Merge branch 'staging-next'

This round is without the systemd CVE,
as we don't have binaries for that yet.
BTW, I just ignore darwin binaries these days,
as I'd have to wait for weeks for them.

pkgs/development/python-modules/cmd2/default.nix

@@ -18,8 +18,8 @@ buildPythonPackage rec {
   postPatch = stdenv.lib.optional stdenv.isDarwin ''
     # Fake the impure dependencies pbpaste and pbcopy
     mkdir bin
-    echo '#/bin/sh' > bin/pbpaste
-    echo '#/bin/sh' > bin/pbcopy
+    echo '#${stdenv.shell}' > bin/pbpaste
+    echo '#${stdenv.shell}' > bin/pbcopy
     chmod +x bin/{pbcopy,pbpaste}
     export PATH=$(realpath bin):$PATH
   '';

pkgs/development/python-modules/cmd2/old.nix

@@ -19,8 +19,8 @@ buildPythonPackage rec {
   postPatch = stdenv.lib.optional stdenv.isDarwin ''
     # Fake the impure dependencies pbpaste and pbcopy
     mkdir bin
-    echo '#/bin/sh' > bin/pbpaste
-    echo '#/bin/sh' > bin/pbcopy
+    echo '#${stdenv.shell}' > bin/pbpaste
+    echo '#${stdenv.shell}' > bin/pbcopy
     chmod +x bin/{pbcopy,pbpaste}
     export PATH=$(realpath bin):$PATH
   '';

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

@@ -97,8 +97,8 @@ in buildPythonPackage rec {
   #       Until then we disable the tests.
   + optionalString isDarwin ''
     # Fake the impure dependencies pbpaste and pbcopy
-    echo "#!/bin/sh" > pbcopy
-    echo "#!/bin/sh" > pbpaste
+    echo "#!${stdenv.shell}" > pbcopy
+    echo "#!${stdenv.shell}" > pbpaste
     chmod a+x pbcopy pbpaste
     export PATH=$(pwd):$PATH
   '' + ''

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

@@ -15,7 +15,7 @@ buildPythonPackage rec {
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "c988d923e0b0627085b9700e2757003552ae9ccd7daa3a4b067ce60a0c7e642f";
+    sha256 = "0bv4gq60mrkw0r5kmakxrnfawlim01bjf3khp62p0qmhw0ixk269";
   };
 
   propagatedBuildInputs = [

pkgs/development/python-modules/scikit-build/default.nix

@@ -0,0 +1,43 @@
+{ lib, buildPythonPackage, fetchPypi, wheel, setuptools, packaging
+, cmake, ninja, cython, codecov, coverage, six, virtualenv, pathpy
+, pytest, pytestcov, pytest-virtualenv, pytest-mock, pytestrunner
+, requests, flake8 }:
+
+buildPythonPackage rec {
+  pname = "scikit-build";
+  version = "0.8.1";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1hh275lj98wgwi53mr9fqk8wh1dajjksch52xjax6a79gld4391a";
+  };
+
+  # Fixes incorrect specified requirement (part of next release)
+  patches = [ ./fix_pytestrunner_req.patch ];
+
+  propagatedBuildInputs = [ wheel setuptools packaging ];
+  checkInputs = [ 
+    cmake ninja cython codecov coverage six virtualenv pathpy
+    pytest pytestcov pytest-mock pytest-virtualenv pytestrunner
+    requests flake8
+  ];
+
+  disabledTests = lib.concatMapStringsSep " and " (s: "not " + s) ([
+    "test_hello_develop" # tries setuptools develop install
+    "test_wheel" # pip has no way to install missing dependencies
+    "test_fortran_compiler" # passes if gfortran is available
+    "test_install_command" # tries to alter out path
+    "test_test_command" # tries to alter out path
+  ]);
+
+  checkPhase = ''
+    py.test -k '${disabledTests}'
+  '';
+
+  meta = with lib; {
+    homepage = http://scikit-build.org/;
+    description = "Improved build system generator for CPython C/C++/Fortran/Cython extensions";
+    license = with licenses; [ mit bsd2 ]; # BSD due to reuses of PyNE code
+    maintainers = [ maintainers.FlorianFranzen ];
+  };
+}

pkgs/development/python-modules/scikit-build/fix_pytestrunner_req.patch

@@ -0,0 +1,13 @@
+diff --git a/setup.py b/setup.py
+index dd348fa..4de89c6 100755
+--- a/setup.py
++++ b/setup.py
+@@ -22,7 +22,7 @@ with open('requirements-dev.txt', 'r') as fp:
+     dev_requirements = list(filter(bool, (line.strip() for line in fp)))
+ 
+ # Require pytest-runner only when running tests
+-pytest_runner = (['pytest-runner>=2.0,<3dev']
++pytest_runner = (['pytest-runner>=2.0']
+                  if any(arg in sys.argv for arg in ('pytest', 'test'))
+                  else [])
+ 

pkgs/development/python-modules/sphinxcontrib-bibtex/default.nix

@@ -8,7 +8,7 @@ buildPythonPackage rec {
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "169afb3a3485775e5473934a0fdff1780e8bdcdd44db7ed286044a074331c729";
+    sha256 = "0af7651hfjh4hv97xns4vpf8n3kqy7ghyjlkfda5wxw56hxgp6hn";
   };
 
   propagatedBuildInputs = [ oset pybtex pybtex-docutils sphinx ];

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

@@ -31,7 +31,7 @@ buildPythonPackage rec {
     description = "Trend Micro Locality Sensitive Hash";
     homepage = https://github.com/trendmicro/tlsh;
     license = licenses.asl20;
-    platforms = platforms.linux;
+    platforms = platforms.unix;
   };
 
 }