REMOVE)
def testMissingInfo(self):
test_input = ["-c", INCOMP_INI]
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue("Missing config val for key 'prot_res_mol_id'" in output)
with capture_stdout(main, test_input) as output:
self.assertTrue("optional arguments" in output)
def testNoArgs(self):
test_input = []
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stdout(main, test_input) as output:
self.assertTrue("arguments:" in output)
with capture_stderr(main, test_input) as output:
self.assertTrue("required" in output)
def testInvalidData(self):
test_input = ["-c", INVALID_INI]
with capture_stderr(main, test_input) as output:
self.assertTrue(
"Problem with config vals on key h3o_o_type: invalid literal for int"
in output)
with capture_stdout(main, test_input) as output:
self.assertTrue("optional arguments" in output)
def testMissingConfig(self):
test_input = ["-c", INCOMP_INI_PATH]
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue("Missing config val for key 'water_o_type'" in output)
with capture_stdout(main, test_input) as output:
self.assertTrue("optional arguments" in output)
def testNoIni(self):
test_input = []
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stdout(main, test_input) as output:
self.assertTrue("usage:" in output)
with capture_stderr(main, test_input) as output:
self.assertTrue(
"Problems reading file: Could not read file" in output)
def testMissingInfo(self):
test_input = ["-c", INCOMP_INI]
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue(
"Missing config val for key 'prot_res_mol_id'" in output)
with capture_stdout(main, test_input) as output:
self.assertTrue("optional arguments" in output)
def testNoSuchOption(self):
test_input = ["-@", DEF_OUT]
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue("unrecognized argument" in output)
self.assertTrue(DEF_OUT in output)
with capture_stdout(main, test_input) as output:
self.assertTrue("optional arguments" in output)
def testCheckCharge(self):
try:
test_input = ["-c", CHECK_CHARGE_INI]
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stdout(main, test_input) as output:
self.assertFalse("total charge" in output)
finally:
silent_remove(VMD_OUT, disable=DISABLE_REMOVE)
silent_remove(WATER_OUT, disable=DISABLE_REMOVE)
def testHO_OO_HH_OHGofR_MaxSteps(self):
test_input = ["-c", HO_OO_HH_OH_GOFR_INI_MAX_STEPS]
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
try:
with capture_stdout(main, test_input) as output:
self.assertTrue(good_long_out_msg in output)
self.assertFalse(diff_lines(DEF_MAX_STEPS_OUT, GOOD_HO_OO_HH_OH_GOFR_OUT_MAX_STEPS))
finally:
silent_remove(DEF_MAX_STEPS_OUT, disable=DISABLE_REMOVE)
def testCsvHeader(self):
"""
This input file has a header that starts with a '#' so is ignored by np.loadtxt
"""
try:
with capture_stdout(main, ["-f", CSV_HEADER_INPUT, "-n", "-d", ","]) as output:
self.assertTrue(GOOD_OUT in output)
self.assertFalse(diff_lines(CSV_HEADER_OUT, GOOD_CSV_HEADER_OUT))
finally:
silent_remove(CSV_HEADER_OUT, disable=DISABLE_REMOVE)
def testMMAfterQM(self):
test_input = ["-f", GLU_FILE_MM_AFTER_QM, "-n", GLU_ATOM_NUM]
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
try:
with capture_stdout(main, test_input) as output:
self.assertTrue("1429 44 0.065 -0.677 -0.401 0.789" in output)
self.assertFalse(diff_lines(GLU_2MM_AFTER_QM_OUT, GOOD_GLU_2QM_OUT, delimiter=" "))
finally:
silent_remove(GLU_2MM_AFTER_QM_OUT, disable=DISABLE_REMOVE)
def testRelativeEnergy(self):
try:
test_input = ["-c", REL_E_INI]
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stdout(main, test_input) as output:
self.assertTrue("44.822" in output)
self.assertFalse(diff_lines(REL_E_OUT, GOOD_REL_E_OUT))
finally:
silent_remove(REL_E_OUT, disable=DISABLE_REMOVE)
def testCsvHeader(self):
"""
This input file has a header that starts with a '#' so is ignored by np.loadtxt
"""
try:
with capture_stdout(main, ["-f", CSV_HEADER_INPUT, "-n", "-d", ","]) as output:
self.assertTrue(GOOD_OUT in output)
self.assertFalse(diff_lines(CSV_HEADER_OUT, GOOD_CSV_HEADER_OUT))
finally:
silent_remove(CSV_HEADER_OUT, disable=DISABLE_REMOVE)
def testGood(self):
try:
# main(["-c", DEF_INI])
with capture_stdout(main, ["-c", DEF_INI]) as output:
self.assertTrue("total charge" in output)
self.assertFalse(diff_lines(VMD_OUT, GOOD_VMD_OUT))
self.assertFalse(diff_lines(WATER_OUT, GOOD_WATER_OUT))
finally:
silent_remove(VMD_OUT)
silent_remove(WATER_OUT)
def testBin(self):
test_input = ["-f", BIN_INPUT, "-c", BIN_INI]
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
try:
with capture_stdout(main, test_input) as output:
self.assertTrue("Keeping 14 of 16 rows based on filtering criteria" in output)
self.assertFalse(diff_lines(DEF_BIN_OUT, GOOD_BIN_OUT))
finally:
silent_remove(DEF_BIN_OUT, disable=DISABLE_REMOVE)
def testGoodAtomNumFile(self):
test_input = ["-f", GLU_FILE, "-n", GLU_ATOM_NUM]
main(test_input)
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
try:
with capture_stdout(main, test_input) as output:
self.assertTrue("1429 47 -0.215 0.156 -0.387 0.470" in output)
self.assertFalse(diff_lines(GLU_OUT1, GOOD_GLU_OUT1, delimiter=" "))
finally:
silent_remove(GLU_OUT1, disable=DISABLE_REMOVE)
def testRMSDEnergy(self):
try:
test_input = ["-c", RMSD_ENE_INI]
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stdout(main, test_input) as output:
self.assertTrue("23.760125" in output)
print(REL_ENE_OUT2)
print(GOOD_RMSD_ENE_OUT)
self.assertFalse(diff_lines(REL_ENE_OUT2, GOOD_RMSD_ENE_OUT))
finally:
silent_remove(REL_ENE_OUT2, disable=DISABLE_REMOVE)
def testGood(self):
try:
test_input = ["-c", DEF_INI]
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stdout(main, test_input) as output:
self.assertTrue("total charge" in output)
self.assertFalse(diff_lines(VMD_OUT, GOOD_VMD_OUT))
self.assertFalse(diff_lines(WATER_OUT, GOOD_WATER_OUT))
finally:
silent_remove(VMD_OUT)
silent_remove(WATER_OUT)
def testCsv(self):
"""
This input file has a header that starts with a '#' so is ignored by np.loadtxt
"""
if logger.isEnabledFor(logging.DEBUG):
main(["-f", CSV_INPUT, "-d", ","])
try:
with capture_stdout(main, ["-f", CSV_INPUT, "-d", ","]) as output:
self.assertTrue(GOOD_OUT in output)
self.assertFalse(diff_lines(CSV_OUT, GOOD_CSV_OUT))
finally:
silent_remove(CSV_OUT, disable=DISABLE_REMOVE)
def testDupKey(self):
# Checking what happens if the key is listed twice. Expect the program to use the last
# key value. In this case, it results in no rows that meet the criteria
test_input = ["-f", DEF_INPUT, "-c", DUP_KEY_INI]
try:
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stdout(main, test_input) as output:
self.assertTrue("Keeping 0 of 4 rows based on filtering criteria" in output)
self.assertFalse(diff_lines(CSV_OUT, GOOD_CSV_NONE_KEPT))
finally:
silent_remove(CSV_OUT, disable=DISABLE_REMOVE)
def testPrintQMMM(self):
try:
# main(["-c", QMMM_OUT_INI])
with capture_stdout(main, ["-c", QMMM_OUT_INI]) as output:
self.assertTrue("Total charge from QM atoms: -1.0" in output)
self.assertFalse(diff_lines(QMMM_OUT, GOOD_QMMM_OUT))
self.assertFalse(diff_lines(MM_KIND_OUT, GOOD_MM_KIND_OUT))
self.assertFalse(diff_lines(VMD_ATOMS_OUT, GOOD_VMD_ATOMS_OUT))
finally:
silent_remove(QMMM_OUT)
silent_remove(MM_KIND_OUT)
silent_remove(VMD_ATOMS_OUT)
def testHO_OO_HH_OHGofR_MaxSteps(self):
test_input = ["-c", HO_OO_HH_OH_GOFR_INI_MAX_STEPS]
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
try:
with capture_stdout(main, test_input) as output:
self.assertTrue(good_long_out_msg in output)
self.assertFalse(
diff_lines(DEF_MAX_STEPS_OUT,
GOOD_HO_OO_HH_OH_GOFR_OUT_MAX_STEPS))
finally:
silent_remove(DEF_MAX_STEPS_OUT, disable=DISABLE_REMOVE)
def testCsv(self):
"""
This input file has a header that starts with a '#' so is ignored by np.loadtxt
"""
if logger.isEnabledFor(logging.DEBUG):
main(["-f", CSV_INPUT, "-d", ","])
try:
with capture_stdout(main, ["-f", CSV_INPUT, "-d", ","]) as output:
self.assertTrue(GOOD_OUT in output)
self.assertFalse(diff_lines(CSV_OUT, GOOD_CSV_OUT))
finally:
silent_remove(CSV_OUT, disable=DISABLE_REMOVE)
def testMissingIncompleteFile(self):
test_input = ["-l", INCOMP_F_LIST]
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
try:
with capture_stderr(main, test_input) as output:
self.assertTrue("Check file" in output)
self.assertTrue("Could not read file" in output)
with capture_stdout(main, test_input) as output:
self.assertTrue("1429 47 -0.215 0.156 -0.387 0.470" in output)
self.assertFalse(diff_lines(GLU_OUT1, GOOD_GLU_OUT1, delimiter=" "))
finally:
silent_remove(GLU_OUT1)
def testBasinHopBounds(self):
# Try hopping + minimization
try:
silent_remove(SCRIPT_OUT)
test_input = ["-c", CONV_HOP_MIN_MAX_INI]
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
silent_remove(SCRIPT_OUT)
with capture_stdout(main, test_input) as output:
self.assertTrue("success condition satisfied. Number of function calls: 83" in output)
finally:
silent_remove(PAR_OUT, disable=DISABLE_REMOVE)
silent_remove(SCRIPT_OUT, disable=DISABLE_REMOVE)
def testHIJArq6(self):
# Test calculating the Maupin form
try:
test_input = ["-c", HIJ_ARQ6_GLU2_INI, "-p"]
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
# because i've turned off printing, there should be no output
with capture_stdout(main, test_input) as output:
self.assertFalse(output)
self.assertFalse(
diff_lines(HIJ_NEW_GLU2_OUT, GOOD_HIJ_NEW_GLU2_OUT))
finally:
silent_remove(HIJ_NEW_GLU2_OUT, disable=DISABLE_REMOVE)
def testHeader(self):
"""
This input file has a header that starts with a '#' so is ignored by np
"""
test_input = ["-f", HEADER_INPUT]
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
try:
with capture_stdout(main, test_input) as output:
self.assertTrue(GOOD_OUT in output)
self.assertFalse(diff_lines(CSV_HEADER_OUT, GOOD_CSV_OUT))
finally:
silent_remove(CSV_HEADER_OUT, disable=DISABLE_REMOVE)
def testNoInputFile(self):
with capture_stderr(main) as output:
self.assertTrue("Problems reading file: Could not read file" in output)
with capture_stdout(main) as output:
self.assertTrue("optional arguments" in output)
def testHelpOption(self):
with capture_stdout(main, ["-h"]) as output:
self.assertTrue("optional arguments" in output)
def testNoArgs(self):
with capture_stdout(main, []) as output:
self.assertTrue("usage:" in output)
with capture_stderr(main, []) as output:
self.assertTrue("too few arguments" in output)
def testNoAction(self):
with capture_stderr(main, ["-c", NO_ACTION_INI_PATH]) as output:
self.assertTrue("No calculations have been requested" in output)
with capture_stdout(main, ["-c", NO_ACTION_INI_PATH]) as output:
self.assertTrue("optional arguments" in output)
def testNoArgsIni(self):
# main([])
with capture_stdout(main, []) as output:
self.assertTrue("optional arguments:" in output)
with capture_stderr(main, []) as output:
self.assertTrue("Problems reading file: Could not read file" in output)
def testMissingConfig(self):
with capture_stderr(evbdump2data.main, ["-c", INCOMP_INI]) as output:
self.assertTrue("Input data missing" in output)
with capture_stdout(evbdump2data.main, ["-c", INCOMP_INI]) as output:
self.assertTrue("optional arguments" in output)
def testNoIni(self):
with capture_stdout(evbdump2data.main, []) as output:
self.assertTrue("usage:" in output)
with capture_stderr(evbdump2data.main, []) as output:
self.assertTrue("Problems reading file: Could not read file" in output)
def testNoArgs(self):
with capture_stdout(main, []) as output:
self.assertTrue("optional arguments" in output)
with capture_stderr(main, []) as output:
self.assertTrue("Problems reading file" in output)
def testNoComboFiles(self):
with capture_stdout(main, ["-d", FES_OUT_NONE]) as output:
self.assertTrue("Found 0 dirs with files to combine" in output)
def testInvalidData(self):
with capture_stderr(main, ["-c", INVALID_INI]) as output:
self.assertTrue("Problem with config vals on key h3o_o_type: invalid literal for int" in output)
with capture_stdout(main, ["-c", INVALID_INI]) as output:
self.assertTrue("optional arguments" in output)
def testNoArgs(self):
with capture_stderr(main, []) as output:
self.assertTrue("Could not read file" in output)
with capture_stdout(main, []) as output:
self.assertTrue("optional arguments" in output)
