python3Packages.dendropy: 4.5.1 -> 5.0.2 (#326199)

pkgs/by-name/pa/paup/package.nix

@@ -0,0 +1,52 @@
+{
+  lib,
+  stdenvNoCC,
+  fetchurl,
+  autoPatchelfHook,
+  curl,
+  gfortran,
+  zlib,
+}:
+
+stdenvNoCC.mkDerivation {
+  pname = "paup";
+  version = "4.0a168";
+
+  src = fetchurl {
+    url = "http://phylosolutions.com/paup-test/paup4a168_centos64.gz";
+    hash = "sha256-41dZswlrIQ05f1zJzId78DKmPf0QH1SfrexzvCAUxq8=";
+  };
+
+  unpackPhase = ''
+    runHook preUnpack
+
+    gunzip -c $src > paup
+
+    runHook postUnpack
+  '';
+
+  nativeBuildInputs = [ autoPatchelfHook ];
+  buildInputs = [
+    curl
+    gfortran
+    zlib
+  ];
+
+  installPhase = ''
+    runHook preInstall
+
+    install -Dm755 paup -t $out/bin
+
+    runHook postInstall
+  '';
+
+  meta = {
+    description = "A software package for inferring evolutionary trees";
+    homepage = "http://phylosolutions.com/paup-test/";
+    license = lib.licenses.unfree;
+    sourceProvenance = [ lib.sourceTypes.binaryNativeCode ];
+    maintainers = with lib.maintainers; [ pandapip1 ];
+    mainProgram = "paup";
+    platforms = [ "x86_64-linux" ];
+  };
+}

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

@@ -1,45 +1,54 @@
 {
   lib,
+  stdenv,
   buildPythonPackage,
   fetchFromGitHub,
   pytestCheckHook,
   pythonOlder,
+  nix-update-script,
+  setuptools,
+  paup,
+  paupIntegration ? false,
 }:
 
+let
+  paupPath = if paupIntegration then lib.getExe paup else "NONE";
+in
 buildPythonPackage rec {
   pname = "dendropy";
-  version = "4.5.1";
-  format = "setuptools";
+  version = "5.0.2";
 
-  disabled = pythonOlder "3.7";
+  pyproject = true;
+  build-system = [ setuptools ];
 
   src = fetchFromGitHub {
     owner = "jeetsukumaran";
-    repo = pname;
-    rev = "v${version}";
-    hash = "sha256-FP0+fJkkFtSysPxoHXjyMgF8pPin7aRyzmHe9bH8LlM=";
+    repo = "dendropy";
+    rev = "refs/tags/v${version}";
+    hash = "sha256-OiFei/6226FDtL4w1XrXL2OVn3/hfQwnIhTzM4OneKc=";
   };
 
+  postPatch = ''
+    substituteInPlace setup.py \
+      --replace '["pytest-runner"],' '[],'
+
+    substituteInPlace src/dendropy/interop/paup.py \
+      --replace 'PAUP_PATH = os.environ.get(metavar.DENDROPY_PAUP_PATH_ENVAR, "paup")' 'PAUP_PATH = os.environ.get(metavar.DENDROPY_PAUP_PATH_ENVAR, "${paupPath}")'
+  '';
+
   nativeCheckInputs = [ pytestCheckHook ];
 
-  disabledTests = [
-    # FileNotFoundError: [Errno 2] No such file or directory: 'paup'
-    "test_basic_split_count_with_incorrect_rootings_raises_error"
-    "test_basic_split_count_with_incorrect_weight_treatment_raises_error"
-    "test_basic_split_counting_under_different_rootings"
-    "test_group1"
-    # AssertionError: 6 != 5
-    "test_by_num_lineages"
-    # AttributeError: module 'collections' has no attribute 'Iterable'
-    "test_findall_multiple"
-  ];
-
   pythonImportsCheck = [ "dendropy" ];
 
-  meta = with lib; {
+  passthru.updateScript = nix-update-script { };
+
+  meta = {
     description = "Python library for phylogenetic computing";
-    homepage = "https://dendropy.org/";
-    license = licenses.bsd3;
-    maintainers = with maintainers; [ unode ];
+    homepage = "https://jeetsukumaran.github.io/DendroPy/";
+    license = lib.licenses.bsd3;
+    maintainers = with lib.maintainers; [
+      unode
+      pandapip1
+    ];
   };
 }