{lang}[iimkl/2023a] SciPy-bundle v2023.07

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

@@ -0,0 +1,117 @@
+easyblock = 'PythonBundle'
+
+name = 'SciPy-bundle'
+version = '2023.07'
+
+homepage = 'https://python.org/'
+description = "Bundle of Python packages for scientific software"
+
+toolchain = {'name': 'iimkl', 'version': '2023a'}
+toolchainopts = {'pic': True, 'lowopt': True, 'strict': 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-1.18.2-mkl.patch',
+            'numpy-1.25.1_disable_fortran_callback_test.patch',
+            'numpy-1.22.3_disable-broken-override-test.patch',
+            'numpy-1.25.1_disable-broken-test_long_long_map.patch',
+            'numpy-1.25.1_fix_selected_kind_for_ifort.patch',
+            'numpy-1.25.1_disable-broken-fortran-docstring-test.patch',
+            'numpy-1.25.1_fix-test_features.patch'
+        ],
+        'checksums': [
+            {'numpy-1.25.1.tar.gz': '9a3a9f3a61480cc086117b426a8bd86869c213fc4072e606f01c4e4b66eb92bf'},
+            {'numpy-1.18.2-mkl.patch': 'ea25ad5c0148c1398d282f0424e642fb9815a1a80f4512659b018e2adc378bcf'},
+            {'numpy-1.25.1_disable_fortran_callback_test.patch':
+             '3c02bd9973b7082fde9f9d18edfeb05798226ccb5731a56f5677269200c345cf'},
+            {'numpy-1.22.3_disable-broken-override-test.patch':
+             '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c'},
+            {'numpy-1.25.1_disable-broken-test_long_long_map.patch':
+             'fa0fb0a16c4f1339a974c1c84b79df21dc9bfdc14e3e68f6aebaf5e30bad3fe9'},
+            {'numpy-1.25.1_fix_selected_kind_for_ifort.patch':
+             '4e6561f44de027edf498ac29ed93115f801348a3398700271ccbf048f433b2d3'},
+            {'numpy-1.25.1_disable-broken-fortran-docstring-test.patch':
+             '8a4d36e3b3a9c9bf43df6e5214f3883234a069b80c5c1027a7c84bd5cb133457'},
+            {'numpy-1.25.1_fix-test_features.patch':
+             '1c05ee5d105fe2f824416dd6dd5c64ed0c1cd710a002b4e6dbfafff19203adc5'},
+        ],
+    }),
+    ('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', {
+        'enable_slow_tests': True,
+        'ignore_test_result': False,
+        'patches': [
+            'scipy-1.11.1_disable-tests.patch',
+            'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch',
+            'scipy-1.11.1_disable-tests-iimkl.patch',
+            'scipy-1.11.1_relaxed_test_accuracy.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'},
+            {'scipy-1.11.1_disable-tests-iimkl.patch':
+             'e85cf95d343fa4fd9e0045df3a030209a8d7b32a47d6da64ae1efd7b8ef827e3'},
+            {'scipy-1.11.1_relaxed_test_accuracy.patch':
+             '2b6a7f7f58a7a8391dff52ae9565270c20c8312558b482f526be5e474ad2e675'},
+        ],
+    }),
+    ('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', {
+        'modulename': 'deap.base',
+        'checksums': ['ffef2921932a0edbe634fcb6d156189e7a364bf638a2af4ae5d59931a9a4c8cc'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'lang'

easybuild/easyconfigs/s/SciPy-bundle/numpy-1.25.1_disable-broken-fortran-docstring-test.patch

@@ -0,0 +1,16 @@
+Disable test for docstrings in fortran extension modules, as it fails due to an error
+in autogenerated test code (int * versus npy_intp*).
+
+Author: Jakob Schiotz (Techn. Univ. Denmark) <schiotz@fysik.dtu.dk>
+
+--- numpy/f2py/tests/test_module_doc.old	2023-10-23 15:49:00.858332420 +0200
++++ numpy/f2py/tests/test_module_doc.py	2023-10-23 15:50:04.072826243 +0200
+@@ -7,7 +7,7 @@
+ from numpy.testing import IS_PYPY
+
+
+-class TestModuleDocString(util.F2PyTest):
++class Disabled_for_intel_TestModuleDocString(util.F2PyTest):
+     sources = [
+         util.getpath("tests", "src", "module_data",
+                      "module_data_docstring.f90")

easybuild/easyconfigs/s/SciPy-bundle/numpy-1.25.1_disable-broken-test_long_long_map.patch

@@ -0,0 +1,15 @@
+Disable test that imports a fortran function, it breaks on iimkl toolchain.
+
+Author: Jakob Schiotz (Techn. Univ. Denmark) <schiotz@fysik.dtu.dk>
+
+--- numpy-1.25.1/numpy/f2py/tests/test_value_attrspec.old	2023-07-08 21:25:45.000000000 +0200
++++ numpy-1.25.1/numpy/f2py/tests/test_value_attrspec.py	2023-09-27 11:21:32.172791528 +0200
+@@ -7,7 +7,7 @@
+     sources = [util.getpath("tests", "src", "value_attrspec", "gh21665.f90")]
+
+     # gh-21665
+-    def test_long_long_map(self):
++    def ignored_test_long_long_map(self):
+         inp = 2
+         out = self.module.fortfuncs.square(inp)
+         exp_out = 4

easybuild/easyconfigs/s/SciPy-bundle/numpy-1.25.1_disable_fortran_callback_test.patch

@@ -0,0 +1,17 @@
+Disable TestF90Callback which fails when compiling the resulting code with ifort.
+The resulting code is incorrect Fortran.
+See https://github.com/numpy/numpy/issues/20157
+
+Åke Sandgren, 20211021
+Updated: Jakob Schiøtz, 20230927
+--- numpy-1.25.1/numpy/f2py/tests/test_callback.old	2023-09-27 14:15:21.076625096 +0200
++++ numpy-1.25.1/numpy/f2py/tests/test_callback.py	2023-09-27 14:15:46.401827839 +0200
+@@ -202,7 +202,7 @@
+     options = ["-DF2PY_USE_PYTHON_TLS"]
+
+
+-class TestF90Callback(util.F2PyTest):
++class Disabled_for_intel_TestF90Callback(util.F2PyTest):
+     sources = [util.getpath("tests", "src", "callback", "gh17797.f90")]
+
+     def test_gh17797(self):

easybuild/easyconfigs/s/SciPy-bundle/numpy-1.25.1_fix_selected_kind_for_ifort.patch

@@ -0,0 +1,65 @@
+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>
+
+--- 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
+@@ -2385,7 +2385,8 @@
+     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:
+@@ -2396,29 +2397,27 @@
+         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
+
++_selected_int_kind_func = _selected_int_kind_func_intel
+
+-def _selected_real_kind_func(p, r=0, radix=0):
++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', 'arm64', 'power', 'ppc', 'riscv', 's390x', 'sparc')):
+-        if p <= 33:
+-            return 16
+-    else:
+-        if p < 19:
+-            return 10
+-        elif p <= 33:
+-            return 16
++    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)

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

@@ -0,0 +1,43 @@
+Skip tests that fail when compiling with iimkl/2023a:
+
+Disable PROPACK test for complex, as it appears to be broken when
+using Intel compiler.  The tests were already skipped in a few other
+cases for similar reasons.
+
+Skip test test_x0_equals_Mb[bicgstab-nonsymposdef-F], it fails to
+converge.  Many other solvers are skipped with this test case for
+similar reasons, although it is worrying that it works with OpenBLAS
+and not with MKL.
+
+Author: Jakob Schiotz (Techn. Univ. Denmark) <schiotz@fysik.dtu.dk>
+
+--- scipy/sparse/linalg/tests/test_propack.py.old	2023-10-24 12:12:17.722133108 +0200
++++ scipy/sparse/linalg/tests/test_propack.py	2023-10-24 12:14:02.072938068 +0200
+@@ -34,14 +34,8 @@
+ for dtype_flavour in TOLS.keys():
+     marks = []
+     if is_complex_type(dtype_flavour):
+-        if is_32bit():
+-            # PROPACK has issues w/ complex on 32-bit; see gh-14433
+-            marks = [pytest.mark.skip]
+-        elif is_windows() and np.dtype(dtype_flavour).itemsize == 16:
+-            # windows crashes for complex128 (so don't xfail); see gh-15108
+-            marks = [pytest.mark.skip]
+-        else:
+-            marks = [pytest.mark.slow]  # type: ignore[list-item]
++        # PROPACK crashes for complex with Intel compiler.
++        marks = [pytest.mark.skip]
+     _dtypes.append(pytest.param(dtype_flavour, marks=marks,
+                                 id=dtype_flavour.__name__))
+ _dtypes = tuple(_dtypes)  # type: ignore[assignment]
+--- scipy/sparse/linalg/_isolve/tests/test_iterative.py.old	2023-10-24 17:07:24.697195558 +0200
++++ scipy/sparse/linalg/_isolve/tests/test_iterative.py	2023-10-24 17:07:46.106361595 +0200
+@@ -162,7 +162,7 @@
+         self.cases.append(Case("nonsymposdef", A,
+                                skip=sym_solvers + [cgs, qmr, bicg, tfqmr]))
+         self.cases.append(Case("nonsymposdef-F", A.astype('F'),
+-                               skip=sym_solvers + [cgs, qmr, bicg, tfqmr]))
++                               skip=sym_solvers + [cgs, qmr, bicg, bicgstab, tfqmr]))
+
+         # Symmetric, non-pd, hitting cgs/bicg/bicgstab/qmr/tfqmr breakdown
+         A = np.array([[0, 0, 0, 0, 0, 1, -1, -0, -0, -0, -0],

easybuild/easyconfigs/s/SciPy-bundle/scipy-1.11.1_relaxed_test_accuracy.patch

@@ -0,0 +1,110 @@
+Backported test from main branch of scipy on Github, relaxing the
+tolerances of a few tests.  Some of these fail with the Intel
+compiler.
+
+The patch has been edited directly to backport it (np.double had been replaced
+by np.float64 in the main branch), and one patch was to code that is not in
+scipy-1.11.1.
+
+Backported by: Jakob Schiotz (Techn. Univ. Denmark) <schiotz@fysik.dtu.dk>
+
+Original description:
+
+From a4fba82078d2e95005343150d821ccd33cb5de20 Mon Sep 17 00:00:00 2001
+From: Ralf Gommers <ralf.gommers@gmail.com>
+Date: Wed, 6 Sep 2023 15:08:59 +0200
+Subject: [PATCH] TST: test tolerance bumps to fix reported failures
+
+Closes gh-19117
+
+The `test_sygst` one was reported in gh-19153.
+---
+ scipy/fft/_pocketfft/tests/test_real_transforms.py | 2 +-
+ scipy/linalg/tests/test_lapack.py                  | 2 +-
+ scipy/ndimage/tests/test_datatypes.py              | 4 +++-
+ scipy/spatial/transform/tests/test_rotation.py     | 8 ++++----
+ scipy/special/tests/test_hyp2f1.py                 | 6 +++---
+ 5 files changed, 12 insertions(+), 10 deletions(-)
+
+diff --git a/scipy/fft/_pocketfft/tests/test_real_transforms.py b/scipy/fft/_pocketfft/tests/test_real_transforms.py
+index d1f4e1d..a217e75 100644
+--- a/scipy/fft/_pocketfft/tests/test_real_transforms.py
++++ b/scipy/fft/_pocketfft/tests/test_real_transforms.py
+@@ -239,7 +239,7 @@ dec_map: DecMapType = {
+     (dst, np.float32, 3): 7,
+
+     (dst, np.double, 4): 13,
+-    (dst, np.float32, 4): 6,
++    (dst, np.float32, 4): 5,
+
+     # IDST
+     (idst, np.double, 1): 14,
+diff --git a/scipy/linalg/tests/test_lapack.py b/scipy/linalg/tests/test_lapack.py
+index 6c64a2a..2c994f6 100644
+--- a/scipy/linalg/tests/test_lapack.py
++++ b/scipy/linalg/tests/test_lapack.py
+@@ -1031,7 +1031,7 @@ def test_sygst():
+
+         eig, _, info = syevd(a)
+         assert_(info == 0)
+-        assert_allclose(eig, eig_gvd, rtol=1e-4)
++        assert_allclose(eig, eig_gvd, rtol=1.2e-4)
+
+
+ def test_hegst():
+diff --git a/scipy/ndimage/tests/test_datatypes.py b/scipy/ndimage/tests/test_datatypes.py
+index 327cc5a..1eb056b 100644
+--- a/scipy/ndimage/tests/test_datatypes.py
++++ b/scipy/ndimage/tests/test_datatypes.py
+@@ -45,7 +45,7 @@ def test_map_coordinates_dts():
+             assert_array_almost_equal(these_data, out)
+
+
+-@pytest.mark.xfail(not sys.platform == 'darwin', reason="runs only on darwin")
++@pytest.mark.xfail(True, reason="Broken on many platforms")
+ def test_uint64_max():
+     # Test interpolation respects uint64 max.  Reported to fail at least on
+     # win32 (due to the 32 bit visual C compiler using signed int64 when
+@@ -53,6 +53,8 @@ def test_uint64_max():
+     # Interpolation is always done in double precision floating point, so
+     # we use the largest uint64 value for which int(float(big)) still fits
+     # in a uint64.
++    # This test was last enabled on macOS only, and there it started failing
++    # on arm64 as well (see gh-19117).
+     big = 2**64 - 1025
+     arr = np.array([big, big, big], dtype=np.uint64)
+     # Tests geometric transform (map_coordinates, affine_transform)
+diff --git a/scipy/special/tests/test_hyp2f1.py b/scipy/special/tests/test_hyp2f1.py
+index 2fe732f..200d4bb 100644
+--- a/scipy/special/tests/test_hyp2f1.py
++++ b/scipy/special/tests/test_hyp2f1.py
+@@ -474,7 +474,7 @@ class TestHyp2f1:
+                     c=-15.5,
+                     z=(1.1578947368421053-1.1578947368421053j),
+                     expected=(0.9778506962676361+0.044083801141231616j),
+-                    rtol=1e-12,
++                    rtol=3e-12,
+                 ),
+             ),
+             pytest.param(
+@@ -1378,7 +1378,7 @@ class TestHyp2f1:
+                     c=-7.949900487447654,
+                     z=(0.4172413793103451-0.8724137931034484j),
+                     expected=(-2258.1590330318213+8860.193389158803j),
+-                    rtol=1e-10,
++                    rtol=1.4e-10,
+                 ),
+             ),
+         ]
+@@ -1433,7 +1433,7 @@ class TestHyp2f1:
+                     c=-15.964218273004214,
+                     z=(0.6448275862068968+0.8724137931034486j),
+                     expected=(85592537010.05054-8061416766688.324j),
+-                    rtol=1e-14,
++                    rtol=2e-14,
+                 ),
+             ),
+             pytest.param(
+-- 
+1.8.3.1
+