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pythonPackages.pymatgen: 2018.8.10 -> 2018.9.1 #46132

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merged 1 commit into from Sep 6, 2018
Merged

pythonPackages.pymatgen: 2018.8.10 -> 2018.9.1 #46132

merged 1 commit into from Sep 6, 2018

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costrouc
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@costrouc costrouc commented Sep 6, 2018 •
edited

Also 2018.8.10 does not build in previous state because auto updating
from pypi did not account for a new requirement networkx. This has
been added.

Contributes to #45960

Motivation for this change

pymatgen does not build in current state.

Things done

pythonPackages.pymatgen: 2018.8.10 -> 2018.9.1
Added networkx as dependency

  • 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.

@costrouc
pythonPackages.pymatgen: 2018.8.10 -> 2018.9.1
63cf879 
Also 2018.8.10 does not build in previous state because auto updating
from pypi did not account for a new requirement `networkx`. This has
been added.
@costrouc costrouc requested a review from FRidh as a code owner September 6, 2018 04:08
@Mic92
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Mic92 commented Sep 6, 2018

@GrahamcOfBorg build pythonPackages.pymatgen

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Success on x86_64-linux (full log)

Attempted: pythonPackages.pymatgen

Partial log (click to expand)

strip is /nix/store/h0lbngpv6ln56hjj59i6l77vxq25flbz-binutils-2.30/bin/strip
stripping (with command strip and flags -S) in /nix/store/4ws66nq18ggiil5pbfqgnqxv0244hijk-python2.7-pymatgen-2018.9.1/lib  /nix/store/4ws66nq18ggiil5pbfqgnqxv0244hijk-python2.7-pymatgen-2018.9.1/bin
patching script interpreter paths in /nix/store/4ws66nq18ggiil5pbfqgnqxv0244hijk-python2.7-pymatgen-2018.9.1
checking for references to /build in /nix/store/4ws66nq18ggiil5pbfqgnqxv0244hijk-python2.7-pymatgen-2018.9.1...
wrapping `/nix/store/4ws66nq18ggiil5pbfqgnqxv0244hijk-python2.7-pymatgen-2018.9.1/bin/feff_plot_dos'...
wrapping `/nix/store/4ws66nq18ggiil5pbfqgnqxv0244hijk-python2.7-pymatgen-2018.9.1/bin/feff_input_generation'...
wrapping `/nix/store/4ws66nq18ggiil5pbfqgnqxv0244hijk-python2.7-pymatgen-2018.9.1/bin/feff_plot_cross_section'...
wrapping `/nix/store/4ws66nq18ggiil5pbfqgnqxv0244hijk-python2.7-pymatgen-2018.9.1/bin/pmg'...
wrapping `/nix/store/4ws66nq18ggiil5pbfqgnqxv0244hijk-python2.7-pymatgen-2018.9.1/bin/get_environment'...
wrapping `/nix/store/4ws66nq18ggiil5pbfqgnqxv0244hijk-python2.7-pymatgen-2018.9.1/bin/gaussian_analyzer'...

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Success on x86_64-darwin (full log)

Attempted: pythonPackages.pymatgen

Partial log (click to expand)

strip is /nix/store/df6k4mgdjxciy0f637lryp7c9ln7n1m3-cctools-binutils-darwin/bin/strip
stripping (with command strip and flags -S) in /nix/store/6y3bysrb4h4prnbxk2nzp3zlh8pgp1sg-python2.7-pymatgen-2018.9.1/lib  /nix/store/6y3bysrb4h4prnbxk2nzp3zlh8pgp1sg-python2.7-pymatgen-2018.9.1/bin
patching script interpreter paths in /nix/store/6y3bysrb4h4prnbxk2nzp3zlh8pgp1sg-python2.7-pymatgen-2018.9.1
wrapping `/nix/store/6y3bysrb4h4prnbxk2nzp3zlh8pgp1sg-python2.7-pymatgen-2018.9.1/bin/feff_input_generation'...
wrapping `/nix/store/6y3bysrb4h4prnbxk2nzp3zlh8pgp1sg-python2.7-pymatgen-2018.9.1/bin/feff_plot_cross_section'...
wrapping `/nix/store/6y3bysrb4h4prnbxk2nzp3zlh8pgp1sg-python2.7-pymatgen-2018.9.1/bin/feff_plot_dos'...
wrapping `/nix/store/6y3bysrb4h4prnbxk2nzp3zlh8pgp1sg-python2.7-pymatgen-2018.9.1/bin/gaussian_analyzer'...
wrapping `/nix/store/6y3bysrb4h4prnbxk2nzp3zlh8pgp1sg-python2.7-pymatgen-2018.9.1/bin/get_environment'...
wrapping `/nix/store/6y3bysrb4h4prnbxk2nzp3zlh8pgp1sg-python2.7-pymatgen-2018.9.1/bin/pmg'...
/nix/store/6y3bysrb4h4prnbxk2nzp3zlh8pgp1sg-python2.7-pymatgen-2018.9.1

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Failure on aarch64-linux (full log)

Attempted: pythonPackages.pymatgen

Partial log (click to expand)

  /nix/store/0fplnr41gl5v4rdmk4hdi47im79zjg5v-python2.7-pandas-0.23.4/lib/python2.7/site-packages/pandas/core/internals.py:312: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.
    return self.values[slicer]
  /nix/store/0fplnr41gl5v4rdmk4hdi47im79zjg5v-python2.7-pandas-0.23.4/lib/python2.7/site-packages/pandas/core/indexes/datetimelike.py:428: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.
    result = getitem(key)

-- Docs: https://docs.pytest.org/en/latest/warnings.html
 5 failed, 16896 passed, 1030 skipped, 11887 deselected, 37 xfailed, 2 xpassed, 6 warnings in 1567.28 seconds
builder for '/nix/store/b5j1ydbjjxkn2nvnxsyc4rsllrzlbkm5-python2.7-pandas-0.23.4.drv' failed with exit code 1
cannot build derivation '/nix/store/za7hrxw4csxq534q2myp0yrmqg5dxc31-python2.7-pymatgen-2018.9.1.drv': 1 dependencies couldn't be built
error: build of '/nix/store/za7hrxw4csxq534q2myp0yrmqg5dxc31-python2.7-pymatgen-2018.9.1.drv' failed

@Mic92 Mic92 merged commit 9a58565 into NixOS:master Sep 6, 2018
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Mic92 commented Sep 6, 2018

backport:

[detached HEAD eedff96] pythonPackages.pymatgen: 2018.8.10 -> 2018.9.1
Author: Chris Ostrouchov chris.ostrouchov@gmail.com
Date: Thu Sep 6 00:04:28 2018 -0400
1 file changed, 5 insertions(+), 6 deletions(-)

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