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Correctly handle the case that the YAML python module is not installed

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Axel Kohlmeyer
2022-05-14 10:13:08 -04:00
parent 9661711a1e
commit 168d3bdd3c
2 changed files with 24 additions and 9 deletions
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11
python/lammps/formats.py
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@ -17,11 +17,18 @@
# and Axel Kohlmeyer <akohlmey@gmail.com> # and Axel Kohlmeyer <akohlmey@gmail.com>
################################################################################ ################################################################################
import re, yaml import re
has_yaml = False
try:
import yaml
has_yaml = True
try: try:
from yaml import CSafeLoader as Loader from yaml import CSafeLoader as Loader
except ImportError: except ImportError:
from yaml import SafeLoader as Loader from yaml import SafeLoader as Loader
except ImportError:
pass
class LogFile: class LogFile:
"""Reads LAMMPS log files and extracts the thermo information """Reads LAMMPS log files and extracts the thermo information
@ -66,6 +73,8 @@ class LogFile:
style = LogFile.STYLE_YAML style = LogFile.STYLE_YAML
yamllog += line; yamllog += line;
current_run = {} current_run = {}
if not has_yaml:
raise Exception('Cannot process YAML format logs without the PyYAML Python module')
elif re.match(r'^\.\.\.$', line): elif re.match(r'^\.\.\.$', line):
thermo = yaml.load(yamllog, Loader=Loader) thermo = yaml.load(yamllog, Loader=Loader)

8
unittest/python/python-formats.py
View File

@ -2,11 +2,16 @@ import os
import unittest import unittest
from lammps.formats import LogFile, AvgChunkFile from lammps.formats import LogFile, AvgChunkFile
has_yaml = False
try:
import yaml import yaml
has_yaml = True
try: try:
from yaml import CSafeLoader as Loader, CSafeDumper as Dumper from yaml import CSafeLoader as Loader, CSafeDumper as Dumper
except ImportError: except ImportError:
from yaml import SafeLoader, SafeDumper from yaml import SafeLoader, SafeDumper
except:
pass
EXAMPLES_DIR=os.path.abspath(os.path.join(__file__, '..', '..', '..', 'examples')) EXAMPLES_DIR=os.path.abspath(os.path.join(__file__, '..', '..', '..', 'examples'))
@ -65,6 +70,7 @@ class Logfiles(unittest.TestCase):
self.assertEqual(run0["Step"], list(range(0,350, 50))) self.assertEqual(run0["Step"], list(range(0,350, 50)))
@unittest.skipIf(not has_yaml,"Missing the PyYAML python module")
def testYamlLogFile(self): def testYamlLogFile(self):
log = LogFile(os.path.join(EXAMPLES_DIR, YAML_STYLE_EXAMPLE_LOG)) log = LogFile(os.path.join(EXAMPLES_DIR, YAML_STYLE_EXAMPLE_LOG))
self.assertEqual(len(log.runs), 2) self.assertEqual(len(log.runs), 2)
@ -127,7 +133,7 @@ try:
except: except:
pass pass
@unittest.skipIf(not has_dump_yaml, "Either atom_style full or dump_style yaml are not available") @unittest.skipIf(not (has_dump_yaml and has_yaml), "Either atom_style full, dump_style yaml, or the python PyYAML module are not available")
class PythonDump(unittest.TestCase): class PythonDump(unittest.TestCase):
def setUp(self): def setUp(self):
machine = None machine = None