def cleanup():
"""
Clean-up the package including the tests.
"""
# Clean the tests (note cleanup_tests has a main() so it runs when imported.
import tests.cleanup_tests as cleanup_tests
cleanup_tests.cleanup_tests()
from sbpipe.utils.io import files_with_pattern_recur
# Remove all files with suffix .pyc recursively
for f in files_with_pattern_recur(SBPIPE, '.pyc'):
remove_file_silently(f)
# Remove all temporary files (*~) recursively
for f in files_with_pattern_recur(SBPIPE, '~'):
remove_file_silently(f)
def sim(self, model, inputdir, outputdir, cluster="local", local_cpus=1, runs=1, output_msg=False):
__doc__ = Simul.sim.__doc__
# check Copasi file
if not self.model_checking(os.path.join(inputdir, model),
os.path.join(inputdir, model.replace('.cps', '_check.txt')),
'Time-Course'):
return False
if not self._run_par_comput(inputdir, model, outputdir, cluster, local_cpus, runs, output_msg):
return False
# removed repeated copasi files
repeated_copasi_files = [f for f in os.listdir(inputdir) if re.match(self._get_model_group(model) + '[0-9]+.*.cps', f)]
for report in repeated_copasi_files:
remove_file_silently(os.path.join(inputdir, report))
return True
def pe(self, model, inputdir, cluster, local_cpus, runs, outputdir, sim_data_dir, output_msg=False):
__doc__ = Simul.pe.__doc__
# check Copasi file
if not self.model_checking(os.path.join(inputdir, model),
os.path.join(inputdir, model.replace('.cps', '_check.txt')),
'Parameter Estimation'):
return False
if not self._run_par_comput(inputdir, model, sim_data_dir, cluster, local_cpus, runs, output_msg):
return False
# move_models
repeated_copasi_files = [f for f in os.listdir(inputdir) if re.match(self._get_model_group(model) + '[0-9]+.*.cps', f)]
for file in repeated_copasi_files:
remove_file_silently(os.path.join(inputdir, file))
return True
def ps1(self, model, scanned_par, simulate_intervals,
single_param_scan_intervals, inputdir, outputdir, cluster="local", local_cpus=1, runs=1, output_msg=False):
__doc__ = Simul.ps1.__doc__
# check Copasi file
if not self.model_checking(os.path.join(inputdir, model),
os.path.join(inputdir, model.replace('.cps', '_check.txt')),
'Scan'):
return False
if not self._run_par_comput(inputdir, model, outputdir, cluster, local_cpus, runs, output_msg):
return False
# removed repeated copasi files
repeated_copasi_files = [f for f in os.listdir(inputdir) if re.match(self._get_model_group(model) + '[0-9]+.*.cps', f)]
for report in repeated_copasi_files:
remove_file_silently(os.path.join(inputdir, report))
self.ps1_postproc(model, scanned_par, simulate_intervals, single_param_scan_intervals, outputdir)
return True
def cleanup_tests():
"""
Clean up the test results.
"""
projects = [f for f in os.listdir(testpath) if isdir(join(testpath, f))]
print('Cleaning tests:')
for file in projects:
if file == '__pycache__':
shutil.rmtree(os.path.join(testpath, file), ignore_errors=True)
continue
print('- ' + file)
if file == 'snakemake':
print("cleaning output files...")
shutil.rmtree(os.path.join(testpath, file, 'Results'), ignore_errors=True)
shutil.rmtree(os.path.join(testpath, file, 'log'), ignore_errors=True)
shutil.rmtree(os.path.join(testpath, file, '.snakemake'), ignore_errors=True)
snake_files = glob.glob(os.path.join(testpath, file, "*.snake"))
for f in snake_files:
remove_file_silently(f)
continue
modelspath = join(testpath, file, 'Models')
replicated_files = glob.glob(os.path.join(modelspath, "*[0-9].cps"))
for f in replicated_files:
remove_file_silently(f)
check_files = glob.glob(os.path.join(modelspath, "*_check.txt"))
for f in check_files:
remove_file_silently(f)
wfpath = join(testpath, file, 'Results')
if file == 'interrupted':
# We keep the generated data sets for these tests
results = [os.path.join(dp, f) for dp, dn, filenames in os.walk(wfpath)
for f in filenames]
for f in results:
if f.find('param_estim_data') == -1:
remove_file_silently(f)
continue
shutil.rmtree(wfpath, ignore_errors=True)