{lang,lib,tools}[gfbf/2023a] SciPy-bundle v2023.07, hypothesis v6.82.0, pybind11 v2.11.1

easybuild/easyconfigs/h/hypothesis/hypothesis-6.82.0-GCCcore-12.3.0.eb

@@ -0,0 +1,27 @@
+easyblock = 'PythonPackage'
+
+name = 'hypothesis'
+version = '6.82.0'
+
+homepage = "https://github.com/HypothesisWorks/hypothesis"
+description = """Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized
+ by a source of examples, and then generates simple and comprehensible examples that make your tests fail. This lets
+ you find more bugs in your code with less work."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['ffece8e40a34329e7112f7408f2c45fe587761978fdbc6f4f91bf0d683a7d4d9']
+
+builddependencies = [('binutils', '2.40')]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),  # required for attrs, sortedcontainers
+]
+
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+moduleclass = 'tools'

easybuild/easyconfigs/p/pybind11/pybind11-2.11.1-GCCcore-12.3.0.eb

@@ -0,0 +1,26 @@
+name = 'pybind11'
+version = '2.11.1'
+
+homepage = 'https://pybind11.readthedocs.io'
+description = """pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa,
+ mainly to create Python bindings of existing C++ code."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://github.com/pybind/pybind11/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['d475978da0cdc2d43b73f30910786759d593a9d8ee05b1b6846d1eb16c6d2e0c']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.26.3'),
+    ('Eigen', '3.4.0'),
+    ('Python-bundle-PyPI', '2023.06'),  # to provide pytest
+]
+dependencies = [
+    ('Python', '3.11.3'),
+]
+
+configopts = "-DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python"
+
+moduleclass = 'lib'

easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-gfbf-2023a.eb

@@ -0,0 +1,92 @@
+easyblock = 'PythonBundle'
+
+name = 'SciPy-bundle'
+version = '2023.07'
+
+homepage = 'https://python.org/'
+description = "Bundle of Python packages for scientific software"
+
+toolchain = {'name': 'gfbf', 'version': '2023a'}
+toolchainopts = {'pic': True, 'lowopt': True}
+
+builddependencies = [
+    ('hypothesis', '6.82.0'),
+    ('UnZip', '6.0'),
+    # scipy >= 1.9.0 uses Meson/Ninja
+    ('Meson', '1.1.1'),
+    ('Ninja', '1.11.1'),
+    ('pkgconf', '1.9.5'),   # required by scipy
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('pybind11', '2.11.1'),  # required by scipy
+]
+
+use_pip = True
+
+# order is important!
+exts_list = [
+    ('numpy', '1.25.1', {
+        'patches': ['numpy-1.22.3_disable-broken-override-test.patch'],
+        'checksums': [
+            {'numpy-1.25.1.tar.gz': '9a3a9f3a61480cc086117b426a8bd86869c213fc4072e606f01c4e4b66eb92bf'},
+            {'numpy-1.22.3_disable-broken-override-test.patch':
+             '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c'},
+        ],
+    }),
+    ('ply', '3.11', {
+        'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'],
+    }),
+    ('gast', '0.5.4', {
+        'checksums': ['9c270fe5f4b130969b54174de7db4e764b09b4f7f67ccfc32480e29f78348d97'],
+    }),
+    ('beniget', '0.4.1', {
+        'checksums': ['75554b3b8ad0553ce2f607627dad3d95c60c441189875b98e097528f8e23ac0c'],
+    }),
+    ('pythran', '0.13.1', {
+        'checksums': ['8aad08162f010e5425a7b254dd68d83311b430bb29f9252dce2eff3ba39497dd'],
+    }),
+    ('versioneer', '0.29', {
+        'checksums': ['5ab283b9857211d61b53318b7c792cf68e798e765ee17c27ade9f6c924235731'],
+    }),
+    ('scipy', '1.11.1', {
+        'patches': [
+            'scipy-1.11.1_disable-tests.patch',
+            'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch',
+        ],
+        'checksums': [
+            {'scipy-1.11.1.tar.gz': 'fb5b492fa035334fd249f0973cc79ecad8b09c604b42a127a677b45a9a3d4289'},
+            {'scipy-1.11.1_disable-tests.patch': '906bfb03397d94882ccdc1b93bc2c8e854e0e060c2d107c83042992394e6a4af'},
+            {'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch':
+             '918c8e6fa8215d459126f267764c961bde729ea4a116c7f6287cddfdc58ffcea'},
+        ],
+        'enable_slow_tests': True,
+        'ignore_test_result': False,
+    }),
+    ('numexpr', '2.8.4', {
+        'checksums': ['d5432537418d18691b9115d615d6daa17ee8275baef3edf1afbbf8bc69806147'],
+    }),
+    ('Bottleneck', '1.3.7', {
+        'checksums': ['e1467e373ad469da340ed0ff283214d6531cc08bfdca2083361a3aa6470681f8'],
+    }),
+    ('tzdata', '2023.3', {
+        'checksums': ['11ef1e08e54acb0d4f95bdb1be05da659673de4acbd21bf9c69e94cc5e907a3a'],
+    }),
+    ('pandas', '2.0.3', {
+        'preinstallopts': "export PANDAS_CI=0 && ",
+        'checksums': ['c02f372a88e0d17f36d3093a644c73cfc1788e876a7c4bcb4020a77512e2043c'],
+    }),
+    ('mpmath', '1.3.0', {
+        'checksums': ['7a28eb2a9774d00c7bc92411c19a89209d5da7c4c9a9e227be8330a23a25b91f'],
+    }),
+    ('deap', '1.4.0', {
+        'checksums': ['ffef2921932a0edbe634fcb6d156189e7a364bf638a2af4ae5d59931a9a4c8cc'],
+        'modulename': 'deap.base',
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'lang'

easybuild/easyconfigs/s/SciPy-bundle/scipy-1.11.1_disable-tests.patch

@@ -0,0 +1,26 @@
+disable problematic tests
+test_hermitian_modes fails with order of magnitude difference
+test_concatenate_int32_overflow fails if not enough memory is available
+author: Kenneth Hoste (HPC-UGent) + Simon Branford (University of Birmingham) + Sebastian Achilles (Juelich Supercomputing Centre)
+diff -ru scipy-1.11.1.orig/scipy/sparse/linalg/_eigen/arpack/tests/test_arpack.py scipy-1.11.1/scipy/sparse/linalg/_eigen/arpack/tests/test_arpack.py
+--- scipy-1.11.1.orig/scipy/sparse/linalg/_eigen/arpack/tests/test_arpack.py    2023-07-28 07:18:00.383649919 +0000
++++ scipy-1.11.1/scipy/sparse/linalg/_eigen/arpack/tests/test_arpack.py 2023-07-28 07:19:08.646148457 +0000
+@@ -410,7 +410,7 @@
+                                       None, sigma, mattype, None, mode)
+
+
+-def test_hermitian_modes():
++def disable_test_hermitian_modes():
+     params = SymmetricParams()
+     k = 2
+     symmetric = True
+diff -ru scipy-1.11.1.orig/scipy/sparse/tests/test_construct.py scipy-1.11.1/scipy/sparse/tests/test_construct.py      --- scipy-1.11.1.orig/scipy/sparse/tests/test_construct.py      2023-07-28 07:18:00.387649832 +0000
++++ scipy-1.11.1/scipy/sparse/tests/test_construct.py   2023-07-29 17:59:26.471992100 +0000
+@@ -446,7 +446,7 @@
+
+     @pytest.mark.slow
+     @pytest.mark.xfail_on_32bit("Can't create large array for test")
+-    def test_concatenate_int32_overflow(self):
++    def disable_test_concatenate_int32_overflow(self):
+         """ test for indptr overflow when concatenating matrices """
+         check_free_memory(30000)

easybuild/easyconfigs/s/SciPy-bundle/scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch

@@ -0,0 +1,15 @@
+also xfail test_maxiter_worsening for Python 3.10 on aarch64
+see also https://github.com/scipy/scipy/issues/13019 + https://github.com/scipy/scipy/pull/13022
+author: Kenneth Hoste (HPC-UGent) + Sebastian Achilles (Juelich Supercomputing Centre)
+diff -ru scipy-1.11.1.orig/scipy/sparse/linalg/_isolve/tests/test_iterative.py scipy-1.11.1/scipy/sparse/linalg/_isolve/tests/test_iterative.py
+--- scipy-1.11.1.orig/scipy/sparse/linalg/_isolve/tests/test_iterative.py       2023-07-28 07:18:00.387649832 +0000
++++ scipy-1.11.1/scipy/sparse/linalg/_isolve/tests/test_iterative.py    2023-07-29 18:17:22.432356816 +0000
+@@ -465,7 +465,7 @@
+     # which they should detect and halt as necessary.
+     # cf. gh-9100
+     if (solver is gmres and platform.machine() == 'aarch64'
+-            and sys.version_info[1] == 9):
++            and sys.version_info[1] >= 9):
+         pytest.xfail(reason="gh-13019")
+     if (solver is lgmres and
+             platform.machine() not in ['x86_64' 'x86', 'aarch64', 'arm64']):