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aports/community/py3-h5py/cython3.patch
Natanael Copa 71a773b061 community/*: rebuild against python 3.12
2024-04-12 11:59:22 +02:00

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From b8cc539ce501f95b7f9720b318c54672c512ec16 Mon Sep 17 00:00:00 2001
From: Thomas Kluyver <thomas@kluyver.me.uk>
Date: Thu, 5 Oct 2023 12:44:12 +0100
Subject: [PATCH 1/9] Fix compiling fileobj file driver with Cython 3.0
---
h5py/api_types_hdf5.pxd | 24 ++++++++++++------------
h5py/h5fd.pyx | 4 ++--
2 files changed, 14 insertions(+), 14 deletions(-)
diff --git a/h5py/api_types_hdf5.pxd b/h5py/api_types_hdf5.pxd
index f3d537c47..a1369e8a7 100644
--- a/h5py/api_types_hdf5.pxd
+++ b/h5py/api_types_hdf5.pxd
@@ -257,27 +257,27 @@ cdef extern from "hdf5.h":
herr_t (*sb_encode)(H5FD_t *file, char *name, unsigned char *p)
herr_t (*sb_decode)(H5FD_t *f, const char *name, const unsigned char *p)
size_t fapl_size
- void * (*fapl_get)(H5FD_t *file)
- void * (*fapl_copy)(const void *fapl)
- herr_t (*fapl_free)(void *fapl)
+ void * (*fapl_get)(H5FD_t *file) except *
+ void * (*fapl_copy)(const void *fapl) except *
+ herr_t (*fapl_free)(void *fapl) except *
size_t dxpl_size
void * (*dxpl_copy)(const void *dxpl)
herr_t (*dxpl_free)(void *dxpl)
- H5FD_t *(*open)(const char *name, unsigned flags, hid_t fapl, haddr_t maxaddr)
- herr_t (*close)(H5FD_t *file)
+ H5FD_t *(*open)(const char *name, unsigned flags, hid_t fapl, haddr_t maxaddr) except *
+ herr_t (*close)(H5FD_t *file) except *
int (*cmp)(const H5FD_t *f1, const H5FD_t *f2)
herr_t (*query)(const H5FD_t *f1, unsigned long *flags)
herr_t (*get_type_map)(const H5FD_t *file, H5FD_mem_t *type_map)
haddr_t (*alloc)(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, hsize_t size)
herr_t (*free)(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, haddr_t addr, hsize_t size)
- haddr_t (*get_eoa)(const H5FD_t *file, H5FD_mem_t type)
- herr_t (*set_eoa)(H5FD_t *file, H5FD_mem_t type, haddr_t addr)
- haddr_t (*get_eof)(const H5FD_t *file, H5FD_mem_t type)
+ haddr_t (*get_eoa)(const H5FD_t *file, H5FD_mem_t type) except *
+ herr_t (*set_eoa)(H5FD_t *file, H5FD_mem_t type, haddr_t addr) except *
+ haddr_t (*get_eof)(const H5FD_t *file, H5FD_mem_t type) except *
herr_t (*get_handle)(H5FD_t *file, hid_t fapl, void**file_handle)
- herr_t (*read)(H5FD_t *file, H5FD_mem_t type, hid_t dxpl, haddr_t addr, size_t size, void *buffer)
- herr_t (*write)(H5FD_t *file, H5FD_mem_t type, hid_t dxpl, haddr_t addr, size_t size, const void *buffer)
- herr_t (*flush)(H5FD_t *file, hid_t dxpl_id, hbool_t closing)
- herr_t (*truncate)(H5FD_t *file, hid_t dxpl_id, hbool_t closing)
+ herr_t (*read)(H5FD_t *file, H5FD_mem_t type, hid_t dxpl, haddr_t addr, size_t size, void *buffer) except *
+ herr_t (*write)(H5FD_t *file, H5FD_mem_t type, hid_t dxpl, haddr_t addr, size_t size, const void *buffer) except *
+ herr_t (*flush)(H5FD_t *file, hid_t dxpl_id, hbool_t closing) except *
+ herr_t (*truncate)(H5FD_t *file, hid_t dxpl_id, hbool_t closing) except *
herr_t (*lock)(H5FD_t *file, hbool_t rw)
herr_t (*unlock)(H5FD_t *file)
H5FD_mem_t fl_map[<int>H5FD_MEM_NTYPES]
diff --git a/h5py/h5fd.pyx b/h5py/h5fd.pyx
index e97460573..f1b4aade7 100644
--- a/h5py/h5fd.pyx
+++ b/h5py/h5fd.pyx
@@ -144,10 +144,10 @@ cdef herr_t H5FD_fileobj_close(H5FD_fileobj_t *f) except -1 with gil:
stdlib_free(f)
return 0
-cdef haddr_t H5FD_fileobj_get_eoa(const H5FD_fileobj_t *f, H5FD_mem_t type):
+cdef haddr_t H5FD_fileobj_get_eoa(const H5FD_fileobj_t *f, H5FD_mem_t type) noexcept nogil:
return f.eoa
-cdef herr_t H5FD_fileobj_set_eoa(H5FD_fileobj_t *f, H5FD_mem_t type, haddr_t addr):
+cdef herr_t H5FD_fileobj_set_eoa(H5FD_fileobj_t *f, H5FD_mem_t type, haddr_t addr) noexcept nogil:
f.eoa = addr
return 0
From c0a7b9848eedbd3b64c248ed579ee629903231f1 Mon Sep 17 00:00:00 2001
From: David Hoese <david.hoese@ssec.wisc.edu>
Date: Tue, 28 Nov 2023 09:57:33 -0600
Subject: [PATCH 2/9] Add minimal except definitions for Cython 3 compatibility
---
h5py/api_types_hdf5.pxd | 38 +++++++++++++++++++-------------------
h5py/h5fd.pyx | 36 ++++++++++++++++++++++++++----------
2 files changed, 45 insertions(+), 29 deletions(-)
diff --git a/h5py/api_types_hdf5.pxd b/h5py/api_types_hdf5.pxd
index a1369e8a7..0523b2feb 100644
--- a/h5py/api_types_hdf5.pxd
+++ b/h5py/api_types_hdf5.pxd
@@ -259,25 +259,25 @@ cdef extern from "hdf5.h":
size_t fapl_size
void * (*fapl_get)(H5FD_t *file) except *
void * (*fapl_copy)(const void *fapl) except *
- herr_t (*fapl_free)(void *fapl) except *
+ herr_t (*fapl_free)(void *fapl) except -1
size_t dxpl_size
void * (*dxpl_copy)(const void *dxpl)
herr_t (*dxpl_free)(void *dxpl)
H5FD_t *(*open)(const char *name, unsigned flags, hid_t fapl, haddr_t maxaddr) except *
- herr_t (*close)(H5FD_t *file) except *
+ herr_t (*close)(H5FD_t *file) except -1
int (*cmp)(const H5FD_t *f1, const H5FD_t *f2)
herr_t (*query)(const H5FD_t *f1, unsigned long *flags)
herr_t (*get_type_map)(const H5FD_t *file, H5FD_mem_t *type_map)
haddr_t (*alloc)(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, hsize_t size)
herr_t (*free)(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, haddr_t addr, hsize_t size)
- haddr_t (*get_eoa)(const H5FD_t *file, H5FD_mem_t type) except *
- herr_t (*set_eoa)(H5FD_t *file, H5FD_mem_t type, haddr_t addr) except *
- haddr_t (*get_eof)(const H5FD_t *file, H5FD_mem_t type) except *
+ haddr_t (*get_eoa)(const H5FD_t *file, H5FD_mem_t type) noexcept
+ herr_t (*set_eoa)(H5FD_t *file, H5FD_mem_t type, haddr_t addr) noexcept
+ haddr_t (*get_eof)(const H5FD_t *file, H5FD_mem_t type) noexcept
herr_t (*get_handle)(H5FD_t *file, hid_t fapl, void**file_handle)
herr_t (*read)(H5FD_t *file, H5FD_mem_t type, hid_t dxpl, haddr_t addr, size_t size, void *buffer) except *
herr_t (*write)(H5FD_t *file, H5FD_mem_t type, hid_t dxpl, haddr_t addr, size_t size, const void *buffer) except *
- herr_t (*flush)(H5FD_t *file, hid_t dxpl_id, hbool_t closing) except *
- herr_t (*truncate)(H5FD_t *file, hid_t dxpl_id, hbool_t closing) except *
+ herr_t (*flush)(H5FD_t *file, hid_t dxpl_id, hbool_t closing) except -1
+ herr_t (*truncate)(H5FD_t *file, hid_t dxpl_id, hbool_t closing) except -1
herr_t (*lock)(H5FD_t *file, hbool_t rw)
herr_t (*unlock)(H5FD_t *file)
H5FD_mem_t fl_map[<int>H5FD_MEM_NTYPES]
@@ -295,27 +295,27 @@ cdef extern from "hdf5.h":
herr_t (*sb_encode)(H5FD_t *file, char *name, unsigned char *p)
herr_t (*sb_decode)(H5FD_t *f, const char *name, const unsigned char *p)
size_t fapl_size
- void * (*fapl_get)(H5FD_t *file)
- void * (*fapl_copy)(const void *fapl)
- herr_t (*fapl_free)(void *fapl)
+ void * (*fapl_get)(H5FD_t *file) except *
+ void * (*fapl_copy)(const void *fapl) except *
+ herr_t (*fapl_free)(void *fapl) except -1
size_t dxpl_size
void * (*dxpl_copy)(const void *dxpl)
herr_t (*dxpl_free)(void *dxpl)
- H5FD_t *(*open)(const char *name, unsigned flags, hid_t fapl, haddr_t maxaddr)
- herr_t (*close)(H5FD_t *file)
+ H5FD_t *(*open)(const char *name, unsigned flags, hid_t fapl, haddr_t maxaddr) except *
+ herr_t (*close)(H5FD_t *file) except -1
int (*cmp)(const H5FD_t *f1, const H5FD_t *f2)
herr_t (*query)(const H5FD_t *f1, unsigned long *flags)
herr_t (*get_type_map)(const H5FD_t *file, H5FD_mem_t *type_map)
haddr_t (*alloc)(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, hsize_t size)
herr_t (*free)(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, haddr_t addr, hsize_t size)
- haddr_t (*get_eoa)(const H5FD_t *file, H5FD_mem_t type)
- herr_t (*set_eoa)(H5FD_t *file, H5FD_mem_t type, haddr_t addr)
- haddr_t (*get_eof)(const H5FD_t *file, H5FD_mem_t type)
+ haddr_t (*get_eoa)(const H5FD_t *file, H5FD_mem_t type) noexcept
+ herr_t (*set_eoa)(H5FD_t *file, H5FD_mem_t type, haddr_t addr) noexcept
+ haddr_t (*get_eof)(const H5FD_t *file, H5FD_mem_t type) noexcept
herr_t (*get_handle)(H5FD_t *file, hid_t fapl, void**file_handle)
- herr_t (*read)(H5FD_t *file, H5FD_mem_t type, hid_t dxpl, haddr_t addr, size_t size, void *buffer)
- herr_t (*write)(H5FD_t *file, H5FD_mem_t type, hid_t dxpl, haddr_t addr, size_t size, const void *buffer)
- herr_t (*flush)(H5FD_t *file, hid_t dxpl_id, hbool_t closing)
- herr_t (*truncate)(H5FD_t *file, hid_t dxpl_id, hbool_t closing)
+ herr_t (*read)(H5FD_t *file, H5FD_mem_t type, hid_t dxpl, haddr_t addr, size_t size, void *buffer) except *
+ herr_t (*write)(H5FD_t *file, H5FD_mem_t type, hid_t dxpl, haddr_t addr, size_t size, const void *buffer) except *
+ herr_t (*flush)(H5FD_t *file, hid_t dxpl_id, hbool_t closing) except -1
+ herr_t (*truncate)(H5FD_t *file, hid_t dxpl_id, hbool_t closing) except -1
herr_t (*lock)(H5FD_t *file, hbool_t rw)
herr_t (*unlock)(H5FD_t *file)
H5FD_mem_t fl_map[<int>H5FD_MEM_NTYPES]
diff --git a/h5py/h5fd.pyx b/h5py/h5fd.pyx
index f1b4aade7..5e2ea9cd1 100644
--- a/h5py/h5fd.pyx
+++ b/h5py/h5fd.pyx
@@ -151,7 +151,7 @@ cdef herr_t H5FD_fileobj_set_eoa(H5FD_fileobj_t *f, H5FD_mem_t type, haddr_t add
f.eoa = addr
return 0
-cdef haddr_t H5FD_fileobj_get_eof(const H5FD_fileobj_t *f, H5FD_mem_t type) except -1 with gil: # HADDR_UNDEF
+cdef haddr_t H5FD_fileobj_get_eof(const H5FD_fileobj_t *f, H5FD_mem_t type) noexcept with gil: # HADDR_UNDEF
(<object>f.fileobj).seek(0, libc.stdio.SEEK_END)
return (<object>f.fileobj).tell()
@@ -191,22 +191,38 @@ cdef herr_t H5FD_fileobj_flush(H5FD_fileobj_t *f, hid_t dxpl, hbool_t closing) e
cdef H5FD_class_t info
memset(&info, 0, sizeof(info))
+# Cython doesn't support "except X" in casting definition currently
+ctypedef herr_t (*file_free_func_ptr)(void *) except -1
+
+ctypedef herr_t (*file_close_func_ptr)(H5FD_t *) except -1
+ctypedef haddr_t (*file_get_eoa_func_ptr)(const H5FD_t *, H5FD_mem_t) noexcept
+ctypedef herr_t (*file_set_eof_func_ptr)(H5FD_t *, H5FD_mem_t, haddr_t) noexcept
+ctypedef haddr_t (*file_get_eof_func_ptr)(const H5FD_t *, H5FD_mem_t) noexcept
+ctypedef herr_t (*file_read_func_ptr)(H5FD_t *, H5FD_mem_t, hid_t, haddr_t, size_t, void*) except -1
+ctypedef herr_t (*file_write_func_ptr)(H5FD_t *, H5FD_mem_t, hid_t, haddr_t, size_t, const void*) except -1
+ctypedef herr_t (*file_truncate_func_ptr)(H5FD_t *, hid_t, hbool_t) except -1
+ctypedef herr_t (*file_flush_func_ptr)(H5FD_t *, hid_t, hbool_t) except -1
+
+
info.name = 'fileobj'
info.maxaddr = libc.stdint.SIZE_MAX - 1
info.fc_degree = H5F_CLOSE_WEAK
info.fapl_size = sizeof(PyObject *)
info.fapl_get = <void *(*)(H5FD_t *)>H5FD_fileobj_fapl_get
info.fapl_copy = <void *(*)(const void *)>H5FD_fileobj_fapl_copy
-info.fapl_free = <herr_t (*)(void *)>H5FD_fileobj_fapl_free
+
+info.fapl_free = <file_free_func_ptr>H5FD_fileobj_fapl_free
+
info.open = <H5FD_t *(*)(const char *name, unsigned flags, hid_t fapl, haddr_t maxaddr)>H5FD_fileobj_open
-info.close = <herr_t (*)(H5FD_t *)>H5FD_fileobj_close
-info.get_eoa = <haddr_t (*)(const H5FD_t *, H5FD_mem_t)>H5FD_fileobj_get_eoa
-info.set_eoa = <herr_t (*)(H5FD_t *, H5FD_mem_t, haddr_t)>H5FD_fileobj_set_eoa
-info.get_eof = <haddr_t (*)(const H5FD_t *, H5FD_mem_t)>H5FD_fileobj_get_eof
-info.read = <herr_t (*)(H5FD_t *, H5FD_mem_t, hid_t, haddr_t, size_t, void *)>H5FD_fileobj_read
-info.write = <herr_t (*)(H5FD_t *, H5FD_mem_t, hid_t, haddr_t, size_t, const void *)>H5FD_fileobj_write
-info.truncate = <herr_t (*)(H5FD_t *, hid_t, hbool_t)>H5FD_fileobj_truncate
-info.flush = <herr_t (*)(H5FD_t *, hid_t, hbool_t)>H5FD_fileobj_flush
+
+info.close = <file_close_func_ptr>H5FD_fileobj_close
+info.get_eoa = <file_get_eoa_func_ptr>H5FD_fileobj_get_eoa
+info.set_eoa = <file_set_eof_func_ptr>H5FD_fileobj_set_eoa
+info.get_eof = <file_get_eof_func_ptr>H5FD_fileobj_get_eof
+info.read = <file_read_func_ptr>H5FD_fileobj_read
+info.write = <file_write_func_ptr>H5FD_fileobj_write
+info.truncate = <file_truncate_func_ptr>H5FD_fileobj_truncate
+info.flush = <file_flush_func_ptr>H5FD_fileobj_flush
# H5FD_FLMAP_DICHOTOMY
info.fl_map = [H5FD_MEM_SUPER, # default
H5FD_MEM_SUPER, # super
From 8a1c2ed5cfe7527244ec452ddb0cdb6b14e9595f Mon Sep 17 00:00:00 2001
From: David Hoese <david.hoese@ssec.wisc.edu>
Date: Tue, 28 Nov 2023 09:58:49 -0600
Subject: [PATCH 3/9] Force Cython to version 3 during build
---
pyproject.toml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/pyproject.toml b/pyproject.toml
index ee573d2fc..3bc08b762 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
[build-system]
requires = [
- "Cython >=0.29.31,<1",
+ "Cython >=3",
"oldest-supported-numpy",
"pkgconfig",
"setuptools >=61",
From 2f7c05123ca3490dd2617b7a6e4545c1063e7082 Mon Sep 17 00:00:00 2001
From: David Hoese <david.hoese@ssec.wisc.edu>
Date: Tue, 28 Nov 2023 14:12:29 -0600
Subject: [PATCH 4/9] Update remaining except/nogil cython 3 issues
---
h5py/_errors.pxd | 2 +-
h5py/_errors.pyx | 4 ++--
h5py/_locks.pxi | 2 +-
h5py/_proxy.pyx | 4 ++--
4 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/h5py/_errors.pxd b/h5py/_errors.pxd
index df9c1bbe4..f56d7353a 100644
--- a/h5py/_errors.pxd
+++ b/h5py/_errors.pxd
@@ -425,4 +425,4 @@ ctypedef struct err_cookie:
cdef err_cookie set_error_handler(err_cookie handler)
# Set the default error handler set by silence_errors/unsilence_errors
-cdef void set_default_error_handler() nogil
+cdef void set_default_error_handler() noexcept nogil
diff --git a/h5py/_errors.pyx b/h5py/_errors.pyx
index c3bd184ee..2a7524b2c 100644
--- a/h5py/_errors.pyx
+++ b/h5py/_errors.pyx
@@ -94,7 +94,7 @@ cdef struct err_data_t:
H5E_error_t err
int n
-cdef herr_t walk_cb(unsigned int n, const H5E_error_t *desc, void *e) nogil noexcept:
+cdef herr_t walk_cb(unsigned int n, const H5E_error_t *desc, void *e) noexcept nogil:
cdef err_data_t *ee = <err_data_t*>e
@@ -168,7 +168,7 @@ cdef err_cookie _error_handler # Store error handler used by h5py
_error_handler.func = NULL
_error_handler.data = NULL
-cdef void set_default_error_handler() nogil:
+cdef void set_default_error_handler() noexcept nogil:
"""Set h5py's current default error handler"""
H5Eset_auto(<hid_t>H5E_DEFAULT, _error_handler.func, _error_handler.data)
diff --git a/h5py/_locks.pxi b/h5py/_locks.pxi
index bc8b2dd92..c6cea88dd 100644
--- a/h5py/_locks.pxi
+++ b/h5py/_locks.pxi
@@ -111,7 +111,7 @@ cdef bint _acquire_lock(FastRLock lock, long current_thread, int wait) nogil:
lock._count = 1
return 1
-cdef inline void unlock_lock(FastRLock lock) nogil:
+cdef inline void unlock_lock(FastRLock lock) noexcept nogil:
# Note that this function *must* hold the GIL when being called.
# We just use 'nogil' in the signature to make sure that no Python
# code execution slips in that might free the GIL
diff --git a/h5py/_proxy.pyx b/h5py/_proxy.pyx
index 46b4fe0d8..e40504f53 100644
--- a/h5py/_proxy.pyx
+++ b/h5py/_proxy.pyx
@@ -241,7 +241,7 @@ ctypedef struct h5py_scatter_t:
void* buf
cdef herr_t h5py_scatter_cb(void* elem, hid_t type_id, unsigned ndim,
- const hsize_t *point, void *operator_data) nogil except -1:
+ const hsize_t *point, void *operator_data) except -1 nogil:
cdef h5py_scatter_t* info = <h5py_scatter_t*>operator_data
memcpy(elem, (<char*>info[0].buf)+((info[0].i)*(info[0].elsize)),
@@ -252,7 +252,7 @@ cdef herr_t h5py_scatter_cb(void* elem, hid_t type_id, unsigned ndim,
return 0
cdef herr_t h5py_gather_cb(void* elem, hid_t type_id, unsigned ndim,
- const hsize_t *point, void *operator_data) nogil except -1:
+ const hsize_t *point, void *operator_data) except -1 nogil:
cdef h5py_scatter_t* info = <h5py_scatter_t*>operator_data
memcpy((<char*>info[0].buf)+((info[0].i)*(info[0].elsize)), elem,
From d6b267d980b391561047af0e573d26140c7d35bd Mon Sep 17 00:00:00 2001
From: David Hoese <david.hoese@ssec.wisc.edu>
Date: Fri, 1 Dec 2023 09:49:29 -0600
Subject: [PATCH 5/9] Fix get_eof exception definition
---
h5py/api_types_hdf5.pxd | 4 ++--
h5py/h5fd.pyx | 4 ++--
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/h5py/api_types_hdf5.pxd b/h5py/api_types_hdf5.pxd
index 6e2fc2399..099e0f588 100644
--- a/h5py/api_types_hdf5.pxd
+++ b/h5py/api_types_hdf5.pxd
@@ -272,7 +272,7 @@ cdef extern from "hdf5.h":
herr_t (*free)(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, haddr_t addr, hsize_t size)
haddr_t (*get_eoa)(const H5FD_t *file, H5FD_mem_t type) noexcept
herr_t (*set_eoa)(H5FD_t *file, H5FD_mem_t type, haddr_t addr) noexcept
- haddr_t (*get_eof)(const H5FD_t *file, H5FD_mem_t type) noexcept
+ haddr_t (*get_eof)(const H5FD_t *file, H5FD_mem_t type) except -1
herr_t (*get_handle)(H5FD_t *file, hid_t fapl, void**file_handle)
herr_t (*read)(H5FD_t *file, H5FD_mem_t type, hid_t dxpl, haddr_t addr, size_t size, void *buffer) except *
herr_t (*write)(H5FD_t *file, H5FD_mem_t type, hid_t dxpl, haddr_t addr, size_t size, const void *buffer) except *
@@ -310,7 +310,7 @@ cdef extern from "hdf5.h":
herr_t (*free)(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, haddr_t addr, hsize_t size)
haddr_t (*get_eoa)(const H5FD_t *file, H5FD_mem_t type) noexcept
herr_t (*set_eoa)(H5FD_t *file, H5FD_mem_t type, haddr_t addr) noexcept
- haddr_t (*get_eof)(const H5FD_t *file, H5FD_mem_t type) noexcept
+ haddr_t (*get_eof)(const H5FD_t *file, H5FD_mem_t type) except -1
herr_t (*get_handle)(H5FD_t *file, hid_t fapl, void**file_handle)
herr_t (*read)(H5FD_t *file, H5FD_mem_t type, hid_t dxpl, haddr_t addr, size_t size, void *buffer) except *
herr_t (*write)(H5FD_t *file, H5FD_mem_t type, hid_t dxpl, haddr_t addr, size_t size, const void *buffer) except *
diff --git a/h5py/h5fd.pyx b/h5py/h5fd.pyx
index 5e2ea9cd1..d39cf68f2 100644
--- a/h5py/h5fd.pyx
+++ b/h5py/h5fd.pyx
@@ -151,7 +151,7 @@ cdef herr_t H5FD_fileobj_set_eoa(H5FD_fileobj_t *f, H5FD_mem_t type, haddr_t add
f.eoa = addr
return 0
-cdef haddr_t H5FD_fileobj_get_eof(const H5FD_fileobj_t *f, H5FD_mem_t type) noexcept with gil: # HADDR_UNDEF
+cdef haddr_t H5FD_fileobj_get_eof(const H5FD_fileobj_t *f, H5FD_mem_t type) except -1 with gil: # HADDR_UNDEF
(<object>f.fileobj).seek(0, libc.stdio.SEEK_END)
return (<object>f.fileobj).tell()
@@ -197,7 +197,7 @@ ctypedef herr_t (*file_free_func_ptr)(void *) except -1
ctypedef herr_t (*file_close_func_ptr)(H5FD_t *) except -1
ctypedef haddr_t (*file_get_eoa_func_ptr)(const H5FD_t *, H5FD_mem_t) noexcept
ctypedef herr_t (*file_set_eof_func_ptr)(H5FD_t *, H5FD_mem_t, haddr_t) noexcept
-ctypedef haddr_t (*file_get_eof_func_ptr)(const H5FD_t *, H5FD_mem_t) noexcept
+ctypedef haddr_t (*file_get_eof_func_ptr)(const H5FD_t *, H5FD_mem_t) except -1
ctypedef herr_t (*file_read_func_ptr)(H5FD_t *, H5FD_mem_t, hid_t, haddr_t, size_t, void*) except -1
ctypedef herr_t (*file_write_func_ptr)(H5FD_t *, H5FD_mem_t, hid_t, haddr_t, size_t, const void*) except -1
ctypedef herr_t (*file_truncate_func_ptr)(H5FD_t *, hid_t, hbool_t) except -1
From f0aa23d35b69343d3ca0f7697d96e42cc2403c73 Mon Sep 17 00:00:00 2001
From: David Hoese <david.hoese@ssec.wisc.edu>
Date: Fri, 1 Dec 2023 21:09:23 -0600
Subject: [PATCH 6/9] Fix numpy warning about array to scalar conversion
---
h5py/tests/test_dataset.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/h5py/tests/test_dataset.py b/h5py/tests/test_dataset.py
index e104dd53d..0ffa5c800 100644
--- a/h5py/tests/test_dataset.py
+++ b/h5py/tests/test_dataset.py
@@ -1939,9 +1939,9 @@ def test_numpy_commutative(self,):
dset = self.f.create_dataset("test", shape, dtype=float,
data=np.random.rand(*shape))
- # grab a value from the elements, ie dset[0]
+ # grab a value from the elements, ie dset[0, 0]
# check that mask arrays are commutative wrt ==, !=
- val = np.float64(dset[0])
+ val = np.float64(dset[0, 0])
assert np.all((val == dset) == (dset == val))
assert np.all((val != dset) == (dset != val))
From 51d3c3a7db33ab3ee9e69d680cd08a149dd05335 Mon Sep 17 00:00:00 2001
From: David Hoese <david.hoese@ssec.wisc.edu>
Date: Fri, 1 Dec 2023 21:09:37 -0600
Subject: [PATCH 7/9] Fix compatibility with numpy 2
---
h5py/api_compat.h | 13 ++++++-------
1 file changed, 6 insertions(+), 7 deletions(-)
diff --git a/h5py/api_compat.h b/h5py/api_compat.h
index 52917f4d0..a359e8278 100644
--- a/h5py/api_compat.h
+++ b/h5py/api_compat.h
@@ -24,7 +24,6 @@ typedef void *PyMPI_MPI_Message;
#include <stddef.h>
#include "Python.h"
#include "numpy/arrayobject.h"
-#include "hdf5.h"
/* The HOFFSET macro can't be used from Cython. */
@@ -35,14 +34,14 @@ typedef void *PyMPI_MPI_Message;
#define h5py_size_n256 (sizeof(npy_complex256))
#endif
-#define h5py_offset_n64_real (HOFFSET(npy_complex64, real))
-#define h5py_offset_n64_imag (HOFFSET(npy_complex64, imag))
-#define h5py_offset_n128_real (HOFFSET(npy_complex128, real))
-#define h5py_offset_n128_imag (HOFFSET(npy_complex128, imag))
+#define h5py_offset_n64_real (0)
+#define h5py_offset_n64_imag (sizeof(float))
+#define h5py_offset_n128_real (0)
+#define h5py_offset_n128_imag (sizeof(double))
#ifdef NPY_COMPLEX256
-#define h5py_offset_n256_real (HOFFSET(npy_complex256, real))
-#define h5py_offset_n256_imag (HOFFSET(npy_complex256, imag))
+#define h5py_offset_n256_real (0)
+#define h5py_offset_n256_imag (sizeof(long double))
#endif
#endif
From 502be1786591076ad7012e6abe1576d5f6ba48a6 Mon Sep 17 00:00:00 2001
From: David Hoese <david.hoese@ssec.wisc.edu>
Date: Mon, 4 Dec 2023 13:52:52 -0600
Subject: [PATCH 8/9] Add explicit noexcept to lock functions
---
h5py/_locks.pxi | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/h5py/_locks.pxi b/h5py/_locks.pxi
index c6cea88dd..1ec4e2fc9 100644
--- a/h5py/_locks.pxi
+++ b/h5py/_locks.pxi
@@ -63,7 +63,7 @@ cdef class FastRLock:
return self._owner == pythread.PyThread_get_thread_ident()
-cdef inline bint lock_lock(FastRLock lock, long current_thread, bint blocking) nogil:
+cdef inline bint lock_lock(FastRLock lock, long current_thread, bint blocking) noexcept nogil:
# Note that this function *must* hold the GIL when being called.
# We just use 'nogil' in the signature to make sure that no Python
# code execution slips in that might free the GIL
@@ -83,7 +83,7 @@ cdef inline bint lock_lock(FastRLock lock, long current_thread, bint blocking) n
lock, current_thread,
pythread.WAIT_LOCK if blocking else pythread.NOWAIT_LOCK)
-cdef bint _acquire_lock(FastRLock lock, long current_thread, int wait) nogil:
+cdef bint _acquire_lock(FastRLock lock, long current_thread, int wait) noexcept nogil:
# Note that this function *must* hold the GIL when being called.
# We just use 'nogil' in the signature to make sure that no Python
# code execution slips in that might free the GIL
From 5531827d7687b966243e8c8aa430ec3206a1328a Mon Sep 17 00:00:00 2001
From: David Hoese <david.hoese@ssec.wisc.edu>
Date: Mon, 4 Dec 2023 13:53:50 -0600
Subject: [PATCH 9/9] Update Cython version limits to include 0.29 and up to 4
---
pyproject.toml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/pyproject.toml b/pyproject.toml
index 3bc08b762..717200efa 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
[build-system]
requires = [
- "Cython >=3",
+ "Cython >=0.29.31,<4",
"oldest-supported-numpy",
"pkgconfig",
"setuptools >=61",
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