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Add patch to fix permission denied issue during PyTables installation. #22975

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dagonzalezfo wants to merge 3 commits into from
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Add patch to fix permission denied issue during PyTables installation. #22975

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72360b0
Add patch changing copy by copyfile to solve permission denied issue
dagonzalezfo May 29, 2025
5b393e1
Add patch to fix permission issue
dagonzalezfo May 29, 2025
1ac1eba
Update easybuild/easyconfigs/p/PyTables/PyTables-3.9.2-foss-2023b.eb
Micket May 30, 2025
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3 changes: 3 additions & 0 deletions easybuild/easyconfigs/p/PyTables/PyTables-3.9.2-foss-2023b.eb
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Original file line number Diff line number Diff line change
Expand Up @@ -49,12 +49,15 @@ exts_list = [
'patches': [
'PyTables-3.8.0_fix-libs.patch',
'PyTables-3.9.2_fix-find-blosc2-dep.patch',
'PyTables-3.9.2_fix-filecopy-permissions.patch'
],
'checksums': [
{'tables-3.9.2.tar.gz': 'd470263c2e50c4b7c8635a0d99ac1ff2f9e704c24d71e5fa33c4529e7d0ad9c3'},
{'PyTables-3.8.0_fix-libs.patch': '7a1e6fa1f9169e52293e2b433a4302fa13c5d31e7709cd4fe0e087199b9e3f8a'},
{'PyTables-3.9.2_fix-find-blosc2-dep.patch':
'e2149f43da12d9ba26cca4c838f6e8a4694adab75c0f055b186674a017e41a55'},
{'PyTables-3.9.2_fix-filecopy-permissions.patch':
'9965914c1924e16b35cd005098879c00ab769da4ffb69f5efbb1d95bce6b59b7'},
],
}),
]
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13 changes: 13 additions & 0 deletions easybuild/easyconfigs/p/PyTables/PyTables-3.9.2_fix-filecopy-permissions.patch
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Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
change copy by copyfile to avoid permission issues
author: Danilo Gonzalez (DoitNow)
--- setup.py.orig 2025-05-29 16:30:25.438309725 +0200
+++ setup.py 2025-05-29 16:31:20.932235168 +0200
@@ -962,7 +962,7 @@
)
platform_system = platform.system()
if platform_system == "Linux":
- shutil.copy(libdir / "libblosc2.so", ROOT / "tables")
+ shutil.copyfile(libdir / "libblosc2.so", ROOT / "tables" / "libblosc2.so")
copy_libs += ["libblosc2.so"]

dll_dir = "/tmp/hdf5/lib"