Merge pull request #192695 from bcdarwin/edlib-init

python310Packages.edlib: init at 1.3.9

pkgs/development/libraries/science/biology/edlib/default.nix

@@ -0,0 +1,30 @@
+{ lib, stdenv, fetchFromGitHub, cmake }:
+
+stdenv.mkDerivation rec {
+  pname = "edlib";
+  version = "unstable-2021-08-20";
+
+  src = fetchFromGitHub {
+    owner = "Martinsos";
+    repo = pname;
+    rev = "f8afceb49ab0095c852e0b8b488ae2c88e566afd";
+    hash = "sha256-P/tFbvPBtA0MYCNDabW+Ypo3ltwP4S+6lRDxwAZ1JFo=";
+  };
+
+  nativeBuildInputs = [ cmake ];
+
+  doCheck = true;
+  checkPhase = ''
+    runHook preCheck
+    bin/runTests
+    runHook postCheck
+  '';
+
+  meta = with lib; {
+    homepage = "https://martinsos.github.io/edlib";
+    description = "Lightweight, fast C/C++ library for sequence alignment using edit distance";
+    maintainers = with maintainers; [ bcdarwin ];
+    license = licenses.mit;
+    platforms = platforms.unix;
+  };
+}

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

@@ -0,0 +1,36 @@
+{ lib
+, buildPythonPackage
+, pythonOlder
+, fetchFromGitHub
+, edlib
+, cython
+, python
+}:
+
+buildPythonPackage {
+  inherit (edlib) pname src meta;
+  version = "1.3.9";
+
+  disabled = pythonOlder "3.6";
+
+  sourceRoot = "source/bindings/python";
+
+  preBuild = ''
+    ln -s ${edlib.src}/edlib .
+  '';
+
+  EDLIB_OMIT_README_RST = 1;
+  EDLIB_USE_CYTHON = 1;
+
+  nativeBuildInputs = [ cython ];
+  buildInputs = [ edlib ];
+
+  checkPhase = ''
+    runHook preCheck
+    ${python.interpreter} test.py
+    runHook postCheck
+  '';
+
+  pythonImportsCheck = [ "edlib" ];
+
+}

pkgs/top-level/all-packages.nix

@@ -6675,6 +6675,8 @@ with pkgs;
 
   edk2-uefi-shell = callPackage ../tools/misc/edk2-uefi-shell { };
 
+  edlib = callPackage ../development/libraries/science/biology/edlib { };
+
   eff = callPackage ../development/interpreters/eff { };
 
   eflite = callPackage ../applications/audio/eflite {};

pkgs/top-level/python-packages.nix

@@ -2937,6 +2937,10 @@ self: super: with self; {
 
   editorconfig = callPackage ../development/python-modules/editorconfig { };
 
+  edlib = callPackage ../development/python-modules/edlib {
+    inherit (pkgs) edlib;
+  };
+
   edward = callPackage ../development/python-modules/edward { };
 
   effect = callPackage ../development/python-modules/effect { };