Merge master into staging-next

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

@@ -0,0 +1,26 @@
+{ stdenv
+, buildPythonPackage
+, fetchPypi
+, nose
+}:
+
+buildPythonPackage rec {
+  version = "1.15.2";
+  pname = "annoy";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1i5bkf8mwd1pyrbhfwncir2r8yq8s9qz5j13vv2qz92n9g57sr3m";
+  };
+
+  checkInputs = [
+    nose
+  ];
+
+  meta = with stdenv.lib; {
+    description = "Approximate Nearest Neighbors in C++/Python optimized for memory usage and loading/saving to disk";
+    homepage = https://github.com/spotify/annoy;
+    license = licenses.asl20;
+    maintainers = with maintainers; [ timokau ];
+  };
+}

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

@@ -1,16 +1,16 @@
 { stdenv, buildPythonPackage
-, fetchPypi, isPy3k, linuxPackages, gcc5
+, fetchPypi, isPy3k, linuxPackages
 , fastrlock, numpy, six, wheel, pytest, mock
 , cudatoolkit, cudnn, nccl
 }:
 
 buildPythonPackage rec {
   pname = "cupy";
-  version = "5.2.0";
+  version = "5.4.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "664acff0e1094f0135acca8899318d300258b704e049b1ef0c59154912da53b2";
+    sha256 = "1qms1kmzr543hz30jmcmx20cf9xbgzl97a9k44xizsk785dwakbn";
   };
 
   checkInputs = [
@@ -18,10 +18,6 @@ buildPythonPackage rec {
     mock
   ];
 
-  nativeBuildInputs = [
-    gcc5
-  ];
-
   propagatedBuildInputs = [
     cudatoolkit
     cudnn

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

@@ -1,6 +1,7 @@
 { lib
 , buildPythonPackage
 , fetchPypi
+, pythonOlder
 , pytest
 , numpy
 , nbconvert
@@ -8,21 +9,22 @@
 , mock
 , jinja2
 , branca
-, six
 , requests
 }:
 
 buildPythonPackage rec {
   pname = "folium";
-  version = "0.8.3";
+  version = "0.9.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "b7a1e907caac6ddaf0614555f58ba9af2ed65356ccc77f6ba6fc3df202d8f146";
+    sha256 = "66901483808839ed895a685ca7bc4731379f4a627d73a83b77f0df1847b14892";
   };
 
+  disabled = pythonOlder "3.5";
+
   checkInputs = [ pytest nbconvert pandas mock ];
-  propagatedBuildInputs = [ jinja2 branca six requests numpy ];
+  propagatedBuildInputs = [ jinja2 branca requests numpy ];
 
   # No tests in archive
   doCheck = false;

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

@@ -5,13 +5,13 @@
 
 buildPythonPackage rec {
   pname = "hetzner";
-  version = "0.8.1";
+  version = "0.8.2";
 
   src = fetchFromGitHub {
     repo = "hetzner";
     owner = "aszlig";
     rev = "v${version}";
-    sha256 = "1xd1klvjskv0pg8ginih597jkk491a55b8dq80dsm61m5sbsx3vq";
+    sha256 = "152fklxff08s71v0b78yp5ajwpqyszm3sd7j0qsrwa2x9ik4968h";
   };
 
   meta = with stdenv.lib; {
@@ -20,5 +20,4 @@ buildPythonPackage rec {
     license = licenses.bsd3;
     maintainers = with maintainers; [ aszlig ];
   };
-
 }

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

@@ -7,11 +7,11 @@
 
 buildPythonPackage rec {
   pname = "isbnlib";
-  version = "3.9.6";
+  version = "3.9.8";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "d4ae098cb31d6c678a6eac074a24f8ba4adfe7df65db13b0b2ab7355f28d6e3b";
+    sha256 = "ca27dc15763759d038a22f4e05d849acc121ffcb8ffe008768f09a0d844f7172";
   };
 
   checkInputs = [

pkgs/development/python-modules/mpi4py/default.nix

@@ -13,6 +13,12 @@ buildPythonPackage rec {
     inherit mpi;
   };
 
+  patches = [ ( fetchpatch {
+    # Upstream patch to ensure compatibility with openmpi-4.0.1
+    url = "https://github.com/mpi4py/mpi4py/commit/42f5e35a6a90454516c11131549a08cd766edbb0.patch";
+    sha256 = "1dm0i3amwj1cddzz1m9ssd7qp655c8rv1wzjs9ww3kzd90fm4w72";
+  })];
+
   postPatch = ''
     substituteInPlace test/test_spawn.py --replace \
                       "unittest.skipMPI('openmpi(<3.0.0)')" \

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

@@ -2,13 +2,13 @@
 
 buildPythonPackage rec {
   pname = "pyhomematic";
-  version = "0.1.58";
+  version = "0.1.59";
 
   disabled = !isPy3k;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "b390400169a4d57b3ddc3bf2123d71f2c9ef9042a50906e13253aa67311f5183";
+    sha256 = "4406d9bf49d570ef0ba80be9cf8eb4bd75c08a2909369ebd90b8e94ff07f116e";
   };
 
   # PyPI tarball does not include tests/ directory

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

@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "python-axolotl";
-  version = "0.2.2";
+  version = "0.2.3";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1had4dq4n26c3hp62rbmhvs1dj3j3z2jhcbddnbsmqmiky8dqs39";
+    sha256 = "1bwdp24fmriffwx91aigs9k162albb51iskp23nc939z893q23py";
   };
 
   propagatedBuildInputs = [ cryptography python-axolotl-curve25519 protobuf ];

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

@@ -17,7 +17,7 @@ buildPythonPackage rec {
 
   meta = with lib; {
     description = "Library to implement a well-behaved Unix daemon process";
-    homepage = https://alioth.debian.org/projects/python-daemon/;
+    homepage = "https://pagure.io/python-daemon/";
     license = [ licenses.gpl3Plus licenses.asl20 ];
   };
 }

pkgs/development/python-modules/rl-coach/default.nix

@@ -0,0 +1,98 @@
+{ stdenv
+, lib
+, buildPythonPackage
+, pythonOlder
+, fetchPypi
+, tensorflow
+, annoy
+, pillow
+, matplotlib
+, numpy
+, pandas
+, pygame
+, pyopengl
+, scipy
+, scikitimage
+, gym
+, bokeh
+, kubernetes
+, redis
+, minio
+, pytest
+, psutil
+}:
+
+buildPythonPackage rec {
+  version = "0.12.0";
+  pname = "rl-coach";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0kfm699rsy63726hpz3fyppl7zbl0fzf0vk2kkfgg718mcjxmdnh";
+  };
+
+  propagatedBuildInputs = [
+    tensorflow
+    annoy
+    pillow
+    matplotlib
+    numpy
+    pandas
+    pygame
+    pyopengl
+    scipy
+    scikitimage
+    gym
+    bokeh
+    kubernetes
+    redis
+    minio
+    psutil
+  ];
+
+  checkInputs = [
+    pytest
+  ];
+
+  # run only some tests that do not need any optional dependencies
+  # available tests: https://github.com/NervanaSystems/coach/tree/master/rl_coach/tests
+  testsToRun = [
+    # test only the tensorflow backend (not mxnet)
+    "architectures/tensorflow_components"
+    "agents"
+    "exploration_policies"
+    "filters"
+    "memories"
+    "utils"
+  ];
+  checkPhase = let
+    fullTestPaths = map (testfile: "rl_coach/tests/${testfile}") testsToRun;
+    escapedPaths = map lib.escapeShellArg fullTestPaths;
+    pytestArgs = builtins.concatStringsSep " " escapedPaths;
+  in
+  ''
+    pytest ${pytestArgs}
+  '';
+
+  postPatch = ''
+    # pinned to 8.0.1 for unknown reason, at least basic functionallity seems to work without it
+    # https://github.com/NervanaSystems/coach/pull/149#issuecomment-495915804
+    sed -i '/kubernetes/d' requirements.txt
+
+    # this is just an "intel-optimized" version of tensorflow, e.g. an implementation detail
+    sed -i 's/intel-tensorflow/tensorflow/g' setup.py
+
+    # backports of python3 features not needed
+    # https://github.com/NervanaSystems/coach/issues/324
+    sed -i '/futures/d' requirements.txt
+  '';
+
+  disabled = pythonOlder "3.5"; # minimum required version
+
+  meta = with stdenv.lib; {
+    description = "Enables easy experimentation with state of the art Reinforcement Learning algorithms";
+    homepage = "https://nervanasystems.github.io/coach/";
+    license = licenses.asl20;
+    maintainers = with maintainers; [ timokau ];
+  };
+}

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

@@ -1,24 +1,13 @@
 { lib
-, python
+, buildPythonPackage
+, fetchPypi
+, pytest
+, boto3
+, six
+, pyyaml
+, mock
 }:
 
-let
-  py = python.override {
-    packageOverrides = self: super: {
-      pyyaml = super.pyyaml.overridePythonAttrs (oldAttrs: rec {
-        version = "3.12";
-        src = oldAttrs.src.override {
-          inherit version;
-          sha256 = "592766c6303207a20efc445587778322d7f73b161bd994f227adaa341ba212ab";
-        };
-      });
-    };
-  };
-
-in
-
-with py.pkgs;
-
 buildPythonPackage rec {
   pname = "serverlessrepo";
   version = "0.1.8";
@@ -40,6 +29,10 @@ buildPythonPackage rec {
     pytest tests/unit
   '';
 
+  postPatch = ''
+    substituteInPlace setup.py --replace "pyyaml~=3.12" "pyyaml~=5.1"
+  '';
+
   meta = with lib; {
     homepage = https://github.com/awslabs/aws-serverlessrepo-python;
     description = "Helpers for working with the AWS Serverless Application Repository";

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

@@ -4,12 +4,12 @@
 }:
 
 buildPythonPackage rec {
-  pname = "python-setproctitle";
-  version = "1.1.9";
+  pname = "setproctitle";
+  version = "1.1.10";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1mqadassxcm0m9r1l02m5vr4bbandn48xz8gifvxmb4wiz8i8d0w";
+    sha256 = "6283b7a58477dd8478fbb9e76defb37968ee4ba47b05ec1c053cb39638bd7398";
   };
 
   meta = with stdenv.lib; {

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

@@ -31,7 +31,8 @@ buildPythonPackage rec {
 
   # Disable test_tcp_async because fails on sandbox build
   checkPhase = ''
-    pytest --deselect=streamz/tests/test_sources.py::test_tcp_async
+    pytest --deselect=streamz/tests/test_sources.py::test_tcp_async \
+      --deselect=streamz/tests/test_sources.py::test_tcp
   '';
 
   meta = with lib; {

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

@@ -23,7 +23,7 @@
 
 buildPythonPackage rec {
   pname = "weasyprint";
-  version = "45";
+  version = "47";
   disabled = !isPy3k;
 
   # ignore failing pytest
@@ -55,7 +55,7 @@ buildPythonPackage rec {
   src = fetchPypi {
     inherit version;
     pname = "WeasyPrint";
-    sha256 = "04bf2p2x619g4q4scg8v6v57c24vwn7qckvz81rckj8clzifyr82";
+    sha256 = "0hd1zwrkfnj7g0jaaf6jvarlj6l5imar6ar78zxdgv17a3s3k3dg";
   };
 
   meta = with stdenv.lib; {

pkgs/development/python-modules/xhtml2pdf/default.nix

@@ -0,0 +1,28 @@
+{ stdenv
+, buildPythonPackage
+, fetchPypi
+, pillow
+, html5lib
+, pypdf2
+, reportlab
+, six
+}:
+
+buildPythonPackage rec {
+  pname = "xhtml2pdf";
+  version = "0.2.3";
+
+  propagatedBuildInputs = [pillow html5lib pypdf2 reportlab six];
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "10kg8cmn7zgql2lb6cfmqj94sa0jkraksv3lc4kvpn58sxw7x8w6";
+  };
+
+  meta = with stdenv.lib; {
+    description = "A PDF generator using HTML and CSS";
+    homepage = https://github.com/xhtml2pdf/xhtml2pdf;
+    license = licenses.asl20;
+  };
+
+}