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python3Packages.scikit-tda: init at 0.0.4 #64689

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merged 6 commits into from Jul 14, 2019

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costrouc
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Motivation for this change

Went to scipy and saw an awesome package for Topological Data Analysis and wanted to add it to nixpkgs. Thanks @sauln for the great talk!

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 nix-review --run "nix-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)
  • Ensured that relevant documentation is up to date
  • Fits CONTRIBUTING.md.

@costrouc costrouc requested a review from FRidh as a code owner July 13, 2019 00:39
@costrouc costrouc changed the title Python scikit tda init python3Packages.scikit-tda: init at 0.0.4 Jul 13, 2019
@costrouc
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Result of nix-review pr 64689 1

11 package were build:
  • python27Packages.kmapper
  • python27Packages.persim
  • python27Packages.ripser
  • python27Packages.tadasets
  • python27Packages.umap-learn
  • python37Packages.kmapper
  • python37Packages.persim
  • python37Packages.ripser
  • python37Packages.scikit-tda
  • python37Packages.tadasets
  • python37Packages.umap-learn

@sauln
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sauln commented Jul 13, 2019

❤️❤️This is great! Thank you @costrouc!

@risicle
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risicle commented Jul 13, 2019

Interesting - umap-learn (both py27 and py37) on macos 10.13 gives me

running install tests
....................................................F.......................
======================================================================
FAIL: umap.tests.test_umap.test_umap_transform_on_iris
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/nix/store/7zlrb2lkq5rv24x4a60vjpli2b9hl712-python3.7-nose-1.3.7/lib/python3.7/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/private/tmp/nix-build-python3.7-umap-learn-0.3.9.drv-0/source/umap/tests/test_umap.py", line 767, in test_umap_transform_on_iris
    trust),
AssertionError: 0.889159891598916 not greater than or equal to 0.89 : Insufficiently trustworthy transform foriris dataset: 0.889159891598916

Which... I'm not sure what to do about 🤷‍♂

@risicle
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risicle commented Jul 13, 2019

persim requires exactly the same fix as trackpy in #64692 (comment) for the tests to pass on macos 10.13.

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risicle commented Jul 13, 2019

Same for ripser!

@risicle
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risicle commented Jul 13, 2019

If I disable the problematic test in umap-learn, and make the mentioned other fixes, everything does indeed build fine on macos 10.13.

@costrouc
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Thanks @risicle I appreciate the testing on darwin. I will make the changes tomorrow.

@costrouc
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Result of nix-review pr 64689 1

11 package were build:
  • python27Packages.kmapper
  • python27Packages.persim
  • python27Packages.ripser
  • python27Packages.tadasets
  • python27Packages.umap-learn
  • python37Packages.kmapper
  • python37Packages.persim
  • python37Packages.ripser
  • python37Packages.scikit-tda
  • python37Packages.tadasets
  • python37Packages.umap-learn

@costrouc
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@GrahamcOfBorg build python3Packages.scikit-tda

@FRidh FRidh merged commit c610eb4 into NixOS:master Jul 14, 2019
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4 participants