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dendropy: init at 4.3.0 #34533

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merged 1 commit into from Feb 8, 2018
Merged

dendropy: init at 4.3.0 #34533

merged 1 commit into from Feb 8, 2018

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unode
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@unode unode commented Feb 2, 2018

Motivation for this change

Dendropy is a versatile python module to handle several phylogenetic formats and build phylogenetic pipelines.

Things done
  • Tested using sandboxing (nix.useSandbox on NixOS, or option build-use-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/)
  • Fits CONTRIBUTING.md.

}:

buildPythonPackage rec {
name = "${pname}-${version}";
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no name

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I tried omitting name but that resulted in a failure when I tried locally

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There shouldn't be any. Did you rebase on latest master?
Btw, name is optional only for buildPythonPackage and buildPythonApplication.

sha256 = "bd5b35ce1a1c9253209b7b5f3939ac22beaa70e787f8129149b4f7ffe865d510";
};

preCheck = ''
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This might be better suited for postPatch.

@dotlambda
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@GrahamcOfBorg build python2.pkgs.dendropy python3.pkgs.dendropy

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Failure on x86_64-linux (full log)

Partial log (click to expand)

test_colless_tree_imbalance2 (dendropy.test.test_tree_calculations_and_metrics.TreeUnaryMetricsTest) ... ok
test_gamma2 (dendropy.test.test_tree_calculations_and_metrics.TreeUnaryMetricsTest) ... ok
test_sackin_index (dendropy.test.test_tree_calculations_and_metrics.TreeUnaryMetricsTest) ... ok
test_treeness (dendropy.test.test_tree_calculations_and_metrics.TreeUnaryMetricsTest) ... ok

----------------------------------------------------------------------
Ran 829 tests in 538.029s

OK
error: build of ‘/nix/store/x0iqrgf8i4z931y69dmvzjps53r9yvx8-python3.6-DendroPy-4.3.0.drv’ failed

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unode commented Feb 2, 2018

Looks like a few more tests need to be disabled. Doesn't seem like nixpkgs fault here.

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Failure on aarch64-linux (full log)

Partial log (click to expand)

test_plot_by_age (dendropy.test.test_asciitree.AsciiTreeTest) ... ok
test_plot_by_depth (dendropy.test.test_asciitree.AsciiTreeTest) ... ok
test_plot_by_length (dendropy.test.test_asciitree.AsciiTreeTest) ... ok
test_plot_by_level (dendropy.test.test_asciitree.AsciiTreeTest) ... ok

----------------------------------------------------------------------
Ran 829 tests in 2189.740s

OK
error: build of '/nix/store/w7zq8jbpfrk1h845jm0g3slndigqwf7s-python3.6-DendroPy-4.3.0.drv' failed

@FRidh
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FRidh commented Feb 3, 2018

The errors are:

UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 181: ordinal not in range(128)

Solution:

preCheck = ''
  export LC_ALL="en_US.UTF-8"
'';
checkInputs = [ pkgs.glibcLocales ];

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unode commented Feb 5, 2018

@GrahamcOfBorg build python2.pkgs.dendropy python3.pkgs.dendropy

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Success on x86_64-linux (full log)

Partial log (click to expand)

test_gamma2 (dendropy.test.test_tree_calculations_and_metrics.TreeUnaryMetricsTest) ... ok
test_sackin_index (dendropy.test.test_tree_calculations_and_metrics.TreeUnaryMetricsTest) ... ok
test_treeness (dendropy.test.test_tree_calculations_and_metrics.TreeUnaryMetricsTest) ... ok

----------------------------------------------------------------------
Ran 829 tests in 513.991s

OK
/nix/store/s2mnwid4aamhma08qqc5mkpqd0kxw7pw-python2.7-DendroPy-4.3.0
/nix/store/3wh11zyq28p0mqx0c1yqsf094a1hzipi-python3.6-DendroPy-4.3.0

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Just move the rm command to prePatch and then this should be good to go.


meta = {
homepage = http://dendropy.org/;
description = "a Python library for phylogenetic computing";
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Capitalize first letter please.

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Success on aarch64-linux (full log)

Partial log (click to expand)

test_plot_by_depth (dendropy.test.test_asciitree.AsciiTreeTest) ... ok
test_plot_by_length (dendropy.test.test_asciitree.AsciiTreeTest) ... ok
test_plot_by_level (dendropy.test.test_asciitree.AsciiTreeTest) ... ok

----------------------------------------------------------------------
Ran 829 tests in 2070.668s

OK
/nix/store/i8d05ga34bw8k8i2wy78ci312zj4g07q-python2.7-DendroPy-4.3.0
/nix/store/mwxiwrbr4labarx04ycm6pl36k474n5i-python3.6-DendroPy-4.3.0

@FRidh FRidh merged commit c0c366c into NixOS:master Feb 8, 2018
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4 participants