Merge branch 'master' into staging-next

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

@@ -0,0 +1,39 @@
+{ stdenv, buildPythonPackage, fetchFromGitHub, pytest }:
+
+buildPythonPackage rec {
+  pname = "boltons";
+  version = "2019-01-07";
+
+  # No tests in PyPi Tarball
+  src = fetchFromGitHub {
+    owner = "mahmoud";
+    repo = "boltons";
+    rev = "3584ac9399f227a2a11b74153140ee171fd49783";
+    sha256 = "13xngjw249sk4vmr5kqqnia0npw0kpa0gm020a4dqid0cjyvj0rv";
+  };
+
+  checkInputs = [ pytest ];
+  checkPhase = "pytest tests";
+
+  meta = with stdenv.lib; {
+    homepage = https://github.com/mahmoud/boltons;
+    description = "220+ constructs, recipes, and snippets extending (and relying on nothing but) the Python standard library";
+    longDescription = ''
+      Boltons is a set of over 220 BSD-licensed, pure-Python utilities
+      in the same spirit as — and yet conspicuously missing from — the
+      standard library, including:
+
+      - Atomic file saving, bolted on with fileutils
+      - A highly-optimized OrderedMultiDict, in dictutils
+      - Two types of PriorityQueue, in queueutils
+      - Chunked and windowed iteration, in iterutils
+      - Recursive data structure iteration and merging, with iterutils.remap
+      - Exponential backoff functionality, including jitter, through
+      iterutils.backoff
+      - A full-featured TracebackInfo type, for representing stack
+      traces, in tbutils
+    '';
+    license = licenses.bsd3;
+    maintainers = with maintainers; [ twey ];
+  };
+}

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

@@ -11,11 +11,11 @@
 
 buildPythonPackage rec {
   pname = "elpy";
-  version = "1.27.0";
+  version = "1.28.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0fpxxmxjzcam3kharbmvprf4kagspya1rx9piacmxbgcp6w2lc4s";
+    sha256 = "0lx6bf6ajx6wmnns03gva5sh1mmmxahjaqrn735cgwn6j4ikyqfs";
   };
 
   propagatedBuildInputs = [ flake8 autopep8 jedi importmagic ]

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

@@ -0,0 +1,31 @@
+{ stdenv, buildPythonPackage, fetchPypi, boltons, pytest }:
+
+buildPythonPackage rec {
+  pname = "face";
+  version = "0.1.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0zdp5qlrhxf4dypvvd0zr7zxj2svkz9wblp37vgw01wvcy9b1ds7";
+  };
+
+  propagatedBuildInputs = [ boltons ];
+
+  checkInputs = [ pytest ];
+  checkPhase = "pytest face/test";
+
+  # ironically, test_parse doesn't parse, but fixed in git so no point
+  # reporting
+  doCheck = false;
+
+  meta = with stdenv.lib; {
+    homepage = https://github.com/mahmoud/face;
+    description = "A command-line interface parser and framework";
+    longDescription = ''
+      A command-line interface parser and framework, friendly for
+      users, full-featured for developers.
+    '';
+    license = licenses.bsd3;
+    maintainers = with maintainers; [ twey ];
+  };
+}

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

@@ -0,0 +1,38 @@
+{ stdenv
+, buildPythonPackage
+, fetchPypi
+, boltons
+, attrs
+, face
+, pytest
+, pyyaml
+, isPy37
+}:
+
+buildPythonPackage rec {
+  pname = "glom";
+  version = "18.4.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0rfikq27a9wwfkd4k3bk7x4fssw6r7z138g9i3wpzvjc7anlzk24";
+  };
+
+  propagatedBuildInputs = [ boltons attrs face ];
+
+  checkInputs = [ pytest pyyaml ];
+  checkPhase = "pytest glom/test";
+
+  doCheck = !isPy37; # https://github.com/mahmoud/glom/issues/72
+
+  meta = with stdenv.lib; {
+    homepage = https://github.com/mahmoud/glom;
+    description = "Restructuring data, the Python way";
+    longDescription = ''
+      glom helps pull together objects from other objects in a
+      declarative, dynamic, and downright simple way.
+    '';
+    license = licenses.bsd3;
+    maintainers = with maintainers; [ twey ];
+  };
+}

pkgs/development/python-modules/graph-tool/2.x.x.nix

@@ -3,6 +3,8 @@
 , gobject-introspection, pygobject3, gtk3, matplotlib, ncurses
 , buildPythonPackage
 , fetchpatch
+, pythonAtLeast
+, lib
 }:
 
 buildPythonPackage rec {
@@ -29,7 +31,14 @@ buildPythonPackage rec {
       url = "https://git.skewed.de/count0/graph-tool/commit/aa39e4a6b42d43fac30c841d176c75aff92cc01a.patch";
       sha256 = "1578inb4jqwq2fhhwscn5z95nzmaxvmvk30nzs5wirr26iznap4m";
     })
-  ];
+  ] ++ (lib.optionals (pythonAtLeast "3.7") [
+    # # python 3.7 compatibility (`async` is now reserved)
+    (fetchpatch {
+      name = "async-reserved.patch";
+      url = "https://git.skewed.de/count0/graph-tool/commit/0407f41a35b6be7c670927fb5dc578cbd0e88be4.patch";
+      sha256 = "1fklznhmfvbb3ykwzyf8p2hiczby6y7r0xnkkjl2jkxlvr24000q";
+    })
+  ]);
 
   configureFlags = [
     "--with-python-module-path=$(out)/${python.sitePackages}"

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

@@ -1,25 +1,51 @@
-{ stdenv
+{ lib
 , buildPythonPackage
-, fetchPypi
-, pkgs
+, fetchFromGitHub
+, substituteAll
+, graphviz
+, makeFontsConf
+, freefont_ttf
+, mock
+, pytest
+, pytest-mock
+, pytestcov
 }:
 
 buildPythonPackage rec {
   pname = "graphviz";
   version = "0.10.1";
 
-  src = fetchPypi {
-    inherit pname version;
-    extension = "zip";
-    sha256 = "d311be4fddfe832a56986ac5e1d6e8715d7fcb0208560da79d1bb0f72abef41f";
+  # patch does not apply to PyPI tarball due to different line endings
+  src = fetchFromGitHub {
+    owner = "xflr6";
+    repo = "graphviz";
+    rev = version;
+    sha256 = "1vqk4xy45c72la56j24z9jmjp5a0aa2k32fybnlbkzqjvvbl72d8";
   };
 
-  propagatedBuildInputs = [ pkgs.graphviz ];
+  patches = [
+    (substituteAll {
+      src = ./hardcode-graphviz-path.patch;
+      inherit graphviz;
+    })
+  ];
 
-  meta = with stdenv.lib; {
+  # Fontconfig error: Cannot load default config file 
+  FONTCONFIG_FILE = makeFontsConf { 
+    fontDirectories = [ freefont_ttf ]; 
+  };
+
+  checkInputs = [ mock pytest pytest-mock pytestcov ];
+
+  checkPhase = ''
+    pytest
+  '';
+
+  meta = with lib; {
     description = "Simple Python interface for Graphviz";
     homepage = https://github.com/xflr6/graphviz;
     license = licenses.mit;
+    maintainers = with maintainers; [ dotlambda ];
   };
 
 }

pkgs/development/python-modules/graphviz/hardcode-graphviz-path.patch

@@ -0,0 +1,95 @@
+diff --git a/graphviz/backend.py b/graphviz/backend.py
+index 704017b..fe4aefe 100644
+--- a/graphviz/backend.py
++++ b/graphviz/backend.py
+@@ -114,7 +114,7 @@ def command(engine, format, filepath=None, renderer=None, formatter=None):
+     suffix = '.'.join(reversed(format_arg))
+     format_arg = ':'.join(format_arg)
+ 
+-    cmd = [engine, '-T%s' % format_arg]
++    cmd = [os.path.join('@graphviz@/bin', engine), '-T%s' % format_arg]
+     rendered = None
+     if filepath is not None:
+         cmd.extend(['-O', filepath])
+@@ -217,7 +217,7 @@ def version():
+         subprocess.CalledProcessError: If the exit status is non-zero.
+         RuntimmeError: If the output cannot be parsed into a version number.
+     """
+-    cmd = ['dot', '-V']
++    cmd = ['@graphviz@/bin/dot', '-V']
+     out, _ = run(cmd, check=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
+ 
+     info = out.decode('ascii')
+diff --git a/tests/test_backend.py b/tests/test_backend.py
+index 7ec12f7..2e8550d 100644
+--- a/tests/test_backend.py
++++ b/tests/test_backend.py
+@@ -47,6 +47,7 @@ def test_render_formatter_unknown():
+         render('dot', 'ps', 'nonfilepath', 'ps', '')
+ 
+ 
++@pytest.mark.skip(reason='empty $PATH has no effect')
+ @pytest.mark.usefixtures('empty_path')
+ def test_render_missing_executable():
+     with pytest.raises(ExecutableNotFound, match=r'execute'):
+@@ -85,7 +86,7 @@ def test_render_mocked(capsys, mocker, Popen, quiet):
+ 
+     assert render('dot', 'pdf', 'nonfilepath', quiet=quiet) == 'nonfilepath.pdf'
+ 
+-    Popen.assert_called_once_with(['dot', '-Tpdf', '-O', 'nonfilepath'],
++    Popen.assert_called_once_with(['@graphviz@/bin/dot', '-Tpdf', '-O', 'nonfilepath'],
+                                   stdout=subprocess.PIPE,
+                                   stderr=subprocess.PIPE,
+                                   startupinfo=mocker.ANY)
+@@ -94,6 +95,7 @@ def test_render_mocked(capsys, mocker, Popen, quiet):
+     assert capsys.readouterr() == ('', '' if quiet else 'stderr')
+ 
+ 
++@pytest.mark.skip(reason='empty $PATH has no effect')
+ @pytest.mark.usefixtures('empty_path')
+ def test_pipe_missing_executable():
+     with pytest.raises(ExecutableNotFound, match=r'execute'):
+@@ -143,7 +145,7 @@ def test_pipe_pipe_invalid_data_mocked(mocker, py2, Popen, quiet):  # noqa: N803
+     assert e.value.returncode is mocker.sentinel.returncode
+     assert e.value.stdout is mocker.sentinel.out
+     assert e.value.stderr is err
+-    Popen.assert_called_once_with(['dot', '-Tpng'],
++    Popen.assert_called_once_with(['@graphviz@/bin/dot', '-Tpng'],
+                                   stdin=subprocess.PIPE,
+                                   stdout=subprocess.PIPE,
+                                   stderr=subprocess.PIPE,
+@@ -166,7 +168,7 @@ def test_pipe_mocked(capsys, mocker, Popen, quiet):  # noqa: N803
+ 
+     assert pipe('dot', 'png', b'nongraph', quiet=quiet) is mocker.sentinel.out
+ 
+-    Popen.assert_called_once_with(['dot', '-Tpng'],
++    Popen.assert_called_once_with(['@graphviz@/bin/dot', '-Tpng'],
+                                   stdin=subprocess.PIPE,
+                                   stdout=subprocess.PIPE,
+                                   stderr=subprocess.PIPE,
+@@ -176,6 +178,7 @@ def test_pipe_mocked(capsys, mocker, Popen, quiet):  # noqa: N803
+     assert capsys.readouterr() == ('', '' if quiet else 'stderr')
+ 
+ 
++@pytest.mark.skip(reason='empty $PATH has no effect')
+ @pytest.mark.usefixtures('empty_path')
+ def test_version_missing_executable():
+     with pytest.raises(ExecutableNotFound, match=r'execute'):
+@@ -196,7 +199,7 @@ def test_version_parsefail_mocked(mocker, Popen):
+     with pytest.raises(RuntimeError):
+         version()
+ 
+-    Popen.assert_called_once_with(['dot', '-V'],
++    Popen.assert_called_once_with(['@graphviz@/bin/dot', '-V'],
+                                   stdout=subprocess.PIPE,
+                                   stderr=subprocess.STDOUT,
+                                   startupinfo=mocker.ANY)
+@@ -211,7 +214,7 @@ def test_version_mocked(mocker, Popen):
+ 
+     assert version() == (1, 2, 3)
+ 
+-    Popen.assert_called_once_with(['dot', '-V'],
++    Popen.assert_called_once_with(['@graphviz@/bin/dot', '-V'],
+                                   stdout=subprocess.PIPE,
+                                   stderr=subprocess.STDOUT,
+                                   startupinfo=mocker.ANY)

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

@@ -2,6 +2,8 @@
 , buildPythonPackage
 , fetchPypi
 , isPyPy
+, substituteAll
+, graphvizPkg
 , graphviz
 , mock
 }:
@@ -18,6 +20,13 @@ buildPythonPackage rec {
   # Tests fail with PyPy.
   disabled = isPyPy;
 
+  patches = [
+    (substituteAll {
+      src = ./hardcode-graphviz-path.patch;
+      graphviz = graphvizPkg;
+    })
+  ];
+
   propagatedBuildInputs = [ graphviz ];
 
   checkInputs = [ mock ];

pkgs/development/python-modules/objgraph/hardcode-graphviz-path.patch

@@ -0,0 +1,61 @@
+diff --git a/objgraph.py b/objgraph.py
+index 88e307b..0369f49 100755
+--- a/objgraph.py
++++ b/objgraph.py
+@@ -1045,12 +1045,12 @@ def _present_graph(dot_filename, filename=None):
+     if not filename and _program_in_path('xdot'):
+         print("Spawning graph viewer (xdot)")
+         subprocess.Popen(['xdot', dot_filename], close_fds=True)
+-    elif _program_in_path('dot'):
++    elif True: # path to dot is hardcoded and hence always in $PATH
+         if not filename:
+             print("Graph viewer (xdot) not found, generating a png instead")
+             filename = dot_filename[:-4] + '.png'
+         stem, ext = os.path.splitext(filename)
+-        cmd = ['dot', '-T' + ext[1:], '-o' + filename, dot_filename]
++        cmd = ['@graphviz@/bin/dot', '-T' + ext[1:], '-o' + filename, dot_filename]
+         dot = subprocess.Popen(cmd, close_fds=False)
+         dot.wait()
+         if dot.returncode != 0:
+diff --git a/tests.py b/tests.py
+index 7db2888..bdb666e 100755
+--- a/tests.py
++++ b/tests.py
+@@ -557,7 +557,7 @@ class PresentGraphTest(CaptureMixin, TemporaryDirectoryMixin,
+         self.programsInPath(['dot'])
+         objgraph._present_graph('foo.dot', 'bar.png')
+         self.assertOutput("""
+-            subprocess.Popen(['dot', '-Tpng', '-obar.png', 'foo.dot'])
++            subprocess.Popen(['@graphviz@/bin/dot', '-Tpng', '-obar.png', 'foo.dot'])
+             Image generated as bar.png
+         """)
+ 
+@@ -566,11 +566,12 @@ class PresentGraphTest(CaptureMixin, TemporaryDirectoryMixin,
+         objgraph.subprocess.should_fail = True
+         objgraph._present_graph('f.dot', 'b.png')
+         self.assertOutput("""
+-            subprocess.Popen(['dot', '-Tpng', '-ob.png', 'f.dot'])
+-            dot failed (exit code 1) while executing "dot -Tpng -ob.png f.dot"
++            subprocess.Popen(['@graphviz@/bin/dot', '-Tpng', '-ob.png', 'f.dot'])
++            dot failed (exit code 1) while executing "@graphviz@/bin/dot -Tpng -ob.png f.dot"
+         """)
+ 
+-    def test_present_png_no_dot(self):
++    @unittest.skip("empty $PATH has no effect")
++    def no_test_present_png_no_dot(self):
+         self.programsInPath([])
+         objgraph._present_graph('foo.dot', 'bar.png')
+         self.assertOutput("""
+@@ -591,10 +592,11 @@ class PresentGraphTest(CaptureMixin, TemporaryDirectoryMixin,
+         objgraph._present_graph('foo.dot')
+         self.assertOutput("""
+             Graph viewer (xdot) not found, generating a png instead
+-            subprocess.Popen(['dot', '-Tpng', '-ofoo.png', 'foo.dot'])
++            subprocess.Popen(['@graphviz@/bin/dot', '-Tpng', '-ofoo.png', 'foo.dot'])
+             Image generated as foo.png
+         """)
+ 
++    @unittest.skip("empty $PATH has no effect")
+     def test_present_no_xdot_and_no_not(self):
+         self.programsInPath([])
+         objgraph._present_graph('foo.dot')

pkgs/development/python-modules/plone-testing/default.nix

@@ -1,6 +1,7 @@
 { lib
 , buildPythonPackage
 , fetchPypi
+, six
 , zope_testing
 , setuptools
 }:
@@ -14,7 +15,7 @@ buildPythonPackage rec {
     sha256 = "db71bde0d4d3c273dbba8c7a2ab259a42f038eca74184da36c5aab61e90e8dd7";
   };
 
-  propagatedBuildInputs = [ setuptools zope_testing ];
+  propagatedBuildInputs = [ six setuptools zope_testing ];
 
   # Huge amount of testing dependencies (including Zope2)
   doCheck = false;
@@ -24,4 +25,4 @@ buildPythonPackage rec {
     homepage = https://github.com/plone/plone.testing;
     license = lib.licenses.bsd3;
   };
-}
+}

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

@@ -1,23 +1,44 @@
 { lib
 , buildPythonPackage
 , fetchPypi
+, substituteAll
+, graphviz
+, python
 , chardet
 , pyparsing
-, graphviz
 }:
 
 buildPythonPackage rec {
   pname = "pydot";
-  version = "1.4.0";
+  version = "1.4.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "02yp2k7p1kh0azwd932jhvfc3nxxdv9dimh7hdgwdnmp05yms6cq";
+    sha256 = "d49c9d4dd1913beec2a997f831543c8cbd53e535b1a739e921642fe416235f01";
   };
+
+  patches = [
+    (substituteAll {
+      src = ./hardcode-graphviz-path.patch;
+      inherit graphviz;
+    })
+  ];
+
+  postPatch = ''
+    # test_graphviz_regression_tests also fails upstream: https://github.com/pydot/pydot/pull/198
+    substituteInPlace test/pydot_unittest.py \
+      --replace "test_graphviz_regression_tests" "no_test_graphviz_regression_tests"
+  '';
+
+  propagatedBuildInputs = [ pyparsing ];
+
   checkInputs = [ chardet ];
-  # No tests in archive
-  doCheck = false;
-  propagatedBuildInputs = [pyparsing graphviz];
+
+  checkPhase = ''
+    cd test
+    ${python.interpreter} pydot_unittest.py
+  '';
+
   meta = {
     homepage = https://github.com/erocarrera/pydot;
     description = "Allows to easily create both directed and non directed graphs from Python";

pkgs/development/python-modules/pydot/hardcode-graphviz-path.patch

@@ -0,0 +1,13 @@
+diff --git a/pydot.py b/pydot.py
+index 3c7da4d..582c5bc 100644
+--- a/pydot.py
++++ b/pydot.py
+@@ -124,7 +124,7 @@ def call_graphviz(program, arguments, working_dir, **kwargs):
+         'LD_LIBRARY_PATH': os.environ.get('LD_LIBRARY_PATH', ''),
+     }
+ 
+-    program_with_args = [program, ] + arguments
++    program_with_args = ['@graphviz@/bin/' + program, ] + arguments
+ 
+     process = subprocess.Popen(
+         program_with_args,

pkgs/development/python-modules/r2pipe/default.nix

@@ -0,0 +1,51 @@
+{ stdenv
+, lib
+, python
+, buildPythonPackage
+, fetchPypi
+, radare2
+, coreutils
+}:
+
+buildPythonPackage rec {
+  pname = "r2pipe";
+  version = "1.2.0";
+
+  postPatch = let
+    r2lib = "${lib.getOutput "lib" radare2}/lib";
+    libr_core = "${r2lib}/libr_core${stdenv.hostPlatform.extensions.sharedLibrary}";
+  in
+  ''
+    # Fix find_library, can be removed after
+    # https://github.com/NixOS/nixpkgs/issues/7307 is resolved.
+    substituteInPlace r2pipe/native.py --replace "find_library('r_core')" "'${libr_core}'"
+
+    # Fix the default r2 executable
+    substituteInPlace r2pipe/open_sync.py --replace "r2e = 'radare2'" "r2e = '${radare2}/bin/radare2'"
+    substituteInPlace r2pipe/open_base.py --replace 'which("radare2")' "'${radare2}/bin/radare2'"
+  '';
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1qs3xqmi9alahsgr8akzw06ia4c3554dz8pran1h7z5llk262nj4";
+  };
+
+  # Tiny sanity check to make sure r2pipe finds radare2 (since r2pipe doesn't
+  # provide its own tests):
+  # Analyze ls with the fastest analysis and do nothing with the result.
+  postCheck = ''
+    ${python.interpreter} <<EOF
+    import r2pipe
+    r2 = r2pipe.open('${coreutils}/bin/ls')
+    r2.cmd('a')
+    r2.quit()
+    EOF
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Interact with radare2";
+    homepage = https://github.com/radare/radare2-r2pipe;
+    license = licenses.mit;
+    maintainers = with maintainers; [ timokau ];
+  };
+}

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

@@ -25,6 +25,7 @@ buildPythonPackage rec {
 
   preConfigure = ''
     chmod +x ./deps/pjsip/configure ./deps/pjsip/aconfigure
+    export LD=$CC
   '';
 
   nativeBuildInputs = [ pkgs.pkgconfig ];

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

@@ -9,11 +9,11 @@
 
 buildPythonPackage rec {
   pname = "xarray";
-  version = "0.11.0";
+  version = "0.11.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "06580fg3kgnwci070ivgqzfilmldjk5lxb10jbbfb87wrjx68sb3";
+    sha256 = "1cnghx1xcgdq675abmrys311vspmzgjgiji4wh8iyw194qalfwdg";
   };
 
   checkInputs = [ pytest ];

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

@@ -8,18 +8,19 @@
 
 buildPythonPackage rec {
   pname = "xdis";
-  version = "3.8.8";
+  version = "3.8.9";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "4d212df8a85ab55a35f6ad71b2c29818d903c3e6a95e31eb26d5f3fc66a4e015";
+    sha256 = "1q2dg3hnsmmpjcc7lzjf5nd041mpbwa2bq3dgr4p6wv65vncny9v";
   };
 
   checkInputs = [ pytest ];
   propagatedBuildInputs = [ six click ];
 
-  # newest release moves to pytest (tests not packaged with release)
-  doCheck = false;
+  checkPhase = ''
+    make check
+  '';
 
   meta = with stdenv.lib; {
     description = "Python cross-version byte-code disassembler and marshal routines";

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

@@ -3,7 +3,6 @@
 , fetchPypi
 , setuptoolsDarcs
 , pyutil
-, argparse
 , isPyPy
 }:
 
@@ -18,7 +17,12 @@ buildPythonPackage rec {
   };
 
   buildInputs = [ setuptoolsDarcs ];
-  propagatedBuildInputs = [ pyutil argparse ];
+  propagatedBuildInputs = [ pyutil ];
+
+  # argparse is in the stdlib but zfec doesn't know that.
+  postPatch = ''
+    sed -i -e '/argparse/d' setup.py
+  '';
 
   meta = with stdenv.lib; {
     homepage = http://allmydata.org/trac/zfec;