Merge remote-tracking branch 'upstream/master' into HEAD

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

@@ -19,6 +19,8 @@ buildPythonPackage rec {
   '';
 
   propagatedBuildInputs = [ vega pandas ipython traitlets ];
+  # Disabling checks, MockRequest object has no method send()
+  doCheck = false;
 
   meta = with stdenv.lib; {
     description = "A declarative statistical visualization library for Python.";

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

@@ -1,7 +1,7 @@
 { gui ? true,
   buildPythonPackage, fetchFromGitHub, lib,
   sphinx_1_2, lxml, isodate, numpy, pytest,
-  tkinter ? null,
+  tkinter ? null, py3to2,
   ... }:
 
 let
@@ -26,6 +26,7 @@ buildPythonPackage {
   buildInputs = [
     sphinx_1_2
     pytest
+    py3to2
   ];
   propagatedBuildInputs = [
     lxml

pkgs/development/python-modules/cachetools/1.nix

@@ -0,0 +1,18 @@
+{ stdenv, buildPythonPackage, fetchPypi, isPyPy }:
+
+buildPythonPackage rec {
+  name = "${pname}-${version}";
+  pname = "cachetools";
+  version = "1.1.3";
+  disabled = isPyPy;  # a test fails
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0js7qx5pa8ibr8487lcf0x3a7w0xml0wa17snd6hjs0857kqhn20";
+  };
+
+  meta = with stdenv.lib; {
+    homepage = "https://github.com/tkem/cachetools";
+    license = licenses.mit;
+  };
+}

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

@@ -0,0 +1,18 @@
+{ stdenv, buildPythonPackage, fetchPypi, isPyPy }:
+
+buildPythonPackage rec {
+  name = "${pname}-${version}";
+  pname = "cachetools";
+  version = "2.0.1";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0pdw2fr29pxlyn1g5fhdrrqbpn0iw062nv716ngdqvdx7hnizq7d";
+  };
+
+  meta = with stdenv.lib; {
+    description = "Extensible memoizing collections and decorators";
+    homepage = "https://github.com/tkem/cachetools";
+    license = licenses.mit;
+  };
+}

pkgs/development/python-modules/cld2-cffi/default.nix

@@ -0,0 +1,27 @@
+{ stdenv, buildPythonPackage, fetchPypi, six, cffi, nose }:
+
+buildPythonPackage rec {
+  name = "${pname}-${version}";
+  pname = "cld2-cffi";
+  version = "0.1.4";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0rvcdx4fdh5yk4d2nlddq1q1r2r0xqp86hpmbdn447pdcj1r8a9s";
+  };
+
+  propagatedBuildInputs = [ six cffi ];
+  checkInputs = [ nose ];
+
+  # gcc doesn't approve of this code, so disable -Werror
+  NIX_CFLAGS_COMPILE = "-w";
+
+  checkPhase = "nosetests -v";
+
+  meta = with stdenv.lib; {
+    description = "CFFI bindings around Google Chromium's embedded compact language detection library (CLD2)";
+    homepage = "https://github.com/GregBowyer/cld2-cffi";
+    license = licenses.asl20;
+    maintainers = with maintainers; [ rvl ];
+  };
+}

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

@@ -26,7 +26,7 @@ buildPythonPackage rec {
     #COVERAGE=${coverage}/bin/coverage $out/bin/cram tests
     #${coverage}/bin/coverage report --fail-under=100
     COVERAGE=coverage $out/bin/cram tests
-    coverage report --fail-under=100 --omit="*/_encoding.py"
+    coverage report --fail-under=100 --omit="*/_encoding.py,*/__main__.py"
   '';
 
   meta = {

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

@@ -0,0 +1,23 @@
+{ stdenv, buildPythonPackage, fetchPypi, cryptography, boto3, pyyaml, docutils }:
+
+buildPythonPackage rec {
+  pname    = "credstash";
+  version = "1.13.3";
+  name = "${pname}-${version}";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1x2dh4rs5sahb8h2xznhq7srcm2zl9ykc72a8iqpq4dz7l9k7x7i";
+  };
+
+  propagatedBuildInputs = [ cryptography boto3 pyyaml docutils ];
+
+  # No tests in archive
+  doCheck = false;
+
+  meta = with stdenv.lib; {
+    description = "A utility for managing secrets in the cloud using AWS KMS and DynamoDB";
+    homepage = https://github.com/LuminalOSS/credstash;
+    license = licenses.asl20;
+  };
+}

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

@@ -0,0 +1,28 @@
+{ stdenv, buildPythonPackage, fetchPypi, isPyPy, isPy35, ncurses }:
+
+buildPythonPackage rec {
+  pname = "cx_Freeze";
+  version = "5.0.2";
+  name  = "${pname}-${version}";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0zbx9j5z5l06bvwvlqvvn7h9dm7zjcjgxm7agbb625nymkq6cd15";
+  };
+
+  propagatedBuildInputs = [ ncurses ];
+
+  # timestamp need to come after 1980 for zipfiles and nix store is set to epoch
+  prePatch = ''
+    substituteInPlace cx_Freeze/freezer.py --replace "os.stat(module.file).st_mtime" "time.time()"
+  '';
+
+  # fails to find Console even though it exists on python 3.x
+  doCheck = false;
+
+  meta = with stdenv.lib; {
+    description = "A set of scripts and modules for freezing Python scripts into executables";
+    homepage = "http://cx-freeze.sourceforge.net/";
+    license = licenses.psfl;
+  };
+}

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

@@ -0,0 +1,21 @@
+{ stdenv, buildPythonPackage, fetchPypi }:
+
+buildPythonPackage rec {
+  name = "${pname}-${version}";
+  pname = "ijson";
+  version = "2.3";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0x7l9k2dvxzd5mjgiq15nl9b0sxcqy1cqaz744bjwkz4z5mrypzg";
+  };
+
+  doCheck = false; # something about yajl
+
+  meta = with stdenv.lib; {
+    description = "Iterative JSON parser with a standard Python iterator interface";
+    homepage = "https://github.com/isagalaev/ijson";
+    license = licenses.bsd3;
+    maintainers = with maintainers; [ rvl ];
+  };
+}

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

@@ -1,9 +1,4 @@
-{ lib
-, buildPythonPackage
-, fetchPypi
-, pytest
-, glibcLocales
-}:
+{ stdenv, buildPythonPackage, fetchPypi, pytest, glibcLocales, tox, pytestcov }:
 
 buildPythonPackage rec {
   pname = "jedi";
@@ -15,19 +10,19 @@ buildPythonPackage rec {
     sha256 = "7abb618cac6470ebbd142e59c23daec5e6e063bfcecc8a43a037d2ab57276f4e";
   };
 
-  checkInputs = [ pytest glibcLocales ];
+  checkInputs = [ pytest glibcLocales tox pytestcov ];
 
   checkPhase = ''
     LC_ALL="en_US.UTF-8" py.test test
   '';
 
-  # 7 failed
-  #doCheck = false;
+  # tox required for tests: https://github.com/davidhalter/jedi/issues/808
+  doCheck = false;
 
-  meta = {
+  meta = with stdenv.lib; {
     homepage = https://github.com/davidhalter/jedi;
     description = "An autocompletion tool for Python that can be used for text editors";
-    license = lib.licenses.lgpl3Plus;
-    maintainers = with lib.maintainers; [ garbas ];
+    license = licenses.lgpl3Plus;
+    maintainers = with maintainers; [ garbas ];
   };
 }

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

@@ -0,0 +1,25 @@
+{ stdenv, buildPythonPackage, fetchPypi, pytest_29, future, numpy }:
+
+buildPythonPackage rec {
+  pname = "MDP";
+  version = "3.5";
+  name  = "${pname}-${version}";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0aw1zxmyvx6gfmmnixbqmdaah28jl7rmqkzhxv53091asc23iw9k";
+  };
+
+  checkInputs = [ pytest_29 ];
+  propagatedBuildInputs = [ future numpy ];
+
+  # Tests disabled because of missing dependencies not in nix
+  doCheck = false;
+
+  meta = with stdenv.lib; {
+    description = "Library for building complex data processing software by combining widely used machine learning algorithms";
+    homepage = http://mdp-toolkit.sourceforge.net;
+    license = licenses.bsd3;
+    maintainers = with maintainers; [ nico202 ];
+  };
+}

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

@@ -0,0 +1,32 @@
+{ stdenv, buildPythonPackage, fetchPypi, jinja2, werkzeug, flask, requests, pytz
+, six, boto, httpretty, xmltodict, nose, sure, boto3, freezegun, dateutil }:
+
+buildPythonPackage rec {
+  pname = "moto";
+  version = "0.4.31";
+  name    = "moto-${version}";
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "19s8hfz4mzzzdksa0ddlvrga5mxdaqahk89p5l29a5id8127shr8";
+  };
+
+  propagatedBuildInputs = [
+    boto
+    dateutil
+    flask
+    httpretty
+    jinja2
+    pytz
+    werkzeug
+    requests
+    six
+    xmltodict
+  ];
+
+  checkInputs = [ boto3 nose sure freezegun ];
+
+  checkPhase = "nosetests";
+
+  # TODO: make this true; I think lots of the tests want network access but we can probably run the others
+  doCheck = false;
+}

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

@@ -0,0 +1,31 @@
+{ stdenv, buildPythonPackage, fetchPypi, nose, nibabel, numpy, scikitlearn
+, scipy, matplotlib }:
+
+buildPythonPackage rec {
+  pname = "nilearn";
+  version = "0.3.1";
+  name = "nilearn-${version}";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0kkarh5cdcd2czs0bf0s1g51qas84mfxfq0dzd7k5h5l0qr4zy06";
+  };
+
+  checkPhase = "nosetests --exclude with_expand_user nilearn/tests";
+
+  buildInputs = [ nose ];
+
+  propagatedBuildInputs = [
+    matplotlib
+    nibabel
+    numpy
+    scikitlearn
+    scipy
+  ];
+
+  meta = with stdenv.lib; {
+    homepage = http://nilearn.github.io;
+    description = "A module for statistical learning on neuroimaging data";
+    license = licenses.bsd3;
+  };
+}

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

@@ -0,0 +1,25 @@
+{ stdenv, buildPythonPackage, fetchPypi, wcwidth, six, prompt_toolkit, docopt
+, jedi, pygments }:
+
+buildPythonPackage rec {
+  pname = "ptpython";
+  version = "0.41";
+  name  = "${pname}-${version}";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1hcaaadkp5n37hxggraynifa33wx1akklzvf6y4rvgjxbjl2g2x7";
+  };
+
+  propagatedBuildInputs = [ wcwidth six prompt_toolkit docopt jedi pygments ];
+
+  # no tests to run
+  doCheck = false;
+
+  meta = with stdenv.lib; {
+    description = "An advanced Python REPL";
+    license = licenses.bsd3;
+    maintainers = with maintainers; [ mlieberman85 ];
+    platforms = platforms.all;
+  };
+}

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

@@ -0,0 +1,22 @@
+{ stdenv, buildPythonPackage, fetchPypi, numpy, cython }:
+
+buildPythonPackage rec {
+  name = "${pname}-${version}";
+  pname = "pyemd";
+  version = "0.4.4";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "13y06y7r1697cv4r430g45fxs40i2yk9xn0dk9nqlrpddw3a0mr4";
+  };
+
+  propagatedBuildInputs = [ numpy ];
+  buildInputs = [ cython ];
+
+  meta = with stdenv.lib; {
+    description = "A Python wrapper for Ofir Pele and Michael Werman's implementation of the Earth Mover's Distance";
+    homepage = http://github.com/wmayner/pyemd;
+    license = licenses.mit;
+    maintainers = with maintainers; [ rvl ];
+  };
+}

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

@@ -0,0 +1,19 @@
+{ stdenv, buildPythonPackage, fetchPypi }:
+
+buildPythonPackage rec {
+  name = "${pname}-${version}";
+  pname = "Pyphen";
+  version = "0.9.4";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1mqb5jrigxipxzp1d8nbwkq0cfjw77pnn6hc4mp1yd2mn059mymb";
+  };
+
+  meta = with stdenv.lib; {
+    description = "Pure Python module to hyphenate text";
+    homepage = "https://github.com/Kozea/Pyphen";
+    license = with licenses; [gpl2 lgpl21 mpl20];
+    maintainers = with maintainers; [ rvl ];
+  };
+}

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

@@ -1,18 +1,18 @@
-{ lib, fetchurl, buildPythonPackage, isPy3k }:
+{ stdenv, fetchPypi, buildPythonPackage, isPy3k }:
 
 buildPythonPackage rec {
-  pname = "pywebdav";
-  name = "${pname}-${version}";
+  pname = "PyWebDAV";
   version = "0.9.8";
+  name = "${pname}-${version}";
   disabled = isPy3k;
-  src = fetchurl {
-    url = "mirror://pypi/p/pywebdav/${name}.tar.gz";
+  src = fetchPypi {
+    inherit pname version;
     sha256 = "1v10vg79h85milnq8w7yd75qq5z6297ywkn9b2kxajldzwqxn3ji";
   };
-  meta = {
+  meta = with stdenv.lib; {
     homepage = http://code.google.com/p/pywebdav/;
     description = "WebDAV library including a standalone server for python";
-    maintainers = with lib.maintainers; [ johbo ];
-    license = lib.licenses.gpl2Plus;
+    maintainers = with maintainers; [ johbo ];
+    license = licenses.gpl2Plus;
   };
 }

pkgs/development/python-modules/spacy/models.json

@@ -0,0 +1,42 @@
+[{
+  "pname": "es_core_web_md",
+  "version": "1.0.0",
+  "sha256": "0ikyakdhnj6rrfpr8k83695d1gd3z9n60a245hwwchv94jmr7r6s",
+  "license": "cc-by-sa-40"
+},
+{
+  "pname": "fr_depvec_web_lg",
+  "version": "1.0.0",
+  "sha256": "0nxmdszs1s5by2874cz37azrmwamh1ngdsiylffkfihzq6s8bhka",
+  "license": "cc-by-nc-sa-40"
+},
+{
+  "pname": "en_core_web_md",
+  "version": "1.2.1",
+  "sha256": "12prr4hcbfdaky9rcna1y1ykr417jkhkks2r8l06g8fb7am3pvp3",
+  "license": "cc-by-sa-40"
+},
+{
+  "pname": "en_depent_web_md",
+  "version": "1.2.1",
+  "sha256": "0giyr35q5lpp5drpcamyvb5gsjnhj62mk3ndfr49nm1s6d5f6m52",
+  "license": "cc-by-sa-40"
+},
+{
+  "pname": "en_core_web_sm",
+  "version": "1.2.0",
+  "sha256": "0vc4l77dcwa9lmzyqdci8ikjc0m2rhasl2zvyba547vf76qb0528",
+  "license": "cc-by-sa-40"
+},
+{
+  "pname": "de_core_news_md",
+  "version": "1.0.0",
+  "sha256": "072jz2rdi1nckny7k16avp86vjg4didfdsw816kfl9zwr88iny6g",
+  "license": "cc-by-sa-40"
+},
+{
+  "pname": "en_vectors_glove_md",
+  "version": "1.0.0",
+  "sha256": "1jbr27xnh5fdww8yphpvk2brfnzb174wfnxkzdqwv3iyi02zsin6",
+  "license": "cc-by-sa-40"
+}]

pkgs/development/python-modules/spacy/models.nix

@@ -0,0 +1,26 @@
+{ stdenv, buildPythonPackage, fetchurl, spacy }:
+let
+  buildModelPackage = { pname, version, sha256, license }: buildPythonPackage {
+    name = "${pname}-${version}";
+    inherit pname version;
+
+    src = fetchurl {
+      url = "https://github.com/explosion/spacy-models/releases/download/${pname}-${version}/${pname}-${version}.tar.gz";
+      inherit sha256;
+    };
+
+    propagatedBuildInputs = [ spacy ];
+
+    meta = with stdenv.lib; {
+      description = "Models for the spaCy NLP library";
+      homepage    = "https://github.com/explosion/spacy-models";
+      license     = licenses."${license}";
+      maintainers = with maintainers; [ rvl ];
+    };
+  };
+
+  makeModelSet = models: with stdenv.lib; listToAttrs (map (m: nameValuePair m.pname (buildModelPackage m)) models);
+
+in makeModelSet (stdenv.lib.importJSON ./models.json)
+
+# cat models.json | jq -r '.[] | @uri "https://github.com/explosion/spacy-models/releases/download/\(.pname)-\(.version)/\(.pname)-\(.version).tar.gz"' | xargs -n1 nix-prefetch-url

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

@@ -0,0 +1,65 @@
+{ stdenv
+, buildPythonPackage
+, isPy27
+, fetchPypi
+, cachetools
+, cld2-cffi
+, cython
+, cytoolz
+, ftfy
+, ijson
+, matplotlib
+, networkx
+, numpy
+, pyemd
+, pyphen
+, python-Levenshtein
+, requests
+, scikitlearn
+, scipy
+, spacy
+, tqdm
+, unidecode
+}:
+
+buildPythonPackage rec {
+  name = "${pname}-${version}";
+  pname = "textacy";
+  version = "0.4.1";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "04wf3a7zgzz83nmgkh488wkl50zm9yfdpv3sl12sm2zj685plqcz";
+  };
+
+  disabled = isPy27; # 2.7 requires backports.csv
+
+  propagatedBuildInputs = [
+    cachetools
+    cld2-cffi
+    cytoolz
+    ftfy
+    ijson
+    matplotlib
+    networkx
+    numpy
+    pyemd
+    pyphen
+    python-Levenshtein
+    requests
+    scikitlearn
+    scipy
+    spacy
+    tqdm
+    unidecode
+  ];
+
+  doCheck = false;  # tests want to download data files
+
+  meta = with stdenv.lib; {
+    description = "Higher-level text processing, built on spaCy";
+    homepage = "http://textacy.readthedocs.io/";
+    license = licenses.asl20;
+    maintainers = with maintainers; [ rvl ];
+  };
+}

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

@@ -0,0 +1,23 @@
+{ stdenv, buildPythonPackage, fetchPypi, glibcLocales }:
+
+buildPythonPackage rec {
+  name = "${pname}-${version}";
+  pname = "Unidecode";
+  version = "0.04.21";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0lfhp9c5xrbpjvbpr12ji52g1lx04404bzzdg6pvabhzisw6l2i8";
+  };
+
+  LC_ALL="en_US.UTF-8";
+
+  buildInputs = [ glibcLocales ];
+
+  meta = with stdenv.lib; {
+    homepage = http://pypi.python.org/pypi/Unidecode/;
+    description = "ASCII transliterations of Unicode text";
+    license = licenses.gpl2;
+    maintainers = with maintainers; [ domenkozar ];
+  };
+}

pkgs/development/python-modules/ws4py/default.nix

@@ -0,0 +1,26 @@
+{ stdenv, buildPythonPackage, fetchPypi, pytest, mock, git, asyncio
+, cherrypy, gevent, tornado }:
+
+buildPythonPackage rec {
+  name = "${pname}-${version}";
+  pname = "ws4py";
+  version = "0.4.2";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0zr3254ky6r7q15l3dhdczfa8i723055zdkqssjifsgcwvirriks";
+  };
+
+  checkInputs = [ pytest mock git ];
+  propagatedBuildInputs = [ asyncio cherrypy gevent tornado ];
+
+  checkPhase = ''
+    pytest test
+  '';
+
+  meta = with stdenv.lib; {
+    homepage = https://ws4py.readthedocs.org;
+    description = "A WebSocket package for Python";
+    maintainers = with maintainers; [ rickynils ];
+  };
+}