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Fix build in Docker

This commit is contained in:
Roman Yurchak 2018-10-11 12:03:32 +02:00
parent 3b906e4b68
commit 27319bc675
9 changed files with 316 additions and 118 deletions
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2
.circleci/config.yml
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@ -19,6 +19,8 @@ jobs:
- run:
name: dependencies
command: |
sudo apt-get install gfortran f2c
# Download BLAS/LAPACK
git clone https://github.com/adrianbg/CLAPACK-WA.git packages/scipy/CLAPACK-WA

2
emsdk/patches/num_params.patch
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@ -7,7 +7,7 @@ index 013e9403..d95fc282 100644
// to match when dynamically linking, and also dynamic linking is why we
// can't just detect this automatically in the module we see.)
-static const int NUM_PARAMS = 15;
+static const int NUM_PARAMS = 37;
+static const int NUM_PARAMS = 45;
// Converts a value to the ABI type of i64.
static Expression* toABI(Expression* value, Module* module) {

5
packages/scipy/meta.yaml
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@ -20,10 +20,11 @@ source:
- patches/fix-build-gcc5-a80460.patch
- patches/force_malloc.patch
- patches/disable_scipy_stats_mvn.patch
- patches/skip-scipy-special-_ufuncs.patch
- patches/skip-fortran-fails-to-link.patch
- patches/disable_FuncCastEmulation_num_params.patch
build:
cflags: -I/home/rth/src/pyodide/packages/scipy/CLAPACK-WA/INCLUDE -Wno-implicit-function-declaration
cflags: -I../../CLAPACK-WA/INCLUDE -Wno-implicit-function-declaration
cxxflags:
requirements:

77
packages/scipy/patches/disable_FuncCastEmulation_num_params.patch Normal file
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@ -0,0 +1,77 @@
commit dbfb06104aa7f3f36737f394b66a76a29018d5e7
Author: Roman Yurchak <rth.yurchak@pm.me>
Date: Fri Oct 12 10:36:48 2018 +0200
Disable F2C function that need larger FuncCastEmulation::NUM_PARAMS
scipy/interpolate/_fitpack seems to require NUM_PARAMS
43 then 45 then 47 (each requiring to rebuild emsdk), so disabling this
for now.
scipy/ord/_odrpack requires NUM_PARAMS 57
diff --git a/scipy/interpolate/setup.py b/scipy/interpolate/setup.py
index 2c8279403..9934376e8 100755
--- a/scipy/interpolate/setup.py
+++ b/scipy/interpolate/setup.py
@@ -22,18 +22,18 @@ def configuration(parent_package='',top_path=None):
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('_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'],
diff --git a/scipy/odr/setup.py b/scipy/odr/setup.py
index 9974dfac6..d7560896f 100644
--- a/scipy/odr/setup.py
+++ b/scipy/odr/setup.py
@@ -22,18 +22,18 @@ def configuration(parent_package='', top_path=None):
libodr_files.append('d_lpkbls.f')
odrpack_src = [join('odrpack', x) for x in libodr_files]
- config.add_library('odrpack', sources=odrpack_src)
+ #config.add_library('odrpack', sources=odrpack_src)
sources = ['__odrpack.c']
libraries = ['odrpack'] + blas_info.pop('libraries', [])
include_dirs = ['.'] + blas_info.pop('include_dirs', [])
- config.add_extension('__odrpack',
- sources=sources,
- libraries=libraries,
- include_dirs=include_dirs,
- depends=(['odrpack.h'] + odrpack_src),
- **blas_info
- )
+ #config.add_extension('__odrpack',
+ # sources=sources,
+ # libraries=libraries,
+ # include_dirs=include_dirs,
+ # depends=(['odrpack.h'] + odrpack_src),
+ # **blas_info
+ #)
config.add_data_dir('tests')
return config

65
packages/scipy/patches/force_malloc.patch
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@ -1,3 +1,68 @@
commit d755dab2147732e9213af29f55ab38c38b7ba8d2
Author: Roman Yurchak <rth.yurchak@pm.me>
Date: Mon Oct 8 12:13:55 2018 +0200
Force malloc
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/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

83
packages/scipy/patches/skip-fortran-fails-to-link.patch Normal file
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@ -0,0 +1,83 @@
commit 0822e53ae255433469257625e8f292abd13ae562
Author: Roman Yurchak <rth.yurchak@pm.me>
Date: Thu Oct 11 17:10:36 2018 +0200
Skip fortran code that fails to link
scipy.integrate.odepack
diff --git a/scipy/integrate/setup.py b/scipy/integrate/setup.py
index 9d607af8d..2be454c70 100755
--- 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)
# 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)
config.add_data_dir('tests')
return config

114
packages/scipy/patches/skip-scipy-special-_ufuncs.patch
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@ -1,114 +0,0 @@
commit 066faced67d1d0a8a4a89588194fcbd2faa0a525
Author: Roman Yurchak <rth.yurchak@pm.me>
Date: Wed Oct 10 17:48:17 2018 +0200
Skip scipy.special._ufuncs
diff --git a/scipy/special/__init__.py b/scipy/special/__init__.py
index f013b818e..ab4956825 100644
--- a/scipy/special/__init__.py
+++ b/scipy/special/__init__.py
@@ -624,7 +624,11 @@ Convenience Functions
from __future__ import division, print_function, absolute_import
-from ._ufuncs import *
+try:
+ from ._ufuncs import *
+except ImportError:
+ # TODO
+ pass
from .basic import *
from . import specfun
diff --git a/scipy/special/_ellip_harm.py b/scipy/special/_ellip_harm.py
index 6972c2ad1..0558ee6d3 100644
--- a/scipy/special/_ellip_harm.py
+++ b/scipy/special/_ellip_harm.py
@@ -3,7 +3,11 @@ from __future__ import division, print_function, absolute_import
import threading
import numpy as np
-from ._ufuncs import _ellip_harm
+try:
+ from ._ufuncs import _ellip_harm
+except ImportError:
+ # TODO
+ pass
from ._ellip_harm_2 import _ellipsoid, _ellipsoid_norm
diff --git a/scipy/special/basic.py b/scipy/special/basic.py
index bb251e745..f1c788c3d 100644
--- a/scipy/special/basic.py
+++ b/scipy/special/basic.py
@@ -11,9 +11,13 @@ from scipy._lib.six import xrange
from numpy import (pi, asarray, floor, isscalar, iscomplex, real, imag, sqrt,
where, mgrid, sin, place, issubdtype, extract,
less, inexact, nan, zeros, atleast_1d, sinc)
-from ._ufuncs import (ellipkm1, mathieu_a, mathieu_b, iv, jv, gamma, psi, zeta,
- hankel1, hankel2, yv, kv, gammaln, ndtri, errprint, poch,
- binom)
+try:
+ from ._ufuncs import (ellipkm1, mathieu_a, mathieu_b, iv, jv, gamma, psi, zeta,
+ hankel1, hankel2, yv, kv, gammaln, ndtri, errprint, poch,
+ binom)
+except ImportError:
+ # TODO
+ pass
from . import specfun
from . import orthogonal
diff --git a/scipy/special/lambertw.py b/scipy/special/lambertw.py
index 4bdac30f9..8a890ce51 100644
--- a/scipy/special/lambertw.py
+++ b/scipy/special/lambertw.py
@@ -1,6 +1,10 @@
from __future__ import division, print_function, absolute_import
-from ._ufuncs import _lambertw
+try:
+ from ._ufuncs import _lambertw
+except ImportError:
+ # TODO
+ pass
def lambertw(z, k=0, tol=1e-8):
diff --git a/scipy/special/orthogonal.py b/scipy/special/orthogonal.py
index c2b8dead3..b33ab96ac 100755
--- a/scipy/special/orthogonal.py
+++ b/scipy/special/orthogonal.py
@@ -102,8 +102,12 @@ from scipy import linalg
from scipy.special import airy
# Local imports.
-from . import _ufuncs as cephes
-_gam = cephes.gamma
+try:
+ from . import _ufuncs as cephes
+ _gam = cephes.gamma
+except ImportError:
+ # TODO
+ pass
from . import specfun
__all__ = ['legendre', 'chebyt', 'chebyu', 'chebyc', 'chebys',
@@ -1657,8 +1661,12 @@ def sh_legendre(n, monic=False):
# -----------------------------------------------------------------------------
# Vectorized functions for evaluation
# -----------------------------------------------------------------------------
-from ._ufuncs import (binom, eval_jacobi, eval_sh_jacobi, eval_gegenbauer,
- eval_chebyt, eval_chebyu, eval_chebys, eval_chebyc,
- eval_sh_chebyt, eval_sh_chebyu, eval_legendre,
- eval_sh_legendre, eval_genlaguerre, eval_laguerre,
- eval_hermite, eval_hermitenorm)
+try:
+ from ._ufuncs import (binom, eval_jacobi, eval_sh_jacobi, eval_gegenbauer,
+ eval_chebyt, eval_chebyu, eval_chebys, eval_chebyc,
+ eval_sh_chebyt, eval_sh_chebyu, eval_legendre,
+ eval_sh_legendre, eval_genlaguerre, eval_laguerre,
+ eval_hermite, eval_hermitenorm)
+except ImportError:
+ # TODO
+ pass

3
test/conftest.py
View File

@ -16,7 +16,8 @@ import shutil
TEST_PATH = pathlib.Path(__file__).parents[0].resolve()
BUILD_PATH = TEST_PATH / '..' / 'build'
sys.path.append(TEST_PATH / '..')
sys.path.append(str(TEST_PATH / '..'))
print(sys.path)
from pyodide_build._fixes import _selenium_is_connectable # noqa: E402
import selenium.webdriver.common.utils # noqa: E402

83
test/test_scipy.py Normal file
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@ -0,0 +1,83 @@
from pathlib import Path
import subprocess
import sys
from textwrap import dedent
import pytest
sys.path.append(str(Path(__file__).parents[1]))
from pyodide_build.common import HOSTPYTHON # noqa: E402
def test_scipy_import(selenium_standalone):
from selenium.common.exceptions import JavascriptException
selenium = selenium_standalone
selenium.load_package("scipy")
selenium.run("""
import scipy
""")
# supported modules
for module in ['constants', 'fftpack']:
selenium.run(f"import scipy.{module}")
# not yet built modules
for module in ['cluster', # needs sparse
'spatial', # needs sparse
'sparse',
'integrate', # needs special
'interpolate', # needs linalg
'linalg',
'misc', # needs special
'odrpack',
'signal', # needs special
'ndimage', # needs special
'stats', # need special
'optimize', # needs minpack2
'special']:
print(module)
with pytest.raises(JavascriptException) as err:
selenium.run(f"import scipy.{module}")
assert ('ModuleNotFoundError' in str(err.value)
or 'ImportError' in str(err.value))
print(selenium.logs)
def test_built_so(selenium_standalone):
selenium = selenium_standalone
selenium.load_package("scipy")
cmd = dedent(r"""
import scipy as sp
import os
base_dir = os.path.dirname(sp.__file__)
out = []
for (dirpath, dirnames, filenames) in os.walk(base_dir):
for path in filenames:
if path.endswith('.so'):
rel_path = os.path.relpath(dirpath, base_dir)
out.append(os.path.join(rel_path, path))
print("\n".join(out))
out
""")
out = subprocess.check_output(
[HOSTPYTHON / 'bin' / 'python3', '-c', cmd])
modules_host = out.decode('utf-8').split('\n')
def _get_modules_name(modules):
return set([path.split('.')[0] for path in modules if path])
modules_host = _get_modules_name(modules_host)
modules_target = selenium.run(cmd)
modules_target = _get_modules_name(modules_target)
print(f'Included modules: {len(modules_target)}')
print(f' {modules_target} ')
print(f'\nMissing modules: {len(modules_host.difference(modules_target))}')
print(f' {modules_host.difference(modules_target)}')