More patches for ellip_harm_2.pyx that uses ctypes

.circleci/config.yml

@@ -19,6 +19,7 @@ jobs:
       - run:
            name: dependencies
            command: |
+             sudo apt-get update
              sudo apt-get install gfortran f2c
 
              # Download BLAS/LAPACK

packages/scipy/meta.yaml

@@ -22,6 +22,7 @@ source:
     - patches/skip-fortran-fails-to-link.patch
     - patches/dummy_threading.patch
     - patches/skip-blas-imports.patch
+    - patches/skip_ellip_harm_2_pyx_ctypes.patch
 
 build:
   cflags: -I../../CLAPACK-WA/INCLUDE -Wno-implicit-function-declaration

packages/scipy/patches/disable_modules_with_blas.patch

-commit 5c2a77219d5bd92c48d8d5d5e71ba28228c282a1
+commit 771537885db80fb664d5671af5048e445b6fa821
 Author: Roman Yurchak <rth.yurchak@pm.me>
 Date:   Mon Oct 8 10:53:11 2018 +0200
 
     Removes files that require LAPACK
 
-diff --git a/scipy/linalg/__init__.py b/scipy/linalg/__init__.py
-index fd02851bf..faa6723d2 100644
---- a/scipy/linalg/__init__.py
-+++ b/scipy/linalg/__init__.py
-@@ -181,13 +181,16 @@ from ._decomp_qz import *
- from .decomp_svd import *
- from .decomp_schur import *
- from ._decomp_polar import *
--from .matfuncs import *
--from .blas import *
--from .lapack import *
--from .special_matrices import *
--from ._solvers import *
--from ._procrustes import *
--from ._decomp_update import *
-+try:
-+    from .matfuncs import *
-+    from .blas import *
-+    from .lapack import *
-+    from .special_matrices import *
-+    from ._solvers import *
-+    from ._procrustes import *
-+    from ._decomp_update import *
-+except ImportError:
-+    pass
- 
- __all__ = [s for s in dir() if not s.startswith('_')]
- 
 diff --git a/scipy/linalg/setup.py b/scipy/linalg/setup.py
 index 2c9b9ba22..035b4bb80 100755
 --- a/scipy/linalg/setup.py

packages/scipy/patches/dummy_threading.patch

-commit 055d7fcf48996f9619ddd68f4ac0ccb611e8706d
+commit cfd6c4b18c5f338842d2ee509bfb2d3a3c6f6439
 Author: Roman Yurchak <rth.yurchak@pm.me>
 Date:   Mon Oct 15 15:40:48 2018 +0200
 
@@ -102,14 +102,14 @@ index ba33fadbe..644a57eaf 100644
  cimport numpy as np
  cimport cython
 diff --git a/scipy/special/_ellip_harm.py b/scipy/special/_ellip_harm.py
-index 6972c2ad1..76a828201 100644
+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_threadng as threading
++import dummy_threading as threading
  import numpy as np
  
  from ._ufuncs import _ellip_harm

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')

test/test_scipy.py → test/packages/test_scipy.py

@@ -5,7 +5,7 @@ from textwrap import dedent
 
 import pytest
 
-sys.path.append(str(Path(__file__).parents[1]))
+sys.path.append(str(Path(__file__).parents[2]))
 
 from pyodide_build.common import HOSTPYTHON   # noqa: E402
 
@@ -23,7 +23,10 @@ def test_scipy_import(selenium_standalone, request):
         """)
 
     # supported modules
-    for module in ['constants', 'fftpack', 'odr', 'sparse']:
+    for module in ['constants', 'fftpack', 'odr', 'sparse',
+                   'linalg',  # heavily patched
+                   'misc', 'ndimage', 'special'
+                   ]:
         selenium.run(f"import scipy.{module}")
 
     # not yet built modules
@@ -31,13 +34,10 @@ def test_scipy_import(selenium_standalone, request):
                    'spatial',  # needs sparse
                    'integrate',  # needs special
                    'interpolate',  # needs linalg
-                   'linalg',
-                   'misc',   # needs special
                    'signal',  # needs special
-                   'ndimage',  # needs special
                    'stats',  # need special
-                   'optimize',  # needs minpack2
-                   'special']:
+                   'optimize',  # needs _odepack
+                   ]:
         print(module)
         with pytest.raises(JavascriptException) as err:
             selenium.run(f"import scipy.{module}")