{lang}[gfbf/2026.1] SciPy-bundle v2026.05 by pavelToman · Pull Request #26109 · easybuilders/easybuild-easyconfigs

pavelToman · 2026-05-28T13:39:05Z

(created using eb --new-pr)
resolves vscentrum/vsc-software-stack#650
requires:

set ulimit -s or wait for enhance PythonPackage easyblock to limit ulimit stack size when unlimited easybuild-easyblocks#4144
- fixes TEST_BUG: NumPy v2.4.6 tests hang on recursive/self-referential object arrays with CPython 3.14.2 numpy/numpy#31512
update test command in custom easyblock for scipy easyblock for scipy >= 1.17 easybuild-easyblocks#4143
{devel,tools}[GCCcore/15.2.0] meson-python v0.19.0, hypothesis v6.153.2, spin v0.18, ... #26098
{lib}[GCCcore/15.2.0] pybind11 v3.0.4, Catch2 v2.13.10, Eigen v5.0.0 #26083

test cmd:
ulimit -s 8192 && eb --from-pr 26109 --include-easyblocks-from-pr 4143 --upload-test-report --rebuild --robot
or
eb --from-pr 26109 --include-easyblocks-from-pr 4144,4143 --upload-test-report --rebuild --robot
NOT: --include-easyblocks-from-pr 4143,4144 this will skip the 4144 and fail on tests

…scipy-1.17.1_relax-tests-py314.patch

github-actions · 2026-05-28T13:39:39Z

Updated software `SciPy-bundle-2026.05-gfbf-2026.1.eb`

Diff against SciPy-bundle-2023.11-iimkl-2023b.eb

easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.11-iimkl-2023b.eb

diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.11-iimkl-2023b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2026.05-gfbf-2026.1.eb
index 2a4b77fcaa..eb79590783 100644
--- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.11-iimkl-2023b.eb
+++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2026.05-gfbf-2026.1.eb
@@ -1,120 +1,85 @@
 easyblock = 'PythonBundle'
 
 name = 'SciPy-bundle'
-# using 2023.11 as version to keep it aligned with gfbf/2023b version
-version = '2023.11'
+version = '2026.05'
 
 homepage = 'https://python.org/'
 description = "Bundle of Python packages for scientific software"
 
-toolchain = {'name': 'iimkl', 'version': '2023b'}
-toolchainopts = {
-    'pic': True, 'lowopt': True, 'strict': True,
-    'oneapi': True, 'optarch': False,  # prevents -xHost
-}
+toolchain = {'name': 'gfbf', 'version': '2026.1'}
+toolchainopts = {'pic': True, 'lowopt': True}
 
 builddependencies = [
-    ('hypothesis', '6.90.0'),
+    ('hypothesis', '6.153.2'),
     ('UnZip', '6.0'),
     # scipy >= 1.9.0 uses Meson/Ninja
-    ('Meson', '1.2.3'),
-    ('meson-python', '0.15.0'),
-    ('Ninja', '1.11.1'),
-    ('pkgconf', '2.0.3'),   # required by scipy
+    ('Meson', '1.10.2'),
+    ('meson-python', '0.19.0'),
+    ('Ninja', '1.13.2'),
+    ('pkgconf', '2.5.1'),  # required by scipy
+    ('Cython', '3.2.4'),  # required by numpy and scipy
+    ('pybind11', '3.0.4'),  # required by scipy
+    ('spin', '0.18'),  # required for testing numpy
 ]
-
 dependencies = [
-    ('Python', '3.11.5'),
-    ('Python-bundle-PyPI', '2023.10'),
-    ('pybind11', '2.11.1'),  # required by scipy
+    ('Python', '3.14.2'),
+    ('Python-bundle-PyPI', '2026.04'),
 ]
 
-
 # order is important!
 exts_list = [
-    ('numpy', '1.26.2', {
-        'easyblock': 'PythonPackage',  # pip install builds numpy v1.26.x via spin/meson/ninja
-        'patches': [
-            'numpy-1.25.1_disable_fortran_callback_test.patch',
-            'numpy-1.25.1_disable-broken-test_long_long_map.patch',
-            'numpy-1.26.2_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-1.26.2.tar.gz': 'f65738447676ab5777f11e6bbbdb8ce11b785e105f690bc45966574816b6d3ea'},
-            {'numpy-1.25.1_disable_fortran_callback_test.patch':
-             '3c02bd9973b7082fde9f9d18edfeb05798226ccb5731a56f5677269200c345cf'},
-            {'numpy-1.25.1_disable-broken-test_long_long_map.patch':
-             'fa0fb0a16c4f1339a974c1c84b79df21dc9bfdc14e3e68f6aebaf5e30bad3fe9'},
-            {'numpy-1.26.2_fix_selected_kind_for_ifort.patch':
-             '3622bacbe4063373cc0b1c0aa0ffe3d30dfe132f6a763b15b45cc6387cbd51d7'},
-            {'numpy-1.25.1_disable-broken-fortran-docstring-test.patch':
-             '8a4d36e3b3a9c9bf43df6e5214f3883234a069b80c5c1027a7c84bd5cb133457'},
-            {'numpy-1.25.1_fix-test_features.patch':
-             '1c05ee5d105fe2f824416dd6dd5c64ed0c1cd710a002b4e6dbfafff19203adc5'},
-        ],
+    ('numpy', '2.4.6', {
+        'checksums': ['f3a3570c4a2a16746ac2c31a7c7c7b0c186b95ce902e33db6f28094ed7387dda'],
     }),
     ('ply', '3.11', {
         'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'],
     }),
-    ('gast', '0.5.4', {
-        'checksums': ['9c270fe5f4b130969b54174de7db4e764b09b4f7f67ccfc32480e29f78348d97'],
+    ('gast', '0.6.0', {
+        'checksums': ['88fc5300d32c7ac6ca7b515310862f71e6fdf2c029bbec7c66c0f5dd47b6b1fb'],
     }),
-    ('beniget', '0.4.1', {
-        'checksums': ['75554b3b8ad0553ce2f607627dad3d95c60c441189875b98e097528f8e23ac0c'],
+    ('beniget', '0.4.2.post1', {
+        'checksums': ['a0258537e65e7e14ec33a86802f865a667f949bb6c73646d55e42f7c45a052ae'],
     }),
-    ('pythran', '0.14.0', {
-        'checksums': ['42f3473946205964844eff7f750e2541afb2006d53475d708f5ff2d048db89bd'],
+    ('pythran', '0.18.1', {
+        'checksums': ['8803ed948bf841a11bbbb10472a8ff6ea24ebd70e67c3f77b77be3db900eccfe'],
     }),
     ('versioneer', '0.29', {
         'checksums': ['5ab283b9857211d61b53318b7c792cf68e798e765ee17c27ade9f6c924235731'],
     }),
-    ('scipy', '1.12.0', {
+    ('mpmath', '1.4.1', {
+        'checksums': ['efd6d1b75f09d69524a67609949812668b28e81ecbfe0ab449ced8c13e92642e'],
+    }),
+    ('scipy', '1.17.1', {
         '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-1.11.4_disable-test_branch_cut.patch',  # intel might need -assume=minus0
-            'scipy-1.12.0_disable-tests-iimkl.patch',
+            'scipy-1.16.0_skip-tests-broken-grace.patch',
+            'scipy-1.17.1_relax-tests-py314.patch',
         ],
         'checksums': [
-            {'scipy-1.12.0.tar.gz': '4bf5abab8a36d20193c698b0f1fc282c1d083c94723902c447e5d2f1780936a3'},
-            {'scipy-1.11.1_disable-tests.patch': '906bfb03397d94882ccdc1b93bc2c8e854e0e060c2d107c83042992394e6a4af'},
-            {'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch':
-             '918c8e6fa8215d459126f267764c961bde729ea4a116c7f6287cddfdc58ffcea'},
-            {'scipy-1.11.4_disable-test_branch_cut.patch':
-             '3433d284e4074ee8a5b10bfc65c729214bc75670c36d8b7a983bb5ccddc5cf61'},
-            {'scipy-1.12.0_disable-tests-iimkl.patch':
-             'edf575be62b77bb8984e87e75f69a0799d719fc8b5c801c79e4f9592e1c8203f'},
+            {'scipy-1.17.1.tar.gz': '95d8e012d8cb8816c226aef832200b1d45109ed4464303e997c5b13122b297c0'},
+            {'scipy-1.16.0_skip-tests-broken-grace.patch':
+             '33885518a572f843a0edeb7a58aa938202aae70267f6de1ce60acef97f393126'},
+            {'scipy-1.17.1_relax-tests-py314.patch':
+             '4a54394854f14b3f1300629e00c19fbce1b7780fa38044e3a1f0b2b2cff6f988'},
         ],
-        'runtest': ' && '.join((
-            'unset LDFLAGS',
-            'cd ..',  # avoid running the test suite from the build dir which will cause import related failures
-            "python -c 'import sys; import numpy; sys.exit(not numpy.test(verbose=2))'",
-        )),
-        'testinstall': True,
-    }),
-    ('numexpr', '2.8.7', {
-        'checksums': ['596eeb3bbfebc912f4b6eaaf842b61ba722cebdb8bc42dfefa657d3a74953849'],
     }),
-    ('Bottleneck', '1.3.7', {
-        'checksums': ['e1467e373ad469da340ed0ff283214d6531cc08bfdca2083361a3aa6470681f8'],
+    ('numexpr', '2.14.1', {
+        'checksums': ['4be00b1086c7b7a5c32e31558122b7b80243fe098579b170967da83f3152b48b'],
     }),
-    ('tzdata', '2023.3', {
-        'checksums': ['11ef1e08e54acb0d4f95bdb1be05da659673de4acbd21bf9c69e94cc5e907a3a'],
+    ('bottleneck', '1.6.0', {
+        'checksums': ['028d46ee4b025ad9ab4d79924113816f825f62b17b87c9e1d0d8ce144a4a0e31'],
     }),
-    ('pandas', '2.1.3', {
+    ('pandas', '3.0.3', {
         'preinstallopts': "export PANDAS_CI=0 && ",
-        'checksums': ['22929f84bca106921917eb73c1521317ddd0a4c71b395bcf767a106e3494209f'],
+        'checksums': ['696a4a00a2a2a35d4e5deb3fc946641b96c944f02230e4f76137fe35d806c4fc'],
     }),
-    ('mpmath', '1.3.0', {
-        'checksums': ['7a28eb2a9774d00c7bc92411c19a89209d5da7c4c9a9e227be8330a23a25b91f'],
+    ('moocore', '0.3.1', {
+        'checksums': ['a8f83cfbc0aa81c1c9dd33e473adbc9b638dc3b1a6943753f8146770bb76bae4'],
     }),
-    ('deap', '1.4.1', {
+    ('deap', '1.4.4', {
         'modulename': 'deap.base',
-        'checksums': ['cc01de9892dfa7d1bc9803dab28892fead177f0182c81db47360a240ead778ff'],
+        'checksums': ['50d4bd924fca5a16a3dba8bfdb1140a55e9c24ce50816ab4f5683d2f31c2d734'],
     }),
 ]

Diff against SciPy-bundle-2025.07-lfbf-2025b.eb

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

diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2025.07-lfbf-2025b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2026.05-gfbf-2026.1.eb
index 05c3d1b8c6..eb79590783 100644
--- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2025.07-lfbf-2025b.eb
+++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2026.05-gfbf-2026.1.eb
@@ -1,53 +1,35 @@
 easyblock = 'PythonBundle'
 
 name = 'SciPy-bundle'
-version = '2025.07'
+version = '2026.05'
 
 homepage = 'https://python.org/'
 description = "Bundle of Python packages for scientific software"
 
-toolchain = {'name': 'lfbf', 'version': '2025b'}
+toolchain = {'name': 'gfbf', 'version': '2026.1'}
 toolchainopts = {'pic': True, 'lowopt': True}
 
 builddependencies = [
-    ('hypothesis', '6.136.6'),
+    ('hypothesis', '6.153.2'),
     ('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
+    ('Meson', '1.10.2'),
+    ('meson-python', '0.19.0'),
+    ('Ninja', '1.13.2'),
+    ('pkgconf', '2.5.1'),  # required by scipy
+    ('Cython', '3.2.4'),  # required by numpy and scipy
+    ('pybind11', '3.0.4'),  # required by scipy
+    ('spin', '0.18'),  # required for testing numpy
 ]
-
 dependencies = [
-    ('Python', '3.13.5'),
-    ('Python-bundle-PyPI', '2025.07'),
+    ('Python', '3.14.2'),
+    ('Python-bundle-PyPI', '2026.04'),
 ]
 
 # order is important!
 exts_list = [
-    ('numpy', '2.3.2', {
-        'patches': [
-            'numpy-1.22.3_disable-broken-override-test.patch',
-            'numpy-2.3.2_fix-llvm-tests.patch',
-            'numpy-2.3.2_fix-selected-real-kind-for-flang.patch',
-            # Adds proper processing of object files for f2py
-            # Fixed in 2.4.0, see https://github.com/numpy/numpy/pull/29572
-            'numpy-2.3.1_fix_f2py_object_files.patch',
-        ],
-        'checksums': [
-            {'numpy-2.3.2.tar.gz': 'e0486a11ec30cdecb53f184d496d1c6a20786c81e55e41640270130056f8ee48'},
-            {'numpy-1.22.3_disable-broken-override-test.patch':
-             '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c'},
-            {'numpy-2.3.2_fix-llvm-tests.patch': 'dac856f521e2b5175f0edb09ee65ba9246af2a7d52d36dfb2dbb1b516b8cfaff'},
-            {'numpy-2.3.2_fix-selected-real-kind-for-flang.patch':
-             '0e947fc7730bc87d10279c4393db9b1585e7f1ae6932c989f37c1080479d7cb7'},
-            {'numpy-2.3.1_fix_f2py_object_files.patch':
-             'b586083c384becc9ef7908af171c9034473514f8c8741d15b8bda23da503718f'},
-        ],
+    ('numpy', '2.4.6', {
+        'checksums': ['f3a3570c4a2a16746ac2c31a7c7c7b0c186b95ce902e33db6f28094ed7387dda'],
     }),
     ('ply', '3.11', {
         'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'],
@@ -58,56 +40,46 @@ exts_list = [
     ('beniget', '0.4.2.post1', {
         'checksums': ['a0258537e65e7e14ec33a86802f865a667f949bb6c73646d55e42f7c45a052ae'],
     }),
-    ('pythran', '0.18.0', {
-        'checksums': ['5c003e8cbedf6dbb68c2869c49fc110ce8b5e8982993078a4a819f1dadc4fc6a'],
+    ('pythran', '0.18.1', {
+        'checksums': ['8803ed948bf841a11bbbb10472a8ff6ea24ebd70e67c3f77b77be3db900eccfe'],
     }),
     ('versioneer', '0.29', {
         'checksums': ['5ab283b9857211d61b53318b7c792cf68e798e765ee17c27ade9f6c924235731'],
     }),
-    ('scipy', '1.16.1', {
+    ('mpmath', '1.4.1', {
+        'checksums': ['efd6d1b75f09d69524a67609949812668b28e81ecbfe0ab449ced8c13e92642e'],
+    }),
+    ('scipy', '1.17.1', {
         '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-1.17.1_relax-tests-py314.patch',
         ],
         'checksums': [
-            {'scipy-1.16.1.tar.gz': '44c76f9e8b6e8e488a586190ab38016e4ed2f8a038af7cd3defa903c0a2238b3'},
-            {'scipy-1.11.1_disable-tests.patch': '906bfb03397d94882ccdc1b93bc2c8e854e0e060c2d107c83042992394e6a4af'},
+            {'scipy-1.17.1.tar.gz': '95d8e012d8cb8816c226aef832200b1d45109ed4464303e997c5b13122b297c0'},
             {'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-1.17.1_relax-tests-py314.patch':
+             '4a54394854f14b3f1300629e00c19fbce1b7780fa38044e3a1f0b2b2cff6f988'},
         ],
     }),
-    ('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'],
+    ('numexpr', '2.14.1', {
+        'checksums': ['4be00b1086c7b7a5c32e31558122b7b80243fe098579b170967da83f3152b48b'],
     }),
-    ('tzdata', '2025.2', {
-        'checksums': ['b60a638fcc0daffadf82fe0f57e53d06bdec2f36c4df66280ae79bce6bd6f2b9'],
+    ('bottleneck', '1.6.0', {
+        'checksums': ['028d46ee4b025ad9ab4d79924113816f825f62b17b87c9e1d0d8ce144a4a0e31'],
     }),
-    ('pandas', '2.3.1', {
+    ('pandas', '3.0.3', {
         'preinstallopts': "export PANDAS_CI=0 && ",
-        'checksums': ['0a95b9ac964fe83ce317827f80304d37388ea77616b1425f0ae41c9d2d0d7bb2'],
+        'checksums': ['696a4a00a2a2a35d4e5deb3fc946641b96c944f02230e4f76137fe35d806c4fc'],
     }),
-    ('mpmath', '1.3.0', {
-        'checksums': ['7a28eb2a9774d00c7bc92411c19a89209d5da7c4c9a9e227be8330a23a25b91f'],
+    ('moocore', '0.3.1', {
+        'checksums': ['a8f83cfbc0aa81c1c9dd33e473adbc9b638dc3b1a6943753f8146770bb76bae4'],
     }),
-    ('deap', '1.4.3', {
+    ('deap', '1.4.4', {
         'modulename': 'deap.base',
-        'checksums': ['7c97088fb05835bdc255bec475cb0e778de2b43e44cbefbf2bcd655aeec865fd'],
+        'checksums': ['50d4bd924fca5a16a3dba8bfdb1140a55e9c24ce50816ab4f5683d2f31c2d734'],
     }),
 ]

Diff against SciPy-bundle-2025.07-iimkl-2025b.eb

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

diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2025.07-iimkl-2025b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2026.05-gfbf-2026.1.eb
index e9f398831b..eb79590783 100644
--- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2025.07-iimkl-2025b.eb
+++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2026.05-gfbf-2026.1.eb
@@ -1,56 +1,35 @@
 easyblock = 'PythonBundle'
 
 name = 'SciPy-bundle'
-version = '2025.07'
+version = '2026.05'
 
 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'}
+toolchain = {'name': 'gfbf', 'version': '2026.1'}
+toolchainopts = {'pic': True, 'lowopt': True}
 
 builddependencies = [
-    ('hypothesis', '6.136.6'),
+    ('hypothesis', '6.153.2'),
     ('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
+    ('Meson', '1.10.2'),
+    ('meson-python', '0.19.0'),
+    ('Ninja', '1.13.2'),
+    ('pkgconf', '2.5.1'),  # required by scipy
+    ('Cython', '3.2.4'),  # required by numpy and scipy
+    ('pybind11', '3.0.4'),  # required by scipy
+    ('spin', '0.18'),  # required for testing numpy
 ]
-
 dependencies = [
-    ('Python', '3.13.5'),
-    ('Python-bundle-PyPI', '2025.07'),
+    ('Python', '3.14.2'),
+    ('Python-bundle-PyPI', '2026.04'),
 ]
 
 # 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',
-            # Adds proper processing of object files for f2py
-            # Fixed in 2.4.0, see https://github.com/numpy/numpy/pull/29572
-            'numpy-2.3.1_fix_f2py_object_files.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'},
-            {'numpy-2.3.1_fix_f2py_object_files.patch':
-             'b586083c384becc9ef7908af171c9034473514f8c8741d15b8bda23da503718f'},
-        ],
+    ('numpy', '2.4.6', {
+        'checksums': ['f3a3570c4a2a16746ac2c31a7c7c7b0c186b95ce902e33db6f28094ed7387dda'],
     }),
     ('ply', '3.11', {
         'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'],
@@ -61,58 +40,46 @@ exts_list = [
     ('beniget', '0.4.2.post1', {
         'checksums': ['a0258537e65e7e14ec33a86802f865a667f949bb6c73646d55e42f7c45a052ae'],
     }),
-    ('pythran', '0.18.0', {
-        'checksums': ['5c003e8cbedf6dbb68c2869c49fc110ce8b5e8982993078a4a819f1dadc4fc6a'],
+    ('pythran', '0.18.1', {
+        'checksums': ['8803ed948bf841a11bbbb10472a8ff6ea24ebd70e67c3f77b77be3db900eccfe'],
     }),
     ('versioneer', '0.29', {
         'checksums': ['5ab283b9857211d61b53318b7c792cf68e798e765ee17c27ade9f6c924235731'],
     }),
-    ('scipy', '1.16.1', {
+    ('mpmath', '1.4.1', {
+        'checksums': ['efd6d1b75f09d69524a67609949812668b28e81ecbfe0ab449ced8c13e92642e'],
+    }),
+    ('scipy', '1.17.1', {
         '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',
+            'scipy-1.17.1_relax-tests-py314.patch',
         ],
         'checksums': [
-            {'scipy-1.16.1.tar.gz': '44c76f9e8b6e8e488a586190ab38016e4ed2f8a038af7cd3defa903c0a2238b3'},
-            {'scipy-1.11.1_disable-tests.patch': '906bfb03397d94882ccdc1b93bc2c8e854e0e060c2d107c83042992394e6a4af'},
+            {'scipy-1.17.1.tar.gz': '95d8e012d8cb8816c226aef832200b1d45109ed4464303e997c5b13122b297c0'},
             {'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'},
+            {'scipy-1.17.1_relax-tests-py314.patch':
+             '4a54394854f14b3f1300629e00c19fbce1b7780fa38044e3a1f0b2b2cff6f988'},
         ],
     }),
-    ('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'],
+    ('numexpr', '2.14.1', {
+        'checksums': ['4be00b1086c7b7a5c32e31558122b7b80243fe098579b170967da83f3152b48b'],
     }),
-    ('tzdata', '2025.2', {
-        'checksums': ['b60a638fcc0daffadf82fe0f57e53d06bdec2f36c4df66280ae79bce6bd6f2b9'],
+    ('bottleneck', '1.6.0', {
+        'checksums': ['028d46ee4b025ad9ab4d79924113816f825f62b17b87c9e1d0d8ce144a4a0e31'],
     }),
-    ('pandas', '2.3.1', {
+    ('pandas', '3.0.3', {
         'preinstallopts': "export PANDAS_CI=0 && ",
-        'checksums': ['0a95b9ac964fe83ce317827f80304d37388ea77616b1425f0ae41c9d2d0d7bb2'],
+        'checksums': ['696a4a00a2a2a35d4e5deb3fc946641b96c944f02230e4f76137fe35d806c4fc'],
     }),
-    ('mpmath', '1.3.0', {
-        'checksums': ['7a28eb2a9774d00c7bc92411c19a89209d5da7c4c9a9e227be8330a23a25b91f'],
+    ('moocore', '0.3.1', {
+        'checksums': ['a8f83cfbc0aa81c1c9dd33e473adbc9b638dc3b1a6943753f8146770bb76bae4'],
     }),
-    ('deap', '1.4.3', {
+    ('deap', '1.4.4', {
         'modulename': 'deap.base',
-        'checksums': ['7c97088fb05835bdc255bec475cb0e778de2b43e44cbefbf2bcd655aeec865fd'],
+        'checksums': ['50d4bd924fca5a16a3dba8bfdb1140a55e9c24ce50816ab4f5683d2f31c2d734'],
     }),
 ]

pavelToman · 2026-05-28T15:03:05Z

Test report by @pavelToman
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#4143
SUCCESS
Build succeeded for 1 out of 1 (total: 1 hour 3 mins 46 secs) (1 easyconfigs in total)
node4210.shinx.os - Linux RHEL 9.6, x86_64, AMD EPYC 9654 96-Core Processor, Python 3.9.21
See https://gist.github.com/pavelToman/0ae41befa900d4299f6e2d42610fe5b7 for a full test report.

pavelToman · 2026-05-28T15:20:41Z

Test report by @pavelToman
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#4143
SUCCESS
Build succeeded for 1 out of 1 (total: 1 hour 21 mins 28 secs) (1 easyconfigs in total)
node4011.donphan.os - Linux RHEL 9.6, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz, 1 x NVIDIA NVIDIA A2, 595.71.05, Python 3.9.21
See https://gist.github.com/pavelToman/622b6c1594fd1522234d5d4d447e9c75 for a full test report.

Thyre · 2026-05-28T15:52:16Z

Test report by @Thyre
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#4144, easybuilders/easybuild-easyblocks#4143
SUCCESS
Build succeeded for 5 out of 5 (total: 43 mins 38 secs) (1 easyconfigs in total)
jrc0900.jureca - Linux Rocky Linux 9.7, AArch64, ARM UNKNOWN (neoverse_v2), 1 x NVIDIA NVIDIA GH200 480GB, 595.71.05, Python 3.9.25
See https://gist.github.com/Thyre/c895d3565a8b2d10b633e4cf5406ec47 for a full test report.

pavelToman · 2026-05-28T16:14:56Z

Test report by @pavelToman
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#4143, easybuilders/easybuild-easyblocks#4144
FAILED
Build succeeded for 0 out of 1 (total: 5 mins 45 secs) (1 easyconfigs in total)
node4015.donphan.os - Linux RHEL 9.6, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz, 1 x NVIDIA NVIDIA A2, 595.71.05, Python 3.9.21
See https://gist.github.com/pavelToman/a86b34a754c512f6901343fa28d00ab5 for a full test report.

Failed on numpy/_core/tests/test_dtype.py::TestMonsterType::test_list_recursion - should be ok with easybuilders/easybuild-easyblocks#4144
@Thyre do you know please why it failed? For you it seems it works

Flamefire · 2026-05-28T18:54:11Z

Test report by @Flamefire
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#4144, easybuilders/easybuild-easyblocks#4143
FAILED
Build succeeded for 34 out of 40 (total: 2 hours 34 mins 49 secs) (1 easyconfigs in total)
n1152.barnard.hpc.tu-dresden.de - Linux RHEL 9.6, x86_64, Intel(R) Xeon(R) Platinum 8470 (sapphirerapids), Python 3.9.21
See https://gist.github.com/Flamefire/0c814c29b39c75e2920fcea142bd5438 for a full test report.

Thyre · 2026-05-29T07:43:19Z

Test report by @Thyre
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#4144, easybuilders/easybuild-easyblocks#4143
FAILED
Build succeeded for 27 out of 28 (total: 1 hour 28 mins 56 secs) (1 easyconfigs in total)
Linux - Linux Arch Linux UNKNOWN, x86_64, AMD Ryzen 7 7800X3D 8-Core Processor (zen4), 1 x AMD Navi 48 [Radeon RX 9070/9070 XT/9070 GRE] (device id: 0x7550, gfx: gfx1201, driver: Linuxversion7.0.9-arch1-1(linux@archlinux)(gcc(GCC)16.1.120260430,GNUld(GNUBinutils)2.46.0)#1SMPPREEMPT_DYNAMICSun,17May202617:23:07+0000), 1 x AMD Raphael (device id: 0x164e, gfx: gfx1036, driver: Linuxversion7.0.9-arch1-1(linux@archlinux)(gcc(GCC)16.1.120260430,GNUld(GNUBinutils)2.46.0)#1SMPPREEMPT_DYNAMICSun,17May202617:23:07+0000), Python 3.14.5
See https://gist.github.com/Thyre/3ecda4f79700b46f56a36fa96d554351 for a full test report.

Three SciPy tests failed. This seems similar to #24464.

Details

_________________________________________________________________________________________________________________ TestVectorNorms.test_stable _________________________________________________________________________________________________________________

self = <scipy.linalg.tests.test_basic.TestVectorNorms object at 0x14b2f6e25350>

    def test_stable(self):
        # more stable than numpy's norm
        a = array([1e4] + [1]*10000, dtype=float32)
        try:
            # snrm in double precision; we obtain the same as for float64
            # -- large atol needed due to varying blas implementations
>           assert_allclose(norm(a) - 1e4, 0.5, atol=1e-2)
E           AssertionError: 
E           Not equal to tolerance rtol=1e-07, atol=0.01
E           
E           Mismatched elements: 1 / 1 (100%)
E           Max absolute difference among violations: 0.015625
E           Max relative difference among violations: 0.03125
E            ACTUAL: array(0.484375)
E            DESIRED: array(0.5)

scipy/linalg/tests/test_basic.py:2386: AssertionError

During handling of the above exception, another exception occurred:

self = <scipy.linalg.tests.test_basic.TestVectorNorms object at 0x14b2f6e25350>

    def test_stable(self):
        # more stable than numpy's norm
        a = array([1e4] + [1]*10000, dtype=float32)
        try:
            # snrm in double precision; we obtain the same as for float64
            # -- large atol needed due to varying blas implementations
            assert_allclose(norm(a) - 1e4, 0.5, atol=1e-2)
        except AssertionError:
            # snrm implemented in single precision, == np.linalg.norm result
            msg = ": Result should equal either 0.0 or 0.5 (depending on " \
                  "implementation of snrm2)."
>           assert_almost_equal(norm(a) - 1e4, 0.0, err_msg=msg)
E           AssertionError: 
E           Arrays are not almost equal to 7 decimals
E           : Result should equal either 0.0 or 0.5 (depending on implementation of snrm2).
E            ACTUAL: 0.484375
E            DESIRED: 0.0

scipy/linalg/tests/test_basic.py:2391: AssertionError
_____________________________________________________________________________________________________________ TestBatch.test_solve[float32-bdim2] _____________________________________________________________________________________________________________

self = <scipy.linalg.tests.test_batch.TestBatch object at 0x14b2f5c29b30>, bdim = (2, 3, 5, 4), dtype = <class 'numpy.float32'>

    @pytest.mark.parametrize('bdim', [(5,), (5, 4), (2, 3, 5, 4)])
    @pytest.mark.parametrize('dtype', floating)
    def test_solve(self, bdim, dtype):
        rng = np.random.default_rng(8342310302941288912051)
        A = get_random((2, 3, 5, 5), dtype=dtype, rng=rng)
        b = get_random(bdim, dtype=dtype, rng=rng)
        x = linalg.solve(A, b)
        if len(bdim) == 1:
            x = x[..., np.newaxis]
            b = b[..., np.newaxis]
        assert_allclose(A @ x - b, 0, atol=2e-6)
>       assert_allclose(x, np.linalg.solve(A, b), atol=3e-6)
E       AssertionError: 
E       Not equal to tolerance rtol=1e-07, atol=3e-06
E       
E       Mismatched elements: 1 / 120 (0.833%)
E       Mismatch at index:
E        [0, 2, 3, 2]: 6.206988334655762 (ACTUAL), 6.206984519958496 (DESIRED)
E       Max absolute difference among violations: 3.8146973e-06
E       Max relative difference among violations: 6.145814e-07
E        ACTUAL: array([[[[-0.043413,  0.581656,  1.552659,  1.236517],
E                [ 0.55996 , -0.884823,  1.266554, -0.218998],
E                [-0.074441,  0.693561, -2.024928, -0.646222],...
E        DESIRED: array([[[[-0.043413,  0.581656,  1.552659,  1.236518],
E                [ 0.55996 , -0.884823,  1.266554, -0.218998],
E                [-0.074441,  0.693562, -2.024928, -0.646223],...

scipy/linalg/tests/test_batch.py:456: AssertionError
___________________________________________________________________________________________________________ TestBatch.test_lu_solve[float32-bdim2] ____________________________________________________________________________________________________________

self = <scipy.linalg.tests.test_batch.TestBatch object at 0x14b2f5c2a2b0>, bdim = (2, 3, 5, 4), dtype = <class 'numpy.float32'>

    @pytest.mark.parametrize('bdim', [(5,), (5, 4), (2, 3, 5, 4)])
    @pytest.mark.parametrize('dtype', floating)
    def test_lu_solve(self, bdim, dtype):
        rng = np.random.default_rng(8342310302941288912051)
        A = get_random((2, 3, 5, 5), dtype=dtype, rng=rng)
        b = get_random(bdim, dtype=dtype, rng=rng)
        lu_and_piv = linalg.lu_factor(A)
        x = linalg.lu_solve(lu_and_piv, b)
        if len(bdim) == 1:
            x = x[..., np.newaxis]
            b = b[..., np.newaxis]
        assert_allclose(A @ x - b, 0, atol=2e-6)
>       assert_allclose(x, np.linalg.solve(A, b), atol=3e-6)
E       AssertionError: 
E       Not equal to tolerance rtol=1e-07, atol=3e-06
E       
E       Mismatched elements: 1 / 120 (0.833%)
E       Mismatch at index:
E        [0, 2, 3, 2]: 6.206988334655762 (ACTUAL), 6.206984519958496 (DESIRED)
E       Max absolute difference among violations: 3.8146973e-06
E       Max relative difference among violations: 6.145814e-07
E        ACTUAL: array([[[[-0.043413,  0.581656,  1.552659,  1.236517],
E                [ 0.55996 , -0.884823,  1.266554, -0.218998],
E                [-0.074441,  0.693561, -2.024928, -0.646222],...
E        DESIRED: array([[[[-0.043413,  0.581656,  1.552659,  1.236518],
E                [ 0.55996 , -0.884823,  1.266554, -0.218998],
E                [-0.074441,  0.693562, -2.024928, -0.646223],...

scipy/linalg/tests/test_batch.py:470: AssertionError

Micket · 2026-05-29T12:57:58Z

It is exactly the same issue @Thyre . I assume you use AOCL-BLAS here?
It's a minor difference from blas implementations.
OpenBLAS is extra accurate
BLIS is very inaccurate
AOCL-BLAS is somewhat accurate
but scipy only wrote the test to accept the really good, and really bad implementations. The somewhat accurate isn't accepted. Makes no sense.

Thyre · 2026-05-29T13:01:07Z

It is exactly the same issue @Thyre . I assume you use AOCL-BLAS here? It's a minor difference from blas implementations. OpenBLAS is extra accurate BLIS is very inaccurate AOCL-BLAS is somewhat accurate but scipy only wrote the test to accept the really good, and really bad implementations. The somewhat accurate isn't accepted. Makes no sense.

Yeah, looks like I had this still set in my config, but forgot about it:

Default BLAS:
    System:       OPENBLAS
    User:         AOCL_MT
    Host:         (none)
    Active Default: AOCL_MT (User)
Run-time properties:
   verbose = 0 (User)

Thyre · 2026-05-29T13:07:25Z

Test report by @pavelToman
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#4143, easybuilders/easybuild-easyblocks#4144
FAILED Build succeeded for 0 out of 1 (total: 5 mins 45 secs) (1 easyconfigs in total)
node4015.donphan.os - Linux RHEL 9.6, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz, 1 x NVIDIA NVIDIA A2, 595.71.05, Python 3.9.21
See https://gist.github.com/pavelToman/a86b34a754c512f6901343fa28d00ab5 for a full test report.

Given that it fails and did not hang, maybe you're hitting something different here. The logs probably should tell you more. The ulimit command should correctly show up in the shell command.

Thyre · 2026-05-29T13:42:36Z

Test report by @Thyre
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#4144, easybuilders/easybuild-easyblocks#4143
SUCCESS
Build succeeded for 1 out of 1 (total: 36 mins 43 secs) (1 easyconfigs in total)
Linux - Linux Arch Linux UNKNOWN, x86_64, AMD Ryzen 7 7800X3D 8-Core Processor (zen4), 1 x AMD Navi 48 [Radeon RX 9070/9070 XT/9070 GRE] (device id: 0x7550, gfx: gfx1201, driver: Linuxversion7.0.10-arch1-1(linux@archlinux)(gcc(GCC)16.1.120260430,GNUld(GNUBinutils)2.46.0)#1SMPPREEMPT_DYNAMICSat,23May202614:21:20+0000), 1 x AMD Raphael (device id: 0x164e, gfx: gfx1036, driver: Linuxversion7.0.10-arch1-1(linux@archlinux)(gcc(GCC)16.1.120260430,GNUld(GNUBinutils)2.46.0)#1SMPPREEMPT_DYNAMICSat,23May202614:21:20+0000), Python 3.14.5
See https://gist.github.com/Thyre/9ff0d55bfe18ddb25797a384fe5eb7f5 for a full test report.

pavelToman · 2026-05-29T13:53:57Z

Test report by @pavelToman
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#4143, easybuilders/easybuild-easyblocks#4144
FAILED Build succeeded for 0 out of 1 (total: 5 mins 45 secs) (1 easyconfigs in total)
node4015.donphan.os - Linux RHEL 9.6, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz, 1 x NVIDIA NVIDIA A2, 595.71.05, Python 3.9.21
See https://gist.github.com/pavelToman/a86b34a754c512f6901343fa28d00ab5 for a full test report.

Given that it fails and did not hang, maybe you're hitting something different here. The logs probably should tell you more. The ulimit command should correctly show up in the shell command.

It always failed like that for me when ulimit -s unlimited - then tests crash without the error and the last test has no PASSED/FAILED and it is always one of these:

numpy/_core/tests/test_dtype.py::TestMonsterType::test_list_recursion
numpy/_core/tests/test_dtype.py::TestMonsterType::test_dict_recursion
numpy/_core/tests/test_multiarray.py::TestConversion::test_to_bool_scalar_not_convertible
numpy/_core/tests/test_regression.py::TestRegression::test_object_array_self_reference
numpy/_core/tests/test_regression.py::TestRegression::test_object_array_circular_reference

It only hangs when I run tests from cmd.sh.
I am gonna run it again and check the log for details.

EDIT:
The easyblock PR 4144 must be first in --include-easyblocks-from-pr to set ulimit -s correctly

pavelToman · 2026-05-29T15:58:04Z

Test report by @pavelToman
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#4144, easybuilders/easybuild-easyblocks#4143
SUCCESS
Build succeeded for 1 out of 1 (total: 1 hour 28 mins 33 secs) (1 easyconfigs in total)
node4001.donphan.os - Linux RHEL 9.6, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz, 1 x NVIDIA NVIDIA A2, 595.71.05, Python 3.9.21
See https://gist.github.com/pavelToman/53ea15431be6ffa903b3d8b1a3e39026 for a full test report.

Flamefire · 2026-05-29T16:51:09Z

Python-bundlePyPI has an extensions using JavaScript now? Triggered my $HOME-access check:

  ENOTDIR: not a directory, stat '/home/s3248973/.npm/_cacache/content-v2/sha512/08/2d/5b38bf3b3c85920610dc4eb75e2e8e9e193ee6085b6b834b8826da89505c8af9e267ce5f00d67887e7abaeeca31ae5716bb6257e010b873b79fb0ec1e72d'

pavelToman · 2026-05-29T17:05:44Z

Test report by @pavelToman
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#4144, easybuilders/easybuild-easyblocks#4143
SUCCESS
Build succeeded for 1 out of 1 (total: 1 hour 0 mins 30 secs) (1 easyconfigs in total)
node4207.shinx.os - Linux RHEL 9.6, x86_64, AMD EPYC 9654 96-Core Processor, Python 3.9.21
See https://gist.github.com/pavelToman/0e3e28fe46bf2dec0f9fcef5b9368eb7 for a full test report.

Micket · 2026-05-29T21:57:53Z

Test report by @Micket
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#4144, easybuilders/easybuild-easyblocks#4143
SUCCESS
Build succeeded for 4 out of 4 (total: 2 hours 0 mins 20 secs) (1 easyconfigs in total)
vera-icelake-build - Linux Rocky Linux 9.6, x86_64, Intel(R) Xeon(R) Silver 4316 CPU @ 2.30GHz, Python 3.9.21
See https://gist.github.com/Micket/15bd6928ac09b1f66aa50083517d5f49 for a full test report.

Thyre · 2026-05-30T10:27:31Z

@boegelbot please test @ jsc-zen3

boegelbot · 2026-05-30T10:30:08Z

@Thyre: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=26109 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_26109 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 10548

Test results coming soon (I hope)...

Details

- notification for comment with ID 4582536370 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2026-05-30T11:41:29Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (total: 1 hour 8 mins 20 secs) (1 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.7, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.25
See https://gist.github.com/boegelbot/5fe50d57b235b21566a35341558ad783 for a full test report.

Thyre · 2026-05-31T08:25:36Z

Python-bundlePyPI has an extensions using JavaScript now? Triggered my $HOME-access check:

  ENOTDIR: not a directory, stat '/home/s3248973/.npm/_cacache/content-v2/sha512/08/2d/5b38bf3b3c85920610dc4eb75e2e8e9e193ee6085b6b834b8826da89505c8af9e267ce5f00d67887e7abaeeca31ae5716bb6257e010b873b79fb0ec1e72d'

We should keep track of this in an issue. Writing to $HOME seems incorrect, downloading npm during the build even more so.

pavelToman · 2026-06-01T09:02:29Z

Python-bundlePyPI has an extensions using JavaScript now? Triggered my $HOME-access check:
  ENOTDIR: not a directory, stat '/home/s3248973/.npm/_cacache/content-v2/sha512/08/2d/5b38bf3b3c85920610dc4eb75e2e8e9e193ee6085b6b834b8826da89505c8af9e267ce5f00d67887e7abaeeca31ae5716bb6257e010b873b79fb0ec1e72d'
We should keep track of this in an issue. Writing to $HOME seems incorrect, downloading npm during the build even more so.

I was asked to add furo to the PYPI-Python-bundle, but it needs also nodeenv and sphinx-theme-builder during the build and installation.
So one way is to install furo from wheels or remove it from the bundle. What do you think?

EDIT:
PyPI-bundle updated:

update Python-bundle-PyPI 2026.04 to use wheel for furo extension, to avoid use of js/npm #26140

Micket

lgtm

jfgrimm · 2026-06-01T14:03:52Z

Test report by @jfgrimm
SUCCESS
Build succeeded for 2 out of 2 (total: 1 hour 26 mins 43 secs) (2 easyconfigs in total)
node032.viking2.yor.alces.network - Linux Rocky Linux 8.10, x86_64, AMD EPYC 7643 48-Core Processor, Python 3.6.8
See https://gist.github.com/jfgrimm/13a8b25e33e7e49395f5a2ca8fcee5c3 for a full test report.

adding easyconfigs: SciPy-bundle-2026.05-gfbf-2026.1.eb and patches: …

6a9b61d

…scipy-1.17.1_relax-tests-py314.patch

pavelToman added the update label May 28, 2026

github-actions Bot added the 2026.1 issues & PRs related to 2026.1 common toolchains label May 28, 2026

This was referenced May 28, 2026

PhyStack - python bundles with foss/2026.1 vscentrum/vsc-software-stack#650

Open

TEST_BUG: NumPy v2.4.6 tests hang on recursive/self-referential object arrays with CPython 3.14.2 numpy/numpy#31512

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Micket added this to the next release (5.3.1?) milestone May 29, 2026

Thyre added the ready-to-review label May 31, 2026

pavelToman mentioned this pull request Jun 1, 2026

update Python-bundle-PyPI 2026.04 to use wheel for furo extension, to avoid use of js/npm #26140

Merged

Micket approved these changes Jun 1, 2026

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Micket merged commit 2775fcd into easybuilders:develop Jun 1, 2026
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Updated software SciPy-bundle-2026.05-gfbf-2026.1.eb

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