Accepting request 1282932 from devel:languages:python

- Switch to pyproject macros.
- Do not mark everything as pycache_only.

OBS-URL: https://build.opensuse.org/request/show/1282932
OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/python-mrcz?expand=0&rev=5

new-pythons.patch

@@ -0,0 +1,67 @@
+From ce031b069262cfd1a21c76bf2d54f7bf31a178c6 Mon Sep 17 00:00:00 2001
+From: Eric Prestat <eric.prestat@gmail.com>
+Date: Sun, 13 Oct 2024 11:21:06 +0100
+Subject: [PATCH 1/2] Remove use of distutils, use packaging library instead
+
+---
+ mrcz/ioMRC.py                 | 8 ++++----
+ requirements.txt              | 1 +
+ utils/update_mrcz_to_0.5.0.py | 1 -
+ 3 files changed, 5 insertions(+), 5 deletions(-)
+
+diff --git a/utils/update_mrcz_to_0.5.0.py b/utils/update_mrcz_to_0.5.0.py
+index ba84d2b..515bd01 100644
+--- a/utils/update_mrcz_to_0.5.0.py
++++ b/utils/update_mrcz_to_0.5.0.py
+@@ -1,7 +1,6 @@
+ import glob, sys, os, os.path as path
+ import numpy as np
+ import mrcz
+-from distutils.version import StrictVersion
+ import shutil
+ 
+ args = sys.argv
+
+From 6c196f6602a50f14545c197234e0b8fdd7711e0f Mon Sep 17 00:00:00 2001
+From: Eric Prestat <eric.prestat@gmail.com>
+Date: Sun, 13 Oct 2024 11:57:13 +0100
+Subject: [PATCH 2/2] Fix deprecated `unittest.makeSuite` and explicitly list
+ python supported version
+
+---
+ mrcz/test_mrcz.py | 4 ++--
+ setup.py          | 5 +++++
+ 2 files changed, 7 insertions(+), 2 deletions(-)
+
+diff --git a/mrcz/test_mrcz.py b/mrcz/test_mrcz.py
+index d76f5fa..fe58e38 100644
+--- a/mrcz/test_mrcz.py
++++ b/mrcz/test_mrcz.py
+@@ -573,9 +573,9 @@ def test(verbosity=2):
+     
+     theSuite = unittest.TestSuite()
+ 
+-    theSuite.addTest(unittest.makeSuite(PythonMrczTests))
++    theSuite.addTest(unittest.defaultTestLoader.loadTestsFromTestCase(PythonMrczTests))
+     if cmrczProg is not None:
+-        theSuite.addTest(unittest.makeSuite(PythonToCMrczTests))
++        theSuite.addTest(unittest.defaultTestLoader.loadTestsFromTestCase(PythonToCMrczTests))
+ 
+     test_result = unittest.TextTestRunner(verbosity=verbosity).run(theSuite)
+     return test_result
+diff --git a/setup.py b/setup.py
+index ebda8b3..47914a7 100644
+--- a/setup.py
++++ b/setup.py
+@@ -62,6 +62,11 @@ def exit_with_error(message):
+ Programming Language :: Python :: 3.6
+ Programming Language :: Python :: 3.7
+ Programming Language :: Python :: 3.8
++Programming Language :: Python :: 3.9
++Programming Language :: Python :: 3.10
++Programming Language :: Python :: 3.11
++Programming Language :: Python :: 3.12
++Programming Language :: Python :: 3.13
+ Topic :: Software Development :: Libraries :: Python Modules
+ Topic :: System :: Archiving :: Compression
+ Operating System :: Microsoft :: Windows

numpy2.patch

@@ -0,0 +1,265 @@
+From 07c01ce360fd3bad884f2a3c03c5f33c0f8348cf Mon Sep 17 00:00:00 2001
+From: Eric Prestat <eric.prestat@gmail.com>
+Date: Sat, 22 Jun 2024 20:05:46 +0100
+Subject: [PATCH 2/5] Replace `==/!=` with `is`/`is not` when comparing to
+ `None`
+
+---
+ mrcz/ReliablePy.py |  8 ++++----
+ mrcz/ioMRC.py      | 20 ++++++++++----------
+ mrcz/test_mrcz.py  |  2 +-
+ 3 files changed, 15 insertions(+), 15 deletions(-)
+
+diff --git a/mrcz/ReliablePy.py b/mrcz/ReliablePy.py
+index 64e3274..db0dc6e 100644
+--- a/mrcz/ReliablePy.py
++++ b/mrcz/ReliablePy.py
+@@ -398,7 +398,7 @@ def pruneParticlesNearImageEdge( self, box = None, shapeImage = [3838,3710] ):
+         Image size is not stored anywhere obvious in Relion, so it must be passed in in terms of 
+         it's shape in [y,x]
+         """
+-        if box == None:
++        if box is None:
+             try: 
+                 box = self.star[b'data_model_general'][b'OriginalImageSize']
+             except:
+@@ -570,7 +570,7 @@ def saveDataStar( self, outputName, particleKey = b"data_" ):
+         Outputs a relion ..._data.star file that has been pruned, regrouped, etc. to outputName
+         """
+         
+-        if outputName == None:
++        if outputName is None:
+             # Need to store input star names, and figure out which was the last loaded particles.star file.
+             # [outFront, outExt] = os.path.splitext()
+             raise IOError( "Default filenames for saveDataStar not implemented yet" )
+@@ -652,11 +652,11 @@ def saveDataAsPar( self, outputPrefix, N_classes = 1, mag = None, pixelsize=None
+         # kept track of in Relion with Magnification and DetectorPixelSize (which
+         # defaults to 14.0)
+         
+-        if pixelsize == None:
++        if pixelsize is None:
+             # Detector pixel size in um, we need pixelsize in Angstrom
+             pixelsize = self.star[b'data_'][b'DetectorPixelSize'][0]*1E4 / self.star[b'data_'][b'Magnification'][0]
+             print( "Found pixelsize of %0.f" % pixelsize )
+-        if mag == None:
++        if mag is None:
+             print( "Using Relion magnification of %.f and DSTEP=%.1f" % ( self.star[b'data_'][b'Magnification'][0], self.star[b'data_'][b'DetectorPixelSize'][0]) )
+             print( "For a K2 (DSTEP=5.0) the appropriate magnification would be %0.f" % 50000/pixelsize )
+         else:
+diff --git a/mrcz/ioMRC.py b/mrcz/ioMRC.py
+index 998de75..c5b234b 100644
+--- a/mrcz/ioMRC.py
++++ b/mrcz/ioMRC.py
+@@ -282,16 +282,16 @@ def readMRC(MRCfilename, idx=None, endian='le',
+         
+         if ( (header['compressor'] in REVERSE_COMPRESSOR_ENUM) 
+             and (REVERSE_COMPRESSOR_ENUM[header['compressor']] > 0) 
+-            and idx == None ):
++            and idx is None ):
+             return __MRCZImport(f, header, slices, endian=endian, fileConvention=fileConvention, 
+                                 n_threads=n_threads)
+         # Else load as uncompressed MRC file
+ 
+-        if idx != None:
++        if idx is not None:
+         # If specific images were requested:
+         # TO DO: add support to read all images within a range at once
+ 
+-            if header['compressor'] != None:
++            if header['compressor'] is not None:
+                 raise RuntimeError('Reading from arbitrary positions not supported for compressed files. Compressor = %s'%header['compressor'])
+             if np.isscalar( idx ):
+                 indices = np.array([idx, idx], dtype='int')
+@@ -370,7 +370,7 @@ def __MRCZImport(f, header, slices, endian='le', fileConvention='ccpem',
+     if not BLOSC_PRESENT:
+         raise ImportError( '`blosc` is not installed, cannot decompress file.' )
+         
+-    if n_threads == None:
++    if n_threads is None:
+         blosc.nthreads = DEFAULT_N_THREADS
+     else:
+         blosc.nthreads = n_threads
+@@ -751,7 +751,7 @@ def writeMRC(input_image, MRCfilename, meta=None, endian='le', dtype=None,
+     # the file exists, but idx is 'None', it will be replaced by a new file 
+     # with new header anyway:
+     if os.path.isfile(MRCfilename):
+-        if idx == None:
++        if idx is None:
+             idxnewfile = True
+         else:
+             idxnewfile = False
+@@ -760,11 +760,11 @@ def writeMRC(input_image, MRCfilename, meta=None, endian='le', dtype=None,
+ 
+     
+     if idxnewfile:
+-        if dtype == 'uint4' and compressor != None:
++        if dtype == 'uint4' and compressor is not None:
+             raise TypeError('uint4 packing is not compatible with compression, use int8 datatype.')
+             
+         header = {'meta': meta}
+-        if dtype == None:
++        if dtype is None:
+             if slices > 0:
+                 header['dtype'] = endchar + input_image[0].dtype.descr[0][1].strip('<>|')
+             else:
+@@ -816,7 +816,7 @@ def writeMRC(input_image, MRCfilename, meta=None, endian='le', dtype=None,
+         
+         header['compressor'] = compressor
+         header['clevel'] = clevel
+-        if n_threads == None and BLOSC_PRESENT:
++        if n_threads is None and BLOSC_PRESENT:
+             n_threads = DEFAULT_N_THREADS
+         header['n_threads'] = n_threads
+         
+@@ -848,8 +848,8 @@ def writeMRC(input_image, MRCfilename, meta=None, endian='le', dtype=None,
+             header['meta'] = meta
+ 
+     # Now that we have a proper header, we go into the details of writing to a specific position:
+-    if idx != None:
+-        if header['compressor'] != None:
++    if idx is not None:
++        if header['compressor'] is not None:
+             raise RuntimeError('Writing at arbitrary positions not supported for compressed files. Compressor = %s' % header['compressor'])
+ 
+         idx = int(idx)
+diff --git a/mrcz/test_mrcz.py b/mrcz/test_mrcz.py
+index d76f5fa..9701cdc 100644
+--- a/mrcz/test_mrcz.py
++++ b/mrcz/test_mrcz.py
+@@ -23,7 +23,7 @@ def which(program):
+         program_ext = os.path.splitext(program)[1]
+         if program_ext == '':
+             prog_exe = which(program + '.exe')
+-            if prog_exe != None:
++            if prog_exe is not None:
+                 return prog_exe
+             return which(program + '.com')
+             
+
+From 92e1b2397e2024c25b61d9eef1ed700c5bc00a4e Mon Sep 17 00:00:00 2001
+From: Eric Prestat <eric.prestat@gmail.com>
+Date: Sat, 22 Jun 2024 20:18:25 +0100
+Subject: [PATCH 3/5] Replace deprecated `disutils.version.StrictVersion` with
+ `packaging.version.Version`
+
+---
+ mrcz/ioMRC.py | 8 ++++----
+ 1 file changed, 4 insertions(+), 4 deletions(-)
+
+diff --git a/mrcz/ioMRC.py b/mrcz/ioMRC.py
+index c5b234b..115044e 100644
+--- a/mrcz/ioMRC.py
++++ b/mrcz/ioMRC.py
+@@ -27,7 +27,7 @@
+         raise ImportError('Get the backport for `concurrent.futures` for Py2.7 as `pip install futures`')
+     raise e
+ from mrcz.__version__ import __version__
+-from distutils.version import StrictVersion
++from packaging.version import Version
+ 
+ import logging
+ logger = logging.getLogger('MRCZ')
+@@ -195,7 +195,7 @@ def _getMRCZVersion(label):
+ 
+     Returns
+     -------
+-    version: Optional[distutils.version.StrictVersion]
++    version: Optional[packaging.version.Version]
+         areturns ``None`` if `label` cannot be parsed.
+     """
+     if isinstance(label, bytes):
+@@ -207,7 +207,7 @@ def _getMRCZVersion(label):
+ 
+     label = label[4:]
+     try:
+-        version = StrictVersion(label)
++        version = Version(label)
+         return version
+     except ValueError:
+         return None
+@@ -537,7 +537,7 @@ def readMRCHeader(MRCfilename, slices=None, endian='le', fileConvention = 'ccpem
+             # is essentially unknown (and wrong). So we have this version 
+             # check where we force slices to be 1 (i.e. we assume it is a 
+             # stack of 2D images).
+-            if mrcz_version is not None and mrcz_version < StrictVersion('0.5.0'):
++            if mrcz_version is not None and mrcz_version < Version('0.5.0'):
+                 logger.warning('MRCZ version < 0.5.0 for file {}, assuming slices == 1.'.format(MRCfilename))
+                 slices = 1
+             else:
+
+From 1c367b3c3a5bfbffbebf36e2bf6a1eab9a668252 Mon Sep 17 00:00:00 2001
+From: Eric Prestat <eric.prestat@gmail.com>
+Date: Sat, 22 Jun 2024 20:20:13 +0100
+Subject: [PATCH 4/5] Replace deprecated `warn` method with `warning`
+
+---
+ mrcz/ioMRC.py | 8 ++++----
+ 1 file changed, 4 insertions(+), 4 deletions(-)
+
+diff --git a/mrcz/ioMRC.py b/mrcz/ioMRC.py
+index 115044e..872ee2e 100644
+--- a/mrcz/ioMRC.py
++++ b/mrcz/ioMRC.py
+@@ -711,12 +711,12 @@ def writeMRC(input_image, MRCfilename, meta=None, endian='le', dtype=None,
+ 
+             if z_slice.dtype == np.float64 or z_slice.dtype == float:
+                 if not WARNED_ABOUT_CASTING_F64:
+-                    logger.warn('Casting {} to `numpy.float32`, further warnings will be suppressed.'.format(MRCfilename))
++                    logger.warning('Casting {} to `numpy.float32`, further warnings will be suppressed.'.format(MRCfilename))
+                     WARNED_ABOUT_CASTING_F64 = True
+                 input_image[J] = z_slice.astype(np.float32)
+             elif z_slice.dtype == np.complex128:
+                 if not WARNED_ABOUT_CASTING_C128:
+-                    logger.warn('Casting {} to `numpy.complex64`, further warnings will be suppressed.'.format(MRCfilename))
++                    logger.warning('Casting {} to `numpy.complex64`, further warnings will be suppressed.'.format(MRCfilename))
+                     WARNED_ABOUT_CASTING_C128 = True
+                 input_image[J] = z_slice.astype(np.complex64)
+             else:
+@@ -732,12 +732,12 @@ def writeMRC(input_image, MRCfilename, meta=None, endian='le', dtype=None,
+         # Cast float64 -> float32, and complex128 -> complex64
+         if input_image.dtype == np.float64 or input_image.dtype == float:
+             if not WARNED_ABOUT_CASTING_F64:
+-                logger.warn('Casting {} to `numpy.float64`'.format(MRCfilename))
++                logger.warning('Casting {} to `numpy.float64`'.format(MRCfilename))
+                 WARNED_ABOUT_CASTING_F64 = True
+             input_image = input_image.astype(np.float32)
+         elif input_image.dtype == np.complex128:
+             if not WARNED_ABOUT_CASTING_C128:
+-                logger.warn('Casting {} to `numpy.complex64`'.format(MRCfilename))
++                logger.warning('Casting {} to `numpy.complex64`'.format(MRCfilename))
+                 WARNED_ABOUT_CASTING_C128 = True
+             input_image = input_image.astype(np.complex64)
+ 
+
+From 97644c4a957946deb1c510d83dba3d3e2fa155ba Mon Sep 17 00:00:00 2001
+From: Eric Prestat <eric.prestat@gmail.com>
+Date: Sat, 22 Jun 2024 20:23:15 +0100
+Subject: [PATCH 5/5] Fix numpy deprecation warning on conversion of an array
+ with ndim > 0 to a scalar
+
+---
+ mrcz/ioMRC.py | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/mrcz/ioMRC.py b/mrcz/ioMRC.py
+index 872ee2e..7a61b16 100644
+--- a/mrcz/ioMRC.py
++++ b/mrcz/ioMRC.py
+@@ -542,7 +542,7 @@ def readMRCHeader(MRCfilename, slices=None, endian='le', fileConvention = 'ccpem
+                 slices = 1
+             else:
+                 f.seek(36)
+-                slices = int(np.fromfile(f, dtype=dtype_i4, count=1))
++                slices = int(np.fromfile(f, dtype=dtype_i4, count=1)[0])
+ 
+         # Read in pixelsize
+         f.seek(40)
+@@ -572,7 +572,7 @@ def readMRCHeader(MRCfilename, slices=None, endian='le', fileConvention = 'ccpem
+ 
+         # Size of meta-data
+         f.seek(92)
+-        header['extendedBytes'] = int(np.fromfile(f, dtype=dtype_i4, count=1))
++        header['extendedBytes'] = int(np.fromfile(f, dtype=dtype_i4, count=1)[0])
+         if header['extendedBytes'] > 0:
+             f.seek(104)
+             header['metaId'] = f.read(4)

python-mrcz-0.5.6.tar.gz

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:8568a9d9fbf3fa8d1097f4b00edd0ed7ab9dcfda97fe236e05076e67b62fae13
-size 56897

python-mrcz-0.5.7.tar.gz

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:dfb729604436942e912d5034ea2df72ba0055e00b31ec403b113222b827f4fa4
+size 56956

python-mrcz.changes

@@ -1,3 +1,22 @@
+-------------------------------------------------------------------
+Thu Jun  5 04:39:19 UTC 2025 - Steve Kowalik <steven.kowalik@suse.com>
+
+- Switch to pyproject macros.
+- Do not mark everything as pycache_only.
+
+-------------------------------------------------------------------
+Wed Nov 27 11:40:39 UTC 2024 - Markéta Machová <mmachova@suse.com>
+
+- Update to 0.5.7
+  * Renamed np.product to np.prod as the old name is deprecated in NumPy 2.0.
+- Add patch new-pythons.patch to fix build with Python 3.13
+- Python 2 can be finally gone
+
+-------------------------------------------------------------------
+Mon Sep  9 13:39:13 UTC 2024 - Markéta Machová <mmachova@suse.com>
+
+- Add patch numpy2.patch to fix build with the new numpy
+
 -------------------------------------------------------------------
 Thu Apr 22 06:21:32 UTC 2021 - Steve Kowalik <steven.kowalik@suse.com>
 

python-mrcz.spec

@@ -1,7 +1,7 @@
 #
 # spec file for package python-mrcz
 #
-# Copyright (c) 2021 SUSE LLC
+# Copyright (c) 2025 SUSE LLC
 #
 # All modifications and additions to the file contributed by third parties
 # remain the property of their copyright owners, unless otherwise agreed
@@ -16,33 +16,30 @@
 #
 
 
-%{?!python_module:%define python_module() python-%{**} python3-%{**}}
+%{?sle15_python_module_pythons}
-%bcond_without python2
-%define skip_python36 1
 Name:           python-mrcz
-Version:        0.5.6
+Version:        0.5.7
 Release:        0
 Summary:        MRCZ meta-compressed image file-format library
 License:        BSD-3-Clause
 URL:            https://github.com/em-MRCZ/python-mrcz
 Source:         https://github.com/em-MRCZ/python-mrcz/archive/v%{version}.tar.gz#/%{name}-%{version}.tar.gz
+# PATCH-FIX-UPSTREAM https://github.com/em-MRCZ/python-mrcz/pull/15 Numpy 2.0 and deprecation fixes
+Patch:          numpy2.patch
+# PATCH-FIX-UPSTREAM https://github.com/em-MRCZ/python-mrcz/pull/16 Remove distutils / support python >=3.12
+Patch:          new-pythons.patch
 BuildRequires:  %{python_module blosc}
 BuildRequires:  %{python_module numpy}
+BuildRequires:  %{python_module pip}
 BuildRequires:  %{python_module pytest}
 BuildRequires:  %{python_module setuptools}
+BuildRequires:  %{python_module wheel}
+BuildRequires:  dos2unix
 BuildRequires:  fdupes
 BuildRequires:  python-rpm-macros
-Requires:       python-blosc
 Requires:       python-numpy
+Recommends:     python-blosc
 BuildArch:      noarch
-%if %{with python2}
-BuildRequires:  python-enum34
-BuildRequires:  python-futures
-%endif
-%ifpython2
-Requires:       python-enum34
-Requires:       python-futures
-%endif
 %python_subpackages
 
 %description
@@ -53,13 +50,14 @@ file input/output for the era of "Big Data" in electron and optical
 microscopy.
 
 %prep
-%setup -q
+%autosetup -p1
+dos2unix README.rst
 
 %build
-%python_build
+%pyproject_wheel
 
 %install
-%python_install
+%pyproject_install
 %python_expand %fdupes %{buildroot}%{$python_sitelib}
 
 %check
@@ -68,9 +66,7 @@ microscopy.
 %files %{python_files}
 %doc AUTHORS.txt README.rst
 %license LICENSE.txt
-%dir %{python_sitelib}/mrcz/
+%{python_sitelib}/mrcz
-%pycache_only %{python_sitelib}/mrcz-%{version}-py%{python_version}.egg-info/
+%{python_sitelib}/mrcz-%{version}.dist-info
-%pycache_only %{python_sitelib}/mrcz/*.py
-%pycache_only %{python_sitelib}/mrcz/__pycache__/
 
 %changelog