[22.05] backport python39Packages.numba-scipy: update stale substituteInPlace

[risicle]

Description of changes

#174152 - needed to include a commit from #174720 to get arviz patch to apply.

Backport of #174152 & #174720

This fixes several packages.

ZHF: #172160

Things done

• Built on platform(s)
  • x86_64-linux
  • aarch64-linux
  • x86_64-darwin
  • aarch64-darwin
• For non-Linux: Is sandbox = true set in nix.conf? (See Nix manual)
• Tested, as applicable:
  • NixOS test(s) (look inside nixos/tests)
  • and/or package tests
  • or, for functions and "core" functionality, tests in lib/tests or pkgs/test
  • made sure NixOS tests are linked to the relevant packages
• Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage
• Tested basic functionality of all binary files (usually in ./result/bin/)
• 22.05 Release Notes (or backporting 21.11 Release notes)
  • (Package updates) Added a release notes entry if the change is major or breaking
  • (Module updates) Added a release notes entry if the change is significant
  • (Module addition) Added a release notes entry if adding a new NixOS module
  • (Release notes changes) Ran nixos/doc/manual/md-to-db.sh to update generated release notes
• Fits CONTRIBUTING.md.

[mweinelt]

error: builder for '/nix/store/k5j9k8lx8z19jj6h93fcjn4cqbrbw0r1-python3.10-graspologic-1.0.0.drv' failed with exit code 1;
       last 10 log lines:
       > removing build/bdist.linux-x86_64/wheel
       > Finished executing setuptoolsBuildPhase
       > installing
       > Executing pipInstallPhase
       > /build/source/dist /build/source
       > Processing ./graspologic-1.0.0-py3-none-any.whl
       > ERROR: Could not find a version that satisfies the requirement beartype>=0.10.0 (from graspologic) (from versions: none)
       > ERROR: No matching distribution found for beartype>=0.10.0
       >
       > builder for '/nix/store/k5j9k8lx8z19jj6h93fcjn4cqbrbw0r1-python3.10-graspologic-1.0.0.drv' failed with exit code 1
       For full logs, run 'nix log /nix/store/k5j9k8lx8z19jj6h93fcjn4cqbrbw0r1-python3.10-graspologic-1.0.0.drv'.

error: builder for '/nix/store/dd59iz763as2404swdaq96bnilmzq1xg-python3.9-graspologic-1.0.0.drv' failed with exit code 1;
       last 10 log lines:
       > removing build/bdist.linux-x86_64/wheel
       > Finished executing setuptoolsBuildPhase
       > installing
       > Executing pipInstallPhase
       > /build/source/dist /build/source
       > Processing ./graspologic-1.0.0-py3-none-any.whl
       > ERROR: Could not find a version that satisfies the requirement graspologic-native>=1.1.1 (from graspologic) (from versions: none)
       > ERROR: No matching distribution found for graspologic-native>=1.1.1
       >
       > builder for '/nix/store/dd59iz763as2404swdaq96bnilmzq1xg-python3.9-graspologic-1.0.0.drv' failed with exit code 1
       For full logs, run 'nix log /nix/store/dd59iz763as2404swdaq96bnilmzq1xg-python3.9-graspologic-1.0.0.drv'.

Has been marked broken due to missing graspologic-native dependency on master, but not on release-22.05

[mweinelt]

Result of nixpkgs-review pr 175286 run on x86_64-linux 1

4 packages marked as broken and skipped:

• python310Packages.pygbm
• python310Packages.shap
• python39Packages.pygbm
• python39Packages.shap

2 packages failed to build:

• python310Packages.graspologic
• python39Packages.graspologic

73 packages built:

• python310Packages.aeppl
• python310Packages.aesara
• python310Packages.awkward
• python310Packages.clifford
• python310Packages.cppe
• python310Packages.dask-ml
• python310Packages.datashader
• python310Packages.fastparquet
• python310Packages.ffcv
• python310Packages.gumath
• python310Packages.hyppo
• python310Packages.intake
• python310Packages.intake-parquet
• python310Packages.librosa
• python310Packages.numba
• python310Packages.numba-scipy
• python310Packages.numbaWithCuda
• python310Packages.numdifftools
• python310Packages.persim
• python310Packages.phik
• python310Packages.pygmo
• python310Packages.pynndescent
• python310Packages.pyscf
• python310Packages.qiskit
• python310Packages.qiskit-machine-learning
• python310Packages.resampy
• python310Packages.ripser
• python310Packages.scikit-tda
• python310Packages.sparse
• python310Packages.stumpy
• python310Packages.stytra
• python310Packages.tensorly
• python310Packages.timezonefinder
• python310Packages.trackpy
• python310Packages.umap-learn
• python310Packages.uproot
• python39Packages.aeppl
• python39Packages.aesara
• python39Packages.awkward
• python39Packages.clifford
• python39Packages.cppe
• python39Packages.dask-ml
• python39Packages.datashader
• python39Packages.fastparquet
• python39Packages.ffcv
• python39Packages.gumath
• python39Packages.hyppo
• python39Packages.intake
• python39Packages.intake-parquet
• python39Packages.librosa
• python39Packages.numba
• python39Packages.numba-scipy
• python39Packages.numbaWithCuda
• python39Packages.numdifftools
• python39Packages.persim
• python39Packages.phik
• python39Packages.pygmo
• python39Packages.pynndescent
• python39Packages.pyscf
• python39Packages.qiskit
• python39Packages.qiskit-machine-learning
• python39Packages.resampy
• python39Packages.ripser
• python39Packages.scikit-tda
• python39Packages.sparse
• python39Packages.stumpy
• python39Packages.stytra
• python39Packages.tensorly
• python39Packages.timezonefinder
• python39Packages.trackpy
• python39Packages.umap-learn
• python39Packages.uproot
• tts

[mweinelt]

python310.pkgs.arviz

Before

error: numba-0.55.1 not supported for interpreter python3.10

Now

SIGILL, probably related to my builder.... nvm

error: builder for '/nix/store/dpfsyawij8gxysjjcg7h2c1lckprbqpd-python3.10-arviz-0.12.1.drv' failed with exit code 1;
       last 10 log lines:
       > running install tests
       > no Makefile or custom installCheckPhase, doing nothing
       > pythonCatchConflictsPhase
       > pythonRemoveBinBytecodePhase
       > pythonImportsCheckPhase
       > Executing pythonImportsCheckPhase
       > Check whether the following modules can be imported: arviz
       > Matplotlib created a temporary config/cache directory at /build/matplotlib-dr1pk2zu because the default path (/homeless-shelter/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.
       > /nix/store/acjcrvqk7cz8690jh0chz6jbi2znlyx9-python-imports-check-hook.sh/nix-support/setup-hook: line 9:   422 Illegal instruction     (core dumped) /nix/store/40n9pd613v8fc3x39yjrgs1i7d4q8yl0-python3-3.10.4/bin/python3.10 -c 'import os; import importlib; list(map(lambda mod: importlib.import_module(mod), os.environ["pythonImportsCheck"].split()))'
       > builder for '/nix/store/dpfsyawij8gxysjjcg7h2c1lckprbqpd-python3.10-arviz-0.12.1.drv' failed with exit code 132
       For full logs, run 'nix log /nix/store/dpfsyawij8gxysjjcg7h2c1lckprbqpd-python3.10-arviz-0.12.1.drv'.

[mweinelt]

Pick 9102b1c to mark graspologic as broken.

[risicle]

Should already be #175318

[risicle]

Do you get the arviz SIGILL on master?

[mweinelt]

It just gets SIGILL on older x86_64 models, nothing we can do about that. Works on my desktop.