Merge branch 'master' into staging-next

Hydra nixpkgs: ?compare=1530372

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

@@ -18,11 +18,11 @@
 
 buildPythonPackage rec {
   pname = "ansible";
-  version = "2.8.1";
+  version = "2.8.2";
 
   src = fetchurl {
     url = "https://releases.ansible.com/ansible/${pname}-${version}.tar.gz";
-    sha256 = "0ia4x17ywym3r1m96ar4h0wc2xlylhbjp6x4wzwkh4p2i0x1vmg1";
+    sha256 = "1e5ba829ca0602c55b33da399b06f99b135a34014b661d1c36d8892a1e2d3730";
   };
 
   prePatch = ''

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

@@ -0,0 +1,45 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, pbr
+, prettytable
+, pyparsing
+, six
+, stevedore
+, pyyaml
+, unicodecsv
+, cmd2
+}:
+
+buildPythonPackage rec {
+  pname = "cliff";
+  version = "2.15.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "fe044273539250a99a5b9915843902e40e4e9b32ac5698c1fae89e31200d649f";
+  };
+
+  propagatedBuildInputs = [
+    pbr
+    prettytable
+    pyparsing
+    six
+    stevedore
+    pyyaml
+    cmd2
+    unicodecsv
+  ];
+
+  # test dependencies are complex
+  # and would require about 20 packages
+  # to be added
+  doCheck = false;
+
+  meta = with lib; {
+    description = "Command Line Interface Formulation Framework";
+    homepage = https://docs.openstack.org/cliff/latest/;
+    license = licenses.asl20;
+    maintainers = [ maintainers.costrouc ];
+  };
+}

pkgs/development/python-modules/github-webhook/default.nix

@@ -1,28 +1,25 @@
-{ stdenv
-, buildPythonPackage
-, fetchgit
+{ lib, buildPythonPackage, fetchPypi
 , flask
+, six
 }:
 
 buildPythonPackage rec {
   pname = "github-webhook";
-  version = "unstable-2016-03-11";
+  version = "1.0.2";
 
-  # There is a PyPI package but an older one.
-  src = fetchgit {
-    url = "https://github.com/bloomberg/python-github-webhook.git";
-    rev = "ca1855479ee59c4373da5425dbdce08567605d49";
-    sha256 = "0mqwig9281iyzbphp1d21a4pqdrf98vs9k8lqpqx6spzgqaczx5f";
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "04jdf595gv97s4br0ym8izca3i6d1nfwcrpi4s26hkvn3czz84sv";
   };
 
-  propagatedBuildInputs = [ flask ];
-  # No tests
+  propagatedBuildInputs = [ flask six ];
+
+  # touches network
   doCheck = false;
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     description = "A framework for writing webhooks for GitHub";
+    homepage = "https://github.com/bloomberg/python-github-webhook";
     license = licenses.mit;
-    homepage = https://github.com/bloomberg/python-github-webhook;
   };
-
 }

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

@@ -0,0 +1,51 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, scikitlearn
+, numpy
+, scipy
+, jinja2
+, pytest
+, networkx
+, matplotlib
+, python-igraph
+, plotly
+, ipywidgets
+}:
+
+buildPythonPackage rec {
+  pname = "kmapper";
+  version = "1.2.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0879294680c5d01a928847b818a3c4e07eded3f602f96e510858e68e74fa3783";
+  };
+
+  propagatedBuildInputs = [
+    scikitlearn
+    numpy
+    scipy
+    jinja2
+  ];
+
+  checkInputs = [
+    pytest
+    networkx
+    matplotlib
+    python-igraph
+    plotly
+    ipywidgets
+  ];
+
+  checkPhase = ''
+    pytest test --ignore test/test_drawing.py
+  '';
+
+  meta = with lib; {
+    description = "Python implementation of Mapper algorithm for Topological Data Analysis";
+    homepage = http://kepler-mapper.scikit-tda.org;
+    license = licenses.mit;
+    maintainers = [ maintainers.costrouc ];
+  };
+}

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

@@ -0,0 +1,44 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, cmake
+, numpy
+, scipy
+, scikitlearn
+}:
+
+buildPythonPackage rec {
+  pname = "lightgbm";
+  version = "2.2.3";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "40354d21da6bfa73c7ada4d01b2e0b22eaae00f93e90bdaf3fc423020c273890";
+  };
+
+  nativeBuildInputs = [
+    cmake
+  ];
+
+  propagatedBuildInputs = [
+    numpy
+    scipy
+    scikitlearn
+  ];
+
+  postConfigure = ''
+    export HOME=$(mktemp -d)
+  '';
+
+  # The pypi package doesn't distribute the tests from the GitHub
+  # repository. It contains c++ tests which don't seem to wired up to
+  # `make check`.
+  doCheck = false;
+
+  meta = with lib; {
+    description = "A fast, distributed, high performance gradient boosting (GBDT, GBRT, GBM or MART) framework";
+    homepage = https://github.com/Microsoft/LightGBM;
+    license = licenses.mit;
+    maintainers = with lib.maintainers; [ teh costrouc ];
+  };
+}

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

@@ -16,12 +16,18 @@ buildPythonPackage rec {
     sha256 = "efa66e9e3045aa7cb1dd4bf0106e07dec9f80bc781a993fbaf8162a36c20af5c";
   };
 
+  patches = [ ./python37.patch ];
+
   buildInputs = [ cython ];
 
   propagatedBuildInputs = [ ipython ];
 
   disabled = isPyPy;
 
+  preBuild = ''
+    rm -f _line_profiler.c
+  '';
+
   checkPhase = ''
     ${python.interpreter} -m unittest discover -s tests
   '';
@@ -32,4 +38,4 @@ buildPythonPackage rec {
     license = lib.licenses.bsd3;
     maintainers = with lib.maintainers; [ fridh ];
   };
-}
+}

pkgs/development/python-modules/line_profiler/python37.patch

@@ -0,0 +1,36 @@
+From 542baf59f3b2eada13bde48e8a89e484c2cfeeef Mon Sep 17 00:00:00 2001
+From: Hanaasagi <ambiguous404@gmail.com>
+Date: Wed, 17 Apr 2019 06:46:03 +0000
+Subject: [PATCH] Support Python 3.7 Generator (PEP 479)
+
+---
+ kernprof.py      | 2 ++
+ line_profiler.py | 2 ++
+ 2 files changed, 4 insertions(+)
+
+diff --git a/kernprof.py b/kernprof.py
+index 108d36e..6461cf6 100755
+--- a/kernprof.py
++++ b/kernprof.py
+@@ -102,6 +102,8 @@ def wrapper(*args, **kwds):
+                 self.enable_by_count()
+                 try:
+                     item = g.send(input)
++                except StopIteration:
++                    return
+                 finally:
+                     self.disable_by_count()
+                 input = (yield item)
+diff --git a/line_profiler.py b/line_profiler.py
+index a481dd2..5744d05 100755
+--- a/line_profiler.py
++++ b/line_profiler.py
+@@ -100,6 +100,8 @@ def wrapper(*args, **kwds):
+                 self.enable_by_count()
+                 try:
+                     item = g.send(input)
++                except StopIteration:
++                    return
+                 finally:
+                     self.disable_by_count()
+                 input = (yield item)

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

@@ -0,0 +1,81 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, pytest
+, mock
+, bokeh
+, plotly
+, chainer
+, xgboost
+, mpi4py
+, lightgbm
+, Keras
+, mxnet
+, scikit-optimize
+, tensorflow
+, sqlalchemy
+, numpy
+, scipy
+, six
+, cliff
+, colorlog
+, pandas
+, alembic
+, typing
+, pythonOlder
+, isPy27
+}:
+
+buildPythonPackage rec {
+  pname = "optuna";
+  version = "0.13.0";
+  disabled = isPy27;
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "915b9d7b28f7f7cdf015d8617c689ca90eda7a5bbd59c5fc232c9eccc9a91585";
+  };
+
+  checkInputs = [
+    pytest
+    mock
+    bokeh
+    plotly
+    chainer
+    xgboost
+    mpi4py
+    lightgbm
+    Keras
+    mxnet
+    scikit-optimize
+    tensorflow
+  ];
+
+  propagatedBuildInputs = [
+    sqlalchemy
+    numpy
+    scipy
+    six
+    cliff
+    colorlog
+    pandas
+    alembic
+  ] ++ lib.optionals (pythonOlder "3.5") [ typing ];
+
+  configurePhase = if !(pythonOlder "3.5") then ''
+    substituteInPlace setup.py \
+      --replace "'typing'" ""
+  '' else "";
+
+  checkPhase = ''
+    pytest --ignore tests/test_cli.py \
+           --ignore tests/integration_tests/test_chainermn.py
+  '';
+
+  meta = with lib; {
+    description = "A hyperparameter optimization framework";
+    homepage = https://optuna.org/;
+    license = licenses.mit;
+    maintainers = [ maintainers.costrouc ];
+  };
+}

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

@@ -1,11 +1,11 @@
 { lib, buildPythonPackage, fetchPypi, dateutil, requests, pytz, pyproj , pytest } :
 buildPythonPackage rec {
   pname = "OWSLib";
-  version = "0.17.1";
+  version = "0.18.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "19dm6dxj9hsiq0bnb4d6ms3sh2hcss9d9fhpjgkwxzrw9mlzvrxj";
+    sha256 = "018p2ypmpbbcgl0hp92s0vig1wirh41lj0wy62aafn5050pmqr7m";
   };
 
   buildInputs = [ pytest ];

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

@@ -0,0 +1,50 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, scikitlearn
+, numpy
+, matplotlib
+, scipy
+, hopcroftkarp
+, pytest
+}:
+
+buildPythonPackage rec {
+  pname = "persim";
+  version = "0.0.9";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "52ce59856de25eec74c6f20951301b13e7d98c434e712d2225653e2087d54fbc";
+  };
+
+  propagatedBuildInputs = [
+    scikitlearn
+    numpy
+    matplotlib
+    scipy
+    hopcroftkarp
+  ];
+
+  checkInputs = [
+    pytest
+  ];
+
+  checkPhase = ''
+    # specifically needed for darwin
+    export HOME=$(mktemp -d)
+    mkdir -p $HOME/.matplotlib
+    echo "backend: ps" > $HOME/.matplotlib/matplotlibrc
+
+    # ignore tests due to python 2.7 fail
+    pytest --ignore test/test_plots.py \
+           --ignore test/test_visuals.py
+  '';
+
+  meta = with lib; {
+    description = "Distances and representations of persistence diagrams";
+    homepage = https://persim.scikit-tda.org;
+    license = licenses.mit;
+    maintainers = [ maintainers.costrouc ];
+  };
+}

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

@@ -0,0 +1,48 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, cython
+, numpy
+, scipy
+, scikitlearn
+, persim
+, pytest
+}:
+
+buildPythonPackage rec {
+  pname = "ripser";
+  version = "0.3.2";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "ff9f50fba911f0e9212077b78014f83e30c97526194dd6bd1df3d81896e6cb58";
+  };
+
+  checkInputs = [
+    pytest
+  ];
+
+  propagatedBuildInputs = [
+    cython
+    numpy
+    scipy
+    scikitlearn
+    persim
+  ];
+
+  checkPhase = ''
+    # specifically needed for darwin
+    export HOME=$(mktemp -d)
+    mkdir -p $HOME/.matplotlib
+    echo "backend: ps" > $HOME/.matplotlib/matplotlibrc
+
+    pytest
+  '';
+
+  meta = with lib; {
+    description = "A Lean Persistent Homology Library for Python";
+    homepage = https://ripser.scikit-tda.org;
+    license = licenses.mit;
+    maintainers = [ maintainers.costrouc ];
+  };
+}

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

@@ -0,0 +1,44 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, numpy
+, scipy
+, scikitlearn
+, pyaml
+, pytest
+}:
+
+buildPythonPackage rec {
+  pname = "scikit-optimize";
+  version = "0.6";
+
+  src = fetchFromGitHub {
+    owner = "scikit-optimize";
+    repo = "scikit-optimize";
+    rev = "v${version}";
+    sha256 = "1srbb20k8ddhpcfxwdflapfh6xfyrd3dnclcg3bsfq1byrcmv0d4";
+  };
+
+  propagatedBuildInputs = [
+    numpy
+    scipy
+    scikitlearn
+    pyaml
+  ];
+
+  checkInputs = [
+    pytest
+  ];
+
+  # remove --ignore at next release > 0.6
+  checkPhase = ''
+    pytest skopt --ignore skopt/tests/test_searchcv.py
+  '';
+
+  meta = with lib; {
+    description = "Sequential model-based optimization toolbox";
+    homepage = https://scikit-optimize.github.io/;
+    license = licenses.bsd3;
+    maintainers = [ maintainers.costrouc ];
+  };
+}

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

@@ -0,0 +1,64 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, numpy
+, scipy
+, scikitlearn
+, matplotlib
+, numba
+, umap-learn
+, cython
+, ripser
+, persim
+, pillow
+, kmapper
+, tadasets
+, pytest
+, isPy27
+}:
+
+buildPythonPackage rec {
+  pname = "scikit-tda";
+  version = "0.0.4";
+  disabled = isPy27;
+
+  src = fetchFromGitHub {
+    owner = "scikit-tda";
+    repo = "scikit-tda";
+    rev = version;
+    sha256 = "0a90k6i9fkmc9gf250b4fidx2fzd2qrn025l74mjk51fvf23q13a";
+  };
+
+  propagatedBuildInputs = [
+    numpy
+    scipy
+    scikitlearn
+    matplotlib
+    numba
+    umap-learn
+    cython
+    ripser
+    persim
+    pillow
+    kmapper
+    tadasets
+  ];
+
+  checkInputs = [
+    pytest
+  ];
+
+  checkPhase = ''
+    pytest test
+  '';
+
+  # tests will be included in next release
+  doCheck = false;
+
+  meta = with lib; {
+    description = "Topological Data Analysis for humans";
+    homepage = https://github.com/scikit-tda/scikit-tda;
+    license = licenses.mit;
+    maintainers = [ maintainers.costrouc ];
+  };
+}

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

@@ -0,0 +1,35 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, numpy
+, matplotlib
+, pytest
+, scipy
+}:
+
+buildPythonPackage rec {
+  pname = "tadasets";
+  version = "0.0.4";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "a0e6c14678750315febd97fcf334bbbfd2695ebd91b4fe7707bb1220d7348416";
+  };
+
+  propagatedBuildInputs = [
+    numpy
+    matplotlib
+  ];
+
+  checkInputs = [
+    pytest
+    scipy
+  ];
+
+  meta = with lib; {
+    description = "Great data sets for Topological Data Analysis";
+    homepage = https://tadasets.scikit-tda.org;
+    license = licenses.mit;
+    maintainers = [ maintainers.costrouc ];
+  };
+}

pkgs/development/python-modules/umap-learn/default.nix

@@ -0,0 +1,49 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, nose
+, numpy
+, scikitlearn
+, scipy
+, numba
+}:
+
+buildPythonPackage rec {
+  pname = "umap-learn";
+  version = "0.3.9";
+
+  src = fetchFromGitHub {
+    owner = "lmcinnes";
+    repo = "umap";
+    rev = version;
+    sha256 = "1cdc7hs3vwzxvzs34l9a06q8rvks29wj6swyj8zvwr32knxch8a9";
+  };
+
+  checkInputs = [
+    nose
+  ];
+
+  propagatedBuildInputs = [
+    numpy
+    scikitlearn
+    scipy
+    numba
+  ];
+
+  postConfigure = ''
+   substituteInPlace umap/tests/test_umap.py \
+     --replace "def test_umap_transform_on_iris()" "@SkipTest
+def test_umap_transform_on_iris()"
+  '';
+
+  checkPhase = ''
+    nosetests -s umap
+  '';
+
+  meta = with lib; {
+    description = "Uniform Manifold Approximation and Projection";
+    homepage = http://github.com/lmcinnes/umap;
+    license = licenses.bsd3;
+    maintainers = [ maintainers.costrouc ];
+  };
+}

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

@@ -0,0 +1,22 @@
+{ lib, buildPythonPackage, fetchPypi, nose }:
+
+buildPythonPackage rec {
+  pname = "yappi";
+  version = "1.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1gs48c5sy771lsjhca3m4j8ljc6yhk5qnim3n5idnlaxa4ql30bz";
+  };
+
+  patches = [ ./tests.patch ];
+
+  checkInputs = [ nose ];
+
+  meta = with lib; {
+    homepage = https://github.com/sumerc/yappi;
+    description = "Python profiler that supports multithreading and measuring CPU time";
+    license = licenses.mit;
+    maintainers = with maintainers; [ orivej ];
+  };
+}

pkgs/development/python-modules/yappi/tests.patch

@@ -0,0 +1,12 @@
+--- a/tests/test_functionality.py
++++ b/tests/test_functionality.py
+@@ -74,2 +74,3 @@ class BasicUsage(utils.YappiUnitTestCase):
+    
++    @_unittest.skip('wall-clock-time-sensitive')
+     def test_get_clock(self):
+--- a/tests/test_hooks.py
++++ b/tests/test_hooks.py
+@@ -124,2 +124,3 @@ class ContextIdCallbackTest(utils.YappiUnitTestCase):
+ 
++    @unittest.skip('wall-clock-time-sensitive')
+     def test_pause_resume(self):