Unverified Commit 14fc170c authored by kirillrdy's avatar kirillrdy Committed by GitHub
Browse files

python3Packages.biom-format: cleanup, fix build; python3Packages.scikit-bio:... 

python3Packages.biom-format: cleanup, fix build; python3Packages.scikit-bio: 0.7.1.post1 -> 0.7.2 (#495656)
parents 713ac536 f07ec8da

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 ];

  };

pkgs/development/python-modules/scikit-bio/default.nix

+7 −8
Original line number Diff line number Diff line
@@ -5,9 +5,9 @@ 
  fetchFromGitHub,



  # build-system

  setuptools,

  cython,

  oldest-supported-numpy,

  numpy,

  setuptools,



  # dependencies

  array-api-compat,
@@ -15,7 +15,6 @@ 
  decorator,

  h5py,

  natsort,

  numpy,

  pandas,

  patsy,

  requests,
@@ -29,20 +28,20 @@ 


buildPythonPackage (finalAttrs: {

  pname = "scikit-bio";

  version = "0.7.1.post1";

  version = "0.7.2";

  pyproject = true;



  src = fetchFromGitHub {

    owner = "scikit-bio";

    repo = "scikit-bio";

    tag = finalAttrs.version;

    hash = "sha256-fnZpLhn2F/KoP3q7WmdaDXeC9i7hduGRkUWlCwwME3Q=";

    hash = "sha256-zBOUZukqLhTxKG9BluWB+2zTCx5ALhM1s+YP2itqg9A=";

  };



  build-system = [

    setuptools

    cython

    oldest-supported-numpy

    numpy

    setuptools

  ];



  dependencies = [
@@ -76,7 +75,7 @@ buildPythonPackage (finalAttrs: { 
    description = "Data structures, algorithms and educational resources for bioinformatics";

    homepage = "http://scikit-bio.org/";

    downloadPage = "https://github.com/scikit-bio/scikit-bio";

    changelog = "https://github.com/scikit-bio/scikit-bio/blob/${finalAttrs.src.rev}/CHANGELOG.md";

    changelog = "https://github.com/scikit-bio/scikit-bio/blob/${finalAttrs.src.tag}/CHANGELOG.md";

    license = lib.licenses.bsd3;

    maintainers = with lib.maintainers; [ tomasajt ];

  };