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[#1237] Update SciPy to 1.9.3 #1359

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[#1237] Update SciPy to 1.9.3 #1359

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10 changes: 8 additions & 2 deletions server/pypi/packages/scipy/meta.yaml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,12 @@
{% if PY_VER == "3.8" %}
{% set numpy_version = "1.19.5" %}
{% elif PY_VER in ["3.9", "3.10", "3.11"] %}
{% set numpy_version = "1.23.3" %}
{% endif %}
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There's no need for this, because we aren't building new packages for Python 3.8 anymore.


package:
name: scipy
version: "1.8.1"
version: "1.9.3"

build:
number: 1
Expand All @@ -13,4 +19,4 @@ requirements:
host:
- chaquopy-libgfortran 4.9
- chaquopy-openblas 0.2.20
- numpy 1.23.3
- numpy {{ numpy_version }}
228 changes: 156 additions & 72 deletions server/pypi/packages/scipy/patches/chaquopy.patch
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Original file line number Diff line number Diff line change
@@ -1,10 +1,27 @@
diff -aur src-orig/scipy/__init__.py src/scipy/__init__.py
--- src-orig/scipy/__init__.py 2023-09-20 11:08:01.936923429 +0200
+++ src/scipy/__init__.py 2023-09-21 13:13:09.267906353 +0200
@@ -64,50 +64,54 @@
diff --git a/pyproject.toml b/pyproject.toml
index 6dc1d4070..7797510a2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -8,9 +8,8 @@
# "pybind11>=2.4.3,<2.5.0",

__all__ = __dir__()
[build-system]
-build-backend = 'mesonpy'
requires = [
- "meson-python>=0.9.0", # we need more fixes in meson-python, so no upper bound now
+ "setuptools<60.0.0", # Chaquopy: Use setuptools instead of meson
"Cython>=0.29.32,<3.0",
"pybind11>=2.4.3,<2.11.0",
"pythran>=0.9.12,<0.13.0",
diff --git a/scipy/__init__.py b/scipy/__init__.py
index 0e132c394..ee125c418 100644
--- a/scipy/__init__.py
+++ b/scipy/__init__.py
@@ -69,53 +69,54 @@ if sys.version_info >= (3, 12):
raise RuntimeError(_msg)
del sys

-
-from numpy import show_config as show_numpy_config
-if show_numpy_config is None:
- raise ImportError(
Expand All @@ -13,42 +30,44 @@ diff -aur src-orig/scipy/__init__.py src/scipy/__init__.py
-
-# Import numpy symbols to scipy name space (DEPRECATED)
-from ._lib.deprecation import _deprecated
-import numpy as _num
-linalg = None
-import numpy as np
-_msg = ('scipy.{0} is deprecated and will be removed in SciPy 2.0.0, '
- 'use numpy.{0} instead')
-# deprecate callable objects, skipping classes
-for _key in _num.__all__:
- _fun = getattr(_num, _key)
-
-# deprecate callable objects from numpy, skipping classes and modules
-import types as _types # noqa: E402
-for _key in np.__all__:
- if _key.startswith('_'):
- continue
- _fun = getattr(np, _key)
- if isinstance(_fun, _types.ModuleType):
- continue
- if callable(_fun) and not isinstance(_fun, type):
- _fun = _deprecated(_msg.format(_key))(_fun)
- globals()[_key] = _fun
-del np, _types
-
-from numpy.random import rand, randn
-_msg = ('scipy.{0} is deprecated and will be removed in SciPy 2.0.0, '
- 'use numpy.random.{0} instead')
-rand = _deprecated(_msg.format('rand'))(rand)
-randn = _deprecated(_msg.format('randn'))(randn)
-
-# fft is especially problematic, so was removed in SciPy 1.6.0
-from numpy.fft import ifft
-ifft = _deprecated('scipy.ifft is deprecated and will be removed in SciPy '
- '2.0.0, use scipy.fft.ifft instead')(ifft)
-import numpy.lib.scimath as _sci
-
-from numpy.lib import scimath # noqa: E402
-_msg = ('scipy.{0} is deprecated and will be removed in SciPy 2.0.0, '
- 'use numpy.lib.scimath.{0} instead')
-for _key in _sci.__all__:
- _fun = getattr(_sci, _key)
-for _key in scimath.__all__:
- _fun = getattr(scimath, _key)
- if callable(_fun):
- _fun = _deprecated(_msg.format(_key))(_fun)
- globals()[_key] = _fun
-
-__all__ += _num.__all__
-__all__ += ['randn', 'rand', 'ifft']
-
-del _num
-# Remove the linalg imported from NumPy so that the scipy.linalg package can be
-# imported.
-del linalg
-__all__.remove('linalg')
-del scimath
-del _msg, _fun, _key, _deprecated
+# Chaquopy: don't import numpy during build.
+try:
+ __SCIPY_SETUP__
Expand Down Expand Up @@ -100,21 +119,42 @@ diff -aur src-orig/scipy/__init__.py src/scipy/__init__.py

# We first need to detect if we're being called as part of the SciPy
# setup procedure itself in a reliable manner.
@@ -121,6 +125,10 @@
import sys as _sys
_sys.stderr.write('Running from SciPy source directory.\n')
del _sys
@@ -129,6 +130,10 @@ if __SCIPY_SETUP__:
import sys
sys.stderr.write('Running from SciPy source directory.\n')
del sys
+
+ # Chaquopy: the module namespace was originally empty in this mode, but the following
+ # things are neded by the scikit-learn build.
+ from scipy.version import version as __version__
else:
try:
from scipy.__config__ import show as show_config
diff -aur src-orig/scipy/_lib/_testutils.py src/scipy/_lib/_testutils.py
--- src-orig/scipy/_lib/_testutils.py 2023-09-20 11:08:01.940923505 +0200
+++ src/scipy/_lib/_testutils.py 2023-09-21 13:13:08.763896205 +0200
@@ -86,9 +86,10 @@
diff --git a/scipy/_lib/_c99compat.h b/scipy/_lib/_c99compat.h
index 7d285137d..f0ce4f63f 100644
--- a/scipy/_lib/_c99compat.h
+++ b/scipy/_lib/_c99compat.h
@@ -120,9 +120,12 @@
/* Hopefully fail in fewer cases */

/* For compilers which aren't MSVC and haven't defined isnan */
- #ifndef isnan
- #define isnan(x) ((x) != (x))
- #endif
+ /* Chaquopy: Prevent C/C++ macro collision */
+ #ifndef __cplusplus
+ #ifndef isnan
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Why is this patch necessary – what error message do you get without it?

And why is __cplusplus the appropriate way of doing it? Is this file included in any C++ code? If not, then the __cplusplus check is just equivalent to disabling the code completely.

If the patch is necessary, then the inner #ifndef should be left at its original indentation to make the patch easier to read.

+ #define isnan(x) ((x) != (x))
+ #endif
+ #endif

#ifndef isfinite
#ifdef _MSC_VER
diff --git a/scipy/_lib/_testutils.py b/scipy/_lib/_testutils.py
index def797954..f94ff6a39 100644
--- a/scipy/_lib/_testutils.py
+++ b/scipy/_lib/_testutils.py
@@ -86,9 +86,10 @@ class _TestPythranFunc:
`self.partialfunc`: A function used to freeze some non-array argument
that of no interests in the original function
'''
Expand All @@ -128,10 +168,23 @@ diff -aur src-orig/scipy/_lib/_testutils.py src/scipy/_lib/_testutils.py

def setup_method(self):
self.arguments = {}
diff -aur src-orig/scipy/sparse/linalg/_propack/setup.py src/scipy/sparse/linalg/_propack/setup.py
--- src-orig/scipy/sparse/linalg/_propack/setup.py 2023-09-20 11:08:03.624955562 +0200
+++ src/scipy/sparse/linalg/_propack/setup.py 2023-09-21 13:13:09.407909172 +0200
@@ -1,12 +1,14 @@
diff --git a/scipy/integrate/setup.py b/scipy/integrate/setup.py
index 1ba82d18c..e18391dd3 100644
--- a/scipy/integrate/setup.py
+++ b/scipy/integrate/setup.py
@@ -3,7 +3,6 @@ from os.path import join

from scipy._build_utils import numpy_nodepr_api

-
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This change appears to be insignificant.

def configuration(parent_package='',top_path=None):
from numpy.distutils.misc_util import Configuration
from scipy._build_utils.system_info import get_info
diff --git a/scipy/sparse/linalg/_propack/setup.py b/scipy/sparse/linalg/_propack/setup.py
index 5c8f252ac..def2dde17 100644
--- a/scipy/sparse/linalg/_propack/setup.py
+++ b/scipy/sparse/linalg/_propack/setup.py
@@ -1,11 +1,14 @@
from os.path import join
+from os import getenv
import pathlib
Expand All @@ -142,43 +195,53 @@ diff -aur src-orig/scipy/sparse/linalg/_propack/setup.py src/scipy/sparse/linalg

def _is_32bit():
- return np.intp(0).itemsize < 8
-
+ # Chaquopy: check 32/64 bit based on ABI instead of numpy
+ # np.intp(0).itemsize < 8
+ return getenv('HOST') in ["arm-linux-androideabi", "i686-linux-android"]
+ # return np.intp(0).itemsize < 8
+ return getenv('HOST') in ["arm-linux-androideabi", "i686-linux-android"]


def check_propack_submodule():
if not (pathlib.Path(__file__).parent / 'PROPACK/README').exists():
diff -aur src-orig/scipy/special/ellint_carlson_cpp_lite/ellint_arith_aux.hh src/scipy/special/ellint_carlson_cpp_lite/ellint_arith_aux.hh
--- src-orig/scipy/special/ellint_carlson_cpp_lite/ellint_arith_aux.hh 2023-09-20 11:08:03.696956933 +0200
+++ src/scipy/special/ellint_carlson_cpp_lite/ellint_arith_aux.hh 2023-09-21 13:13:09.439909816 +0200
@@ -5,6 +5,8 @@
#include <cstddef>
#include "ellint_typing.hh"

+// Chaquopy: added <algorithm>
+#include <algorithm>

/* Auxiliary floating-point manipulation utilities.
* Ref:
diff -aur src-orig/scipy/special/_generate_pyx.py src/scipy/special/_generate_pyx.py
--- src-orig/scipy/special/_generate_pyx.py 2023-09-20 11:08:03.676956552 +0200
+++ src/scipy/special/_generate_pyx.py 2023-09-21 13:13:09.443909897 +0200
@@ -230,7 +230,7 @@
diff --git a/scipy/spatial/_qhull.pyx b/scipy/spatial/_qhull.pyx
index 8c9135adc..b6ff2d86f 100644
--- a/scipy/spatial/_qhull.pyx
+++ b/scipy/spatial/_qhull.pyx
@@ -17,6 +17,7 @@ cimport cython
from . cimport _qhull
from . cimport setlist
from libc cimport stdlib
+from libc.stdio cimport FILE # Chaquopy
from scipy._lib.messagestream cimport MessageStream

import os
@@ -992,7 +993,7 @@ cdef class _Qhull:
return extremes_arr


-cdef void _visit_voronoi(qhT *_qh, void *ptr, vertexT *vertex, vertexT *vertexA,
+cdef void _visit_voronoi(qhT *_qh, FILE *ptr, vertexT *vertex, vertexT *vertexA,
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Please add a "Chaquopy: " comment saying that you changed void to FILE, and explaining why that was necessary.

setT *centers, boolT unbounded):
cdef _Qhull qh = <_Qhull>ptr
cdef int point_1, point_2, ix
diff --git a/scipy/special/_generate_pyx.py b/scipy/special/_generate_pyx.py
index 21b401629..15f84e553 100644
--- a/scipy/special/_generate_pyx.py
+++ b/scipy/special/_generate_pyx.py
@@ -232,8 +232,7 @@ import re
import textwrap
from typing import List

-import numpy
-
+# Chaquopy: skip "import numpy"
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Was there some reason to change this? The previous version was less disruptive, as it retained the two lines after the imports.



BASE_DIR = os.path.abspath(os.path.dirname(__file__))
@@ -923,7 +923,13 @@

@@ -925,7 +924,13 @@ class FusedFunc(Func):
all_codes = tuple([codes for _unused, codes in fused_types])

codelens = [len(x) for x in all_codes]
- last = numpy.prod(codelens) - 1
+
+
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Please avoid insignificant whitespace changes.

+ # Chaquopy: replace numpy.prod(codelens) - 1
+ last = 1
+ for x in codelens:
Expand All @@ -188,23 +251,34 @@ diff -aur src-orig/scipy/special/_generate_pyx.py src/scipy/special/_generate_py
for m, codes in enumerate(itertools.product(*all_codes)):
fused_codes, decs = [], []
for n, fused_type in enumerate(fused_types):
diff -aur src-orig/scipy/special/utils/makenpz.py src/scipy/special/utils/makenpz.py
--- src-orig/scipy/special/utils/makenpz.py 2023-09-20 11:08:03.708957161 +0200
+++ src/scipy/special/utils/makenpz.py 2023-09-21 13:13:09.447909977 +0200
@@ -6,7 +6,8 @@
diff --git a/scipy/special/utils/makenpz.py b/scipy/special/utils/makenpz.py
index f7dd6622a..dc670fe49 100644
--- a/scipy/special/utils/makenpz.py
+++ b/scipy/special/utils/makenpz.py
@@ -6,7 +6,8 @@ Build a npz containing all data files in the directory.
"""

import os
-import numpy as np
+# Chaquopy: removed `import numpy`: we will "Skip rebuilding if no sources" below, so it's not
+# needed.
import argparse
from stat import ST_MTIME

from distutils.util import newer # type: ignore
diff -aur src-orig/scipy/stats/_generate_pyx.py src/scipy/stats/_generate_pyx.py
--- src-orig/scipy/stats/_generate_pyx.py 2023-09-20 11:08:03.708957161 +0200
+++ src/scipy/stats/_generate_pyx.py 2023-09-21 13:13:09.463910299 +0200
@@ -8,6 +8,10 @@
@@ -47,6 +48,8 @@ def main():
outdir_abs = os.path.join(os.getcwd(), args.outdir)
outp = os.path.join(outdir_abs, args.dirname + ".npz")

+ # Chaquopy: Force return
+ return
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This says what you're doing, but it doesn't explain why. If the rest of the function would cause some problem, then include a comment saying what it was.

# Skip rebuilding if no sources
if os.path.isfile(outp) and not os.path.isdir(inp):
return
diff --git a/scipy/stats/_generate_pyx.py b/scipy/stats/_generate_pyx.py
index 07861467f..4bba6e623 100644
--- a/scipy/stats/_generate_pyx.py
+++ b/scipy/stats/_generate_pyx.py
@@ -10,6 +10,10 @@ def isNPY_OLD():
A new random C API was added in 1.18 and became stable in 1.19.
Prefer the new random C API when building with recent numpy.
'''
Expand All @@ -215,14 +289,25 @@ diff -aur src-orig/scipy/stats/_generate_pyx.py src/scipy/stats/_generate_pyx.py
import numpy as np
ver = tuple(int(num) for num in np.__version__.split('.')[:2])
return ver < (1, 19)
diff -aur src-orig/setup.py src/setup.py
--- src-orig/setup.py 2023-09-20 11:08:03.732957618 +0200
+++ src/setup.py 2023-09-21 13:13:08.707895078 +0200
@@ -32,6 +32,15 @@
diff --git a/setup.py b/setup.py
index de1c702af..85f76a66e 100755
--- a/setup.py
+++ b/setup.py
@@ -28,12 +28,25 @@ from tools.version_utils import write_version_py, get_version_info
from tools.version_utils import IS_RELEASE_BRANCH
import importlib

+# Chaquopy: Force use of cross-compilers for Fortran
+os.environ["FC"] = os.path.join(os.path.expanduser("~"), "Downloads/gcc-arm64-linux-x86_64/aarch64-linux-android-4.9/bin/aarch64-linux-android-gfortran")
+os.environ["F77"] = os.path.join(os.path.expanduser("~"), "Downloads/gcc-arm64-linux-x86_64/aarch64-linux-android-4.9/bin/aarch64-linux-android-gfortran")
+os.environ["F90"] = os.path.join(os.path.expanduser("~"), "Downloads/gcc-arm64-linux-x86_64/aarch64-linux-android-4.9/bin/aarch64-linux-android-gfortran")
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@mhsmith mhsmith Apr 20, 2025 •
edited
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One thing to note is that I had to hardcode some paths for Fortran in SciPy's setup.py file (despite seemingly placing the Fortran library for Android in the proper folder).

The proper folder is not ~/Downloads, but chaquopy/server/pypi/fortran, as it says in pypi/README.md. build-wheel.py sets these environment variables to point into that location.


if sys.version_info[:2] < (3, 8):
raise RuntimeError("Python version >= 3.8 required.")

import builtins

+# Chaquopy
+# Chaquopy: Use OpenBLAS from Chaquopy package index
+with open(os.path.join(os.path.dirname(__file__), "site.cfg"), "w") as site_file:
+ site_file.write("[openblas]\n"
+ "library_dirs = {reqs_dir}/lib\n"
Expand All @@ -234,4 +319,3 @@ diff -aur src-orig/setup.py src/setup.py

CLASSIFIERS = """\
Development Status :: 5 - Production/Stable