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Use scipy 0.17.1

This commit is contained in:
Roman Yurchak 2018-10-05 15:26:21 +02:00
parent b071d37e1a
commit 40605620f8
6 changed files with 417 additions and 5 deletions
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6
.circleci/config.yml
View File

@ -16,6 +16,12 @@ jobs:
command: |
make lint
- run:
name: dependencies
command: |
# Download BLAS/LAPACK
git clone https://github.com/adrianbg/CLAPACK-WA.git packages/scipy/CLAPACK-WA
- restore_cache:
keys:
- v1-emsdk-{{ checksum "emsdk/Makefile" }}-v11-

2
Makefile
View File

@ -208,6 +208,8 @@ $(LZ4LIB):
$(SIX_LIBS): $(CPYTHONLIB)
make -C six
$(LAPACK): $(CPYTHONLIB)
emmake make -C packages/scipy/CLAPACK-WA
$(CLAPACK): $(CPYTHONLIB)
make -C CLAPACK

5
packages/Makefile
View File

@ -1,9 +1,12 @@
PYODIDE_ROOT=$(abspath ..)
include ../Makefile.envs
all:
all: deps
../bin/pyodide buildall . ../build \
--ldflags="$(SIDE_LDFLAGS)" --host=$(HOSTPYTHONROOT) --target=$(TARGETPYTHONROOT)
deps:
# Temporary workaround to install build dependencies
$(HOSTPYTHON) -m pip install Cython Tempita
clean:
rm -rf ./*/build

17
packages/scipy/meta.yaml
View File

@ -1,13 +1,22 @@
package:
name: scipy
version: 1.1.0
version: 0.17.1
source:
url: https://files.pythonhosted.org/packages/07/76/7e844757b9f3bf5ab9f951ccd3e4a8eed91ab8720b0aac8c2adcc2fdae9f/scipy-1.1.0.tar.gz
sha256: 878352408424dffaa695ffedf2f9f92844e116686923ed9aa8626fc30d32cfd1
# 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
patches:
- patches/disable_modules_with_blas.patch
- patches/fix-build-gcc5-a80460.patch
build:
cflags: -ICLAPACK-WA/F2CLIBS/libf2c/ -Wno-implicit-function-declaration
cflags: -I../../CLAPACK-WA/F2CLIBS/libf2c/ -Wno-implicit-function-declaration
cxxflags:
requirements:

338
packages/scipy/patches/disable_modules_with_blas.patch Normal file
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@ -0,0 +1,338 @@
diff --git a/scipy/interpolate/setup.py b/scipy/interpolate/setup.py
deleted file mode 100755
index b42d3345c..000000000
--- a/scipy/interpolate/setup.py
+++ /dev/null
@@ -1,49 +0,0 @@
-#!/usr/bin/env python
-from __future__ import division, print_function, absolute_import
-
-from os.path import join
-
-
-def configuration(parent_package='',top_path=None):
- from numpy.distutils.misc_util import Configuration
- from numpy.distutils.system_info import get_info
-
- lapack_opt = get_info('lapack_opt', notfound_action=2)
-
- config = Configuration('interpolate', parent_package, top_path)
-
- fitpack_src = [join('fitpack', '*.f')]
- config.add_library('fitpack', sources=fitpack_src)
-
- config.add_extension('interpnd',
- sources=['interpnd.c'])
-
- config.add_extension('_ppoly',
- sources=['_ppoly.c'],
- **lapack_opt)
-
- config.add_extension('_fitpack',
- sources=['src/_fitpackmodule.c'],
- libraries=['fitpack'],
- depends=(['src/__fitpack.h','src/multipack.h']
- + fitpack_src)
- )
-
- config.add_extension('dfitpack',
- sources=['src/fitpack.pyf'],
- libraries=['fitpack'],
- depends=fitpack_src,
- )
-
- config.add_extension('_interpolate',
- sources=['src/_interpolate.cpp'],
- include_dirs=['src'],
- depends=['src/interpolate.h'])
-
- config.add_data_dir('tests')
-
- return config
-
-if __name__ == '__main__':
- from numpy.distutils.core import setup
- setup(**configuration(top_path='').todict())
diff --git a/scipy/linalg/setup.py b/scipy/linalg/setup.py
deleted file mode 100755
index 2c9b9ba22..000000000
--- a/scipy/linalg/setup.py
+++ /dev/null
@@ -1,173 +0,0 @@
-#!/usr/bin/env python
-from __future__ import division, print_function, absolute_import
-
-import os
-from os.path import join
-
-
-def configuration(parent_package='', top_path=None):
- from distutils.sysconfig import get_python_inc
- from numpy.distutils.system_info import get_info, NotFoundError, numpy_info
- from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
- from scipy._build_utils import (get_sgemv_fix, get_g77_abi_wrappers,
- split_fortran_files)
-
- config = Configuration('linalg', parent_package, top_path)
-
- lapack_opt = get_info('lapack_opt')
-
- if not lapack_opt:
- raise NotFoundError('no lapack/blas resources found')
-
- atlas_version = ([v[3:-3] for k, v in lapack_opt.get('define_macros', [])
- if k == 'ATLAS_INFO']+[None])[0]
- if atlas_version:
- print(('ATLAS version: %s' % atlas_version))
-
- # fblas:
- sources = ['fblas.pyf.src']
- sources += get_g77_abi_wrappers(lapack_opt)
- sources += get_sgemv_fix(lapack_opt)
-
- config.add_extension('_fblas',
- sources=sources,
- depends=['fblas_l?.pyf.src'],
- extra_info=lapack_opt
- )
-
- # flapack:
- sources = ['flapack.pyf.src']
- 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']
- sources += deprecated_lapack_routines
-
- config.add_extension('_flapack',
- sources=sources,
- depends=['flapack_user.pyf.src'],
- extra_info=lapack_opt
- )
-
- if atlas_version is not None:
- # cblas:
- config.add_extension('_cblas',
- sources=['cblas.pyf.src'],
- depends=['cblas.pyf.src', 'cblas_l1.pyf.src'],
- extra_info=lapack_opt
- )
-
- # clapack:
- config.add_extension('_clapack',
- sources=['clapack.pyf.src'],
- depends=['clapack.pyf.src'],
- extra_info=lapack_opt
- )
-
- # _flinalg:
- config.add_extension('_flinalg',
- sources=[join('src', 'det.f'), join('src', 'lu.f')],
- extra_info=lapack_opt
- )
-
- # _interpolative:
- routines_to_split = [
- 'dfftb1',
- 'dfftf1',
- 'dffti1',
- 'dsint1',
- 'dzfft1',
- 'id_srand',
- 'idd_copyints',
- 'idd_id2svd0',
- 'idd_pairsamps',
- 'idd_permute',
- 'idd_permuter',
- 'idd_random_transf0',
- 'idd_random_transf0_inv',
- 'idd_random_transf_init0',
- 'idd_subselect',
- 'iddp_asvd0',
- 'iddp_rsvd0',
- 'iddr_asvd0',
- 'iddr_rsvd0',
- 'idz_estrank0',
- 'idz_id2svd0',
- 'idz_permute',
- 'idz_permuter',
- 'idz_random_transf0_inv',
- 'idz_random_transf_init0',
- 'idz_random_transf_init00',
- 'idz_realcomp',
- 'idz_realcomplex',
- 'idz_reco',
- 'idz_subselect',
- 'idzp_aid0',
- 'idzp_aid1',
- 'idzp_asvd0',
- 'idzp_rsvd0',
- 'idzr_asvd0',
- 'idzr_reco',
- 'idzr_rsvd0',
- 'zfftb1',
- 'zfftf1',
- 'zffti1',
- ]
- print('Splitting linalg.interpolative Fortran source files')
- dirname = os.path.split(os.path.abspath(__file__))[0]
- 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
- )
-
- # _calc_lwork:
- config.add_extension('_calc_lwork',
- [join('src', 'calc_lwork.f')],
- extra_info=lapack_opt)
-
- # _solve_toeplitz:
- config.add_extension('_solve_toeplitz',
- sources=[('_solve_toeplitz.c')],
- include_dirs=[get_numpy_include_dirs()])
-
- config.add_data_dir('tests')
-
- # Cython BLAS/LAPACK
- config.add_data_files('cython_blas.pxd')
- config.add_data_files('cython_lapack.pxd')
-
- sources = ['_blas_subroutine_wrappers.f', '_lapack_subroutine_wrappers.f']
- sources += get_g77_abi_wrappers(lapack_opt)
- sources += get_sgemv_fix(lapack_opt)
- includes = numpy_info().get_include_dirs() + [get_python_inc()]
- config.add_library('fwrappers', sources=sources, include_dirs=includes)
-
- config.add_extension('cython_blas',
- sources=['cython_blas.c'],
- depends=['cython_blas.pyx', 'cython_blas.pxd',
- 'fortran_defs.h', '_blas_subroutines.h'],
- include_dirs=['.'],
- libraries=['fwrappers'],
- extra_info=lapack_opt)
-
- config.add_extension('cython_lapack',
- sources=['cython_lapack.c'],
- depends=['cython_lapack.pyx', 'cython_lapack.pxd',
- 'fortran_defs.h', '_lapack_subroutines.h'],
- include_dirs=['.'],
- libraries=['fwrappers'],
- extra_info=lapack_opt)
-
- config.add_extension('_decomp_update',
- sources=['_decomp_update.c'])
-
- return config
-
-
-if __name__ == '__main__':
- from numpy.distutils.core import setup
- from linalg_version import linalg_version
-
- setup(version=linalg_version,
- **configuration(top_path='').todict())
diff --git a/scipy/sparse/linalg/eigen/arpack/setup.py b/scipy/sparse/linalg/eigen/arpack/setup.py
deleted file mode 100755
index a8175a9d5..000000000
--- a/scipy/sparse/linalg/eigen/arpack/setup.py
+++ /dev/null
@@ -1,44 +0,0 @@
-#!/usr/bin/env python
-from __future__ import division, print_function, absolute_import
-
-from os.path import join
-
-
-def configuration(parent_package='',top_path=None):
- from numpy.distutils.system_info import get_info, NotFoundError
- from numpy.distutils.misc_util import Configuration
- from scipy._build_utils import get_g77_abi_wrappers, get_sgemv_fix
-
- config = Configuration('arpack',parent_package,top_path)
-
- lapack_opt = get_info('lapack_opt')
-
- if not lapack_opt:
- raise NotFoundError('no lapack/blas resources found')
-
- config = Configuration('arpack', parent_package, top_path)
-
- arpack_sources = [join('ARPACK','SRC', '*.f')]
- arpack_sources.extend([join('ARPACK','UTIL', '*.f')])
- arpack_sources.extend([join('ARPACK','LAPACK', '*.f')])
-
- arpack_sources += get_g77_abi_wrappers(lapack_opt)
-
- config.add_library('arpack_scipy', sources=arpack_sources,
- include_dirs=[join('ARPACK', 'SRC')])
-
- ext_sources = ['arpack.pyf.src']
- ext_sources += get_sgemv_fix(lapack_opt)
- config.add_extension('_arpack',
- sources=ext_sources,
- libraries=['arpack_scipy'],
- extra_info=lapack_opt,
- depends=arpack_sources,
- )
-
- config.add_data_dir('tests')
- return config
-
-if __name__ == '__main__':
- from numpy.distutils.core import setup
- setup(**configuration(top_path='').todict())
diff --git a/scipy/sparse/linalg/isolve/setup.py b/scipy/sparse/linalg/isolve/setup.py
deleted file mode 100755
index becb9237a..000000000
--- a/scipy/sparse/linalg/isolve/setup.py
+++ /dev/null
@@ -1,48 +0,0 @@
-#!/usr/bin/env python
-from __future__ import division, print_function, absolute_import
-
-from os.path import join
-
-
-def configuration(parent_package='',top_path=None):
- from numpy.distutils.system_info import get_info, NotFoundError
- from numpy.distutils.misc_util import Configuration
- from scipy._build_utils import get_g77_abi_wrappers
-
- config = Configuration('isolve',parent_package,top_path)
-
- lapack_opt = get_info('lapack_opt')
-
- if not lapack_opt:
- raise NotFoundError('no lapack/blas resources found')
-
- # iterative methods
- methods = ['BiCGREVCOM.f.src',
- 'BiCGSTABREVCOM.f.src',
- 'CGREVCOM.f.src',
- 'CGSREVCOM.f.src',
-# 'ChebyREVCOM.f.src',
- 'GMRESREVCOM.f.src',
-# 'JacobiREVCOM.f.src',
- 'QMRREVCOM.f.src',
-# 'SORREVCOM.f.src'
- ]
-
- Util = ['STOPTEST2.f.src','getbreak.f.src']
- sources = Util + methods + ['_iterative.pyf.src']
- sources = [join('iterative', x) for x in sources]
- sources += get_g77_abi_wrappers(lapack_opt)
-
- config.add_extension('_iterative',
- sources=sources,
- extra_info=lapack_opt)
-
- config.add_data_dir('tests')
-
- return config
-
-
-if __name__ == '__main__':
- from numpy.distutils.core import setup
-
- setup(**configuration(top_path='').todict())

54
packages/scipy/patches/fix-build-gcc5-a80460.patch Normal file
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@ -0,0 +1,54 @@
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