Merge branch 'master' into staging

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

@@ -1,4 +1,4 @@
-{ stdenv, buildPythonPackage, fetchPypi, iana-etc, libredirect,
+{ stdenv, buildPythonPackage, fetchPypi, fetchpatch, iana-etc, libredirect,
   pytest, case, kombu, billiard, pytz, anyjson, amqp, eventlet
 }:
 
@@ -11,6 +11,13 @@ buildPythonPackage rec {
     sha256 = "ff727c115533edbc7b81b2b4ba1ec88d1c2fc4836e1e2f4c3c33a76ff53e5d7f";
   };
 
+  # Skip test_RedisBackend.test_timeouts_in_url_coerced
+  # See https://github.com/celery/celery/pull/4847
+  patches = fetchpatch {
+    url = https://github.com/celery/celery/commit/b2668607c909c61becd151905b4525190c19ff4a.patch;
+    sha256 = "11w0z2ycyh8kccj4y69zb7bxppiipcwwigg6jn1q9yrcsvz170jq";
+  };
+
   # make /etc/protocols accessible to fix socket.getprotobyname('tcp') in sandbox
   preCheck = stdenv.lib.optionalString stdenv.isLinux ''
     export NIX_REDIRECTS=/etc/protocols=${iana-etc}/etc/protocols \

pkgs/development/python-modules/cmd2/default.nix

@@ -1,17 +1,15 @@
-{ stdenv, fetchPypi, buildPythonPackage, pythonOlder
-, pyperclip, six, pyparsing, vim
+{ stdenv, fetchPypi, buildPythonPackage, pythonOlder, isPy3k
+, pyperclip, six, pyparsing, vim, wcwidth, colorama
 , contextlib2 ? null, subprocess32 ? null
 , pytest, mock, which, fetchFromGitHub, glibcLocales
 }:
 buildPythonPackage rec {
   pname = "cmd2";
-  version = "0.8.0";
+  version = "0.9.1";
 
-  src = fetchFromGitHub {
-    owner = "python-cmd2";
-    repo = "cmd2";
-    rev = version;
-    sha256 = "0nw2b7n7zg51bc3glxw0l9fn91mwjnjshklhmxhyvjbsg7khf64z";
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1wpw4f9zix30hfncm0hwxjjdx78zq26x3r8s9nvsq9vnxf41xb49";
   };
 
   LC_ALL="en_US.UTF-8";
@@ -31,14 +29,16 @@ buildPythonPackage rec {
     py.test -k 'not test_path_completion_user_expansion'
   '';
   doCheck = !stdenv.isDarwin;
+  disabled = !isPy3k;
 
   propagatedBuildInputs = [
+    colorama
     pyperclip
     six
     pyparsing
+    wcwidth
   ]
   ++ stdenv.lib.optional (pythonOlder "3.5") contextlib2
-  ++ stdenv.lib.optional (pythonOlder "3.0") subprocess32
   ;
 
   meta = with stdenv.lib; {

pkgs/development/python-modules/cmd2/old.nix

@@ -0,0 +1,49 @@
+{ stdenv, fetchPypi, buildPythonPackage, pythonOlder
+, pyperclip, six, pyparsing, vim
+, contextlib2 ? null, subprocess32 ? null
+, pytest, mock, which, fetchFromGitHub, glibcLocales
+}:
+buildPythonPackage rec {
+  pname = "cmd2";
+  version = "0.8.0";
+
+  src = fetchFromGitHub {
+    owner = "python-cmd2";
+    repo = "cmd2";
+    rev = version;
+    sha256 = "0nw2b7n7zg51bc3glxw0l9fn91mwjnjshklhmxhyvjbsg7khf64z";
+  };
+
+  LC_ALL="en_US.UTF-8";
+
+  postPatch = stdenv.lib.optional stdenv.isDarwin ''
+    # Fake the impure dependencies pbpaste and pbcopy
+    mkdir bin
+    echo '#/bin/sh' > bin/pbpaste
+    echo '#/bin/sh' > bin/pbcopy
+    chmod +x bin/{pbcopy,pbpaste}
+    export PATH=$(realpath bin):$PATH
+  '';
+
+  checkInputs= [ pytest mock which vim glibcLocales ];
+  checkPhase = ''
+    # test_path_completion_user_expansion might be fixed in the next release
+    py.test -k 'not test_path_completion_user_expansion'
+  '';
+  doCheck = !stdenv.isDarwin;
+
+  propagatedBuildInputs = [
+    pyperclip
+    six
+    pyparsing
+  ]
+  ++ stdenv.lib.optional (pythonOlder "3.5") contextlib2
+  ++ stdenv.lib.optional (pythonOlder "3.0") subprocess32
+  ;
+
+  meta = with stdenv.lib; {
+    description = "Enhancements for standard library's cmd module";
+    homepage = https://github.com/python-cmd2/cmd2;
+    maintainers = with maintainers; [ teto ];
+  };
+}

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

@@ -46,6 +46,11 @@ buildPythonPackage rec {
     export CVXOPT_FFTW_INC_DIR=${fftw.dev}/include
   '';
 
+  # https://github.com/cvxopt/cvxopt/issues/122
+  # This is fixed on staging (by #43234, status 2018-07-15), but until that
+  # lands we should disable the tests. Otherwise the 99% of use cases that
+  # should be unaffected by that failure are affected.
+  doCheck = false;
   checkPhase = ''
     ${python.interpreter} -m unittest discover -s tests
   '';

pkgs/development/python-modules/cypari2/default.nix

@@ -7,16 +7,15 @@
 , gmp
 , cython
 , cysignals
-, six
 }:
 
 buildPythonPackage rec {
   pname = "cypari2";
-  version = "1.1.4"; # remove six dependency on upgrade to >1.1.4
+  version = "1.2.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0n0mp8qmvvzmfaawg39d3mkyzf65q2zkz7bnqyk4sfjbz4xwc6mb";
+    sha256 = "0v2kikwf0advq8j76nwzhlacwj1yys9cvajm4fqgmasjdsnf1q4k";
   };
 
   # This differs slightly from the default python installPhase in that it pip-installs
@@ -39,7 +38,6 @@ buildPythonPackage rec {
   propagatedBuildInputs = [
     cysignals
     cython
-    six # after 1.1.4: will not be needed
   ];
 
   checkPhase = ''

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

@@ -1,5 +1,6 @@
-{ lib, buildPythonPackage, fetchPypi,
-  celery, django, psycopg2
+{ lib, buildPythonPackage, fetchPypi
+, glibcLocales
+, celery, django, psycopg2
 }:
 
 buildPythonPackage rec {
@@ -7,7 +8,7 @@ buildPythonPackage rec {
   version = "1.1.0";
 
   meta = {
-    description = "Simple, powerfull and nonobstructive django email middleware.";
+    description = "Simple, powerfull and nonobstructive django email middleware";
     homepage = https://github.com/bameda/djmail;
     license = lib.licenses.bsd3;
   };
@@ -17,6 +18,10 @@ buildPythonPackage rec {
     sha256 = "87d2a8b4bdf67ae9b312e127ccc873a53116cf297ec786460d782ce82eaa76b5";
   };
 
+  nativeBuildInputs = [ glibcLocales ];
+
+  LC_ALL = "en_US.UTF-8";
+
   propagatedBuildInputs = [ celery django psycopg2 ];
 
   # django.core.exceptions.ImproperlyConfigured: Requested setting DEFAULT_INDEX_TABLESPACE, but settings are not configured. You must either define the environment variable DJANGO_SETTINGS_MODULE or call settings.configure() before accessing settings.

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

@@ -4,17 +4,12 @@
 buildPythonPackage rec {
   pname = "Eve";
   version = "0.8";
-  name  = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
     sha256 = "9f926c715f88c7a92dc2b950ccc09cccd91f72fe0e93cde806b85d25b947df2f";
   };
 
-  patches = [
-    ./setup.patch
-  ];
-
   propagatedBuildInputs = [
     cerberus
     events

pkgs/development/python-modules/eve/setup.patch

@@ -1,21 +0,0 @@
-diff --git i/setup.py w/setup.py
-index 0176467..2b74988 100755
---- i/setup.py
-+++ w/setup.py
-@@ -9,11 +9,11 @@ install_requires = [
-     'cerberus>=0.9.2,<0.10',
-     'events>=0.2.1,<0.3',
-     'simplejson>=3.3.0,<4.0',
--    'werkzeug>=0.9.4,<=0.11.15',
--    'markupsafe>=0.23,<1.0',
--    'jinja2>=2.8,<3.0',
--    'itsdangerous>=0.24,<1.0',
--    'flask>=0.10.1,<=0.12',
-+    'werkzeug>=0.9.4',
-+    'markupsafe>=0.23',
-+    'jinja2>=2.8',
-+    'itsdangerous>=0.24',
-+    'flask>=0.10.1',
-     'pymongo>=3.4',
-     'flask-pymongo>=0.4',
- ]

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

@@ -0,0 +1,17 @@
+{ lib, buildPythonPackage, fetchPypi }:
+
+buildPythonPackage rec {
+  pname = "Events";
+  version = "0.3";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "f4d9c41a5c160ce504278f219fe56f44242ca63794a0ad638b52d1e087ac2a41";
+  };
+
+  meta = with lib; {
+    homepage = http://events.readthedocs.org;
+    description = "Bringing the elegance of C# EventHanlder to Python";
+    license = licenses.bsd3;
+  };
+}

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

@@ -0,0 +1,25 @@
+{ lib, buildPythonPackage, fetchPypi, pytest, case, pytz, amqp }:
+
+buildPythonPackage rec {
+    pname = "kombu";
+    version = "4.2.1";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "86adec6c60f63124e2082ea8481bbe4ebe04fde8ebed32c177c7f0cd2c1c9082";
+  };
+
+  postPatch = ''
+    substituteInPlace requirements/test.txt --replace "pytest-sugar" ""
+  '';
+
+  checkInputs = [ pytest case pytz ];
+
+  propagatedBuildInputs = [ amqp ];
+
+  meta = with lib; {
+    description = "Messaging library for Python";
+    homepage    = https://github.com/celery/kombu;
+    license     = licenses.bsd3;
+  };
+}

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

@@ -14,6 +14,10 @@ buildPythonPackage rec {
     sha256 = "5ca0ad32ee04abe0d4ba02c8d89d501b4e5e0304bdf4d45c2e9875a735b323a0";
   };
 
+  # basically https://github.com/scikit-learn/scikit-learn/pull/10723,
+  # but rebased onto 0.19.1
+  patches = [ ./n_iter-should-be-less-than-max_iter-using-lbgfs.patch ];
+
   buildInputs = [ nose pillow gfortran glibcLocales ];
   propagatedBuildInputs = [ numpy scipy numpy.blas ];
 

pkgs/development/python-modules/scikitlearn/n_iter-should-be-less-than-max_iter-using-lbgfs.patch

@@ -0,0 +1,73 @@
+diff --git a/sklearn/linear_model/huber.py b/sklearn/linear_model/huber.py
+index e17dc1e..665654d 100644
+--- a/sklearn/linear_model/huber.py
++++ b/sklearn/linear_model/huber.py
+@@ -181,7 +181,11 @@ class HuberRegressor(LinearModel, RegressorMixin, BaseEstimator):
+ 
+     n_iter_ : int
+         Number of iterations that fmin_l_bfgs_b has run for.
+-        Not available if SciPy version is 0.9 and below.
++
++        .. versionchanged:: 0.20
++
++            In SciPy <= 1.0.0 the number of lbfgs iterations may exceed
++            ``max_iter``. ``n_iter_`` will now report at most ``max_iter``.
+ 
+     outliers_ : array, shape (n_samples,)
+         A boolean mask which is set to True where the samples are identified
+@@ -272,7 +276,9 @@ class HuberRegressor(LinearModel, RegressorMixin, BaseEstimator):
+             raise ValueError("HuberRegressor convergence failed:"
+                              " l-BFGS-b solver terminated with %s"
+                              % dict_['task'].decode('ascii'))
+-        self.n_iter_ = dict_.get('nit', None)
++        # In scipy <= 1.0.0, nit may exceed maxiter.
++        # See https://github.com/scipy/scipy/issues/7854.
++        self.n_iter_ = min(dict_.get('nit', None), self.max_iter)
+         self.scale_ = parameters[-1]
+         if self.fit_intercept:
+             self.intercept_ = parameters[-2]
+diff --git a/sklearn/linear_model/logistic.py b/sklearn/linear_model/logistic.py
+index 8646c9a..c72a7d9 100644
+--- a/sklearn/linear_model/logistic.py
++++ b/sklearn/linear_model/logistic.py
+@@ -718,7 +718,9 @@ def logistic_regression_path(X, y, pos_class=None, Cs=10, fit_intercept=True,
+                 warnings.warn("lbfgs failed to converge. Increase the number "
+                               "of iterations.")
+             try:
+-                n_iter_i = info['nit'] - 1
++                # In scipy <= 1.0.0, nit may exceed maxiter.
++                # See https://github.com/scipy/scipy/issues/7854.
++                n_iter_i = min(info['nit'], max_iter)
+             except:
+                 n_iter_i = info['funcalls'] - 1
+         elif solver == 'newton-cg':
+@@ -1115,6 +1117,11 @@ class LogisticRegression(BaseEstimator, LinearClassifierMixin,
+         it returns only 1 element. For liblinear solver, only the maximum
+         number of iteration across all classes is given.
+ 
++        .. versionchanged:: 0.20
++
++            In SciPy <= 1.0.0 the number of lbfgs iterations may exceed
++            ``max_iter``. ``n_iter_`` will now report at most ``max_iter``.
++
+     See also
+     --------
+     SGDClassifier : incrementally trained logistic regression (when given
+diff --git a/sklearn/linear_model/tests/test_huber.py b/sklearn/linear_model/tests/test_huber.py
+index 08f4fdf..ca1092f 100644
+--- a/sklearn/linear_model/tests/test_huber.py
++++ b/sklearn/linear_model/tests/test_huber.py
+@@ -42,6 +42,13 @@ def test_huber_equals_lr_for_high_epsilon():
+     assert_almost_equal(huber.intercept_, lr.intercept_, 2)
+ 
+ 
++def test_huber_max_iter():
++    X, y = make_regression_with_outliers()
++    huber = HuberRegressor(max_iter=1)
++    huber.fit(X, y)
++    assert huber.n_iter_ == huber.max_iter
++
++
+ def test_huber_gradient():
+     # Test that the gradient calculated by _huber_loss_and_gradient is correct
+     rng = np.random.RandomState(1)

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

@@ -0,0 +1,26 @@
+{ stdenv, fetchurl, buildPythonPackage }:
+
+buildPythonPackage rec {
+    name = "wcwidth-${version}";
+    version = "0.1.7";
+
+    src = fetchurl {
+      url = "mirror://pypi/w/wcwidth/${name}.tar.gz";
+      sha256 = "0pn6dflzm609m4r3i8ik5ni9ijjbb5fa3vg1n7hn6vkd49r77wrx";
+    };
+
+    # Checks fail due to missing tox.ini file:
+    doCheck = false;
+
+    meta = with stdenv.lib; {
+      description = "Measures number of Terminal column cells of wide-character codes";
+      longDescription = ''
+        This API is mainly for Terminal Emulator implementors -- any Python
+        program that attempts to determine the printable width of a string on
+        a Terminal. It is implemented in python (no C library calls) and has
+        no 3rd-party dependencies.
+      '';
+      homepage = https://github.com/jquast/wcwidth;
+      license = licenses.mit;
+    };
+  }