hdf5: make possible to use the v1.10 API #118454
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@FRidh you mentioned an issue with |
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This needs to target pandas segfaults in a tables test. tables is the pytables package that uses hdf5. https://hydra.nixos.org/build/140676472 |
vigra is not yet compatible with the v1.12 API [0][1]. [0] ukoethe/vigra#476 [1] ukoethe/vigra#476
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10.rebuild-darwin: 101-500
10.rebuild-linux: 101-500
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10.rebuild-darwin: 1-10
10.rebuild-linux: 1-10
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It looks like this solves the issue for vigra but pandas still segfault :/ |
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Good vigra is fixed. Pandas could have another cause then, or it is the update itself despite using the old api. To check, it is worthwhile building pandas against the old hdf5. |
It tried to revert the upgrade and build pandas and the segfault does not happen. I'm trying to see what's wrong with the upgrade. |
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In case we won't figure out (within a day or two, so staging-next can proceed), the alternative is to keep 1.11 in just for pandas. |
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This reverts commit b86327e. This is a temporary hack which can't be merged into master at some point because the package is actually broken. The real issue will likely be fixed in NixOS#118454.
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I have not made significant progress on this topic and I'm not sure I will in a timely manner. Maybe someone with more experience of the Python ecosystem/pandas could take a look and have more success than me. In the meantime to unblock the situation I have updated the PR to introduce |
Introduce hdf5_1_10 so it can be used by packages encountering issues hdf5 1.12.0.
Without that, the test suite of python3Packages.pandas segfault.
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This is a semi-automatic executed nixpkgs-review with nixpkgs-review-checks extension. It is checked by a human on a best effort basis and does not build all packages (e.g. lumo, tensorflow or pytorch). Result of 37 packages marked as broken and skipped:
18 packages failed to build and already failed to build on hydra master:
2 packages failed to build and are new build failures:
336 packages built:
the two build failures are probably not reproducible. Merging right now because I want to test home-assistant on staging/staging-next. |
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Motivation for this change
hdf5 v1.12 has introduced breaking changes to the API and some dependent packages are not yet compatible with it. This contribution adds a way to build the hdf5 library with the v1.10 API.
Things done
sandboxinnix.confon non-NixOS linux)nix-shell -p nixpkgs-review --run "nixpkgs-review wip"./result/bin/)nix path-info -Sbefore and after)