Hello community,
here is the log from the commit of package python-oiffile for openSUSE:Factory
checked in at 2020-11-29 12:31:21
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Comparing /work/SRC/openSUSE:Factory/python-oiffile (Old)
and /work/SRC/openSUSE:Factory/.python-oiffile.new.5913 (New)
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "python-oiffile"
Sun Nov 29 12:31:21 2020 rev:2 rq:851384 version:2020.9.18
Changes:
--------
--- /work/SRC/openSUSE:Factory/python-oiffile/python-oiffile.changes
2020-08-14 13:11:28.905259402 +0200
+++ /work/SRC/openSUSE:Factory/.python-oiffile.new.5913/python-oiffile.changes
2020-11-29 12:33:16.990296800 +0100
@@ -1,0 +2,8 @@
+Thu Nov 26 06:52:36 UTC 2020 - andy great <andythe_gr...@pm.me>
+
+- Update to version 2020.9.18.
+ * Remove support for Python 3.6.
+ * Support os.PathLike file names.
+ * Fix unclosed files.
+
+-------------------------------------------------------------------
Old:
----
oiffile-2020.1.18.tar.gz
New:
----
oiffile-2020.9.18.tar.gz
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Other differences:
------------------
++++++ python-oiffile.spec ++++++
--- /var/tmp/diff_new_pack.jRLVH9/_old 2020-11-29 12:33:18.486298313 +0100
+++ /var/tmp/diff_new_pack.jRLVH9/_new 2020-11-29 12:33:18.486298313 +0100
@@ -20,20 +20,20 @@
%define skip_python2 1
%{?!python_module:%define python_module() python-%{**} python3-%{**}}
Name: python-oiffile
-Version: 2020.1.18
+Version: 2020.9.18
Release: 0
Summary: Read Olympus(r) image files (OIF and OIB)
License: BSD-3-Clause
Group: Development/Languages/Python
URL: https://www.lfd.uci.edu/~gohlke/
Source:
https://github.com/cgohlke/oiffile/archive/v%{version}.tar.gz#/%{packagename}-%{version}.tar.gz
-BuildRequires: %{python_module numpy >= 1.14}
-BuildRequires: %{python_module tifffile >= 2019.1.1}
+BuildRequires: %{python_module numpy >= 1.15}
+BuildRequires: %{python_module tifffile >= 2020.6.3}
BuildRequires: %{python_module setuptools}
BuildRequires: fdupes
BuildRequires: python-rpm-macros
-Requires: python-numpy >= 1.14
-Requires: python-tifffile >= 2019.1.1
+Requires: python-numpy >= 1.15
+Requires: python-tifffile >= 2020.6.3
BuildArch: noarch
%python_subpackages
++++++ oiffile-2020.1.18.tar.gz -> oiffile-2020.9.18.tar.gz ++++++
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/oiffile-2020.1.18/README.rst
new/oiffile-2020.9.18/README.rst
--- old/oiffile-2020.1.18/README.rst 2020-01-19 10:33:48.000000000 +0100
+++ new/oiffile-2020.9.18/README.rst 2020-09-19 06:59:59.000000000 +0200
@@ -22,16 +22,20 @@
:License: BSD 3-Clause
-:Version: 2020.1.18
+:Version: 2020.9.18
Requirements
------------
-* `CPython >= 3.6 <https://www.python.org>`_
-* `Numpy 1.14 <https://www.numpy.org>`_
-* `Tifffile 2019.1.1 <https://pypi.org/project/tifffile/>`_
+* `CPython >= 3.7 <https://www.python.org>`_
+* `Numpy 1.15 <https://www.numpy.org>`_
+* `Tifffile 2020.6.3 <https://pypi.org/project/tifffile/>`_
Revisions
---------
+2020.9.18
+ Remove support for Python 3.6 (NEP 29).
+ Support os.PathLike file names.
+ Fix unclosed files.
2020.1.18
Fix indentation error.
2020.1.1
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/oiffile-2020.1.18/oiffile/oiffile.py
new/oiffile-2020.9.18/oiffile/oiffile.py
--- old/oiffile-2020.1.18/oiffile/oiffile.py 2020-01-19 10:33:48.000000000
+0100
+++ new/oiffile-2020.9.18/oiffile/oiffile.py 2020-09-19 06:59:59.000000000
+0200
@@ -52,16 +52,20 @@
:License: BSD 3-Clause
-:Version: 2020.1.18
+:Version: 2020.9.18
Requirements
------------
-* `CPython >= 3.6 <https://www.python.org>`_
-* `Numpy 1.14 <https://www.numpy.org>`_
-* `Tifffile 2019.1.1 <https://pypi.org/project/tifffile/>`_
+* `CPython >= 3.7 <https://www.python.org>`_
+* `Numpy 1.15 <https://www.numpy.org>`_
+* `Tifffile 2020.6.3 <https://pypi.org/project/tifffile/>`_
Revisions
---------
+2020.9.18
+ Remove support for Python 3.6 (NEP 29).
+ Support os.PathLike file names.
+ Fix unclosed files.
2020.1.18
Fix indentation error.
2020.1.1
@@ -136,7 +140,7 @@
"""
-__version__ = '2020.1.18'
+__version__ = '2020.9.18'
__all__ = (
'imread',
@@ -201,7 +205,7 @@
def __init__(self, filename):
"""Open OIF or OIB file and read main settings."""
- self.filename = filename
+ self.filename = filename = os.fspath(filename)
if filename.lower().endswith('.oif'):
self.filesystem = OifFileSystem(filename)
self.is_oib = False
@@ -210,14 +214,16 @@
self.is_oib = True
self.mainfile = self.filesystem.settings
# map file names to storage names (flattened name space)
- self._files_flat = {os.path.basename(f): f
- for f in self.filesystem.files()}
+ self._files_flat = {
+ os.path.basename(f): f for f in self.filesystem.files()
+ }
def open_file(self, filename):
"""Return open file object from path name."""
try:
return self.filesystem.open_file(
- self._files_flat.get(filename, filename))
+ self._files_flat.get(filename, filename)
+ )
except (KeyError, OSError) as exc:
raise FileNotFoundError(f'No such file: {filename}') from exc
@@ -238,8 +244,9 @@
def shape(self):
"""Return shape of image data from mainfile."""
size = {
- self.mainfile[f'Axis {i} Parameters Common']['AxisCode']:
- int(self.mainfile[f'Axis {i} Parameters Common']['MaxSize'])
+ self.mainfile[f'Axis {i} Parameters Common']['AxisCode']: int(
+ self.mainfile[f'Axis {i} Parameters Common']['MaxSize']
+ )
for i in range(8)
}
return tuple(size[ax] for ax in self.axes)
@@ -248,7 +255,8 @@
def dtype(self):
"""Return dtype of image data from mainfile."""
bitcount = int(
- self.mainfile['Reference Image Parameter']['ValidBitCounts'])
+ self.mainfile['Reference Image Parameter']['ValidBitCounts']
+ )
return numpy.dtype('<u2' if bitcount > 8 else '<u2')
@lazyattr
@@ -256,18 +264,23 @@
"""Return tuple of TiffSequence of sorted TIFF files."""
series = {}
for fname in self.glob('*.tif'):
- key = ''.join(c for c in os.path.split(fname)[-1][:-4]
- if c.isalpha())
+ key = ''.join(
+ c for c in os.path.split(fname)[-1][:-4] if c.isalpha()
+ )
if key in series:
series[key].append(fname)
else:
series[key] = [fname]
- series = [TiffSequence(natural_sorted(files),
- imread=self.asarray, pattern='axes')
- for files in series.values()]
+ series = [
+ TiffSequence(
+ natural_sorted(files), imread=self.asarray, pattern='axes'
+ )
+ for files in series.values()
+ ]
if len(series) > 1:
- series = tuple(reversed(sorted(series,
- key=lambda x: len(x.files))))
+ series = tuple(
+ reversed(sorted(series, key=lambda x: len(x.files)))
+ )
return series
@property
@@ -288,8 +301,12 @@
"""
if isinstance(series, int):
return self.series[series].asarray(**kwargs)
- with TiffFile(self.open_file(series), name=series) as tif:
- result = tif.asarray(**kwargs)
+ try:
+ fh = self.open_file(series)
+ with TiffFile(fh, name=series) as tif:
+ result = tif.asarray(**kwargs)
+ finally:
+ fh.close()
return result
def close(self):
@@ -325,7 +342,7 @@
def __init__(self, filename, storage_ext='.files'):
"""Open OIF file and read settings."""
- self.filename = filename
+ self.filename = filename = os.fspath(filename)
self._path, self.mainfile = os.path.split(os.path.abspath(filename))
self.settings = SettingsFile(filename, name=self.mainfile)
self.name = self.settings['ProfileSaveInfo']['Name']
@@ -334,7 +351,8 @@
storage = os.path.join(self._path, self.mainfile + storage_ext)
if not os.path.exists(storage) or not os.path.isdir(storage):
raise OSError(
- f'OIF storage path not found: {self.mainfile}{storage_ext}')
+ f'OIF storage path not found: {self.mainfile}{storage_ext}'
+ )
# list all files
pathlen = len(self._path + os.path.sep)
self._files = [self.mainfile]
@@ -342,7 +360,11 @@
self._files.append(f[pathlen:])
def open_file(self, filename):
- """Return file object from path name."""
+ """Return file object from path name.
+
+ File object must be closed.
+
+ """
return open(os.path.join(self._path, filename), 'rb')
def files(self):
@@ -366,13 +388,15 @@
def __str__(self):
"""Return string with information about OifFileSystem."""
- return '\n '.join((
- self.__class__.__name__,
- os.path.normpath(os.path.normcase(self.filename)),
- f'name: {self.name}',
- f'version: {self.version}',
- f'mainfile: {self.mainfile}',
- ))
+ return '\n '.join(
+ (
+ self.__class__.__name__,
+ os.path.normpath(os.path.normcase(self.filename)),
+ f'name: {self.name}',
+ f'version: {self.version}',
+ f'mainfile: {self.mainfile}',
+ )
+ )
class OibFileSystem:
@@ -380,24 +404,28 @@
def __init__(self, filename):
"""Open compound document and read OibInfo.txt settings."""
- self.filename = filename
+ self.filename = filename = os.fspath(filename)
self.com = CompoundFile(filename)
- info = SettingsFile(self.com.open_file('OibInfo.txt'),
- 'OibInfo.txt')['OibSaveInfo']
+ info = SettingsFile(self.com.open_file('OibInfo.txt'), 'OibInfo.txt')[
+ 'OibSaveInfo'
+ ]
self.name = info.get('Name', None)
self.version = info.get('Version', None)
self.compression = info.get('Compression', None)
self.mainfile = info[info['MainFileName']]
# map OIB file names to CompoundFile file names
oibfiles = {os.path.split(i)[-1]: i for i in self.com.files()}
- self._files = {v: oibfiles[k] for k, v in info.items()
- if k.startswith('Stream')}
+ self._files = {
+ v: oibfiles[k] for k, v in info.items() if k.startswith('Stream')
+ }
# map storage names to directory names
- self._folders = {i[0]: i[1] for i in info.items()
- if i[0].startswith('Storage')}
+ self._folders = {
+ i[0]: i[1] for i in info.items() if i[0].startswith('Storage')
+ }
# read main settings file
- self.settings = SettingsFile(self.open_file(self.mainfile),
- name=self.mainfile)
+ self.settings = SettingsFile(
+ self.open_file(self.mainfile), name=self.mainfile
+ )
def open_file(self, filename):
"""Return file object from case sensitive path name."""
@@ -456,14 +484,16 @@
def __str__(self):
"""Return string with information about OibFileSystem."""
- return '\n '.join((
- self.__class__.__name__,
- os.path.normpath(os.path.normcase(self.filename)),
- f'name: {self.name}',
- f'version: {self.version}',
- f'mainfile: {self.mainfile}',
- f'compression: {self.compression}',
- ))
+ return '\n '.join(
+ (
+ self.__class__.__name__,
+ os.path.normpath(os.path.normcase(self.filename)),
+ f'name: {self.name}',
+ f'version: {self.version}',
+ f'mainfile: {self.mainfile}',
+ f'compression: {self.compression}',
+ )
+ )
class SettingsFile(dict):
@@ -490,8 +520,8 @@
"""
dict.__init__(self)
- if isinstance(arg, str):
- self.name = arg
+ if isinstance(arg, (str, os.PathLike)):
+ self.name = os.fspath(arg)
stream = open(arg, 'rb')
else:
self.name = str(name)
@@ -506,19 +536,23 @@
# UTF16 BOM
content = content.rsplit(
b'[\x00C\x00o\x00l\x00o\x00r\x00L\x00U\x00T\x00'
- b'D\x00a\x00t\x00a\x00]\x00\x0D\x00\x0A\x00', 1)
+ b'D\x00a\x00t\x00a\x00]\x00\x0D\x00\x0A\x00',
+ 1,
+ )
if len(content) > 1:
self['ColorLUTData'] = numpy.fromstring(
- content[1], 'uint8').reshape(-1, 4)
+ content[1], 'uint8'
+ ).reshape(-1, 4)
content = content[0].decode('utf-16')
elif content[:1] == b'[':
# try UTF-8
content = content.rsplit(b'[ColorLUTData]\r\n', 1)
if len(content) > 1:
self['ColorLUTData'] = numpy.fromstring(
- content[1], 'uint8').reshape(-1, 4)
+ content[1], 'uint8'
+ ).reshape(-1, 4)
try:
- content = content[0].decode('utf-8')
+ content = content[0].decode()
except Exception as exc:
raise ValueError('not a valid settings file') from exc
else:
@@ -559,6 +593,7 @@
def __init__(self, filename):
"""Initialize instance from file."""
+ self.filename = filename = os.fspath(filename)
self._fh = open(filename, 'rb')
if self._fh.read(8) != b'\xd0\xcf\x11\xe0\xa1\xb1\x1a\xe1':
self.close()
@@ -594,23 +629,27 @@
if self.version_minor != 0x3E:
raise OifFileError(
- f'cannot handle version_minor {self.version_minor}')
+ f'cannot handle version_minor {self.version_minor}'
+ )
if mini_sector_shift != 0x0006:
raise OifFileError(
- f'cannot handle mini_sector_shift {mini_sector_shift}')
+ f'cannot handle mini_sector_shift {mini_sector_shift}'
+ )
if not (
- (self.version_major == 0x4 and sector_shift == 0x000C) or
- (self.version_major == 0x3 and sector_shift == 0x0009 and
- self.dir_len == 0)
+ (self.version_major == 0x4 and sector_shift == 0x000C)
+ or (
+ self.version_major == 0x3
+ and sector_shift == 0x0009
+ and self.dir_len == 0
+ )
):
raise OifFileError(
f'cannot handle version_major {self.version_major} '
f'and sector_shift {sector_shift}'
)
- self.filename = filename
- self.sec_size = 2**sector_shift
- self.short_sec_size = 2**mini_sector_shift
+ self.sec_size = 2 ** sector_shift
+ self.short_sec_size = 2 ** mini_sector_shift
secfmt = '<' + ('I' * (self.sec_size // 4))
# read DIFAT
@@ -625,7 +664,7 @@
self._difat.extend(sec[:-1])
nextsec = sec[-1]
# if nextsec != CompoundFile.ENDOFCHAIN: raise OifFileError()
- self._difat = self._difat[:self.fat_len]
+ self._difat = self._difat[: self.fat_len]
# read FAT
self._fat = []
for secid in self._difat:
@@ -640,15 +679,16 @@
self._dirs = []
for sector in self._sec_chain(self.dir_start):
for i in range(0, self.sec_size, 128):
- direntry = DirectoryEntry(sector[i:i+128], self.version_major)
+ direntry = DirectoryEntry(
+ sector[i : i + 128], self.version_major
+ )
self._dirs.append(direntry)
# read root storage
if len(self._dirs) <= 0:
raise OifFileError('no directories found')
root = self._dirs[0]
if root.name != 'Root Entry':
- raise OifFileError(
- f"no root directory found, got {root.name}")
+ raise OifFileError(f"no root directory found, got {root.name}")
if root.create_time is not None: # and root.modify_time is None
raise OifFileError(f'invalid root.create_time {root.create_time}')
if root.stream_size % self.short_sec_size != 0:
@@ -658,7 +698,7 @@
)
# read mini stream
self._ministream = b''.join(self._sec_chain(root.sector_start))
- self._ministream = self._ministream[:root.stream_size]
+ self._ministream = self._ministream[: root.stream_size]
# map stream/file names to directory entries
nostream = CompoundFile.NOSTREAM
join = '/'.join # os.path.sep.join
@@ -687,7 +727,7 @@
result = b''.join(self._mini_sec_chain(direntry.sector_start))
else:
result = b''.join(self._sec_chain(direntry.sector_start))
- return result[:direntry.stream_size]
+ return result[: direntry.stream_size]
def _sec_read(self, secid):
"""Return content of sector from file."""
@@ -704,7 +744,7 @@
def _mini_sec_read(self, secid):
"""Return content of sector from mini stream."""
pos = secid * self.short_sec_size
- return self._ministream[pos: pos+self.short_sec_size]
+ return self._ministream[pos : pos + self.short_sec_size]
def _mini_sec_chain(self, secid):
"""Return iterator over mini FAT sector chain content."""
@@ -746,9 +786,18 @@
os.path.normpath(os.path.normcase(self.filename)),
]
for attr in (
- 'clsid', 'version_minor', 'version_major', 'byteorder',
- 'dir_len', 'fat_len', 'dir_start', 'mini_stream_cutof_size',
- 'minifat_start', 'minifat_len', 'difat_start', 'difat_len'
+ 'clsid',
+ 'version_minor',
+ 'version_major',
+ 'byteorder',
+ 'dir_len',
+ 'fat_len',
+ 'dir_start',
+ 'mini_stream_cutof_size',
+ 'minifat_start',
+ 'minifat_len',
+ 'difat_start',
+ 'difat_len',
):
s.append(f'{attr}: {getattr(self, attr)}')
return '\n '.join(s)
@@ -758,9 +807,20 @@
"""Compound Document Directory Entry."""
__slots__ = (
- 'name', 'entry_type', 'color', 'left_sibling_id', 'right_sibling_id',
- 'child_id', 'clsid', 'user_flags', 'create_time', 'modify_time',
- 'sector_start', 'stream_size', 'is_stream', 'is_storage'
+ 'name',
+ 'entry_type',
+ 'color',
+ 'left_sibling_id',
+ 'right_sibling_id',
+ 'child_id',
+ 'clsid',
+ 'user_flags',
+ 'create_time',
+ 'modify_time',
+ 'sector_start',
+ 'stream_size',
+ 'is_stream',
+ 'is_storage',
)
def __init__(self, data, version_major):
@@ -791,7 +851,7 @@
if self.color not in (0, 1):
raise OifFileError(f'invalid color {self.color}')
- self.name = name[:name_len-2].decode('utf-16')
+ self.name = name[: name_len - 2].decode('utf-16')
self.create_time = filetime(create_time)
self.modify_time = filetime(modify_time)
self.is_stream = self.entry_type == 2
@@ -805,16 +865,24 @@
return '\n '.join(s)
-def format_dict(adict, prefix=' ', indent=' ', bullets=('', ''),
- excludes=('_', ), linelen=79, trim=1):
+def format_dict(
+ adict,
+ prefix=' ',
+ indent=' ',
+ bullets=('', ''),
+ excludes=('_',),
+ linelen=79,
+ trim=1,
+):
"""Return pretty-print of nested dictionary."""
result = []
for k, v in sorted(adict.items(), key=lambda x: str(x[0]).lower()):
if any(k.startswith(e) for e in excludes):
continue
if isinstance(v, dict):
- v = '\n' + format_dict(v, prefix=prefix+indent, excludes=excludes,
- trim=0)
+ v = '\n' + format_dict(
+ v, prefix=prefix + indent, excludes=excludes, trim=0
+ )
result.append(f'{prefix}{bullets[1]}{k}: {v}')
else:
result.append((f'{prefix}{bullets[0]}{k}: {v}')[:linelen].rstrip())
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/oiffile-2020.1.18/setup.py
new/oiffile-2020.9.18/setup.py
--- old/oiffile-2020.1.18/setup.py 2020-01-19 10:33:48.000000000 +0100
+++ new/oiffile-2020.9.18/setup.py 2020-09-19 06:59:59.000000000 +0200
@@ -14,14 +14,21 @@
description = re.search(r'"""(.*)\.(?:\r\n|\r|\n)', code).groups()[0]
-readme = re.search(r'(?:\r\n|\r|\n){2}"""(.*)"""(?:\r\n|\r|\n){2}__version__',
- code, re.MULTILINE | re.DOTALL).groups()[0]
+readme = re.search(
+ r'(?:\r\n|\r|\n){2}"""(.*)"""(?:\r\n|\r|\n){2}__version__',
+ code,
+ re.MULTILINE | re.DOTALL,
+).groups()[0]
-readme = '\n'.join([description, '=' * len(description)]
- + readme.splitlines()[1:])
+readme = '\n'.join(
+ [description, '=' * len(description)] + readme.splitlines()[1:]
+)
-license = re.search(r'(# Copyright.*?(?:\r\n|\r|\n))(?:\r\n|\r|\n)+""', code,
- re.MULTILINE | re.DOTALL).groups()[0]
+license = re.search(
+ r'(# Copyright.*?(?:\r\n|\r|\n))(?:\r\n|\r|\n)+""',
+ code,
+ re.MULTILINE | re.DOTALL,
+).groups()[0]
license = license.replace('# ', '').replace('#', '')
@@ -40,10 +47,15 @@
author='Christoph Gohlke',
author_email='cgoh...@uci.edu',
url='https://www.lfd.uci.edu/~gohlke/',
+ project_urls={
+ 'Bug Tracker': 'https://github.com/cgohlke/oiffile/issues',
+ 'Source Code': 'https://github.com/cgohlke/oiffile',
+ # 'Documentation': 'https://',
+ },
license='BSD',
packages=['oiffile'],
python_requires='>=3.6',
- install_requires=['numpy>=1.14.5', 'tifffile>=2019.1.1'],
+ install_requires=['numpy>=1.15.1', 'tifffile>=2020.6.3'],
platforms=['any'],
classifiers=[
'Development Status :: 4 - Beta',
@@ -52,8 +64,8 @@
'Intended Audience :: Developers',
'Operating System :: OS Independent',
'Programming Language :: Python :: 3 :: Only',
- 'Programming Language :: Python :: 3.6',
'Programming Language :: Python :: 3.7',
'Programming Language :: Python :: 3.8',
+ 'Programming Language :: Python :: 3.9',
],
)
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