def _parse_zgoubi_log(run_dir):
path = run_dir.join(_ZGOUBI_LOG_FILE)
if not path.exists():
return ''
res = ''
element_by_num = PKDict()
text = pkio.read_text(str(path))
for line in text.split("\n"):
match = re.search(r'^ (\'\w+\'.*?)\s+(\d+)$', line)
if match:
element_by_num[match.group(2)] = match.group(1)
continue
if re.search('all particles lost', line):
res += '{}\n'.format(line)
continue
if re.search('charge found null', line):
res += '{}\n'.format(line)
match = re.search(r'Enjob occured at element # (\d+)', line)
if match:
res += '{}\n'.format(line)
num = match.group(1)
if num in element_by_num:
res += ' element # {}: {}\n'.format(num, element_by_num[num])
path = run_dir.join(template_common.RUN_LOG)
if res == '' and path.exists():
text = pkio.read_text(str(path))
for line in text.split("\n"):
match = re.search(r'Fortran runtime error: (.*)', line)
if match:
res += '{}\n'.format(match.group(1))
return res
def tox_get_python_executable(envconfig):
if tox.INFO.IS_WIN:
path = envconfig.envdir.join("python.exe")
else:
path = envconfig.envdir.join("bin", "python")
if path.exists():
return path
def test_compressed_images(dials_regression, compression, extension,
image_to_test, tmp_path):
path = Path(dials_regression) / "image_examples" / image_to_test
if not path.exists():
pytest.skip(str(path) + " not present in dials_regression")
# Compress this file and write to disk
test_image_for_reading = str(tmp_path / (path.name + "." + extension))
with path.open("rb") as f_in:
with compression(test_image_for_reading, "wb") as f_out:
shutil.copyfileobj(f_in, f_out)
# Find and instantiate the format class
format_class = dxtbx.format.Registry.get_format_class_for_file(
test_image_for_reading)
assert format_class is not None, "no matching format class found"
instance = format_class(test_image_for_reading)
# Test metadata reading
assert instance.get_goniometer()
assert instance.get_beam()
assert instance.get_scan()
assert instance.get_detector()
# Test data reading
assert instance.get_raw_data()
def copy_lib_files(data, source, target):
"""Copy auxiliary files to target
Args:
data (dict): simulation db
target (py.path): destination directory
"""
for f in lib_files(data, source):
path = target.join(f.basename)
pkio.mkdir_parent_only(path)
if not path.exists():
if not f.exists():
sim_resource = resource_dir(data.simulationType)
r = sim_resource.join(f.basename)
# the file doesn't exist in the simulation lib, check the resource lib
if r.exists():
pkio.mkdir_parent_only(f)
r.copy(f)
else:
pkdlog('No file in lib or resource: {}', f)
continue
if source:
# copy files from another session
f.copy(path)
else:
# symlink into the run directory
path.mksymlinkto(f, absolute=False)
def _mtime_or_now(path):
"""mtime for path if exists else time.time()
Args:
path (py.path):
Returns:
int: modification time
"""
return int(path.mtime() if path.exists() else time.time())
def _mtime_or_now(path):
"""mtime for path if exists else time.time()
Args:
path (py.path):
Returns:
int: modification time
"""
return int(path.mtime() if path.exists() else time.time())
def __call__(self):
if self._fixture:
return self._fixture
self.ensure(self.directory, bool(self.lineage))
path = self.path(self.directory)
if not path.exists():
self.create()
self.install(self.directory)
module = self.load(self.root, path, self.lineage)
if self.module_name is None:
module_name = self.lineage[-1]
else:
module_name = self.module_name
self._fixture = ModuleFixture(module_name, module, path)
return self._fixture
def _parse_zgoubi_log(run_dir):
path = run_dir.join(_ZGOUBI_LOG_FILE)
if not path.exists():
return ''
res = ''
element_by_num = {}
text = pkio.read_text(str(path))
for line in text.split("\n"):
match = re.search(r'^ (\'\w+\'.*?)\s+(\d+)$', line)
if match:
element_by_num[match.group(2)] = match.group(1)
continue
if re.search('all particles lost', line):
res += '{}\n'.format(line)
continue
match = re.search(r'Enjob occured at element # (\d+)', line)
if match:
res += '{}\n'.format(line)
num = match.group(1)
if num in element_by_num:
res += ' element # {}: {}\n'.format(num, element_by_num[num])
return res
def _parse_zgoubi_log(run_dir):
path = run_dir.join(_ZGOUBI_LOG_FILE)
if not path.exists():
return ''
res = ''
element_by_num = {}
text = pkio.read_text(str(path))
for line in text.split("\n"):
match = re.search(r'^ (\'\w+\'.*?)\s+(\d+)$', line)
if match:
element_by_num[match.group(2)] = match.group(1)
continue
if re.search('all particles lost', line):
res += '{}\n'.format(line)
continue
match = re.search(r'Enjob occured at element # (\d+)', line)
if match:
res += '{}\n'.format(line)
num = match.group(1)
if num in element_by_num:
res += ' element # {}: {}\n'.format(num, element_by_num[num])
return res
def path(self, directory):
path = super(SetsUpPyWithOutOfDatePyc, self).path(directory)
pyc = self.directory.join(self.PYC_FN)
if path.exists() and path.mtime() < pyc.mtime():
path.remove()
return path
