Merge staging-next into staging

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

@@ -0,0 +1,24 @@
+{ stdenv, buildPythonPackage, fetchPypi
+, requests }:
+
+buildPythonPackage rec {
+  pname = "WazeRouteCalculator";
+  version = "0.6";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0zmnw4198a2kvqvsz1i4a3aa20r4afp2lai6fxbpq1ppv120h857";
+  };
+
+  propagatedBuildInputs = [ requests ];
+
+  # there are no tests
+  doCheck = false;
+
+  meta = with stdenv.lib; {
+    description = "Calculate actual route time and distance with Waze API";
+    homepage = https://github.com/kovacsbalu/WazeRouteCalculator;
+    license = licenses.gpl3;
+    maintainers = with maintainers; [ peterhoeg ];
+  };
+}

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

@@ -0,0 +1,30 @@
+{ pkgs
+, buildPythonPackage
+, fetchPypi
+, astropy
+, requests
+, keyring
+, beautifulsoup4
+, html5lib
+}:
+
+buildPythonPackage rec {
+  pname = "astroquery";
+  version = "0.3.8";
+
+  doCheck = false; # Tests require the pytest-astropy package
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "800d9730c9e2bd299f14c29b4d709d1605c82833223a2e4f784fea7ad805c168";
+  };
+
+  propagatedBuildInputs = [ astropy requests keyring beautifulsoup4 html5lib ];
+
+  meta = with pkgs.lib; {
+    description = "Functions and classes to access online data resources";
+    homepage = "https://astroquery.readthedocs.io/";
+    license = licenses.bsd3;
+    maintainers = [ maintainers.smaret ];
+  };
+}

pkgs/development/python-modules/bt-proximity/default.nix

@@ -0,0 +1,27 @@
+{ stdenv, buildPythonPackage, fetchFromGitHub
+, pybluez }:
+
+buildPythonPackage rec {
+  pname = "bt-proximity";
+  version = "0.0.20180217";
+
+  # pypi only has a pre-compiled wheel and no sources
+  src = fetchFromGitHub {
+    owner  = "FrederikBolding";
+    repo   = "bluetooth-proximity";
+    rev    = "463bade8a9080b47f09bf4a47830b31c69c5dffd";
+    sha256 = "0anfh90cj3c2g7zqrjvq0d6dzpb4hjl6gk8zw0r349j2zw9i4h7y";
+  };
+
+  propagatedBuildInputs = [ pybluez ];
+
+  # there are no tests
+  doCheck = false;
+
+  meta = with stdenv.lib; {
+    description = "Bluetooth Proximity Detection using Python";
+    homepage = https://github.com/FrederikBolding/bluetooth-proximity;
+    maintainers = with maintainers; [ peterhoeg ];
+    license = licenses.asl20;
+  };
+}

pkgs/development/python-modules/eyed3/default.nix

@@ -1,23 +1,41 @@
 { stdenv
 , buildPythonPackage
-, fetchurl
+, fetchPypi
+, pythonAtLeast
+, pythonOlder
 , paver
 , python
 , isPyPy
+, six
+, pathlib
+, python_magic
+, isPy3k
+, lib
 }:
 
 buildPythonPackage rec {
-  version = "0.7.8";
+  version = "0.8.7";
   pname    = "eyeD3";
   disabled = isPyPy;
 
-  src = fetchurl {
-    url = "http://eyed3.nicfit.net/releases/${pname}-${version}.tar.gz";
-    sha256 = "1nv7nhfn1d0qm7rgkzksbccgqisng8klf97np0nwaqwd5dbmdf86";
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1fzqy6hkg73xvpapdjrdzr3r0fsamnplvjfl7dz7rzgzx2r4x4pg";
   };
 
+  # https://github.com/nicfit/eyeD3/pull/284
+  postPatch = lib.optionalString (pythonAtLeast "3.4") ''
+    sed -ie '/pathlib/d' requirements/requirements.yml
+  '';
+
   buildInputs = [ paver ];
 
+  # requires special test data:
+  # https://github.com/nicfit/eyeD3/blob/103198e265e3279384f35304e8218be6717c2976/Makefile#L97
+  doCheck = false;
+
+  propagatedBuildInputs = [ six python_magic ] ++ lib.optional (pythonOlder "3.4") pathlib;
+
   postInstall = ''
     for prog in "$out/bin/"*; do
       wrapProgram "$prog" --prefix PYTHONPATH : "$PYTHONPATH" \

pkgs/development/python-modules/hoomd-blue/default.nix

@@ -0,0 +1,67 @@
+{ stdenv, buildPythonPackage, fetchgit
+, cmake, pkgconfig
+, python
+, mpi ? null
+}:
+
+let components = {
+     cgcmm = true;
+     depreciated = true;
+     hpmc = true;
+     md = true;
+     metal = true;
+     testing = false;
+   };
+   onOffBool = b: if b then "ON" else "OFF";
+   withMPI = (mpi != null);
+in
+stdenv.mkDerivation rec {
+  version = "2.3.4";
+  name = "hoomd-blue-${version}";
+
+  src = fetchgit {
+    url = "https://bitbucket.org/glotzer/hoomd-blue";
+    rev = "v${version}";
+    sha256 = "0in49f1dvah33nl5n2qqbssfynb31pw1ds07j8ziryk9w252j1al";
+  };
+
+  passthru = {
+    inherit components mpi;
+  };
+
+  nativeBuildInputs = [ cmake pkgconfig ];
+  buildInputs = stdenv.lib.optionals withMPI [ mpi ];
+  propagatedBuildInputs = [ python.pkgs.numpy ]
+   ++ stdenv.lib.optionals withMPI [ python.pkgs.mpi4py ];
+
+  enableParallelBuilding = true;
+
+  dontAddPrefix = true;
+  cmakeFlags = [
+       "-DENABLE_MPI=${onOffBool withMPI}"
+       "-DBUILD_CGCMM=${onOffBool components.cgcmm}"
+       "-DBUILD_DEPRECIATED=${onOffBool components.depreciated}"
+       "-DBUILD_HPMC=${onOffBool components.hpmc}"
+       "-DBUILD_MD=${onOffBool components.md}"
+       "-DBUILD_METAL=${onOffBool components.metal}"
+       "-DBUILD_TESTING=${onOffBool components.testing}"
+  ];
+
+  preConfigure = ''
+    # Since we can't expand $out in `cmakeFlags`
+    cmakeFlags="$cmakeFlags -DCMAKE_INSTALL_PREFIX=$out/${python.sitePackages}"
+  '';
+
+  # tests fail but have tested that package runs properly
+  doCheck = false;
+  checkTarget = "test";
+
+  meta = with stdenv.lib; {
+    homepage = http://glotzerlab.engin.umich.edu/hoomd-blue/;
+    description = "HOOMD-blue is a general-purpose particle simulation toolkit";
+    license = licenses.bsdOriginal;
+    platforms = [ "x86_64-linux" ];
+    maintainers = [ maintainers.costrouc ];
+  };
+
+}

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

@@ -1,46 +1,41 @@
-{ stdenv, buildPythonPackage, fetchFromGitHub, pytest, six, clint, pyyaml, docopt
-, requests, jsonpatch, args, schema, responses, backports_csv }:
+{ buildPythonPackage, fetchFromGitHub, pytest, six, clint, pyyaml, docopt
+, requests, jsonpatch, args, schema, responses, backports_csv, isPy3k
+, lib, glibcLocales }:
 
 buildPythonPackage rec {
-
   pname = "internetarchive";
-  version = "1.7.2";
+  version = "1.8.1";
 
   # Can't use pypi, data files for tests missing
   src = fetchFromGitHub {
     owner = "jjjake";
     repo = "internetarchive";
     rev = "v${version}";
-    sha256 = "1cijagy22qi8ydrvizqmi1whnc3qr94yk0910lwgpxjywcygggir";
+    sha256 = "1fdb0kr9hzgyh0l8d02khcjpsgyd63nbablhc49ncdsav3dhhr3f";
   };
-    # It is hardcoded to specific versions, I don't know why.
-    preConfigure = ''
-        sed "s/schema>=.*/schema>=0.4.0',/" -i setup.py
-        sed "/backports.csv/d" -i setup.py
-    '';
 
-    #phases = [ "unpackPhase" "configurePhase" "installPhase" "fixupPhase" "installCheckPhase" ];
-    buildInputs = [ pytest responses ];
-    propagatedBuildInputs = [
-      six
-      clint
-      pyyaml
-      docopt
-      requests
-      jsonpatch
-      args
-      schema
-      backports_csv
-    ];
+  propagatedBuildInputs = [
+    six
+    clint
+    pyyaml
+    docopt
+    requests
+    jsonpatch
+    args
+    schema
+  ] ++ lib.optional (!isPy3k) backports_csv;
 
-    # Tests disabled because ia binary doesn't exist when tests run
-    doCheck = false;
+  checkInputs = [ pytest responses glibcLocales ];
 
-    checkPhase = "pytest tests";
+  # tests depend on network
+  doCheck = false;
 
+  checkPhase = ''
+    LC_ALL=en_US.utf-8 pytest tests
+  '';
 
-  meta = with stdenv.lib; {
-      description = "A python wrapper for the various Internet Archive APIs";
+  meta = with lib; {
+    description = "A python wrapper for the various Internet Archive APIs";
     homepage = https://github.com/jjjake/internetarchive;
     license = licenses.agpl3;
   };

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

@@ -17,6 +17,11 @@ buildPythonPackage rec {
 
   LC_ALL="en_US.UTF-8";
 
+  preCheck = ''
+    # Remove tests that rely on networking (breaks sandboxed builds)
+    rm test/test_submit.py
+  '';
+
   meta = with stdenv.lib; {
     homepage = http://alastair/python-musicbrainz-ngs;
     description = "Python bindings for musicbrainz NGS webservice";

pkgs/development/python-modules/netcdf4/default.nix

@@ -3,13 +3,13 @@
 }:
 buildPythonPackage rec {
   pname = "netCDF4";
-  version = "1.4.1";
+  version = "1.4.2";
 
   disabled = isPyPy;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "d4fc65b98e348c39d082ab6b4b7f6d636b1b4e63bec016e5bca189fee5d46403";
+    sha256 = "0c0sklgrmv15ygliin8qq0hp7vanmbi74m6zpi0r1ksr0hssyd5r";
   };
 
   checkInputs = [ pytest ];

pkgs/development/python-modules/nose-cov/default.nix

@@ -0,0 +1,20 @@
+{ buildPythonPackage, fetchPypi, lib, nose, covCore }:
+
+buildPythonPackage rec {
+  pname = "nose-cov";
+  version = "1.6";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "04j4fw01bv648gimqqj4z88606lcczbm1k326agcc74gb4sh7v4b";
+  };
+
+  propagatedBuildInputs = [ nose covCore ];
+
+  meta = with lib; {
+    homepage = https://pypi.org/project/nose-cov/;
+    license = licenses.mit;
+    description = "This plugin produces coverage reports. It also supports coverage of subprocesses.";
+    maintainers = with maintainers; [ ma27 ];
+  };
+}

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

@@ -22,9 +22,8 @@ in buildPythonPackage rec {
     sha256 = "01vm8mqhpdrwlxw6rxbg3wz51njq69yn862141mja00mllg3j7pg";
   };
 
-  buildInputs = stdenv.lib.optionals doCheck [ vmprof pyqt4 ];
-
-  propagatedBuildInputs = [ scons ];
+  checkInputs = [ vmprof pyqt4 ];
+  nativeBuildInputs = [ scons ];
 
   postPatch = ''
     patchShebangs tests/run-tests

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

@@ -0,0 +1,33 @@
+{ stdenv, fetchgit
+, cmake
+, qtbase, libav, netcdf, qscintilla, zlib, boost, git, fftw, hdf5, libssh
+, pythonPackages
+}:
+
+stdenv.mkDerivation rec {
+  # compilation error in 2.9.0 https://gitlab.com/stuko/ovito/issues/40
+  # This is not the "released" 3.0.0 just a commit
+  version = "3.0.0";
+  name = "ovito-${version}";
+
+  src = fetchgit {
+    url = "https://gitlab.com/stuko/ovito";
+    rev = "a28c28182a879d2a1b511ec56f9845306dd8a4db";
+    sha256 = "1vqzv3gzwf8r0g05a7fj8hdyvnzq2h3wdfck7j6n1av6rvp7hi5r";
+  };
+
+  buildInputs = [ cmake libav netcdf qscintilla zlib boost zlib git fftw hdf5 libssh ];
+  propagatedBuildInputs = with pythonPackages; [ sphinx numpy sip pyqt5 matplotlib ase ];
+
+  enableParallelBuilding = true;
+
+  meta = with stdenv.lib; {
+    description = "Scientific visualization and analysis software for atomistic simulation data";
+    homepage = https://www.ovito.org;
+    license = licenses.gpl3;
+    maintainers = [ maintainers.costrouc ];
+    # ensures not built on hydra
+    # https://github.com/NixOS/nixpkgs/pull/46846#issuecomment-436388048
+    hydraPlatforms = [ ];
+  };
+}

pkgs/development/python-modules/pyexiv2/default.nix

@@ -10,13 +10,12 @@ buildPythonPackage rec {
     sha256 = "09r1ga6kj5cnmrldpkqzvdhh7xi7aad9g4fbcr1gawgsd9y13g0a";
   };
 
-  buildPhase = ''
+  preBuild = ''
     sed -i -e "s@env = Environment()@env = Environment( ENV = os.environ )@" src/SConscript
-    scons
   '';
-  installPhase = ''
+
+  preInstall = ''
     sed -i -e "s@    python_lib_path = get_python_lib(plat_specific=True)@    python_lib_path = \'/lib/python2.7/site-packages\'@" src/SConscript
-    scons install DESTDIR=$out
   '';
 
   buildInputs = [ python exiv2 scons boost ];

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

@@ -0,0 +1,24 @@
+{ stdenv, buildPythonPackage, fetchPypi
+, requests }:
+
+buildPythonPackage rec {
+  pname = "pyfttt";
+  version = "0.3.2";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "10iq7c9c832ssl2xrvf62xf7znfvqzax6sq8ppsibq6wpb8dlnj5";
+  };
+
+  propagatedBuildInputs = [ requests ];
+
+  # tests need a server to run against
+  doCheck = false;
+
+  meta = with stdenv.lib; {
+    description = "Package for sending events to the IFTTT Webhooks Channel";
+    homepage = https://github.com/briandconnelly/pyfttt;
+    maintainers = with maintainers; [ peterhoeg ];
+    license = licenses.bsd2;
+  };
+}

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

@@ -1,34 +1,32 @@
 { stdenv, buildPythonPackage, fetchPypi, python
-, nose, pillow
 , gfortran, glibcLocales
-, numpy, scipy
+, numpy, scipy, pytest, pillow
 }:
 
 buildPythonPackage rec {
   pname = "scikit-learn";
-  version = "0.19.2";
+  version = "0.20.0";
   # UnboundLocalError: local variable 'message' referenced before assignment
-  doCheck = false;
   disabled = stdenv.isi686;  # https://github.com/scikit-learn/scikit-learn/issues/5534
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "b276739a5f863ccacb61999a3067d0895ee291c95502929b2ae56ea1f882e888";
+    sha256 = "064cbxsis6m7l6pr09ijjwqdv0c0yrfnazabwq8p09gcz1qxklcp";
   };
 
-  buildInputs = [ nose pillow gfortran glibcLocales ];
+  buildInputs = [ pillow gfortran glibcLocales ];
   propagatedBuildInputs = [ numpy scipy numpy.blas ];
+  checkInputs = [ pytest ];
 
   LC_ALL="en_US.UTF-8";
 
-  # Disable doctests on OSX: https://github.com/scikit-learn/scikit-learn/issues/10213
-  # Disable doctests everywhere: https://github.com/NixOS/nixpkgs/issues/35436
+  doCheck = !stdenv.isAarch64;
+  # Skip test_feature_importance_regression - does web fetch
   checkPhase = ''
-    HOME=$TMPDIR OMP_NUM_THREADS=1 nosetests --doctest-options=+SKIP $out/${python.sitePackages}/sklearn/
+    cd $TMPDIR
+    HOME=$TMPDIR OMP_NUM_THREADS=1 pytest -k "not test_feature_importance_regression" --pyargs sklearn
   '';
 
-
-
   meta = with stdenv.lib; {
     description = "A set of python modules for machine learning and data mining";
     homepage = http://scikit-learn.org;

pkgs/development/python-modules/uncompyle6/default.nix

@@ -30,7 +30,7 @@ buildPythonPackage rec {
   meta = with stdenv.lib; {
     description = "Python cross-version byte-code deparser";
     homepage = https://github.com/rocky/python-uncompyle6/;
-    license = licenses.mit;
+    license = licenses.gpl3;
   };
 
 }

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

@@ -24,7 +24,7 @@ buildPythonPackage rec {
   meta = with stdenv.lib; {
     description = "Python cross-version byte-code disassembler and marshal routines";
     homepage = https://github.com/rocky/python-xdis/;
-    license = licenses.mit;
+    license = licenses.gpl2;
   };
 
 }