diff --git a/pkgs/development/python-modules/ffcv/default.nix b/pkgs/development/python-modules/ffcv/default.nix
index 2aee132e294fc..809a9ca696d81 100644
--- a/pkgs/development/python-modules/ffcv/default.nix
+++ b/pkgs/development/python-modules/ffcv/default.nix
@@ -35,7 +35,8 @@ buildPythonPackage rec {
       --replace "'webdataset'," ""
   '';
 
-  buildInputs = [ libjpeg pkgconfig ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ libjpeg ];
   propagatedBuildInputs = [ opencv4 numba pandas pytorch-pfn-extras terminaltables tqdm ];
 
   # `ffcv._libffcv*.so` cannot be loaded in the nix build environment for some
diff --git a/pkgs/development/python-modules/onnx/default.nix b/pkgs/development/python-modules/onnx/default.nix
index e873f3256084d..2846042e8d457 100644
--- a/pkgs/development/python-modules/onnx/default.nix
+++ b/pkgs/development/python-modules/onnx/default.nix
@@ -1,5 +1,6 @@
 { lib
 , buildPythonPackage
+, bash
 , cmake
 , fetchPypi
 , isPy27
@@ -43,8 +44,9 @@ buildPythonPackage rec {
 
   postPatch = ''
     chmod +x tools/protoc-gen-mypy.sh.in
-    patchShebangs tools/protoc-gen-mypy.sh.in tools/protoc-gen-mypy.py
-
+    patchShebangs tools/protoc-gen-mypy.py
+    substituteInPlace tools/protoc-gen-mypy.sh.in \
+      --replace "/bin/bash" "${bash}/bin/bash"
     substituteInPlace setup.py \
       --replace "setup_requires.append('pytest-runner')" ""
   '';
diff --git a/pkgs/development/python-modules/pycapnp/default.nix b/pkgs/development/python-modules/pycapnp/default.nix
index 8c63a11862239..cd2e8f450cd2b 100644
--- a/pkgs/development/python-modules/pycapnp/default.nix
+++ b/pkgs/development/python-modules/pycapnp/default.nix
@@ -20,16 +20,18 @@ buildPythonPackage rec {
     sha256 = "1xi6df93ggkpmwckwbi356v7m32zv5qry8s45hvsps66dz438kmi";
   };
 
-  buildInputs = [ capnproto cython pkgconfig ];
+  nativeBuildInputs = [ cython pkgconfig ];
 
-  # Tests disabled due to dependency on jinja and various other libraries.
+  buildInputs = [ capnproto ];
+
+  # Tests depend on schema_capnp which fails to generate
   doCheck = false;
 
   pythonImportsCheck = [ "capnp" ];
 
   meta = with lib; {
+    homepage = "https://capnproto.github.io/pycapnp/";
     maintainers = with maintainers; [ cstrahan lukeadams ];
     license = licenses.bsd2;
-    homepage = "https://capnproto.github.io/pycapnp/";
   };
 }
diff --git a/pkgs/development/python-modules/pyvips/default.nix b/pkgs/development/python-modules/pyvips/default.nix
index b25d9d3b5ae44..3974767856677 100644
--- a/pkgs/development/python-modules/pyvips/default.nix
+++ b/pkgs/development/python-modules/pyvips/default.nix
@@ -1,23 +1,23 @@
-{ buildPythonPackage, fetchPypi, pytest-runner, pytestCheckHook, glib, vips, cffi
-, pkg-config, pkgconfig, lib }:
+{ buildPythonPackage, fetchFromGitHub, pytestCheckHook, glib, vips, cffi
+, pkgconfig, lib }:
 
 buildPythonPackage rec {
   pname = "pyvips";
   version = "2.1.16";
 
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "654c03014a15f846786807a2ece6f525a8fec883d1c857742c8e37da149a81ed";
+  src = fetchFromGitHub {
+    owner = "libvips";
+    repo = "pyvips";
+    rev = "v${version}";
+    sha256 = "sha256-8CeQbx3f2i0lEU0wxPeUwHlUGtzOztzTOdFNjIDy8s0=";
   };
 
-  nativeBuildInputs = [ pytest-runner pkgconfig pkg-config ];
+  nativeBuildInputs = [ pkgconfig ];
 
   buildInputs = [ glib vips ];
 
   propagatedBuildInputs = [ cffi ];
 
-  # tests are not included in pypi tarball
-  doCheck = false;
   checkInputs = [ pytestCheckHook ];
 
   pythonImportsCheck = [ "pyvips" ];