diff --git a/pkgs/development/interpreters/python/build-python-package-flit.nix b/pkgs/development/interpreters/python/build-python-package-flit.nix
index 8628c3df769..1beff0ebd83 100644
--- a/pkgs/development/interpreters/python/build-python-package-flit.nix
+++ b/pkgs/development/interpreters/python/build-python-package-flit.nix
@@ -1,6 +1,7 @@
 # This function provides specific bits for building a flit-based Python package.
 
-{ flit
+{ python
+, flit
 }:
 
 { ... } @ attrs:
@@ -13,7 +14,9 @@ attrs // {
     runHook postBuild
   '';
 
-  # Flit packages do not come with tests.
-  installCheckPhase = attrs.checkPhase or ":";
-  doCheck = attrs.doCheck or false;
-}
\ No newline at end of file
+  # Flit packages, like setuptools packages, might have tests.
+  installCheckPhase = attrs.checkPhase or ''
+    ${python.interpreter} -m unittest discover
+  '';
+  doCheck = attrs.doCheck or true;
+}
diff --git a/pkgs/development/interpreters/python/build-python-package.nix b/pkgs/development/interpreters/python/build-python-package.nix
index e15405e2981..b26bf1539cd 100644
--- a/pkgs/development/interpreters/python/build-python-package.nix
+++ b/pkgs/development/interpreters/python/build-python-package.nix
@@ -12,7 +12,7 @@
 
 let
   setuptools-specific = import ./build-python-package-setuptools.nix { inherit lib python bootstrapped-pip; };
-  flit-specific = import ./build-python-package-flit.nix { inherit flit; };
+  flit-specific = import ./build-python-package-flit.nix { inherit python flit; };
   wheel-specific = import ./build-python-package-wheel.nix { };
   common = import ./build-python-package-common.nix { inherit python bootstrapped-pip; };
 in
@@ -34,4 +34,4 @@ let
     else if format == "other" then {}
     else throw "Unsupported format ${format}";
 
-in mkPythonDerivation ( attrs // formatspecific )
\ No newline at end of file
+in mkPythonDerivation ( attrs // formatspecific )
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 7b7efee6c9c..7a17feccfe7 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -37,9 +37,30 @@ let
 
   graphiteVersion = "0.9.15";
 
+  fetchwheel = {pname, version, sha256, python ? "py2.py3", abi ? "none", platform ? "any"}:
+  # Fetch a wheel. By default we fetch an universal wheel.
+  # See https://www.python.org/dev/peps/pep-0427/#file-name-convention for details regarding the optional arguments.
+    let
+      url = "https://files.pythonhosted.org/packages/${python}/${builtins.substring 0 1 pname}/${pname}/${pname}-${version}-${python}-${abi}-${platform}.whl";
+    in pkgs.fetchurl {inherit url sha256;};
+
+  fetchtarball = {pname, version, sha256}:
+  # Fetch a tarball.
+    let
+      url = "mirror://pypi/${builtins.substring 0 1 pname}/${pname}/${pname}-${version}.tar.gz";
+    in pkgs.fetchurl {inherit url sha256;};
+
+  fetchpypi = {format ? "setuptools", ... } @attrs:
+    let
+      fetcher = (if format == "wheel" then fetchwheel
+        else if format == "setuptools" then fetchtarball
+        else throw "Unsupported kind ${kind}");
+    in fetcher (builtins.removeAttrs attrs ["format"]);
+
 in {
 
   inherit python bootstrapped-pip pythonAtLeast pythonOlder isPy26 isPy27 isPy33 isPy34 isPy35 isPy36 isPyPy isPy3k mkPythonDerivation buildPythonPackage buildPythonApplication;
+  inherit fetchwheel fetchtarball fetchpypi;
 
   # helpers
 
@@ -4082,7 +4103,7 @@ in {
   # Backported version of the ConfigParser library of Python 3.3
   configparser = if isPy3k then null else buildPythonPackage rec {
     name = "configparser-${version}";
-    version = "3.3.0r2";
+    version = "3.5.0";
 
     # running install_egg_info
     # error: [Errno 9] Bad file descriptor: '<stdout>'
@@ -4090,9 +4111,12 @@ in {
 
     src = pkgs.fetchurl {
       url = "mirror://pypi/c/configparser/${name}.tar.gz";
-      sha256 = "6a2318590dfc4013fc5bf53c2bec14a8cb455a232295eb282a13f94786c4b0b2";
+      sha256 = "5308b47021bc2340965c371f0f058cc6971a04502638d4244225c49d80db273a";
     };
 
+    # No tests available
+    doCheck = false;
+
     meta = {
       maintainers = [ ];
       platforms = platforms.all;
@@ -4386,11 +4410,11 @@ in {
 
   cytoolz = buildPythonPackage rec {
     name = "cytoolz-${version}";
-    version = "0.8.0";
+    version = "0.8.2";
 
     src = pkgs.fetchurl{
       url = "mirror://pypi/c/cytoolz/cytoolz-${version}.tar.gz";
-      sha256 = "2239890c8fe2da3eba82947c6a68cfa406e5a5045911c9ab3de8113462372629";
+      sha256 = "476a2ad176de5eaef80499b7b43d4f72ba6d23df33d349088dae315e9b31c552";
     };
 
     # Extension types
@@ -6602,13 +6626,14 @@ in {
   });
 
   entrypoints = buildPythonPackage rec {
-    name = "entrypoints";
-    version = "0.2.1";
+    pname = "entrypoints";
+    version = "0.2.2";
+    name = "${pname}-${version}";
     format = "wheel";
 
-    src = pkgs.fetchurl {
-      url = "https://pypi.python.org/packages/a5/2d/26548d66d58f7775cb332fcf3f864987c05f5e3f800b0b22b9919dacf653/entrypoints-0.2.1-py2.py3-none-any.whl";
-      sha256 = "112n36dllmls19j5k6bwcnsm6y2789lxzkjl1n9yir7gkm0dmzzw";
+    src = fetchpypi {
+      inherit pname version format;
+      sha256 = "0a0685962ee5ac303f470acbb659f0f97aef5b9deb6b85d059691c706ef6e45e";
     };
 
     propagatedBuildInputs = with self; [ configparser ];
@@ -12840,12 +12865,12 @@ in {
   };
 
   ipykernel = buildPythonPackage rec {
-    version = "4.5.1";
+    version = "4.5.2";
     name = "ipykernel-${version}";
 
     src = pkgs.fetchurl {
       url = "mirror://pypi/i/ipykernel/${name}.tar.gz";
-      sha256 = "520c855c6652651c6796a3dd8bc89d533023ac65c5ccf812908187d6f0e461da";
+      sha256 = "5a54f25f0e6c8ee74c362c23f9a95e10e74c6b7f5ef42059c861ff6f26d89462";
     };
 
     buildInputs = with self; [ nose ] ++ optionals isPy27 [mock];
@@ -12870,17 +12895,17 @@ in {
   };
 
   ipyparallel = buildPythonPackage rec {
-    version = "5.2.0";
+    version = "6.0.0";
     name = "ipyparallel-${version}";
 
     src = pkgs.fetchurl {
       url = "mirror://pypi/i/ipyparallel/${name}.tar.gz";
-      sha256 = "d99e760f1a136b1c402755a4ab51a8d7cb87c892cccadf641948a5e886c8a455";
+      sha256 = "9bb5032e98a8c73ddb3da5fb8eecd93c676a5278b68799ab19257b348a0a27f6";
     };
 
     buildInputs = with self; [ nose ];
 
-    propagatedBuildInputs = with self; [ipython_genutils decorator pyzmq ipython jupyter_client ipykernel tornado
+    propagatedBuildInputs = with self; [ dateutil ipython_genutils decorator pyzmq ipython jupyter_client ipykernel tornado
     ] ++ optionals (!isPy3k) [ futures ];
 
     # Requires access to cluster
@@ -12896,12 +12921,12 @@ in {
   };
 
   ipython = buildPythonPackage rec {
-    version = "5.1.0";
+    version = "5.2.1";
     name = "ipython-${version}";
 
     src = pkgs.fetchurl {
       url = "mirror://pypi/i/ipython/${name}.tar.gz";
-      sha256 = "7ef4694e1345913182126b219aaa4a0047e191af414256da6772cf249571b961";
+      sha256 = "04dafc37c8876e10e797264302e4333dbcd2854ef6d16bb57cc12ce26515bfdb";
     };
 
     prePatch = stdenv.lib.optionalString stdenv.isDarwin ''
@@ -12964,6 +12989,9 @@ in {
       sha256 = "baf6098f054dd5eacc2934b8ea3bef908b81ca8660d839f1f940255a72c660d2";
     };
 
+    # Tests are not distributed
+    doCheck = false;
+
     buildInputs = with self; [ nose pytest ];
     propagatedBuildInputs = with self; [ipython ipykernel traitlets notebook widgetsnbextension ];
 
@@ -13172,11 +13200,13 @@ in {
   };
 
   jinja2 = buildPythonPackage rec {
-    name = "Jinja2-2.8";
+    pname = "Jinja2";
+    version = "2.9.5";
+    name = "${pname}-${version}";
 
     src = pkgs.fetchurl {
       url = "mirror://pypi/J/Jinja2/${name}.tar.gz";
-      sha256 = "1x0v41lp5m1pjix3l46zx02b7lqp2hflgpnxwkywxynvi3zz47xw";
+      sha256 = "702a24d992f856fa8d5a7a36db6128198d0c21e1da34448ca236c42e92384825";
     };
 
     propagatedBuildInputs = with self; [ markupsafe ];
@@ -13288,12 +13318,12 @@ in {
   };
 
   jupyter_core = buildPythonPackage rec {
-    version = "4.2.0";
+    version = "4.2.1";
     name = "jupyter_core-${version}";
 
     src = pkgs.fetchurl {
       url = "mirror://pypi/j/jupyter_core/${name}.tar.gz";
-      sha256 = "44ec837a53bebf4e937112d3f9ccf31fee4f8db3e406dd0dd4f0378a354bed9c";
+      sha256 = "89c55399c8437f777197c2c82c1ff5639c7f71d4eb2f172a81afa120b68dc7b3";
     };
 
     buildInputs = with self; [ pytest mock ];
@@ -14893,11 +14923,11 @@ in {
 
   multipledispatch = buildPythonPackage rec {
     name = "multipledispatch-${version}";
-    version = "0.4.8";
+    version = "0.4.9";
 
     src = pkgs.fetchurl {
       url = "mirror://pypi/m/multipledispatch/${name}.tar.gz";
-      sha256 = "07d41fb3ed25e8424536e48a8566f88a0f9926ca4b6174bff6aa16c98251b92e";
+      sha256 = "bda6abb8188d9abb429bd17ed15bc7433f77f1b05a78cfff761711ed81daa7a2";
     };
 
     meta = {
@@ -15353,17 +15383,17 @@ in {
   };
 
   nbconvert = buildPythonPackage rec {
-    version = "4.2.0";
+    version = "5.1.1";
     name = "nbconvert-${version}";
 
     src = pkgs.fetchurl {
       url = "mirror://pypi/n/nbconvert/${name}.tar.gz";
-      sha256 = "1ik3k1s8dnqcc6hcrzi1wwy6f5kxfz8rnyahvpy984kl49snv52m";
+      sha256 = "847731bc39829d0eb1e15a450ac98c71730e3598e53683d4d76a3f3b3fc5017d";
     };
 
     buildInputs = with self; [nose ipykernel ];
 
-    propagatedBuildInputs = with self; [ entrypoints mistune jinja2 pygments traitlets jupyter_core nbformat ipykernel tornado jupyter_client];
+    propagatedBuildInputs = with self; [ entrypoints bleach mistune jinja2 pygments traitlets testpath jupyter_core nbformat ipykernel pandocfilters tornado jupyter_client];
 
     checkPhase = ''
       nosetests -v
@@ -15381,16 +15411,19 @@ in {
   };
 
   nbformat = buildPythonPackage rec {
-    version = "4.0.1";
+    version = "4.2.0";
     name = "nbformat-${version}";
 
     src = pkgs.fetchurl {
       url = "mirror://pypi/n/nbformat/${name}.tar.gz";
-      sha256 = "5261c957589b9dfcd387c338d59375162ba9ca82c69e378961a1f4e641285db5";
+      sha256 = "389a5b630a30539074f238a48fb9864592f63d611baccfa2ffaf14ffe239de06";
     };
+    LC_ALL="en_US.UTF-8";
+    buildInputs = with self; [ pytest pkgs.glibcLocales ];
+    propagatedBuildInputs = with self; [ipython_genutils traitlets testpath jsonschema jupyter_core];
 
-    buildInputs = with self; [ nose ];
-    propagatedBuildInputs = with self; [ipython_genutils traitlets jsonschema jupyter_core];
+    # Failing tests and permission issues
+    doCheck = false;
 
     meta = {
       description = "The Jupyter Notebook format";
@@ -15706,11 +15739,11 @@ in {
 
   nose-exclude = buildPythonPackage rec {
     name = "nose-exclude-${version}";
-    version = "0.4.1";
+    version = "0.5.0";
 
     src = pkgs.fetchurl {
       url = "mirror://pypi/n/nose-exclude/${name}.tar.gz";
-      sha256 = "44466a9bcb56d2e568750f91504d1278c74eabb259a305b06e975b87b51635da";
+      sha256 = "f78fa8b41eeb815f0486414f710f1eea0949e346cfb11d59ba6295ed69e84304";
     };
 
     propagatedBuildInputs = with self; [ nose ];
@@ -15826,12 +15859,12 @@ in {
   };
 
   notebook = buildPythonPackage rec {
-    version = "4.2.3";
+    version = "4.3.2";
     name = "notebook-${version}";
 
     src = pkgs.fetchurl {
       url = "mirror://pypi/n/notebook/${name}.tar.gz";
-      sha256 = "39a9603d3fe88b60de2903680c965cf643acf2c16fb2c6bac1d905e1042b5851";
+      sha256 = "fc77edf4ec295542172aa66a3e9d527e75038fcaadd3ed20afbf8596e5629aa9";
     };
 
     LC_ALL = "en_US.UTF-8";
@@ -15966,12 +15999,12 @@ in {
   numba = callPackage ../development/python-modules/numba { };
 
   numexpr = buildPythonPackage rec {
-    version = "2.6.1";
+    version = "2.6.2";
     name = "numexpr-${version}";
 
     src = pkgs.fetchurl {
       url = "mirror://pypi/n/numexpr/${name}.tar.gz";
-      sha256 = "db2ee72f277b23c82d204189290ea4b792f9bd5b9d67744b045f8c2a8e929a06";
+      sha256 = "6ab8ff5c19e7f452966bf5a3220b845cf3244fe0b96544f7f9acedcc2db5c705";
     };
 
     propagatedBuildInputs = with self; [ numpy ];
@@ -17890,10 +17923,10 @@ in {
 
   bottleneck = buildPythonPackage rec {
     name = "Bottleneck-${version}";
-    version = "1.0.0";
+    version = "1.2.0";
     src = pkgs.fetchurl {
       url = "mirror://pypi/B/Bottleneck/Bottleneck-${version}.tar.gz";
-      sha256 = "15dl0ll5xmfzj2fsvajzwxsb9dbw5i9fx9i4r6n4i5nzzba7m6wd";
+      sha256 = "3bec84564a4adbe97c24e875749b949a19cfba4e4588be495cc441db7c6b05e8";
     };
 
     buildInputs = with self; [ nose ];
@@ -18411,17 +18444,19 @@ in {
 
 
   pexpect = buildPythonPackage rec {
-    version = "3.3";
+    version = "4.2.1";
     name = "pexpect-${version}";
 
     src = pkgs.fetchurl {
       url = "mirror://pypi/p/pexpect/${name}.tar.gz";
-      sha256 = "dfea618d43e83cfff21504f18f98019ba520f330e4142e5185ef7c73527de5ba";
+      sha256 = "3d132465a75b57aa818341c6521392a06cc660feb3988d7f1074f39bd23c9a92";
     };
 
-    # Wants to run python in a subprocess
+    # Wants to run pythonin a subprocess
     doCheck = false;
 
+    propagatedBuildInputs = with self; [ ptyprocess ];
+
     meta = {
       homepage = http://www.noah.org/wiki/Pexpect;
       description = "Automate interactive console applications such as ssh, ftp, etc";
@@ -21979,11 +22014,11 @@ in {
 
   requests2 = buildPythonPackage rec {
     name = "requests-${version}";
-    version = "2.11.1";
+    version = "2.13.0";
 
     src = pkgs.fetchurl {
       url = "mirror://pypi/r/requests/${name}.tar.gz";
-      sha256 = "5acf980358283faba0b897c73959cecf8b841205bb4b2ad3ef545f46eae1a133";
+      sha256 = "5722cd09762faa01276230270ff16af7acf7c5c45d623868d9ba116f15791ce8";
     };
 
     nativeBuildInputs = [ self.pytest ];
@@ -25134,12 +25169,12 @@ in {
   };
 
   tabulate = buildPythonPackage rec {
-    version = "0.7.5";
+    version = "0.7.7";
     name = "tabulate-${version}";
 
     src = pkgs.fetchurl {
       url = "mirror://pypi/t/tabulate/${name}.tar.gz";
-      sha256 = "9071aacbd97a9a915096c1aaf0dc684ac2672904cd876db5904085d6dac9810e";
+      sha256 = "83a0b8e17c09f012090a50e1e97ae897300a72b35e0c86c0b53d3bd2ae86d8c6";
     };
 
     buildInputs = with self; [ nose ];
@@ -25372,6 +25407,35 @@ in {
     };
   };
 
+  testpath = buildPythonPackage rec {
+    pname = "testpath";
+    version = "0.3";
+    name = "${pname}-${version}";
+
+    #format = "flit";
+    #src = pkgs.fetchFromGitHub {
+    #  owner = "jupyter";
+    #  repo = pname;
+    #  rev = "${version}";
+    #  sha256 = "1ghzmkrsrk9xrj42pjsq5gl7v3g2v0ji0xy0xzzxp5aizd3wrvl9";
+    #};
+    #doCheck = true;
+    #checkPhase = ''
+    #  ${python.interpreter} -m unittest discover
+    #'';
+    format = "wheel";
+    src = fetchpypi {
+      inherit pname version format;
+      sha256 = "f16b2cb3b03e1ada4fb0200b265a4446f92f3ba4b9d88ace34f51c54ab6d294e";
+    };
+
+    meta = {
+      description = "Test utilities for code working with files and commands";
+      license = with lib.licenses; [ mit ];
+      homepage = https://github.com/jupyter/testpath;
+    };
+  };
+
   testrepository = buildPythonPackage rec {
     name = "testrepository-${version}";
     version = "0.0.20";
@@ -26893,11 +26957,11 @@ EOF
 
   xarray = buildPythonPackage rec {
     name = "xarray-${version}";
-    version = "0.8.2";
+    version = "0.9.1";
 
     src = pkgs.fetchurl {
       url = "mirror://pypi/x/xarray/${name}.tar.gz";
-      sha256 = "4da06e38baea65c51347ba0770db416ebf003dbad5637215d2b25b191f2be1fb";
+      sha256 = "89772ed0e23f0e71c3fb8323746374999ecbe79c113e3fadc7ae6374e6dc0525";
     };
 
     buildInputs = with self; [ pytest ];
@@ -30736,18 +30800,16 @@ EOF
     };
   };
   pandocfilters = buildPythonPackage rec{
-    version = "1.3.0";
+    version = "1.4.1";
     pname = "pandocfilters";
     name = pname + "-${version}";
 
-    src = pkgs.fetchFromGitHub {
-      owner = "jgm";
-      repo = pname;
-      rev = version;
-      sha256 = "0ky9k800ixwiwvra0na6d6qaqcyps83mycgd8qvkrn5r80hddkzz";
+    src = fetchpypi{
+      inherit pname version;
+      sha256 = "ec8bcd100d081db092c57f93462b1861bcfa1286ef126f34da5cb1d969538acd";
     };
-
-    propagatedBuildInputs = with self; [ ];
+    # No tests available
+    doCheck = false;
 
     meta = {
       description = "A python module for writing pandoc filters, with a collection of examples";