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Accepting request 1226889 from home:mcalabkova:branches:devel:languages:python

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- 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

OBS-URL: https://build.opensuse.org/request/show/1226889
OBS-URL: https://build.opensuse.org/package/show/devel:languages:python/python-mrcz?expand=0&rev=9
This commit is contained in:
Nico Krapp
2024-11-27 16:10:59 +00:00
committed by Git OBS Bridge
parent fbe02815e4
commit 79a37f54d5
6 changed files with 81 additions and 78 deletions
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66
numpy2.patch
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@@ -1,69 +1,3 @@
From f28e1a2b90c04ac47c586fa7398d1e694029174a Mon Sep 17 00:00:00 2001
From: Eric Prestat <eric.prestat@gmail.com>
Date: Sat, 22 Jun 2024 20:02:09 +0100
Subject: [PATCH 1/5] Replace `np.product` with `np.prod` since it has been
removed in numpy 2
---
mrcz/ioMRC.py | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/mrcz/ioMRC.py b/mrcz/ioMRC.py
index b1184bb..998de75 100644
--- a/mrcz/ioMRC.py
+++ b/mrcz/ioMRC.py
@@ -318,7 +318,7 @@ def readMRC(MRCfilename, idx=None, endian='le',
header['dimensions'][0] = n
# This offset will be applied to f.seek():
- offset = idx * np.product(header['dimensions'][1:])*np.dtype(header['dtype']).itemsize
+ offset = idx * np.prod(header['dimensions'][1:])*np.dtype(header['dtype']).itemsize
else:
offset = 0
@@ -331,7 +331,7 @@ def readMRC(MRCfilename, idx=None, endian='le',
else: # Load entire file into memory
dims = header['dimensions']
if slices > 0: # List of NumPy 2D-arrays
- frame_size = slices * np.product(dims[1:])
+ frame_size = slices * np.prod(dims[1:])
n_frames = dims[0] // slices
dtype = header['dtype']
@@ -343,12 +343,12 @@ def readMRC(MRCfilename, idx=None, endian='le',
image.append(buffer)
else: # monolithic NumPy ndarray
- image = np.fromfile(f, dtype=header['dtype'], count=np.product(dims))
+ image = np.fromfile(f, dtype=header['dtype'], count=np.prod(dims))
if header['MRCtype'] == 101:
# Seems the 4-bit is interlaced ...
interlaced_image = image
- image = np.empty(np.product(dims), dtype=header['dtype'])
+ image = np.empty(np.prod(dims), dtype=header['dtype'])
image[0::2] = np.left_shift(interlaced_image,4) / 15
image[1::2] = np.right_shift(interlaced_image,4)
@@ -429,7 +429,7 @@ def __MRCZImport(f, header, slices, endian='le', fileConvention='ccpem',
raise NotImplementedError('MRC type 101 (uint4) not supported with return as `list`')
interlaced_image = image
- image = np.empty(np.product(header['dimensions']), dtype=dtype)
+ image = np.empty(np.prod(header['dimensions']), dtype=dtype)
# Bit-shift and Bit-and to seperate decimated pixels
image[0::2] = np.left_shift(interlaced_image, 4) / 15
image[1::2] = np.right_shift(interlaced_image, 4)
@@ -872,7 +872,7 @@ def writeMRC(input_image, MRCfilename, meta=None, endian='le', dtype=None,
header['dimensions'] = np.array([idx + input_image.shape[0], header['dimensions'][1], header['dimensions'][2]])
# This offset will be applied to f.seek():
- offset = idx * np.product(header['dimensions'][1:]) * np.dtype(header['dtype']).itemsize
+ offset = idx * np.prod(header['dimensions'][1:]) * np.dtype(header['dtype']).itemsize
else:
offset = 0
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