pythonPackages.phonopy: refactor

[costrouc]

Fixing phonopy not building. Tests were moved on Jul 30.

Motivation for this change

Fixing #45960 phonopy not building.

Things done

• Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS)
• 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 nox --run "nox-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)
• Fits CONTRIBUTING.md.

---

[FRidh]

@GrahamcOfBorg build python2.pkgs.phonopy python3.pkgs.phonopy

[GrahamcOfBorg]

Failure on x86_64-linux (full log)

Attempted: python2.pkgs.phonopy, python3.pkgs.phonopy

Partial log (click to expand)

 y: array([2.990558e+01, 8.017501e+00, 3.839426e+00, 2.339812e+00,
       1.633024e+00, 1.245578e+00, 6.772900e-05, 3.625850e-04,
       2.829889e-02, 5.767737e-03])

----------------------------------------------------------------------
Ran 51 tests in 22.281s

FAILED (failures=1)
builder for '/nix/store/x3rp47k1syl5vnk7mk76i80nk7vlvsw5-python3.6-phonopy-1.13.2.107.drv' failed with exit code 1
error: build of '/nix/store/kbr90ysi7m4h0p05r7cqw20izn4h6x3w-python2.7-phonopy-1.13.2.107.drv', '/nix/store/x3rp47k1syl5vnk7mk76i80nk7vlvsw5-python3.6-phonopy-1.13.2.107.drv' failed

[GrahamcOfBorg]

Success on aarch64-linux (full log)

Attempted: python2.pkgs.phonopy, python3.pkgs.phonopy

Partial log (click to expand)

Ran 51 tests in 127.852s

OK
...................................................
----------------------------------------------------------------------
Ran 51 tests in 134.172s

OK
/nix/store/m4k3b93pilpg9mmv6354mx7yip08vp5d-python2.7-phonopy-1.13.2.107
/nix/store/lh4cc7cc0f7424lp3c0aswcgs7ymx9b5-python3.6-phonopy-1.13.2.107

[costrouc]

That is a weird test failure on x86_64-linux. I cannot reproduce and I am using sandbox...

[FRidh]

Likely the tolerances are incorrect. You can disable the specific test.

[costrouc]

@FRidh I have removed that test and added a comment about the issue. Test on x86 should pass now

[FRidh]

@GrahamcOfBorg build python2.pkgs.phonopy python3.pkgs.phonopy

[GrahamcOfBorg]

Success on x86_64-linux (full log)

Attempted: python2.pkgs.phonopy, python3.pkgs.phonopy

Partial log (click to expand)

wrapping `/nix/store/i8cia332pdffs46kz3ccms88qm7jlqvl-python3.6-phonopy-1.13.2.107/bin/phonopy-pdosplot'...
wrapping `/nix/store/i8cia332pdffs46kz3ccms88qm7jlqvl-python3.6-phonopy-1.13.2.107/bin/phonopy-qha'...
running install tests
..................................................
----------------------------------------------------------------------
Ran 50 tests in 20.756s

OK
/nix/store/6jmlxjlyb0gfnp3989pzwlcg1l43f4k4-python2.7-phonopy-1.13.2.107
/nix/store/i8cia332pdffs46kz3ccms88qm7jlqvl-python3.6-phonopy-1.13.2.107

[GrahamcOfBorg]

Success on aarch64-linux (full log)

Attempted: python2.pkgs.phonopy, python3.pkgs.phonopy

Partial log (click to expand)

Ran 50 tests in 120.894s

OK
..................................................
----------------------------------------------------------------------
Ran 50 tests in 132.809s

OK
/nix/store/d7i796j6dhagkvlg813cycxr1a9dcmf8-python2.7-phonopy-1.13.2.107
/nix/store/vihbwmqag9rsj1yn58ryhh6b899iqg3c-python3.6-phonopy-1.13.2.107

[GrahamcOfBorg]

Success on x86_64-darwin (full log)

Attempted: python2.pkgs.phonopy, python3.pkgs.phonopy

Partial log (click to expand)

wrapping `/nix/store/j0pwxab08b611vag5g0rrckn1fcp48ah-python3.6-phonopy-1.13.2.107/bin/phonopy-vasp-born'...
wrapping `/nix/store/j0pwxab08b611vag5g0rrckn1fcp48ah-python3.6-phonopy-1.13.2.107/bin/phonopy-vasp-efe'...
running install tests
..................................................
----------------------------------------------------------------------
Ran 50 tests in 17.749s

OK
/nix/store/zla7xa5gr2xnk2p5smqw3r94615qaswn-python2.7-phonopy-1.13.2.107
/nix/store/j0pwxab08b611vag5g0rrckn1fcp48ah-python3.6-phonopy-1.13.2.107

[xeji]

backported: 53b9062