Merge master into staging-next

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

@@ -0,0 +1,22 @@
+{ buildPythonPackage, pytest, lib, fetchPypi }:
+
+buildPythonPackage rec {
+  pname = "affine";
+  version = "2.2.1";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0j3mvcnmgjvvm0znqyf7xylq7i89zjf4dq0g8280xs6bwbl5cvih";
+  };
+
+  checkInputs = [ pytest ];
+  checkPhase = "py.test";
+
+  meta = with lib; {
+    description = "Matrices describing affine transformation of the plane";
+    license = licenses.bsd3;
+    homepage = https://github.com/sgillies/affine;
+    maintainers = with maintainers; [ mredaelli ];
+  };
+
+}

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

@@ -1,16 +1,27 @@
-{ stdenv, fetchPypi, buildPythonPackage, six }:
+{ stdenv
+, fetchPypi
+, buildPythonPackage
+, six
+, wheel
+ }:
 
 buildPythonPackage rec {
   pname = "astunparse";
-  version =  "1.5.0";
+  version =  "1.6.1";
+
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1kc9lm2jvfcip3z8snj04dar5a9jh857a704m6lvcv4xclm3rpsm";
+    sha256 = "d27b16fb33dea0778c5a2c01801554eae0d3f8a8d6f604f15627589c3d6f11ca";
   };
-  propagatedBuildInputs = [ six ];
-  doCheck = false; # no tests
+
+  propagatedBuildInputs = [ six wheel ];
+
+  # tests not included with pypi release
+  doCheck = false;
+
   meta = with stdenv.lib; {
     description = "This is a factored out version of unparse found in the Python source distribution";
+    homepage = https://github.com/simonpercivall/astunparse;
     license = licenses.bsd3;
     maintainers = with maintainers; [ jyp ];
   };

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

@@ -1,4 +1,4 @@
-{ lib, buildPythonPackage, fetchPypi, pythonOlder, pytest, pytest-asyncio }:
+{ lib, buildPythonPackage, fetchPypi, pythonOlder, isPy35, pytest, pytest-asyncio }:
 
 buildPythonPackage rec {
   pname = "async_generator";
@@ -17,6 +17,9 @@ buildPythonPackage rec {
     pytest -W error -ra -v --pyargs async_generator
   '';
 
+  # disable tests on python3.5 to avoid circular dependency with pytest-asyncio
+  doCheck = !isPy35;
+
   meta = with lib; {
     description = "Async generators and context managers for Python 3.5+";
     homepage = https://github.com/python-trio/async_generator;

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

@@ -3,7 +3,7 @@
 
 buildPythonPackage rec {
   pname = "bugzilla";
-  version = "1.1.0";
+  version = "2.2.0";
 
   src = fetchPypi {
     inherit pname version;

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

@@ -0,0 +1,46 @@
+{ buildPythonPackage, lib, fetchPypi
+, pytest, filelock, mock, pep8
+, cython, isPy37, glibcLocales
+, six, pyshp, shapely, geos, proj, numpy
+, gdal, pillow, matplotlib, pyepsg, pykdtree, scipy, owslib, fiona
+}:
+
+buildPythonPackage rec {
+  pname = "cartopy";
+  version = "0.17.0";
+
+  src = fetchPypi {
+    inherit version;
+    pname = "Cartopy";
+    sha256 = "0q9ckfi37cxj7jwnqnzij62vwcf4krccx576vv5lhvpgvplxjjs2";
+  };
+
+  checkInputs = [ filelock mock pytest pep8 ];
+
+  # several tests require network connectivity: we disable them
+  checkPhase = ''
+    export HOME=$(mktemp -d)
+    pytest --pyargs cartopy \
+      -m "not network and not natural_earth" \
+      -k "not test_nightshade_image"
+  '';
+
+  buildInputs = [ cython glibcLocales ];
+  LC_ALL = "en_US.UTF-8";
+
+  propagatedBuildInputs = [
+    # required
+    six pyshp shapely geos proj numpy
+
+    # optional
+    gdal pillow matplotlib pyepsg pykdtree scipy fiona owslib
+  ];
+
+  meta = with lib; {
+    description = "Process geospatial data to create maps and perform analyses";
+    license = licenses.lgpl3;
+    homepage = https://scitools.org.uk/cartopy/docs/latest/;
+    maintainers = with maintainers; [ mredaelli ];
+  };
+
+}

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

@@ -0,0 +1,21 @@
+{ stdenv, fetchFromGitHub, buildPythonPackage, pyparsing, six }:
+
+buildPythonPackage rec {
+  pname = "configshell";
+  version = "1.1.fb25";
+
+  src = fetchFromGitHub {
+    owner = "open-iscsi";
+    repo ="${pname}-fb";
+    rev = "v${version}";
+    sha256 = "0zpr2n4105qqsklyfyr9lzl1rhxjcv0mnsl57hgk0m763w6na90h";
+  };
+
+  propagatedBuildInputs = [ pyparsing six ];
+
+  meta = with stdenv.lib; {
+    description = "A Python library for building configuration shells";
+    homepage = https://github.com/open-iscsi/configshell-fb;
+    license = licenses.asl20;
+  };
+}

pkgs/development/python-modules/fs-s3fs/default.nix

@@ -0,0 +1,23 @@
+{ buildPythonPackage, fetchPypi, lib, fs, six, boto3 }:
+
+buildPythonPackage rec {
+  pname = "fs-s3fs";
+  version = "1.0.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1czv67zs4sl5l3rv9l3hzn22zzzqm372lq1wlhihigir4cfyslak";
+  };
+
+  propagatedBuildInputs = [ fs six boto3 ];
+
+  # tests try to integrate an s3 bucket which can't be tested properly in an isolated environment.
+  doCheck = false;
+
+  meta = with lib; {
+    homepage = https://pypi.org/project/fs-s3fs/;
+    license = licenses.mit;
+    description = "Amazon S3 filesystem for PyFilesystem2";
+    maintainers = with maintainers; [ ma27 ];
+  };
+}

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

@@ -0,0 +1,31 @@
+{ buildPythonPackage, lib, fetchFromGitHub, pytest
+, typing, funcsigs, pythonOlder
+}:
+
+buildPythonPackage rec {
+  pname = "gentools";
+  version = "1.1.0";
+
+  # Pypi doesn't ship the tests, so we fetch directly from GitHub
+  src = fetchFromGitHub {
+    owner = "ariebovenberg";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "1sm6cqi7fv2k3pc68r7wvvjjz8y6cjmz8bvxgqfa4v4wxibwnwrl";
+  };
+
+  propagatedBuildInputs =
+    lib.optionals (pythonOlder "3.5") [ typing ] ++
+    lib.optionals (pythonOlder "3.4") [ funcsigs ];
+
+  checkInputs = [ pytest ];
+  checkPhase = "pytest";
+
+  meta = with lib; {
+    description = "Tools for generators, generator functions, and generator-based coroutines";
+    license = licenses.mit;
+    homepage = http://gentools.readthedocs.io/;
+    maintainers = with maintainers; [ mredaelli ];
+  };
+
+}

pkgs/development/python-modules/grpcio-tools/default.nix

@@ -2,16 +2,16 @@
 
 buildPythonPackage rec {
   pname = "grpcio-tools";
-  version = "1.14.2";
+  version = "1.16.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "b3fd64a5b8c1d981f6d68a331449109633710a346051c44e0f0cca1812e2b4b0";
+    sha256 = "0h0w7jlggm8nc250wwqai7lihw8mymx9jjpkl0cdmqmwbypj72vd";
   };
 
   enableParallelBuilding = true;
 
-  propagatedBuildInputs = [ grpc grpcio ];
+  propagatedBuildInputs = [ grpcio ];
 
   # no tests in the package
   doCheck = false;

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

@@ -4,11 +4,11 @@
 with stdenv.lib;
 buildPythonPackage rec {
   pname = "grpcio";
-  version = "1.15.0";
+  version = "1.16.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1lhh76kgyibgsk6c54nbzzhkskknkbvn71xvixsk0prfp8izr98m";
+    sha256 = "0am76f8r4v5kcvbar593n2c1mp25cxi67cxigjhd0rnncmk4bgs1";
   };
 
   nativeBuildInputs = [ pkgconfig ] ++ optional stdenv.isDarwin darwin.cctools;

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

@@ -0,0 +1,24 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+}:
+
+buildPythonPackage rec {
+  pname = "hopcroftkarp";
+  version = "1.2.4";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "cc6fc7ad348bbe5c9451f8116845c46ae26290c92b2dd14690aae2d55ba5e3a6";
+  };
+
+  # tests fail due to bad package name
+  doCheck = false;
+
+  meta = with lib; {
+    description = "Implementation of HopcroftKarp's algorithm";
+    homepage = https://github.com/sofiat-olaosebikan/hopcroftkarp;
+    license = licenses.gpl1;
+    maintainers = [ maintainers.costrouc ];
+  };
+}

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

@@ -7,14 +7,15 @@
 
 buildPythonPackage rec {
   pname = "manuel";
-  version = "1.8.0";
+  version = "1.10.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1diyj6a8bvz2cdf9m0g2bbx9z2yjjnn3ylbg1zinpcjj6vldfx59";
+    sha256 = "1bdzay7j70fly5fy6wbdi8fbrxjrrlxnxnw226rwry1c8a351rpy";
   };
 
-  propagatedBuildInputs = [ six zope_testing ];
+  propagatedBuildInputs = [ six ];
+  checkInputs = [ zope_testing ];
 
   meta = with stdenv.lib; {
     description = "A documentation builder";

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

@@ -0,0 +1,33 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, hopcroftkarp
+, multiset
+, pytest
+, pytestrunner
+, hypothesis
+, setuptools_scm
+, isPy27
+}:
+
+buildPythonPackage rec {
+  pname = "matchpy";
+  version = "0.4.6";
+  disabled = isPy27;
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "eefa1e50a10e1255db61bc2522a6768ad0701f8854859f293ebaa442286faadd";
+  };
+
+  buildInputs = [ setuptools_scm pytestrunner ];
+  checkInputs = [ pytest hypothesis ];
+  propagatedBuildInputs = [ hopcroftkarp multiset ];
+
+  meta = with lib; {
+    description = "A library for pattern matching on symbolic expressions";
+    homepage = https://github.com/HPAC/matchpy;
+    license = licenses.mit;
+    maintainers = [ maintainers.costrouc ];
+  };
+}

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

@@ -0,0 +1,27 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, setuptools_scm
+, pytestrunner
+, pytest
+}:
+
+buildPythonPackage rec {
+  pname = "multiset";
+  version = "2.1.1";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "4801569c08bfcecfe7b0927b17f079c90f8607aca8fecaf42ded92b737162bc7";
+  };
+
+  buildInputs = [ setuptools_scm pytestrunner ];
+  checkInputs = [ pytest ];
+
+  meta = with lib; {
+    description = "An implementation of a multiset";
+    homepage = https://github.com/wheerd/multiset;
+    license = licenses.mit;
+    maintainers = [ maintainers.costrouc ];
+  };
+}

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

@@ -0,0 +1,41 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, coverage
+, ipykernel
+, jupyter_client
+, nbformat
+, pytest
+, six
+, glibcLocales
+, matplotlib
+, sympy
+, pytestcov
+}:
+
+buildPythonPackage rec {
+  pname = "nbval";
+  version = "0.9.1";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "3f18b87af4e94ccd073263dd58cd3eebabe9f5e4d6ab535b39d3af64811c7eda";
+  };
+
+  LC_ALL = "en_US.UTF-8";
+
+  buildInputs = [ glibcLocales ];
+  checkInputs = [ matplotlib sympy pytestcov ];
+  propagatedBuildInputs = [ coverage ipykernel jupyter_client nbformat pytest six ];
+
+  checkPhase = ''
+    pytest tests --current-env --ignore tests/test_timeouts.py
+  '';
+
+  meta = with lib; {
+    description = "A py.test plugin to validate Jupyter notebooks";
+    homepage = https://github.com/computationalmodelling/nbval;
+    license = licenses.bsd3;
+    maintainers = [ maintainers.costrouc ];
+  };
+}

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

@@ -18,7 +18,10 @@ buildPythonPackage rec {
   buildInputs = [ pkgs.glibcLocales pytest ];
 
   checkPhase = ''
-    py.test netaddr/tests
+    # fails on python3.7: https://github.com/drkjam/netaddr/issues/182
+    py.test \
+      -k 'not test_ip_splitter_remove_prefix_larger_than_input_range' \
+      netaddr/tests
   '';
 
   patches = [

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

@@ -0,0 +1,43 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, six
+, statistics
+, pythonOlder
+, nose
+, psutil
+, contextlib2
+, mock
+, unittest2
+, isPy27
+, python
+}:
+
+buildPythonPackage rec {
+  pname = "perf";
+  version = "1.5.1";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "5aae76e58bd3edd0c50adcc7c16926ebb9ed8c0e5058b435a30d58c6bb0394a8";
+  };
+
+  checkInputs = [ nose psutil ] ++
+    lib.optionals isPy27 [ contextlib2 mock unittest2 ];
+  propagatedBuildInputs = [ six ] ++
+    lib.optionals (pythonOlder "3.4") [ statistics ];
+
+  # tests not included in pypi repository
+  doCheck = false;
+
+  checkPhase = ''
+    ${python.interpreter} -m nose
+  '';
+
+  meta = with lib; {
+    description = "Python module to generate and modify perf";
+    homepage = https://github.com/vstinner/perf;
+    license = licenses.mit;
+    maintainers = [ maintainers.costrouc ];
+  };
+}

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

@@ -1,4 +1,4 @@
-{ stdenv, python, buildPythonPackage
+{ stdenv, fetchpatch, python, buildPythonPackage
 , protobuf, google_apputils, pyext, libcxx
 , disabled, doCheck ? true }:
 
@@ -16,6 +16,15 @@ buildPythonPackage rec {
   propagatedBuildInputs = [ protobuf google_apputils ];
   buildInputs = [ google_apputils pyext ];
 
+  patches = [
+    # Python 3.7 compatibility (remove when protobuf 3.7 is released)
+    (fetchpatch {
+      url = "https://github.com/protocolbuffers/protobuf/commit/0a59054c30e4f0ba10f10acfc1d7f3814c63e1a7.patch";
+      sha256 = "09hw22y3423v8bbmc9xm07znwdxfbya6rp78d4zqw6fisdvjkqf1";
+      stripLen = 1;
+    })
+  ];
+
   prePatch = ''
     while [ ! -d python ]; do
       cd *

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

@@ -0,0 +1,23 @@
+{ buildPythonPackage, lib, fetchPypi, requests }:
+
+buildPythonPackage rec {
+  pname = "pyepsg";
+  version = "0.3.2";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0ng0k140kzq3xcffi4vy10py4cmwzfy8anccysw3vgn1x30ghzjr";
+  };
+
+  propagatedBuildInputs = [ requests ];
+
+  doCheck = false;
+
+  meta = with lib; {
+    description = "Simple Python interface to epsg.io";
+    license = licenses.lgpl3;
+    homepage = https://pyepsg.readthedocs.io/en/latest/;
+    maintainers = with maintainers; [ mredaelli ];
+  };
+
+}

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

@@ -20,9 +20,9 @@ buildPythonPackage rec {
   checkInputs = [ mock psutil ];
   propagatedBuildInputs = [ pyopenssl pysendfile ];
 
-  checkPhase = ''
-    ${python.interpreter} pyftpdlib/test/runner.py
-  '';
+  # impure filesystem-related tests cause timeouts
+  # on Hydra: https://hydra.nixos.org/build/84374861
+  doCheck = false;
 
   meta = with stdenv.lib; {
     homepage = https://github.com/giampaolo/pyftpdlib/;

pkgs/development/python-modules/pytest-asyncio/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, buildPythonPackage, fetchPypi, pytest, isPy3k }:
+{ stdenv, buildPythonPackage, fetchPypi, pytest, isPy3k, isPy35, async_generator }:
 buildPythonPackage rec {
   pname = "pytest-asyncio";
   version = "0.9.0";
@@ -10,7 +10,8 @@ buildPythonPackage rec {
     sha256 = "fbd92c067c16111174a1286bfb253660f1e564e5146b39eeed1133315cf2c2cf";
   };
 
-  buildInputs = [ pytest ];
+  buildInputs = [ pytest ]
+    ++ stdenv.lib.optionals isPy35 [ async_generator ];
 
   # No tests in archive
   doCheck = false;

pkgs/development/python-modules/pytest-mypy/default.nix

@@ -0,0 +1,25 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, pytest
+, mypy
+}:
+
+buildPythonPackage rec {
+  pname = "pytest-mypy";
+  version = "0.3.2";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "acc653210e7d8d5c72845a5248f00fd33f4f3379ca13fe56cfc7b749b5655c3e";
+  };
+
+  propagatedBuildInputs = [ pytest mypy ];
+
+  meta = with lib; {
+    description = "Mypy static type checker plugin for Pytest";
+    homepage = https://github.com/dbader/pytest-mypy;
+    license = licenses.mit;
+    maintainers = [ maintainers.costrouc ];
+  };
+}

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

@@ -0,0 +1,28 @@
+{ stdenv, buildPythonPackage, fetchPypi, isPy3k
+, requests }:
+
+buildPythonPackage rec {
+  pname = "pyupdate";
+  version = "0.2.16";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1p4zpjvwy6h9kr0dp80z5k04s14r9f75jg9481gpx8ygxj0l29bi";
+  };
+
+  propagatedBuildInputs = [ requests ];
+
+  # As of 0.2.16, pyupdate is intimately tied to Home Assistant which is py3 only
+  disabled = !isPy3k;
+
+  # no tests
+  doCheck = false;
+
+  meta = with stdenv.lib; {
+    # This description is terrible, but it's what upstream uses.
+    description = "Package to update stuff";
+    homepage = https://github.com/ludeeus/pyupdate;
+    license = licenses.mit;
+    maintainers = with maintainers; [ peterhoeg ];
+  };
+}

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

@@ -0,0 +1,29 @@
+{ buildPythonPackage, lib, fetchFromGitHub
+, cython
+, numpy, affine, attrs, cligj, click-plugins, snuggs, gdal
+, pytest, pytestcov, packaging, hypothesis, boto3
+}:
+
+buildPythonPackage rec {
+  pname = "rasterio";
+  version = "1.0.10";
+
+  # Pypi doesn't ship the tests, so we fetch directly from GitHub
+  src = fetchFromGitHub {
+    owner = "mapbox";
+    repo = "rasterio";
+    rev = version;
+    sha256 = "0gnck9y3n31nnazlrw54swab8wql9qjx5r5x9r7hrmzy72xlzjqq";
+  };
+
+  checkInputs = [ boto3 pytest pytestcov packaging hypothesis ];
+  buildInputs = [ cython ];
+  propagatedBuildInputs = [ gdal numpy attrs affine cligj click-plugins snuggs ];
+
+  meta = with lib; {
+    description = "Python package to read and write geospatial raster data";
+    license = licenses.bsd3;
+    homepage = https://rasterio.readthedocs.io/en/latest/;
+    maintainers = with maintainers; [ mredaelli ];
+  };
+}

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

@@ -1,4 +1,4 @@
-{ stdenv, buildPythonPackage, fetchPypi }:
+{ stdenv, buildPythonPackage, fetchPypi, nose }:
 
 buildPythonPackage rec {
   pname = "rope";
@@ -9,6 +9,12 @@ buildPythonPackage rec {
     sha256 = "a108c445e1cd897fe19272ab7877d172e7faf3d4148c80e7d20faba42ea8f7b2";
   };
 
+  checkInputs = [ nose ];
+  checkPhase = ''
+    # tracked upstream here https://github.com/python-rope/rope/issues/247
+    NOSE_IGNORE_FILES=type_hinting_test.py nosetests ropetest
+  '';
+
   meta = with stdenv.lib; {
     description = "Python refactoring library";
     homepage = https://github.com/python-rope/rope;

pkgs/development/python-modules/rpy2/default.nix

@@ -1,10 +1,13 @@
 { lib
+, python
 , buildPythonPackage
 , fetchPypi
 , isPyPy
 , isPy27
 , readline
 , R
+, rWrapper
+, rPackages
 , pcre
 , lzma
 , bzip2
@@ -13,7 +16,11 @@
 , singledispatch
 , six
 , jinja2
+, pytz
+, numpy
 , pytest
+, mock
+, extraRPackages ? []
 }:
 
 buildPythonPackage rec {
@@ -38,18 +45,54 @@ buildPythonPackage rec {
       bzip2
       zlib
       icu
+    ] ++ (with rPackages; [
+      # packages expected by the test framework
+      ggplot2
+      dplyr
+      RSQLite
+      broom
+      DBI
+      dbplyr
+      hexbin
+      lme4
+      tidyr
+    ]) ++ extraRPackages ++ rWrapper.recommendedPackages;
+
+    patches = [
+      # R_LIBS_SITE is used by the nix r package to point to the installed R libraries.
+      # This patch sets R_LIBS_SITE when rpy2 is imported.
+      ./r-libs-site.patch
     ];
+    postPatch = ''
+      substituteInPlace rpy/rinterface/__init__.py --replace '@NIX_R_LIBS_SITE@' "$R_LIBS_SITE"
+    '';
+
     propagatedBuildInputs = [
       singledispatch
       six
       jinja2
+      pytz
+      numpy
     ];
-    checkInputs = [ pytest ];
-    # Tests fail with `assert not _relpath.startswith('..'), "Path must be within the project"`
-    # in the unittest `loader.py`. I don't know what causes this.
+
+    checkInputs = [
+      pytest
+      mock
+    ];
+    # One remaining test failure caused by different unicode encoding.
+    # https://bitbucket.org/rpy2/rpy2/issues/488
     doCheck = false;
-    # without this tests fail when looking for libreadline.so
-    LD_LIBRARY_PATH = lib.makeLibraryPath buildInputs;
+    checkPhase = ''
+      ${python.interpreter} -m 'rpy2.tests'
+    '';
+
+    # For some reason libreadline.so is not found. Curiously `ldd _rinterface.so | grep readline` shows two readline entries:
+    # libreadline.so.6 => not found
+    # libreadline.so.6 => /nix/store/z2zhmrg6jcrn5iq2779mav0nnq4vm2q6-readline-6.3p08/lib/libreadline.so.6 (0x00007f333ac43000)
+    # There must be a better way to fix this, but I don't know it.
+    postFixup = ''
+      patchelf --add-needed ${readline}/lib/libreadline.so "$out/${python.sitePackages}/rpy2/rinterface/"_rinterface*.so
+    '';
 
     meta = {
       homepage = http://rpy.sourceforge.net/rpy2;

pkgs/development/python-modules/rpy2/r-libs-site.patch

@@ -0,0 +1,20 @@
+diff --git a/rpy/rinterface/__init__.py b/rpy/rinterface/__init__.py
+index 9362e57..1af258e 100644
+--- a/rpy/rinterface/__init__.py
++++ b/rpy/rinterface/__init__.py
+@@ -43,6 +43,15 @@ if not R_HOME:
+ if not os.environ.get("R_HOME"):
+     os.environ['R_HOME'] = R_HOME
+ 
++# path to libraries
++existing = os.environ.get('R_LIBS_SITE')
++if existing is not None:
++    prefix = existing + ':'
++else:
++    prefix = ''
++additional = '@NIX_R_LIBS_SITE@'
++os.environ['R_LIBS_SITE'] = prefix + additional
++
+ if sys.platform == 'win32':
+     _load_r_dll(R_HOME)
+ 

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

@@ -0,0 +1,21 @@
+{ stdenv, fetchFromGitHub, buildPythonPackage, six, pyudev, pygobject3 }:
+
+buildPythonPackage rec {
+  pname = "rtslib";
+  version = "2.1.fb69";
+
+  src = fetchFromGitHub {
+    owner = "open-iscsi";
+    repo ="${pname}-fb";
+    rev = "v${version}";
+    sha256 = "17rlcrd9757nq91pa8xjr7147k7mxxp8zdka7arhlgsp3kcnbsfd";
+  };
+
+  propagatedBuildInputs = [ six pyudev pygobject3 ];
+
+  meta = with stdenv.lib; {
+    description = "A Python object API for managing the Linux LIO kernel target";
+    homepage = https://github.com/open-iscsi/rtslib-fb;
+    license = licenses.asl20;
+  };
+}

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

@@ -0,0 +1,37 @@
+{ buildPythonPackage, lib, fetchFromGitHub, glibcLocales
+, pytest, pytest-mock, gentools
+, typing, singledispatch, pythonOlder
+}:
+
+buildPythonPackage rec {
+  pname = "snug";
+  version = "1.3.4";
+
+  # Pypi doesn't ship the tests, so we fetch directly from GitHub
+  src = fetchFromGitHub {
+    owner = "ariebovenberg";
+    repo = "snug";
+    rev = "v${version}";
+    sha256 = "0jmg0sivz9ljazlnsrrqaizrb3r7asy5pa0dj3idx49gbig4589i";
+  };
+
+  # Prevent unicode decoding error in setup.py
+  # while reading README.rst and HISTORY.rst
+  buildInputs = [ glibcLocales ];
+  LC_ALL = "en_US.UTF-8";
+
+  propagatedBuildInputs =
+    lib.optionals (pythonOlder "3.4") [ singledispatch ] ++
+    lib.optionals (pythonOlder "3.5") [ typing ];
+
+  checkInputs = [ pytest pytest-mock gentools ];
+  checkPhase = "pytest";
+
+  meta = with lib; {
+    description = "Tiny toolkit for writing reusable interactions with web APIs";
+    license = licenses.mit;
+    homepage = https://snug.readthedocs.io/en/latest/;
+    maintainers = with maintainers; [ mredaelli ];
+  };
+
+}

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

@@ -0,0 +1,29 @@
+{ buildPythonPackage, lib, fetchFromGitHub
+, click, numpy, pyparsing
+, pytest
+}:
+
+buildPythonPackage rec {
+  pname = "snuggs";
+  version = "1.4.2";
+
+  # Pypi doesn't ship the tests, so we fetch directly from GitHub
+  src = fetchFromGitHub {
+    owner = "mapbox";
+    repo = pname;
+    rev = version;
+    sha256 = "1q6jqwai4qgghdjgwhyx3yz8mlrm7p1vvnwc339lfl028hrgb5kb";
+  };
+
+  propagatedBuildInputs = [ click numpy pyparsing ];
+
+  checkInputs = [ pytest ];
+  checkPhase = "pytest test_snuggs.py";
+
+  meta = with lib; {
+    description = "S-expressions for Numpy";
+    license = licenses.mit;
+    homepage = https://github.com/mapbox/snuggs;
+    maintainers = with maintainers; [ mredaelli ];
+  };
+}

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

@@ -1,31 +1,28 @@
 { stdenv
 , buildPythonPackage
 , fetchPypi
-, nose
+, rednose
 , six
 , mock
-, pkgs
 , isPyPy
 }:
 
 buildPythonPackage rec {
   pname = "sure";
-  version = "1.2.24";
+  version = "1.4.11";
   disabled = isPyPy;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1lyjq0rvkbv585dppjdq90lbkm6gyvag3wgrggjzyh7cpyh5c12w";
+    sha256 = "3c8d5271fb18e2c69e2613af1ad400d8df090f1456081635bd3171847303cdaa";
   };
 
-  LC_ALL="en_US.UTF-8";
-
-  buildInputs = [ nose pkgs.glibcLocales ];
+  buildInputs = [ rednose ];
   propagatedBuildInputs = [ six mock ];
 
   meta = with stdenv.lib; {
     description = "Utility belt for automated testing";
-    homepage = https://falcao.it/sure/;
+    homepage = https://sure.readthedocs.io/en/latest/;
     license = licenses.gpl3Plus;
   };
 

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

@@ -0,0 +1,44 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, matchpy
+, numpy
+, astunparse
+, typing-extensions
+, black
+, pytest
+, pytestcov
+, numba
+, nbval
+, python
+, isPy37
+}:
+
+buildPythonPackage rec {
+  pname = "uarray";
+  version = "0.4";
+  format = "flit";
+  # will have support soon see
+  # https://github.com/Quansight-Labs/uarray/pull/64
+  disabled = isPy37;
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "4ec88f477d803a914d58fdf83aeedfb1986305355775cf55525348c62cce9aa4";
+  };
+
+  checkInputs = [ pytest nbval pytestcov numba ];
+  propagatedBuildInputs = [ matchpy numpy astunparse typing-extensions black ];
+
+  checkPhase = ''
+    ${python.interpreter} extract_readme_tests.py
+    pytest
+  '';
+
+  meta = with lib; {
+    description = "Universal array library";
+    homepage = https://github.com/Quansight-Labs/uarray;
+    license = licenses.bsd0;
+    maintainers = [ maintainers.costrouc ];
+  };
+}