python38Packages.h5py: 3.1.0 -> 3.2.1

[SuperSandro2000]

Motivation for this change

Things done

• Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS linux)
• Built on platform(s)
  • NixOS
  • macOS
  • other Linux distributions
• Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
• Tested compilation of all pkgs that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review wip"
• Tested execution of all binary files (usually in ./result/bin/)
• Determined the impact on package closure size (by running nix path-info -S before and after)
• Ensured that relevant documentation is up to date
• Fits CONTRIBUTING.md.

[fabaff]

Could you please update the license in the process? BSD3 and not BSD2.

[fabaff]

hickle want h5py<3.0.0.

  ERROR: Could not find a version that satisfies the requirement h5py<3.0.0,>=2.8.0 (from hickle)

[r-rmcgibbo]

Result of nixpkgs-review pr 118844 at 0f56dbe1 run on x86_64-linux 1

13 packages marked as broken and skipped:

• python38Packages.arviz
• python38Packages.clifford
• python38Packages.dm-sonnet
• python38Packages.graph_nets
• python38Packages.optuna
• python38Packages.pymc3
• python38Packages.rl-coach
• python38Packages.tensorflow-probability
• python39Packages.dm-sonnet
• python39Packages.graph_nets
• ...

2 packages failed to build:

• python38Packages.hickle
• python39Packages.hickle

30 packages skipped due to time constraints:

• gpt2tc
• python38Packages.baselines
• python38Packages.caffe
• python38Packages.dipy
• python38Packages.edward
• python38Packages.mask-rcnn
• python38Packages.nilearn
• python38Packages.pywick
• python38Packages.scikit-tda
• python38Packages.sfepy
• ...

55 packages built successfully:

• python38Packages.Keras
• python38Packages.annoy
• python38Packages.aplpy
• python38Packages.asdf
• python38Packages.bayespy
• python38Packages.dicom2nifti
• python38Packages.h5netcdf
• python38Packages.h5py
• python38Packages.h5py-mpi
• python38Packages.keras-applications
• python38Packages.meshio
• python38Packages.nibabel
• python38Packages.nipy
• python38Packages.nipype
• python38Packages.nitime
• python38Packages.phonopy
• python38Packages.pybids
• python38Packages.pyregion
• python38Packages.pytest-astropy
• python38Packages.pytest-astropy-header
• python38Packages.python-openems
• python38Packages.qiskit
• python38Packages.qiskit-aqua
• python38Packages.radio_beam
• python38Packages.reproject
• python38Packages.sumo
• python38Packages.sunpy
• python39Packages.Keras
• python39Packages.annoy
• python39Packages.aplpy
• python39Packages.asdf
• python39Packages.bayespy
• python39Packages.dicom2nifti
• python39Packages.h5netcdf
• python39Packages.h5py
• python39Packages.h5py-mpi
• python39Packages.keras-applications
• python39Packages.meshio
• python39Packages.nibabel
• python39Packages.nipy
• python39Packages.nipype
• python39Packages.nitime
• python39Packages.phonopy
• python39Packages.pybids
• python39Packages.pyregion
• python39Packages.pytest-astropy
• python39Packages.pytest-astropy-header
• python39Packages.python-openems
• python39Packages.qiskit
• python39Packages.qiskit-aqua
• python39Packages.radio_beam
• python39Packages.reproject
• python39Packages.sumo
• python39Packages.worldengine
• visidata

4 suggestions:

• warning: unused-argument

  Unused argument: python.
  Near pkgs/development/python-modules/h5py/default.nix:1:27:

    |
  1 | { lib, fetchPypi, isPy27, python, buildPythonPackage, pythonOlder
    |                           ^
  

• warning: unused-argument

  Unused argument: fetchpatch.
  Near pkgs/development/python-modules/h5py/default.nix:2:51:

    |
  2 | , numpy, hdf5, cython, six, pkgconfig, unittest2, fetchpatch
    |                                                   ^
  

• warning: duplicate-check-inputs

  Dependencies listed in propagatedBuildInputs should not be repeated in checkInputs.

  Detected duplicates:

  • openssh-8.5p1

  Near pkgs/development/python-modules/h5py/default.nix:39:3:

     |
  39 |   checkInputs = lib.optional isPy27 unittest2 ++ [ pytestCheckHook openssh ];
     |   ^
  

  Near pkgs/development/python-modules/h5py/default.nix:43:3:

     |
  43 |   propagatedBuildInputs = [ numpy six]
     |   ^
  

• warning: maintainers-missing

  Package does not have a maintainer. Consider adding yourself?

  Near pkgs/development/python-modules/h5py/default.nix:49:3:

     |
  49 |   meta = with lib; {
     |   ^
  

Note that build failures may predate this PR, and could be nondeterministic or hardware dependent.
Please exercise your independent judgement.

[SuperSandro2000]

hickle want h5py<3.0.0.

  ERROR: Could not find a version that satisfies the requirement h5py<3.0.0,>=2.8.0 (from hickle)

That was already broken before this update. Let me run nixpkgs-review and then we can decide what to do with the failures.

[fabaff]

That was already broken before this update. Let me run nixpkgs-review and then we can decide what to do with the failures.

Yes, it was. telegraphic/hickle#143

[SuperSandro2000]

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).
If you have any questions or problems please reach out to SuperSandro2000 on IRC.

Result of nixpkgs-review pr 118844 run on x86_64-linux 1

11 packages marked as broken and skipped:

• python38Packages.arviz
• python38Packages.clifford
• python38Packages.dm-sonnet
• python38Packages.graph_nets
• python38Packages.optuna
• python38Packages.pymc3
• python38Packages.rl-coach
• python39Packages.dm-sonnet
• python39Packages.graph_nets
• python39Packages.optuna
• python39Packages.rl-coach

6 packages failed to build and already failed to build on hydra master:

• python38Packages.hickle: log was empty
• python38Packages.nilearn: log was empty
• python38Packages.pywick: log was empty
• python39Packages.hickle: log was empty
• python39Packages.nilearn: log was empty
• python39Packages.pywick: log was empty

2 packages failed to build and are new build failures:

• python38Packages.qiskit: log was empty
• python38Packages.qiskit-aqua: log was empty

64 packages built:

• gpt2tc
• python38Packages.Keras
• python38Packages.annoy
• python38Packages.aplpy
• python38Packages.asdf
• python38Packages.bayespy
• python38Packages.caffe
• python38Packages.dicom2nifti
• python38Packages.dipy
• python38Packages.h5netcdf
• python38Packages.h5py
• python38Packages.h5py-mpi
• python38Packages.keras-applications
• python38Packages.meshio
• python38Packages.nibabel
• python38Packages.nipy
• python38Packages.nipype
• python38Packages.nitime
• python38Packages.phonopy
• python38Packages.pybids
• python38Packages.pyregion
• python38Packages.pytest-astropy
• python38Packages.pytest-astropy-header
• python38Packages.python-openems
• python38Packages.radio_beam
• python38Packages.reproject
• python38Packages.sfepy
• python38Packages.spectral-cube
• python38Packages.sumo
• python38Packages.sunpy
• python38Packages.worldengine
• python39Packages.Keras
• python39Packages.annoy
• python39Packages.aplpy
• python39Packages.asdf
• python39Packages.bayespy
• python39Packages.caffe
• python39Packages.dicom2nifti
• python39Packages.dipy
• python39Packages.h5netcdf
• python39Packages.h5py
• python39Packages.h5py-mpi
• python39Packages.keras-applications
• python39Packages.meshio
• python39Packages.nibabel
• python39Packages.nipy
• python39Packages.nipype
• python39Packages.nitime
• python39Packages.phonopy
• python39Packages.pybids
• python39Packages.pyregion
• python39Packages.pytest-astropy
• python39Packages.pytest-astropy-header
• python39Packages.python-openems
• python39Packages.qiskit
• python39Packages.qiskit-aqua
• python39Packages.radio_beam
• python39Packages.reproject
• python39Packages.sfepy
• python39Packages.spectral-cube
• python39Packages.sumo
• python39Packages.sunpy
• python39Packages.worldengine
• visidata

---

python38Packages.qiskit has a separate PR fixing and updating all of the dependencies.