diff --git a/pkgs/development/python-modules/persim/default.nix b/pkgs/development/python-modules/persim/default.nix
index d016d1ccea8..65f3529e60c 100644
--- a/pkgs/development/python-modules/persim/default.nix
+++ b/pkgs/development/python-modules/persim/default.nix
@@ -1,12 +1,14 @@
 { lib
 , buildPythonPackage
 , fetchPypi
-, scikitlearn
-, numpy
-, matplotlib
-, scipy
+, deprecated
 , hopcroftkarp
-, pytest
+, joblib
+, matplotlib
+, numpy
+, scikitlearn
+, scipy
+, pytestCheckHook
 }:
 
 buildPythonPackage rec {
@@ -19,26 +21,24 @@ buildPythonPackage rec {
   };
 
   propagatedBuildInputs = [
-    scikitlearn
-    numpy
-    matplotlib
-    scipy
+    deprecated
     hopcroftkarp
+    joblib
+    matplotlib
+    numpy
+    scikitlearn
+    scipy
   ];
 
   checkInputs = [
-    pytest
+    pytestCheckHook
   ];
 
-  checkPhase = ''
+  preCheck = ''
     # specifically needed for darwin
     export HOME=$(mktemp -d)
     mkdir -p $HOME/.matplotlib
     echo "backend: ps" > $HOME/.matplotlib/matplotlibrc
-
-    # ignore tests due to python 2.7 fail
-    pytest --ignore test/test_plots.py \
-           --ignore test/test_visuals.py
   '';
 
   meta = with lib; {
diff --git a/pkgs/development/python-modules/pynndescent/default.nix b/pkgs/development/python-modules/pynndescent/default.nix
index aab8f4e743a..8cddeb8873f 100644
--- a/pkgs/development/python-modules/pynndescent/default.nix
+++ b/pkgs/development/python-modules/pynndescent/default.nix
@@ -1,7 +1,6 @@
 { lib
 , buildPythonPackage
 , fetchPypi
-, fetchpatch
 , nose
 , scikitlearn
 , scipy
@@ -12,25 +11,13 @@
 
 buildPythonPackage rec {
   pname = "pynndescent";
-  version = "0.5.1";
+  version = "0.5.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "74a05a54d13573a38878781d44812ac6df97d8762a56f9bb5dd87a99911820fe";
+    sha256 = "0w87c2v0li2rdbx6qfc2lb6y6bxpdy3jwfgzfs1kcr4d1chj5zfr";
   };
 
-  patches = [
-    # fixes tests, included in 0.5.2
-    (fetchpatch {
-      url = "https://github.com/lmcinnes/pynndescent/commit/ef5d8c3c3bfe976063b6621e3e0734c0c22d813b.patch";
-      sha256 = "sha256-49n3kevs3wpzd4FfZVKmNpF2o1V8pJs4KOx8zCAhR3s=";
-    })
-  ];
-
-  checkInputs = [
-    nose
-  ];
-
   propagatedBuildInputs = [
     scikitlearn
     scipy
@@ -39,6 +26,10 @@ buildPythonPackage rec {
     joblib
   ];
 
+  checkInputs = [
+    nose
+  ];
+
   checkPhase = ''
     nosetests
   '';
diff --git a/pkgs/development/python-modules/umap-learn/default.nix b/pkgs/development/python-modules/umap-learn/default.nix
index b9abe2bb768..f888704e6a8 100644
--- a/pkgs/development/python-modules/umap-learn/default.nix
+++ b/pkgs/development/python-modules/umap-learn/default.nix
@@ -13,21 +13,15 @@
 
 buildPythonPackage rec {
   pname = "umap-learn";
-  version = "0.5.0";
+  version = "0.5.1";
 
   src = fetchFromGitHub {
     owner = "lmcinnes";
     repo = "umap";
     rev = version;
-    sha256 = "sha256-2Z5RDi4bz8hh8zMwkcCQY9NrGaVd1DJEBOmrCl2oSvM=";
+    sha256 = "0favphngcz5jvyqs06x07hk552lvl9qx3vka8r4x0xmv88gsg349";
   };
 
-  checkInputs = [
-    nose
-    tensorflow
-    pytestCheckHook
-  ];
-
   propagatedBuildInputs = [
     numpy
     scikitlearn
@@ -36,6 +30,12 @@ buildPythonPackage rec {
     pynndescent
   ];
 
+  checkInputs = [
+    nose
+    tensorflow
+    pytestCheckHook
+  ];
+
   preCheck = ''
     export HOME=$TMPDIR
   '';