Unverified Commit 1f5ba0c9 authored by Gaétan Lepage's avatar Gaétan Lepage Committed by GitHub
Browse files

python3Packages.scanpy: 1.12.0 -> 1.12.1 (#508669)

parents 35a9c338 4fa3c00d

pkgs/development/python-modules/fast-array-utils/default.nix

+5 −11
Original line number Diff line number Diff line
@@ -6,7 +6,6 @@ 
  # build-system

  hatch-docstring-description,

  hatch-fancy-pypi-readme,

  hatch-min-requirements,

  hatch-vcs,

  hatchling,
@@ -22,13 +21,12 @@ 
  furo,

  pytest,

  sphinx,

  sphinx-autodoc-typehints,

  # full

  h5py,

  zarr,

  # test

  anndata,

  numcodecs,

  scikit-learn,

  # test-min

  coverage,

  pytest-codspeed,
@@ -44,14 +42,14 @@ 


buildPythonPackage (finalAttrs: {

  pname = "fast-array-utils";

  version = "1.3.1";

  version = "1.4.1";

  pyproject = true;



  src = fetchFromGitHub {

    owner = "scverse";

    repo = "fast-array-utils";

    tag = "v${finalAttrs.version}";

    hash = "sha256-FUzCdDFDqP+izlSWruWzslfPayzRN7MFx1LOikyMDss=";

    hash = "sha256-9tB8cV3i9WPbdLeS5/FmQzLu8rk/jRVtUZ35X/XSCx8=";

  };



  # hatch-min-requirements tries to talk to PyPI by default. See https://github.com/tlambert03/hatch-min-requirements?tab=readme-ov-file#environment-variables.
@@ -60,7 +58,6 @@ buildPythonPackage (finalAttrs: { 
  build-system = [

    hatch-docstring-description

    hatch-fancy-pypi-readme

    hatch-min-requirements

    hatch-vcs

    hatchling

  ];
@@ -79,9 +76,7 @@ buildPythonPackage (finalAttrs: { 
    doc = [

      furo

      pytest

      # scanpydoc

      sphinx

      sphinx-autodoc-typehints

      # sphinx-autofixture

    ];

    full = [
@@ -96,11 +91,10 @@ buildPythonPackage (finalAttrs: { 
    ];

    test = [

      anndata

      numcodecs

      scikit-learn

      zarr

    ]

    ++ self.accel

    ++ self.test-min;

    ++ self.accel;

    test-min = [

      coverage

      pytest

pkgs/development/python-modules/scanpy/default.nix

+11 −5
Original line number Diff line number Diff line
@@ -2,6 +2,7 @@ 
  lib,

  buildPythonPackage,

  fetchFromGitHub,

  pythonOlder,



  # build-system

  hatch-vcs,
@@ -9,6 +10,7 @@ 


  # dependencies

  anndata,

  certifi,

  fast-array-utils,

  h5py,

  joblib,
@@ -28,8 +30,9 @@ 
  session-info2,

  statsmodels,

  tqdm,

  typing-extensions,

  umap-learn,

  # python<3.13 only:

  typing-extensions,



  # optional-attrs

  # dask
@@ -60,14 +63,14 @@ 


buildPythonPackage (finalAttrs: {

  pname = "scanpy";

  version = "1.12.0";

  version = "1.12.1";

  pyproject = true;



  src = fetchFromGitHub {

    owner = "scverse";

    repo = "scanpy";

    tag = finalAttrs.version;

    hash = "sha256-jpi3SyTaG5mxCqUNSM564MMIrNdz4LBYo9+dn5nYmeY=";

    hash = "sha256-r8kicjCFyEKLxQtFYuZg0NKK7gRBoaLSSFGWqcQtBqM=";

  };



  # Otherwise, several tests fail to be collected:
@@ -86,6 +89,7 @@ buildPythonPackage (finalAttrs: { 


  dependencies = [

    anndata

    certifi

    fast-array-utils

    h5py

    joblib
@@ -105,11 +109,13 @@ buildPythonPackage (finalAttrs: { 
    session-info2

    statsmodels

    tqdm

    typing-extensions

    umap-learn

  ]

  ++ fast-array-utils.optional-dependencies.accel

  ++ fast-array-utils.optional-dependencies.sparse;

  ++ fast-array-utils.optional-dependencies.sparse

  ++ lib.optionals (pythonOlder "3.13") [

    typing-extensions

  ];



  optional-dependencies = {

    # commented attributes are due to some dependencies not being in Nixpkgs

pkgs/development/python-modules/umap-learn/default.nix

+7 −9
Original line number Diff line number Diff line
@@ -32,16 +32,16 @@ 
  writableTmpDirAsHomeHook,

}:



buildPythonPackage rec {

buildPythonPackage (finalAttrs: {

  pname = "umap-learn";

  version = "0.5.11";

  version = "0.5.12";

  pyproject = true;



  src = fetchFromGitHub {

    owner = "lmcinnes";

    repo = "umap";

    tag = "release-${version}";

    hash = "sha256-V63W9ax7iOq5+oZFRWaQbAws942JBeufnQ3IF4rcgko=";

    tag = "release-${finalAttrs.version}";

    hash = "sha256-NORv3wJliKfft/+kMNKL133PKPN88Pt23yqbT1LjUKE=";

  };



  build-system = [ setuptools ];
@@ -55,7 +55,7 @@ buildPythonPackage rec { 
    tqdm

  ];



  optional-dependencies = rec {

  optional-dependencies = {

    plot = [

      bokeh

      colorcet
@@ -77,8 +77,6 @@ buildPythonPackage rec { 
      # Not packaged.

      #tbb

    ];



    all = plot ++ parametric_umap ++ tbb;

  };



  nativeCheckInputs = [
@@ -104,8 +102,8 @@ buildPythonPackage rec { 
  meta = {

    description = "Uniform Manifold Approximation and Projection";

    homepage = "https://github.com/lmcinnes/umap";

    changelog = "https://github.com/lmcinnes/umap/releases/tag/release-${src.tag}";

    changelog = "https://github.com/lmcinnes/umap/releases/tag/${finalAttrs.src.tag}";

    license = lib.licenses.bsd3;

    maintainers = [ ];

  };

}
 
})