Merge master into staging-next

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

@@ -18,13 +18,13 @@
 
 buildPythonPackage rec {
   pname = "ansible";
-  version = "2.8.4";
+  version = "2.8.7";
 
   src = fetchFromGitHub {
     owner = "ansible";
     repo = "ansible";
     rev = "v${version}";
-    sha256 = "1fp7zz8awfv70nn8i6x0ggx4472377hm7787x16qv2kz4nb069ki";
+    sha256 = "08vqjk85j0g1x0iad03d7ysws433dikii8j2lr3a1mlx6d186vv8";
   };
 
   prePatch = ''

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

@@ -0,0 +1,25 @@
+{ lib, pkgs, buildPythonPackage, fetchPypi, isPy3k
+, numpy
+}:
+
+buildPythonPackage rec {
+  pname = "arrayqueues";
+  version = "1.2.0b0";
+  disabled = !isPy3k;
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1gvrxb2rw0dk469wq5azylar7hhanfp07gl5mc6ajdbgz9gsd6ln";
+  };
+
+  propagatedBuildInputs = [
+    numpy
+  ];
+
+  meta = {
+    homepage = "https://github.com/portugueslab/arrayqueues";
+    description = "Multiprocessing queues for numpy arrays using shared memory";
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ tbenst ];
+  };
+}

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

@@ -0,0 +1,24 @@
+{ lib, pkgs, buildPythonPackage, fetchPypi, isPy3k
+, numpy
+}:
+
+buildPythonPackage rec {
+  pname = "colorspacious";
+  version = "1.1.2";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "065n24zbm9ymy2gvf03vx5cggk1258vcjdaw8jn9v26arpl7542y";
+  };
+
+  propagatedBuildInputs = [
+    numpy
+  ];
+
+  meta = {
+    homepage = "https://github.com/njsmith/colorspacious";
+    description = "A powerful, accurate, and easy-to-use Python library for doing colorspace conversions ";
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ tbenst ];
+  };
+}

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

@@ -0,0 +1,29 @@
+{ lib, buildPythonPackage, fetchPypi, requests, pytest }:
+
+buildPythonPackage rec {
+  version = "0.1.2";
+  pname = "etelemetry";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0m3dqvs3xbckmjiwppy366qmgzx0z917j1d7dadfl3bprgipy51j";
+  };
+
+  propagatedBuildInputs = [ requests ];
+
+  # all 2 of the tests both try to pull down from a url
+  doCheck = false;
+
+  pythonImportsCheck = [
+    "etelemetry"
+    "etelemetry.client"
+    "etelemetry.config"
+  ];
+
+  meta = with lib; {
+    description = "Lightweight python client to communicate with the etelemetry server";
+    homepage = "https://github.com/mgxd/etelemetry-client";
+    license = licenses.asl20;
+    maintainers = with maintainers; [ ];
+  };
+}

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

@@ -0,0 +1,36 @@
+{ lib, pkgs, buildPythonPackage, fetchPypi, isPy27
+, numpy
+, scipy
+, tables
+, pandas
+, nose
+, configparser
+}:
+
+buildPythonPackage rec {
+  pname = "flammkuchen";
+  version = "0.9.1";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "e9aab9b229ace70d879b85618a9ce0e88dd6ce35d4dbcdfd60c6b61c33a1b4fb";
+  };
+
+  checkInputs = [
+    nose
+  ];
+
+  propagatedBuildInputs = [
+    numpy
+    scipy
+    tables
+    pandas
+  ] ++ lib.optionals isPy27 [ configparser ];
+
+  meta = {
+    homepage = "https://github.com/portugueslab/flammkuchen";
+    description = "Flexible HDF5 saving/loading library forked from deepdish (University of Chicago) and maintained by the Portugues lab";
+    license = lib.licenses.bsd3;
+    maintainers = with lib.maintainers; [ tbenst ];
+  };
+}

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

@@ -0,0 +1,28 @@
+{ lib, pkgs, buildPythonPackage, fetchPypi, isPy3k
+, numpy
+}:
+
+buildPythonPackage rec {
+  pname = "lightparam";
+  version = "0.3.7";
+  disabled = !isPy3k;
+  format = "wheel";
+
+  src = fetchPypi {
+    inherit pname version;
+    format = "wheel";
+    python = "py3";
+    sha256 = "53d5d5b225bac27bc14929c9ad4e51ece4f692813dd367f317fb1586145d93f1";
+  };
+
+  propagatedBuildInputs = [
+    numpy
+  ];
+
+  meta = {
+    homepage = "https://github.com/portugueslab/lightparam";
+    description = "Another attempt at parameters in Python";
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ tbenst ];
+  };
+}

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

@@ -4,7 +4,8 @@
 
 buildPythonPackage rec {
   pname = "mesa";
-  version = "0.8.6";
+  # contains several fixes for networkx 2.4 bump
+  version = "unstable-2019-12-09";
 
   # According to their docs, this library is for Python 3+.
   disabled = isPy27;
@@ -12,8 +13,8 @@ buildPythonPackage rec {
   src = fetchFromGitHub {
     owner = "projectmesa";
     repo = "mesa";
-    rev = "v${version}";
-    sha256 = "0d8c636zhswxd91ldlmdxxlyym2fj3bk1iqmpc1jp3hg7vvc7w03";
+    rev = "86b343b42630e94d939029ff2cc609ff04ed40e9";
+    sha256 = "1y41s1vd89vcsm4aia18ayfff4w2af98lwn5l9fcwp157li985vw";
   };
 
   checkInputs = [ pytest ];

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

@@ -6,6 +6,8 @@
 , click
 , configparser ? null
 , dateutil
+, etelemetry
+, filelock
 , funcsigs
 , future
 , futures
@@ -14,6 +16,7 @@
 , nibabel
 , numpy
 , packaging
+, pathlib2
 , prov
 , psutil
 , pybids
@@ -60,6 +63,8 @@ buildPythonPackage rec {
   propagatedBuildInputs = [
     click
     dateutil
+    etelemetry
+    filelock
     funcsigs
     future
     networkx
@@ -77,6 +82,7 @@ buildPythonPackage rec {
   ] ++ stdenv.lib.optional (!isPy3k) [
     configparser
     futures
+    pathlib2 # darwin doesn't receive this transitively, but it is in install_requires
   ];
 
   checkInputs = [
@@ -91,6 +97,8 @@ buildPythonPackage rec {
     which
   ];
 
+  # checks on darwin inspect memory which doesn't work in build environment
+  doCheck = !stdenv.isDarwin;
   # ignore tests which incorrect fail to detect xvfb
   checkPhase = ''
     LC_ALL="en_US.UTF-8" pytest -v nipype -k 'not display'

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

@@ -13,7 +13,7 @@
 
 buildPythonPackage rec {
   pname = "odo";
-  version= "unstable-2019-07-16";
+  version= "unstable-2018-09-21";
 
   src = fetchFromGitHub {
     owner = "blaze";
@@ -54,5 +54,6 @@ buildPythonPackage rec {
     description = "Data migration utilities";
     license = licenses.bsdOriginal;
     maintainers = with maintainers; [ fridh costrouc ];
+    broken = true; # no longer compatible with dask>=2.0
   };
 }

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

@@ -1,28 +1,30 @@
-{ stdenv, buildPythonPackage, python, fetchFromGitHub, six, pycryptodome, chardet, nose, pytest, sortedcontainers }:
+{ stdenv, buildPythonPackage, fetchFromGitHub, isPy3k, six, pycryptodome, chardet, nose, sortedcontainers }:
 
 buildPythonPackage rec {
   pname = "pdfminer_six";
-  version = "20181108";
+  version = "20191020";
 
+  # No tests in PyPi Tarball
   src = fetchFromGitHub {
     owner = "pdfminer";
     repo = "pdfminer.six";
     rev = version;
-    sha256 = "1v8pcx43fgidv1g54s92k85anvcss08blkhm4yi1hn1ybl0mmw6c";
+    sha256 = "1fqn4ilcscvw6ws9a1yqiprha9d3rgw3d0280clkbk6s4l26wm9h";
   };
 
-  propagatedBuildInputs = [ six pycryptodome chardet sortedcontainers ];
+  propagatedBuildInputs = [ six pycryptodome sortedcontainers ]
+    ++ stdenv.lib.optionals isPy3k [ chardet ];
 
-  checkInputs = [ nose pytest ];
+  checkInputs = [ nose ];
   checkPhase = ''
-    ${python.interpreter} -m pytest
+    nosetests
   '';
 
   meta = with stdenv.lib; {
     description = "fork of PDFMiner using six for Python 2+3 compatibility";
     homepage = https://github.com/pdfminer/pdfminer.six;
     license = licenses.mit;
-    maintainers = with maintainers; [ psyanticy ];
+    maintainers = with maintainers; [ psyanticy marsam ];
   };
 }
 

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

@@ -22,12 +22,12 @@
 
 buildPythonPackage rec {
   pname = "pikepdf";
-  version = "1.8.0";
+  version = "1.8.1";
   disabled = ! isPy3k;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0pxcx3xc6c0plgxa4w9sjdf4rs1sxpx152b1vqvad2i3392n77ga";
+    sha256 = "a57a295296820087e66a3c62569d288958f29d1a354701ace6639a7692cc3022";
   };
 
   buildInputs = [

pkgs/development/python-modules/qimage2ndarray/default.nix

@@ -0,0 +1,32 @@
+{ lib, pkgs, buildPythonPackage, fetchPypi, isPy3k
+, numpy
+, pyqt5
+, nose
+}:
+
+buildPythonPackage rec {
+  pname = "qimage2ndarray";
+  version = "1.8";
+  disabled = !isPy3k;
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "7b9eb08a9be27f5439289d90d7d5a5942aad403d5634fe336eb915678c65db48";
+  };
+
+  checkInputs = [
+    nose
+  ];
+
+  propagatedBuildInputs = [
+    numpy
+    pyqt5
+  ];
+
+  meta = {
+    homepage = "https://github.com/hmeine/qimage2ndarray";
+    description = "A small python extension for quickly converting between QImages and numpy.ndarrays (in both directions)";
+    license = lib.licenses.bsd3;
+    maintainers = with lib.maintainers; [ tbenst ];
+  };
+}

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

@@ -4,13 +4,13 @@
 
 buildPythonPackage rec {
   pname = "sasmodels";
-  version = "1.0.0";
+  version = "1.0.1";
 
   src = fetchFromGitHub {
     owner = "SasView";
     repo = "sasmodels";
     rev = "v${version}";
-    sha256 = "082wnk10axincc4a62zxyr33l7v80yf7iz630y3421b50fwwyd8j";
+    sha256 = "0k4334nxf1n6gwb9m57sqcchmlssglfd116mpl72glmmdc451d5j";
   };
 
   buildInputs = [ opencl-headers ];

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

@@ -1,11 +1,9 @@
-{ lib
-, buildPythonPackage
-, fetchPypi
+{ lib, buildPythonPackage, fetchPypi, fetchpatch
 , tornado
 , toolz
 , zict
 , six
-, pytest_4
+, pytest
 , networkx
 , distributed
 , confluent-kafka
@@ -22,7 +20,21 @@ buildPythonPackage rec {
     sha256 = "127rpdjgkcyjifmkqbhmqfbzlgi32n54rybrdxja610qr906y40c";
   };
 
+  patches = [
+    # fix networkx rename issue of GiGraph.node -> DiGraph.nodes, remove on next bump
+    ( fetchpatch {
+      url = "https://github.com/python-streamz/streamz/commit/f8b7bdb6bcb9dd107677e82e755ff4695bf0c4be.patch";
+      sha256 = "1b2frp0j369gf55plxk2pigblhsc44m0rm9az01y83cjlcm26x2s";
+    })
+    # also, fix networkx rename issue of GiGraph.node -> DiGraph.nodes, remove on next bump
+    ( fetchpatch {
+      url = "https://github.com/python-streamz/streamz/commit/f7603f4cbea54f1548885881206a3ca9d6e52250.patch";
+      sha256 = "1125kqiaz6b3cifz0yk1zrkxj5804lfzl4kc58jhqajv8rsrbs45";
+    })
+  ];
+
   propagatedBuildInputs = [
+    networkx
     tornado
     toolz
     zict
@@ -33,20 +45,21 @@ buildPythonPackage rec {
     confluent-kafka
     distributed
     graphviz
-    networkx
-    pytest_4
+    pytest
     requests
   ];
 
   # Disable test_tcp_async because fails on sandbox build
+  # disable kafka tests
   checkPhase = ''
     pytest --deselect=streamz/tests/test_sources.py::test_tcp_async \
-      --deselect=streamz/tests/test_sources.py::test_tcp
+      --deselect=streamz/tests/test_sources.py::test_tcp \
+      --ignore=streamz/tests/test_kafka.py
   '';
 
   meta = with lib; {
     description = "Pipelines to manage continuous streams of data";
-    homepage = "https://github.com/mrocklin/streamz";
+    homepage = "https://github.com/python-streamz/streamz";
     license = licenses.bsd3;
     maintainers = [ maintainers.costrouc ];
   };

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

@@ -0,0 +1,81 @@
+{ lib, pkgs, buildPythonPackage, fetchPypi, isPy3k, callPackage
+, opencv3
+, pyqt5
+, pyqtgraph
+, numpy
+, scipy
+, numba
+, pandas
+, tables
+, git
+, ffmpeg
+, scikitimage
+, matplotlib
+, qdarkstyle
+, GitPython
+, anytree
+, pims
+, imageio
+, imageio-ffmpeg
+, av
+, nose
+, pytest
+, pyserial
+, arrayqueues
+, colorspacious
+, qimage2ndarray
+, flammkuchen
+, lightparam
+}:
+
+buildPythonPackage rec {
+  pname = "stytra";
+  version = "0.8.26";
+  disabled = !isPy3k;
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "81842a957e3114230c2d628f64325cd89d166913b68c3f802c89282f40918587";
+  };
+  doCheck = false;
+  checkInputs = [
+    nose
+    pytest
+    pyserial
+  ];
+
+
+  propagatedBuildInputs = [
+    opencv3
+    pyqt5
+    pyqtgraph
+    numpy
+    scipy
+    numba
+    pandas
+    tables
+    git
+    ffmpeg
+    scikitimage
+    matplotlib
+    qdarkstyle
+    GitPython
+    anytree
+    qimage2ndarray
+    flammkuchen
+    pims
+    colorspacious
+    lightparam
+    imageio
+    imageio-ffmpeg
+    arrayqueues
+    av
+  ];
+
+  meta = {
+    homepage = "https://github.com/portugueslab/stytra";
+    description = "A modular package to control stimulation and track behaviour";
+    license = lib.licenses.gpl3;
+    maintainers = with lib.maintainers; [ tbenst ];
+  };
+}

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

@@ -9,14 +9,14 @@
 
 buildPythonPackage rec {
   pname = "tqdm";
-  version = "4.36.1";
+  version = "4.40.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "abc25d0ce2397d070ef07d8c7e706aede7920da163c64997585d42d3537ece3d";
+    sha256 = "f0ab01cf3ae5673d18f918700c0165e5fad0f26b5ebe4b34f62ead92686b5340";
   };
 
-  buildInputs = [ nose coverage glibcLocales flake8 ];
+  checkInputs = [ nose coverage glibcLocales flake8 ];
 
   postPatch = ''
     # Remove performance testing.

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

@@ -1,8 +1,24 @@
-{ buildPythonPackage, fetchPypi, stdenv
-, nose, pillow, prettytable, pyyaml, dateutil, gdata
-, requests, mechanize, feedparser, lxml, gnupg, pyqt5
-, libyaml, simplejson, cssselect, pdfminer
-, termcolor, google_api_python_client, html2text
+{ lib, buildPythonPackage, fetchPypi, isPy27
+, cssselect
+, dateutil
+, feedparser
+, futures
+, gdata
+, gnupg
+, google_api_python_client
+, html2text
+, libyaml
+, lxml
+, mechanize
+, nose
+, pdfminer
+, pillow
+, prettytable
+, pyqt5
+, pyyaml
+, requests
+, simplejson
+, termcolor
 , unidecode
 }:
 
@@ -34,10 +50,27 @@ buildPythonPackage rec {
 
   nativeBuildInputs = [ pyqt5 ];
 
-  propagatedBuildInputs = [ pillow prettytable pyyaml dateutil
-    gdata requests mechanize feedparser lxml gnupg pyqt5 libyaml
-    simplejson cssselect pdfminer termcolor
-    google_api_python_client html2text unidecode ];
+  propagatedBuildInputs = [
+    cssselect
+    dateutil
+    feedparser
+    gdata
+    gnupg
+    google_api_python_client
+    html2text
+    libyaml
+    lxml
+    mechanize
+    pdfminer
+    pillow
+    prettytable
+    pyqt5
+    pyyaml
+    requests
+    simplejson
+    termcolor
+    unidecode
+  ] ++ lib.optionals isPy27 [ futures ];
 
   checkPhase = ''
     nosetests
@@ -46,6 +79,6 @@ buildPythonPackage rec {
   meta = {
     homepage = http://weboob.org;
     description = "Collection of applications and APIs to interact with websites without requiring the user to open a browser";
-    license = stdenv.lib.licenses.agpl3;
+    license = lib.licenses.agpl3;
   };
 }