{lang}[foss/2021.04] SciPy-bundle v2021.05

easybuild/easyconfigs/h/hypothesis/hypothesis-6.13.1-GCCcore-10.3.0.eb

@@ -0,0 +1,24 @@
+easyblock = 'PythonPackage'
+
+name = 'hypothesis'
+version = '6.13.1'
+
+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': '10.3.0'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['074e27e514b305ba0b0c6bc0037faad1abbe2ea641ab4a8ec90e12a5e3238009']
+
+builddependencies = [('binutils', '2.36.1')]
+
+dependencies = [('Python', '3.9.5')]
+
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+moduleclass = 'tools'

easybuild/easyconfigs/p/pybind11/pybind11-2.6.2-GCCcore-10.3.0.eb

@@ -0,0 +1,23 @@
+name = 'pybind11'
+version = '2.6.2'
+
+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': '10.3.0'}
+
+source_urls = ['https://github.com/pybind/pybind11/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['8ff2fff22df038f5cd02cea8af56622bc67f5b64534f1b83b9f133b8366acff2']
+
+builddependencies = [
+    ('binutils', '2.36.1'),
+    ('CMake', '3.20.1'),
+    ('Eigen', '3.3.9'),
+]
+dependencies = [('Python', '3.9.5')]
+
+configopts = "-DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python"
+
+moduleclass = 'lib'

easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-foss-2021.04.eb

@@ -0,0 +1,62 @@
+easyblock = 'PythonBundle'
+
+name = 'SciPy-bundle'
+version = '2021.05'
+
+homepage = 'https://python.org/'
+description = "Bundle of Python packages for scientific software"
+
+toolchain = {'name': 'foss', 'version': '2021.04'}
+toolchainopts = {'pic': True, 'lowopt': True}
+
+builddependencies = [('hypothesis', '6.13.1')]
+
+dependencies = [
+    ('Python', '3.9.5'),
+    ('pybind11', '2.6.2'),  # required by scipy
+]
+
+use_pip = True
+
+# order is important!
+exts_list = [
+    ('numpy', '1.20.3', {
+        'sources': [SOURCE_ZIP],
+        'patches': [
+            'numpy-1.20.3_skip-ppc-long-complex-test.patch',
+            'numpy-1.20.3_xfail-test-nan.patch',
+        ],
+        'checksums': [
+            'e55185e51b18d788e49fe8305fd73ef4470596b33fc2c1ceb304566b99c71a69',  # numpy-1.20.3.zip
+            # numpy-1.20.3_skip-ppc-long-complex-test.patch
+            '2f9a12e3a352b39076db84a7622fc8f4796abd3cb7f97f71958a495e864659a4',
+            'f0ce961f7d79551598e23050d92f46e827e300f6a7e5a6112e58efcc10385d4d',  # numpy-1.20.3_xfail-test-nan.patch
+        ],
+    }),
+    ('scipy', '1.6.3', {
+        'checksums': ['a75b014d3294fce26852a9d04ea27b5671d86736beb34acdfc05859246260707'],
+    }),
+    ('mpi4py', '3.0.3', {
+        'checksums': ['012d716c8b9ed1e513fcc4b18e5af16a8791f51e6d1716baccf988ad355c5a1f'],
+    }),
+    ('numexpr', '2.7.3', {
+        'checksums': ['43616529f9b7d1afc83386f943dc66c4da5e052f00217ba7e3ad8dd1b5f3a825'],
+    }),
+    ('Bottleneck', '1.3.2', {
+        'checksums': ['20179f0b66359792ea283b69aa16366419132f3b6cf3adadc0c48e2e8118e573'],
+    }),
+    ('pandas', '1.2.4', {
+        'preinstallopts': """sed -i 's@extra_compile_args = \["-Werror"\]@extra_compile_args = []@g' setup.py && """,
+        'checksums': ['649ecab692fade3cbfcf967ff936496b0cfba0af00a55dfaacd82bdda5cb2279'],
+    }),
+    ('mpmath', '1.2.1', {
+        'checksums': ['79ffb45cf9f4b101a807595bcb3e72e0396202e0b1d25d689134b48c4216a81a'],
+    }),
+    ('deap', '1.3.1', {
+        'checksums': ['11f54493ceb54aae10dde676577ef59fc52d52f82729d5a12c90b0813c857a2f'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'lang'

easybuild/easyconfigs/s/SciPy-bundle/numpy-1.20.3_skip-ppc-long-complex-test.patch

@@ -0,0 +1,37 @@
+Include a PPC detection for the inaccurate trig functions
+See https://github.com/numpy/numpy/issues/15763
+
+Author: Alexander Grund (TU Dresden), ported to numpy 1.20.3 by Kenneth Hoste (HPC-UGent)
+
+--- numpy-1.20.3/numpy/core/tests/test_umath.py.orig	2021-05-23 16:30:32.532283122 +0200
++++ numpy-1.20.3/numpy/core/tests/test_umath.py	2021-05-23 16:35:26.122552207 +0200
+@@ -23,20 +23,25 @@
+
+
+ def bad_arcsinh():
+-    """The blocklisted trig functions are not accurate on aarch64 for
++    """The blocklisted trig functions are not accurate on aarch64/PPC for
+     complex256. Rather than dig through the actual problem skip the
+     test. This should be fixed when we can move past glibc2.17
+     which is the version in manylinux2014
+     """
+-    x = 1.78e-10
++    if platform.machine() == 'aarch64':
++        x = 1.78e-10
++    elif on_powerpc():
++        x = 2.16e-10
++    else:
++        return False
+     v1 = np.arcsinh(np.float128(x))
+     v2 = np.arcsinh(np.complex256(x)).real
+     # The eps for float128 is 1-e33, so this is way bigger
+     return abs((v1 / v2) - 1.0) > 1e-23
+
+-if platform.machine() == 'aarch64' and bad_arcsinh():
++if bad_arcsinh():
+     skip_longcomplex_msg = ('Trig functions of np.longcomplex values known to be '
+-                            'inaccurate on aarch64 for some compilation '
++                            'inaccurate on aarch64 and PPC for some compilation '
+                             'configurations, should be fixed by building on a '
+                             'platform using glibc>2.17')
+ else:

easybuild/easyconfigs/s/SciPy-bundle/numpy-1.20.3_xfail-test-nan.patch

@@ -0,0 +1,57 @@
+mark test_nan as expected failure (xfail), see https://github.com/numpy/numpy/issues/18914
+and https://github.com/numpy/numpy/pull/18943
+
+From acf249e0c663f148ee6389327f0b35298fc14833 Mon Sep 17 00:00:00 2001
+From: Ralf Gommers <[email protected]>
+Date: Sat, 8 May 2021 14:52:03 +0200
+Subject: [PATCH] TST: xfail `TestCond.test_nan` unconditionally
+
+This is happening on too many build configurations, and it's not
+completely clear if it's just an OpenBLAS version or also depends
+on something else. Reported as happening mostly on macOS, but
+also on Fedora.
+---
+ numpy/linalg/tests/test_linalg.py | 9 ++++++---
+ 1 file changed, 6 insertions(+), 3 deletions(-)
+
+diff --git a/numpy/linalg/tests/test_linalg.py b/numpy/linalg/tests/test_linalg.py
+index 8a270f194147..c6e8cdd039f1 100644
+--- a/numpy/linalg/tests/test_linalg.py
++++ b/numpy/linalg/tests/test_linalg.py
+@@ -684,7 +684,7 @@ def hermitian(mat):
+             axes = list(range(mat.ndim))
+             axes[-1], axes[-2] = axes[-2], axes[-1]
+             return np.conj(np.transpose(mat, axes=axes))
+-        
++
+         assert_almost_equal(np.matmul(u, hermitian(u)), np.broadcast_to(np.eye(u.shape[-1]), u.shape))
+         assert_almost_equal(np.matmul(vt, hermitian(vt)), np.broadcast_to(np.eye(vt.shape[-1]), vt.shape))
+         assert_equal(np.sort(s)[..., ::-1], s)
+@@ -766,6 +766,9 @@ def test_singular(self):
+         for A, p in itertools.product(As, p_neg):
+             linalg.cond(A, p)
+
++    @pytest.mark.xfail(True, run=False,
++                       reason="Platform/LAPACK-dependent failure, "
++                              "see gh-18914")
+     def test_nan(self):
+         # nans should be passed through, not converted to infs
+         ps = [None, 1, -1, 2, -2, 'fro']
+@@ -981,7 +984,7 @@ def test_incompatible_dims(self):
+             linalg.lstsq(A, y, rcond=None)
+
+
+[email protected]('dt', [np.dtype(c) for c in '?bBhHiIqQefdgFDGO']) 
+[email protected]('dt', [np.dtype(c) for c in '?bBhHiIqQefdgFDGO'])
+ class TestMatrixPower:
+
+     rshft_0 = np.eye(4)
+@@ -1010,7 +1013,7 @@ def tz(M):
+             mz = matrix_power(M, 0)
+             assert_equal(mz, identity_like_generalized(M))
+             assert_equal(mz.dtype, M.dtype)
+-        
++
+         for mat in self.rshft_all:
+             tz(mat.astype(dt))
+             if dt != object: