def testSpecificTimestep(self):
try:
test_input = ["-c", ONLY_STEPS_INI]
main(test_input)
self.assertFalse(diff_lines(ONLY_STEPS_OUT, GOOD_ONLY_STEPS_OUT))
finally:
silent_remove(ONLY_STEPS_OUT, disable=DISABLE_REMOVE)
def testMaxSteps(self):
try:
test_input = ["-c", MAX_STEPS_INI]
main(test_input)
self.assertFalse(diff_lines(MAX_STEPS_OUT, GOOD_MAX_STEPS_OUT))
finally:
silent_remove(MAX_STEPS_OUT, disable=DISABLE_REMOVE)
def testWaterMolCombine(self):
# Should skip the timestep with only 1 state
try:
main(["-c", WATER_MOL_COMB_INI])
self.assertFalse(diff_lines(WATER_MOL_COMB_OUT, GOOD_WATER_MOL_COMB_OUT))
finally:
silent_remove(WATER_MOL_COMB_OUT)
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 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 testRepeatedTimestep(self):
try:
test_input = ["-c", REPEATED_EVB_STEP_INI]
main(test_input)
self.assertFalse(
diff_lines(REPEATED_EVB_STEP_OUT, GOOD_REPEATED_EVB_STEP_OUT))
finally:
silent_remove(REPEATED_EVB_STEP_OUT, disable=DISABLE_REMOVE)
def testWaterMol(self):
try:
main(["-c", WATER_MOL_INI])
self.assertFalse(diff_lines(WATER_MOL_OUT1, GOOD_WATER_MOL_OUT1))
self.assertFalse(diff_lines(WATER_MOL_OUT2, GOOD_WATER_MOL_OUT2))
finally:
silent_remove(WATER_MOL_OUT1, disable=DISABLE_REMOVE)
silent_remove(WATER_MOL_OUT2, disable=DISABLE_REMOVE)
def testWaterMol(self):
try:
main(["-c", WATER_MOL_INI, "-p"])
self.assertFalse(diff_lines(DEF_CI_OUT1, GOOD_WATER_MOL_OUT1))
self.assertFalse(diff_lines(DEF_CI_OUT2, GOOD_WATER_MOL_OUT2))
finally:
silent_remove(DEF_CI_OUT1, disable=DISABLE_REMOVE)
silent_remove(DEF_CI_OUT2, disable=DISABLE_REMOVE)
def testWaterMolCombine(self):
# Should skip the timestep with only 1 state
try:
main(["-c", WATER_MOL_COMB_INI, "-p"])
self.assertFalse(
diff_lines(WATER_MOL_COMB_OUT, GOOD_WATER_MOL_COMB_OUT))
finally:
silent_remove(WATER_MOL_COMB_OUT, disable=DISABLE_REMOVE)
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 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 testCiInfo(self):
try:
main(["-c", CI_INI])
self.assertFalse(diff_lines(DEF_CI_OUT1, GOOD_CI_OUT1))
self.assertEqual(1, len(diff_lines(DEF_CI_OUT2, BAD_CI_OUT2)))
self.assertFalse(diff_lines(DEF_CI_OUT2, GOOD_CI_OUT2))
finally:
silent_remove(DEF_CI_OUT1, disable=DISABLE_REMOVE)
silent_remove(DEF_CI_OUT2, disable=DISABLE_REMOVE)
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 testRelEnergyMissingInfo(self):
# Check that prints "nan" instead of printing a stack trace (uncaught error)
try:
main(["-c", REL_ENE_INI2, "-p"])
print(REL_ENE_OUT2)
print(GOOD_REL_ENE_OUT2)
self.assertFalse(diff_lines(REL_ENE_OUT2, GOOD_REL_ENE_OUT2))
finally:
silent_remove(REL_ENE_OUT2, disable=DISABLE_REMOVE)
def testRelEnergy(self):
# calculates relative energy
try:
main(["-c", REL_ENE_INI, "-p"])
print(REL_ENE_OUT)
print(GOOD_REL_ENE_OUT)
self.assertFalse(diff_lines(REL_ENE_OUT, GOOD_REL_ENE_OUT))
finally:
silent_remove(REL_ENE_OUT, disable=DISABLE_REMOVE)
def testCiInfo(self):
try:
main(["-c", CI_INI])
self.assertFalse(diff_lines(DEF_CI_OUT1, GOOD_CI_OUT1))
self.assertEquals(1, len(diff_lines(DEF_CI_OUT2, BAD_CI_OUT2)))
self.assertFalse(diff_lines(DEF_CI_OUT2, GOOD_CI_OUT2))
finally:
silent_remove(DEF_CI_OUT1)
silent_remove(DEF_CI_OUT2)
def testOneStateCiInfo(self):
"""
Make sure can handle input that only has one state (such steps have a vector instead of a matrix)
and does not skip them
Also, check that properly reads to make a summary file
"""
try:
main(["-c", CI_ONE_STATE_INI])
self.assertFalse(diff_lines(DEF_LIST_OUT, GOOD_LIST_OUT))
finally:
silent_remove(DEF_LIST_OUT)
def testOneStateCiInfo(self):
"""
Make sure can handle input that only has one state (such steps have a vector instead of a matrix)
and does not skip them
Also, check that properly reads to make a summary file
"""
try:
main(["-c", CI_ONE_STATE_INI])
self.assertFalse(diff_lines(DEF_LIST_OUT, GOOD_LIST_OUT))
finally:
silent_remove(DEF_LIST_OUT, disable=DISABLE_REMOVE)
def testMultiFileSum(self):
try:
test_input = ["-c", MULTI_SUM_INI]
silent_remove(MULTI_SUM_OUT)
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue(
"setting 'print_output_file_list' to 'True'" in output)
self.assertFalse(diff_lines(MULTI_SUM_OUT, GOOD_MULTI_SUM_OUT))
finally:
silent_remove(MULTI_SUM_OUT, 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 testOneStateEachFileCiInfo(self):
"""
Make sure can handle input that only has one state (such steps have a vector instead of a matrix)
this time, printing a separate output for each file
And, skip one-state-steps
"""
try:
main(["-c", CI_ONE_STATE_EACH_FILE_INI])
self.assertFalse(diff_lines(DEF_ONE_STATE_OUT, GOOD_ONE_STATE_OUT))
self.assertFalse(diff_lines(DEF_ONE_STATE_OUT2, GOOD_ONE_STATE_OUT2))
finally:
silent_remove(DEF_ONE_STATE_OUT)
silent_remove(DEF_ONE_STATE_OUT2)
def testOneStateEachFileCiInfo(self):
"""
Make sure can handle input that only has one state (such steps have a vector instead of a matrix)
this time, printing a separate output for each file
And, skip one-state-steps
"""
try:
main(["-c", CI_ONE_STATE_EACH_FILE_INI])
self.assertFalse(diff_lines(DEF_ONE_STATE_OUT, GOOD_ONE_STATE_OUT))
self.assertFalse(
diff_lines(DEF_ONE_STATE_OUT2, GOOD_ONE_STATE_OUT2))
finally:
silent_remove(DEF_ONE_STATE_OUT, disable=DISABLE_REMOVE)
silent_remove(DEF_ONE_STATE_OUT2, disable=DISABLE_REMOVE)
def testNonIntTimestep(self):
test_input = ["-c", REF_ENE_NON_INT_TIME_INI]
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue("Could not convert" in output)
def testKeyProps(self):
try:
main(["-c", KEY_PROPS_INI])
self.assertFalse(diff_lines(KEY_PROPS_OUT, GOOD_KEY_PROPS_OUT))
finally:
silent_remove(KEY_PROPS_OUT, disable=DISABLE_REMOVE)
def testDecomposedEnergyInfo(self):
try:
main(["-c", DECOMP_ENE_INI, "-p"])
self.assertFalse(diff_lines(REL_ENE_OUT2, GOOD_DECOMP_ENE_OUT))
finally:
silent_remove(REL_ENE_OUT2, disable=DISABLE_REMOVE)
def testNoPath(self):
test_input = ["-c", NO_PATH_INI]
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue("Found no evb file names" in output)
def testKeyProps(self):
try:
main(["-c", KEY_PROPS_INI])
self.assertFalse(diff_lines(KEY_PROPS_OUT, GOOD_KEY_PROPS_OUT))
finally:
silent_remove(KEY_PROPS_OUT)
def testBadPath(self):
test_input = ["-c", BAD_PATH_INI]
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue("No such file or directory:" in output)
def testBadPath(self):
test_input = ["-c", BAD_PATH_INI]
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue("Found no evb file names to read" in output)
