From 4f25a138612ff62df020ff74753bd47d6fbd91f9 Mon Sep 17 00:00:00 2001
From: Chris Ostrouchov <chris.ostrouchov@gmail.com>
Date: Wed, 10 Oct 2018 21:21:58 -0400
Subject: [PATCH] pythonPackages.scikit-bio: init at 0.5.4

---
 .../python-modules/scikit-bio/default.nix     | 55 +++++++++++++++++++
 pkgs/top-level/python-packages.nix            |  2 +
 2 files changed, 57 insertions(+)
 create mode 100644 pkgs/development/python-modules/scikit-bio/default.nix

diff --git a/pkgs/development/python-modules/scikit-bio/default.nix b/pkgs/development/python-modules/scikit-bio/default.nix
new file mode 100644
index 000000000000..7a2ab097a71e
--- /dev/null
+++ b/pkgs/development/python-modules/scikit-bio/default.nix
@@ -0,0 +1,55 @@
+{ stdenv
+, buildPythonPackage
+, fetchPypi
+, cython
+, lockfile
+, cachecontrol
+, decorator
+, ipython
+, matplotlib
+, natsort
+, numpy
+, pandas
+, scipy
+, hdmedians
+, scikitlearn
+, pytest
+, coverage
+, python
+, isPy3k
+}:
+
+buildPythonPackage rec {
+  version = "0.5.4";
+  pname = "scikit-bio";
+  disabled = !isPy3k;
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "3243f1995ef24643c09ff4d9391a79528aadd8232e5aa5d66c38d7b2e0c92f24";
+  };
+
+  buildInputs = [ cython ];
+  checkInputs = [ coverage ];
+  propagatedBuildInputs = [ lockfile cachecontrol decorator ipython matplotlib natsort numpy pandas scipy hdmedians scikitlearn ];
+
+  # remove on when version > 0.5.4
+  postPatch = ''
+    sed -i "s/numpy >= 1.9.2, < 1.14.0/numpy/" setup.py
+    sed -i "s/pandas >= 0.19.2, < 0.23.0/pandas/" setup.py
+  '';
+
+  # cython package not included for tests
+  doCheck = false;
+
+  checkPhase = ''
+    ${python.interpreter} -m skbio.test
+  '';
+
+  meta = with stdenv.lib; {
+    homepage = http://scikit-bio.org/;
+    description = "Data structures, algorithms and educational resources for bioinformatics";
+    license = licenses.bsd3;
+    maintainers = [ maintainers.costrouc ];
+  };
+}
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 505874ecf6c1..a2935c111943 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -11715,6 +11715,8 @@ in {
     inherit (pkgs) gfortran glibcLocales;
   };
 
+  scikit-bio = callPackage ../development/python-modules/scikit-bio { };
+
   scp = callPackage ../development/python-modules/scp {};
 
   scripttest = buildPythonPackage rec {