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Update to Scipy 1.7.3 (#2065)

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Hood Chatham 2022-01-03 14:07:13 -08:00 committed by GitHub
parent 6f318244f9
commit 5309d21371
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32 changed files with 1843 additions and 1729 deletions
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1
Makefile.envs
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@ -30,6 +30,7 @@ export PYODIDE_BASE_URL?=./
# For packages that depend on numpy.
# TODO: maybe move this somewhere else?
export NUMPY_LIB_BASE=$(PYODIDE_ROOT)/packages/numpy/build/numpy-1.21.4/install/lib/python$(PYMAJOR).$(PYMINOR)/site-packages/numpy/
export NUMPY_LIB=$(PYODIDE_ROOT)/packages/numpy/build/numpy-1.21.4/install/lib/python$(PYMAJOR).$(PYMINOR)/site-packages/numpy/core/lib/
# This environment variable is used for packages to detect if they are built

12
docs/project/changelog.md
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@ -184,7 +184,17 @@ async function runPythonAsync(code, globals) {
- {{ Enhancement }} upgraded numpy to 1.21.4
{pr}`1934`
- {{ Fix }} The built-in pwd module of Python, which provides Unix specific
- {{ Enhancement }} Upgraded SciPy to 1.7.3. Note that there are still known issues with
some SciPy components.
{pr}`2065`
- {{ Enhancement }} Upgraded scikit-learn to version 1.0.2
{pr}`2065`
- {{ Enhancement }} Added threadpoolctl (a dependency of scikit-learn)
{pr}`2065`
- {{ Fix }} The built-in pwd module of Python, which provides a Unix specific
feature, is now unvendored.
{pr}`1883`

8
packages/CLAPACK/meta.yaml
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@ -31,11 +31,7 @@ build:
sed -i 's/^ ar /^ $(ARCH)/' **/Makefile
sed -i 's/^ ld /^ $(LD)/' **/Makefile
# We build BLAS/LAPACK only for target.
# On host we include -LCLAPACK-3.2.1 path which has no effect on host.
# On target it gets rewritten by pywasmcross to the full patch of
# blas_WA.a, lapack_WA.a which are linked statically in scipy
# in each module that needs them.
emmake make -j ${PYODIDE_JOBS:-3} blaslib lapacklib
mkdir -p install/lib
emcc blas_WA.a lapack_WA.a F2CLIBS/libf2c.a -sSIDE_MODULE -o install/lib/clapack_all.so
emcc blas_WA.a lapack_WA.a F2CLIBS/libf2c.a -sSIDE_MODULE -o install/lib/clapack_all.so

8
packages/scikit-learn/meta.yaml
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@ -1,13 +1,14 @@
package:
name: scikit-learn
version: 0.22.2
version: 1.0.2
source:
url: https://github.com/scikit-learn/scikit-learn/archive/0.22.2.tar.gz
sha256: 54ae27be30ef26718c9e517c4c8f23b6af26c66e52cf16d38799ba4262d4fd3b
url: https://files.pythonhosted.org/packages/75/44/074b780d8ac0b0899937e9b8ba6d5d8873a71b99aa915219251ef85a8890/scikit-learn-1.0.2.tar.gz
sha256: b5870959a5484b614f26d31ca4c17524b1b0317522199dc985c3b4256e030767
patches:
- patches/disable-openmp.patch
- patches/0001-Cythonize-_cython_blas.pyx-with-include-path-pointin.patch
build:
cflags: -Wno-implicit-function-declaration
@ -17,6 +18,7 @@ requirements:
- numpy
- scipy
- joblib
- threadpoolctl
test:
imports:

33
packages/scikit-learn/patches/0001-Cythonize-_cython_blas.pyx-with-include-path-pointin.patch Normal file
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@ -0,0 +1,33 @@
From f1d8f0b92b17765a2e8b6ac508cfa77a79fb73a0 Mon Sep 17 00:00:00 2001
From: Hood Chatham <roberthoodchatham@gmail.com>
Date: Sun, 26 Dec 2021 22:39:25 -0800
Subject: [PATCH] Cythonize _cython_blas.pyx with include path pointing to
scipy
---
sklearn/utils/setup.py | 2 ++
1 file changed, 2 insertions(+)
diff --git a/sklearn/utils/setup.py b/sklearn/utils/setup.py
index ed78ecc5d..ea1a61b40 100644
--- a/sklearn/utils/setup.py
+++ b/sklearn/utils/setup.py
@@ -2,6 +2,7 @@ import os
from os.path import join
from sklearn._build_utils import gen_from_templates
+from Cython.Build import cythonize
def configuration(parent_package="", top_path=None):
@@ -18,6 +19,7 @@ def configuration(parent_package="", top_path=None):
"sparsefuncs_fast", sources=["sparsefuncs_fast.pyx"], libraries=libraries
)
+ cythonize("sklearn/utils/_cython_blas.pyx", include_path=[f"{os.environ['PYODIDE_ROOT']}/packages/scipy/build/scipy-1.7.3/"])
config.add_extension(
"_cython_blas", sources=["_cython_blas.pyx"], libraries=libraries
)
--
2.25.1

60
packages/scikit-learn/test_scikit-learn.py
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@ -1,26 +1,48 @@
import pytest
from conftest import selenium_context_manager
@pytest.mark.driver_timeout(40)
def test_scikit_learn(selenium_standalone, request):
selenium = selenium_standalone
selenium.load_package("scikit-learn")
assert (
def test_scikit_learn(selenium_module_scope):
if selenium_module_scope.browser == "chrome":
pytest.xfail("Times out in chrome")
with selenium_context_manager(selenium_module_scope) as selenium:
selenium.load_package("scikit-learn")
assert (
selenium.run(
"""
import numpy as np
import sklearn
from sklearn.linear_model import LogisticRegression
rng = np.random.RandomState(42)
X = rng.rand(100, 20)
y = rng.randint(5, size=100)
estimator = LogisticRegression(solver='liblinear')
estimator.fit(X, y)
print(estimator.predict(X))
estimator.score(X, y)
"""
)
> 0
)
@pytest.mark.driver_timeout(40)
def test_logistic_regression(selenium_module_scope):
if selenium_module_scope.browser == "chrome":
pytest.xfail("Times out in chrome")
with selenium_context_manager(selenium_module_scope) as selenium:
selenium.load_package("scikit-learn")
selenium.run(
"""
import numpy as np
import sklearn
from sklearn.linear_model import LogisticRegression
rng = np.random.RandomState(42)
X = rng.rand(100, 20)
y = rng.randint(5, size=100)
estimator = LogisticRegression(solver='liblinear')
estimator.fit(X, y)
print(estimator.predict(X))
estimator.score(X, y)
"""
from sklearn.datasets import load_iris
from sklearn.linear_model import LogisticRegression
X, y = load_iris(return_X_y=True)
clf = LogisticRegression(random_state=0).fit(X, y)
print(clf.predict(X[:2, :]))
print(clf.predict_proba(X[:2, :]))
print(clf.score(X, y))
"""
)
> 0
)

95
packages/scipy/info.md Normal file
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@ -0,0 +1,95 @@
The biggest issue that comes up in building scipy is that we don't have a good
fotran to wasm compiler. Some version of flang classic might work.
Instead of compiling from fortran directly, we rely on f2c to cross compile
the code to C and then compile C to wasm. We rely on f2c both directly and via
CLAPACK which is f2c'd LAPACK.
Unfortunately, f2c only handles fortran 77 code and it doesn't work perfectly
even on that. After LAPACK version 3.2 (released in 2008), LAPACK started
adding methods that use newer fortran features, so they cannot be f2c'd. Hence
it's unlikely that new versions of CLAPACK will be released and we can't use
any newer version of CLAPACK.
Scipy is built based on a newer version of CLAPACK and I couldn't figure out
how to remove the newer functions. They cause dynamic linking errors when
scipy is imported. To find the list of problem functions I used:
```sh
wasm-objdump clapack_all.so -d | sed -n 's/.*func.*<\(.*\)>:/\1/p' | sort -u > clapack_exports.txt
```
to list the symbols exported from our clapack and
```
wasm-objdump _flapack.so -d | sed -E -n 's/.*global.get [0-9]* <([a-z]*_?)>/\1/p' | sort -u > symbols.txt
```
to list the symbols that `_flapack.so` expects to see. There are 36 symbols in
this list. Conveniently, LAPACK defines one function per file, so I just
download a copy of LAPACK and cat these functions into
`scipy/linalg/src/lapack_deprecations/cgegv.f` which is chosen arbitrarily from
the `.f` source files that are linked into `_flapack.so` (there aren't that many
options though). Using an existing file allows us to avoid fiddling with build
scripts. Of the 36 missing symbol, 32 of them are written in Fortran 77 and work
fine. The remaining 4 need removing but I couldn't figure out how to take them
out in any sensible way (I can't understand all the layers of codegen that
happen in scipy), so I give them do-nothing definitions, and then in the build
script remove lines containing them with `sed`.
Another big problem with f2c is that it cannot handle implicit casts of function
arguments, because it tries to guess the types of the arguments of the function
being called based on the types of the arguments at the call site. There are two
distinct versions of this:
1. casts between number types -- we deal with this automatically in
`fix_inconsistent_decls` in `_f2c_fixes.py`
2. casts between char\* and int -- this is too annoying to deal with
automatically, so we write manual patches.
Type 1: the fortran equivalent of the following C code:
```C
double f(double x){
return x + 5;
}
double g(int x){
return f(x);
}
```
gets f2c'd to
```C
double f(double x){
return x + 5;
}
double g(int x){
double f(int);
return f(x);
}
```
When we try to compile this, we get an error saying that f has been declared
with two different types.
Type 2: For each string argument, the Fortran ABI adds arguments at the end of
the argument list. LAPACK never declares functions as taking strings, preferring
to call them integers:
```C
int some_lapack_func(int *some_string, int *some_string_length){
// ...
}
```
But then when we call it: `some_lapack_func("a string here", 14);` the f2c'd
version looks like:
```C
int str_len = 14;
int some_lapack_func(int *some_string, int *some_string_length, fortranlen some_string_length_again);
some_lapack_func("a string here", &str_len, 14);
```

141
packages/scipy/meta.yaml
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@ -1,60 +1,105 @@
package:
name: scipy
version: 0.17.1
version: 1.7.3 # when updating version make sure to update pip install scipy==1.7.3 below too.
# See extra explanation in info.md
#
# For future reference: if you see the following errors:
# Declaration error: adjustable dimension on non-argument
# or:
# nonconstant array size
# you are trying to compile code that isn't written to the fortran 77 standard.
# The line number in the error points to the last line of the problematic
# subroutine. Try deleting it.
source:
# We can't use the version from PyPI as it includes Cythonized files
# generated with an older Cython that does not support Python 3.7
# This requires,
# pip install Cython Tempita
# on the host for the build
url: https://github.com/scipy/scipy/archive/v0.17.1.tar.gz
sha256: bf22383d9e2526ffdc53a6c7d3d66dab45a86291ed35d8e281bd1a5d2c34187b
url: https://files.pythonhosted.org/packages/61/67/1a654b96309c991762ee9bc39c363fc618076b155fe52d295211cf2536c7/scipy-1.7.3.tar.gz
sha256: ab5875facfdef77e0a47d5fd39ea178b58e60e454a4c85aa1e52fcb80db7babf
patches:
# these patches can be found as commits in
# https://github.com/rth/scipy/tree/0.17.1-pyodide
# on top of the v0.17.1 tag
- patches/fix-blas.patch
- patches/fix-build-gcc5-a80460.patch
- patches/force_malloc.patch
- patches/disable_scipy_stats_mvn.patch
- patches/skip-fortran-fails-to-link.patch
- patches/skip_ellip_harm_2_pyx_ctypes.patch
- patches/add-lapack_extras-to-flapack.patch
- patches/convert-xerrwv-message-arg-from-int-to-str.patch
- patches/disable-blas-detection.patch
- patches/fix-fortran-files-minpack.patch
- patches/gemm_-no-const.patch
- patches/make-int-return-values.patch
- patches/add-missing-extern.patch
- patches/fix-typo-flapack-pyf.patch
- patches/remove-cuncsd-dorcsd-sorcsd-zuncsd.patch
- patches/remove-mvnun-not-fortran-77-compliant.patch
- patches/sasum-returns-double-not-float.patch
- patches/skip-fortran-fails-to-link.patch
- patches/rename-_page_trend_test.patch
build:
# set linker and C flags to error on anything to do with function declarations being wrong.
# In webassembly, any conflicts mean that a randomly selected 50% of calls to the function
# will fail. Better to fail at compile or link time.
cflags: |
-I $(PYODIDE_ROOT)/packages/numpy/config
-I$(PYODIDE_ROOT)/packages/numpy/config
-I$(PYODIDE_ROOT)/packages/CLAPACK/build/CLAPACK-3.2.1/INCLUDE
-I$(PYODIDE_ROOT)/packages/.artifacts/include/
-I$(PYODIDE_ROOT)/packages/.artifacts/pythran/
-DUNDERSCORE_G77
-Werror=implicit-function-declaration
-Werror=mismatched-parameter-types
-Werror=mismatched-return-types
-Wno-return-type
ldflags: |
-L$(NUMPY_LIB)
-L$(NUMPY_LIB_BASE)/random/lib
-Wl,--fatal-warnings
# IMPORTANT: Other locations important in scipy build process:
# There are two files built in the "capture" pass that need patching:
# _blas_subroutines.h, and _cython
# Scipy has a bunch of custom logic implemented in
# pyodide-build/pyodide_build/_f2c_fixes.py.
script: |
# Some fixes were extracted from patches/make-int-return-values.patch as regex.
pip install scipy==1.7.3 pybind11[global] pythran
pip install --upgrade pybind11[global] pythran -t $PYODIDE_ROOT/packages/.artifacts/
# We get linker errors because the following 36 functions are missing
# Copying them from a more recent LAPACK seems to work fine.
wget https://github.com/Reference-LAPACK/lapack/archive/refs/tags/v3.10.0.tar.gz
tar xzf v3.10.0.tar.gz
cd lapack-3.10.0/SRC
cat \
cgemqrt.f cgeqrfp.f cgeqrt.f clahqr.f csyconv.f csyconvf.f csyconvf_rook.f ctpmqrt.f ctpqrt.f \
dgemqrt.f dgeqrfp.f dgeqrt.f dlahqr.f dsyconv.f dsyconvf.f dsyconvf_rook.f dtpmqrt.f dtpqrt.f \
sgemqrt.f sgeqrfp.f sgeqrt.f slahqr.f ssyconv.f ssyconvf.f ssyconvf_rook.f stpmqrt.f stpqrt.f \
zgemqrt.f zgeqrfp.f zgeqrt.f zlahqr.f zsyconv.f zsyconvf.f zsyconvf_rook.f ztpmqrt.f ztpqrt.f \
>> ../../scipy/linalg/lapack_extras.f
cd ../..
# The additional four functions cuncsd, dorcsd, sorcsd, and zuncsd are also
# missing but they use features of Fortran that aren't Fortran 77 compatible
# so f2c can't handle them. We stub them with C definitions that do nothing.
# These stubs come from f2cpatches/wrap_dummy_g77_abi.patch
# Change many functions that return void into functions that return int
find scipy -name "*.c*" | xargs sed -i 's/extern void F_FUNC/extern int F_FUNC/g'
sed -i 's/void F_FUNC/int F_FUNC/g' scipy/odr/__odrpack.c
sed -i 's/extern void/extern int/g' scipy/optimize/__minpack.h scipy/fftpack/src/zfftnd.c scipy/fftpack/src/zrfft.c
sed -i 's/void f_/int f_/g' scipy/cluster/cluster_blas.pxd
sed -i 's/void @pref/int @pref/g' scipy/fftpack/src/dct.c.src scipy/fftpack/src/dst.c.src
sed -i 's/^void/int/g' scipy/interpolate/src/__fitpack.h scipy/integrate/__quadpack.h scipy/fftpack/src/drfft.c scipy/fftpack/src/zfft.c
sed -i 's/static void/static int/g' scipy/interpolate/src/__fitpack.h
sed -i 's/ILAENV/ILAENZ/g' scipy/linalg/src/calc_lwork.f
# Regenerate header files after make-int-return-values patch to fix return
# types of f2c functions.
echo "Regenerating cython wrappers"
cd scipy/linalg
python _cython_wrapper_generators.py
cd ../..
sed -i 's/extern void/extern int/g' scipy/optimize/__minpack.h
sed -i 's/^void/int/g' scipy/interpolate/src/_fitpackmodule.c
sed -i 's/void/int/g' scipy/linalg/cython_blas_signatures.txt
# Missing declaration from cython_lapack_signatures.txt
echo "void ilaenv(int *ispec, char *name, char *opts, int *n1, int *n2, int *n3, int *n4)" \
>> scipy/linalg/cython_lapack_signatures.txt
# Input error causes "duplicate symbol" linker errors. Empty out the file.
echo "" > scipy/sparse/linalg/dsolve/SuperLU/SRC/input_error.c
echo 'import sys' >> scipy/__init__.py
echo 'if "pyodide_js" in sys.modules:' >> scipy/__init__.py
echo ' from pyodide_js._module import loadDynamicLibrary' >> scipy/__init__.py
echo ' loadDynamicLibrary("/lib/python3.9/site-packages/scipy/linalg/_flapack.so")' >> scipy/__init__.py
prereplay: |
sed -i 's/void F_FUNC/int F_FUNC/g' scipy/linalg/_lapack_subroutines.h
sed -i 's/void F_FUNC/int F_FUNC/g' scipy/linalg/_blas_subroutines.h
find -name '*.c' | xargs sed -i 's/extern void F_WRAPPEDFUNC/extern int F_WRAPPEDFUNC/g'
find -name '*.c' | xargs sed -i 's/void (\*f2py_func)/int (*f2py_func)/g'
find -name '*.c' | xargs sed -i 's/static void cb_/static int cb_/g'
find -name '*.c' | xargs sed -i 's/typedef void(\*cb_/typedef int(*cb_/g'
sed -i 's/,size_t//' build/src.linux-x86_64-3.9/build/src.linux-x86_64-3.9/scipy/linalg/_flapackmodule.c
sed -i 's/,slen([a-z]*))/)/g' build/src.linux-x86_64-3.9/build/src.linux-x86_64-3.9/scipy/linalg/_flapackmodule.c
sed -i 's/ float (\*f2py_func)/ double (\*f2py_func)/g' build/src.linux-x86_64-3.9/build/src.linux-x86_64-3.9/scipy/linalg/_fblasmodule.c
requirements:
run:
@ -65,14 +110,38 @@ test:
imports:
- scipy
- scipy.cluster
- scipy.cluster.vq
- scipy.cluster.hierarchy
- scipy.constants
- scipy.fft
- scipy.fftpack
- scipy.odr
- scipy.sparse
- scipy.interpolate
- scipy.integrate
- scipy.interpolate
- scipy.io
- scipy.io.arff
- scipy.io.matlab
- scipy.io.wavfile
- scipy.linalg
- scipy.linalg.blas
- scipy.linalg.cython_blas
- scipy.linalg.lapack
- scipy.linalg.cython_lapack
- scipy.linalg.interpolative
- scipy.misc
- scipy.ndimage
- scipy.odr
- scipy.optimize
- scipy.signal
- scipy.signal.windows
- scipy.sparse
- scipy.sparse.linalg
- scipy.sparse.csgraph
- scipy.spatial
- scipy.spatial.distance
- scipy.spatial.transform
- scipy.special
- scipy.stats
- scipy.stats.contingency
- scipy.stats.distributions
- scipy.stats.mstats
- scipy.stats.qmc

25
packages/scipy/patches/add-lapack_extras-to-flapack.patch Normal file
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@ -0,0 +1,25 @@
From 117b00d72c0472eb6a33e8fcbf17e3bfe3337a88 Mon Sep 17 00:00:00 2001
From: Hood Chatham <roberthoodchatham@gmail.com>
Date: Fri, 31 Dec 2021 22:27:07 -0800
Subject: [PATCH] Add lapack_extras to linalg/setup.py
---
scipy/linalg/setup.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/scipy/linalg/setup.py b/scipy/linalg/setup.py
index 2f0ef0a48..d384081a2 100644
--- a/scipy/linalg/setup.py
+++ b/scipy/linalg/setup.py
@@ -43,7 +43,7 @@ def configuration(parent_package='', top_path=None):
ext._pre_build_hook = blas_ilp64_pre_build_hook(lapack_ilp64_opt)
# flapack:
- sources = ['flapack.pyf.src']
+ sources = ['flapack.pyf.src', 'lapack_extras.f']
sources += get_g77_abi_wrappers(lapack_opt)
dep_pfx = join('src', 'lapack_deprecations')
deprecated_lapack_routines = [join(dep_pfx, c + 'gegv.f') for c in 'cdsz']
--
2.25.1

12
packages/scipy/patches/add-missing-extern.patch
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@ -1,12 +0,0 @@
Add a missing extern in specfunc_wrappers.c
--- a/scipy/special/specfun_wrappers.c
+++ b/scipy/special/specfun_wrappers.c
@@ -35,6 +35,7 @@
extern void F_FUNC(itairy,ITAIRY)(double*,double*,double*,double*,double*);
extern void F_FUNC(e1xb,E1XB)(double*,double*);
extern void F_FUNC(e1z,E1Z)(npy_cdouble*,npy_cdouble*);
+extern void F_FUNC(eixz,EIXZ)(npy_cdouble*,npy_cdouble*);
extern void F_FUNC(eix,EIX)(double*,double*);
extern void F_FUNC(cerror,CERROR)(npy_cdouble*,npy_cdouble*);
extern void F_FUNC(stvh0,STVH0)(double*,double*);

30
packages/scipy/patches/convert-xerrwv-message-arg-from-int-to-str.patch Normal file
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@ -0,0 +1,30 @@
From 109051fc810881a7291b47ba9353a69a36b600e3 Mon Sep 17 00:00:00 2001
From: Hood Chatham <roberthoodchatham@gmail.com>
Date: Sat, 25 Dec 2021 18:04:18 -0800
Subject: [PATCH] int to string
f2c does not handle implicit casts of function arguments correctly. The msg
argument of `xerrwv` is defined to be an `int *`, and then implicitly cast
from a string at the call site. This doesn't work correctly.
We redefine the type of the first argument to be string to fix the problem.
---
scipy/integrate/odepack/xerrwv.f | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/scipy/integrate/odepack/xerrwv.f b/scipy/integrate/odepack/xerrwv.f
index 7e180e4f8..b940bb702 100644
--- a/scipy/integrate/odepack/xerrwv.f
+++ b/scipy/integrate/odepack/xerrwv.f
@@ -1,5 +1,6 @@
subroutine xerrwv (msg, nmes, nerr, level, ni, i1, i2, nr, r1, r2)
- integer msg, nmes, nerr, level, ni, i1, i2, nr,
+ character msg*1
+ integer nmes, nerr, level, ni, i1, i2, nr,
1 i, lun, lunit, mesflg, ncpw, nch, nwds
double precision r1, r2
dimension msg(nmes)
--
2.25.1

24
packages/scipy/patches/disable-blas-detection.patch Normal file
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@ -0,0 +1,24 @@
commit 7352fc4a977a3414cf3194faf6ef990638a6329c
Author: Roman Yurchak <rth.yurchak@gmail.com>
Date: Sat Feb 27 11:13:29 2021 +0100
disable-blas-detection.patch
BLAS and LAPACK aren't available on host because we only cross compile these
libraries (see CLAPACK/meta.yaml). Scipy tries to detect these libraries and
if it fails to find them errors out the build. But we have them installed
correctly for our target, so we just disable this detection mechanism.
diff --git a/setup.py b/setup.py
index 0e11de60f..8c28c613d 100755
--- a/setup.py
+++ b/setup.py
@@ -484,7 +484,7 @@ def configuration(parent_package='', top_path=None):
lapack_opt = get_info('lapack_opt')
- if not lapack_opt:
+ if not lapack_opt and False:
if sys.platform == "darwin":
msg = ('No BLAS/LAPACK libraries found. '
'Note: Accelerate is no longer supported.')

39
packages/scipy/patches/disable_scipy_stats_mvn.patch
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@ -1,39 +0,0 @@
commit d6740caa7400105a578ace74f8c25bbb3434178c
Author: Roman Yurchak <rth.yurchak@pm.me>
Date: Wed Oct 10 14:47:12 2018 +0200
Disable scipy.stats.mvn
diff --git a/scipy/stats/kde.py b/scipy/stats/kde.py
index 7c702a038..8b0ab0254 100644
--- a/scipy/stats/kde.py
+++ b/scipy/stats/kde.py
@@ -32,7 +32,10 @@ import numpy as np
from numpy.random import randint, multivariate_normal
# Local imports.
-from . import mvn
+try:
+ from . import mvn
+except ImportError:
+ mvn = None
__all__ = ['gaussian_kde']
diff --git a/scipy/stats/setup.py b/scipy/stats/setup.py
index f1a02df4e..7366ec12d 100755
--- a/scipy/stats/setup.py
+++ b/scipy/stats/setup.py
@@ -32,9 +32,9 @@ def configuration(parent_package='',top_path=None):
)
# add mvn module
- config.add_extension('mvn',
- sources=['mvn.pyf','mvndst.f'],
- )
+ #config.add_extension('mvn',
+ # sources=['mvn.pyf','mvndst.f'],
+ #)
return config

89
packages/scipy/patches/fix-blas.patch
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@ -1,89 +0,0 @@
commit f03d85c00ae993c3c87a5a7b2ea0c1215f57ee04
Author: Roman Yurchak <rth.yurchak@pm.me>
Date: Mon Oct 8 10:53:11 2018 +0200
Partial fixes for BLAS/LAPACK
diff --git a/scipy/linalg/setup.py b/scipy/linalg/setup.py
index 2c9b9ba22..e8c7336d5 100755
--- a/scipy/linalg/setup.py
+++ b/scipy/linalg/setup.py
@@ -14,7 +14,13 @@ def configuration(parent_package='', top_path=None):
config = Configuration('linalg', parent_package, top_path)
- lapack_opt = get_info('lapack_opt')
+ lapack_opt = { # libraries will be auto-generated by pywasmcross
+ 'libraries': [],
+ 'include_dirs': [],
+ 'library_dirs': ['../../../CLAPACK/build/CLAPACK-3.2.1/'],
+ 'language': 'f77',
+ 'define_macros': [('NO_ATLAS_INFO', 1),
+ ('HAVE_CBLAS', None)]}
if not lapack_opt:
raise NotFoundError('no lapack/blas resources found')
@@ -117,9 +123,22 @@ def configuration(parent_package='', top_path=None):
fnames = split_fortran_files(join(dirname, 'src', 'id_dist', 'src'),
routines_to_split)
fnames = [join('src', 'id_dist', 'src', f) for f in fnames]
- config.add_extension('_interpolative', fnames + ["interpolative.pyf"],
- extra_info=lapack_opt
- )
+ # TODO: The following fails with,
+ # scipy/linalg/src/id_dist/src/idd_sfft.c:114:22: error: conflicting types for 'idd_sffti1__'
+ # /* Subroutine */ int idd_sffti1__(integer *ind, integer *n, doublereal *wsave)
+ # ^
+ # scipy/linalg/src/id_dist/src/idd_sfft.c:72:33: note: previous declaration is here
+ # extern /* Subroutine */ int idd_sffti1__(integer *, integer *,
+ # ^
+ # scipy/linalg/src/id_dist/src/idd_sfft.c:371:22: error: conflicting types for 'idd_sfft1__'
+ # /* Subroutine */ int idd_sfft1__(integer *ind, integer *n, doublereal *v,
+ # ^
+ # scipy/linalg/src/id_dist/src/idd_sfft.c:311:33: note: previous declaration is here
+ # extern /* Subroutine */ int idd_sfft1__(integer *, integer *, doublereal *<Paste>
+ #
+ #config.add_extension('_interpolative', fnames + ["interpolative.pyf"],
+ # extra_info=lapack_opt
+ # )
# _calc_lwork:
config.add_extension('_calc_lwork',
diff --git a/scipy/sparse/linalg/eigen/arpack/setup.py b/scipy/sparse/linalg/eigen/arpack/setup.py
index a8175a9d5..88a717fe6 100755
--- a/scipy/sparse/linalg/eigen/arpack/setup.py
+++ b/scipy/sparse/linalg/eigen/arpack/setup.py
@@ -11,7 +11,13 @@ def configuration(parent_package='',top_path=None):
config = Configuration('arpack',parent_package,top_path)
- lapack_opt = get_info('lapack_opt')
+ lapack_opt = { # libraries will be auto-generated by pywasmcross
+ 'libraries': [],
+ 'include_dirs': [],
+ 'library_dirs': ['../../../CLAPACK/build/CLAPACK-3.2.1/'],
+ 'language': 'f77',
+ 'define_macros': [('NO_ATLAS_INFO', 1),
+ ('HAVE_CBLAS', None)]}
if not lapack_opt:
raise NotFoundError('no lapack/blas resources found')
diff --git a/scipy/sparse/linalg/isolve/setup.py b/scipy/sparse/linalg/isolve/setup.py
index becb9237a..707e3f49d 100755
--- a/scipy/sparse/linalg/isolve/setup.py
+++ b/scipy/sparse/linalg/isolve/setup.py
@@ -11,7 +11,13 @@ def configuration(parent_package='',top_path=None):
config = Configuration('isolve',parent_package,top_path)
- lapack_opt = get_info('lapack_opt')
+ lapack_opt = { # libraries will be auto-generated by pywasmcross
+ 'libraries': [],
+ 'include_dirs': [],
+ 'library_dirs': ['../../../CLAPACK/build/CLAPACK-3.2.1/'],
+ 'language': 'f77',
+ 'define_macros': [('NO_ATLAS_INFO', 1),
+ ('HAVE_CBLAS', None)]}
if not lapack_opt:
raise NotFoundError('no lapack/blas resources found')

54
packages/scipy/patches/fix-build-gcc5-a80460.patch
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@ -1,54 +0,0 @@
commit a80460f1b45035d34575866e6394107396ac62e2
Author: Michael Danilov <mike402@users.noreply.github.com>
Date: Thu Apr 20 18:08:39 2017 +0200
Fix build with GCC5.
diff --git a/scipy/odr/odrpack/d_lpkbls.f b/scipy/odr/odrpack/d_lpkbls.f
index 324b7a8a2..1e6624d63 100644
--- a/scipy/odr/odrpack/d_lpkbls.f
+++ b/scipy/odr/odrpack/d_lpkbls.f
@@ -136,8 +136,8 @@ C***FIRST EXECUTABLE STATEMENT DAXPY
IF(N.LE.0.OR.DA.EQ.0.D0) RETURN
- IF (INCX.EQ.INCY) IF(INCX.lt.1) GOTO 5
- IF (INCX.EQ.INCY) IF(INCX.eq.1) GOTO 20
+ IF (INCX.EQ.INCY .AND. INCX.lt.1) GOTO 5
+ IF (INCX.EQ.INCY .AND. INCX.eq.1) GOTO 20
GOTO 60
5 CONTINUE
@@ -483,8 +483,8 @@ C***FIRST EXECUTABLE STATEMENT DCOPY
IF(N.LE.0)RETURN
- IF (INCX.EQ.INCY) IF(INCX.lt.1) GOTO 5
- IF (INCX.EQ.INCY) IF(INCX.eq.1) GOTO 20
+ IF (INCX.EQ.INCY .AND. INCX.lt.1) GOTO 5
+ IF (INCX.EQ.INCY .AND. INCX.eq.1) GOTO 20
GOTO 60
5 CONTINUE
@@ -589,8 +589,8 @@ C***FIRST EXECUTABLE STATEMENT DDOT
DDOT = 0.D0
IF(N.LE.0)RETURN
- IF (INCX.EQ.INCY) IF(INCX.lt.1) GOTO 5
- IF (INCX.EQ.INCY) IF(INCX.eq.1) GOTO 20
+ IF (INCX.EQ.INCY .AND. INCX.lt.1) GOTO 5
+ IF (INCX.EQ.INCY .AND. INCX.eq.1) GOTO 20
GOTO 60
5 CONTINUE
@@ -1772,8 +1772,8 @@ C***FIRST EXECUTABLE STATEMENT DSWAP
IF(N.LE.0)RETURN
- IF (INCX.EQ.INCY) IF(INCX.lt.1) GOTO 5
- IF (INCX.EQ.INCY) IF(INCX.eq.1) GOTO 20
+ IF (INCX.EQ.INCY .AND. INCX.lt.1) GOTO 5
+ IF (INCX.EQ.INCY .AND. INCX.eq.1) GOTO 20
GOTO 60
5 CONTINUE

253
packages/scipy/patches/fix-fortran-files-minpack.patch Normal file
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@ -0,0 +1,253 @@
diff --git a/scipy/optimize/minpack/chkder.f b/scipy/optimize/minpack/chkder.f
index 0657ab56a..29578fc41 100644
--- a/scipy/optimize/minpack/chkder.f
+++ b/scipy/optimize/minpack/chkder.f
@@ -1,5 +1,4 @@
- recursive
- *subroutine chkder(m,n,x,fvec,fjac,ldfjac,xp,fvecp,mode,err)
+ subroutine chkder(m,n,x,fvec,fjac,ldfjac,xp,fvecp,mode,err)
integer m,n,ldfjac,mode
double precision x(n),fvec(m),fjac(ldfjac,n),xp(n),fvecp(m),
* err(m)
diff --git a/scipy/optimize/minpack/dogleg.f b/scipy/optimize/minpack/dogleg.f
index d9626c911..b812f1966 100644
--- a/scipy/optimize/minpack/dogleg.f
+++ b/scipy/optimize/minpack/dogleg.f
@@ -1,5 +1,4 @@
- recursive
- *subroutine dogleg(n,r,lr,diag,qtb,delta,x,wa1,wa2)
+ subroutine dogleg(n,r,lr,diag,qtb,delta,x,wa1,wa2)
integer n,lr
double precision delta
double precision r(lr),diag(n),qtb(n),x(n),wa1(n),wa2(n)
diff --git a/scipy/optimize/minpack/dpmpar.f b/scipy/optimize/minpack/dpmpar.f
index 3fd3b4ef8..cb6545a92 100644
--- a/scipy/optimize/minpack/dpmpar.f
+++ b/scipy/optimize/minpack/dpmpar.f
@@ -1,5 +1,4 @@
- recursive
- *double precision function dpmpar(i)
+ double precision function dpmpar(i)
integer i
c **********
c
diff --git a/scipy/optimize/minpack/enorm.f b/scipy/optimize/minpack/enorm.f
index 21557c147..2cb5b607e 100644
--- a/scipy/optimize/minpack/enorm.f
+++ b/scipy/optimize/minpack/enorm.f
@@ -1,5 +1,4 @@
- recursive
- *double precision function enorm(n,x)
+ double precision function enorm(n,x)
integer n
double precision x(n)
c **********
diff --git a/scipy/optimize/minpack/fdjac1.f b/scipy/optimize/minpack/fdjac1.f
index 2a7d84cc1..031ed4652 100644
--- a/scipy/optimize/minpack/fdjac1.f
+++ b/scipy/optimize/minpack/fdjac1.f
@@ -1,5 +1,4 @@
- recursive
- *subroutine fdjac1(fcn,n,x,fvec,fjac,ldfjac,iflag,ml,mu,epsfcn,
+ subroutine fdjac1(fcn,n,x,fvec,fjac,ldfjac,iflag,ml,mu,epsfcn,
* wa1,wa2)
integer n,ldfjac,iflag,ml,mu
double precision epsfcn
diff --git a/scipy/optimize/minpack/fdjac2.f b/scipy/optimize/minpack/fdjac2.f
index 5f4c1338f..218ab94c1 100644
--- a/scipy/optimize/minpack/fdjac2.f
+++ b/scipy/optimize/minpack/fdjac2.f
@@ -1,5 +1,4 @@
- recursive
- *subroutine fdjac2(fcn,m,n,x,fvec,fjac,ldfjac,iflag,epsfcn,wa)
+ subroutine fdjac2(fcn,m,n,x,fvec,fjac,ldfjac,iflag,epsfcn,wa)
integer m,n,ldfjac,iflag
double precision epsfcn
double precision x(n),fvec(m),fjac(ldfjac,n),wa(m)
diff --git a/scipy/optimize/minpack/hybrd.f b/scipy/optimize/minpack/hybrd.f
index 75f450c9c..fc0b4c26a 100644
--- a/scipy/optimize/minpack/hybrd.f
+++ b/scipy/optimize/minpack/hybrd.f
@@ -1,5 +1,4 @@
- recursive
- *subroutine hybrd(fcn,n,x,fvec,xtol,maxfev,ml,mu,epsfcn,diag,
+ subroutine hybrd(fcn,n,x,fvec,xtol,maxfev,ml,mu,epsfcn,diag,
* mode,factor,nprint,info,nfev,fjac,ldfjac,r,lr,
* qtf,wa1,wa2,wa3,wa4)
integer n,maxfev,ml,mu,mode,nprint,info,nfev,ldfjac,lr
diff --git a/scipy/optimize/minpack/hybrd1.f b/scipy/optimize/minpack/hybrd1.f
index 87660fe18..c0a859275 100644
--- a/scipy/optimize/minpack/hybrd1.f
+++ b/scipy/optimize/minpack/hybrd1.f
@@ -1,5 +1,4 @@
- recursive
- *subroutine hybrd1(fcn,n,x,fvec,tol,info,wa,lwa)
+ subroutine hybrd1(fcn,n,x,fvec,tol,info,wa,lwa)
integer n,info,lwa
double precision tol
double precision x(n),fvec(n),wa(lwa)
diff --git a/scipy/optimize/minpack/hybrj.f b/scipy/optimize/minpack/hybrj.f
index 4f676832e..3070dad3f 100644
--- a/scipy/optimize/minpack/hybrj.f
+++ b/scipy/optimize/minpack/hybrj.f
@@ -1,5 +1,4 @@
- recursive
- *subroutine hybrj(fcn,n,x,fvec,fjac,ldfjac,xtol,maxfev,diag,mode,
+ subroutine hybrj(fcn,n,x,fvec,fjac,ldfjac,xtol,maxfev,diag,mode,
* factor,nprint,info,nfev,njev,r,lr,qtf,wa1,wa2,
* wa3,wa4)
integer n,ldfjac,maxfev,mode,nprint,info,nfev,njev,lr
diff --git a/scipy/optimize/minpack/hybrj1.f b/scipy/optimize/minpack/hybrj1.f
index afa9d80f1..9f51c4965 100644
--- a/scipy/optimize/minpack/hybrj1.f
+++ b/scipy/optimize/minpack/hybrj1.f
@@ -1,5 +1,4 @@
- recursive
- *subroutine hybrj1(fcn,n,x,fvec,fjac,ldfjac,tol,info,wa,lwa)
+ subroutine hybrj1(fcn,n,x,fvec,fjac,ldfjac,tol,info,wa,lwa)
integer n,ldfjac,info,lwa
double precision tol
double precision x(n),fvec(n),fjac(ldfjac,n),wa(lwa)
diff --git a/scipy/optimize/minpack/lmder.f b/scipy/optimize/minpack/lmder.f
index 684925592..8797d8bed 100644
--- a/scipy/optimize/minpack/lmder.f
+++ b/scipy/optimize/minpack/lmder.f
@@ -1,5 +1,4 @@
- recursive
- *subroutine lmder(fcn,m,n,x,fvec,fjac,ldfjac,ftol,xtol,gtol,
+ subroutine lmder(fcn,m,n,x,fvec,fjac,ldfjac,ftol,xtol,gtol,
* maxfev,diag,mode,factor,nprint,info,nfev,njev,
* ipvt,qtf,wa1,wa2,wa3,wa4)
integer m,n,ldfjac,maxfev,mode,nprint,info,nfev,njev
diff --git a/scipy/optimize/minpack/lmder1.f b/scipy/optimize/minpack/lmder1.f
index 6be29477d..d691940fd 100644
--- a/scipy/optimize/minpack/lmder1.f
+++ b/scipy/optimize/minpack/lmder1.f
@@ -1,5 +1,4 @@
- recursive
- *subroutine lmder1(fcn,m,n,x,fvec,fjac,ldfjac,tol,info,ipvt,wa,
+ subroutine lmder1(fcn,m,n,x,fvec,fjac,ldfjac,tol,info,ipvt,wa,
* lwa)
integer m,n,ldfjac,info,lwa
integer ipvt(n)
diff --git a/scipy/optimize/minpack/lmdif.f b/scipy/optimize/minpack/lmdif.f
index fcb61d138..dd3d4ee25 100644
--- a/scipy/optimize/minpack/lmdif.f
+++ b/scipy/optimize/minpack/lmdif.f
@@ -1,5 +1,4 @@
- recursive
- *subroutine lmdif(fcn,m,n,x,fvec,ftol,xtol,gtol,maxfev,epsfcn,
+ subroutine lmdif(fcn,m,n,x,fvec,ftol,xtol,gtol,maxfev,epsfcn,
* diag,mode,factor,nprint,info,nfev,fjac,ldfjac,
* ipvt,qtf,wa1,wa2,wa3,wa4)
integer m,n,maxfev,mode,nprint,info,nfev,ldfjac
diff --git a/scipy/optimize/minpack/lmdif1.f b/scipy/optimize/minpack/lmdif1.f
index 6f28ed2f7..70f8aae05 100644
--- a/scipy/optimize/minpack/lmdif1.f
+++ b/scipy/optimize/minpack/lmdif1.f
@@ -1,5 +1,4 @@
- recursive
- *subroutine lmdif1(fcn,m,n,x,fvec,tol,info,iwa,wa,lwa)
+ subroutine lmdif1(fcn,m,n,x,fvec,tol,info,iwa,wa,lwa)
integer m,n,info,lwa
integer iwa(n)
double precision tol
diff --git a/scipy/optimize/minpack/lmpar.f b/scipy/optimize/minpack/lmpar.f
index e25eb0d3e..26c422a79 100644
--- a/scipy/optimize/minpack/lmpar.f
+++ b/scipy/optimize/minpack/lmpar.f
@@ -1,5 +1,4 @@
- recursive
- *subroutine lmpar(n,r,ldr,ipvt,diag,qtb,delta,par,x,sdiag,wa1,
+ subroutine lmpar(n,r,ldr,ipvt,diag,qtb,delta,par,x,sdiag,wa1,
* wa2)
integer n,ldr
integer ipvt(n)
diff --git a/scipy/optimize/minpack/lmstr.f b/scipy/optimize/minpack/lmstr.f
index 2b6bbbfc2..d9a7893f8 100644
--- a/scipy/optimize/minpack/lmstr.f
+++ b/scipy/optimize/minpack/lmstr.f
@@ -1,5 +1,4 @@
- recursive
- *subroutine lmstr(fcn,m,n,x,fvec,fjac,ldfjac,ftol,xtol,gtol,
+ subroutine lmstr(fcn,m,n,x,fvec,fjac,ldfjac,ftol,xtol,gtol,
* maxfev,diag,mode,factor,nprint,info,nfev,njev,
* ipvt,qtf,wa1,wa2,wa3,wa4)
integer m,n,ldfjac,maxfev,mode,nprint,info,nfev,njev
diff --git a/scipy/optimize/minpack/lmstr1.f b/scipy/optimize/minpack/lmstr1.f
index 225e8736f..2fa8ee1c5 100644
--- a/scipy/optimize/minpack/lmstr1.f
+++ b/scipy/optimize/minpack/lmstr1.f
@@ -1,5 +1,4 @@
- recursive
- *subroutine lmstr1(fcn,m,n,x,fvec,fjac,ldfjac,tol,info,ipvt,wa,
+ subroutine lmstr1(fcn,m,n,x,fvec,fjac,ldfjac,tol,info,ipvt,wa,
* lwa)
integer m,n,ldfjac,info,lwa
integer ipvt(n)
diff --git a/scipy/optimize/minpack/qform.f b/scipy/optimize/minpack/qform.f
index 1f368587e..087b2478b 100644
--- a/scipy/optimize/minpack/qform.f
+++ b/scipy/optimize/minpack/qform.f
@@ -1,5 +1,4 @@
- recursive
- *subroutine qform(m,n,q,ldq,wa)
+ subroutine qform(m,n,q,ldq,wa)
integer m,n,ldq
double precision q(ldq,m),wa(m)
c **********
diff --git a/scipy/optimize/minpack/qrfac.f b/scipy/optimize/minpack/qrfac.f
index fa6789086..cb686086c 100644
--- a/scipy/optimize/minpack/qrfac.f
+++ b/scipy/optimize/minpack/qrfac.f
@@ -1,5 +1,4 @@
- recursive
- *subroutine qrfac(m,n,a,lda,pivot,ipvt,lipvt,rdiag,acnorm,wa)
+ subroutine qrfac(m,n,a,lda,pivot,ipvt,lipvt,rdiag,acnorm,wa)
integer m,n,lda,lipvt
integer ipvt(lipvt)
logical pivot
diff --git a/scipy/optimize/minpack/qrsolv.f b/scipy/optimize/minpack/qrsolv.f
index 3dc009721..5580087ca 100644
--- a/scipy/optimize/minpack/qrsolv.f
+++ b/scipy/optimize/minpack/qrsolv.f
@@ -1,5 +1,4 @@
- recursive
- *subroutine qrsolv(n,r,ldr,ipvt,diag,qtb,x,sdiag,wa)
+ subroutine qrsolv(n,r,ldr,ipvt,diag,qtb,x,sdiag,wa)
integer n,ldr
integer ipvt(n)
double precision r(ldr,n),diag(n),qtb(n),x(n),sdiag(n),wa(n)
diff --git a/scipy/optimize/minpack/r1mpyq.f b/scipy/optimize/minpack/r1mpyq.f
index 1410b9ad6..ec99b96ce 100644
--- a/scipy/optimize/minpack/r1mpyq.f
+++ b/scipy/optimize/minpack/r1mpyq.f
@@ -1,5 +1,4 @@
- recursive
- *subroutine r1mpyq(m,n,a,lda,v,w)
+ subroutine r1mpyq(m,n,a,lda,v,w)
integer m,n,lda
double precision a(lda,n),v(n),w(n)
c **********
diff --git a/scipy/optimize/minpack/r1updt.f b/scipy/optimize/minpack/r1updt.f
index e809d8402..e034973d9 100644
--- a/scipy/optimize/minpack/r1updt.f
+++ b/scipy/optimize/minpack/r1updt.f
@@ -1,5 +1,4 @@
- recursive
- *subroutine r1updt(m,n,s,ls,u,v,w,sing)
+ subroutine r1updt(m,n,s,ls,u,v,w,sing)
integer m,n,ls
logical sing
double precision s(ls),u(m),v(n),w(m)
diff --git a/scipy/optimize/minpack/rwupdt.f b/scipy/optimize/minpack/rwupdt.f
index 61a7928bb..05282b556 100644
--- a/scipy/optimize/minpack/rwupdt.f
+++ b/scipy/optimize/minpack/rwupdt.f
@@ -1,5 +1,4 @@
- recursive
- *subroutine rwupdt(n,r,ldr,w,b,alpha,cos,sin)
+ subroutine rwupdt(n,r,ldr,w,b,alpha,cos,sin)
integer n,ldr
double precision alpha
double precision r(ldr,n),w(n),b(n),cos(n),sin(n)

317
packages/scipy/patches/fix-implicit-cast-args-from-newer-lapack.patch Normal file
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@ -0,0 +1,317 @@
We are hijacking dfft.f to inject missing functions from future versions of LAPACK.
This patch is applied to the generated dfft.c after f2c is applied to dfft.f.
This must be done in between when f2c is applied to dfft.f and when dfft.c is compiled.
This is arranged in _f2c_fixes.py.
f2c does not correctly handle implicit casts of function arguments. If the implicit casts
are between integer types then we can handle that automatically in _f2c_fixes.py. This
patch fixes implicit casts from char* to int, which we need to deal with manually.
--- a/scipy/linalg/src/id_dist/src/dfft.c
+++ b/scipy/linalg/src/id_dist/src/dfft.c
@@ -2855,8 +2855,7 @@ f_rook.f"> */
extern /* Subroutine */ int xerbla_(char *, integer *, ftnlen), ctprfb_(
char *, char *, char *, char *, integer *, integer *, integer *,
integer *, complex *, integer *, complex *, integer *, complex *,
- integer *, complex *, integer *, complex *, integer *, ftnlen,
- ftnlen, ftnlen, ftnlen);
+ integer *, complex *, integer *, complex *, integer *);
static logical notran;
@@ -2967,8 +2966,7 @@ f_rook.f"> */
}
ctprfb_("L", "C", "F", "C", &mb, n, &ib, &lb, &v[i__ * v_dim1 + 1]
, ldv, &t[i__ * t_dim1 + 1], ldt, &a[i__ + a_dim1], lda, &
- b[b_offset], ldb, &work[1], &ib, (ftnlen)1, (ftnlen)1, (
- ftnlen)1, (ftnlen)1);
+ b[b_offset], ldb, &work[1], &ib);
}
} else if (right && notran) {
@@ -2989,8 +2987,7 @@ f_rook.f"> */
}
ctprfb_("R", "N", "F", "C", m, &mb, &ib, &lb, &v[i__ * v_dim1 + 1]
, ldv, &t[i__ * t_dim1 + 1], ldt, &a[i__ * a_dim1 + 1],
- lda, &b[b_offset], ldb, &work[1], m, (ftnlen)1, (ftnlen)1,
- (ftnlen)1, (ftnlen)1);
+ lda, &b[b_offset], ldb, &work[1], m);
}
} else if (left && notran) {
@@ -3011,8 +3008,7 @@ f_rook.f"> */
}
ctprfb_("L", "N", "F", "C", &mb, n, &ib, &lb, &v[i__ * v_dim1 + 1]
, ldv, &t[i__ * t_dim1 + 1], ldt, &a[i__ + a_dim1], lda, &
- b[b_offset], ldb, &work[1], &ib, (ftnlen)1, (ftnlen)1, (
- ftnlen)1, (ftnlen)1);
+ b[b_offset], ldb, &work[1], &ib);
}
} else if (right && tran) {
@@ -3033,8 +3029,7 @@ f_rook.f"> */
}
ctprfb_("R", "C", "F", "C", m, &mb, &ib, &lb, &v[i__ * v_dim1 + 1]
, ldv, &t[i__ * t_dim1 + 1], ldt, &a[i__ * a_dim1 + 1],
- lda, &b[b_offset], ldb, &work[1], m, (ftnlen)1, (ftnlen)1,
- (ftnlen)1, (ftnlen)1);
+ lda, &b[b_offset], ldb, &work[1], m);
}
}
@@ -3247,8 +3242,7 @@ f"> */
extern /* Subroutine */ int xerbla_(char *, integer *, ftnlen), ctprfb_(
char *, char *, char *, char *, integer *, integer *, integer *,
integer *, complex *, integer *, complex *, integer *, complex *,
- integer *, complex *, integer *, complex *, integer *, ftnlen,
- ftnlen, ftnlen, ftnlen), ctpqrt2_(integer *, integer *, integer *,
+ integer *, complex *, integer *, complex *, integer *), ctpqrt2_(integer *, integer *, integer *,
complex *, integer *, complex *, integer *, complex *, integer *,
integer *);
@@ -3342,7 +3336,7 @@ f"> */
ctprfb_("L", "C", "F", "C", &mb, &i__3, &ib, &lb, &b[i__ * b_dim1
+ 1], ldb, &t[i__ * t_dim1 + 1], ldt, &a[i__ + (i__ + ib)
* a_dim1], lda, &b[(i__ + ib) * b_dim1 + 1], ldb, &work[1]
- , &ib, (ftnlen)1, (ftnlen)1, (ftnlen)1, (ftnlen)1);
+ , &ib);
}
}
return 0;
@@ -6041,11 +6035,13 @@ f_rook.f"> */
static integer ldvq;
extern logical lsame_(char *, char *, ftnlen, ftnlen);
static logical right;
- extern /* Subroutine */ int xerbla_(char *, integer *, ftnlen), dtprfb_(
+ extern /* Subroutine */ int xerbla_(char *, integer *, ftnlen),
+
+ dtprfb_(
char *, char *, char *, char *, integer *, integer *, integer *,
integer *, doublereal *, integer *, doublereal *, integer *,
doublereal *, integer *, doublereal *, integer *, doublereal *,
- integer *, ftnlen, ftnlen, ftnlen, ftnlen);
+ integer *);
static logical notran;
@@ -6156,8 +6152,7 @@ f_rook.f"> */
}
dtprfb_("L", "T", "F", "C", &mb, n, &ib, &lb, &v[i__ * v_dim1 + 1]
, ldv, &t[i__ * t_dim1 + 1], ldt, &a[i__ + a_dim1], lda, &
- b[b_offset], ldb, &work[1], &ib, (ftnlen)1, (ftnlen)1, (
- ftnlen)1, (ftnlen)1);
+ b[b_offset], ldb, &work[1], &ib);
}
} else if (right && notran) {
@@ -6178,8 +6173,7 @@ f_rook.f"> */
}
dtprfb_("R", "N", "F", "C", m, &mb, &ib, &lb, &v[i__ * v_dim1 + 1]
, ldv, &t[i__ * t_dim1 + 1], ldt, &a[i__ * a_dim1 + 1],
- lda, &b[b_offset], ldb, &work[1], m, (ftnlen)1, (ftnlen)1,
- (ftnlen)1, (ftnlen)1);
+ lda, &b[b_offset], ldb, &work[1], m);
}
} else if (left && notran) {
@@ -6200,8 +6194,7 @@ f_rook.f"> */
}
dtprfb_("L", "N", "F", "C", &mb, n, &ib, &lb, &v[i__ * v_dim1 + 1]
, ldv, &t[i__ * t_dim1 + 1], ldt, &a[i__ + a_dim1], lda, &
- b[b_offset], ldb, &work[1], &ib, (ftnlen)1, (ftnlen)1, (
- ftnlen)1, (ftnlen)1);
+ b[b_offset], ldb, &work[1], &ib);
}
} else if (right && tran) {
@@ -6222,8 +6215,7 @@ f_rook.f"> */
}
dtprfb_("R", "T", "F", "C", m, &mb, &ib, &lb, &v[i__ * v_dim1 + 1]
, ldv, &t[i__ * t_dim1 + 1], ldt, &a[i__ * a_dim1 + 1],
- lda, &b[b_offset], ldb, &work[1], m, (ftnlen)1, (ftnlen)1,
- (ftnlen)1, (ftnlen)1);
+ lda, &b[b_offset], ldb, &work[1], m);
}
}
@@ -6433,13 +6425,12 @@ f"> */
/* Local variables */
static integer i__, ib, lb, mb, iinfo;
- extern /* Subroutine */ int xerbla_(char *, integer *, ftnlen), dtprfb_(
- char *, char *, char *, char *, integer *, integer *, integer *,
- integer *, doublereal *, integer *, doublereal *, integer *,
- doublereal *, integer *, doublereal *, integer *, doublereal *,
- integer *, ftnlen, ftnlen, ftnlen, ftnlen), dtpqrt2_(integer *,
- integer *, integer *, doublereal *, integer *, doublereal *,
- integer *, doublereal *, integer *, integer *);
+ extern /* Subroutine */ int xerbla_(char *, integer *, ftnlen),
+
+dtprfb_(char *, char *, char *, char *, integer *, integer *, integer *, integer *, doublereal *, integer *, doublereal *, integer *,
+ doublereal *, integer *, doublereal *, integer *, doublereal *, integer *),
+
+ dtpqrt2_(integer *, integer *, integer *, doublereal *, integer *, doublereal *, integer *, doublereal *, integer *, integer *);
/* -- LAPACK computational routine -- */
@@ -6531,9 +6522,8 @@ f"> */
dtprfb_("L", "T", "F", "C", &mb, &i__3, &ib, &lb, &b[i__ * b_dim1
+ 1], ldb, &t[i__ * t_dim1 + 1], ldt, &a[i__ + (i__ + ib)
* a_dim1], lda, &b[(i__ + ib) * b_dim1 + 1], ldb, &work[1]
- , &ib, (ftnlen)1, (ftnlen)1, (ftnlen)1, (ftnlen)1);
- }
- }
+ , &ib);
+ }}
return 0;
/* End of DTPQRT */
@@ -9226,8 +9216,7 @@ f_rook.f"> */
extern /* Subroutine */ int xerbla_(char *, integer *, ftnlen), stprfb_(
char *, char *, char *, char *, integer *, integer *, integer *,
integer *, real *, integer *, real *, integer *, real *, integer *
- , real *, integer *, real *, integer *, ftnlen, ftnlen, ftnlen,
- ftnlen);
+ , real *, integer *, real *, integer *);
static logical notran;
@@ -9338,8 +9327,7 @@ f_rook.f"> */
}
stprfb_("L", "T", "F", "C", &mb, n, &ib, &lb, &v[i__ * v_dim1 + 1]
, ldv, &t[i__ * t_dim1 + 1], ldt, &a[i__ + a_dim1], lda, &
- b[b_offset], ldb, &work[1], &ib, (ftnlen)1, (ftnlen)1, (
- ftnlen)1, (ftnlen)1);
+ b[b_offset], ldb, &work[1], &ib);
}
} else if (right && notran) {
@@ -9360,8 +9348,7 @@ f_rook.f"> */
}
stprfb_("R", "N", "F", "C", m, &mb, &ib, &lb, &v[i__ * v_dim1 + 1]
, ldv, &t[i__ * t_dim1 + 1], ldt, &a[i__ * a_dim1 + 1],
- lda, &b[b_offset], ldb, &work[1], m, (ftnlen)1, (ftnlen)1,
- (ftnlen)1, (ftnlen)1);
+ lda, &b[b_offset], ldb, &work[1], m);
}
} else if (left && notran) {
@@ -9382,8 +9369,7 @@ f_rook.f"> */
}
stprfb_("L", "N", "F", "C", &mb, n, &ib, &lb, &v[i__ * v_dim1 + 1]
, ldv, &t[i__ * t_dim1 + 1], ldt, &a[i__ + a_dim1], lda, &
- b[b_offset], ldb, &work[1], &ib, (ftnlen)1, (ftnlen)1, (
- ftnlen)1, (ftnlen)1);
+ b[b_offset], ldb, &work[1], &ib);
}
} else if (right && tran) {
@@ -9404,8 +9390,7 @@ f_rook.f"> */
}
stprfb_("R", "T", "F", "C", m, &mb, &ib, &lb, &v[i__ * v_dim1 + 1]
, ldv, &t[i__ * t_dim1 + 1], ldt, &a[i__ * a_dim1 + 1],
- lda, &b[b_offset], ldb, &work[1], m, (ftnlen)1, (ftnlen)1,
- (ftnlen)1, (ftnlen)1);
+ lda, &b[b_offset], ldb, &work[1], m);
}
}
@@ -9618,8 +9603,7 @@ f"> */
extern /* Subroutine */ int xerbla_(char *, integer *, ftnlen), stprfb_(
char *, char *, char *, char *, integer *, integer *, integer *,
integer *, real *, integer *, real *, integer *, real *, integer *
- , real *, integer *, real *, integer *, ftnlen, ftnlen, ftnlen,
- ftnlen), stpqrt2_(integer *, integer *, integer *, real *,
+ , real *, integer *, real *, integer *), stpqrt2_(integer *, integer *, integer *, real *,
integer *, real *, integer *, real *, integer *, integer *);
@@ -9712,7 +9696,7 @@ f"> */
stprfb_("L", "T", "F", "C", &mb, &i__3, &ib, &lb, &b[i__ * b_dim1
+ 1], ldb, &t[i__ * t_dim1 + 1], ldt, &a[i__ + (i__ + ib)
* a_dim1], lda, &b[(i__ + ib) * b_dim1 + 1], ldb, &work[1]
- , &ib, (ftnlen)1, (ftnlen)1, (ftnlen)1, (ftnlen)1);
+ , &ib);
}
}
return 0;
@@ -12502,8 +12486,7 @@ f_rook.f"> */
extern /* Subroutine */ int ztprfb_(char *, char *, char *, char *,
integer *, integer *, integer *, integer *, doublecomplex *,
integer *, doublecomplex *, integer *, doublecomplex *, integer *,
- doublecomplex *, integer *, doublecomplex *, integer *, ftnlen,
- ftnlen, ftnlen, ftnlen);
+ doublecomplex *, integer *, doublecomplex *, integer *);
/* -- LAPACK computational routine -- */
@@ -12613,8 +12596,7 @@ f_rook.f"> */
}
ztprfb_("L", "C", "F", "C", &mb, n, &ib, &lb, &v[i__ * v_dim1 + 1]
, ldv, &t[i__ * t_dim1 + 1], ldt, &a[i__ + a_dim1], lda, &
- b[b_offset], ldb, &work[1], &ib, (ftnlen)1, (ftnlen)1, (
- ftnlen)1, (ftnlen)1);
+ b[b_offset], ldb, &work[1], &ib);
}
} else if (right && notran) {
@@ -12635,8 +12617,7 @@ f_rook.f"> */
}
ztprfb_("R", "N", "F", "C", m, &mb, &ib, &lb, &v[i__ * v_dim1 + 1]
, ldv, &t[i__ * t_dim1 + 1], ldt, &a[i__ * a_dim1 + 1],
- lda, &b[b_offset], ldb, &work[1], m, (ftnlen)1, (ftnlen)1,
- (ftnlen)1, (ftnlen)1);
+ lda, &b[b_offset], ldb, &work[1], m);
}
} else if (left && notran) {
@@ -12657,8 +12638,7 @@ f_rook.f"> */
}
ztprfb_("L", "N", "F", "C", &mb, n, &ib, &lb, &v[i__ * v_dim1 + 1]
, ldv, &t[i__ * t_dim1 + 1], ldt, &a[i__ + a_dim1], lda, &
- b[b_offset], ldb, &work[1], &ib, (ftnlen)1, (ftnlen)1, (
- ftnlen)1, (ftnlen)1);
+ b[b_offset], ldb, &work[1], &ib);
}
} else if (right && tran) {
@@ -12679,8 +12659,7 @@ f_rook.f"> */
}
ztprfb_("R", "C", "F", "C", m, &mb, &ib, &lb, &v[i__ * v_dim1 + 1]
, ldv, &t[i__ * t_dim1 + 1], ldt, &a[i__ * a_dim1 + 1],
- lda, &b[b_offset], ldb, &work[1], m, (ftnlen)1, (ftnlen)1,
- (ftnlen)1, (ftnlen)1);
+ lda, &b[b_offset], ldb, &work[1], m);
}
}
@@ -12894,7 +12873,7 @@ f"> */
char *, char *, char *, char *, integer *, integer *, integer *,
integer *, doublecomplex *, integer *, doublecomplex *, integer *,
doublecomplex *, integer *, doublecomplex *, integer *,
- doublecomplex *, integer *, ftnlen, ftnlen, ftnlen, ftnlen),
+ doublecomplex *, integer *),
ztpqrt2_(integer *, integer *, integer *, doublecomplex *,
integer *, doublecomplex *, integer *, doublecomplex *, integer *,
integer *);
@@ -12989,7 +12968,7 @@ f"> */
ztprfb_("L", "C", "F", "C", &mb, &i__3, &ib, &lb, &b[i__ * b_dim1
+ 1], ldb, &t[i__ * t_dim1 + 1], ldt, &a[i__ + (i__ + ib)
* a_dim1], lda, &b[(i__ + ib) * b_dim1 + 1], ldb, &work[1]
- , &ib, (ftnlen)1, (ftnlen)1, (ftnlen)1, (ftnlen)1);
+ , &ib);
}
}
return 0;
@@ -12998,3 +12977,10 @@ f"> */
} /* ztpqrt_ */
+
+typedef struct { float real, imag; } npy_complex64;
+typedef struct { double real, imag; } npy_complex128;
+int sorcsd_(char *jobu1, char *jobu2, char *jobv1t, char *jobv2t, char *trans, char *signs, int *m, int *p, int *q, float *x11, int *ldx11, float *x12, int *ldx12, float *x21, int *ldx21, float *x22, int *ldx22, float *theta, float *u1, int *ldu1, float *u2, int *ldu2, float *v1t, int *ldv1t, float *v2t, int *ldv2t, float *work, int *lwork, int *iwork, int *info){ return 0; }
+int dorcsd_(char *jobu1, char *jobu2, char *jobv1t, char *jobv2t, char *trans, char *signs, int *m, int *p, int *q, double *x11, int *ldx11, double *x12, int *ldx12, double *x21, int *ldx21, double *x22, int *ldx22, double *theta, double *u1, int *ldu1, double *u2, int *ldu2, double *v1t, int *ldv1t, double *v2t, int *ldv2t, double *work, int *lwork, int *iwork, int *info){ return 0; }
+int zuncsd_(char *jobu1, char *jobu2, char *jobv1t, char *jobv2t, char *trans, char *signs, int *m, int *p, int *q, npy_complex128 *x11, int *ldx11, npy_complex128 *x12, int *ldx12, npy_complex128 *x21, int *ldx21, npy_complex128 *x22, int *ldx22, double *theta, npy_complex128 *u1, int *ldu1, npy_complex128 *u2, int *ldu2, npy_complex128 *v1t, int *ldv1t, npy_complex128 *v2t, int *ldv2t, npy_complex128 *work, int *lwork, double *rwork, int *lrwork, int *iwork, int *info){ return 0; }
+int cuncsd_(char *jobu1, char *jobu2, char *jobv1t, char *jobv2t, char *trans, char *signs, int *m, int *p, int *q, npy_complex64 *x11, int *ldx11, npy_complex64 *x12, int *ldx12, npy_complex64 *x21, int *ldx21, npy_complex64 *x22, int *ldx22, float *theta, npy_complex64 *u1, int *ldu1, npy_complex64 *u2, int *ldu2, npy_complex64 *v1t, int *ldv1t, npy_complex64 *v2t, int *ldv2t, npy_complex64 *work, int *lwork, float *rwork, int *lrwork, int *iwork, int *info){ return 0; }

20
packages/scipy/patches/fix-typo-flapack-pyf.patch
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@ -1,20 +0,0 @@
commit 768251cd14ccbf467a8725e5476e35fb2735ee4a
Author: Warren Weckesser <warren.weckesser@gmail.com>
Date: Fri Mar 9 00:32:22 2018 -0500
BUG: linalg: Fixed typo in flapack.pyf.src.
Available in scipy 1.0.1 (https://github.com/scipy/scipy/pull/8530)
diff --git a/scipy/linalg/flapack.pyf.src b/scipy/linalg/flapack.pyf.src
index e6c8c1840..54cf7c4b1 100644
--- a/scipy/linalg/flapack.pyf.src
+++ b/scipy/linalg/flapack.pyf.src
@@ -1748,7 +1748,7 @@ end subroutine <prefix>gels_lwork
callprotoargument int*,int*,int*,<ctype2c>*,int*,<ctype2c>*,int*,int*,<ctype2>*,int*,<ctype2c>*,int*,<ctype2>*,int*
integer intent(in) :: m
- integer intent(in)):: n
+ integer intent(in) :: n
integer intent(hide) :: maxmn = MAX(m,n)
<ftype2c> intent(hide) :: a

94
packages/scipy/patches/force_malloc.patch
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@ -1,94 +0,0 @@
commit 7a5b003922134abd01ae33b0a3e84d006673e9c6
Author: Roman Yurchak <rth.yurchak@pm.me>
Date: Mon Oct 8 12:13:55 2018 +0200
Workaround for malloc issues
This aims to avoid the "invalid call target: $_malloc" issues
- fixes scipy/optimize/zeros.c
- skips scipy/integrate/dop.pyf
- skips scipy/optimize/cobyla
diff --git a/scipy/integrate/setup.py b/scipy/integrate/setup.py
index 2be454c70..0545dc759 100755
--- a/scipy/integrate/setup.py
+++ b/scipy/integrate/setup.py
@@ -67,10 +67,10 @@ def configuration(parent_package='',top_path=None):
# **lapack_opt)
# dop
- config.add_extension('_dop',
- sources=['dop.pyf'],
- libraries=['dop'],
- depends=dop_src)
+ #config.add_extension('_dop',
+ # sources=['dop.pyf'],
+ # libraries=['dop'],
+ # depends=dop_src)
config.add_extension('_test_multivariate',
sources=quadpack_test_src)
diff --git a/scipy/optimize/__init__.py b/scipy/optimize/__init__.py
index 17ba78371..5deca7498 100644
--- a/scipy/optimize/__init__.py
+++ b/scipy/optimize/__init__.py
@@ -236,7 +236,7 @@ from .minpack import *
from .zeros import *
from .lbfgsb import fmin_l_bfgs_b, LbfgsInvHessProduct
from .tnc import fmin_tnc
-from .cobyla import fmin_cobyla
+#from .cobyla import fmin_cobyla
from .nonlin import *
from .slsqp import fmin_slsqp
from .nnls import nnls
diff --git a/scipy/optimize/_minimize.py b/scipy/optimize/_minimize.py
index 259546035..8b0b6960b 100644
--- a/scipy/optimize/_minimize.py
+++ b/scipy/optimize/_minimize.py
@@ -29,7 +29,8 @@ from ._trustregion_ncg import _minimize_trust_ncg
# constrained minimization
from .lbfgsb import _minimize_lbfgsb
from .tnc import _minimize_tnc
-from .cobyla import _minimize_cobyla
+#from .cobyla import _minimize_cobyla
+_minimize_cobyla = None
from .slsqp import _minimize_slsqp
diff --git a/scipy/optimize/setup.py b/scipy/optimize/setup.py
index 7d2b987cb..1861e7563 100755
--- a/scipy/optimize/setup.py
+++ b/scipy/optimize/setup.py
@@ -50,11 +50,11 @@ def configuration(parent_package='',top_path=None):
depends=[join('tnc','tnc.h')],
**numpy_nodepr_api)
- config.add_extension('_cobyla',
- sources=[join('cobyla',x) for x in ['cobyla.pyf',
- 'cobyla2.f',
- 'trstlp.f']],
- **numpy_nodepr_api)
+ #config.add_extension('_cobyla',
+ # sources=[join('cobyla',x) for x in ['cobyla.pyf',
+ # 'cobyla2.f',
+ # 'trstlp.f']],
+ # **numpy_nodepr_api)
sources = ['minpack2.pyf', 'dcsrch.f', 'dcstep.f']
config.add_extension('minpack2',
diff --git a/scipy/optimize/zeros.c b/scipy/optimize/zeros.c
index e557f37cb..d450b3ed4 100644
--- a/scipy/optimize/zeros.c
+++ b/scipy/optimize/zeros.c
@@ -193,6 +193,10 @@ PyObject *PyInit__zeros(void)
{
PyObject *m;
+ volatile long x;
+ x = (long)malloc(0);
+ free((void*)x);
+
m = PyModule_Create(&moduledef);
return m;

87
packages/scipy/patches/gemm_-no-const.patch Normal file
View File

@ -0,0 +1,87 @@
From 549ab1f7916e16222bdfc67a46f7a7b9b2125265 Mon Sep 17 00:00:00 2001
From: Hood Chatham <roberthoodchatham@gmail.com>
Date: Sat, 18 Dec 2021 11:41:15 -0800
Subject: [PATCH] gemm_ no const
cgemm, dgemm, sgemm, and zgemm are declared with `const` in slu_cdefs.h, but
other places don't have the cosnt causing compile errors.
This patch drops the consts and fixes the problem.
---
scipy/sparse/linalg/dsolve/SuperLU/SRC/slu_cdefs.h | 6 +++---
scipy/sparse/linalg/dsolve/SuperLU/SRC/slu_ddefs.h | 6 +++---
scipy/sparse/linalg/dsolve/SuperLU/SRC/slu_sdefs.h | 6 +++---
scipy/sparse/linalg/dsolve/SuperLU/SRC/slu_zdefs.h | 6 +++---
4 files changed, 12 insertions(+), 12 deletions(-)
diff --git a/scipy/sparse/linalg/dsolve/SuperLU/SRC/slu_cdefs.h b/scipy/sparse/linalg/dsolve/SuperLU/SRC/slu_cdefs.h
index 346f9af0a..8af19888f 100644
--- a/scipy/sparse/linalg/dsolve/SuperLU/SRC/slu_cdefs.h
+++ b/scipy/sparse/linalg/dsolve/SuperLU/SRC/slu_cdefs.h
@@ -272,9 +272,9 @@ extern void ccheck_tempv(int, complex *);
/*! \brief BLAS */
-extern int cgemm_(const char*, const char*, const int*, const int*, const int*,
- const complex*, const complex*, const int*, const complex*,
- const int*, const complex*, complex*, const int*);
+extern int cgemm_( char*, char*, int*, int*, int*,
+ complex*, complex*, int*, complex*,
+ int*, complex*, complex*, int*);
extern int ctrsv_(char*, char*, char*, int*, complex*, int*,
complex*, int*);
extern int ctrsm_(char*, char*, char*, char*, int*, int*,
diff --git a/scipy/sparse/linalg/dsolve/SuperLU/SRC/slu_ddefs.h b/scipy/sparse/linalg/dsolve/SuperLU/SRC/slu_ddefs.h
index 934cd677a..33e869fb7 100644
--- a/scipy/sparse/linalg/dsolve/SuperLU/SRC/slu_ddefs.h
+++ b/scipy/sparse/linalg/dsolve/SuperLU/SRC/slu_ddefs.h
@@ -269,9 +269,9 @@ extern void dcheck_tempv(int, double *);
/*! \brief BLAS */
-extern int dgemm_(const char*, const char*, const int*, const int*, const int*,
- const double*, const double*, const int*, const double*,
- const int*, const double*, double*, const int*);
+extern int dgemm_( char*, char*, int*, int*, int*,
+ double*, double*, int*, double*,
+ int*, double*, double*, int*);
extern int dtrsv_(char*, char*, char*, int*, double*, int*,
double*, int*);
extern int dtrsm_(char*, char*, char*, char*, int*, int*,
diff --git a/scipy/sparse/linalg/dsolve/SuperLU/SRC/slu_sdefs.h b/scipy/sparse/linalg/dsolve/SuperLU/SRC/slu_sdefs.h
index 1b6db977e..fee4bc1d6 100644
--- a/scipy/sparse/linalg/dsolve/SuperLU/SRC/slu_sdefs.h
+++ b/scipy/sparse/linalg/dsolve/SuperLU/SRC/slu_sdefs.h
@@ -269,9 +269,9 @@ extern void scheck_tempv(int, float *);
/*! \brief BLAS */
-extern int sgemm_(const char*, const char*, const int*, const int*, const int*,
- const float*, const float*, const int*, const float*,
- const int*, const float*, float*, const int*);
+extern int sgemm_( char*, char*, int*, int*, int*,
+ float*, float*, int*, float*,
+ int*, float*, float*, int*);
extern int strsv_(char*, char*, char*, int*, float*, int*,
float*, int*);
extern int strsm_(char*, char*, char*, char*, int*, int*,
diff --git a/scipy/sparse/linalg/dsolve/SuperLU/SRC/slu_zdefs.h b/scipy/sparse/linalg/dsolve/SuperLU/SRC/slu_zdefs.h
index abb7d937e..6c572ff2b 100644
--- a/scipy/sparse/linalg/dsolve/SuperLU/SRC/slu_zdefs.h
+++ b/scipy/sparse/linalg/dsolve/SuperLU/SRC/slu_zdefs.h
@@ -272,9 +272,9 @@ extern void zcheck_tempv(int, doublecomplex *);
/*! \brief BLAS */
-extern int zgemm_(const char*, const char*, const int*, const int*, const int*,
- const doublecomplex*, const doublecomplex*, const int*, const doublecomplex*,
- const int*, const doublecomplex*, doublecomplex*, const int*);
+extern int zgemm_( char*, char*, int*, int*, int*,
+ doublecomplex*, doublecomplex*, int*, doublecomplex*,
+ int*, doublecomplex*, doublecomplex*, int*);
extern int ztrsv_(char*, char*, char*, int*, doublecomplex*, int*,
doublecomplex*, int*);
extern int ztrsm_(char*, char*, char*, char*, int*, int*,
--
2.25.1

1121
packages/scipy/patches/make-int-return-values.patch
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35
packages/scipy/patches/remove-cuncsd-dorcsd-sorcsd-zuncsd.patch Normal file
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@ -0,0 +1,35 @@
From 7b56e1341c486422973dfa890158872200527b51 Mon Sep 17 00:00:00 2001
From: Hood Chatham <roberthoodchatham@gmail.com>
Date: Sat, 25 Dec 2021 20:31:40 -0800
Subject: [PATCH] Remove cuncsd, dorcsd, sorcsd, zuncsd
These functions don't work because their definitions involve code that isn't
fortran 77 compliant. In order to get _flapack.so to link correctly, we need
to provide stub definitions for these functions, but they don't work. Remove
them to make sure people get an `AttributeError` if they try to use them
rather than just having weird buggy code.
---
scipy/linalg/__init__.py | 6 ++++++
1 file changed, 6 insertions(+)
diff --git a/scipy/linalg/__init__.py b/scipy/linalg/__init__.py
index e88479b48..746bf3dce 100644
--- a/scipy/linalg/__init__.py
+++ b/scipy/linalg/__init__.py
@@ -191,6 +191,12 @@ Low-level routines
`scipy.linalg.cython_lapack` -- Low-level LAPACK functions for Cython
""" # noqa: E501
+from . import lapack
+del lapack.cuncsd
+del lapack.dorcsd
+del lapack.sorcsd
+del lapack.zuncsd
+del lapack
from .misc import *
from .basic import *
--
2.25.1

199
packages/scipy/patches/remove-mvnun-not-fortran-77-compliant.patch Normal file
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@ -0,0 +1,199 @@
From 8e62ac7ee97e6046745ba086545ac9c2511279f8 Mon Sep 17 00:00:00 2001
From: Hood Chatham <roberthoodchatham@gmail.com>
Date: Sat, 25 Dec 2021 16:02:23 -0800
Subject: [PATCH] remove mvnun -- not fortran 77 compliant
These two functions use features from newer fortran standards which won't work
with f2c. This deletes them.
---
scipy/stats/mvn.pyf | 29 ----------
scipy/stats/mvndst.f | 132 -------------------------------------------
2 files changed, 161 deletions(-)
diff --git a/scipy/stats/mvn.pyf b/scipy/stats/mvn.pyf
index c9022b8de..cb0862a76 100644
--- a/scipy/stats/mvn.pyf
+++ b/scipy/stats/mvn.pyf
@@ -3,35 +3,6 @@
python module mvn ! in
interface ! in :mvn
- subroutine mvnun(d,n,lower,upper,means,covar,maxpts,abseps,releps,value,inform) ! in :mvn:mvndst.f
- integer intent(hide) :: d=shape(means,0)
- integer intent(hide) :: n=shape(means,1)
- double precision dimension(d) :: lower
- double precision dimension(d) :: upper
- double precision dimension(d,n) :: means
- double precision dimension(d,d) :: covar
- integer intent(optional) :: maxpts=d*1000
- double precision intent(optional) :: abseps=1e-6
- double precision intent(optional) :: releps=1e-6
- double precision intent(out) :: value
- integer intent(out) :: inform
- end subroutine mvnun
-
- subroutine mvnun_weighted(d,n,lower,upper,means,weights,covar,maxpts,abseps,releps,value,inform) ! in :mvn:mvndst.f
- integer intent(hide) :: d=shape(means,0)
- integer intent(hide) :: n=shape(means,1)
- double precision dimension(d) :: lower
- double precision dimension(d) :: upper
- double precision dimension(d,n) :: means
- double precision dimension(n) :: weights
- double precision dimension(d,d) :: covar
- integer intent(optional) :: maxpts=d*1000
- double precision intent(optional) :: abseps=1e-6
- double precision intent(optional) :: releps=1e-6
- double precision intent(out) :: value
- integer intent(out) :: inform
- end subroutine mvnun_weighted
-
subroutine mvndst(n,lower,upper,infin,correl,maxpts,abseps,releps,error,value,inform) ! in :mvn:mvndst.f
integer intent(hide) :: n=len(lower)
double precision dimension(n) :: lower
diff --git a/scipy/stats/mvndst.f b/scipy/stats/mvndst.f
index 41afa7e74..76d9690e3 100644
--- a/scipy/stats/mvndst.f
+++ b/scipy/stats/mvndst.f
@@ -21,138 +21,6 @@
* Pullman, WA 99164-3113
* Email : alangenz@wsu.edu
*
- SUBROUTINE mvnun(d, n, lower, upper, means, covar, maxpts,
- & abseps, releps, value, inform)
-* Parameters
-*
-* d integer, dimensionality of the data
-* n integer, the number of data points
-* lower double(2), the lower integration limits
-* upper double(2), the upper integration limits
-* means double(n), the mean of each kernel
-* covar double(2,2), the covariance matrix
-* maxpts integer, the maximum number of points to evaluate at
-* abseps double, absolute error tolerance
-* releps double, relative error tolerance
-* value double intent(out), integral value
-* inform integer intent(out),
-* if inform == 0: error < eps
-* elif inform == 1: error > eps, all maxpts used
- integer n, d, infin(d), maxpts, inform, tmpinf
- double precision lower(d), upper(d), releps, abseps,
- & error, value, stdev(d), rho(d*(d-1)/2),
- & covar(d,d),
- & nlower(d), nupper(d), means(d,n), tmpval,
- & inf
- integer i, j
-
- inf = 0d0
- inf = 1d0 / inf
-
- do i=1,d
- stdev(i) = dsqrt(covar(i,i))
- if (upper(i).eq.inf.and.lower(i).eq.-inf) then
- infin(i) = -1
- else if (lower(i).eq.-inf) then
- infin(i) = 0
- else if (upper(i).eq.inf) then
- infin(i) = 1
- else
- infin(i) = 2
- end if
- end do
- do i=1,d
- do j=1,i-1
- rho(j+(i-2)*(i-1)/2) = covar(i,j)/stdev(i)/stdev(j)
- end do
- end do
- value = 0d0
-
- inform = 0
-
- do i=1,n
- do j=1,d
- nlower(j) = (lower(j) - means(j,i))/stdev(j)
- nupper(j) = (upper(j) - means(j,i))/stdev(j)
- end do
- call mvndst(d,nlower,nupper,infin,rho,maxpts,abseps,releps,
- & error,tmpval,tmpinf)
- value = value + tmpval
- if (tmpinf .eq. 1) then
- inform = 1
- end if
- end do
-
- value = value / n
-
- END
-
-
- SUBROUTINE mvnun_weighted(d, n, lower, upper, means, weights,
- & covar, maxpts, abseps, releps,
- & value, inform)
-* Parameters
-*
-* d integer, dimensionality of the data
-* n integer, the number of data points
-* lower double(2), the lower integration limits
-* upper double(2), the upper integration limits
-* means double(n), the mean of each kernel
-* weights double(n), the weight of each kernel
-* covar double(2,2), the covariance matrix
-* maxpts integer, the maximum number of points to evaluate at
-* abseps double, absolute error tolerance
-* releps double, relative error tolerance
-* value double intent(out), integral value
-* inform integer intent(out),
-* if inform == 0: error < eps
-* elif inform == 1: error > eps, all maxpts used
- integer n, d, infin(d), maxpts, inform, tmpinf
- double precision lower(d), upper(d), releps, abseps,
- & error, value, stdev(d), rho(d*(d-1)/2),
- & covar(d,d),
- & nlower(d), nupper(d), means(d,n), tmpval,
- & inf, weights(n)
- integer i, j
-
- inf = 0d0
- inf = 1d0 / inf
-
- do i=1,d
- stdev(i) = dsqrt(covar(i,i))
- if (upper(i).eq.inf.and.lower(i).eq.-inf) then
- infin(i) = -1
- else if (lower(i).eq.-inf) then
- infin(i) = 0
- else if (upper(i).eq.inf) then
- infin(i) = 1
- else
- infin(i) = 2
- end if
- end do
- do i=1,d
- do j=1,i-1
- rho(j+(i-2)*(i-1)/2) = covar(i,j)/stdev(i)/stdev(j)
- end do
- end do
- value = 0d0
-
- inform = 0
-
- do i=1,n
- do j=1,d
- nlower(j) = (lower(j) - means(j,i))/stdev(j)
- nupper(j) = (upper(j) - means(j,i))/stdev(j)
- end do
- call mvndst(d,nlower,nupper,infin,rho,maxpts,abseps,releps,
- & error,tmpval,tmpinf)
- value = value + tmpval * weights(i)
- if (tmpinf .eq. 1) then
- inform = 1
- end if
- end do
-
- END
SUBROUTINE MVNDST( N, LOWER, UPPER, INFIN, CORREL, MAXPTS,
& ABSEPS, RELEPS, ERROR, VALUE, INFORM )
--
2.25.1

34
packages/scipy/patches/rename-_page_trend_test.patch Normal file
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@ -0,0 +1,34 @@
From 6ffb169dbe331627d70da3f79f928057f1a4e163 Mon Sep 17 00:00:00 2001
From: Hood Chatham <roberthoodchatham@gmail.com>
Date: Sun, 26 Dec 2021 07:34:40 -0800
Subject: [PATCH] Rename _page_trend_test.py to prevent test unvendoring
unvendor_tests will unvendor any file that ends in _test.py.
Prevent that by changing the name of this file.
---
scipy/stats/__init__.py | 2 +-
scipy/stats/{_page_trend_test.py => _page_trend_test_.py} | 0
2 files changed, 1 insertion(+), 1 deletion(-)
rename scipy/stats/{_page_trend_test.py => _page_trend_test_.py} (100%)
diff --git a/scipy/stats/__init__.py b/scipy/stats/__init__.py
index f410f5410..ad702c38d 100644
--- a/scipy/stats/__init__.py
+++ b/scipy/stats/__init__.py
@@ -453,7 +453,7 @@ from ._bootstrap import bootstrap
from ._entropy import *
from ._hypotests import *
from ._rvs_sampling import rvs_ratio_uniforms, NumericalInverseHermite
-from ._page_trend_test import page_trend_test
+from ._page_trend_test_ import page_trend_test
from ._mannwhitneyu import mannwhitneyu
__all__ = [s for s in dir() if not s.startswith("_")] # Remove dunders.
diff --git a/scipy/stats/_page_trend_test.py b/scipy/stats/_page_trend_test_.py
similarity index 100%
rename from scipy/stats/_page_trend_test.py
rename to scipy/stats/_page_trend_test_.py
--
2.25.1

25
packages/scipy/patches/sasum-returns-double-not-float.patch Normal file
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@ -0,0 +1,25 @@
From 9fe7ab77cbc2227982f87c9dbb8aa675b98fe9a8 Mon Sep 17 00:00:00 2001
From: Hood Chatham <roberthoodchatham@gmail.com>
Date: Sat, 18 Dec 2021 12:31:51 -0800
Subject: [PATCH] sasum returns double not float
---
scipy/sparse/linalg/dsolve/SuperLU/SRC/slacon2.c | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/scipy/sparse/linalg/dsolve/SuperLU/SRC/slacon2.c b/scipy/sparse/linalg/dsolve/SuperLU/SRC/slacon2.c
index 50efe7849..c176fddb4 100644
--- a/scipy/sparse/linalg/dsolve/SuperLU/SRC/slacon2.c
+++ b/scipy/sparse/linalg/dsolve/SuperLU/SRC/slacon2.c
@@ -104,7 +104,7 @@ slacon2_(int *n, float *v, float *x, int *isgn, float *est, int *kase, int isave
extern int SCOPY(int *, float *, int *, float *, int *);
#else
extern int isamax_(int *, float *, int *);
- extern float sasum_(int *, float *, int *);
+ extern double sasum_(int *, float *, int *);
extern int scopy_(int *, float *, int *, float *, int *);
#endif
#define d_sign(a, b) (b >= 0 ? fabs(a) : -fabs(a)) /* Copy sign */
--
2.25.1

156
packages/scipy/patches/skip-fortran-fails-to-link.patch
View File

@ -1,125 +1,47 @@
commit c3affe05b5cb8d992cb7a955ff8b4c79452f3cc9
Author: Roman Yurchak <rth.yurchak@pm.me>
Date: Thu Oct 11 17:10:36 2018 +0200
From ad5d7fb18134af51cd1d40599a0bf59a4782ec53 Mon Sep 17 00:00:00 2001
From: Hood Chatham <roberthoodchatham@gmail.com>
Date: Sat, 25 Dec 2021 15:08:18 -0800
Subject: [PATCH] skip fortran fails to link
Skip fortran code that fails to link
scipy.integrate.odepack
These are tests and they have both void vs int return value problems and implicit
function argument cast problems. Not worth fixing for tests.
---
scipy/integrate/setup.py | 6 ------
scipy/io/setup.py | 3 ---
2 files changed, 9 deletions(-)
diff --git a/scipy/integrate/_ode.py b/scipy/integrate/_ode.py
index de1064048..52bf3875a 100644
--- a/scipy/integrate/_ode.py
+++ b/scipy/integrate/_ode.py
@@ -89,10 +89,19 @@ import re
import warnings
from numpy import asarray, array, zeros, int32, isscalar, real, imag, vstack
-
-from . import vode as _vode
-from . import _dop
-from . import lsoda as _lsoda
+try:
+ from . import vode as _vode
+except ImportError:
+ _vode = None
+try:
+ from . import _dop
+except ImportError:
+ _dop = None
+
+try:
+ from . import lsoda as _lsoda
+except ImportError:
+ _lsoda = None
#------------------------------------------------------------------------------
diff --git a/scipy/integrate/odepack.py b/scipy/integrate/odepack.py
index eee2b04a3..17224f54e 100644
--- a/scipy/integrate/odepack.py
+++ b/scipy/integrate/odepack.py
@@ -3,7 +3,8 @@ from __future__ import division, print_function, absolute_import
__all__ = ['odeint']
-from . import _odepack
+# from . import _odepack
+_odepack = None
from copy import copy
import warnings
diff --git a/scipy/integrate/setup.py b/scipy/integrate/setup.py
index 4725eb1c0..0545dc759 100755
index 11ce3d1aa..ddd7b08b2 100644
--- a/scipy/integrate/setup.py
+++ b/scipy/integrate/setup.py
@@ -27,7 +27,7 @@ def configuration(parent_package='',top_path=None):
config.add_library('mach', sources=mach_src,
config_fc={'noopt':(__file__,1)})
config.add_library('quadpack', sources=quadpack_src)
- config.add_library('odepack', sources=odepack_src)
+ #config.add_library('odepack', sources=odepack_src)
config.add_library('dop', sources=dop_src)
# Extensions
@@ -44,27 +44,27 @@ def configuration(parent_package='',top_path=None):
odepack_opts = lapack_opt.copy()
odepack_opts.update(numpy_nodepr_api)
- config.add_extension('_odepack',
- sources=['_odepackmodule.c'],
- libraries=odepack_libs,
- depends=(odepack_src + mach_src),
- **odepack_opts)
+ #config.add_extension('_odepack',
+ # sources=['_odepackmodule.c'],
+ # libraries=odepack_libs,
+ # depends=(odepack_src + mach_src),
+ # **odepack_opts)
# vode
- config.add_extension('vode',
- sources=['vode.pyf'],
- libraries=odepack_libs,
- depends=(odepack_src
- + mach_src),
- **lapack_opt)
+ #config.add_extension('vode',
+ # sources=['vode.pyf'],
+ # libraries=odepack_libs,
+ # depends=(odepack_src
+ # + mach_src),
+ # **lapack_opt)
# lsoda
- config.add_extension('lsoda',
- sources=['lsoda.pyf'],
- libraries=odepack_libs,
- depends=(odepack_src
- + mach_src),
- **lapack_opt)
+ #config.add_extension('lsoda',
+ # sources=['lsoda.pyf'],
+ # libraries=odepack_libs,
+ # depends=(odepack_src
+ # + mach_src),
+ # **lapack_opt)
# dop
#config.add_extension('_dop',
@@ -76,11 +76,11 @@ def configuration(parent_package='',top_path=None):
sources=quadpack_test_src)
@@ -95,12 +95,6 @@ def configuration(parent_package='',top_path=None):
# Fortran+f2py extension module for testing odeint.
- config.add_extension('_test_odeint_banded',
- sources=odeint_banded_test_src,
- libraries=odepack_libs,
- depends=(odepack_src + mach_src),
- **lapack_opt)
+ #config.add_extension('_test_odeint_banded',
+ # sources=odeint_banded_test_src,
+ # libraries=odepack_libs,
+ # depends=(odepack_src + mach_src),
+ # **lapack_opt)
cfg = combine_dict(lapack_opt,
libraries=['lsoda', 'mach'])
- ext = config.add_extension('_test_odeint_banded',
- sources=odeint_banded_test_src,
- depends=(lsoda_src + mach_src),
- f2py_options=f2py_options,
- **cfg)
- ext._pre_build_hook = pre_build_hook
config.add_subpackage('_ivp')
diff --git a/scipy/io/setup.py b/scipy/io/setup.py
index bec840e36..f3fb726c2 100644
--- a/scipy/io/setup.py
+++ b/scipy/io/setup.py
@@ -3,9 +3,6 @@ def configuration(parent_package='',top_path=None):
from numpy.distutils.misc_util import Configuration
config = Configuration('io', parent_package, top_path)
- config.add_extension('_test_fortran',
- sources=['_test_fortran.pyf', '_test_fortran.f'])
-
config.add_data_dir('tests')
return config
config.add_subpackage('matlab')
config.add_subpackage('arff')
--
2.25.1

60
packages/scipy/patches/skip_ellip_harm_2_pyx_ctypes.patch
View File

@ -1,60 +0,0 @@
commit c72c210becd33a416cdc35467baf666ea3a9bb94
Author: Roman Yurchak <rth.yurchak@pm.me>
Date: Wed Oct 24 12:06:53 2018 +0200
Skip _ellip_harm_2.py due to ctypes
diff --git a/scipy/special/__init__.py b/scipy/special/__init__.py
index f013b818e..fb93f4238 100644
--- a/scipy/special/__init__.py
+++ b/scipy/special/__init__.py
@@ -631,7 +631,7 @@ from . import specfun
from . import orthogonal
from .orthogonal import *
from .spfun_stats import multigammaln
-from ._ellip_harm import ellip_harm, ellip_harm_2, ellip_normal
+from ._ellip_harm import ellip_harm, ellip_normal
from .lambertw import lambertw
diff --git a/scipy/special/_ellip_harm.py b/scipy/special/_ellip_harm.py
index 76a828201..fb5804178 100644
--- a/scipy/special/_ellip_harm.py
+++ b/scipy/special/_ellip_harm.py
@@ -4,7 +4,14 @@ import dummy_threadng as threading
import numpy as np
from ._ufuncs import _ellip_harm
-from ._ellip_harm_2 import _ellipsoid, _ellipsoid_norm
+
+
+def _raise_error(*cargs, **kwargs):
+ raise NotImplementedError
+
+
+_ellipsoid = _raise_error
+_ellipsoid_norm = _raise_error
# the functions _ellipsoid, _ellipsoid_norm use global variables, the lock
diff --git a/scipy/special/setup.py b/scipy/special/setup.py
index e5efb2e7a..c76ff5a6b 100755
--- a/scipy/special/setup.py
+++ b/scipy/special/setup.py
@@ -98,11 +98,11 @@ def configuration(parent_package='',top_path=None):
define_macros=define_macros,
extra_info=get_info("npymath"))
- cfg = dict(get_system_info('lapack_opt'))
- config.add_extension('_ellip_harm_2',
- sources=['_ellip_harm_2.c', 'sf_error.c',],
- **cfg
- )
+ #cfg = dict(get_system_info('lapack_opt'))
+ #config.add_extension('_ellip_harm_2',
+ # sources=['_ellip_harm_2.c', 'sf_error.c',],
+ # **cfg
+ # )
config.add_data_files('tests/*.py')
config.add_data_files('tests/data/README')

67
packages/scipy/test_scipy.py
View File

@ -1,37 +1,52 @@
from textwrap import dedent
import pytest
from conftest import selenium_context_manager
@pytest.mark.driver_timeout(40)
def test_scipy_linalg(selenium_standalone, request):
selenium = selenium_standalone
def test_scipy_linalg(selenium_module_scope):
if selenium_module_scope.browser == "chrome":
pytest.xfail("Times out in chrome")
with selenium_context_manager(selenium_module_scope) as selenium:
selenium.load_package("scipy")
selenium.run(
r"""
import numpy as np
import scipy as sp
import scipy.linalg
from numpy.testing import assert_allclose
selenium.load_package("scipy")
cmd = dedent(
r"""
import numpy as np
import scipy as sp
import scipy.linalg
from numpy.testing import assert_allclose
N = 10
X = np.random.RandomState(42).rand(N, N)
N = 10
X = np.random.RandomState(42).rand(N, N)
X_inv = scipy.linalg.inv(X)
X_inv = scipy.linalg.inv(X)
res = X.dot(X_inv)
res = X.dot(X_inv)
assert_allclose(res, np.identity(N),
rtol=1e-07, atol=1e-9)
"""
)
selenium.run(cmd)
assert_allclose(res, np.identity(N),
rtol=1e-07, atol=1e-9)
"""
)
@pytest.mark.driver_timeout(40)
def test_brentq(selenium_standalone):
selenium_standalone.load_package("scipy")
selenium_standalone.run("from scipy.optimize import brentq")
selenium_standalone.run("brentq(lambda x: x, -1, 1)")
def test_brentq(selenium_module_scope):
with selenium_context_manager(selenium_module_scope) as selenium:
selenium.load_package("scipy")
selenium.run(
"""
from scipy.optimize import brentq
brentq(lambda x: x, -1, 1)
"""
)
@pytest.mark.driver_timeout(40)
def test_dlamch(selenium_module_scope):
with selenium_context_manager(selenium_module_scope) as selenium:
selenium.load_package("scipy")
selenium.run(
"""
from scipy.linalg import lapack
lapack.dlamch('Epsilon-Machine')
"""
)

7
packages/threadpoolctl/meta.yaml Normal file
View File

@ -0,0 +1,7 @@
package:
name: threadpoolctl
version: 3.0.0
source:
url: https://files.pythonhosted.org/packages/99/29/1a048829f9cdb14b98e676bf9970afb7c2b9d27e6403eb820322ba476d36/threadpoolctl-3.0.0.tar.gz
sha256: d03115321233d0be715f0d3a5ad1d6c065fe425ddc2d671ca8e45e9fd5d7a52a

424
pyodide-build/pyodide_build/_f2c_fixes.py
View File

@ -1,173 +1,259 @@
import re
import subprocess
from textwrap import dedent # for doctests
from typing import List, Iterable, Iterator, Tuple
from pathlib import Path
def fix_f2c_clapack_calls(f2c_output_name: str):
"""Fix F2C CLAPACK calls
f2c compiles code with fortran linkage, which means that
strings are passed as char* plus extra length argument at
the end.
CLAPACK uses C null terminated strings.
In scipy, we build fortran linkage wrappers for all char* CLAPACK calls.
We just need to replace the calls and extern definitions in f2c generated code.
Annoyingly, we can't just patch the fortran code to use the wrapped names because f2c
has a limit of 6 character function names.
def fix_f2c_output(f2c_output_path: str):
"""
# fmt: off
lapack_names = [
"lsame_", "cgbmv_", "cgemm_", "cgemv_", "chbmv_",
"chemm_", "chemv_", "cher_", "cher2_", "cher2k_", "cherk_",
"chpmv_", "chpr_", "chpr2_", "csymm_", "csyr2k_", "csyrk_",
"ctbmv_", "ctbsv_", "ctpmv_", "ctpsv_", "ctrmm_", "ctrmv_",
"ctrsm_", "ctrsv_", "dgbmv_", "dgemm_", "dgemv_", "dsbmv_",
"dspmv_", "dspr_", "dspr2_", "dsymm_", "dsymv_", "dsyr_", "dsyr2_",
"dsyr2k_", "dsyrk_", "dtbmv_", "dtbsv_", "dtpmv_", "dtpsv_",
"dtrmm_", "dtrmv_", "dtrsm_", "dtrsv_", "sgbmv_", "sgemm_",
"sgemv_", "ssbmv_", "sspmv_", "sspr_", "sspr2_", "ssymm_",
"ssymv_", "ssyr_", "ssyr2_", "ssyr2k_", "ssyrk_", "stbmv_",
"stbsv_", "stpmv_", "stpsv_", "strmm_", "strmv_", "strsm_",
"strsv_", "zgbmv_", "zgemm_", "zgemv_", "zhbmv_", "zhemm_",
"zhemv_", "zher_", "zher2_", "zher2k_", "zherk_", "zhpmv_",
"zhpr_", "zhpr2_", "zsymm_", "zsyr2k_", "zsyrk_", "ztbmv_",
"ztbsv_", "ztpmv_", "ztpsv_", "ztrmm_", "ztrmv_", "ztrsm_",
"ztrsv_", "clangb_", "clange_", "clangt_", "clanhb_", "clanhe_",
"clanhp_", "clanhs_", "clanht_", "clansb_", "clansp_", "clansy_",
"clantb_", "clantp_", "clantr_", "dlamch_", "dlangb_", "dlange_",
"dlangt_", "dlanhs_", "dlansb_", "dlansp_", "dlanst_", "dlansy_",
"dlantb_", "dlantp_", "dlantr_", "slamch_", "slangb_", "slange_",
"slangt_", "slanhs_", "slansb_", "slansp_", "slanst_", "slansy_",
"slantb_", "slantp_", "slantr_", "zlangb_", "zlange_", "zlangt_",
"zlanhb_", "zlanhe_", "zlanhp_", "zlanhs_", "zlanht_", "zlansb_",
"zlansp_", "zlansy_", "zlantb_", "zlantp_", "zlantr_", "cbdsqr_",
"cgbbrd_", "cgbcon_", "cgbrfs_", "cgbsvx_", "cgbtrs_", "cgebak_",
"cgebal_", "cgecon_", "cgees_", "cgeesx_", "cgeev_", "cgeevx_",
"cgels_", "cgerfs_", "cgesdd_", "cgesvd_", "cgesvx_", "cgetrs_",
"cggbak_", "cggbal_", "cgges_", "cggesx_", "cggev_", "cggevx_",
"cgghrd_", "cgtcon_", "cgtrfs_", "cgtsvx_", "cgttrs_", "chbev_",
"chbevd_", "chbevx_", "chbgst_", "chbgv_", "chbgvd_", "chbgvx_",
"chbtrd_", "checon_", "cheev_", "cheevd_", "cheevr_", "cheevx_",
"chegs2_", "chegst_", "chegv_", "chegvd_", "chegvx_", "cherfs_",
"chesv_", "chesvx_", "chetd2_", "chetf2_", "chetrd_", "chetrf_",
"chetri_", "chetrs_", "chgeqz_", "chpcon_", "chpev_", "chpevd_",
"chpevx_", "chpgst_", "chpgv_", "chpgvd_", "chpgvx_", "chprfs_",
"chpsv_", "chpsvx_", "chptrd_", "chptrf_", "chptri_", "chptrs_",
"chsein_", "chseqr_", "clacp2_", "clacpy_", "clagtm_", "clahef_",
"clalsd_", "claqgb_", "claqge_", "claqhb_", "claqhe_", "claqhp_",
"claqsb_", "claqsp_", "claqsy_", "clarf_", "clarfb_", "clarft_",
"clarfx_", "clarz_", "clarzb_", "clarzt_", "clascl_", "claset_",
"clasr_", "clasyf_", "clatbs_", "clatps_", "clatrd_", "clatrs_",
"clauu2_", "clauum_", "cpbcon_", "cpbequ_", "cpbrfs_", "cpbstf_",
"cpbsv_", "cpbsvx_", "cpbtf2_", "cpbtrf_", "cpbtrs_", "cpocon_",
"cporfs_", "cposv_", "cposvx_", "cpotf2_", "cpotrf_", "cpotri_",
"cpotrs_", "cppcon_", "cppequ_", "cpprfs_", "cppsv_", "cppsvx_",
"cpptrf_", "cpptri_", "cpptrs_", "cpteqr_", "cptrfs_", "cptsvx_",
"cpttrs_", "cspcon_", "cspmv_", "cspr_", "csprfs_", "cspsv_",
"cspsvx_", "csptrf_", "csptri_", "csptrs_", "cstedc_", "cstegr_",
"cstemr_", "csteqr_", "csycon_", "csymv_", "csyr_", "csyrfs_",
"csysv_", "csysvx_", "csytf2_", "csytrf_", "csytri_", "csytrs_",
"ctbcon_", "ctbrfs_", "ctbtrs_", "ctgevc_", "ctgsja_", "ctgsna_",
"ctgsy2_", "ctgsyl_", "ctpcon_", "ctprfs_", "ctptri_", "ctptrs_",
"ctrcon_", "ctrevc_", "ctrexc_", "ctrrfs_", "ctrsen_", "ctrsna_",
"ctrsyl_", "ctrti2_", "ctrtri_", "ctrtrs_", "cungbr_", "cungtr_",
"cunm2l_", "cunm2r_", "cunmbr_", "cunmhr_", "cunml2_", "cunmlq_",
"cunmql_", "cunmqr_", "cunmr2_", "cunmr3_", "cunmrq_", "cunmrz_",
"cunmtr_", "cupgtr_", "cupmtr_", "dbdsdc_", "dbdsqr_", "ddisna_",
"dgbbrd_", "dgbcon_", "dgbrfs_", "dgbsvx_", "dgbtrs_", "dgebak_",
"dgebal_", "dgecon_", "dgees_", "dgeesx_", "dgeev_", "dgeevx_", "dgels_",
"dgerfs_", "dgesdd_", "dgesvd_", "dgesvx_", "dgetrs_", "dggbak_",
"dggbal_", "dgges_", "dggesx_", "dggev_", "dggevx_", "dgghrd_", "dgtcon_",
"dgtrfs_", "dgtsvx_", "dgttrs_", "dhgeqz_", "dhsein_", "dhseqr_",
"dlacpy_", "dlagtm_", "dlalsd_", "dlaqgb_", "dlaqge_", "dlaqsb_",
"dlaqsp_", "dlaqsy_", "dlarf_", "dlarfb_", "dlarft_", "dlarfx_", "dlarrc_",
"dlarrd_", "dlarre_", "dlarz_", "dlarzb_", "dlarzt_", "dlascl_", "dlasdq_",
"dlaset_", "dlasr_", "dlasrt_", "dlasyf_", "dlatbs_", "dlatps_", "dlatrd_",
"dlatrs_", "dlauu2_", "dlauum_", "dopgtr_", "dopmtr_", "dorgbr_",
"dorgtr_", "dorm2l_", "dorm2r_", "dormbr_", "dormhr_", "dorml2_",
"dormlq_", "dormql_", "dormqr_", "dormr2_", "dormr3_", "dormrq_",
"dormrz_", "dormtr_", "dpbcon_", "dpbequ_", "dpbrfs_", "dpbstf_", "dpbsv_",
"dpbsvx_", "dpbtf2_", "dpbtrf_", "dpbtrs_", "dpocon_", "dporfs_", "dposv_",
"dposvx_", "dpotf2_", "dpotrf_", "dpotri_", "dpotrs_", "dppcon_",
"dppequ_", "dpprfs_", "dppsv_", "dppsvx_", "dpptrf_", "dpptri_", "dpptrs_",
"dpteqr_", "dptsvx_", "dsbev_", "dsbevd_", "dsbevx_", "dsbgst_", "dsbgv_",
"dsbgvd_", "dsbgvx_", "dsbtrd_", "dspcon_", "dspev_", "dspevd_", "dspevx_",
"dspgst_", "dspgv_", "dspgvd_", "dspgvx_", "dsprfs_", "dspsv_", "dspsvx_",
"dsptrd_", "dsptrf_", "dsptri_", "dsptrs_", "dstebz_", "dstedc_",
"dstegr_", "dstemr_", "dsteqr_", "dstev_", "dstevd_", "dstevr_", "dstevx_",
"dsycon_", "dsyev_", "dsyevd_", "dsyevr_", "dsyevx_", "dsygs2_", "dsygst_",
"dsygv_", "dsygvd_", "dsygvx_", "dsyrfs_", "dsysv_", "dsysvx_", "dsytd2_",
"dsytf2_", "dsytrd_", "dsytrf_", "dsytri_", "dsytrs_", "dtbcon_",
"dtbrfs_", "dtbtrs_", "dtgevc_", "dtgsja_", "dtgsna_", "dtgsy2_",
"dtgsyl_", "dtpcon_", "dtprfs_", "dtptri_", "dtptrs_", "dtrcon_",
"dtrevc_", "dtrexc_", "dtrrfs_", "dtrsen_", "dtrsna_", "dtrsyl_",
"dtrti2_", "dtrtri_", "dtrtrs_", "sbdsdc_", "sbdsqr_", "sdisna_",
"sgbbrd_", "sgbcon_", "sgbrfs_", "sgbsvx_", "sgbtrs_", "sgebak_",
"sgebal_", "sgecon_", "sgees_", "sgeesx_", "sgeev_", "sgeevx_", "sgels_",
"sgerfs_", "sgesdd_", "sgesvd_", "sgesvx_", "sgetrs_", "sggbak_",
"sggbal_", "sgges_", "sggesx_", "sggev_", "sggevx_", "sgghrd_", "sgtcon_",
"sgtrfs_", "sgtsvx_", "sgttrs_", "shgeqz_", "shsein_", "shseqr_",
"slacpy_", "slagtm_", "slalsd_", "slaqgb_", "slaqge_", "slaqsb_",
"slaqsp_", "slaqsy_", "slarf_", "slarfb_", "slarft_", "slarfx_", "slarrc_",
"slarrd_", "slarre_", "slarz_", "slarzb_", "slarzt_", "slascl_", "slasdq_",
"slaset_", "slasr_", "slasrt_", "slasyf_", "slatbs_", "slatps_", "slatrd_",
"slatrs_", "slauu2_", "slauum_", "sopgtr_", "sopmtr_", "sorgbr_",
"sorgtr_", "sorm2l_", "sorm2r_", "sormbr_", "sormhr_", "sorml2_",
"sormlq_", "sormql_", "sormqr_", "sormr2_", "sormr3_", "sormrq_",
"sormrz_", "sormtr_", "spbcon_", "spbequ_", "spbrfs_", "spbstf_", "spbsv_",
"spbsvx_", "spbtf2_", "spbtrf_", "spbtrs_", "spocon_", "sporfs_", "sposv_",
"sposvx_", "spotf2_", "spotrf_", "spotri_", "spotrs_", "sppcon_",
"sppequ_", "spprfs_", "sppsv_", "sppsvx_", "spptrf_", "spptri_", "spptrs_",
"spteqr_", "sptsvx_", "ssbev_", "ssbevd_", "ssbevx_", "ssbgst_", "ssbgv_",
"ssbgvd_", "ssbgvx_", "ssbtrd_", "sspcon_", "sspev_", "sspevd_", "sspevx_",
"sspgst_", "sspgv_", "sspgvd_", "sspgvx_", "ssprfs_", "sspsv_", "sspsvx_",
"ssptrd_", "ssptrf_", "ssptri_", "ssptrs_", "sstebz_", "sstedc_",
"sstegr_", "sstemr_", "ssteqr_", "sstev_", "sstevd_", "sstevr_", "sstevx_",
"ssycon_", "ssyev_", "ssyevd_", "ssyevr_", "ssyevx_", "ssygs2_", "ssygst_",
"ssygv_", "ssygvd_", "ssygvx_", "ssyrfs_", "ssysv_", "ssysvx_", "ssytd2_",
"ssytf2_", "ssytrd_", "ssytrf_", "ssytri_", "ssytrs_", "stbcon_",
"stbrfs_", "stbtrs_", "stgevc_", "stgsja_", "stgsna_", "stgsy2_",
"stgsyl_", "stpcon_", "stprfs_", "stptri_", "stptrs_", "strcon_",
"strevc_", "strexc_", "strrfs_", "strsen_", "strsna_", "strsyl_",
"strti2_", "strtri_", "strtrs_", "zbdsqr_", "zgbbrd_", "zgbcon_",
"zgbrfs_", "zgbsvx_", "zgbtrs_", "zgebak_", "zgebal_", "zgecon_", "zgees_",
"zgeesx_", "zgeev_", "zgeevx_", "zgels_", "zgerfs_", "zgesdd_", "zgesvd_",
"zgesvx_", "zgetrs_", "zggbak_", "zggbal_", "zgges_", "zggesx_", "zggev_",
"zggevx_", "zgghrd_", "zgtcon_", "zgtrfs_", "zgtsvx_", "zgttrs_", "zhbev_",
"zhbevd_", "zhbevx_", "zhbgst_", "zhbgv_", "zhbgvd_", "zhbgvx_", "zhbtrd_",
"zhecon_", "zheev_", "zheevd_", "zheevr_", "zheevx_", "zhegs2_", "zhegst_",
"zhegv_", "zhegvd_", "zhegvx_", "zherfs_", "zhesv_", "zhesvx_", "zhetd2_",
"zhetf2_", "zhetrd_", "zhetrf_", "zhetri_", "zhetrs_", "zhgeqz_",
"zhpcon_", "zhpev_", "zhpevd_", "zhpevx_", "zhpgst_", "zhpgv_", "zhpgvd_",
"zhpgvx_", "zhprfs_", "zhpsv_", "zhpsvx_", "zhptrd_", "zhptrf_", "zhptri_",
"zhptrs_", "zhsein_", "zhseqr_", "zlacp2_", "zlacpy_", "zlagtm_",
"zlahef_", "zlalsd_", "zlaqgb_", "zlaqge_", "zlaqhb_", "zlaqhe_",
"zlaqhp_", "zlaqsb_", "zlaqsp_", "zlaqsy_", "zlarf_", "zlarfb_", "zlarft_",
"zlarfx_", "zlarz_", "zlarzb_", "zlarzt_", "zlascl_", "zlaset_", "zlasr_",
"zlasyf_", "zlatbs_", "zlatps_", "zlatrd_", "zlatrs_", "zlauu2_",
"zlauum_", "zpbcon_", "zpbequ_", "zpbrfs_", "zpbstf_", "zpbsv_", "zpbsvx_",
"zpbtf2_", "zpbtrf_", "zpbtrs_", "zpocon_", "zporfs_", "zposv_", "zposvx_",
"zpotf2_", "zpotrf_", "zpotri_", "zpotrs_", "zppcon_", "zppequ_",
"zpprfs_", "zppsv_", "zppsvx_", "zpptrf_", "zpptri_", "zpptrs_", "zpteqr_",
"zptrfs_", "zptsvx_", "zpttrs_", "zspcon_", "zspmv_", "zspr_", "zsprfs_",
"zspsv_", "zspsvx_", "zsptrf_", "zsptri_", "zsptrs_", "zstedc_", "zstegr_",
"zstemr_", "zsteqr_", "zsycon_", "zsymv_", "zsyr_", "zsyrfs_", "zsysv_",
"zsysvx_", "zsytf2_", "zsytrf_", "zsytri_", "zsytrs_", "ztbcon_",
"ztbrfs_", "ztbtrs_", "ztgevc_", "ztgsja_", "ztgsna_", "ztgsy2_",
"ztgsyl_", "ztpcon_", "ztprfs_", "ztptri_", "ztptrs_", "ztrcon_",
"ztrevc_", "ztrexc_", "ztrrfs_", "ztrsen_", "ztrsna_", "ztrsyl_",
"ztrti2_", "ztrtri_", "ztrtrs_", "zungbr_", "zungtr_", "zunm2l_",
"zunm2r_", "zunmbr_", "zunmhr_", "zunml2_", "zunmlq_", "zunmql_",
"zunmqr_", "zunmr2_", "zunmr3_", "zunmrq_", "zunmrz_", "zunmtr_",
"zupgtr_", "zupmtr_", "ilaenv_",
]
# fmt: on
code = None
with open(f2c_output_name, "r") as f:
code = f.read()
for cur_name in lapack_names:
code = re.sub(rf"\b{cur_name}\b", "w" + cur_name, code)
if code:
with open(f2c_output_name, "w") as f:
f.write(code)
This function is called on the name of each C output file. It fixes up the C
output in various ways to compensate for the lack of f2c support for Fortan
90 and Fortran 95.
"""
f2c_output = Path(f2c_output_path)
if f2c_output.name == "lapack_extras.c":
# dfft.c has a bunch of implicit cast args coming from functions copied
# out of future lapack versions. fix_inconsistent_decls will fix all
# except string to int.
subprocess.check_call(
[
"patch",
str(f2c_output_path),
f"../../patches/fix-implicit-cast-args-from-newer-lapack.patch",
]
)
with open(f2c_output, "r") as f:
lines = f.readlines()
if "id_dist" in f2c_output_path:
# Fix implicit casts in id_dist.
lines = fix_inconsistent_decls(lines)
if "odepack" in f2c_output_path or f2c_output.name == "mvndst.c":
# Mark all but one declaration of each struct as extern.
if f2c_output.name == "blkdta000.c":
# extern marking in blkdata000.c doesn't work properly so we let it
# define the one copy of the structs. It doesn't talk about lsa001
# at all though, so we need to add a definition of it.
lines.append(
"""
struct { doublereal rownd2, pdest, pdlast, ratio, cm1[12], cm2[5], pdnorm;
integer iownd2[3], icount, irflag, jtyp, mused, mxordn, mxords;
} lsa001_;
"""
)
else:
add_externs_to_structs(lines)
if f2c_output.name in [
"wrap_dummy_g77_abi.c",
"_lapack_subroutine_wrappers.c",
"_blas_subroutine_wrappers.c",
"_flapack-f2pywrappers.c",
]:
lines = remove_ftnlen_args(lines)
with open(f2c_output, "w") as f:
f.writelines(lines)
def prepare_doctest(x):
return dedent(x).strip().split("\n")
def remove_ftnlen_args(lines: List[str]) -> List[str]:
"""
Functions with "character" arguments have these extra ftnlen arguments at
the end (which are never used). Other places declare these arguments as
"integer" which don't get length arguments. This automates the removal of
the problematic arguments.
>>> print("\\n".join(remove_ftnlen_args(prepare_doctest('''
... /* Subroutine */ int chla_transtypewrp__(char *ret, integer *trans, ftnlen
... ret_len)
... '''))))
/* Subroutine */ int chla_transtypewrp__(char *ret, integer *trans)
>>> print("\\n".join(remove_ftnlen_args(prepare_doctest('''
... /* Subroutine */ int clanhfwrp_(real *ret, char *norm, char *transr, char *
... uplo, integer *n, complex *a, real *work, ftnlen norm_len, ftnlen
... transr_len, ftnlen uplo_len)
... '''))))
/* Subroutine */ int clanhfwrp_(real *ret, char *norm, char *transr, char * uplo, integer *n, complex *a, real *work)
"""
new_lines = []
for line in regroup_lines(lines):
if line.startswith("/* Subroutine */"):
line = re.sub(r",\s*ftnlen [a-z]*_len", "", line)
new_lines.append(line)
return new_lines
def add_externs_to_structs(lines: List[str]):
"""
The fortran "common" keyword is supposed to share variables between a bunch
of files. f2c doesn't handle this correctly (it isn't possible for it to
handle it correctly because it only looks one file at a time).
We mark all the structs as externs and then (separately) add one non extern
version to each file.
>>> lines = prepare_doctest('''
... struct { doublereal rls[218];
... integer ils[39];
... } ls0001_;
... struct { doublereal rlsa[22];
... integer ilsa[9];
... } lsa001_;
... struct { integer ieh[2];
... } eh0001_;
... ''')
>>> add_externs_to_structs(lines)
>>> print("\\n".join(lines))
extern struct { doublereal rls[218];
integer ils[39];
} ls0001_;
extern struct { doublereal rlsa[22];
integer ilsa[9];
} lsa001_;
extern struct { integer ieh[2];
} eh0001_;
"""
for idx, line in enumerate(lines):
if line.startswith("struct"):
lines[idx] = "extern " + lines[idx]
def regroup_lines(lines: Iterable[str]) -> Iterator[str]:
"""
Make sure that functions and declarations have their argument list only on
one line.
>>> print("\\n".join(regroup_lines(prepare_doctest('''
... /* Subroutine */ int clanhfwrp_(real *ret, char *norm, char *transr, char *
... uplo, integer *n, complex *a, real *work, ftnlen norm_len, ftnlen
... transr_len, ftnlen uplo_len)
... {
... static doublereal psum[52];
... extern /* Subroutine */ int dqelg_(integer *, doublereal *, doublereal *,
... doublereal *, doublereal *, integer *);
... '''))))
/* Subroutine */ int clanhfwrp_(real *ret, char *norm, char *transr, char * uplo, integer *n, complex *a, real *work, ftnlen norm_len, ftnlen transr_len, ftnlen uplo_len)
{
static doublereal psum[52];
extern /* Subroutine */ int dqelg_(integer *, doublereal *, doublereal *, doublereal *, doublereal *, integer *);
"""
line_iter = iter(lines)
for line in line_iter:
if not "/* Subroutine */" in line:
yield line
continue
is_definition = line.startswith("/* Subroutine */")
stop = ")" if is_definition else ";"
if stop in line:
yield line
continue
sub_lines = [line.rstrip()]
for line in line_iter:
sub_lines.append(line.strip())
if stop in line:
break
joined_line = " ".join(sub_lines)
if is_definition:
yield joined_line
else:
yield from (x + ";" for x in joined_line.split(";")[:-1])
def fix_inconsistent_decls(lines: List[str]) -> List[str]:
"""
Fortran functions in id_dist use implicit casting of function args which f2c
doesn't support.
The fortran equivalent of the following code:
double f(double x){
return x + 5;
}
double g(int x){
return f(x);
}
gets f2c'd to:
double f(double x){
return x + 5;
}
double g(int x){
double f(int);
return f(x);
}
which fails to compile because the declaration of f type clashes with the
definition. Gather up all the definitions in each file and then gathers the
declarations and fixes them if necessary so that the declaration matches the
definition.
>>> print("\\n".join(fix_inconsistent_decls(prepare_doctest('''
... /* Subroutine */ double f(double x){
... return x + 5;
... }
... /* Subroutine */ double g(int x){
... extern /* Subroutine */ double f(int);
... return f(x);
... }
... '''))))
/* Subroutine */ double f(double x){
return x + 5;
}
/* Subroutine */ double g(int x){
extern /* Subroutine */ double f(double);
return f(x);
}
"""
func_types = {}
lines = list(regroup_lines(lines))
for line in lines:
if not line.startswith("/* Subroutine */"):
continue
[func_name, types] = get_subroutine_decl(line)
func_types[func_name] = types
for idx, line in enumerate(lines):
if not "extern /* Subroutine */" in line:
continue
decls = line.split(")")[:-1]
for decl in decls:
[func_name, types] = get_subroutine_decl(decl)
if func_name not in func_types or types == func_types[func_name]:
continue
types = func_types[func_name]
l = list(line.partition(func_name + "("))
l[2:] = list(l[2].partition(")"))
l[2] = ", ".join(types)
line = "".join(l)
lines[idx] = line
return lines
def get_subroutine_decl(sub: str) -> Tuple[str, List[str]]:
"""
>>> get_subroutine_decl(
... "extern /* Subroutine */ int dqelg_(integer *, doublereal *, doublereal *, doublereal *, doublereal *, integer *);"
... )
('dqelg_', ['integer *', 'doublereal *', 'doublereal *', 'doublereal *', 'doublereal *', 'integer *'])
"""
func_name = sub.partition("(")[0].rpartition(" ")[2]
args_str = sub.partition("(")[2].partition(")")[0]
args = args_str.split(",")
types = []
for arg in args:
arg = arg.strip()
if "*" in arg:
type = "".join(arg.partition("*")[:-1])
else:
type = arg.partition(" ")[0]
types.append(type.strip())
return (func_name, types)

15
pyodide-build/pyodide_build/pywasmcross.py
View File

@ -39,7 +39,7 @@ from typing import List, Dict, Set, Optional, overload
# absolute import is necessary as this file will be symlinked
# under tools
from pyodide_build import common
from pyodide_build._f2c_fixes import fix_f2c_clapack_calls
from pyodide_build._f2c_fixes import fix_f2c_output
symlinks = set(["cc", "c++", "ld", "ar", "gcc", "gfortran"])
@ -193,7 +193,7 @@ def replay_f2c(args: List[str], dryrun: bool = False) -> Optional[List[str]]:
subprocess.check_call(
["f2c", os.path.basename(filename)], cwd=os.path.dirname(filename)
)
fix_f2c_clapack_calls(arg[:-2] + ".c")
fix_f2c_output(arg[:-2] + ".c")
new_args.append(arg[:-2] + ".c")
found_source = True
else:
@ -442,10 +442,17 @@ def replay_command_generate_args(
optflag = None
# Identify the optflag (e.g. -O3) in cflags/cxxflags/ldflags. Last one has
# priority.
for arg in new_args[::-1]:
for arg in reversed(new_args):
if arg in optflags_valid:
optflag = arg
break
debugflag = None
# Identify the debug flag (e.g. -g0) in cflags/cxxflags/ldflags. Last one has
# priority.
for arg in reversed(new_args):
if arg.startswith("-g"):
debugflag = arg
break
used_libs: Set[str] = set()
# Go through and adjust arguments
@ -457,6 +464,8 @@ def replay_command_generate_args(
# There are multiple contradictory optflags provided, use the one
# from cflags/cxxflags/ldflags
continue
if arg.startswith("-g") and debugflag is not None:
continue
if new_args[-1].startswith("-B") and "compiler_compat" in arg:
# conda uses custom compiler search paths with the compiler_compat folder.
# Ignore it.

27
pyodide-build/pyodide_build/tests/test_f2c_fixes.py
View File

@ -1,27 +0,0 @@
from textwrap import dedent
from pyodide_build._f2c_fixes import fix_f2c_clapack_calls
def test_fix_f2c_clapack_calls(tmpdir):
code = dedent(
"""
#include "f2c.h"
int sgemv_(char *trans, integer *m, integer *n, real *alpha)
{
return 0;
}
"""
)
source_file = tmpdir / "sgemv.c"
with open(source_file, "w") as fh:
fh.write(code)
fix_f2c_clapack_calls(str(source_file))
with open(source_file, "r") as fh:
code_fixed = fh.read()
assert code_fixed == code.replace("sgemv_", "wsgemv_")