1 files changed, 71 insertions, 0 deletions
diff --git a/pkgs/development/python-modules/biom-format/default.nix b/pkgs/development/python-modules/biom-format/default.nix
new file mode 100644
index 0000000000000..ca5ff3a83fb78
--- /dev/null
+++ b/pkgs/development/python-modules/biom-format/default.nix
@@ -0,0 +1,71 @@
+{
+  lib,
+  buildPythonPackage,
+  fetchFromGitHub,
+  fetchpatch,
+  setuptools,
+  cython,
+  click,
+  numpy,
+  scipy,
+  pandas,
+  h5py,
+  pytestCheckHook,
+}:
+
+buildPythonPackage rec {
+  pname = "biom-format";
+  version = "2.1.15";
+  pyproject = true;
+
+  src = fetchFromGitHub {
+    owner = "biocore";
+    repo = "biom-format";
+    rev = "refs/tags/${version}";
+    hash = "sha256-WRBc+C/UWme7wYogy4gH4KTIdIqU3KmBm2jWzGNxGQg=";
+  };
+
+  patches = [
+    # fixes a test, can be removed in next version after 2.1.15
+    (fetchpatch {
+      name = "fix-dataframe-comparison.patch";
+      url = "https://github.com/biocore/biom-format/commit/5d1c921ca2cde5d7332508503ce990a7209d1fdc.patch";
+      hash = "sha256-nyHi469ivjJSQ01yIk/6ZMXFdoo9wVuazJHnFdy2nBg=";
+    })
+  ];
+
+  build-system = [
+    setuptools
+    cython
+    numpy
+  ];
+
+  dependencies = [
+    click
+    numpy
+    scipy
+    pandas
+    h5py
+  ];
+
+  # make pytest resolve the package from $out
+  # some tests don't work if we change the level of directory nesting
+  preCheck = ''
+    mkdir biom_tests
+    mv biom/tests biom_tests/tests
+    rm -r biom
+  '';
+
+  nativeCheckInputs = [ pytestCheckHook ];
+
+  pytestFlagsArray = [ "biom_tests/tests" ];
+
+  pythonImportsCheck = [ "biom" ];
+
+  meta = {
+    homepage = "http://biom-format.org/";
+    description = "Biological Observation Matrix (BIOM) format";
+    license = lib.licenses.bsd3;
+    maintainers = with lib.maintainers; [ tomasajt ];
+  };
+}