Merge branch 'master' into staging

This apparently fixes some broken src fetches (gnuradio, twisted).

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

@@ -1,21 +1,24 @@
 { lib, buildPythonPackage, fetchFromGitHub, pythonOlder
-, nose, asynctest, mock, pytz, tzlocal, imaplib2, docutils }:
+, nose, asynctest, mock, pytz, tzlocal, imaplib2, docutils, pyopenssl }:
 
 buildPythonPackage rec {
   pname = "aioimaplib";
-  version = "0.7.13";
+  version = "0.7.14";
 
   # PyPI tarball doesn't ship tests
   src = fetchFromGitHub {
     owner = "bamthomas";
     repo = pname;
     rev = version;
-    sha256 = "19yhk4ixfw46d0bvx6a40r23nvia5a83dzn5rzwaq1wdjr186bbn";
+    sha256 = "150v3czh53sqakfqgjyj1w39mdfcxmpnrk2pbmq63jkq7r6njl0l";
   };
 
-  disbaled = pythonOlder "3.4";
+  disabled = pythonOlder "3.4";
 
-  checkInputs = [ nose asynctest mock pytz tzlocal imaplib2 docutils ];
+  checkInputs = [ nose asynctest mock pytz tzlocal imaplib2 docutils pyopenssl ];
+
+  # https://github.com/bamthomas/aioimaplib/issues/35
+  doCheck = false;
 
   meta = with lib; {
     description = "Python asyncio IMAP4rev1 client library";

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

@@ -2,16 +2,13 @@
 
 buildPythonPackage rec {
   pname = "asynctest";
-  version = "0.12.0";
+  version = "0.12.2";
 
   disabled = pythonOlder "3.4";
 
-  # PyPI tarball doesn't ship test/__init__.py
-  src = fetchFromGitHub {
-    owner = "Martiusweb";
-    repo = pname;
-    rev = "v${version}";
-    sha256 = "0rcb3kz2m0iwvgxpx2avfz9cqsd9xbaq93zykr2fki3ikmnp3vyg";
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "77520850ae21620ec31738f4a7b467acaa44de6d3752d8ac7a9f4dcf55d77853";
   };
 
   postPatch = ''

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

@@ -2,9 +2,11 @@
 , fetchPypi
 , buildPythonPackage
 , cython
-, sphinx
+, pariSupport ? true, pari # for interfacing with the PARI/GP signal handler
 }:
 
+assert pariSupport -> pari != null;
+
 buildPythonPackage rec {
   pname = "cysignals";
   version = "1.7.1";
@@ -14,6 +16,8 @@ buildPythonPackage rec {
     sha256 = "15nky8siwlc7s8v23vv4m0mnxa1z6jcs2qfr26m2mkw9j9g2na2j";
   };
 
+  # explicit check:
+  # build/src/cysignals/implementation.c:27:2: error: #error "cysignals must be compiled without _FORTIFY_SOURCE"
   hardeningDisable = [
     "fortify"
   ];
@@ -26,6 +30,10 @@ buildPythonPackage rec {
     export PATH="$out/bin:$PATH"
   '';
 
+  buildInputs = lib.optionals pariSupport [
+    pari
+  ];
+
   propagatedBuildInputs = [
     cython
   ];

pkgs/development/python-modules/django-allauth/default.nix

@@ -1,5 +1,5 @@
 { stdenv, buildPythonPackage, fetchFromGitHub, requests, requests_oauthlib
-, django, python-openid, mock, coverage }:
+, django, python3-openid, mock, coverage }:
 
 buildPythonPackage rec {
   pname = "django-allauth";
@@ -13,7 +13,7 @@ buildPythonPackage rec {
     sha256 = "1c863cmd521j6cwpyd50jxz5y62fdschrhm15jfqihicyr9imjan";
   };
 
-  propagatedBuildInputs = [ requests requests_oauthlib django python-openid ];
+  propagatedBuildInputs = [ requests requests_oauthlib django python3-openid ];
 
   checkInputs = [ coverage mock ];
 

pkgs/development/python-modules/fido2/default.nix

@@ -0,0 +1,23 @@
+{ lib, buildPythonPackage, fetchPypi, six, cryptography }:
+
+buildPythonPackage rec {
+  pname = "fido2";
+  version = "0.3.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0ddbhg4nsabi9w66l8vkr0i5r80jqihlic5yrdl3v1aqahvxph1j";
+  };
+
+  # The pypi package does not include tests
+  # Check https://github.com/Yubico/python-fido2/pull/8
+  doCheck = false;
+
+  propagatedBuildInputs = [ six cryptography ];
+
+  meta = with lib; {
+    description = "Provides library functionality for FIDO 2.0, including communication with a device over USB.";
+    homepage = https://github.com/Yubico/python-fido2;
+    license = licenses.mpl20;
+  };
+}

pkgs/development/python-modules/flask-autoindex/default.nix

@@ -1,7 +1,6 @@
 { stdenv
 , buildPythonPackage
-, fetchpatch
-, fetchPypi
+, fetchFromGitHub
 , flask
 , flask-silk
 , future
@@ -9,11 +8,16 @@
 
 buildPythonPackage rec {
   pname = "Flask-AutoIndex";
-  version = "0.6";
+  version = "2018-06-28";
 
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "19b10mb1nrqfjyafki6wnrbn8mqi30bbyyiyvp5xssc74pciyfqs";
+  # master fixes various issues (binary generation, flask syntax) and has no
+  # major changes
+  # new release requested: https://github.com/sublee/flask-autoindex/issues/38
+  src = fetchFromGitHub {
+    owner = "sublee";
+    repo = "flask-autoindex";
+    rev = "e3d449a89d56bf4c171c7c8d90af028e579782cf";
+    sha256 = "0bwq2nid4h8vrxspggk064vra4wd804cl2ryyx4j2d1dyywmgjgy";
   };
 
   propagatedBuildInputs = [
@@ -22,15 +26,6 @@ buildPythonPackage rec {
     future
   ];
 
-  patches = [
-    # fix generated binary, see https://github.com/sublee/flask-autoindex/pull/32
-    (fetchpatch {
-      name = "fix_binary.patch";
-      url = "https://github.com/sublee/flask-autoindex/pull/32.patch";
-      sha256 = "1v2r0wvi7prhipjq89774svv6aqj0a13mdfj07pdlkpzfbf029dn";
-    })
-  ];
-
   meta = with stdenv.lib; {
     description = "The mod_autoindex for Flask";
     longDescription = ''

pkgs/development/python-modules/flask-silk/default.nix

@@ -1,16 +1,20 @@
 { stdenv
 , buildPythonPackage
-, fetchPypi
+, fetchFromGitHub
 , flask
 }:
 
 buildPythonPackage rec {
   pname = "Flask-Silk";
-  version = "0.2";
+  version = "2018-06-28";
 
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "1gjzighx4f0w39sq9xvzr1kwb4y7yv9qrgzvli1p89gy16piz8l0";
+  # master fixes flask import syntax and has no major changes
+  # new release requested: https://github.com/sublee/flask-silk/pull/6
+  src = fetchFromGitHub {
+    owner = "sublee";
+    repo = "flask-silk";
+    rev = "3a8166550f9a0ec52edae7bf31d9818c4c15c531";
+    sha256 = "0mplziqw52jfspas6vsm210lmxqqzgj0dxm8y0i3gpbyyykwcmh0";
   };
 
   propagatedBuildInputs = [

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

@@ -27,7 +27,7 @@ buildPythonPackage rec {
 
   meta = with lib; {
     description = "A toolkit for working with and comparing the standardized codes for languages, such as ‘en’ for English or ‘es’ for Spanish";
-    homepage =  http://github.com/LuminosoInsight/langcodes;
+    homepage =  https://github.com/LuminosoInsight/langcodes;
     license = licenses.mit;
     maintainers = with maintainers; [ ixxie ];
   };

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

@@ -20,8 +20,8 @@ buildPythonPackage rec {
 
   meta = {
     description = "Pythonic binding for the libxml2 and libxslt libraries";
-    homepage = http://lxml.de;
+    homepage = https://lxml.de;
     license = stdenv.lib.licenses.bsd3;
     maintainers = with stdenv.lib.maintainers; [ sjourdois ];
   };
-}
+}

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

@@ -1,4 +1,5 @@
-{ stdenv, fetchPypi, buildPythonPackage, dateutil, pytzdata, tzlocal }:
+{ lib, fetchPypi, buildPythonPackage, pythonOlder
+, dateutil, pytzdata, typing }:
 
 buildPythonPackage rec {
   pname = "pendulum";
@@ -9,12 +10,12 @@ buildPythonPackage rec {
     sha256 = "544e44d8a92954e5ef4db4fa8b662d3282f2ac7b7c2cbf4227dc193ba78b9e1e";
   };
 
-  propagatedBuildInputs = [ dateutil pytzdata tzlocal ];
+  propagatedBuildInputs = [ dateutil pytzdata ] ++ lib.optional (pythonOlder "3.5") typing;
 
   # No tests
   doCheck = false;
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     description = "Python datetimes made easy";
     homepage = https://github.com/sdispater/pendulum;
     license = licenses.mit;

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

@@ -0,0 +1,24 @@
+{ stdenv, buildPythonPackage, fetchPypi
+, requests, mock }:
+
+buildPythonPackage rec {
+  pname = "PyBrowserID";
+  version = "0.14.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1qvi79kfb8x9kxkm5lw2mp42hm82cpps1xknmsb5ghkwx1lpc8kc";
+  };
+
+  propagatedBuildInputs = [ requests ];
+
+  checkInputs = [ mock ];
+
+  meta = with stdenv.lib; {
+    description = "Python library for the BrowserID Protocol";
+    homepage    = https://github.com/mozilla/PyBrowserID;
+    license     = licenses.mpl20;
+    maintainers = with maintainers; [ worldofpeace ];
+  };
+}
+

pkgs/development/python-modules/pymc3/default.nix

@@ -57,7 +57,7 @@ buildPythonPackage rec {
 
   meta = {
     description = "Bayesian estimation, particularly using Markov chain Monte Carlo (MCMC)";
-    homepage = http://github.com/pymc-devs/pymc3;
+    homepage = https://github.com/pymc-devs/pymc3;
     license = lib.licenses.asl20;
     maintainers = with lib.maintainers; [ ilya-kolpakov ];
   };

pkgs/development/python-modules/pytest-httpbin/default.nix

@@ -28,6 +28,9 @@ buildPythonPackage rec {
     py.test
   '';
 
+  # https://github.com/kevin1024/pytest-httpbin/pull/51
+  doCheck = false;
+
   meta = {
     description = "Easily test your HTTP library against a local copy of httpbin.org";
     homepage = https://github.com/kevin1024/pytest-httpbin;

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

@@ -1,19 +0,0 @@
-{ stdenv, buildPythonPackage, fetchPypi }:
-
-buildPythonPackage rec {
-  pname = "python-openid";
-  version = "2.2.5";
-
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "1vvhxlghjan01snfdc4k7ykd80vkyjgizwgg9bncnin8rqz1ricj";
-  };
-
-  doCheck = false;
-
-  meta = with stdenv.lib; {
-    description = "OpenID support for modern servers and consumers";
-    homepage = https://github.com/openid/python-openid;
-    license = licenses.asl20;
-  };
-}

pkgs/development/python-modules/python3-openid/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, buildPythonPackage, fetchPypi, defusedxml }:
+{ stdenv, isPy3k, buildPythonPackage, fetchPypi, defusedxml }:
 
 buildPythonPackage rec {
   pname = "python3-openid";
@@ -13,9 +13,11 @@ buildPythonPackage rec {
 
   doCheck = false;
 
+  disabled = !isPy3k;
+
   meta = with stdenv.lib; {
     description = "OpenID support for modern servers and consumers";
-    homepage = http://github.com/necaris/python3-openid;
+    homepage = https://github.com/necaris/python3-openid;
     license = licenses.asl20;
   };
 }

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

@@ -0,0 +1,28 @@
+{ lib, buildPythonPackage, fetchPypi, xmltodict, requests
+
+# Test dependencies
+, pytest, pytestcov, coveralls, pylint, flake8, graphviz, mock, sphinx
+, sphinx_rtd_theme
+}:
+
+buildPythonPackage rec {
+  pname = "soco";
+  version = "0.15";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "18bxpbd7l9gns0jpvx09z023kbbz7b6i4f99i8silsb1jv682kg0";
+  };
+
+  propagatedBuildInputs = [ xmltodict requests ];
+  checkInputs = [
+    pytest pytestcov coveralls pylint flake8 graphviz mock sphinx
+    sphinx_rtd_theme
+  ];
+
+  meta = {
+    homepage = http://python-soco.com/;
+    description = "A CLI and library to control Sonos speakers";
+    license = lib.licenses.mit;
+  };
+}

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

@@ -1,6 +1,7 @@
 { lib
 , buildPythonPackage
 , fetchPypi
+, fetchpatch
 , glibcLocales
 , mpmath
 }:
@@ -25,10 +26,26 @@ buildPythonPackage rec {
     export LANG="en_US.UTF-8"
   '';
 
+  patches = [
+    # see https://trac.sagemath.org/ticket/20204 and https://github.com/sympy/sympy/issues/12825
+    # There is also an upstream patch for this, included in the next release (PR #128826).
+    # However that doesn't quite fix the issue yet. Apparently some changes by sage are required.
+    # TODO re-evaluate the change once a new sympy version is released (open a sage trac ticket about
+    # it).
+    (fetchpatch {
+      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/sympy/patches/03_undeffun_sage.patch?id=07d6c37d18811e2b377a9689790a7c5e24da16ba";
+      sha256 = "1mh2va1rlgizgvx8yzqwgvbf5wvswarn511002b361mc8yy0bnhr";
+    })
+    (fetchpatch {
+      url = "https://github.com/sympy/sympy/pull/13276.patch";
+      sha256 = "1rz74b5c74vwh3pj9axxgh610i02l3555vvsvr4a15ya7siw7zxh";
+    })
+  ];
+
   meta = {
     description = "A Python library for symbolic mathematics";
     homepage    = http://www.sympy.org/;
     license     = lib.licenses.bsd3;
     maintainers = with lib.maintainers; [ lovek323 ];
   };
-}
+}

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

@@ -17,6 +17,7 @@ buildPythonPackage rec {
 
   src = fetchPypi {
     inherit pname version;
+    extension = "tar.bz2";
     sha256 = "a4cc164a781859c74de47f17f0e85f4bce8a3321a9d0892c015c8f80c4158ad9";
   };