Merge pull request #16912 from boegel/20221215150042_new_pr_SciPy-bun…

…dle202211

{lang}[gfbf/2022b,foss/2022b] SciPy-bundle v2023.02, mpi4py v3.1.4, pybind11 v2.10.3, hypothesis v6.68.2 w/ Python 3.10.8

easybuild/easyconfigs/e/Eigen/Eigen-3.4.0-GCCcore-12.2.0.eb

@@ -0,0 +1,21 @@
+name = 'Eigen'
+version = '3.4.0'
+
+homepage = 'https://eigen.tuxfamily.org'
+description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers,
+ and related algorithms."""
+
+# only includes header files, but requires CMake so using non-system toolchain
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+source_urls = ['https://gitlab.com/libeigen/eigen/-/archive/%(version)s']
+sources = [SOURCELOWER_TAR_BZ2]
+checksums = ['b4c198460eba6f28d34894e3a5710998818515104d6e74e5cc331ce31e46e626']
+
+# using CMake built with GCCcore to avoid relying on the system compiler to build it
+builddependencies = [
+    ('binutils', '2.39'),  # to make CMake compiler health check pass on old systems
+    ('CMake', '3.24.3'),
+]
+
+moduleclass = 'math'

easybuild/easyconfigs/h/hypothesis/hypothesis-6.68.2-GCCcore-12.2.0.eb

@@ -0,0 +1,24 @@
+easyblock = 'PythonPackage'
+
+name = 'hypothesis'
+version = '6.68.2'
+
+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': '12.2.0'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['a7eb2b0c9a18560d8197fe35047ceb58e7e8ab7623a3e5a82613f6a2cd71cffa']
+
+builddependencies = [('binutils', '2.39')]
+
+dependencies = [('Python', '3.10.8')]
+
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+moduleclass = 'tools'

easybuild/easyconfigs/m/mpi4py/mpi4py-3.1.4-gompi-2022b.eb

@@ -0,0 +1,25 @@
+easyblock = 'PythonBundle'
+
+name = 'mpi4py'
+version = '3.1.4'
+
+homepage = 'https://github.com/mpi4py/mpi4py'
+description = """MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for
+ the Python programming language, allowing any Python program to exploit multiple processors."""
+
+toolchain = {'name': 'gompi', 'version': '2022b'}
+
+dependencies = [
+    ('Python', '3.10.8'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    (name, version, {
+        'checksums': ['17858f2ebc623220d0120d1fa8d428d033dde749c4bc35b33d81a66ad7f93480'],
+    }),
+]
+
+moduleclass = 'lib'

easybuild/easyconfigs/p/pybind11/pybind11-2.10.3-GCCcore-12.2.0.eb

@@ -0,0 +1,23 @@
+name = 'pybind11'
+version = '2.10.3'
+
+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': '12.2.0'}
+
+source_urls = ['https://github.com/pybind/pybind11/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['5d8c4c5dda428d3a944ba3d2a5212cb988c2fae4670d58075a5a49075a6ca315']
+
+builddependencies = [
+    ('binutils', '2.39'),
+    ('CMake', '3.24.3'),
+    ('Eigen', '3.4.0'),
+]
+dependencies = [('Python', '3.10.8')]
+
+configopts = "-DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python"
+
+moduleclass = 'lib'

easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb

@@ -0,0 +1,85 @@
+easyblock = 'PythonBundle'
+
+name = 'SciPy-bundle'
+version = '2023.02'
+
+homepage = 'https://python.org/'
+description = "Bundle of Python packages for scientific software"
+
+toolchain = {'name': 'gfbf', 'version': '2022b'}
+toolchainopts = {'pic': True, 'lowopt': True}
+
+builddependencies = [
+    ('hypothesis', '6.68.2'),
+    ('UnZip', '6.0'),
+    # scipy >= 1.9.0 uses Meson/Ninja
+    ('Meson', '0.64.0'),
+    ('Ninja', '1.11.1'),
+    ('pkgconf', '1.9.3'),   # required by scipy
+]
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('pybind11', '2.10.3'),  # required by scipy
+]
+
+use_pip = True
+
+# order is important!
+exts_list = [
+    ('numpy', '1.24.2', {
+        'patches': ['numpy-1.22.3_disable-broken-override-test.patch'],
+        'checksums': [
+            {'numpy-1.24.2.tar.gz': '003a9f530e880cb2cd177cba1af7220b9aa42def9c4afc2a2fc3ee6be7eb2b22'},
+            {'numpy-1.22.3_disable-broken-override-test.patch':
+             '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c'},
+        ],
+    }),
+    ('ply', '3.11', {
+        'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'],
+    }),
+    ('gast', '0.5.3', {
+        'checksums': ['cfbea25820e653af9c7d1807f659ce0a0a9c64f2439421a7bba4f0983f532dea'],
+    }),
+    ('beniget', '0.4.1', {
+        'checksums': ['75554b3b8ad0553ce2f607627dad3d95c60c441189875b98e097528f8e23ac0c'],
+    }),
+    ('pythran', '0.12.1', {
+        'checksums': ['702c2701187cfb38f66c0c20cc85d04d0e156d260a8d92892da65947faa5360e'],
+    }),
+    ('scipy', '1.10.1', {
+        'patches': [
+            'scipy-1.10.1_disable-tests.patch',
+            'scipy-1.10.1_xfail-aarch64_test_maxiter_worsening.patch',
+        ],
+        'checksums': [
+            {'scipy-1.10.1.tar.gz': '2cf9dfb80a7b4589ba4c40ce7588986d6d5cebc5457cad2c2880f6bc2d42f3a5'},
+            {'scipy-1.10.1_disable-tests.patch': '5d36d416fb7ea9297514c3988d9f506793e39dc4c0daedccf6733c3dd7e3dcc0'},
+            {'scipy-1.10.1_xfail-aarch64_test_maxiter_worsening.patch':
+             '48177d6af51cf3e3d46aed8425807f0a65a498f7558f475032e0ad846559a23e'},
+        ],
+        'enable_slow_tests': True,
+        'ignore_test_result': False,
+    }),
+    ('numexpr', '2.8.4', {
+        'checksums': ['d5432537418d18691b9115d615d6daa17ee8275baef3edf1afbbf8bc69806147'],
+    }),
+    ('Bottleneck', '1.3.5', {
+        'checksums': ['2c0d27afe45351f6f421893362621804fa7dea14fe29a78eaa52d4323f646de7'],
+    }),
+    ('pandas', '1.5.3', {
+        'preinstallopts': "export PANDAS_CI=0 && ",
+        'checksums': ['74a3fd7e5a7ec052f183273dc7b0acd3a863edf7520f5d3a1765c04ffdb3b0b1'],
+    }),
+    ('mpmath', '1.2.1', {
+        'checksums': ['79ffb45cf9f4b101a807595bcb3e72e0396202e0b1d25d689134b48c4216a81a'],
+    }),
+    ('deap', '1.3.3', {
+        'checksums': ['8772f1b0fff042d5e516b0aebac2c706243045aa7d0de8e0b8658f380181cf31'],
+        'modulename': 'deap.base',
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'lang'

easybuild/easyconfigs/s/SciPy-bundle/scipy-1.10.1_disable-tests.patch

@@ -0,0 +1,41 @@
+disable problematic tests
+test_milp_timeout_16545 fails intermittently, known issue - see https://github.com/scipy/scipy/issues/17137
+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)
+diff -ru scipy-1.10.1.orig/scipy/optimize/tests/test_milp.py scipy-1.10.1/scipy/optimize/tests/test_milp.py
+--- scipy-1.10.1.orig/scipy/optimize/tests/test_milp.py	1970-01-01 01:00:00.000000000 +0100
++++ scipy-1.10.1/scipy/optimize/tests/test_milp.py	2023-02-25 15:43:57.780477222 +0100
+@@ -283,7 +283,7 @@
+ @pytest.mark.timeout(360)
+ @pytest.mark.parametrize(["options", "msg"], [({"time_limit": 10}, _msg_time),
+                                               ({"node_limit": 1}, _msg_iter)])
+-def test_milp_timeout_16545(options, msg):
++def disabled_test_milp_timeout_16545(options, msg):
+     # Ensure solution is not thrown away if MILP solver times out
+     # -- see gh-16545
+     rng = np.random.default_rng(5123833489170494244)
+diff -ru scipy-1.10.1.orig/scipy/sparse/linalg/_eigen/arpack/tests/test_arpack.py scipy-1.10.1/scipy/sparse/linalg/_eigen/arpack/tests/test_arpack.py
+--- scipy-1.10.1.orig/scipy/sparse/linalg/_eigen/arpack/tests/test_arpack.py	1970-01-01 01:00:00.000000000 +0100
++++ scipy-1.10.1/scipy/sparse/linalg/_eigen/arpack/tests/test_arpack.py	2023-02-25 15:44:06.220493384 +0100
+@@ -418,7 +418,7 @@
+                                       None, sigma, mattype, None, mode)
+
+
+-def test_hermitian_modes():
++def disabled_test_hermitian_modes():
+     params = SymmetricParams()
+     k = 2
+     symmetric = True
+diff -ru scipy-1.10.1.orig/scipy/sparse/tests/test_construct.py scipy-1.10.1/scipy/sparse/tests/test_construct.py
+--- scipy-1.10.1.orig/scipy/sparse/tests/test_construct.py	1970-01-01 01:00:00.000000000 +0100
++++ scipy-1.10.1/scipy/sparse/tests/test_construct.py	2023-02-25 15:44:25.259531626 +0100
+@@ -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-1.10.1_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)
+diff -ru scipy-1.10.1.orig/scipy/sparse/linalg/_isolve/tests/test_iterative.py scipy-1.10.1/scipy/sparse/linalg/_isolve/tests/test_iterative.py
+--- scipy-1.10.1.orig/scipy/sparse/linalg/_isolve/tests/test_iterative.py	1970-01-01 00:00:00.000000000 +0000
++++ scipy-1.10.1/scipy/sparse/linalg/_isolve/tests/test_iterative.py	2023-02-25 17:18:12.432151563 +0000
+@@ -451,7 +451,7 @@
+
+ @pytest.mark.parametrize("solver", [
+     pytest.param(gmres, marks=pytest.mark.xfail(platform.machine() == 'aarch64'
+-                                                and sys.version_info[1] == 9,
++                                                and sys.version_info[1] >= 9,
+                                                 reason="gh-13019")),
+     qmr,
+     pytest.param(lgmres, marks=pytest.mark.xfail(