[med-svn] [Git][med-team/python-loompy][master] add Numpy 2.x patch

[Alexandre Detiste (@detiste-guest)]

Alexandre Detiste pushed to branch master at Debian Med / python-loompy


Commits:
841d306f by Alexandre Detiste at 2025-05-17T19:12:40+02:00
add Numpy 2.x patch

- - - - -


2 changed files:

- + debian/patches/numpy_2x.patch
- debian/patches/series


Changes:

=====================================
debian/patches/numpy_2x.patch
=====================================
@@ -0,0 +1,59 @@
+--- a/loompy/loom_validator.py
++++ b/loompy/loom_validator.py
+@@ -232,7 +232,7 @@
+ 		if self.version == "3.0.0":
+ 			expected_dtype = np.object_
+ 		else:
+-			expected_dtype = np.string_
++			expected_dtype = np.bytes_
+ 		delay_print("Row attributes:")
+ 		if self._check("row_attrs" in file, "'row_attrs' group is missing"):
+ 			for ra in file["row_attrs"]:
+--- a/loompy/normalize.py
++++ b/loompy/normalize.py
+@@ -7,20 +7,19 @@
+ 
+ def normalize_attr_strings(a: np.ndarray) -> np.ndarray:
+ 	"""
+-	Take an np.ndarray of all kinds of string-like elements, and return an array of ascii (np.string_) objects
++	Take an np.ndarray of all kinds of string-like elements, and return an array of ascii (np.bytes_) objects
+ 	"""
+ 	if np.issubdtype(a.dtype, np.object_):
+-		# if np.all([type(x) is str for x in a]) or np.all([type(x) is np.str_ for x in a]) or np.all([type(x) is np.unicode_ for x in a]):
+-		if np.all([(type(x) is str or type(x) is np.str_ or type(x) is np.unicode_) for x in a]):
++		if np.all([(type(x) is str or type(x) is np.str_) for x in a]):
+ 			return np.array([x.encode('ascii', 'xmlcharrefreplace') for x in a])
+-		elif np.all([type(x) is np.string_ for x in a]) or np.all([type(x) is np.bytes_ for x in a]):
+-			return a.astype("string_")
++		elif np.all([type(x) is np.bytes_ for x in a]):
++			return a.astype("bytes_")
+ 		else:
+ 			logging.debug(f"Attribute contains mixed object types ({np.unique([str(type(x)) for x in a])}); casting all to string")
+-			return np.array([str(x) for x in a], dtype="string_")
+-	elif np.issubdtype(a.dtype, np.string_) or np.issubdtype(a.dtype, np.object_):
++			return np.array([str(x) for x in a], dtype="bytes_")
++	elif np.issubdtype(a.dtype, np.bytes_) or np.issubdtype(a.dtype, np.object_):
+ 		return a
+-	elif np.issubdtype(a.dtype, np.str_) or np.issubdtype(a.dtype, np.unicode_):
++	elif np.issubdtype(a.dtype, np.str_):
+ 		return np.array([x.encode('ascii', 'xmlcharrefreplace') for x in a])
+ 	else:
+ 		raise ValueError("String values must be object, ascii or unicode.")
+@@ -88,7 +87,7 @@
+ 		scalar = True
+ 		a = np.array([a])
+ 	result: np.ndarray = None   # This second clause takes care of attributes stored as variable-length ascii, which can be generated by loomR or Seurat
+-	if np.issubdtype(a.dtype, np.string_) or np.issubdtype(a.dtype, np.object_):
++	if np.issubdtype(a.dtype, np.bytes_) or np.issubdtype(a.dtype, np.object_):
+ 		# First ensure that what we load is valid ascii (i.e. ignore anything outside 7-bit range)
+ 		if hasattr(a, "decode"):  # This takes care of Loom files that store strings as UTF8, which comes in as str and doesn't have a decode method
+ 			temp = np.array([x.decode('ascii', 'ignore') for x in a])
+@@ -100,7 +99,7 @@
+ 		except:  # Dirty hack to handle UTF-8 non-break-space in scalar strings. TODO: Rewrite this whole method completely!
+ 			if type(a[0]) == np.bytes_:
+ 				result = [ a[0].replace(b'\xc2\xa0', b'') ]
+-	elif np.issubdtype(a.dtype, np.str_) or np.issubdtype(a.dtype, np.unicode_):
++	elif np.issubdtype(a.dtype, np.str_):
+ 		result = np.array(a.astype(str), dtype=object)
+ 	else:
+ 		result = a


=====================================
debian/patches/series
=====================================
@@ -2,3 +2,4 @@ tests-open-loom-write-permissions.patch
 numpy_1.24.patch
 python3.12.patch
 do_not_generate_a_dep_on_pkg_resources.patch
+numpy_2x.patch



View it on GitLab: https://salsa.debian.org/med-team/python-loompy/-/commit/841d306ff9f0565397ba5211369e84597bbfcc43

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View it on GitLab: https://salsa.debian.org/med-team/python-loompy/-/commit/841d306ff9f0565397ba5211369e84597bbfcc43
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