Merge branch 'staging-next' into staging

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

@@ -0,0 +1,39 @@
+{ lib, fetchFromGitHub, buildPythonPackage, isPy27, numpy, cython, zlib, six
+, python-lzo, nose }:
+
+buildPythonPackage rec {
+  pname = "bx-python";
+  version = "0.8.6";
+  disabled = isPy27;
+
+  src = fetchFromGitHub {
+    owner = "bxlab";
+    repo = "bx-python";
+    rev = "v${version}";
+    sha256 = "1i40vmn8n83vqcpqj843riv9vp16s753jc4wc90p0cmrnhmzcv13";
+  };
+
+  nativeBuildInputs = [ cython ];
+  buildInputs = [ zlib ];
+  propagatedBuildInputs = [ numpy six python-lzo ];
+  checkInputs = [ nose ];
+
+  postInstall = ''
+    cp -r scripts/* $out/bin
+
+    # This is a small hack; the test suit uses the scripts which need to
+    # be patched. Linking the patched scripts in $out back to the
+    # working directory allows the tests to run
+    rm -rf scripts
+    ln -s $out/bin scripts
+  '';
+
+  meta = with lib; {
+    homepage = "https://github.com/bxlab/bx-python";
+    description =
+      "Tools for manipulating biological data, particularly multiple sequence alignments";
+    license = licenses.mit;
+    maintainers = [ maintainers.jbedo ];
+    platforms = [ "x86_64-linux" ];
+  };
+}

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

@@ -0,0 +1,27 @@
+{ stdenv
+, buildPythonPackage
+, fetchPypi
+, pyopenssl
+}:
+
+buildPythonPackage rec {
+  pname = "certipy";
+  version = "0.1.3";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0n980gqpzh0fm58h3i4mi2i10wgj606lscm1r5sk60vbf6vh8mv9";
+  };
+
+  propagatedBuildInputs = [ pyopenssl ];
+  
+  doCheck = false; #no tests were included
+
+  meta = with stdenv.lib; {
+    homepage = https://github.com/LLNL/certipy;
+    description = "wrapper for pyOpenSSL";
+    license = licenses.bsd3;
+    maintainers = with maintainers; [ isgy ];
+  };
+
+}

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

@@ -9,7 +9,7 @@ buildPythonPackage rec {
       sha256 = "01d71vya2x87f3kl9x0s8xp0n7wixn6ksrd054y7idq3n1mjaxzh";
     };
 
-    propagatedBuildInputs = [ aenum ] ++ stdenv.lib.optional (pythonOlder "3.4") [ enum34 ];
+    propagatedBuildInputs = [ aenum ] ++ stdenv.lib.optional (pythonOlder "3.4") enum34;
 
     doCheck = !isPy3k;
     # tests are not yet ported.

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

@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "grpcio-tools";
-  version = "1.25.0";
+  version = "1.26.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "988014c714ca654b3b7ca9f4dabfe487b00e023bfdd9eaf1bb0fed82bf8c4255";
+    sha256 = "5580b86cf49936c9c74f0def44d3582a7a1bb720eba8a14805c3a61efa790c70";
   };
 
   enableParallelBuilding = true;

pkgs/development/python-modules/hass-nabucasa/default.nix

@@ -1,4 +1,4 @@
-{ lib, buildPythonPackage, fetchFromGitHub, acme, aiohttp, snitun, attrs, pytest-aiohttp, warrant, pytest }:
+{ lib, buildPythonPackage, fetchFromGitHub, fetchpatch, acme, aiohttp, snitun, attrs, pytest-aiohttp, warrant, pytest }:
 
 buildPythonPackage rec {
   pname = "hass-nabucasa";
@@ -11,6 +11,12 @@ buildPythonPackage rec {
     sha256 = "182nh5i3hlj0kqkbynk69md0ddq83w02l8lz4m03d8xbjixzi1k1";
   };
 
+  # upstreamed in https://github.com/NabuCasa/hass-nabucasa/pull/119
+  postPatch = ''
+    sed -i 's/"acme.*/"acme>=0.40.0,<2.0"/' setup.py
+    cat setup.py
+  '';
+
   propagatedBuildInputs = [ acme aiohttp snitun attrs warrant ];
 
   checkInputs = [ pytest pytest-aiohttp ];

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

@@ -22,7 +22,7 @@ buildPythonPackage rec {
 
   postUnpack = "sourceRoot=$sourceRoot/hypothesis-python";
 
-  propagatedBuildInputs = [ attrs coverage ] ++ lib.optional (!isPy3k) [ enum34 ];
+  propagatedBuildInputs = [ attrs coverage ] ++ lib.optional (!isPy3k) enum34;
 
   checkInputs = [ pytest pytest_xdist flaky mock pexpect ];
   inherit doCheck;

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

@@ -1,4 +1,5 @@
 { lib
+, stdenv
 , buildPythonPackage
 , fetchPypi
 , fetchpatch
@@ -7,7 +8,7 @@
 , traitlets
 , tornado
 , pythonOlder
-, pytest
+, pytestCheckHook
 , nose
 }:
 
@@ -21,7 +22,6 @@ buildPythonPackage rec {
     sha256 = "04jx6ihj3zpj4c7acqa14gl37mpdnbgmfm4nvv97xkjc1cz920xm";
   };
 
-  checkInputs = [ pytest nose ];
   propagatedBuildInputs = [ ipython jupyter_client traitlets tornado ];
 
   # https://github.com/ipython/ipykernel/pull/377
@@ -32,10 +32,17 @@ buildPythonPackage rec {
     })
   ];
 
-  # For failing tests, see https://github.com/ipython/ipykernel/issues/387
-  checkPhase = ''
-    HOME=$(mktemp -d) pytest ipykernel -k "not (test_sys_path or test_sys_path_profile_dir or test_complete)"
+  checkInputs = [ pytestCheckHook nose ];
+  dontUseSetuptoolsCheck = true;
+  preCheck = ''
+    export HOME=$(mktemp -d)
   '';
+  disabledTests = lib.optionals stdenv.isDarwin [
+    # see https://github.com/NixOS/nixpkgs/issues/76197
+    "test_subprocess_print"
+    "test_subprocess_error"
+    "test_ipython_start_kernel_no_userns"
+  ];
 
   # Some of the tests use localhost networking.
   __darwinAllowLocalNetworking = true;

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

@@ -16,6 +16,8 @@
 , notebook
 , pythonOlder
 , nodePackages
+, oauthlib
+, certipy
 }:
 
 let
@@ -51,12 +53,12 @@ in
 
 buildPythonPackage rec {
   pname = "jupyterhub";
-  version = "0.9.4";
+  version = "1.0.0";
   disabled = pythonOlder "3.5";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "7848bbb299536641a59eb1977ec3c7c95d931bace4a2803d7e9b28b9256714da";
+    sha256 = "0zx6gw9yhgki05j21p6x1x2sf5a2mg2c2mx0ii8rl6q4b98ilm1k";
   };
 
   # Most of this only applies when building from source (e.g. js/css assets are
@@ -107,7 +109,7 @@ buildPythonPackage rec {
 
   propagatedBuildInputs = [
     alembic ipython jinja2 pamela python-oauth2 requests sqlalchemy tornado
-    traitlets prometheus_client async_generator notebook
+    traitlets prometheus_client async_generator notebook certipy oauthlib
   ];
 
   # Disable tests because they take an excessive amount of time to complete.

pkgs/development/python-modules/mautrix-appservice/0001-Remove-coding-annotations.patch

@@ -1,53 +0,0 @@
-From 6750cda26821f703b120ba5c925cc696200570d3 Mon Sep 17 00:00:00 2001
-From: Maximilian Bosch <maximilian@mbosch.me>
-Date: Sat, 26 Oct 2019 10:31:02 +0200
-Subject: [PATCH] Remove coding annotations
-
-Those used to be needed for Python <=3.5. With `pluggy` 0.13.0 this breaks
-tests on newer python3 versions.
----
- mautrix_appservice/appservice.py  | 1 -
- mautrix_appservice/errors.py      | 1 -
- mautrix_appservice/intent_api.py  | 1 -
- mautrix_appservice/state_store.py | 1 -
- 4 files changed, 4 deletions(-)
-
-diff --git a/mautrix_appservice/appservice.py b/mautrix_appservice/appservice.py
-index 3a141b1..47e37fe 100644
---- a/mautrix_appservice/appservice.py
-+++ b/mautrix_appservice/appservice.py
-@@ -1,4 +1,3 @@
--# -*- coding: future_fstrings -*-
- # Partly based on github.com/Cadair/python-appservice-framework (MIT license)
- from contextlib import contextmanager
- from typing import Optional, Callable, Awaitable, Union
-diff --git a/mautrix_appservice/errors.py b/mautrix_appservice/errors.py
-index 90d040f..702f541 100644
---- a/mautrix_appservice/errors.py
-+++ b/mautrix_appservice/errors.py
-@@ -1,4 +1,3 @@
--# -*- coding: future_fstrings -*-
- from typing import Optional
- 
- 
-diff --git a/mautrix_appservice/intent_api.py b/mautrix_appservice/intent_api.py
-index 4021bf8..7236cbb 100644
---- a/mautrix_appservice/intent_api.py
-+++ b/mautrix_appservice/intent_api.py
-@@ -1,4 +1,3 @@
--# -*- coding: future_fstrings -*-
- from urllib.parse import quote as urllib_quote
- from time import time
- from json.decoder import JSONDecodeError
-diff --git a/mautrix_appservice/state_store.py b/mautrix_appservice/state_store.py
-index 47bb970..6ebec2a 100644
---- a/mautrix_appservice/state_store.py
-+++ b/mautrix_appservice/state_store.py
-@@ -1,4 +1,3 @@
--# -*- coding: future_fstrings -*-
- from typing import Optional
- from abc import ABC, abstractmethod
- import json
--- 
-2.23.0
-

pkgs/development/python-modules/mautrix-appservice/default.nix

@@ -1,32 +0,0 @@
-{ lib, buildPythonPackage, fetchPypi, aiohttp, future-fstrings, pythonOlder }:
-
-buildPythonPackage rec {
-  pname = "mautrix-appservice";
-  version = "0.3.11";
-
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "60192920cff75afdd096eea3a43276e33ec15f4f00bd04d2d1dda616c84f22a5";
-  };
-
-  patches = lib.optional (!(pythonOlder "3.6")) [
-    ./0001-Remove-coding-annotations.patch
-  ];
-
-  propagatedBuildInputs = [
-    aiohttp
-    future-fstrings
-  ];
-
-  # No tests available
-  doCheck = false;
-
-  disabled = pythonOlder "3.5";
-
-  meta = with lib; {
-    homepage = https://github.com/tulir/mautrix-appservice-python;
-    description = "A Python 3 asyncio-based Matrix application service framework";
-    license = licenses.mit;
-    maintainers = with maintainers; [ nyanloutre ];
-  };
-}

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

@@ -0,0 +1,43 @@
+{ lib, buildPythonPackage, fetchPypi, aiohttp, future-fstrings, pythonOlder
+, sqlalchemy, ruamel_yaml, CommonMark, lxml, fetchpatch
+}:
+
+buildPythonPackage rec {
+  pname = "mautrix";
+  version = "0.4.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "03m59d683nr547v5xr80wc3j07das2d2sc3i4bf03dpbkfg0h17w";
+  };
+
+  patches = [
+    (fetchpatch {
+      url = "https://github.com/tulir/mautrix-python/commit/ac46f3bb1bea11d22d8a486cc4821604c844da5e.patch";
+      sha256 = "198g63s0iv8g1w22g4g5hb54y41ws82wraglibz33qhrwsfn8axn";
+    })
+  ];
+
+  propagatedBuildInputs = [
+    aiohttp
+    future-fstrings
+
+    # defined in optional-requirements.txt
+    sqlalchemy
+    ruamel_yaml
+    CommonMark
+    lxml
+  ];
+
+  disabled = pythonOlder "3.5";
+
+  # no tests available
+  doCheck = false;
+
+  meta = with lib; {
+    homepage = https://github.com/tulir/mautrix-python;
+    description = "A Python 3 asyncio Matrix framework.";
+    license = licenses.mpl20;
+    maintainers = with maintainers; [ nyanloutre ma27 ];
+  };
+}

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

@@ -79,7 +79,7 @@ buildPythonPackage rec {
     simplejson
     traits
     xvfbwrapper
-  ] ++ stdenv.lib.optional (!isPy3k) [
+  ] ++ stdenv.lib.optionals (!isPy3k) [
     configparser
     futures
     pathlib2 # darwin doesn't receive this transitively, but it is in install_requires

pkgs/development/python-modules/pyside/shiboken.nix

@@ -27,7 +27,7 @@ buildPythonPackage rec {
   # gcc6 patch was also sent upstream: https://github.com/pyside/Shiboken/pull/86
   patches = [ ./gcc6.patch ] ++ (lib.optional (isPy35 || isPy36 || isPy37) ./shiboken_py35.patch);
 
-  cmakeFlags = if isPy3k then "-DUSE_PYTHON3=TRUE" else null;
+  cmakeFlags = lib.optional isPy3k "-DUSE_PYTHON3=TRUE";
 
   meta = {
     description = "Plugin (front-end) for pyside-generatorrunner, that generates bindings for C++ libraries using CPython source code";

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

@@ -19,7 +19,7 @@ buildPythonPackage rec {
     sha256 = "1hslzzinpwc1zqhbpllqh3sllmiyk69pcycl7ahr0rz3micgwczj";
   };
 
-  propagatedBuildInputs = [ pytest py-cpuinfo ] ++ lib.optional (pythonOlder "3.4") [ pathlib statistics ];
+  propagatedBuildInputs = [ pytest py-cpuinfo ] ++ lib.optionals (pythonOlder "3.4") [ pathlib statistics ];
 
   meta = {
     description = "Py.test fixture for benchmarking code";

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

@@ -0,0 +1,18 @@
+{ stdenv, buildPythonPackage, fetchPypi }:
+
+buildPythonPackage rec {
+  version = "0.2.4";
+  pname = "python-lzf";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1l8m6vzwm1m8hn7ldw8j8r2b6r199k8z3q0wnhdyy4p68hahyhni";
+  };
+
+  meta = with stdenv.lib; {
+    description = "liblzf python bindings";
+    homepage = https://github.com/teepark/python-lzf;
+    license = licenses.mit;
+    platforms = platforms.unix;
+  };
+}

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

@@ -0,0 +1,22 @@
+{ lib, fetchPypi, buildPythonPackage, lzo, nose }:
+
+buildPythonPackage rec {
+  pname = "python-lzo";
+  version = "1.12";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0iakqgd51n1cd7r3lpdylm2rgbmd16y74cra9kcapwg84mlf9a4p";
+  };
+
+  buildInputs = [ lzo ];
+  propagatedBuildInputs = [ ];
+  checkInputs = [ nose ];
+
+  meta = with lib; {
+    homepage = "https://github.com/jd-boyd/python-lzo";
+    description = "Python bindings for the LZO data compression library";
+    license = licenses.gpl2;
+    maintainers = [ maintainers.jbedo ];
+  };
+}

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

@@ -40,7 +40,7 @@ buildPythonPackage rec {
     python-dateutil
     six
     more-itertools
-  ] ++ lib.optional (!isPy3k) [
+  ] ++ lib.optionals (!isPy3k) [
     pyOpenSSL
     ndg-httpsclient
     pyasn1

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

@@ -23,7 +23,7 @@ buildPythonPackage rec {
   '';
 
   propagatedBuildInputs = [ numpy ]
-    ++ lib.optional isPy27 [ futures enum34 pathlib ];
+    ++ lib.optionals isPy27 [ futures enum34 pathlib ];
 
   meta = with lib; {
     description = "Read and write image data from and to TIFF files.";