Merge staging-next into staging

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

@@ -1,4 +1,4 @@
-{ stdenv, lib, buildPythonPackage, fetchFromGitHub, isPy3k
+{ stdenv, lib, buildPythonPackage, python, fetchFromGitHub, isPy3k
 , notmuch, urwid, urwidtrees, twisted, python_magic, configobj, mock, file, gpgme
 , service-identity
 , gnupg ? null, sphinx, awk ? null, procps ? null, future ? null
@@ -39,7 +39,9 @@ buildPythonPackage rec {
 
   checkInputs =  [ awk future mock gnupg procps ];
 
-  postInstall = lib.optionalString withManpage ''
+  postInstall = let
+    completionPython = python.withPackages (ps: [ ps.configobj ]);
+  in lib.optionalString withManpage ''
     mkdir -p $out/man
     cp -r docs/build/man $out/man
   ''
@@ -47,6 +49,8 @@ buildPythonPackage rec {
     mkdir -p $out/share/{applications,alot}
     cp -r extra/themes $out/share/alot
 
+    substituteInPlace extra/completion/alot-completion.zsh \
+      --replace "python3" "${completionPython.interpreter}"
     install -D extra/completion/alot-completion.zsh $out/share/zsh/site-functions/_alot
 
     sed "s,/usr/bin,$out/bin,g" extra/alot.desktop > $out/share/applications/alot.desktop

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

@@ -1,18 +1,20 @@
 { stdenv, buildPythonPackage, fetchPypi, pythonOlder
 , attrs, click, toml, appdirs, aiohttp, aiohttp-cors
-, glibcLocales, pytest }:
+, glibcLocales, typed-ast, pathspec, regex
+, setuptools_scm, pytest }:
 
 buildPythonPackage rec {
   pname = "black";
-  version = "19.3b0";
+  version = "19.10b0";
 
   disabled = pythonOlder "3.6";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "073kd5rs02lisp6n3h7yai9lix520xnaa6c7rdmp2sci9pyhz5b8";
+    sha256 = "0f8mr0yzj78q1dx7v6ggbgfir2wv0n5z2shfbbvfdq7910xbgvf2";
   };
 
+  nativeBuildInputs = [ setuptools_scm ];
   checkInputs =  [ pytest glibcLocales ];
 
   # Necessary for the tests to pass on Darwin with sandbox enabled.
@@ -22,12 +24,11 @@ buildPythonPackage rec {
   # Don't know why these tests fails
   checkPhase = ''
     LC_ALL="en_US.UTF-8" pytest \
-      --deselect tests/test_black.py::BlackTestCase::test_expression_diff \
       --deselect tests/test_black.py::BlackTestCase::test_cache_multiple_files \
       --deselect tests/test_black.py::BlackTestCase::test_failed_formatting_does_not_get_cached
   '';
 
-  propagatedBuildInputs = [ attrs appdirs click toml aiohttp aiohttp-cors ];
+  propagatedBuildInputs = [ attrs appdirs click toml aiohttp aiohttp-cors pathspec regex typed-ast ];
 
   meta = with stdenv.lib; {
     description = "The uncompromising Python code formatter";

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

@@ -1,9 +1,9 @@
-{ stdenv, lib, buildPythonPackage, fetchPypi, makeWrapper, isPy3k,
+{ stdenv, lib, buildPythonPackage, fetchPypi, fetchpatch, makeWrapper, isPy3k,
   python, twisted, jinja2, zope_interface, future, sqlalchemy,
   sqlalchemy_migrate, dateutil, txaio, autobahn, pyjwt, pyyaml, treq,
   txrequests, pyjade, boto3, moto, mock, python-lz4, setuptoolsTrial,
-  isort, pylint, flake8, buildbot-worker, buildbot-pkg, parameterized,
-  git, glibcLocales }:
+  isort, pylint, flake8, buildbot-worker, buildbot-pkg, buildbot-plugins,
+  parameterized, git, openssh, glibcLocales }:
 
 let
   withPlugins = plugins: buildPythonPackage {
@@ -29,7 +29,7 @@ let
 
     src = fetchPypi {
       inherit pname version;
-      sha256 = "e4e6b2861c4f29ed5d84ca497ca7053ae1cc9b9a5387389c457ff9f7e651bf19";
+      sha256 = "06dza7kggybz8nf3i1skkadwrq9s0nkpqjfahifysaag3j3b5rp4";
     };
 
     propagatedBuildInputs = [
@@ -63,8 +63,10 @@ let
       flake8
       buildbot-worker
       buildbot-pkg
+      buildbot-plugins.www
       parameterized
       git
+      openssh
       glibcLocales
     ];
 
@@ -72,6 +74,13 @@ let
       # This patch disables the test that tries to read /etc/os-release which
       # is not accessible in sandboxed builds.
       ./skip_test_linux_distro.patch
+      # Work around https://github.com/glyph/automat/issues/117
+      (fetchpatch {
+        url = "https://git.archlinux.org/svntogit/community.git/plain/trunk/buildbot-automat-117.diff?h=packages/buildbot&id=7904292340f98578adfe783a09e9eb4c5b1d4632";
+        name = "buildbot-automat-117.diff";
+        stripLen = 1;
+        sha256 = "0rng6f8nvghkihajz9m925rdp9q3c395bj4wc7r2s1minv613hba";
+      })
     ];
 
     postPatch = ''
@@ -93,7 +102,7 @@ let
     };
 
     meta = with lib; {
-      homepage = http://buildbot.net/;
+      homepage = "https://buildbot.net/";
       description = "Buildbot is an open-source continuous integration framework for automating software build, test, and release processes";
       maintainers = with maintainers; [ nand0p ryansydnor lopsided98 ];
       license = licenses.gpl2;

pkgs/development/python-modules/buildbot/pkg.nix

@@ -1,4 +1,4 @@
-{ lib, buildPythonPackage, fetchPypi }:
+{ lib, buildPythonPackage, fetchPypi, isPy3k }:
 
 buildPythonPackage rec {
   pname = "buildbot-pkg";
@@ -6,7 +6,7 @@ buildPythonPackage rec {
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "7c5b508c8c0d2fef5cdf4001c9f1e848f06fe8d6c30d8dff571a1a1fd251c9d7";
+    sha256 = "1my9a791y6hsazzqs3f3svl6zw28x3qwj0a0vxffybqdij650nvw";
   };
 
   postPatch = ''
@@ -15,8 +15,10 @@ buildPythonPackage rec {
     substituteInPlace buildbot_pkg.py --replace "os.listdir = listdir" ""
   '';
 
+  disabled = !isPy3k;
+
   meta = with lib; {
-    homepage = http://buildbot.net/;
+    homepage = "https://buildbot.net/";
     description = "Buildbot Packaging Helper";
     maintainers = with maintainers; [ nand0p ryansydnor lopsided98 ];
     license = licenses.gpl2;

pkgs/development/python-modules/buildbot/plugins.nix

@@ -1,4 +1,4 @@
-{ lib, buildPythonPackage, fetchPypi, buildbot, buildbot-pkg, mock }:
+{ lib, buildPythonPackage, fetchPypi, buildbot-pkg, mock }:
 
 {
   www = buildPythonPackage rec {
@@ -7,13 +7,23 @@
 
     src = fetchPypi {
       inherit pname version;
-      sha256 = "0l4kyxh62y86cw97101gjs42n1sdw1n18cgh6mm337gzjn42nv3x";
+      sha256 = "0awy96pb9s9g0nrmlrvqf5zi878z6mvj653inf9sm89x601a6lp1";
     };
 
-    buildInputs = [ buildbot buildbot-pkg mock ];
+    # Remove unneccessary circular dependency on buildbot
+    postPatch = ''
+      sed -i setup.py \
+        -e "/import buildbot/d" \
+        -e "s/'buildbot',//"
+    '';
+
+    buildInputs = [ buildbot-pkg mock ];
+
+    # No tests
+    doCheck = false;
 
     meta = with lib; {
-      homepage = http://buildbot.net/;
+      homepage = "https://buildbot.net/";
       description = "Buildbot UI";
       maintainers = with maintainers; [ nand0p ryansydnor lopsided98 ];
       license = licenses.gpl2;
@@ -26,14 +36,16 @@
 
     src = fetchPypi {
       inherit pname version;
-      sha256 = "1s0jl5b9zd7iwxqfb2g145nzf5nx6q44x4y1axkzilkd777162cz";
+      sha256 = "0bp7bbq6rq1kdg3pf8plcpc4amam0pks5dlmyqj6bn29skfa5h1j";
     };
 
     buildInputs = [ buildbot-pkg ];
-    checkInputs = [ buildbot ];
+
+    # No tests
+    doCheck = false;
 
     meta = with lib; {
-      homepage = http://buildbot.net/;
+      homepage = "https://buildbot.net/";
       description = "Buildbot Console View Plugin";
       maintainers = with maintainers; [ nand0p ryansydnor lopsided98 ];
       license = licenses.gpl2;
@@ -46,14 +58,16 @@
 
     src = fetchPypi {
       inherit pname version;
-      sha256 = "0qld1424d4qvf08qz5ibl3pv0qzj0qxrvgra5dr3wagaq3jfh3kz";
+      sha256 = "1mxxkqzh4a6574n2lk2ndi77d9g93hjpkwsqizj911n6ibsn4qw3";
     };
 
     buildInputs = [ buildbot-pkg ];
-    checkInputs = [ buildbot ];
+
+    # No tests
+    doCheck = false;
 
     meta = with lib; {
-      homepage = http://buildbot.net/;
+      homepage = "https://buildbot.net/";
       description = "Buildbot Waterfall View Plugin";
       maintainers = with maintainers; [ nand0p ryansydnor lopsided98 ];
       license = licenses.gpl2;
@@ -66,14 +80,16 @@
 
     src = fetchPypi {
       inherit pname version;
-      sha256 = "1di8w9dzalg3d2k3wff682irbi8dcksysc9n176zncmkbi2pr2ia";
+      sha256 = "1fkrd5crbgqgp8mr8qgfy559f59ys6hrspddzk3fwg5hrsckkjwr";
     };
 
     buildInputs = [ buildbot-pkg ];
-    checkInputs = [ buildbot ];
+
+    # No tests
+    doCheck = false;
 
     meta = with lib; {
-      homepage = http://buildbot.net/;
+      homepage = "https://buildbot.net/";
       description = "Buildbot Grid View Plugin";
       maintainers = with maintainers; [ nand0p lopsided98 ];
       license = licenses.gpl2;
@@ -86,14 +102,16 @@
 
     src = fetchPypi {
       inherit pname version;
-      sha256 = "0gh6ddczlga75n6fh9pkbv39x8p3b6pqviaj287wab27wimd1hxa";
+      sha256 = "0cvbizcc92df08xcs8w6ah51yfilxz7sx9g8bbdrvw6m586ziczb";
     };
 
     buildInputs = [ buildbot-pkg ];
-    checkInputs = [ buildbot ];
+
+    # No tests
+    doCheck = false;
 
     meta = with lib; {
-      homepage = http://buildbot.net/;
+      homepage = "https://buildbot.net/";
       description = "Buildbot WSGI dashboards Plugin";
       maintainers = with maintainers; [ lopsided98 ];
       license = licenses.gpl2;

pkgs/development/python-modules/buildbot/worker.nix

@@ -7,7 +7,7 @@ buildPythonPackage (rec {
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "8330cf314064516648e78d2685b2eaae14fc9481351eb229f1392b38bdc18815";
+    sha256 = "05c8q6ykharry4lv47imh6agq55fxar8a9ldwx46clb480qwyc43";
   };
 
   propagatedBuildInputs = [ twisted future ];
@@ -20,7 +20,7 @@ buildPythonPackage (rec {
   '';
 
   meta = with lib; {
-    homepage = http://buildbot.net/;
+    homepage = "https://buildbot.net/";
     description = "Buildbot Worker Daemon";
     maintainers = with maintainers; [ nand0p ryansydnor lopsided98 ];
     license = licenses.gpl2;

pkgs/development/python-modules/grpcio-tools/default.nix

@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "grpcio-tools";
-  version = "1.24.3";
+  version = "1.25.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "5efc92721a364e049ad3a174d5b20a21009fae9db04b3e5020ed0b534d9c022f";
+    sha256 = "988014c714ca654b3b7ca9f4dabfe487b00e023bfdd9eaf1bb0fed82bf8c4255";
   };
 
   enableParallelBuilding = true;

pkgs/development/python-modules/jsonrpclib-pelix/default.nix

@@ -18,6 +18,6 @@ buildPythonPackage rec {
     description = "JSON RPC client library - Pelix compatible fork";
     homepage = https://pypi.python.org/pypi/jsonrpclib-pelix/;
     license = lib.licenses.asl20;
-    maintainers = with maintainers; [ moredread ];
+    maintainers = with maintainers; [ ];
   };
 }

pkgs/development/python-modules/jupyter_console/5.nix

@@ -11,11 +11,11 @@
 
 buildPythonPackage rec {
   pname = "jupyter_console";
-  version = "6.0.0";
+  version = "5.2.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "308ce876354924fb6c540b41d5d6d08acfc946984bf0c97777c1ddcb42e0b2f5";
+    sha256 = "545dedd3aaaa355148093c5609f0229aeb121b4852995c2accfa64fe3e0e55cd";
   };
 
   checkInputs = [ nose ];

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

@@ -0,0 +1,20 @@
+{ lib, fetchPypi, buildPythonPackage, pbr, six, sympy }:
+
+buildPythonPackage rec {
+  pname = "measurement";
+  version = "2.0.1";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "36ca385ffdccf140a75a7e1d816a4df97a6dd255f16fd2f53dd7ab43632a8835";
+  };
+
+  propagatedBuildInputs = [ pbr six sympy ];
+
+  meta = with lib; {
+    description = "Use and manipulate unit-aware measurement objects in Python";
+    homepage = https://github.com/coddingtonbear/python-measurement;
+    license = licenses.mit;
+    maintainers = with maintainers; [ bhipple ];
+  };
+}

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

@@ -0,0 +1,29 @@
+{ lib, fetchPypi, buildPythonPackage
+, blessed, keyring, keyrings-alt, lxml, measurement, python-dateutil, requests, six
+, mock, nose }:
+
+buildPythonPackage rec {
+  pname = "myfitnesspal";
+  version = "1.13.3";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "4f785341f0499bad8d3400cfcfffd99b7fcf8aac3971390f8ec3dfaed8361b20";
+  };
+
+  # Remove overly restrictive version constraints on keyring and keyrings.alt
+  postPatch = ''
+    sed -i 's/keyring>=.*/keyring/' requirements.txt
+    sed -i 's/keyrings.alt>=.*/keyrings.alt/' requirements.txt
+  '';
+
+  checkInputs = [ mock nose ];
+  propagatedBuildInputs = [ blessed keyring keyrings-alt lxml measurement python-dateutil requests six ];
+
+  meta = with lib; {
+    description = "Access your meal tracking data stored in MyFitnessPal programatically";
+    homepage = https://github.com/coddingtonbear/python-myfitnesspal;
+    license = licenses.mit;
+    maintainers = with maintainers; [ bhipple ];
+  };
+}

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

@@ -1,35 +0,0 @@
-{ stdenv, buildPythonPackage, fetchPypi, isPy3k
-, scipy, numpy, matplotlib, tables, pyaml, urllib3, rpy2, mpi4py }:
-
-buildPythonPackage rec {
-  pname = "NeuroTools";
-  version = "0.3.1";
-  disabled = isPy3k;
-
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "0ly6qa87l3afhksab06vp1iimlbm1kdnsw98mxcnpzz9q07l4nd4";
-  };
-
-  # Tests are not automatically run
-  # Many tests fail (using py.test), and some need R
-  doCheck = false;
-
-  propagatedBuildInputs = [
-    scipy
-    numpy
-    matplotlib
-    tables
-    pyaml
-    urllib3
-    rpy2
-    mpi4py
-  ];
-
-  meta = with stdenv.lib; {
-    description = "Collection of tools to support analysis of neural activity";
-    homepage = https://pypi.python.org/pypi/NeuroTools;
-    license = licenses.gpl2;
-    maintainers = with maintainers; [ nico202 ];
-  };
-}

pkgs/development/python-modules/portend/black-19.10b0.patch

@@ -0,0 +1,13 @@
+diff --git a/test_portend.py b/test_portend.py
+index b2de8c2..3f90276 100644
+--- a/test_portend.py
++++ b/test_portend.py
+@@ -21,7 +21,7 @@ def socket_infos():
+ 
+ 
+ def id_for_info(info):
+-    af, = info[:1]
++    (af,) = info[:1]
+     return str(af)
+ 
+ 

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

@@ -10,6 +10,7 @@ buildPythonPackage rec {
     sha256 = "19dc27bfb3c72471bd30a235a4d5fbefef8a7e31cab367744b5d87a205e7bfd9";
   };
 
+  patches = [ ./black-19.10b0.patch ];
   postPatch = ''
     substituteInPlace pytest.ini --replace "--flake8" ""
   '';

pkgs/development/python-modules/pytest-black/black-version.patch

@@ -0,0 +1,13 @@
+diff --git a/setup.py b/setup.py
+index 5c9ce5f..84b148a 100644
+--- a/setup.py
++++ b/setup.py
+@@ -26,6 +26,6 @@ setup(
+     python_requires=">=2.7",
+     install_requires=[
+         "pytest>=3.5.0",
+-        'black==19.3b0; python_version >= "3.6"',
++        'black; python_version >= "3.6"',
+         "toml",
+     ],
+     use_scm_version=True,

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

@@ -14,6 +14,7 @@ buildPythonPackage rec {
     sha256 = "03gwwy1h3qnfh6vpfhgsa5ag53a9sw1g42sc2s8a2hilwb7yrfvm";
   };
 
+  patches = [ ./black-version.patch ];
   nativeBuildInputs = [ setuptools_scm ];
 
   propagatedBuildInputs = [ black pytest toml ];

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

@@ -5,6 +5,7 @@
 , pillow
 , pymaging_png
 , mock
+, setuptools
 }:
 
 buildPythonPackage rec {
@@ -16,7 +17,7 @@ buildPythonPackage rec {
     sha256 = "505253854f607f2abf4d16092c61d4e9d511a3b4392e60bff957a68592b04369";
   };
 
-  propagatedBuildInputs = [ six pillow pymaging_png ];
+  propagatedBuildInputs = [ six pillow pymaging_png setuptools ];
   checkInputs = [ mock ];
 
   meta = with stdenv.lib; {

pkgs/development/python-modules/spacy/models.json

@@ -76,6 +76,18 @@
   "sha256": "0gxmknd68kajak8jr443799bfd69pp5j0jnmcbnyx5abzyq6wkzx",
   "license": "cc-by-sa-40"
 },
+{
+  "pname": "lt_core_news_sm",
+  "version": "2.2.0",
+  "sha256": "1j63xnp96qavg8c960y83z752mmvp9qx92r458lydrg1ixmffx9r",
+  "license": "cc-by-sa-40"
+},
+{
+  "pname": "nb_core_news_sm",
+  "version": "2.2.0",
+  "sha256": "0s0wf3kxrhdzfkgrbxjc53hzin3w8v06iivazh6bpf6rhbiwzfr0",
+  "license": "mit"
+},
 {
   "pname": "nl_core_news_sm",
   "version": "2.2.1",

pkgs/development/python-modules/spyder-kernels/default.nix

@@ -3,11 +3,11 @@
 
 buildPythonPackage rec {
   pname = "spyder-kernels";
-  version = "1.6.0";
+  version = "0.5.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "e374452af89f507b345431338c6655465b5c15d0b5e49f703be8c30bbe1d1202";
+    sha256 = "01354b7fa180a87212cc005553b31a7300159b108d36828e301d3782291323f7";
   };
 
   propagatedBuildInputs = [

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

@@ -14,6 +14,8 @@ buildPythonPackage rec {
     sha256 = "1z7qw1h3rhca12ycv8xrzw6z2gf81v0j6lfq9kpwh472w4vk75v1";
   };
 
+  nativeBuildInputs = [ pyqtwebengine.wrapQtAppsHook ];
+
   propagatedBuildInputs = [
     jedi pycodestyle psutil pyflakes rope numpy scipy matplotlib pylint keyring
     numpydoc qtconsole qtawesome nbconvert mccabe pyopengl cloudpickle spyder-kernels
@@ -47,6 +49,11 @@ buildPythonPackage rec {
     cp -r $desktopItem/share/applications/ $out/share
   '';
 
+  dontWrapQtApps = true;
+  makeWrapperArgs = [
+    "\${qtWrapperArgs[@]}"
+  ];
+
   meta = with stdenv.lib; {
     description = "Scientific python development environment";
     longDescription = ''

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

@@ -4,12 +4,12 @@
 with stdenv.lib;
 
 buildPythonPackage rec {
-  version = "3.6.0";
+  version = "3.6.1";
   pname = "tables";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0k9xc0b49j311r6yayw7wzjay6ch3jznijhzc4x33yv490hqhd6v";
+    sha256 = "0j8vnxh2m5n0cyk9z3ndcj5n1zj5rdxgc1gb78bqlyn2lyw75aa9";
   };
 
   nativeBuildInputs = [ cython ];

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

@@ -3,11 +3,11 @@
 
 buildPythonPackage rec {
   pname = "todoist-python";
-  version = "8.1.0";
+  version = "8.1.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0f4d402137f02f415f99acaa9d7ab24016687202dec9a191aee4745a9ce67dc6";
+    sha256 = "0khipf8v0gqvspq7m67aqv0ql3rdqyqr8qfhbm1szc1z6mygj8ns";
   };
 
   propagatedBuildInputs = [ requests ];