Merge pull request #211 from rth/scipy

Scipy packaging

.circleci/config.yml

@@ -3,7 +3,7 @@ version: 2
 defaults: &defaults
   working_directory: ~/repo
   docker:
-    - image: iodide/pyodide-env:0.3.0
+    - image: iodide/pyodide-env:0.3.1
 
 jobs:
   build:

.gitignore

@@ -8,6 +8,7 @@
 .pytest_cache/
 __pycache__
 geckodriver.log
+firefox/
 
 build
 downloads

CLAPACK/Makefile

@@ -25,7 +25,6 @@ $(SRC)/lapack_WA.bc:  $(SRC)/Makefile
 $(SRC)/Makefile:
 	wget -q -O clapack.tgz http://www.netlib.org/clapack/clapack.tgz
 	md5sum --quiet --check checksums || (rm -f clapack.tgz; false)
-
 	tar xzf clapack.tgz
 	rm -rf $(SRC)
 	mv CLAPACK-$(CLAPACK_VERSION) $(SRC)

CLAPACK/Makefile.envs

-CFLAGS_OPT=-O2
-LDFLAGS_OPT=-O2
+CFLAGS_OPT=-Os -s INLINING_LIMIT=5
+LDFLAGS_OPT=-Os -s INLINING_LIMIT=5

Makefile

@@ -15,6 +15,7 @@ OPTFLAGS=-O3
 CFLAGS=$(OPTFLAGS) -g -I$(PYTHONINCLUDE) -Wno-warn-absolute-paths
 CXXFLAGS=$(CFLAGS) -std=c++14
 
+
 # __ZNKSt3__220__vector_base_commonILb1EE20__throw_length_errorEv is in
 # EXPORTED_FUNCTIONS to keep the C++ standard library in the core, even though
 # there isn't any C++ there, for the sake of loading dynamic modules written in
@@ -134,7 +135,7 @@ clean:
 	rm -fr src/*.bc
 	make -C packages clean
 	make -C six clean
-	echo "The Emsdk and CPython are not cleaned. cd into those directories to do so."
+	echo "The Emsdk, CPython and CLAPACK are not cleaned. cd into those directories to do so."
 
 
 %.bc: %.c $(CPYTHONLIB) $(LZ4LIB)
@@ -216,6 +217,5 @@ $(CLAPACK): $(CPYTHONLIB)
 build/packages.json: $(CPYTHONLIB) $(CLAPACK)
 	make -C packages
 
-
 emsdk/emsdk/.complete:
 	make -C emsdk

benchmark/benchmark.py

@@ -68,7 +68,7 @@ def parse_numpy_benchmark(filename):
     lines = []
     with open(filename) as fp:
         for line in fp:
-            m = re.match('^#\s*(setup|run): (.*)$', line)
+            m = re.match(r'^#\s*(setup|run): (.*)$', line)
             if m:
                 line = '{} = {!r}\n'.format(m.group(1), m.group(2))
             lines.append(line)

emsdk/patches/num_params.patch

@@ -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 = 32;
++static const int NUM_PARAMS = 61;   // needed by scipy.odr._odrpack
 
  // Converts a value to the ABI type of i64.
  static Expression* toABI(Expression* value, Module* module) {

packages/Makefile

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

packages/scipy/meta.yaml

+package:
+  name: scipy
+  version: 0.17.1
+
+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
+
+  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/dummy_threading.patch
+    - patches/skip_ellip_harm_2_pyx_ctypes.patch
+    - patches/fix_mmap.patch
+
+build:
+  cflags: -I../../../../CLAPACK/CLAPACK-WA/INCLUDE -Wno-implicit-function-declaration
+  cxxflags:
+
+requirements:
+  run:
+    - numpy
+
+test:
+  imports:
+    - scipy
+    - scipy.cluster
+    - scipy.constants
+    - scipy.fftpack
+    - scipy.odr
+    - scipy.sparse
+    - scipy.interpolate
+    - scipy.integrate
+    - scipy.linalg
+    - scipy.misc
+    - scipy.ndimage
+    - scipy.spatial
+    - scipy.special

packages/scipy/patches/disable_scipy_stats_mvn.patch

+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
+ 

packages/scipy/patches/dummy_threading.patch

+commit cfd6c4b18c5f338842d2ee509bfb2d3a3c6f6439
+Author: Roman Yurchak <rth.yurchak@pm.me>
+Date:   Mon Oct 15 15:40:48 2018 +0200
+
+    Use dummy_threading
+
+diff --git a/scipy/interpolate/tests/test_gil.py b/scipy/interpolate/tests/test_gil.py
+index df3ab3bc4..974b68ada 100644
+--- a/scipy/interpolate/tests/test_gil.py
++++ b/scipy/interpolate/tests/test_gil.py
+@@ -1,7 +1,7 @@
+ from __future__ import division, print_function, absolute_import
+ 
+ import itertools
+-import threading
++import dummy_threading as threading
+ import time
+ 
+ import numpy as np
+diff --git a/scipy/ndimage/tests/test_filters.py b/scipy/ndimage/tests/test_filters.py
+index 8c56393a6..8ff85547c 100644
+--- a/scipy/ndimage/tests/test_filters.py
++++ b/scipy/ndimage/tests/test_filters.py
+@@ -129,7 +129,7 @@ def test_gaussian_truncate():
+ 
+ class TestThreading(TestCase):
+     def check_func_thread(self, n, fun, args, out):
+-        from threading import Thread
++        from dummy_threading import Thread
+         thrds = [Thread(target=fun, args=args, kwargs={'output': out[x]}) for x in range(n)]
+         [t.start() for t in thrds]
+         [t.join() for t in thrds]
+diff --git a/scipy/signal/signaltools.py b/scipy/signal/signaltools.py
+index df7107684..2b9a18422 100644
+--- a/scipy/signal/signaltools.py
++++ b/scipy/signal/signaltools.py
+@@ -4,7 +4,7 @@
+ from __future__ import division, print_function, absolute_import
+ 
+ import warnings
+-import threading
++import dummy_threading as threading
+ 
+ from . import sigtools
+ from scipy._lib.six import callable
+diff --git a/scipy/sparse/tests/test_sparsetools.py b/scipy/sparse/tests/test_sparsetools.py
+index 7a3c903cc..cc495d500 100644
+--- a/scipy/sparse/tests/test_sparsetools.py
++++ b/scipy/sparse/tests/test_sparsetools.py
+@@ -4,7 +4,7 @@ import sys
+ import os
+ import gc
+ import re
+-import threading
++import dummy_threading as threading
+ 
+ from nose import SkipTest
+ import numpy as np
+diff --git a/scipy/spatial/ckdtree.pyx b/scipy/spatial/ckdtree.pyx
+index 2f98613a7..c9f657cf3 100644
+--- a/scipy/spatial/ckdtree.pyx
++++ b/scipy/spatial/ckdtree.pyx
+@@ -17,8 +17,7 @@ from libc.string cimport memset, memcpy
+ 
+ cimport cython
+ 
+-from multiprocessing import cpu_count
+-import threading
++import dummy_threading as threading
+ 
+ cdef extern from "limits.h":
+     long LONG_MAX
+@@ -26,7 +25,7 @@ cdef extern from "limits.h":
+ cdef extern from "ckdtree_methods.h":
+     int number_of_processors
+     
+-number_of_processors = cpu_count()
++number_of_processors = 1
+ 
+ from libcpp.vector cimport vector
+ from libc cimport string
+@@ -91,7 +90,7 @@ cdef extern from "cpp_utils.h":
+ # coo_entry wrapper
+ # =================
+ 
+-cdef class coo_entries:
++cdef class coo_entries(object):
+ 
+     cdef: 
+         readonly object __array_interface__
+diff --git a/scipy/spatial/qhull.pyx b/scipy/spatial/qhull.pyx
+index ba33fadbe..644a57eaf 100644
+--- a/scipy/spatial/qhull.pyx
++++ b/scipy/spatial/qhull.pyx
+@@ -10,7 +10,7 @@ Wrappers for Qhull triangulation, plus some additional N-D geometry utilities
+ # Distributed under the same BSD license as Scipy.
+ #
+ 
+-import threading
++import dummy_threading as threading
+ import numpy as np
+ cimport numpy as np
+ cimport cython
+diff --git a/scipy/special/_ellip_harm.py b/scipy/special/_ellip_harm.py
+index 62e50655e..61e9949cc 100644
+--- a/scipy/special/_ellip_harm.py
++++ b/scipy/special/_ellip_harm.py
+@@ -1,6 +1,6 @@
+ from __future__ import division, print_function, absolute_import
+ 
+-import threading
++import dummy_threading as threading
+ import numpy as np
+ 
+ from ._ufuncs import _ellip_harm

packages/scipy/patches/fix-blas.patch

+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/CLAPACK-WA/'],
++                  '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/CLAPACK-WA/'],
++                  '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/CLAPACK-WA/'],
++                  'language': 'f77',
++                  'define_macros': [('NO_ATLAS_INFO', 1),
++                                    ('HAVE_CBLAS', None)]}
+ 
+     if not lapack_opt:
+         raise NotFoundError('no lapack/blas resources found')

packages/scipy/patches/fix-build-gcc5-a80460.patch

+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
+ 

packages/scipy/patches/fix_mmap.patch

+commit 6d4c53df9fecd236cb569b5f1997908af1daea6b
+Author: Roman Yurchak <rth.yurchak@pm.me>
+Date:   Thu Oct 25 15:28:05 2018 +0200
+
+    Fix mmap imports
+
+diff --git a/scipy/io/netcdf.py b/scipy/io/netcdf.py
+index 841e97830..f06759015 100644
+--- a/scipy/io/netcdf.py
++++ b/scipy/io/netcdf.py
+@@ -39,7 +39,6 @@ __all__ = ['netcdf_file']
+ import warnings
+ import weakref
+ from operator import mul
+-import mmap as mm
+ 
+ import numpy as np
+ from numpy.compat import asbytes, asstr
+@@ -219,6 +218,8 @@ class netcdf_file(object):
+     def __init__(self, filename, mode='r', mmap=None, version=1,
+                  maskandscale=False):
+         """Initialize netcdf_file from fileobj (str or file-like)."""
++        import mmap as mm
++
+         if mode not in 'rwa':
+             raise ValueError("Mode must be either 'r', 'w' or 'a'.")
+ 

packages/scipy/patches/force_malloc.patch

+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;

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

+commit c3affe05b5cb8d992cb7a955ff8b4c79452f3cc9
+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/_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
+--- 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

packages/scipy/patches/skip_ellip_harm_2_pyx_ctypes.patch

+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')

pyodide_build/buildpkg.py

@@ -154,7 +154,7 @@ def build_package(path, args):
     os.chdir(dirpath)
     try:
         buildpath = dirpath / 'build'
-        if not buildpath.is_dir():
+        if not buildpath.resolve().is_dir():
             os.makedirs(buildpath)
         srcpath = download_and_extract(buildpath, packagedir, pkg, args)
         patch(path, srcpath, pkg, args)

pyodide_build/pywasmcross.py

@@ -211,6 +211,8 @@ def handle_command(line, args, dryrun=False):
             return
         if arg == '-print-multiarch':
             return
+        if arg.startswith('/tmp'):
+            return
 
     if line[0] == 'gfortran':
         result = f2c(line)
@@ -234,6 +236,8 @@ def handle_command(line, args, dryrun=False):
     elif new_args[0] in ('emcc', 'em++'):
         new_args.extend(args.cflags.split())
 
+    lapack_dir = None
+
     # Go through and adjust arguments
     for arg in line[1:]:
         if arg.startswith('-I'):
@@ -256,6 +260,34 @@ def handle_command(line, args, dryrun=False):
             arg = arg[:-3] + '.wasm'
             output = arg
 
+        # Fix for scipy to link to the correct BLAS/LAPACK files
+        if arg.startswith('-L') and 'CLAPACK-WA' in arg:
+            out_idx = line.index('-o')
+            out_idx += 1
+            module_name = line[out_idx]
+            module_name = Path(module_name).name.split('.')[0]
+
+            lapack_dir = arg.replace('-L', '')
+            # For convinience we determine needed scipy link libraries
+            # here, instead of in patch files
+            link_libs = ['F2CLIBS/libf2c.bc', 'blas_WA.bc']
+            if module_name in ['_flapack', '_flinalg', '_calc_lwork',
+                               'cython_lapack', '_iterative', '_arpack']:
+                link_libs.append('lapack_WA.bc')
+
+            for lib_name in link_libs:
+                arg = os.path.join(lapack_dir, f"{lib_name}")
+                new_args.append(arg)
+
+            new_args.extend(['-s', 'INLINING_LIMIT=5'])
+            continue
+
+        # Use -Os for files that are statically linked to CLAPACK
+        if (arg.startswith('-O') and 'CLAPACK' in ' '.join(line)
+                and '-L' in ' '.join(line)):
+            new_args.append('-Os')
+            continue
+
         new_args.append(arg)
 
     # This can only be used for incremental rebuilds -- it generates
@@ -316,10 +348,10 @@ def install_for_distribution(args):
     try:
         subprocess.check_call(commands)
     except Exception:
-        print(f'Warning: {" ".join(commands)} failed with distutils, possibly '
-              f'due to the use of distutils that does not support the '
-              f'--old-and-unmanageable argument. Re-trying the install '
-              f'without this argument.')
+        print(f'Warning: {" ".join(str(arg) for arg in commands)} failed '
+              f'with distutils, possibly due to the use of distutils '
+              f'that does not support the --old-and-unmanageable '
+              'argument. Re-trying the install without this argument.')
         subprocess.check_call(commands[:-1])
 
 

run_docker

 #!/bin/sh
-docker run --rm -v $PWD:/src --user root -e NB_UID=$UID -e NB_GID=$GID -it iodide/pyodide-env:0.3.0 /bin/bash
+docker run --rm -v $PWD:/src --user root -e NB_UID=$UID -e NB_GID=$GID -it iodide/pyodide-env:0.3.1 /bin/bash

test/conftest.py

@@ -16,7 +16,7 @@ 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 / '..'))
 
 from pyodide_build._fixes import _selenium_is_connectable  # noqa: E402
 import selenium.webdriver.common.utils  # noqa: E402
@@ -84,7 +84,7 @@ class SeleniumWrapper:
         driver.get(f'http://{server_hostname}:{server_port}/test.html')
         try:
             wait.until(PyodideInited())
-        except TimeoutException as exc:
+        except TimeoutException:
             _display_driver_logs(self.browser, driver)
             raise TimeoutException()
         self.wait = wait
@@ -126,7 +126,7 @@ class SeleniumWrapper:
         )
         try:
             self.wait.until(PackageLoaded())
-        except TimeoutException as exc:
+        except TimeoutException:
             _display_driver_logs(self.browser, self.driver)
             print(self.logs)
             raise TimeoutException('runPythonAsync timed out')
@@ -163,7 +163,7 @@ class SeleniumWrapper:
         __tracebackhide__ = True
         try:
             self.wait.until(PackageLoaded())
-        except TimeoutException as exc:
+        except TimeoutException:
             _display_driver_logs(self.browser, self.driver)
             print(self.logs)
             raise TimeoutException('wait_until_packages_loaded timed out')

test/packages/test_scipy.py

+from textwrap import dedent
+
+import pytest
+
+
+def test_scipy_linalg(selenium_standalone, request):
+    selenium = selenium_standalone
+
+    if selenium.browser == 'chrome':
+        request.applymarker(pytest.mark.xfail(
+            run=False, reason='chrome not supported'))
+
+    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)
+
+        X_inv = scipy.linalg.inv(X)
+
+        res = X.dot(X_inv)
+
+        assert_allclose(res, np.identity(N),
+                        rtol=1e-07, atol=1e-9)
+        """)
+
+    selenium.run(cmd)

test/test_common.py

@@ -23,7 +23,7 @@ def registered_packages_meta():
             for name in packages}
 
 
-UNSUPPORTED_PACKAGES = {'chrome': ['pandas'],
+UNSUPPORTED_PACKAGES = {'chrome': ['pandas', 'scipy'],
                         'firefox': []}
 
 
@@ -72,10 +72,15 @@ def test_import(name, selenium_standalone):
         """
     ) == baseline_pyc
 
+    loaded_packages = []
     for import_name in meta.get('test', {}).get('imports', []):
+
+        if name not in loaded_packages:
+            selenium_standalone.load_package(name)
+            loaded_packages.append(name)
         try:
             selenium_standalone.run('import %s' % import_name)
-        except Exception as e:
+        except Exception:
             print(selenium_standalone.logs)
             raise
 

test/test_python.py

@@ -71,7 +71,7 @@ def test_pythonexc2js(selenium):
     try:
         selenium.run_js('return pyodide.runPython("5 / 0")')
     except selenium.JavascriptException as e:
-        assert('ZeroDivisionError' in str(e))
+        assert 'ZeroDivisionError' in str(e)
     else:
         assert False, 'Expected exception'
 
@@ -393,7 +393,7 @@ def test_cpython_core(python_test, selenium, request):
                 if e.code != 0:
                     raise RuntimeError(f'Failed with code: {{e.code}}')
             """.format(name))
-    except selenium.JavascriptException as e:
+    except selenium.JavascriptException:
         print(selenium.logs)
         raise