Commit a9b78d41 authored by Gaetan Lepage's avatar Gaetan Lepage
Browse files

python3Packages.biom-format: cleanup, fix build

parent 6811cf7e

pkgs/development/python-modules/biom-format/default.nix

+22 −8
Original line number Diff line number Diff line
@@ -2,13 +2,19 @@ 
  lib,

  buildPythonPackage,

  fetchFromGitHub,

  setuptools,



  # build-system

  cython,

  click,

  numpy,

  scipy,

  pandas,

  setuptools,



  # dependencies

  click,

  h5py,

  pandas,

  scipy,



  # tests

  pytestCheckHook,

}:
@@ -24,18 +30,24 @@ buildPythonPackage (finalAttrs: { 
    hash = "sha256-FjIC21LoqltixBstbbANByjTNxVm/3YCxdWaD9KbOQ0=";

  };



  # https://numpy.org/doc/stable//release/2.4.0-notes.html#removed-numpy-in1d

  postPatch = ''

    substituteInPlace biom/table.py \

      --replace-fail "np.in1d" "np.isin"

  '';



  build-system = [

    setuptools

    cython

    numpy

    setuptools

  ];



  dependencies = [

    click

    h5py

    numpy

    scipy

    pandas

    h5py

    scipy

  ];



  # make pytest resolve the package from $out
@@ -53,8 +65,10 @@ buildPythonPackage (finalAttrs: { 
  pythonImportsCheck = [ "biom" ];



  meta = {

    homepage = "http://biom-format.org/";

    description = "Biological Observation Matrix (BIOM) format";

    homepage = "http://biom-format.org/";

    downloadPage = "https://github.com/biocore/biom-format";

    changelog = "https://github.com/biocore/biom-format/blob/${finalAttrs.src.tag}/ChangeLog.md";

    license = lib.licenses.bsd3;

    maintainers = with lib.maintainers; [ tomasajt ];

  };