Merge master into staging-next

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

@@ -47,13 +47,13 @@ let
 
 in buildPythonPackage rec {
   pname = "Theano";
-  version = "1.0.4";
+  version = "1.0.5";
 
   disabled = isPyPy || pythonOlder "2.6" || (isPy3k && pythonOlder "3.3");
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "35c9bbef56b61ffa299265a42a4e8f8cb5a07b2997dabaef0f8830b397086913";
+    sha256 = "129f43ww2a6badfdr6b88kzjzz2b0wk0dwkvwb55z6dsagfkk53f";
   };
 
   postPatch = ''

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

@@ -7,11 +7,11 @@
 }:
 buildPythonPackage rec {
   pname = "argcomplete";
-  version = "1.11.1";
+  version = "1.12.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0h1przxffrhqvi46k40pzjsvdrq4zc3sl1pc96kkigqppq0vdrss";
+    sha256 = "0p19rkvh28klkkd1c6y78h6vb9b9cnlyr7qrshkxghfjkz85xgig";
   };
 
   doCheck = false; # meant to be ran with interactive interpreter

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

@@ -0,0 +1,26 @@
+{ lib, buildPythonPackage, fetchFromGitHub, pytestCheckHook, poetry, pytest-asyncio, }:
+
+buildPythonPackage rec {
+  pname = "backoff";
+  version = "1.10.0";
+
+  src = fetchFromGitHub {
+    owner = "litl";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "1jj0l6pjx747d2yyvnzd3qbm4qr73sq6cc56dhvd8wqfbp5279x0";
+  };
+
+  format = "pyproject";
+
+  nativeBuildInputs = [ poetry ];
+
+  checkInputs = [ pytestCheckHook pytest-asyncio ];
+
+  meta = with lib; {
+    description = "Function decoration for backoff and retry";
+    homepage = "https://github.com/litl/backoff";
+    license = licenses.mit;
+    maintainers = with maintainers; [ chkno ];
+  };
+}

pkgs/development/python-modules/chart-studio/default.nix

@@ -10,14 +10,14 @@
 
 buildPythonPackage rec {
   pname = "chart-studio";
-  version = "1.0.0";
+  version = "1.1.0";
 
   # chart-studio was split from plotly
   src = fetchFromGitHub {
     owner = "plotly";
     repo = "plotly.py";
     rev = "${pname}-v${version}";
-    sha256 = "14lyqbjdffnlnkzlfnn60k7yxjd99vx3hfcs23apsiyinzipjlbf";
+    sha256 = "1q3j3ih5k0jhr8ilwffkfxp1nifpnjnx7862bzhxfg4d386hfg4i";
   };
 
   sourceRoot = "source/packages/python/chart-studio";

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

@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "colorlog";
-  version = "4.1.0";
+  version = "4.2.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1lpk8zmfv8vz090h5d0hzb4n39wgasxdd3x3bpn3v1x1n9dfzaih";
+    sha256 = "066i7904vc7814gqnlprksf0ikz2dmviw93r2mr7sf53qci5irbm";
   };
 
   checkInputs = [ pytest ];

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

@@ -10,18 +10,13 @@
 
 buildPythonPackage rec {
   pname = "ftfy";
+  version = "5.8";
 
-  version = "5.7";
-  # ftfy v5 only supports python3. Since at the moment the only
-  # packages that use ftfy are spacy and textacy which both support
-  # python 2 and 3, they have pinned ftfy to the v4 branch.
-  # I propose to stick to v4 until another package requires v5.
-  # At that point we can make a ftfy_v4 package.
   disabled = !isPy3k;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1j143kfpnskksfzs0pnr37kwph6m7c71p8gdldv26x2b7arwiyb7";
+    sha256 = "081p5z20dirrf1i3nshylc31qd5mbxibjc7gzj8x4isbiizpdisi";
   };
 
   propagatedBuildInputs = [

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

@@ -9,14 +9,14 @@
 
 buildPythonPackage rec {
   pname = "jc";
-  version = "1.11.8";
+  version = "1.13.1";
   disabled = isPy27;
 
   src = fetchFromGitHub {
     owner = "kellyjonbrazil";
     repo = "jc";
     rev = "v${version}";
-    sha256 = "0rkckbgm04ql4r48wjgljfiqvsz36n99yqcpcyna8lvlm8h4nmwa";
+    sha256 = "1q5s81izfvxlifa0kzj2qih03d4d0gf7jxkilrcv40rsag5jfb16";
   };
 
   propagatedBuildInputs = [ ruamel_yaml xmltodict pygments ];

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

@@ -8,11 +8,11 @@
 
 buildPythonPackage rec {
   pname = "mecab-python3";
-  version = "0.996.5";
+  version = "1.0.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "e7f09caf136903ce908b8b001ffc178d6caa129c1550d47d8f7f733a213749a8";
+    sha256 = "0246wxfk8v1js75nv8jl15cwpf4rvv4xndi4gbzjrrqbsgj2fvfm";
   };
 
   nativeBuildInputs = [

pkgs/development/python-modules/openapi-spec-validator/default.nix

@@ -4,11 +4,11 @@
 
 buildPythonPackage rec {
   pname = "openapi-spec-validator";
-  version = "0.2.8";
+  version = "0.2.9";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1kav0jlgdpgwx4am09ja7cr8s1g8h8a7j8mcfy1cfjr8fficg2g4";
+    sha256 = "1jw59mmd3n1d5zihdqz2a3j2axxf3m34lqp1190fw8rlndlilf3r";
   };
 
   propagatedBuildInputs = [ jsonschema pyyaml six setuptools ]

pkgs/development/python-modules/opt-einsum/default.nix

@@ -1,12 +1,12 @@
 { buildPythonPackage, fetchPypi, lib, numpy, pytest_4 }:
 
 buildPythonPackage rec {
-  version = "3.2.1";
+  version = "3.3.0";
   pname = "opt_einsum";
 
   src = fetchPypi {
     inherit version pname;
-    sha256 = "165r7rsl5j94kna4q3vsaq71z23lgxd9b20dgb6abrlas6c6mdw3";
+    sha256 = "0jb5lia0q742d1713jk33vlj41y61sf52j6pgk7pvhxvfxglgxjr";
   };
 
   propagatedBuildInputs = [ numpy ];

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

@@ -0,0 +1,29 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, pillow
+, numpy
+}:
+let
+  version = "0.2.1";
+in
+buildPythonPackage {
+  pname = "pyphotonfile";
+  inherit version;
+  propagatedBuildInputs = [ pillow numpy ];
+  
+  src = fetchFromGitHub {
+    owner = "fookatchu";
+    repo = "pyphotonfile";
+    rev = "v${version}";
+    sha256 = "1hh1fcn7q3kyk2413pjs18xnxvzrchrisbpj2cd59jrdp0qzgv2s";
+  };
+
+  meta = with lib; {
+    maintainers = [ maintainers.cab404 ];
+    license = licenses.gpl3Plus;
+    description = "Library for reading and writing files for the Anycubic Photon 3D-Printer";
+    homepage = "https://github.com/fookatchu/pyphotonfile";
+  };
+
+}

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

@@ -104,7 +104,7 @@ let
     "LD_LIBRARY_PATH=${cudaStub}\${LD_LIBRARY_PATH:+:}$LD_LIBRARY_PATH ";
 
 in buildPythonPackage rec {
-  version = "1.5.1";
+  version = "1.6.0";
   pname = "pytorch";
   disabled = !isPy3k;
 
@@ -119,7 +119,7 @@ in buildPythonPackage rec {
     repo   = "pytorch";
     rev    = "v${version}";
     fetchSubmodules = true;
-    sha256 = "1xjbn4hi96m7xslv3p2jc6qcsng0fx3w1m6isqfah81piljf8wng";
+    sha256 = "14hhjsi6fnpaw9m1a3bhvdinsks6fhss6bbcrfk6jgns64abqdaz";
   };
 
   patches = lib.optionals stdenv.isAarch64 [
@@ -129,7 +129,7 @@ in buildPythonPackage rec {
     # Fix from:
     # https://github.com/pytorch/pytorch/pull/40584
     #
-    # This patch can be removed with the next major version (1.6.0).
+    # This patch can be removed with the next major version (1.7.0).
     (fetchpatch {
       name = "qnnpack-neon-fix.patch";
       url = "https://github.com/pytorch/pytorch/commit/7676682584d0caf9243bce74ea0a88711ec4a807.diff";

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

@@ -11,29 +11,29 @@
 
 buildPythonPackage rec {
   pname = "qds_sdk";
-  version = "1.12.0";
+  version = "1.15.2";
 
   # pypi does not contain tests, using github sources instead
   src = fetchFromGitHub {
     owner = "qubole";
     repo = "qds-sdk-py";
     rev = "V${version}";
-    sha256 = "18xhvlcfki8llv7fw2r5yfk20zds3gr78b4klwm9mkvhlhwds9rx";
+    sha256 = "0xxg9s0y6fz7vb1kab4q93q7ryi71z8x6q9qspm6s506yr3mc67l";
   };
 
-  propagatedBuildInputs = [ 
+  propagatedBuildInputs = [
     boto
     inflection
     requests
-    six 
-    urllib3 
+    six
+    urllib3
   ];
 
   checkInputs = [ pytest mock ];
   checkPhase = ''
     py.test --disable-pytest-warnings tests
   '';
- 
+
   meta = with lib; {
     description = "A Python module that provides the tools you need to authenticate with, and use the Qubole Data Service API";
     homepage = "https://github.com/qubole/qds-sdk-py";

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

@@ -1,28 +1,22 @@
-{ stdenv, buildPythonPackage, fetchPypi, fetchpatch, python, coverage, lsof, glibcLocales }:
+{ lib, buildPythonPackage, fetchPypi, fetchpatch, python, coverage, lsof, glibcLocales, coreutils }:
 
 buildPythonPackage rec {
   pname = "sh";
-  version = "1.12.14";
+  version = "1.13.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1z2hx357xp3v4cv44xmqp7lli3frndqpyfmpbxf7n76h7s1zaaxm";
+    sha256 = "18w6wawmpzfh52s0jimwn59a7rfa7blrmg7bhwnq8siwbqhd58wp";
   };
 
   patches = [
-    # Disable tests that fail on Darwin
-    # Some of the failures are due to Nix using GNU coreutils
+    # Disable tests that fail on Darwin sandbox
     ./disable-broken-tests-darwin.patch
-    # Fix tests for Python 3.7. See: https://github.com/amoffat/sh/pull/468
-    (fetchpatch {
-      url = "https://github.com/amoffat/sh/commit/b6202f75706473f02084d819e0765056afa43664.patch";
-      sha256 = "1kzxyxcc88zhgn2kmfg9yrbs4n405b2jq7qykb453l52hy10vi94";
-      excludes = [ ".travis.yml" ];
-    })
   ];
 
   postPatch = ''
     sed -i 's#/usr/bin/env python#${python.interpreter}#' test.py
+    sed -i 's#/bin/sleep#${coreutils.outPath}/bin/sleep#' test.py
   '';
 
   checkInputs = [ coverage lsof glibcLocales ];
@@ -33,9 +27,10 @@ buildPythonPackage rec {
     HOME=$(mktemp -d)
   '';
 
-  meta = {
+  meta = with lib; {
     description = "Python subprocess interface";
     homepage = "https://pypi.python.org/pypi/sh/";
-    license = stdenv.lib.licenses.mit;
+    license = licenses.mit;
+    maintainers = with maintainers; [ siriobalmelli ];
   };
 }

pkgs/development/python-modules/sh/disable-broken-tests-darwin.patch

@@ -1,49 +1,49 @@
-From 264f2f6a04d25156bba43524a6b172d2e99c53f4 Mon Sep 17 00:00:00 2001
-From: Ben Wolsieffer <benwolsieffer@gmail.com>
-Date: Fri, 21 Dec 2018 17:39:45 -0500
-Subject: [PATCH] Disable tests that fail on OSX.
+From c596ad546fe7460b57a62799837757eb641309c1 Mon Sep 17 00:00:00 2001
+From: Sirio Balmelli <sirio@b-ad.ch>
+Date: Mon, 20 Jul 2020 19:51:20 +0200
+Subject: [PATCH] Disable tests that fail on Darwin (macOS) or with sandboxing
 
-Some of the failures are due to the use of GNU ls.
+Signed-off-by: Sirio Balmelli <sirio@b-ad.ch>
 ---
  test.py | 4 ++++
  1 file changed, 4 insertions(+)
 
 diff --git a/test.py b/test.py
-index 68ef40c..2f53360 100644
+index f8029c0..ba1d141 100644
 --- a/test.py
 +++ b/test.py
-@@ -352,6 +352,7 @@ exit(3)
+@@ -404,6 +404,7 @@ exit(3)
          self.assertEqual(sed(_in="one test three", e="s/test/two/").strip(),
-                 "one two three")
+                          "one two three")
  
-+    @not_osx
++    @not_macos
      def test_ok_code(self):
          from sh import ls, ErrorReturnCode_1, ErrorReturnCode_2
  
-@@ -498,6 +499,7 @@ while True:
-         self.assertEqual(out, match)
+@@ -1004,6 +1005,7 @@ print(sys.argv[1])
+         now = time.time()
+         self.assertGreater(now - start, sleep_time)
  
- 
-+    @not_osx
-     def test_environment(self):
-         """ tests that environments variables that we pass into sh commands
-         exist in the environment, and on the sh module """
-@@ -861,6 +863,7 @@ print(sys.argv[1])
-         self.assertTrue(now - start > sleep_time)
- 
- 
-+    @not_osx
++    @not_macos
      def test_background_exception(self):
          from sh import ls, ErrorReturnCode_1, ErrorReturnCode_2
-         p = ls("/ofawjeofj", _bg=True) # should not raise
-@@ -2036,6 +2039,7 @@ else:
-         self.assertEqual(p, "test")
+         p = ls("/ofawjeofj", _bg=True, _bg_exc=False)  # should not raise
+@@ -1801,6 +1803,7 @@ exit(49)
+         p = python(py.name, _ok_code=49, _bg=True)
+         self.assertEqual(49, p.exit_code)
  
++    @not_macos
+     def test_cwd(self):
+         from sh import pwd
+         from os.path import realpath
+@@ -2899,6 +2902,7 @@ print("hi")
+         python(py.name, _in=stdin)
  
-+    @not_osx
-     def test_signal_exception(self):
-         from sh import SignalException_15
+     @requires_utf8
++    @skipUnless(False, "Does not work in sandbox")
+     def test_unicode_path(self):
+         from sh import Command
  
 -- 
-2.20.0
+2.27.0
 

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

@@ -14,6 +14,7 @@
 buildPythonPackage rec {
   pname = "statsmodels";
   version = "0.11.1";
+  disabled = isPy27;
 
   src = fetchPypi {
     inherit pname version;

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

@@ -0,0 +1,53 @@
+{ lib, fetchPypi, buildPythonPackage, isPy3k
+, colorama, configobj, packaging, pyyaml, pykwalify
+}:
+
+buildPythonPackage rec {
+  version = "0.7.2";
+  pname = "west";
+
+  disabled = !isPy3k;
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "11dbzlcg48fymddqjrrs60pr7y33qjjv0y5zrfjc56gkc190gmz6";
+  };
+
+  propagatedBuildInputs = [
+    colorama
+    configobj
+    packaging
+    pyyaml
+    pykwalify
+  ];
+
+  # pypi package does not include tests (and for good reason):
+  # tests run under 'tox' and have west try to git clone repos (not sandboxable)
+  doCheck = false;
+  pythonImportsCheck = [
+    "west"
+  ];
+
+  meta = with lib; {
+    homepage = "https://github.com/zephyrproject-rtos/west";
+    description = "Zephyr RTOS meta tool";
+    longDescription = ''
+      West lets you manage multiple Git repositories under a single directory using a single file,
+      called the west manifest file, or manifest for short.
+
+      The manifest file is named west.yml.
+      You use west init to set up this directory,
+      then west update to fetch and/or update the repositories
+      named in the manifest.
+
+      By default, west uses upstream Zephyr’s manifest file
+      (https://github.com/zephyrproject-rtos/zephyr/blob/master/west.yml),
+      but west doesn’t care if the manifest repository is a Zephyr tree or not.
+
+      For more details, see Multiple Repository Management in the west documentation
+      (https://docs.zephyrproject.org/latest/guides/west/repo-tool.html).
+    '';
+    license = licenses.asl20;
+    maintainers = with maintainers; [ siriobalmelli ];
+  };
+}