SciPy-bundle

Golden_Repo/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022a.eb

+easyblock = 'PythonBundle'
+
+name = 'SciPy-bundle'
+version = '2022.05'
+
+homepage = 'https://python.org/'
+description = "Bundle of Python packages for scientific software"
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+toolchainopts = {'pic': True, 'lowopt': True}
+
+builddependencies = [
+    ('hypothesis', '6.46.7'),
+    ('UnZip', '6.0'),
+]
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('pybind11', '2.9.2'),  # required by scipy
+]
+
+use_pip = True
+
+# order is important!
+exts_list = [
+    ('numpy', '1.22.3', {
+        'patches': [
+            'numpy-1.18.2-mkl.patch',
+            'numpy-1.20.3_disable_fortran_callback_test.patch',
+            'numpy-1.22.3_disable-broken-override-test.patch',
+            '%(name)s-%(version)s_skip-ppc-long-complex-test.patch',
+        ],
+        'sources': ['%(name)s-%(version)s.zip'],
+        'checksums': [
+            'dbc7601a3b7472d559dc7b933b18b4b66f9aa7452c120e87dfb33d02008c8a18',  # numpy-1.22.3.zip
+            # numpy-1.18.2-mkl.patch
+            'ea25ad5c0148c1398d282f0424e642fb9815a1a80f4512659b018e2adc378bcf',
+            # numpy-1.20.3_disable_fortran_callback_test.patch
+            '44975a944544fd0e771b7e63c32590d257a3713070f8f7fdf60105dc516f1d75',
+            # numpy-1.22.3_disable-broken-override-test.patch
+            '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c',
+            # numpy-1.22.3_skip-ppc-long-complex-test.patch
+            '058c8128b9f7158b4d5bedb2f52ccc7e1362b99c352c3d10335f98a6194c880e',
+        ],
+    }),
+    ('ply', '3.11', {
+        'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'],
+    }),
+    ('gast', '0.5.3', {
+        'checksums': ['cfbea25820e653af9c7d1807f659ce0a0a9c64f2439421a7bba4f0983f532dea'],
+    }),
+    ('beniget', '0.4.1', {
+        'checksums': ['75554b3b8ad0553ce2f607627dad3d95c60c441189875b98e097528f8e23ac0c'],
+    }),
+    ('pythran', '0.11.0', {
+        'checksums': ['0b2cba712e09f7630879dff69f268460bfe34a6d6000451b47d598558a92a875'],
+    }),
+    ('scipy', '1.8.1', {
+        # compilation with Pythran enabled fails when using Intel compilers,
+        # see https://github.com/scipy/scipy/issues/14935
+        'prebuildopts': "export SCIPY_USE_PYTHRAN=0 && ",
+        'preinstallopts': "export SCIPY_USE_PYTHRAN=0 && ",
+        'checksums': ['9e3fb1b0e896f14a85aa9a28d5f755daaeeb54c897b746df7a55ccb02b340f33'],
+    }),
+    # ('mpi4py', '3.1.3', {
+    #    'checksums': ['f1e9fae1079f43eafdd9f817cdb3fd30d709edc093b5d5dada57a461b2db3008'],
+    # }),
+    ('numexpr', '2.8.1', {
+        'checksums': ['cd779aa44dd986c4ef10163519239602b027be06a527946656207acf1f58113b'],
+    }),
+    ('Bottleneck', '1.3.4', {
+        'checksums': ['1764a7f4ad58c558723c542847eb367ab0bbb6d880a4e5d5eef30a0ece5cecea'],
+    }),
+    ('pandas', '1.4.2', {
+        'preinstallopts': """sed -i 's@extra_compile_args = \["-Werror"\]@extra_compile_args = []@g' setup.py && """,
+        'checksums': ['92bc1fc585f1463ca827b45535957815b7deb218c549b7c18402c322c7549a12'],
+    }),
+    ('mpmath', '1.2.1', {
+        'checksums': ['79ffb45cf9f4b101a807595bcb3e72e0396202e0b1d25d689134b48c4216a81a'],
+    }),
+    ('deap', '1.3.1', {
+        'patches': ['deap-1.3.1_no_2to3.patch'],
+        'checksums': [
+            '11f54493ceb54aae10dde676577ef59fc52d52f82729d5a12c90b0813c857a2f',  # deap-1.3.1.tar.gz
+            '3fa9fac74b0750ac6667371ce0634c797d62d270c76eee9c258b55f4a5a5e689',  # deap-1.3.1_no_2to3.patch
+        ],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'lang'

Golden_Repo/s/SciPy-bundle/numpy-1.18.2-mkl.patch

+fix issues in numpy distutils pkg w.r.t. detecting BLAS/LAPACK libraries
+by Kenneth Hoste (HPC-UGent)
+
+Remade against numpy-1.18.2, 20200317, Åke Sandgren (HPC2N)
+diff -ru numpy-1.18.2.orig/numpy/distutils/fcompiler/__init__.py numpy-1.18.2/numpy/distutils/fcompiler/__init__.py
+--- numpy-1.18.2.orig/numpy/distutils/fcompiler/__init__.py	2020-03-09 17:18:24.000000000 +0100
++++ numpy-1.18.2/numpy/distutils/fcompiler/__init__.py	2020-03-17 20:05:39.284278141 +0100
+@@ -637,7 +637,10 @@
+         return options
+ 
+     def library_option(self, lib):
+-        return "-l" + lib
++        if lib[0]=='-':
++            return lib
++        else:
++            return "-l" + lib
+     def library_dir_option(self, dir):
+         return "-L" + dir
+ 
+diff -ru numpy-1.18.2.orig/numpy/distutils/system_info.py numpy-1.18.2/numpy/distutils/system_info.py
+--- numpy-1.18.2.orig/numpy/distutils/system_info.py	2020-03-09 17:18:24.000000000 +0100
++++ numpy-1.18.2/numpy/distutils/system_info.py	2020-03-17 20:05:39.284278141 +0100
+@@ -831,7 +831,7 @@
+             if is_string(default):
+                 return [default]
+             return default
+-        return [b for b in [a.strip() for a in libs.split(',')] if b]
++        return [b for b in [a.strip().replace(':',',') for a in libs.split(',')] if b]
+ 
+     def get_libraries(self, key='libraries'):
+         if hasattr(self, '_lib_names'):
+@@ -918,6 +918,9 @@
+         # make sure we preserve the order of libs, as it can be important
+         found_dirs, found_libs = [], []
+         for lib in libs:
++            if lib[0] == '-':
++                found_libs.append(lib)
++                continue
+             for lib_dir in lib_dirs:
+                 found_lib = self._find_lib(lib_dir, lib, exts)
+                 if found_lib:
+diff -ru numpy-1.18.2.orig/numpy/distutils/unixccompiler.py numpy-1.18.2/numpy/distutils/unixccompiler.py
+--- numpy-1.18.2.orig/numpy/distutils/unixccompiler.py	2020-03-09 17:18:24.000000000 +0100
++++ numpy-1.18.2/numpy/distutils/unixccompiler.py	2020-03-17 20:05:39.284278141 +0100
+@@ -137,3 +137,12 @@
+ 
+ replace_method(UnixCCompiler, 'create_static_lib',
+                UnixCCompiler_create_static_lib)
++
++def UnixCCompiler_library_option(self, lib):
++    if lib[0]=='-':
++        return lib
++    else:
++        return "-l" + lib
++
++replace_method(UnixCCompiler, 'library_option',
++               UnixCCompiler_library_option)

acls.yml

@@ -813,6 +813,9 @@ software:
   - name: 'scikit-uplift'
     owner: 'strube1'
     base: True
+  - name: 'SciPy-Bundle'
+    owner: 'strube1'
+    base: True
   - name: 'SciPy-Stack'
     owner: 'strube1'
     base: True

bin/gcc11ize.py

@@ -263,6 +263,7 @@ releases = {
     'Rust':                     ['1.47.0',          '1.54.0'],
     'scikit':                   ['2021',            '2022'],
     'SciPy-Stack':              ['2021',            '2021b'],
+    'SciPy-bundle':             ['2021.10',            '22.05'],
     'Shapely':                  ['1.7.1',           '1.8.0'],
     'SuiteSparse':              ['5.7.1',           '5.10.1'],
     'snappy':                   ['1.1.8',           '1.1.9'],