Merge master into staging-next

2019-12-13 11:43:39 +01:00
parent d5d8b3514d 418ad571c3
commit dfdf1597a7
154 changed files with 2448 additions and 2272 deletions
--- a/pkgs/development/python-modules/arviz/default.nix
+++ b/pkgs/development/python-modules/arviz/default.nix
@@ -0,0 +1,80 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, emcee
+, matplotlib
+, netcdf4
+, numba
+, numpy
+, pandas
+, pytest
+, scipy
+, setuptools
+, tensorflow-probability
+, xarray
+#, h5py (used by disabled tests)
+#, pymc3 (broken)
+#, pyro-ppl (broken)
+#, pystan (not packaged)
+#, numpyro (not packaged)
+}:
+
+buildPythonPackage rec {
+  pname = "arviz";
+  version = "0.5.1";
+
+  src = fetchFromGitHub {
+    owner = "arviz-devs";
+    repo = "arviz";
+    rev = version;
+    sha256 = "0p600cakix24wz2ridnzy6sp3l1p2kr5s60qc7s82wpv7fw0i9ry";
+  };
+
+  propagatedBuildInputs = [
+    # needed to install
+    matplotlib
+    netcdf4
+    pandas
+    xarray
+    # needed to import
+    setuptools
+    # not needed to import, but used by many functions
+    # and is listed as a dependency in the documentation
+    numpy
+    scipy
+  ];
+
+  checkInputs = [
+    emcee
+    numba
+    pytest
+    tensorflow-probability
+    #h5py (used by disabled tests)
+    #pymc3 (broken)
+    #pyro-ppl (broken)
+    #pystan (not packaged)
+    #numpyro (not packaged)
+  ];
+
+  # check requires pymc3 and pyro-ppl, which are currently broken, and pystan
+  # and numpyro, which are not yet packaged, some checks also need to make
+  # directories and do not have permission to do so. So we can only check part
+  # of the package
+  # Additionally, there are some failures with the plots test, which revolve
+  # around attempting to output .mp4 files through an interface that only wants
+  # to output .html files.
+  # The following test have been disabled as a result: data_cmdstanpy,
+  # data_numpyro, data_pyro, data_pystan, and plots.
+  checkPhase = ''
+    cd arviz/tests/
+    HOME=$TMPDIR pytest test_{data_cmdstan,data_emcee,data,data_tfp,\
+    diagnostics,plot_utils,rcparams,stats,stats_utils,utils}.py
+  '';
+
+  meta = with lib; {
+    description = "ArviZ is a Python package for exploratory analysis of Bayesian models";
+    homepage = "https://arviz-devs.github.io/arviz/";
+    license = licenses.asl20;
+    maintainers = [ maintainers.omnipotententity ];
+  };
+}
--- a/pkgs/development/python-modules/azure-mgmt-recoveryservicesbackup/default.nix
+++ b/pkgs/development/python-modules/azure-mgmt-recoveryservicesbackup/default.nix
@@ -9,12 +9,12 @@

 buildPythonPackage rec {
  pname = "azure-mgmt-recoveryservicesbackup";
-  version = "0.4.0";
+  version = "0.5.0";

  src = fetchPypi {
    inherit pname version;
    extension = "zip";
-    sha256 = "0zssvzdip23yzaxlac9rlzg9mlyjl97fwr0gj8y27z8j58pwj72i";
+    sha256 = "0jhq8fi3dn2cncyv2rrgr4kldd254f30zgwf6p85rdgvg2p9k4hl";
  };

  propagatedBuildInputs = [
--- a/pkgs/development/python-modules/cassandra-driver/default.nix
+++ b/pkgs/development/python-modules/cassandra-driver/default.nix
@@ -15,11 +15,11 @@

 buildPythonPackage rec {
  pname = "cassandra-driver";
-  version = "3.19.0";
+  version = "3.20.2";

  src = fetchPypi {
    inherit pname version;
-    sha256 = "1vy9yzsd9c29irq99m8lpkgnc634waai2phvr6b89pmmdirp2wm9";
+    sha256 = "03nycyn5nd1pnrg6fffq3wcjqnw13lgja137zq5zszx68mc15wnl";
  };

  nativeBuildInputs = [ cython ];
--- a/pkgs/development/python-modules/colored/default.nix
+++ b/pkgs/development/python-modules/colored/default.nix
@@ -5,11 +5,11 @@

 buildPythonPackage rec {
  pname = "colored";
-  version = "1.4.0";
+  version = "1.4.1";

  src = fetchPypi {
    inherit pname version;
-    sha256 = "0wlsg7z406q31r5fpwkqfpyfpigazbmq9qm856wfbn861k2773zf";
+    sha256 = "0qf9470fsasimsmsri13jw1d2zpn3g24fv6vss64jq3ifwfkcs14";
  };

  # No proper test suite
--- a/pkgs/development/python-modules/dask-ml/default.nix
+++ b/pkgs/development/python-modules/dask-ml/default.nix
@@ -1,6 +1,7 @@
 { stdenv
 , buildPythonPackage
 , fetchPypi
+, pythonOlder
 , dask
 , numpy, toolz # dask[array]
 , numba
@@ -19,21 +20,41 @@
 }:

 buildPythonPackage rec {
-  version = "1.0.0";
+  version = "1.1.1";
  pname = "dask-ml";
+  disabled = pythonOlder "3.6"; # >= 3.6

  src = fetchPypi {
    inherit pname version;
-    sha256 = "dde926478653bd03a3fbc501d3873a1534836608217b94d04320d1e1c07e59dc";
+    sha256 = "1yad9b9hd02rbdf6m1gfj74cjgcbyp7lxdj22d5h5rhv7xa3127x";
  };

-  checkInputs = [ pytest xgboost tensorflow joblib distributed ];
-  propagatedBuildInputs = [ dask numpy toolz numba pandas scikitlearn scipy dask-glm six multipledispatch packaging ];
+  propagatedBuildInputs = [
+    dask
+    dask-glm
+    distributed
+    multipledispatch
+    numba
+    numpy
+    packaging
+    pandas
+    scikitlearn
+    scipy
+    six
+    toolz
+  ];

-  # dask-ml has some heavy test requirements
-  # and requires some very new packages
+  # has non-standard build from source, and pypi doesn't include tests
  doCheck = false;

+  # in lieu of proper tests
+  pythonImportsCheck = [
+    "dask_ml"
+    "dask_ml.naive_bayes"
+    "dask_ml.wrappers"
+    "dask_ml.utils"
+  ];
+
  meta = with stdenv.lib; {
    homepage = https://github.com/dask/dask-ml;
    description = "Scalable Machine Learn with Dask";
--- a/pkgs/development/python-modules/docker/default.nix
+++ b/pkgs/development/python-modules/docker/default.nix
@@ -1,8 +1,9 @@
-{ stdenv, buildPythonPackage, fetchPypi, isPy27
+{ lib, stdenv, buildPythonPackage, fetchPypi, isPy27
 , backports_ssl_match_hostname
 , mock
 , paramiko
 , pytest
+, pytestCheckHook
 , requests
 , six
 , websocket_client
@@ -17,25 +18,25 @@ buildPythonPackage rec {
    sha256 = "1hdgics03fz2fbhalzys7a7kjj54jnl5a37h6lzdgym41gkwa1kf";
  };

+  nativeBuildInputs = [
+    pytestCheckHook
+  ] ++ lib.optional isPy27 mock;
+
  propagatedBuildInputs = [
    paramiko
    requests
    six
    websocket_client
-  ] ++ stdenv.lib.optional isPy27 backports_ssl_match_hostname;
+  ] ++ lib.optional isPy27 backports_ssl_match_hostname;

-  checkInputs = [
-    mock
-    pytest
-  ];
-
-  # Other tests touch network
+  pytestFlagsArray = [ "tests/unit" ];
  # Deselect socket tests on Darwin because it hits the path length limit for a Unix domain socket
-  checkPhase = ''
-    ${pytest}/bin/pytest tests/unit/ ${stdenv.lib.optionalString stdenv.isDarwin "--deselect=tests/unit/api_test.py::TCPSocketStreamTest"}
-  '';
+  disabledTests = lib.optionals stdenv.isDarwin [ "stream_response" "socket_file" ];

-  meta = with stdenv.lib; {
+  # skip setuptoolsCheckPhase
+  doCheck = false;
+
+  meta = with lib; {
    description = "An API client for docker written in Python";
    homepage = "https://github.com/docker/docker-py";
    license = licenses.asl20;
--- a/pkgs/development/python-modules/fpylll/default.nix
+++ b/pkgs/development/python-modules/fpylll/default.nix
@@ -14,13 +14,13 @@

 buildPythonPackage rec {
  pname = "fpylll";
-  version = "0.4.1dev";
+  version = "0.5.0dev";

  src = fetchFromGitHub {
    owner = "fplll";
    repo = "fpylll";
    rev = version;
-    sha256 = "01x2sqdv0sbjj4g4waj0hj4rcn4bq7h17442xaqwbznym9azmn9w";
+    sha256 = "091zqgsqd5cqma1hvimkq5xpr9f1jw80v9m2fr6k9hvssqjzgnab";
  };

  buildInputs = [
@@ -45,11 +45,16 @@ buildPythonPackage rec {
  ];

  checkPhase = ''
-    py.test
+    # Since upstream introduced --doctest-modules in
+    # https://github.com/fplll/fpylll/commit/9732fdb40cf1bd43ad1f60762ec0a8401743fc79,
+    # it is necessary to ignore import mismatches. Not sure why, but the files
+    # should be identical anyway.
+    PY_IGNORE_IMPORTMISMATCH=1 pytest
  '';

  meta = {
    description = "A Python interface for fplll";
+    changelog = "https://github.com/fplll/fpylll/releases/tag/${version}";
    homepage = https://github.com/fplll/fpylll;
    maintainers = with lib.maintainers; [ timokau ];
    license = lib.licenses.gpl2Plus;
--- a/pkgs/development/python-modules/goocalendar/default.nix
+++ b/pkgs/development/python-modules/goocalendar/default.nix
@@ -16,17 +16,22 @@ buildPythonPackage rec {
  pname = "GooCalendar";
  version = "0.6";

-  disabled = isPy3k;
+  disabled = !isPy3k;

  src = fetchPypi {
    inherit pname version;
    sha256 = "4c22c93e19b933d10d8ea1c67a67f485267af82175ef59419427dd39d1e3af18";
  };
-  nativeBuildInputs = [ pkgconfig gobject-introspection ];
+
+  nativeBuildInputs = [
+    pkgconfig
+    gobject-introspection
+  ];
+
  propagatedBuildInputs = [
-    pygtk
    pygobject3
  ];
+
  buildInputs = [
    gtk3
    goocanvas2
@@ -37,8 +42,8 @@ buildPythonPackage rec {

  meta = with stdenv.lib; {
    description = "A calendar widget for GTK using PyGoocanvas.";
-    homepage    = https://goocalendar.tryton.org/;
-    license     = licenses.gpl2;
+    homepage = https://goocalendar.tryton.org/;
+    license = licenses.gpl2;
    maintainers = [ maintainers.udono ];
  };
 }
--- a/pkgs/development/python-modules/icalendar/default.nix
+++ b/pkgs/development/python-modules/icalendar/default.nix
@@ -7,12 +7,12 @@
 }:

 buildPythonPackage rec {
-  version = "4.0.3";
+  version = "4.0.4";
  pname = "icalendar";

  src = fetchPypi {
    inherit pname version;
-    sha256 = "0mk3dk1dxkcm46jy48v27j2w2349iv4sbimqj1yb5js43mx49hh7";
+    sha256 = "16gjvqv0n05jrb9g228pdjgzd3amz2pdhvcgsn1jypszjg5m2w9l";
  };

  buildInputs = [ setuptools ];
--- a/pkgs/development/python-modules/internetarchive/default.nix
+++ b/pkgs/development/python-modules/internetarchive/default.nix
@@ -1,6 +1,6 @@
 { buildPythonPackage, fetchFromGitHub, pytest, six, clint, pyyaml, docopt
 , requests, jsonpatch, args, schema, responses, backports_csv, isPy3k
-, lib, glibcLocales }:
+, lib, glibcLocales, setuptools }:

 buildPythonPackage rec {
  pname = "internetarchive";
@@ -23,6 +23,7 @@ buildPythonPackage rec {
    jsonpatch
    args
    schema
+    setuptools
  ] ++ lib.optional (!isPy3k) backports_csv;

  checkInputs = [ pytest responses glibcLocales ];
--- a/pkgs/development/python-modules/libsexy/default.nix
+++ b/pkgs/development/python-modules/libsexy/default.nix
@@ -1,27 +0,0 @@
-{ stdenv, fetchurl, buildPythonPackage, libsexy, pkgconfig, libxml2, pygtk, pango, glib, python }:
-
-buildPythonPackage rec {
-  pname = "libsexy";
-  version = "0.1.9";
-  format = "other";
-
-  src = fetchurl {
-    url = "http://releases.chipx86.com/libsexy/sexy-python/sexy-python-${version}.tar.gz";
-    sha256 = "05bgcsxwkp63rlr8wg6znd46cfbhrzc5wh70jabsi654pxxjb39d";
-  };
-
-  nativeBuildInputs = [ pkgconfig pygtk ];
-
-  propagatedBuildInputs = [
-    pygtk libsexy glib pango libxml2
-  ];
-
-  postInstall = ''
-    ln -s $out/${python.sitePackages}/gtk-2.0/* $out/${python.sitePackages}
-  '';
-
-  meta = {
-    description = "Python libsexy bindings";
-    platforms = stdenv.lib.platforms.linux;
-  };
-}
--- a/pkgs/development/python-modules/limnoria/default.nix
+++ b/pkgs/development/python-modules/limnoria/default.nix
@@ -6,11 +6,11 @@

 buildPythonPackage rec {
  pname = "limnoria";
-  version = "2019.09.08";
+  version = "2019.11.09";

  src = fetchPypi {
    inherit pname version;
-    sha256 = "0l50smy3hai6pb6lwvcgzrx6yfzshqlvx8ym5my1ji07ilnasmmp";
+    sha256 = "1ni25jmri0928jj2c24xw5f2fzljjla54zh80fimks1aa5752j29";
  };

  patchPhase = ''
--- a/pkgs/development/python-modules/mapbox/default.nix
+++ b/pkgs/development/python-modules/mapbox/default.nix
@@ -0,0 +1,36 @@
+{ lib
+, buildPythonPackage
+, boto3
+, cachecontrol
+, fetchFromGitHub
+, iso3166
+, python-dateutil
+, requests
+, responses
+, polyline
+, pytestCheckHook
+, uritemplate
+}:
+
+buildPythonPackage rec {
+  pname = "mapbox";
+  version = "0.18.0";
+
+  src = fetchFromGitHub {
+    owner = "mapbox";
+    repo = "mapbox-sdk-py";
+    rev = "0.18.0";
+    sha256 = "123wsa4j11ps5pkjgylbmw4gnzh2vi22swgmvy50w26glkszh075";
+  };
+
+  propagatedBuildInputs = [ boto3 cachecontrol iso3166 python-dateutil requests polyline uritemplate ];
+  checkInputs = [ pytestCheckHook responses ];
+
+  meta = with lib; {
+    homepage = https://github.com/mapbox/mapbox-sdk-py;
+    license = licenses.mit;
+    description = "Mapbox SDK for Python";
+    longDescription = "Low-level client API for Mapbox web services.";
+    maintainers = with maintainers; [ ersin ];
+  };
+}
--- a/pkgs/development/python-modules/matplotlib/2.nix
+++ b/pkgs/development/python-modules/matplotlib/2.nix
@@ -1,9 +1,8 @@
 { stdenv, fetchPypi, python, buildPythonPackage, pycairo, backports_functools_lru_cache
 , which, cycler, dateutil, nose, numpy, pyparsing, sphinx, tornado, kiwisolver
-, freetype, libpng, pkgconfig, mock, pytz, pygobject3, functools32, subprocess32
+, freetype, libpng, pkgconfig, mock, pytz, pygobject3, gobject-introspection, functools32, subprocess32
 , fetchpatch
 , enableGhostscript ? false, ghostscript ? null, gtk3
-, enableGtk2 ? false, pygtk ? null, gobject-introspection
 , enableGtk3 ? false, cairo
 # darwin has its own "MacOSX" backend
 , enableTk ? !stdenv.isDarwin, tcl ? null, tk ? null, tkinter ? null, libX11 ? null
@@ -14,7 +13,6 @@
 }:

 assert enableGhostscript -> ghostscript != null;
-assert enableGtk2 -> pygtk != null;
 assert enableTk -> (tcl != null)
                && (tk != null)
                && (tkinter != null)
@@ -45,7 +43,6 @@ buildPythonPackage rec {
    [ cycler dateutil nose numpy pyparsing tornado freetype kiwisolver
      libpng mock pytz ]
    ++ stdenv.lib.optional (pythonOlder "3.3") backports_functools_lru_cache
-    ++ stdenv.lib.optional enableGtk2 pygtk
    ++ stdenv.lib.optionals enableGtk3 [ cairo pycairo gtk3 gobject-introspection pygobject3 ]
    ++ stdenv.lib.optionals enableTk [ tcl tk tkinter libX11 ]
    ++ stdenv.lib.optionals enableQt [ pyqt4 ]
--- a/pkgs/development/python-modules/matplotlib/default.nix
+++ b/pkgs/development/python-modules/matplotlib/default.nix
@@ -1,8 +1,7 @@
 { stdenv, fetchPypi, python, buildPythonPackage, isPy3k, pycairo, backports_functools_lru_cache
 , which, cycler, dateutil, nose, numpy, pyparsing, sphinx, tornado, kiwisolver
-, freetype, libpng, pkgconfig, mock, pytz, pygobject3
+, freetype, libpng, pkgconfig, mock, pytz, pygobject3, gobject-introspection
 , enableGhostscript ? true, ghostscript ? null, gtk3
-, enableGtk2 ? false, pygtk ? null, gobject-introspection
 , enableGtk3 ? false, cairo
 # darwin has its own "MacOSX" backend
 , enableTk ? !stdenv.isDarwin, tcl ? null, tk ? null, tkinter ? null, libX11 ? null
@@ -13,7 +12,6 @@
 }:

 assert enableGhostscript -> ghostscript != null;
-assert enableGtk2 -> pygtk != null;
 assert enableTk -> (tcl != null)
                && (tk != null)
                && (tkinter != null)
@@ -46,7 +44,6 @@ buildPythonPackage rec {
    [ cycler dateutil nose numpy pyparsing tornado freetype kiwisolver
      libpng mock pytz ]
    ++ stdenv.lib.optional (pythonOlder "3.3") backports_functools_lru_cache
-    ++ stdenv.lib.optional enableGtk2 pygtk
    ++ stdenv.lib.optionals enableGtk3 [ cairo pycairo gtk3 gobject-introspection pygobject3 ]
    ++ stdenv.lib.optionals enableTk [ tcl tk tkinter libX11 ]
    ++ stdenv.lib.optionals enableQt [ pyqt5 ];
--- a/pkgs/development/python-modules/pikepdf/default.nix
+++ b/pkgs/development/python-modules/pikepdf/default.nix
@@ -22,12 +22,12 @@

 buildPythonPackage rec {
  pname = "pikepdf";
-  version = "1.6.5";
+  version = "1.8.0";
  disabled = ! isPy3k;

  src = fetchPypi {
    inherit pname version;
-    sha256 = "ee935eea84fa5fc1879355de38cd47216e5e922553303ee045c35917e13b2fcf";
+    sha256 = "0pxcx3xc6c0plgxa4w9sjdf4rs1sxpx152b1vqvad2i3392n77ga";
  };

  buildInputs = [
--- a/pkgs/development/python-modules/send2trash/default.nix
+++ b/pkgs/development/python-modules/send2trash/default.nix
@@ -12,7 +12,7 @@ buildPythonPackage rec {
    owner = "hsoft";
    repo = "send2trash";
    rev = version;
-    sha256 = "1w502i5h8xaqf03g6h95h4vs1wqfv6kg925dn63phrwmg1hfz2xx";
+    sha256 = "1c76zldhw2ay7q7r00nnzcampjz9lkqfcbzqpm0iqp5i6bmmv30v";
  };

  doCheck = !stdenv.isDarwin;
--- a/pkgs/development/python-modules/simpleeval/default.nix
+++ b/pkgs/development/python-modules/simpleeval/default.nix
@@ -2,10 +2,10 @@

 buildPythonPackage rec {
  pname = "simpleeval";
-  version = "0.9.8";
+  version = "0.9.10";
  src = fetchPypi {
    inherit pname version;
-    sha256 = "00fzwbjg98lsnmfzmbgzg1k8q8iqbahcxjnnlhzhb44phrhcxql5";
+    sha256 = "1skvl467kj83rzkhk01i0wm8m5vmh6j5znrfdizn6r18ii45a839";
  };
  meta = {
    homepage = https://github.com/danthedeckie/simpleeval;
--- a/pkgs/development/python-modules/soundfile/default.nix
+++ b/pkgs/development/python-modules/soundfile/default.nix
@@ -11,12 +11,12 @@

 buildPythonPackage rec {
  pname = "soundfile";
-  version = "0.10.2";
+  version = "0.10.3.post1";

  src = fetchPypi {
    pname = "SoundFile";
    inherit version;
-    sha256 = "0w8mjadairg6av88090kwsridd0k115672b91zlcmf37r0c64zv3";
+    sha256 = "0yqhrfz7xkvqrwdxdx2ydy4h467sk7z3gf984y1x2cq7cm1gy329";
  };

    checkInputs = [ pytest ];
--- a/pkgs/development/python-modules/testresources/default.nix
+++ b/pkgs/development/python-modules/testresources/default.nix
@@ -10,7 +10,7 @@ buildPythonPackage rec {
    sha256 = "ee9d1982154a1e212d4e4bac6b610800bfb558e4fb853572a827bc14a96e4417";
  };

-  buildInputs = [ pbr ];
+  propagatedBuildInputs = [ pbr ];

  checkInputs = [ fixtures testtools ];