Better refactoring

.circleci/config.yml

@@ -19,6 +19,7 @@ jobs:
       - run:
            name: dependencies
            command: |
+             # TODO: update pyodide-env image with the below
              sudo apt-get update
              sudo apt-get install gfortran f2c
 

Makefile

@@ -215,10 +215,6 @@ $(CLAPACK): $(CPYTHONLIB)
 	make -C CLAPACK
 
 
-$(CLAPACK): $(CPYTHONLIB)
-	make -C CLAPACK
-
-
 build/packages.json: $(CPYTHONLIB) $(CLAPACK)
 	make -C packages
 

packages/Makefile

@@ -5,7 +5,7 @@ all: deps
 	../bin/pyodide buildall . ../build \
 		--ldflags="$(SIDE_LDFLAGS)" --host=$(HOSTPYTHONROOT) --target=$(TARGETPYTHONROOT)
 deps:
-	# Temporary workaround to install build dependencies
+	# Install build dependencies
 	$(HOSTPYTHON) -m pip install Cython Tempita
 
 clean:

packages/scipy/meta.yaml

@@ -22,7 +22,6 @@ source:
     - patches/skip-fortran-fails-to-link.patch
     - patches/dummy_threading.patch
     - patches/skip_ellip_harm_2_pyx_ctypes.patch
-    - patches/skip_optimize_cobyla_import.patch
     - patches/fix_mmap.patch
 
 build:

packages/scipy/patches/force_malloc.patch

-commit d755dab2147732e9213af29f55ab38c38b7ba8d2
+commit 7a5b003922134abd01ae33b0a3e84d006673e9c6
 Author: Roman Yurchak <rth.yurchak@pm.me>
 Date:   Mon Oct 8 12:13:55 2018 +0200
 
-    Force malloc
+    Workaround for malloc issues
     
     This aims to avoid the "invalid call target: $_malloc" issues
     
@@ -42,6 +42,20 @@ index 17ba78371..5deca7498 100644
  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

packages/scipy/patches/skip_optimize_cobyla_import.patch

-commit ca74a1078c3955b06d1ab236bdd13256cb7c2551
-Author: Roman Yurchak <rth.yurchak@pm.me>
-Date:   Thu Oct 25 12:43:50 2018 +0200
-
-    Skip scipy.optimize._cobyla import
-
-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
- 
- 

pyodide_build/pywasmcross.py

@@ -238,7 +238,6 @@ def handle_command(line, args, dryrun=False):
 
     lapack_dir = None
 
-    # rebuild = False
     # Go through and adjust arguments
     for arg in line[1:]:
         if arg.startswith('-I'):
@@ -263,19 +262,11 @@ def handle_command(line, args, dryrun=False):
 
         # Fix for scipy to link to the correct BLAS/LAPACK files
         if arg.startswith('-L') and 'CLAPACK-WA' in arg:
-            # rebuild = True
             out_idx = line.index('-o')
             out_idx += 1
             module_name = line[out_idx]
             module_name = Path(module_name).name.split('.')[0]
 
-            if module_name not in ['_fblas', '_flapack', '_flinalg',
-                                   '_calc_lwork', 'cython_blas',
-                                   'cython_lapack', '_iterative',
-                                   '_arpack']:
-                raise ValueError(f"Unsupported module requiring BLAS/LAPACK "
-                                 f"{module_name} in {' '.join(line)}")
-
             lapack_dir = arg.replace('-L', '')
             # For convinience we determine needed scipy link libraries
             # here, instead of in patch files
@@ -288,9 +279,10 @@ def handle_command(line, args, dryrun=False):
                 arg = os.path.join(lapack_dir, f"{lib_name}")
                 new_args.append(arg)
 
-            new_args.extend(['-s', 'INLINING_LIMIT=5', '--llvm-lto', '1'])
+            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')
@@ -300,7 +292,7 @@ def handle_command(line, args, dryrun=False):
 
     # This can only be used for incremental rebuilds -- it generates
     # an error during clean build of numpy
-    # if os.path.isfile(output) and not rebuild:
+    # if os.path.isfile(output):
     #     print('SKIPPING: ' + ' '.join(new_args))
     #     return