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pythonPackages.atomman: init at 1.2.3 #48183

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merged 3 commits into from Oct 31, 2018
Merged

pythonPackages.atomman: init at 1.2.3 #48183

merged 3 commits into from Oct 31, 2018

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costrouc
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Motivation for this change

Material science python packages for molecular dynamics.

Things done

pythonPackages.numericalunits: init at 1.16

pythonPackages.DataModelDict: init at 0.9.4

pythonPackages.atomman: init at 1.2.3

  • 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 costrouc requested a review from FRidh as a code owner October 10, 2018 22:15
FRidh
FRidh requested changes Oct 13, 2018
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pkgs/top-level/python-packages.nix Outdated Show resolved Hide resolved
@costrouc costrouc force-pushed the costrouc/python-atomman branch 2 times, most recently from 89e44dd to e9f3562 Compare October 14, 2018 14:28
@costrouc
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Package name normalize and ready for merge.

dotlambda
dotlambda requested changes Oct 30, 2018
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@dotlambda dotlambda left a comment

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Commit message needs to be fixed and merge conflict needs to be resolved.

dotlambda
dotlambda reviewed Oct 30, 2018
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pkgs/development/python-modules/atomman/default.nix
propagatedBuildInputs = [ xmltodict datamodeldict numpy matplotlib scipy pandas cython numericalunits ];

# tests not included with Pypi release
doCheck = false;
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lmhale99/atomman#2

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You should enable tests once a new version with this PR merged is released.

@costrouc
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@dotlambda fixed merge conflict. I will create a new PR later to include tests if atomman adds them.

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@GrahamcOfBorg build python2.pkgs.atomman python3.pkgs.atomman

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Success on x86_64-darwin (full log)

Attempted: python2.pkgs.atomman, python3.pkgs.atomman

Partial log (click to expand)

Requirement already satisfied: setuptools in /nix/store/lzlwmzcg98hrvr1ri721sbm2jisir07l-python3.6-bootstrapped-pip-18.1/lib/python3.6/site-packages (from kiwisolver>=1.0.1->matplotlib->atomman==1.2.3) (40.4.3)
Installing collected packages: atomman
Successfully installed atomman-1.2.3
/private/tmp/nix-build-python3.6-atomman-1.2.3.drv-0/atomman-1.2.3
post-installation fixup
strip is /nix/store/g5r4apl0za012ffs6ladinwa5w0m1l3k-cctools-binutils-darwin/bin/strip
stripping (with command strip and flags -S) in /nix/store/jj7cy2vmr7vs24gn0pp5f348bzvl5l8a-python3.6-atomman-1.2.3/lib
patching script interpreter paths in /nix/store/jj7cy2vmr7vs24gn0pp5f348bzvl5l8a-python3.6-atomman-1.2.3
/nix/store/8wb5jdl6kyvfpm27jf2l1409md52j50n-python2.7-atomman-1.2.3
/nix/store/jj7cy2vmr7vs24gn0pp5f348bzvl5l8a-python3.6-atomman-1.2.3

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Success on x86_64-linux (full log)

Attempted: python2.pkgs.atomman, python3.pkgs.atomman

Partial log (click to expand)

/build/atomman-1.2.3
post-installation fixup
shrinking RPATHs of ELF executables and libraries in /nix/store/sqfhz8pq0rm59mwfhh30xgm6kjrrvmmm-python3.6-atomman-1.2.3
shrinking /nix/store/sqfhz8pq0rm59mwfhh30xgm6kjrrvmmm-python3.6-atomman-1.2.3/lib/python3.6/site-packages/atomman/core/cythonized.cpython-36m-x86_64-linux-gnu.so
strip is /nix/store/vcc4svb8gy29g4pam2zja6llkbcwsyiq-binutils-2.30/bin/strip
stripping (with command strip and flags -S) in /nix/store/sqfhz8pq0rm59mwfhh30xgm6kjrrvmmm-python3.6-atomman-1.2.3/lib
patching script interpreter paths in /nix/store/sqfhz8pq0rm59mwfhh30xgm6kjrrvmmm-python3.6-atomman-1.2.3
checking for references to /build in /nix/store/sqfhz8pq0rm59mwfhh30xgm6kjrrvmmm-python3.6-atomman-1.2.3...
/nix/store/p6p4cy0d7vwp4qdqfsmmicv6mi2x1xns-python2.7-atomman-1.2.3
/nix/store/sqfhz8pq0rm59mwfhh30xgm6kjrrvmmm-python3.6-atomman-1.2.3

@dotlambda dotlambda merged commit e0772e6 into NixOS:master Oct 31, 2018
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Failure on aarch64-linux (full log)

Attempted: python2.pkgs.atomman, python3.pkgs.atomman

Partial log (click to expand)

  /nix/store/qfdbglqq4rmjv33y3nhi5qlifgxyg34m-python3.6-pandas-0.23.4/lib/python3.6/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/qfdbglqq4rmjv33y3nhi5qlifgxyg34m-python3.6-pandas-0.23.4/lib/python3.6/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, 16897 passed, 1027 skipped, 11896 deselected, 37 xfailed, 2 xpassed, 10 warnings in 595.77 seconds
builder for '/nix/store/k37vq3id2j6pmwr9dc64gghdk5yidw7x-python3.6-pandas-0.23.4.drv' failed with exit code 1
cannot build derivation '/nix/store/jzsaqg7lbr4jcr60fd78daxwly4mblp9-python3.6-atomman-1.2.3.drv': 1 dependencies couldn't be built
error: build of '/nix/store/jzsaqg7lbr4jcr60fd78daxwly4mblp9-python3.6-atomman-1.2.3.drv', '/nix/store/qpyphn5bvp9mwccv6xzq395wi8xgrh7l-python2.7-atomman-1.2.3.drv' failed

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@FRidh FRidh FRidh requested changes

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@costrouc @dotlambda @GrahamcOfBorg @FRidh