diff --git a/pkgs/development/python-modules/billiard/default.nix b/pkgs/development/python-modules/billiard/default.nix
index 5bccf792452..ff87ba2e669 100644
--- a/pkgs/development/python-modules/billiard/default.nix
+++ b/pkgs/development/python-modules/billiard/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, buildPythonPackage, fetchPypi, isPyPy, pytest, case, psutil }:
+{ stdenv, buildPythonPackage, fetchPypi, isPyPy, pytestCheckHook, case, psutil, fetchpatch }:
 
 buildPythonPackage rec {
   pname = "billiard";
@@ -9,11 +9,15 @@ buildPythonPackage rec {
     inherit pname version;
     sha256 = "0spssl3byzqsplra166d59jx8iqfxyzvcbx7vybkmwr5ck72a5yr";
   };
+  patches = [(fetchpatch {
+    # Add Python 3.9 support to spawnv_passfds()
+    # Should be included in next release after 3.6.3.0
+    url = "https://github.com/celery/billiard/pull/310/commits/a508ebafadcfe2e25554b029593f3e66d01ede6c.patch";
+    sha256 = "05zsr1bvjgi01qg7r274c0qvbn65iig3clyz14c08mpfyn38h84i";
+    excludes = [ "tox.ini" ];
+  })];
 
-  checkInputs = [ pytest case psutil ];
-  checkPhase = ''
-    pytest
-  '';
+  checkInputs = [ pytestCheckHook case psutil ];
 
   meta = with stdenv.lib; {
     homepage = "https://github.com/celery/billiard";
diff --git a/pkgs/development/python-modules/clifford/default.nix b/pkgs/development/python-modules/clifford/default.nix
index 9fe60ba55da..68ac9e45bb4 100644
--- a/pkgs/development/python-modules/clifford/default.nix
+++ b/pkgs/development/python-modules/clifford/default.nix
@@ -1,6 +1,7 @@
 { lib
 , buildPythonPackage
 , fetchPypi
+, fetchpatch
 , isPy27
 , future
 , h5py
@@ -21,6 +22,12 @@ buildPythonPackage rec {
     inherit pname version;
     sha256 = "ade11b20d0631dfc9c2f18ce0149f1e61e4baf114108b27cfd68e5c1619ecc0c";
   };
+  patches = [ (fetchpatch {
+    # Compatibility with h5py 3.
+    # Will be included in the next releasse after 1.3.1
+    url = "https://github.com/pygae/clifford/pull/388/commits/955d141662c68d3d61aa50a162b39e656684c208.patch";
+    sha256 = "00m8ias58xycn5n78sy9wywf4wck1v0gb8gzmg40inzdiha93jyz";
+  }) ];
 
   propagatedBuildInputs = [
     future
diff --git a/pkgs/development/python-modules/datasets/default.nix b/pkgs/development/python-modules/datasets/default.nix
index 4214304a9c9..fc349cdc277 100644
--- a/pkgs/development/python-modules/datasets/default.nix
+++ b/pkgs/development/python-modules/datasets/default.nix
@@ -35,6 +35,10 @@ buildPythonPackage rec {
     xxhash
   ];
 
+  postPatch = ''
+    substituteInPlace setup.py --replace '"tqdm>=4.27,<4.50.0"' '"tqdm>=4.27"'
+  '';
+
   # Tests require pervasive internet access.
   doCheck = false;
 
diff --git a/pkgs/development/python-modules/datashader/default.nix b/pkgs/development/python-modules/datashader/default.nix
index 233aac688ab..c49e2e30b80 100644
--- a/pkgs/development/python-modules/datashader/default.nix
+++ b/pkgs/development/python-modules/datashader/default.nix
@@ -1,6 +1,7 @@
 { lib
 , buildPythonPackage
 , fetchPypi
+, fetchpatch
 , dask
 , distributed
 , bokeh
@@ -36,6 +37,12 @@ buildPythonPackage rec {
     inherit pname version;
     sha256 = "b1f80415f72f92ccb660aaea7b2881ddd35d07254f7c44101709d42e819d6be6";
   };
+  patches = [ (fetchpatch {
+    # Unpins pyct==0.46 (Sep. 11, 2020).
+    # Will be incorporated into the next datashader release after 0.11.1
+    url = "https://github.com/holoviz/datashader/pull/960/commits/d7a462fa399106c34fd0d44505a8a73789dbf874.patch";
+    sha256 = "1wqsk9dpxnkxr49fa7y5q6ahin80cvys05lnirs2w2p1dja35y4x";
+  })];
 
   propagatedBuildInputs = [
     dask
diff --git a/pkgs/development/python-modules/fastparquet/default.nix b/pkgs/development/python-modules/fastparquet/default.nix
index 47c7d506309..07922ee19ef 100644
--- a/pkgs/development/python-modules/fastparquet/default.nix
+++ b/pkgs/development/python-modules/fastparquet/default.nix
@@ -3,22 +3,19 @@ thrift, pytest, python-snappy, lz4, zstd }:
 
 buildPythonPackage rec {
   pname = "fastparquet";
-  version = "0.4.1";
+  version = "0.5.0";
 
   src = fetchFromGitHub {
     owner = "dask";
     repo = pname;
     rev = version;
-    sha256 = "ViZRGEv227/RgCBYAQN8F3Z0m8WrNUT5KUdyFosjg9s=";
+    sha256 = "17i091kky34m2xivk29fqsyxxxa7v4352n79w01n7ni93za6wana";
   };
 
   postPatch = ''
     # FIXME: package zstandard
     # removing the test dependency for now
     substituteInPlace setup.py --replace "'zstandard'," ""
-
-    # workaround for https://github.com/dask/fastparquet/issues/517
-    rm fastparquet/test/test_partition_filters_specialstrings.py
   '';
 
   nativeBuildInputs = [ pytestrunner ];
diff --git a/pkgs/development/python-modules/fiona/default.nix b/pkgs/development/python-modules/fiona/default.nix
index 0e90bb10f95..665bb0c8df0 100644
--- a/pkgs/development/python-modules/fiona/default.nix
+++ b/pkgs/development/python-modules/fiona/default.nix
@@ -41,9 +41,7 @@ buildPythonPackage rec {
   checkPhase = ''
     rm -r fiona # prevent importing local fiona
     # Some tests access network, others test packaging
-    pytest -k "not test_*_http \
-           and not test_*_https \
-           and not test_*_wheel"
+    pytest -k "not (http or https or wheel)"
   '';
 
   meta = with lib; {
diff --git a/pkgs/development/python-modules/fixtures/default.nix b/pkgs/development/python-modules/fixtures/default.nix
index 3042acbbe84..9f1549e98f9 100644
--- a/pkgs/development/python-modules/fixtures/default.nix
+++ b/pkgs/development/python-modules/fixtures/default.nix
@@ -5,6 +5,7 @@
 , testtools
 , mock
 , python
+, isPy39
 }:
 
 buildPythonPackage rec {
@@ -26,5 +27,6 @@ buildPythonPackage rec {
     description = "Reusable state for writing clean tests and more";
     homepage = "https://pypi.python.org/pypi/fixtures";
     license = lib.licenses.asl20;
+    broken = isPy39; # see https://github.com/testing-cabal/fixtures/issues/44
   };
 }
diff --git a/pkgs/development/python-modules/flower/default.nix b/pkgs/development/python-modules/flower/default.nix
index b31cbc7424d..605d08d1258 100644
--- a/pkgs/development/python-modules/flower/default.nix
+++ b/pkgs/development/python-modules/flower/default.nix
@@ -22,6 +22,7 @@ buildPythonPackage rec {
     # rely on using example programs (flowers/examples/tasks.py) which
     # are not part of the distribution
     rm tests/load.py
+    substituteInPlace  requirements/default.txt --replace "prometheus_client==0.8.0" "prometheus_client>=0.8.0"
   '';
 
   propagatedBuildInputs = [
@@ -39,5 +40,6 @@ buildPythonPackage rec {
     homepage = "https://github.com/mher/flower";
     license = licenses.bsdOriginal;
     maintainers = [ maintainers.arnoldfarkas ];
+    broken = (celery.version == "5.0.2"); # currently broken with celery>=5.0 by https://github.com/mher/flower/pull/1021
   };
 }
diff --git a/pkgs/development/python-modules/geopandas/default.nix b/pkgs/development/python-modules/geopandas/default.nix
index 200dfffa562..bd38d2663bc 100644
--- a/pkgs/development/python-modules/geopandas/default.nix
+++ b/pkgs/development/python-modules/geopandas/default.nix
@@ -1,6 +1,6 @@
 { stdenv, buildPythonPackage, fetchFromGitHub, isPy27
 , pandas, shapely, fiona, descartes, pyproj
-, pytest, Rtree, fetchpatch }:
+, pytestCheckHook, Rtree, fetchpatch }:
 
 buildPythonPackage rec {
   pname = "geopandas";
@@ -20,13 +20,18 @@ buildPythonPackage rec {
       url = "https://github.com/geopandas/geopandas/pull/1544/commits/6ce868a33a2f483b071089d51e178030fa4414d0.patch";
       sha256 = "1sjgxrqgbhz5krx51hrv230ywszcdl6z8q3bj6830kfad8n8b5dq";
     })
+    # Fix GeoJSON for Fiona>=1.8.16 (Sep. 7, 2020).
+    # https://github.com/geopandas/geopandas/issues/1606
+    # Will be included in next upstream release after 0.8.1
+    (fetchpatch {
+      url = "https://github.com/geopandas/geopandas/commit/72427d3d8c128039bfce1d54a76c0b652887b276.patch";
+      sha256 = "1726mrpddgmba0ngff73a5bsb6ywpsg63a2pdd2grp9339bgvi4a";
+    })
   ];
 
-  checkInputs = [ pytest Rtree ];
-
-  checkPhase = ''
-    py.test geopandas -m "not web"
-  '';
+  checkInputs = [ pytestCheckHook Rtree ];
+  disabledTests = [ "web" ];
+  pytestFlagsArray = [ "geopandas" ];
 
   propagatedBuildInputs = [
     pandas
diff --git a/pkgs/development/python-modules/imageio-ffmpeg/default.nix b/pkgs/development/python-modules/imageio-ffmpeg/default.nix
index d9991ee7845..db59ba70bb2 100644
--- a/pkgs/development/python-modules/imageio-ffmpeg/default.nix
+++ b/pkgs/development/python-modules/imageio-ffmpeg/default.nix
@@ -1,6 +1,7 @@
 { lib
 , buildPythonPackage
 , fetchPypi
+, fetchpatch
 , isPy3k
 }:
 
@@ -9,9 +10,15 @@ buildPythonPackage rec {
   version = "0.4.2";
 
   src = fetchPypi {
-    sha256 = "13b05b17a941a9f4a90b16910b1ffac159448cff051a153da8ba4b4343ffa195";
     inherit pname version;
+    sha256 = "13b05b17a941a9f4a90b16910b1ffac159448cff051a153da8ba4b4343ffa195";
   };
+  patches = [ (fetchpatch {
+    # Fixes compatibility with python3.9
+    # Should be included in the next release after 0.4.2
+    url = "https://github.com/imageio/imageio-ffmpeg/pull/43/commits/b90c39fe3d29418d67d953588ed9fdf4d848f811.patch";
+    sha256 = "0d9kf4w6ldwag3s2dr9zjin6wrj66fnl4fn8379ci4q4qfsqgx3f";
+  })];
 
   disabled = !isPy3k;
 
diff --git a/pkgs/development/python-modules/imbalanced-learn/default.nix b/pkgs/development/python-modules/imbalanced-learn/default.nix
index 1cb3dc2a7b9..21018518ca2 100644
--- a/pkgs/development/python-modules/imbalanced-learn/default.nix
+++ b/pkgs/development/python-modules/imbalanced-learn/default.nix
@@ -1,7 +1,6 @@
 { stdenv, buildPythonPackage, fetchPypi, isPy27
-, nose
 , pandas
-, pytest
+, pytestCheckHook
 , scikitlearn
 , tensorflow
 }:
@@ -17,16 +16,17 @@ buildPythonPackage rec {
   };
 
   propagatedBuildInputs = [ scikitlearn ];
-  checkInputs = [ nose pytest pandas ];
-  checkPhase = ''
+  checkInputs = [ pytestCheckHook pandas ];
+  preCheck = ''
     export HOME=$TMPDIR
-    # skip some tests that fail because of minimal rounding errors
-    # or very large dependencies (keras + tensorflow)
-    py.test imblearn -k 'not estimator \
-                         and not classification \
-                         and not _generator \
-                         and not show_versions'
   '';
+  disabledTests = [
+    "estimator"
+    "classification"
+    "_generator"
+    "show_versions"
+    "test_make_imbalanced_iris"
+  ];
 
   meta = with stdenv.lib; {
     description = "Library offering a number of re-sampling techniques commonly used in datasets showing strong between-class imbalance";
diff --git a/pkgs/development/python-modules/typing-inspect/default.nix b/pkgs/development/python-modules/typing-inspect/default.nix
index 849b56d2d0c..569096cb466 100644
--- a/pkgs/development/python-modules/typing-inspect/default.nix
+++ b/pkgs/development/python-modules/typing-inspect/default.nix
@@ -3,6 +3,7 @@
 , fetchPypi
 , typing-extensions
 , mypy-extensions
+, isPy39
 }:
 
 buildPythonPackage rec {
@@ -25,5 +26,6 @@ buildPythonPackage rec {
     homepage = "https://github.com/ilevkivskyi/typing_inspect";
     license = licenses.mit;
     maintainers = with maintainers; [ albakham ];
+    broken = isPy39;  # see https://github.com/ilevkivskyi/typing_inspect/issues/65
   };
 }