Merge branch 'master' into staging

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

@@ -1,74 +1,55 @@
-{ lib
-, buildPythonPackage
+{ buildPythonPackage
 , fetchPypi
-, isPyPy
-, mock
-, pytest
-, flask
-, jinja2
-, markupsafe
-, werkzeug
-, itsdangerous
-, dateutil
-, requests
-, six
-, pygments
-, pystache
-, markdown
-, pyyaml
-, pyzmq
-, tornado
-, colorama
-, isPy3k
 , futures
-, websocket_client
+, isPy3k
+, isPyPy
+, jinja2
+, lib
+, mock
 , numpy
-, pandas
-, greenlet
-, python
-, bkcharts
+, nodejs
 , pillow
+, pytest
+, python
+, python-dateutil
+, pyyaml
 , selenium
+, six
+, substituteAll
+, tornado
 }:
 
 buildPythonPackage rec {
   pname = "bokeh";
-  version = "1.0.4";
+  version = "1.3.4";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "ceeb6a75afc1b2de00c2b8b6da121dec3fb77031326897b80d4375a70e96aebf";
+    sha256 = "0m27j29jpi977y95k272xc24qkl5bkniy046cil116hrbgnppng2";
   };
 
-  disabled = isPyPy;
+  patches = [
+    (substituteAll {
+      src = ./hardcode-nodejs-npmjs-paths.patch;
+      node_bin = "${nodejs}/bin/node";
+      npm_bin = "${nodejs}/bin/npm";
+    })
+  ];
 
-  # Some test that uses tornado fails
-#   doCheck = false;
+  disabled = isPyPy;
 
   checkInputs = [ mock pytest pillow selenium ];
 
   propagatedBuildInputs = [
     pillow
-    flask
     jinja2
-    markupsafe
-    werkzeug
-    itsdangerous
-    dateutil
-    requests
+    python-dateutil
     six
-    pygments
-    pystache
-    markdown
     pyyaml
-    pyzmq
     tornado
-    colorama
-    bkcharts
+    numpy
   ]
-  ++ lib.optionals ( !isPy3k ) [ futures ]
-  ++ lib.optionals ( !isPy3k && !isPyPy ) [ websocket_client ]
-  ++ lib.optionals ( !isPyPy ) [ numpy pandas greenlet ];
+  ++ lib.optionals ( !isPy3k ) [ futures ];
 
   checkPhase = ''
     ${python.interpreter} -m unittest discover -s bokeh/tests

pkgs/development/python-modules/bokeh/hardcode-nodejs-npmjs-paths.patch

@@ -0,0 +1,15 @@
+diff --git a/bokeh/util/compiler.py b/bokeh/util/compiler.py
+index a752aad7d..8af05ff63 100644
+--- a/bokeh/util/compiler.py
++++ b/bokeh/util/compiler.py
+@@ -442,8 +442,8 @@ def _detect_nodejs():
+     raise RuntimeError('node.js v%s or higher is needed to allow compilation of custom models ' % version +
+                        '("conda install nodejs" or follow https://nodejs.org/en/download/)')
+ 
+-_nodejs = None
+-_npmjs = None
++_nodejs = "@node_bin@"
++_npmjs = "@npm_bin@"
+ 
+ def _nodejs_path():
+     global _nodejs

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

@@ -2,12 +2,12 @@
 , itsdangerous, click, werkzeug, jinja2, pytest }:
 
 buildPythonPackage rec {
-  version = "1.0.3";
+  version = "1.0.4";
   pname = "Flask";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "ad7c6d841e64296b962296c2c2dabc6543752985727af86a975072dea984b6f3";
+    sha256 = "ed1330220a321138de53ec7c534c3d90cf2f7af938c7880fc3da13aa46bf870f";
   };
 
   checkInputs = [ pytest ];

pkgs/development/python-modules/fx2/default.nix

@@ -0,0 +1,45 @@
+{ lib
+, buildPythonPackage
+, python
+, fetchFromGitHub
+, sdcc
+, libusb1
+, crcmod
+}:
+
+buildPythonPackage {
+  pname = "fx2";
+  version = "unstable-2019-08-27";
+
+  src = fetchFromGitHub {
+    owner = "whitequark";
+    repo = "libfx2";
+    rev = "dd1e42c7b46ff410dbb18beab46111bb5491400c";
+    sha256 = "0xvlmx6ym0ylrvnlqzf18d475wa0mfci7wkdbv30gl3hgdhsppjz";
+  };
+
+  nativeBuildInputs = [ sdcc ];
+
+  propagatedBuildInputs = [ libusb1 crcmod ];
+
+  preBuild = ''
+    cd software
+    ${python.pythonForBuild.interpreter} setup.py build_ext
+  '';
+
+  preInstall = ''
+    mkdir -p $out/share/libfx2
+    cp -R ../firmware/library/{.stamp,lib,include,fx2{rules,conf}.mk} \
+      $out/share/libfx2
+  '';
+
+  # installCheckPhase tries to run build_ext again and there are no tests
+  doCheck = false;
+
+  meta = with lib; {
+    description = "Chip support package for Cypress EZ-USB FX2 series microcontrollers";
+    homepage = https://github.com/whitequark/libfx2;
+    license = licenses.bsd0;
+    maintainers = with maintainers; [ emily ];
+  };
+}

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

@@ -0,0 +1,66 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, sdcc
+, nmigen
+, fx2
+, libusb1
+, aiohttp
+, pyvcd
+, bitarray
+, crcmod
+, yosys
+, icestorm
+, nextpnr
+}:
+
+buildPythonPackage rec {
+  pname = "glasgow";
+  version = "unstable-2019-08-31";
+  realVersion = lib.substring 0 7 src.rev;
+
+  src = fetchFromGitHub {
+    owner = "GlasgowEmbedded";
+    repo = "Glasgow";
+    rev = "21641a13c6a0daaf8618aff3c5bfffcb26ef6cca";
+    sha256 = "1dpm1jmm4fg8xf17s6h9g5sc09gq8b6xq955sv2x11nrbqf98l4v";
+  };
+
+  nativeBuildInputs = [ sdcc ];
+
+  propagatedBuildInputs = [
+    nmigen
+    fx2
+    libusb1
+    aiohttp
+    pyvcd
+    bitarray
+    crcmod
+  ];
+
+  postPatch = ''
+    substituteInPlace software/setup.py \
+      --replace 'versioneer.get_version()' '"${realVersion}"'
+  '';
+
+  preBuild = ''
+    make -C firmware LIBFX2=${fx2}/share/libfx2
+    cp firmware/glasgow.ihex software/glasgow
+    cd software
+  '';
+
+  # a couple failing tests and also installCheck tries to build_ext again
+  doInstallCheck = false;
+  doCheck = false;
+
+  checkPhase = ''
+    python -m unittest discover
+  '';
+
+  meta = with lib; {
+    description = "Software for Glasgow, a digital interface multitool";
+    homepage = https://github.com/GlasgowEmbedded/Glasgow;
+    license = licenses.bsd0;
+    maintainers = with maintainers; [ emily ];
+  };
+}

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

@@ -4,28 +4,31 @@
 , appdirs
 , dask
 , holoviews
+, hvplot
 , jinja2
 , msgpack-numpy
 , msgpack-python
 , numpy
 , pandas
+, panel
 , python-snappy
 , requests
 , ruamel_yaml
 , six
 , tornado
 , pytest
-, isPy27
+, pythonOlder
 }:
 
 buildPythonPackage rec {
   pname = "intake";
-  version = "0.4.4";
-  disabled = isPy27;
+  version = "0.5.3";
+
+  disabled = pythonOlder "3.6";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "3fc1b7c2949c9b4200ecbbfdff17da126981a1d8d95ccb7b7bcca3e3dd849d5e";
+    sha256 = "1mbjr4xl4i523bg8k08s5986v2289fznd8cr3j3czn5adi8519j7";
   };
 
   checkInputs = [ pytest ];
@@ -33,11 +36,13 @@ buildPythonPackage rec {
     appdirs
     dask
     holoviews
+    hvplot
     jinja2
     msgpack-numpy
     msgpack-python
     numpy
     pandas
+    panel
     python-snappy
     requests
     ruamel_yaml
@@ -45,10 +50,15 @@ buildPythonPackage rec {
     tornado
   ];
 
+  postPatch = ''
+    # Is in setup_requires but not used in setup.py...
+    substituteInPlace setup.py --replace "'pytest-runner'" ""
+  '';
+
+  # test_discover requires driver_with_entrypoints-0.1.dist-info, which is not included in tarball
+  # test_filtered_compressed_cache requires calvert_uk_filter.tar.gz, which is not included in tarball
   checkPhase = ''
-    # test_filtered_compressed_cache requires calvert_uk_filter.tar.gz, which is not included in tarball
-    # test_which assumes python for executable name
-    PATH=$out/bin:$PATH HOME=$(mktemp -d) pytest -k "not test_filtered_compressed_cache and not test_which"
+    PATH=$out/bin:$PATH HOME=$(mktemp -d) pytest -k "not test_discover and not test_filtered_compressed_cache"
   '';
 
   meta = with lib; {

pkgs/development/python-modules/nmigen-boards/default.nix

@@ -0,0 +1,32 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, nmigen
+}:
+
+buildPythonPackage rec {
+  pname = "nmigen-boards";
+  version = "unstable-2019-08-30";
+  realVersion = lib.substring 0 7 src.rev;
+
+  src = fetchFromGitHub {
+    owner = "m-labs";
+    repo = "nmigen-boards";
+    rev = "3b80b3a3749ae8f123ff258a25e81bd21412aed4";
+    sha256 = "01qynxip8bq23jfjc5wjd97vxfvhld2zb8sxphwf0zixrmmyaspi";
+  };
+
+  propagatedBuildInputs = [ nmigen ];
+
+  postPatch = ''
+    substituteInPlace setup.py \
+      --replace 'versioneer.get_version()' '"${realVersion}"'
+  '';
+
+  meta = with lib; {
+    description = "Board and connector definitions for nMigen";
+    homepage = https://github.com/m-labs/nmigen-boards;
+    license = licenses.bsd0;
+    maintainers = with maintainers; [ emily ];
+  };
+}

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

@@ -0,0 +1,65 @@
+{ lib
+, buildPythonPackage
+, pythonOlder
+, fetchFromGitHub
+, pyvcd
+, bitarray
+, jinja2
+
+# nmigen.{test,build} call out to these
+, yosys
+, symbiyosys
+, nextpnr ? null
+, icestorm ? null
+, trellis ? null
+
+# for tests
+, yices
+}:
+
+buildPythonPackage rec {
+  pname = "nmigen";
+  version = "unstable-2019-08-31";
+  realVersion = lib.substring 0 7 src.rev;
+
+  src = fetchFromGitHub {
+    owner = "m-labs";
+    repo = "nmigen";
+    rev = "2e206220462c67aa6ae97f7515a2191440fd61b3";
+    sha256 = "0y3w6vd493jqm9b8ppgwzs02v1al8w1n5gylljlsw70ci7fyk4qa";
+  };
+
+  disabled = pythonOlder "3.6";
+
+  propagatedBuildInputs = [ pyvcd bitarray jinja2 ];
+
+  checkInputs = [ yosys yices ];
+
+  postPatch = let
+    tool = pkg: name:
+      if pkg == null then {} else { "${name}" = "${pkg}/bin/${name}"; };
+
+    # Only FOSS toolchain supported out of the box, sorry!
+    toolchainOverrides =
+      tool yosys "yosys" //
+      tool symbiyosys "sby" //
+      tool nextpnr "nextpnr-ice40" //
+      tool nextpnr "nextpnr-ecp5" //
+      tool icestorm "icepack" //
+      tool trellis "ecppack";
+  in ''
+    substituteInPlace setup.py \
+      --replace 'versioneer.get_version()' '"${realVersion}"'
+
+    substituteInPlace nmigen/_toolchain.py \
+      --replace 'overrides = {}' \
+                'overrides = ${builtins.toJSON toolchainOverrides}'
+  '';
+
+  meta = with lib; {
+    description = "A refreshed Python toolbox for building complex digital hardware";
+    homepage = https://github.com/m-labs/nmigen;
+    license = licenses.bsd0;
+    maintainers = with maintainers; [ emily ];
+  };
+}

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

@@ -11,18 +11,13 @@
 
 buildPythonPackage rec {
   pname = "panel";
-  version = "0.4.0";
+  version = "0.6.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "21fc6729909dba4ba8c9a84b7fadd293322cc2594d15ac73b0f66a5ceffd1f98";
+    sha256 = "04w8jjlf7yz3k84xnacahczc9mmddqyp756rj3n8hclks9c1ww40";
   };
 
-  postPatch = ''
-    substituteInPlace setup.py \
-      --replace "testpath<0.4" "testpath"
-  '';
-
   propagatedBuildInputs = [
     bokeh
     param

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

@@ -7,11 +7,11 @@
 
 buildPythonPackage rec {
   pname = "param";
-  version = "1.8.2";
+  version = "1.9.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "49927979d4f6c994bcd8f6f7f2b34e3a0a7f0d62404dca6bcae5acde0192bb01";
+    sha256 = "1dbnviszdq3d2k3dfwpimb0adf27yzwm4iyv42rk8xvd8c6p9gdi";
   };
 
   checkInputs = [ flake8 nose ];

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

@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "phonenumbers";
-  version = "8.10.16";
+  version = "8.10.17";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1cfkyz991nbqsak3mdwybaxvzqbdcqivxnl84n8p4dyi5lk45v4b";
+    sha256 = "023rcv3qishd5n33gj22dzgq51kzpk41ckcmim96s1xvdbd2sxg9";
   };
 
   meta = {

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

@@ -22,12 +22,12 @@
 
 buildPythonPackage rec {
   pname = "pikepdf";
-  version = "1.1.0";
+  version = "1.6.2";
   disabled = ! isPy3k;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "14b36r6h3088z2sxp2pqvm171js53hz53mwm1g52iadignjnp0my";
+    sha256 = "1x1b55znr0j4fib69l2h0xq0qmbf2nbxwbwd4f7y8r4sqi20239z";
   };
 
   buildInputs = [
@@ -55,8 +55,11 @@ buildPythonPackage rec {
   propagatedBuildInputs = [ defusedxml lxml ];
 
   postPatch = ''
-    substituteInPlace requirements/test.txt \
-       --replace "pytest >= 3.6.0, < 4.1.0" "pytest >= 4.2.1, < 5"
+    sed -i \
+      -e 's/^pytest .*/pytest/g' \
+      -e 's/^attrs .*/attrs/g' \
+      -e 's/^hypothesis .*/hypothesis/g' \
+      requirements/test.txt
   '';
 
   preBuild = ''
@@ -70,4 +73,3 @@ buildPythonPackage rec {
     maintainers = [ maintainers.kiwi ];
   };
 }
-

pkgs/development/python-modules/pybind11/default.nix

@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "pybind11";
-  version = "2.2.4";
+  version = "2.3.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1kz1z2cg3q901q9spkdhksmcfiskaghzmbb9ivr5mva856yvnak4";
+    sha256 = "0923ngd2cvck3lhl7584y08n36pm6zqihfm1s69sbdc11xg936hr";
   };
 
   patches = [

pkgs/development/python-modules/pytest-random-order/default.nix

@@ -0,0 +1,27 @@
+{ stdenv
+, buildPythonPackage
+, fetchPypi
+, pythonOlder
+, pytest
+}:
+
+buildPythonPackage rec {
+  version = "1.0.4";
+  pname = "pytest-random-order";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "6b2159342a4c8c10855bc4fc6d65ee890fc614cb2b4ff688979b008a82a0ff52";
+  };
+
+  disabled = pythonOlder "3.5";
+
+  propagatedBuildInputs = [ pytest ];
+
+  meta = with stdenv.lib; {
+    homepage = "https://github.com/jbasko/pytest-random-order";
+    description = "Randomise the order of tests with some control over the randomness";
+    license = licenses.mit;
+    maintainers = [ maintainers.prusnak ];
+  };
+}

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

@@ -58,8 +58,23 @@ let
   variant = if cudaSupport then "-gpu" else "";
   pname = "tensorflow${variant}";
 
-  # TODO: remove after there's support for setupPyDistFlags
-  setuppy = ../../../development/interpreters/python/run_setup.py;
+  pythonEnv = python.withPackages (_:
+    [ # python deps needed during wheel build time
+      numpy
+      keras-preprocessing
+      protobuf
+      wrapt
+      gast
+      astor
+      absl-py
+      termcolor
+      keras-applications
+      setuptools
+      wheel
+  ] ++ lib.optionals (!isPy3k)
+  [ future
+    mock
+  ]);
 
   bazel-build = buildBazelPackage {
     name = "${pname}-${version}";
@@ -96,27 +111,15 @@ let
     # https://gitweb.gentoo.org/repo/gentoo.git/tree/sci-libs/tensorflow
 
     nativeBuildInputs = [
-      swig which cython
+      swig which pythonEnv
     ];
 
     buildInputs = [
-      python
       jemalloc
       openmpi
       glibcLocales
       git
 
-      # python deps needed during wheel build time
-      numpy
-      keras-preprocessing
-      protobuf
-      wrapt
-      gast
-      astor
-      absl-py
-      termcolor
-      keras-applications
-
       # libs taken from system through the TF_SYS_LIBS mechanism
       # grpc
       sqlite
@@ -133,20 +136,12 @@ let
       giflib
       re2
       pkgs.lmdb
-
-      # for building the wheel
-      setuptools
-      wheel
-    ] ++ lib.optionals (!isPy3k) [
-      future
-      mock
     ] ++ lib.optionals cudaSupport [
       cudatoolkit
       cudnn
       nvidia_x11
     ];
 
-
     # arbitrarily set to the current latest bazel version, overly careful
     TF_IGNORE_MAX_BAZEL_VERSION = true;
 
@@ -194,8 +189,8 @@ let
 
     INCLUDEDIR = "${includes_joined}/include";
 
-    PYTHON_BIN_PATH = python.interpreter;
- 
+    PYTHON_BIN_PATH = pythonEnv.interpreter;
+
     TF_NEED_GCP = true;
     TF_NEED_HDFS = true;
     TF_ENABLE_XLA = tfFeature xlaSupport;
@@ -237,6 +232,9 @@ let
       export PYTHON_LIB_PATH="$NIX_BUILD_TOP/site-packages"
       export CC_OPT_FLAGS="${lib.concatStringsSep " " opt_flags}"
       mkdir -p "$PYTHON_LIB_PATH"
+
+      # To avoid mixing Python 2 and Python 3
+      unset PYTHONPATH
     '';
 
     configurePhase = ''
@@ -313,13 +311,7 @@ in buildPythonPackage {
     rm $out/bin/tensorboard
   '';
 
-  # TODO: remove after there's support for setupPyDistFlags
-  buildPhase = ''
-    runHook preBuild
-    cp ${setuppy} nix_run_setup
-    ${python.interpreter} nix_run_setup --project_name ${pname} bdist_wheel
-    runHook postBuild
-  '';
+  setupPyGlobalFlags = [ "--project_name ${pname}" ];
 
   # tensorflow/tools/pip_package/setup.py
   propagatedBuildInputs = [

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

@@ -26,9 +26,6 @@ buildPythonPackage rec {
 
   propagatedBuildInputs = [ typing-extensions protobuf hidapi ecdsa mnemonic requests pyblake2 click construct libusb1 rlp shamir-mnemonic ];
 
-  # build requires UTF-8 locale
-  LANG = "en_US.UTF-8";
-
   checkInputs = [
     pytest
   ];
@@ -36,7 +33,7 @@ buildPythonPackage rec {
   # disable test_tx_api.py as it requires being online
   checkPhase = ''
     runHook preCheck
-    ${python.interpreter} -m pytest --pyarg trezorlib.tests.unit_tests --ignore trezorlib/tests/unit_tests/test_tx_api.py
+    ${python.interpreter} -m pytest --pyargs trezorlib.tests.unit_tests --ignore trezorlib/tests/unit_tests/test_tx_api.py
     runHook postCheck
   '';
 

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

@@ -1,23 +1,33 @@
 { lib
+, stdenv
 , buildPythonPackage
 , fetchPypi
 , pyopenssl
 , libuv
 , psutil
 , isPy27
+, CoreServices
+, ApplicationServices
 }:
 
 buildPythonPackage rec {
   pname = "uvloop";
-  version = "0.12.2";
+  version = "0.13.0";
   disabled = isPy27;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "c48692bf4587ce281d641087658eca275a5ad3b63c78297bbded96570ae9ce8f";
+    sha256 = "0blcnrd5vky2k1m1p1skx4516dr1jx76yyb0c6fi82si6mqd0b4l";
   };
 
-  buildInputs = [ libuv ];
+  buildInputs = [
+    libuv
+  ] ++ lib.optionals stdenv.isDarwin [ CoreServices ApplicationServices ];
+
+  postPatch = ''
+    # Removing code linting tests, which we don't care about
+    rm tests/test_sourcecode.py
+  '';
 
   checkInputs = [ pyopenssl psutil ];