Merge branch 'master' into add-missing-licenses

Conflicts:
	pkgs/development/libraries/exiv2/default.nix
        Set license to gpl2Plus

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

@@ -1,5 +1,5 @@
-{ stdenv, buildPythonPackage, fetchPypi
-, pep8, nose, unittest2, docutils, blockdiag  }:
+{ stdenv, buildPythonPackage, fetchPypi, fetchpatch
+, pep8, nose, unittest2, docutils, blockdiag, reportlab }:
 
 buildPythonPackage rec {
   pname = "actdiag";
@@ -10,13 +10,17 @@ buildPythonPackage rec {
     sha256 = "983071777d9941093aaef3be1f67c198a8ac8d2bba264cdd1f337ca415ab46af";
   };
 
+  patches = fetchpatch {
+    name = "drop_test_pep8.py.patch";
+    url = https://bitbucket.org/blockdiag/actdiag/commits/c1f2ed5947a1e93291f5860e4e30cee098bd635d/raw;
+    sha256 = "1zxzwb0fvwlc8xgs45fx65341sjhb3h6l2p6rdj6i127vg1hsxb4";
+  };
+
   buildInputs = [ pep8 nose unittest2 docutils ];
 
   propagatedBuildInputs = [ blockdiag ];
 
-  # One test fails:
-  #   UnicodeEncodeError: 'ascii' codec can't encode character u'\u3042' in position 0: ordinal not in range(128)
-  doCheck = false;
+  checkInputs = [ reportlab ];
 
   meta = with stdenv.lib; {
     description = "Generate activity-diagram image from spec-text file (similar to Graphviz)";

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

@@ -0,0 +1,30 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, gcc
+, wirelesstools
+, isPy27
+, isPyPy
+}:
+
+buildPythonPackage rec {
+  pname = "basiciw";
+  version = "0.2.2";
+
+  disabled = isPy27 || isPyPy;
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1ajmflvvlkflrcmqmkrx0zaira84z8kv4ssb2jprfwvjh8vfkysb";
+  };
+
+  buildInputs = [ gcc ];
+  propagatedBuildInputs = [ wirelesstools ];
+
+  meta = {
+    description = "Get info about wireless interfaces using libiw";
+    homepage = https://github.com/enkore/basiciw;
+    platforms = lib.platforms.linux;
+    license = lib.licenses.gpl2;
+  };
+}

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

@@ -0,0 +1,43 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, nose
+, mock
+, webtest
+, sqlalchemy
+, pycrypto
+, isPy27
+, funcsigs
+, pycryptopp
+}:
+
+buildPythonPackage rec {
+  pname = "Beaker";
+  version = "1.8.0";
+
+  # The pypy release do not contains the tests
+  src = fetchFromGitHub {
+    owner = "bbangert";
+    repo = "beaker";
+    rev = "${version}";
+    sha256 = "17yfr7a307n8rdl09was4j60xqk2s0hk0hywdkigrpj4qnw0is7g";
+  };
+
+  buildInputs =
+    [ nose
+      mock
+      webtest
+    ];
+  propagatedBuildInputs = [
+    sqlalchemy
+    pycrypto
+  ] ++ lib.optionals (isPy27) [
+    funcsigs
+    pycryptopp
+  ];
+
+  meta = {
+    description = "A Session and Caching library with WSGI Middleware";
+    maintainers = with lib.maintainers; [ garbas domenkozar ];
+  };
+}

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

@@ -0,0 +1,24 @@
+{ stdenv, buildPythonPackage, fetchPypi, isPy3k
+, twisted, whisper, txamqp, cachetools, urllib3
+}:
+
+buildPythonPackage rec {
+  pname = "carbon";
+  version = "1.1.3";
+
+  disabled = isPy3k;
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1s7327p30w4l9ak4gc7m5ga521233179n2lr3j0ggfbmfhd6blky";
+  };
+
+  propagatedBuildInputs = [ twisted whisper txamqp cachetools urllib3 ];
+
+  meta = with stdenv.lib; {
+    homepage = http://graphite.wikidot.com/;
+    description = "Backend data caching and persistence daemon for Graphite";
+    maintainers = with maintainers; [ rickynils offline basvandijk ];
+    license = licenses.asl20;
+  };
+}

pkgs/development/python-modules/graphite-web/default.nix

@@ -0,0 +1,54 @@
+{ stdenv, buildPythonPackage, fetchPypi, isPy3k, which
+, django, django_tagging, whisper, pycairo, cairocffi, ldap, memcached, pytz, urllib3, scandir
+}:
+if django.version != "1.8.18"
+|| django_tagging.version != "0.4.3"
+then throw "graphite-web should be build with django_1_8 and django_tagging_0_4_3"
+else buildPythonPackage rec {
+  pname = "graphite-web";
+  version = "1.1.3";
+
+  disabled = isPy3k;
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0nvyq1859abdch2l90avsjk9vb03s7wgxgrjsqvjhf2b9c1ncsfh";
+  };
+
+  propagatedBuildInputs = [
+    django django_tagging whisper pycairo cairocffi
+    ldap memcached pytz urllib3 scandir
+  ];
+
+  postInstall = ''
+    wrapProgram $out/bin/run-graphite-devel-server.py \
+      --prefix PATH : ${which}/bin
+  '';
+
+  preConfigure = ''
+    # graphite is configured by storing a local_settings.py file inside the
+    # graphite python package. Since that package is stored in the immutable
+    # Nix store we can't modify it. So how do we configure graphite?
+    #
+    # First of all we rename "graphite.local_settings" to
+    # "graphite_local_settings" so that the settings are not looked up in the
+    # graphite package anymore. Secondly we place a directory containing a
+    # graphite_local_settings.py on the PYTHONPATH in the graphite module
+    # <nixpkgs/nixos/modules/services/monitoring/graphite.nix>.
+    substituteInPlace webapp/graphite/settings.py \
+      --replace "graphite.local_settings" " graphite_local_settings"
+
+    substituteInPlace webapp/graphite/settings.py \
+      --replace "join(WEBAPP_DIR, 'content')" "join('$out', 'webapp', 'content')"
+  '';
+
+  # error: invalid command 'test'
+  doCheck = false;
+
+  meta = with stdenv.lib; {
+    homepage = http://graphite.wikidot.com/;
+    description = "Enterprise scalable realtime graphing";
+    maintainers = with maintainers; [ rickynils offline basvandijk ];
+    license = licenses.asl20;
+  };
+}

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

@@ -0,0 +1,25 @@
+{ stdenv, buildPythonPackage, fetchPypi
+, tornado, pyyaml, funcparserlib
+}:
+buildPythonPackage rec {
+  pname = "graphite_beacon";
+  version = "0.27.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "03bp4wyfn3xhcqyvs5hnk1n87m4smsmm1p7qp459m7j8hwpbq2ks";
+  };
+
+  propagatedBuildInputs = [ tornado pyyaml funcparserlib ];
+
+  postPatch = ''
+    substituteInPlace requirements.txt --replace "==" ">="
+  '';
+
+  meta = with stdenv.lib; {
+    description = "A simple alerting application for Graphite metrics";
+    homepage = https://github.com/klen/graphite-beacon;
+    maintainers = [ maintainers.offline ];
+    license = licenses.mit;
+  };
+}

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

@@ -0,0 +1,32 @@
+{ stdenv, buildPythonPackage, fetchPypi
+, jinja2, markupsafe, pagerduty, pushbullet, python_magic, python-simple-hipchat
+, pyyaml, redis, requests, six, websocket_client, nose
+}:
+buildPythonPackage rec {
+  pname = "graphitepager";
+  version = "0.2.11";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0v3g1qcgnkpgjzh6phnv13lnk8qjrcs9sq2qg6k0dk5ik31jfk3d";
+  };
+
+  propagatedBuildInputs = [
+    jinja2 markupsafe pagerduty pushbullet python_magic python-simple-hipchat
+    pyyaml redis requests six websocket_client
+  ];
+
+  postPatch = ''
+    substituteInPlace requirements.txt --replace "==" ">="
+  '';
+
+  checkInputs = [ nose ];
+  checkPhase = "nosetests";
+
+  meta = with stdenv.lib; {
+    description = "A simple alerting application for Graphite metrics";
+    homepage = https://github.com/seatgeek/graphite-pager;
+    maintainers = with maintainers; [ offline basvandijk ];
+    license = licenses.bsd2;
+  };
+}

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

@@ -0,0 +1,29 @@
+{ stdenv, buildPythonPackage, fetchPypi, numpy, scipy, scikitimage, opencv3, six }:
+
+buildPythonPackage rec {
+  pname = "imgaug";
+  version = "0.2.6";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1wy8ydkqq0jrwxwdv04q89n3gwsr9pjaspsbw26ipg5a5lnhb9c2";
+  };
+
+  propagatedBuildInputs = [
+    numpy
+    scipy
+    scikitimage
+    opencv3
+    six
+  ];
+
+  # disable tests when there are no tests in the PyPI archive
+  doCheck = false;
+
+  meta = with stdenv.lib; {
+    homepage = https://github.com/aleju/imgaug;
+    description = "Image augmentation for machine learning experiments";
+    license = licenses.mit;
+    maintainers = with maintainers; [ cmcdragonkai ];
+  };
+}

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

@@ -0,0 +1,30 @@
+{ stdenv, buildPythonPackage, fetchPypi, isPy3k
+, influxdb, graphite_api, memcached, gnugrep
+}:
+
+buildPythonPackage rec {
+  pname = "influxgraph";
+  version = "1.5.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0l33sfwdh4bfprmzp2kx0d9098g6yxbnhyyx9qr3kzczpm0jg9vy";
+  };
+
+  patchPhase = stdenv.lib.optionalString isPy3k ''
+    sed 's/python-memcached/python3-memcached/' \
+      -i ./influxgraph.egg-info/requires.txt    \
+      -i ./setup.py
+  '';
+
+  propagatedBuildInputs = [ influxdb graphite_api memcached ];
+
+  passthru.moduleName = "influxgraph.InfluxDBFinder";
+
+  meta = with stdenv.lib; {
+    description = "InfluxDB storage plugin for Graphite-API";
+    homepage = https://github.com/InfluxGraph/influxgraph;
+    license = licenses.asl20;
+    maintainers = with maintainers; [ basvandijk ];
+  };
+}

pkgs/development/python-modules/ipython/5.nix

@@ -2,6 +2,7 @@
 , stdenv
 , buildPythonPackage
 , fetchPypi
+, fetchpatch
 # Build dependencies
 , glibcLocales
 # Test dependencies
@@ -36,6 +37,16 @@ buildPythonPackage rec {
     substituteInPlace setup.py --replace "'gnureadline'" " "
   '';
 
+  patches = [
+    # improve cython support, needed by sage, accepted upstream
+    # https://github.com/ipython/ipython/pull/11139
+    (fetchpatch {
+      name = "signature-use-inspect.patch";
+      url = "https://github.com/ipython/ipython/commit/8d399b98d3ed5c765835594100c4d36fb2f739dc.patch";
+      sha256 = "1r7v9clwwbskmj4y160vcj6g0vzqbvnj4y1bm2n4bskafapm42g0";
+    })
+  ];
+
   buildInputs = [ glibcLocales ];
 
   checkInputs = [ nose pygments testpath ] ++ lib.optional isPy27 mock;

pkgs/development/python-modules/keras-applications/default.nix

@@ -0,0 +1,27 @@
+{ lib, buildPythonPackage, fetchPypi, numpy, h5py }:
+
+buildPythonPackage rec {
+  pname = "Keras_Applications";
+  version = "1.0.4";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "8c95300328630ae74fb0828b6fa38269a25c0228a02f1e5181753bfd48961f49";
+  };
+
+  # Cyclic dependency: keras-applications requires keras, which requires keras-applications
+  postPatch = ''
+    sed -i "s/keras>=[^']*//" setup.py
+  '';
+
+  # No tests in PyPI tarball
+  doCheck = false;
+
+  propagatedBuildInputs = [ numpy h5py ];
+
+  meta = with lib; {
+    description = "Reference implementations of popular deep learning models";
+    homepage = https://github.com/keras-team/keras-applications;
+    license = licenses.mit;
+  };
+}

pkgs/development/python-modules/keras-preprocessing/default.nix

@@ -0,0 +1,27 @@
+{ lib, buildPythonPackage, fetchPypi, numpy, scipy, six }:
+
+buildPythonPackage rec {
+  pname = "Keras_Preprocessing";
+  version = "1.0.2";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "f5306554d2b454d825b36f35e327744f5477bd2ae21017f1a93b2097bed6757e";
+  };
+
+  # Cyclic dependency: keras-preprocessing requires keras, which requires keras-preprocessing
+  postPatch = ''
+    sed -i "s/keras>=[^']*//" setup.py
+  '';
+
+  # No tests in PyPI tarball
+  doCheck = false;
+
+  propagatedBuildInputs = [ numpy scipy six ];
+
+  meta = with lib; {
+    description = "Easy data preprocessing and data augmentation for deep learning models";
+    homepage = https://github.com/keras-team/keras-preprocessing;
+    license = licenses.mit;
+  };
+}

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

@@ -1,15 +1,16 @@
 { stdenv, buildPythonPackage, fetchPypi
 , pytest, pytestcov, pytestpep8, pytest_xdist
 , six, numpy, scipy, pyyaml, h5py
+, keras-applications, keras-preprocessing
 }:
 
 buildPythonPackage rec {
   pname = "Keras";
-  version = "2.2.0";
+  version = "2.2.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "5b8499d157af217f1a5ee33589e774127ebc3e266c833c22cb5afbb0ed1734bf";
+    sha256 = "468d98da104ec5c3dbb10c2ef6bb345ab154f6ca2d722d4c250ef4d6105de17a";
   };
 
   checkInputs = [
@@ -21,6 +22,7 @@ buildPythonPackage rec {
 
   propagatedBuildInputs = [
     six pyyaml numpy scipy h5py
+    keras-applications keras-preprocessing
   ];
 
   # Couldn't get tests working

pkgs/development/python-modules/marionette-harness/mozlog.nix

@@ -16,7 +16,7 @@ buildPythonPackage rec {
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "af3a3252bc58f8642a641601ba59096c22e4aa49cdc1ed4b0df2314f4f027f0d";
+    sha256 = "00x28z6diw06gakb5isbfha5z2n63yyncv4za303nsgzxvlihmx0";
   };
 
   propagatedBuildInputs = [ blessings mozterm six ];

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

@@ -1,4 +1,4 @@
-{ lib, buildPythonPackage, fetchPypi, isPy3k }:
+{ lib, buildPythonPackage, fetchPypi, isPy3k, six }:
 
 buildPythonPackage rec {
   pname = "mozterm";
@@ -7,6 +7,8 @@ buildPythonPackage rec {
   # name 'unicode' is not defined
   disabled = isPy3k;
 
+  propagatedBuildInputs = [six];
+
   src = fetchPypi {
     inherit pname version;
     sha256 = "b1e91acec188de07c704dbb7b0100a7be5c1e06567b3beb67f6ea11d00a483a4";

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

@@ -0,0 +1,19 @@
+{ stdenv, buildPythonPackage, fetchPypi }:
+
+buildPythonPackage rec {
+  pname = "shippai";
+  # Please make sure that vdirsyncer still builds if you update this package.
+  version = "0.2.3";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1ppwywzg4d12h658682ssmingm6ls6a96p4ak26i2w9d4lf8pfsc";
+  };
+
+  meta = with stdenv.lib; {
+    description = "Use Rust failures as Python exceptions";
+    homepage = https://github.com/untitaker/shippai;
+    license = licenses.mit;
+    maintainers = with maintainers; [ gebner ];
+  };
+}

pkgs/development/python-modules/tensorflow/bin.nix

@@ -61,6 +61,15 @@ in buildPythonPackage rec {
   # bleach) Hence we disable dependency checking for now.
   installFlags = lib.optional isPy36 "--no-dependencies";
 
+
+  # Upstream has a pip hack that results in bin/tensorboard being in both tensorflow
+  # and the propageted input tensorflow-tensorboard which causes environment collisions.
+  #
+  # https://github.com/tensorflow/tensorflow/blob/v1.7.1/tensorflow/tools/pip_package/setup.py#L79
+  postInstall = ''
+    rm $out/bin/tensorboard
+  '';
+
   # Note that we need to run *after* the fixup phase because the
   # libraries are loaded at runtime. If we run in preFixup then
   # patchelf --shrink-rpath will remove the cuda libraries.

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

@@ -0,0 +1,20 @@
+{ stdenv, buildPythonPackage, fetchPypi, six }:
+
+buildPythonPackage rec {
+  pname = "whisper";
+  version = "1.1.3";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1ahzsxk52ws8k3kdq52qbsbsx2r9z350j8gg9adw4x5fjwksz4r8";
+  };
+
+  propagatedBuildInputs = [ six ];
+
+  meta = with stdenv.lib; {
+    homepage = http://graphite.wikidot.com/;
+    description = "Fixed size round-robin style database";
+    maintainers = with maintainers; [ rickynils offline basvandijk ];
+    license = licenses.asl20;
+  };
+}