def sort_requirements(filename: PathLike, allow_git: bool = False) -> int:
"""
Sort the requirements in the given file alphabetically.
:param filename: The file to sort the requirements in.
:param allow_git: Whether to allow lines that start with ``git+``, which are allowed by pip but not :pep:`508`.
"""
ret = PASS
filename = PathPlus(filename)
comments: List[str]
requirements: Set[ComparableRequirement]
git_lines: List[str] = []
requirements, comments, invalid_lines = read_requirements(
req_file=filename,
include_invalid=True,
normalize_func=normalize_keep_dot,
)
for line in invalid_lines:
if line.startswith("git+") and allow_git:
git_lines.append(line)
else:
ret |= FAIL
# find and remove pkg-resources==0.0.0
# which is automatically added by broken pip package under Debian
if ComparableRequirement("pkg-resources==0.0.0") in requirements:
requirements.remove(ComparableRequirement("pkg-resources==0.0.0"))
ret |= FAIL
sorted_requirements = sorted(requirements)
buf = StringList(
[*comments, *git_lines, *[str(req) for req in sorted_requirements]])
buf.blankline(ensure_single=True)
if (requirements != sorted_requirements
and buf != filename.read_lines()) or ret:
print('\n'.join(buf))
# print(coloured_diff(
# filename.read_lines(),
# buf,
# str(filename),
# str(filename),
# "(original)",
# "(sorted)",
# lineterm='',
# ))
ret |= FAIL
filename.write_lines(buf)
return ret
def from_jcamp(cls,
file_name: PathLike,
ignore_warnings: bool = True) -> "ReferenceData":
"""
Create a ReferenceData object from a JCAMP-DX file.
:param file_name: Path of the file to read.
:param ignore_warnings: Whether warnings about invalid tags should be shown.
:authors: Qiao Wang, Andrew Isaac, Vladimir Likic, David Kainer, Dominic Davis-Foster
"""
with warnings.catch_warnings():
if ignore_warnings:
warnings.simplefilter("ignore", JcampTagWarning)
file_name = PathPlus(file_name)
# Commented this line because it also gets printed when the MassSpectrum is created
# print(f" -> Reading JCAMP file '{file_name}'")
lines_list = file_name.read_lines()
last_tag = None
header_info: Dict[str, Any] = {
} # Dictionary containing header information
for line in lines_list:
if len(line.strip()):
if line.startswith("##"):
# key word or information
fields = line.split('=', 1)
current_tag = fields[0] = fields[0].lstrip(
"##").upper()
last_tag = fields[0]
fields[1] = fields[1].strip()
if current_tag.upper().startswith("END"):
break
elif current_tag in xydata_tags:
continue
elif current_tag in header_info_fields:
if fields[1].isdigit():
header_info[current_tag] = int(fields[1])
elif is_float(fields[1]):
header_info[current_tag] = float(fields[1])
else:
header_info[current_tag] = fields[1]
else:
warnings.warn(current_tag, JcampTagWarning)
else:
if last_tag in header_info:
header_info[last_tag] += f"{line}"
return cls(
name=header_info["TITLE"],
cas=header_info["CAS REGISTRY NO"],
nist_no=header_info["$NIST MASS SPEC NO"],
contributor=header_info["ORIGIN"],
formula=header_info["MOLFORM"],
mw=header_info["MW"],
mass_spec=MassSpectrum.from_jcamp(file_name),
)