Patch mmap

packages/scipy/meta.yaml

@@ -23,6 +23,7 @@ source:
     - patches/dummy_threading.patch
     - patches/skip_ellip_harm_2_pyx_ctypes.patch
     - patches/skip_optimize_cobyla_import.patch
+    - patches/fix_mmap.patch
 
 build:
   cflags: -I../../CLAPACK-WA/INCLUDE -Wno-implicit-function-declaration

packages/scipy/patches/skip-blas-imports.patch

@@ -1,104 +0,0 @@
-commit 3f9694b956a2c900f92b635e28ea0eed4baed2fa
-Author: Roman Yurchak <rth.yurchak@pm.me>
-Date:   Fri Oct 19 17:16:05 2018 +0200
-
-    Workaround for missing BLAS/LAPACK imports
-
-diff --git a/scipy/linalg/blas.py b/scipy/linalg/blas.py
-index e4bd57aa4..b88d2f7ea 100644
---- a/scipy/linalg/blas.py
-+++ b/scipy/linalg/blas.py
-@@ -152,7 +152,10 @@ __all__ = ['get_blas_funcs', 'find_best_blas_type']
- 
- import numpy as _np
- 
--from scipy.linalg import _fblas
-+try:
-+    from scipy.linalg import _fblas
-+except ImportError:
-+    _fblas = None
- try:
-     from scipy.linalg import _cblas
- except ImportError:
-@@ -160,7 +163,10 @@ except ImportError:
- 
- # Expose all functions (only fblas --- cblas is an implementation detail)
- empty_module = None
--from scipy.linalg._fblas import *
-+try:
-+    from scipy.linalg._fblas import *
-+except ImportError:
-+    pass
- del empty_module
- 
- # 'd' will be default for 'i',..
-diff --git a/scipy/linalg/lapack.py b/scipy/linalg/lapack.py
-index bc712c4ea..29d59085d 100644
---- a/scipy/linalg/lapack.py
-+++ b/scipy/linalg/lapack.py
-@@ -359,7 +359,10 @@ from .blas import _get_funcs
- # Backward compatibility:
- from .blas import find_best_blas_type as find_best_lapack_type
- 
--from scipy.linalg import _flapack
-+try:
-+    from scipy.linalg import _flapack
-+except ImportError:
-+    _flapack = None
- try:
-     from scipy.linalg import _clapack
- except ImportError:
-@@ -367,12 +370,18 @@ except ImportError:
- 
- # Backward compatibility
- from scipy._lib._util import DeprecatedImport as _DeprecatedImport
--clapack = _DeprecatedImport("scipy.linalg.blas.clapack", "scipy.linalg.lapack")
--flapack = _DeprecatedImport("scipy.linalg.blas.flapack", "scipy.linalg.lapack")
-+try:
-+    clapack = _DeprecatedImport("scipy.linalg.blas.clapack", "scipy.linalg.lapack")
-+    flapack = _DeprecatedImport("scipy.linalg.blas.flapack", "scipy.linalg.lapack")
-+except ImportError:
-+    pass
- 
- # Expose all functions (only flapack --- clapack is an implementation detail)
- empty_module = None
--from scipy.linalg._flapack import *
-+try:
-+    from scipy.linalg._flapack import *
-+except ImportError:
-+    pass
- del empty_module
- 
- _dep_message = """The `*gegv` family of routines has been deprecated in
-@@ -380,17 +389,20 @@ LAPACK 3.6.0 in favor of the `*ggev` family of routines.
- The corresponding wrappers will be removed from SciPy in
- a future release."""
- 
--cgegv = _np.deprecate(cgegv, old_name='cgegv', message=_dep_message)
--dgegv = _np.deprecate(dgegv, old_name='dgegv', message=_dep_message)
--sgegv = _np.deprecate(sgegv, old_name='sgegv', message=_dep_message)
--zgegv = _np.deprecate(zgegv, old_name='zgegv', message=_dep_message)
--
--# Modyfy _flapack in this scope so the deprecation warnings apply to
--# functions returned by get_lapack_funcs.
--_flapack.cgegv = cgegv
--_flapack.dgegv = dgegv
--_flapack.sgegv = sgegv
--_flapack.zgegv = zgegv
-+try:
-+    cgegv = _np.deprecate(cgegv, old_name='cgegv', message=_dep_message)
-+    dgegv = _np.deprecate(dgegv, old_name='dgegv', message=_dep_message)
-+    sgegv = _np.deprecate(sgegv, old_name='sgegv', message=_dep_message)
-+    zgegv = _np.deprecate(zgegv, old_name='zgegv', message=_dep_message)
-+
-+    # Modyfy _flapack in this scope so the deprecation warnings apply to
-+    # functions returned by get_lapack_funcs.
-+    _flapack.cgegv = cgegv
-+    _flapack.dgegv = dgegv
-+    _flapack.sgegv = sgegv
-+    _flapack.zgegv = zgegv
-+except Exception:
-+    pass
- 
- # some convenience alias for complex functions
- _lapack_alias = {

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

@@ -1,4 +1,4 @@
-commit 0822e53ae255433469257625e8f292abd13ae562
+commit e85d4402a802160b13e49d34728f4358e5337848
 Author: Roman Yurchak <rth.yurchak@pm.me>
 Date:   Thu Oct 11 17:10:36 2018 +0200
 
@@ -6,8 +6,22 @@ Date:   Thu Oct 11 17:10:36 2018 +0200
     
        scipy.integrate.odepack
 
+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 9d607af8d..2be454c70 100755
+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):
@@ -63,7 +77,7 @@ index 9d607af8d..2be454c70 100755
 +    #                     **lapack_opt)
  
      # dop
-     config.add_extension('_dop',
+     #config.add_extension('_dop',
 @@ -76,11 +76,11 @@ def configuration(parent_package='',top_path=None):
                           sources=quadpack_test_src)
  

test/packages/test_scipy.py

@@ -1,14 +1,7 @@
-from pathlib import Path
-import subprocess
-import sys
 from textwrap import dedent
 
 import pytest
 
-sys.path.append(str(Path(__file__).parents[2]))
-
-from pyodide_build.common import HOSTPYTHON   # noqa: E402
-
 
 def test_scipy_import(selenium_standalone, request):
     from selenium.common.exceptions import JavascriptException
@@ -41,6 +34,32 @@ def test_scipy_import(selenium_standalone, request):
     print(selenium.logs)
 
 
+def test_scipy_linalg(selenium_standalone):
+    selenium = selenium_standalone
+    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)
+
+    print(selenium.logs)
+
+
+@pytest.mark.skip
 def test_built_so(selenium_standalone):
     selenium = selenium_standalone
     selenium.load_package("scipy")
@@ -61,19 +80,11 @@ def test_built_so(selenium_standalone):
         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)}')