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