{lang}[iimkl/2025b] SciPy-bundle v2025.07

easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2025.07-iimkl-2025b.eb

@@ -0,0 +1,112 @@
+easyblock = 'PythonBundle'
+
+name = 'SciPy-bundle'
+version = '2025.07'
+
+homepage = 'https://python.org/'
+description = "Bundle of Python packages for scientific software"
+
+toolchain = {'name': 'iimkl', 'version': '2025b'}
+toolchainopts = {'pic': True, 'lowopt': True, 'strict': True,
+                 # '-fveclib=none' to avoid 'undefined symbol: pow8_h' in numpy
+                 # see https://github.com/numpy/numpy/issues/27111
+                 # '-mllvm -disable-hir-backward-temp-dependencies-resolver' to avoid AVX2 failure in numpy build
+                 # see https://github.com/numpy/numpy/issues/29679
+                 'extra_cflags': '-fveclib=none -mllvm -disable-hir-backward-temp-dependencies-resolver'}
+
+builddependencies = [
+    ('hypothesis', '6.136.6'),
+    ('UnZip', '6.0'),
+    # scipy >= 1.9.0 uses Meson/Ninja
+    ('Meson', '1.8.2'),
+    ('meson-python', '0.18.0'),
+    ('Ninja', '1.13.0'),
+    ('pkgconf', '2.4.3'),  # required by scipy
+    ('Cython', '3.1.2'),  # required by numpy and scipy
+    ('pybind11', '3.0.0'),  # required by scipy
+    ('spin', '0.14'),  # required for testing numpy
+]
+
+dependencies = [
+    ('Python', '3.13.5'),
+    ('Python-bundle-PyPI', '2025.07'),
+]
+
+# order is important!
+exts_list = [
+    ('numpy', '2.3.2', {
+        'patches': ['numpy-1.22.3_disable-broken-override-test.patch',
+                    'numpy-2.3.2_fix_selected_kind_for_ifort.patch'],
+        'checksums': [
+            {'numpy-2.3.2.tar.gz': 'e0486a11ec30cdecb53f184d496d1c6a20786c81e55e41640270130056f8ee48'},
+            {'numpy-1.22.3_disable-broken-override-test.patch':
+             '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c'},
+            {'numpy-2.3.2_fix_selected_kind_for_ifort.patch':
+             '765cd11029acb97729d072171b3c9919bb0b09e6e0ea5134fd3d779de23f1a03'},
+        ],
+    }),
+    ('ply', '3.11', {
+        'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'],
+    }),
+    ('gast', '0.6.0', {
+        'checksums': ['88fc5300d32c7ac6ca7b515310862f71e6fdf2c029bbec7c66c0f5dd47b6b1fb'],
+    }),
+    ('beniget', '0.4.2.post1', {
+        'checksums': ['a0258537e65e7e14ec33a86802f865a667f949bb6c73646d55e42f7c45a052ae'],
+    }),
+    ('pythran', '0.18.0', {
+        'checksums': ['5c003e8cbedf6dbb68c2869c49fc110ce8b5e8982993078a4a819f1dadc4fc6a'],
+    }),
+    ('versioneer', '0.29', {
+        'checksums': ['5ab283b9857211d61b53318b7c792cf68e798e765ee17c27ade9f6c924235731'],
+    }),
+    ('scipy', '1.16.1', {
+        'enable_slow_tests': True,
+        'ignore_test_result': False,
+        'patches': [
+            'scipy-1.11.1_disable-tests.patch',
+            'scipy-1.16.0_skip-tests-broken-grace.patch',
+            'scipy-1.16.0_relax-tests-broken-neoverse-v1.patch',
+            'scipy-1.16.0_remove-float16-differentiate-test.patch',
+            'scipy-1.16.1_bump-orth-memory-efficiency-tolerance.patch',
+            'scipy-1.16.1_relax-tolerance.patch',
+        ],
+        'checksums': [
+            {'scipy-1.16.1.tar.gz': '44c76f9e8b6e8e488a586190ab38016e4ed2f8a038af7cd3defa903c0a2238b3'},
+            {'scipy-1.11.1_disable-tests.patch': '906bfb03397d94882ccdc1b93bc2c8e854e0e060c2d107c83042992394e6a4af'},
+            {'scipy-1.16.0_skip-tests-broken-grace.patch':
+             '33885518a572f843a0edeb7a58aa938202aae70267f6de1ce60acef97f393126'},
+            {'scipy-1.16.0_relax-tests-broken-neoverse-v1.patch':
+             'a72d794b95dc437c03b323f86392b264c7ecfdbfa19e3bc01fba8d5d3ab2f21a'},
+            {'scipy-1.16.0_remove-float16-differentiate-test.patch':
+             'f857fc1e941c196285f2e871e803cf463fc59c040dd2955deda1dd277d4b00db'},
+            {'scipy-1.16.1_bump-orth-memory-efficiency-tolerance.patch':
+             '1eb58b162d04cbf957979897966bfcf318f05a2bdbb61f0b47c0b3881910b354'},
+            {'scipy-1.16.1_relax-tolerance.patch': 'd78b91cd896951cea39f194a64e9f88bb696f2cb805915b34c9021dd186e3de3'},
+        ],
+    }),
+    ('numexpr', '2.11.0', {
+        # workaround for: ValueError: invalid pyproject.toml config: project.license
+        'preinstallopts': "sed -i '/^license =/d' pyproject.toml && ",
+        'checksums': ['75b2c01a4eda2e7c357bc67a3f5c3dd76506c15b5fd4dc42845ef2e182181bad'],
+    }),
+    ('bottleneck', '1.5.0', {
+        'checksums': ['c860242cf20e69d5aab2ec3c5d6c8c2a15f19e4b25b28b8fca2c2a12cefae9d8'],
+    }),
+    ('tzdata', '2025.2', {
+        'checksums': ['b60a638fcc0daffadf82fe0f57e53d06bdec2f36c4df66280ae79bce6bd6f2b9'],
+    }),
+    ('pandas', '2.3.1', {
+        'preinstallopts': "export PANDAS_CI=0 && ",
+        'checksums': ['0a95b9ac964fe83ce317827f80304d37388ea77616b1425f0ae41c9d2d0d7bb2'],
+    }),
+    ('mpmath', '1.3.0', {
+        'checksums': ['7a28eb2a9774d00c7bc92411c19a89209d5da7c4c9a9e227be8330a23a25b91f'],
+    }),
+    ('deap', '1.4.3', {
+        'modulename': 'deap.base',
+        'checksums': ['7c97088fb05835bdc255bec475cb0e778de2b43e44cbefbf2bcd655aeec865fd'],
+    }),
+]
+
+moduleclass = 'lang'

easybuild/easyconfigs/s/SciPy-bundle/numpy-2.3.2_fix_selected_kind_for_ifort.patch

@@ -0,0 +1,68 @@
+Intel Fortran compiler does not support 10-byte reals, nor 16-byte integers.
+The f2py module needs to know the supported types to reliably build Fortran extensions.
+
+This patch was inspired by the discussion at https://github.com/numpy/numpy/issues/13053
+in particular the comments at
+  https://github.com/numpy/numpy/issues/13053#issuecomment-470314843
+and 
+  https://github.com/numpy/numpy/issues/13053#issuecomment-471008975
+by GitHub user @oleksandr-pavlyk
+
+Author: Jakob Schiotz (Tech. U. Denmark)  <schiotz@fysik.dtu.dk>
+Updated: Simon Branford (University of Birmingham)
+
+--- numpy/f2py/crackfortran.py.old	2023-10-23 14:39:51.510964440 +0200
++++ numpy/f2py/crackfortran.py	2023-10-23 15:10:21.963115914 +0200
+@@ -2407,7 +2407,8 @@
+     return 'kind(' + string + ')'
+
+
+-def _selected_int_kind_func(r):
++def _selected_int_kind_func_intel(r):
++    # Intel(R) Fortran compiler only supports kinds 1, 2, 4, 8.
+     # XXX: This should be processor dependent
+     m = 10 ** r
+     if m <= 2 ** 8:
+@@ -2418,29 +2419,31 @@
+         return 4
+     if m <= 2 ** 63:
+         return 8
+-    if m <= 2 ** 128:
+-        return 16
++    # Not supported by ifort
++    #if m <= 2 ** 128:
++    #    return 16
+     return -1
+
+
+-def _selected_real_kind_func(p, r=0, radix=0):
++_selected_int_kind_func = _selected_int_kind_func_intel
++
++
++def _selected_real_kind_func_intel(p, r=0, radix=0):
++    # Intel(R) Fotran compiler only supports kinds 4, 8, 16
+     # XXX: This should be processor dependent
+-    # This is only verified for 0 <= p <= 20, possibly good for p <= 33 and above
++    # This is only good for 0 <= p <= 20
+     if p < 7:
+         return 4
+     if p < 16:
+         return 8
+-    machine = platform.machine().lower()
+-    if machine.startswith(('aarch64', 'alpha', 'arm64', 'loongarch', 'mips', 'power', 'ppc', 'riscv', 's390x', 'sparc')):
+-        if p <= 33:
+-            return 16
+-    elif p < 19:
+-        return 10
+-    elif p <= 33:
++    if p <= 33:
+         return 16
+     return -1
+
+
++_selected_real_kind_func = _selected_real_kind_func_intel
++
++
+ def get_parameters(vars, global_params={}):
+     params = copy.copy(global_params)
+     g_params = copy.copy(global_params)

easybuild/easyconfigs/s/SciPy-bundle/scipy-1.16.1_relax-tolerance.patch

@@ -0,0 +1,22 @@
+Relax tolerance for the following with Intel oneAPI: TestBatch.test_solve and TestBatch.test_lu_solve
+Patch by Simon Branford (University of Birmingham)
+--- scipy/linalg/tests/test_batch.py.orig	2025-09-09 14:48:42.485545000 +0100
++++ scipy/linalg/tests/test_batch.py	2025-09-09 14:48:54.003644602 +0100
+@@ -445,7 +445,7 @@
+         if len(bdim) == 1:
+             x = x[..., np.newaxis]
+             b = b[..., np.newaxis]
+-        assert_allclose(A @ x - b, 0, atol=1.5e-6)
++        assert_allclose(A @ x - b, 0, atol=1.7e-6)
+         assert_allclose(x, np.linalg.solve(A, b), atol=3e-6)
+
+     @pytest.mark.parametrize('bdim', [(5,), (5, 4), (2, 3, 5, 4)])
+@@ -459,7 +459,7 @@
+         if len(bdim) == 1:
+             x = x[..., np.newaxis]
+             b = b[..., np.newaxis]
+-        assert_allclose(A @ x - b, 0, atol=1.5e-6)
++        assert_allclose(A @ x - b, 0, atol=1.7e-6)
+         assert_allclose(x, np.linalg.solve(A, b), atol=3e-6)
+
+     @pytest.mark.parametrize('l_and_u', [(1, 1), ([2, 1, 0], [0, 1 , 2])])