Merge branch 'master' into staging

This commit is contained in:
Vladimír Čunát
2018-06-30 01:41:59 +02:00
998 changed files with 16512 additions and 10378 deletions

View File

@@ -25,8 +25,8 @@ buildPythonPackage rec {
applications which address the needs of current and future work in
bioinformatics.
'';
homepage = http://biopython.org/wiki/Documentation;
homepage = https://biopython.org/wiki/Documentation;
maintainers = with lib.maintainers; [ luispedro ];
license = lib.licenses.bsd3;
};
}
}

View File

@@ -10,7 +10,7 @@ buildPythonPackage rec {
};
meta = with stdenv.lib; {
homepage = http://pythonhosted.org/blinker/;
homepage = https://pythonhosted.org/blinker/;
description = "Fast, simple object-to-object and broadcast signaling";
license = licenses.mit;
maintainers = with maintainers; [ garbas ];

View File

@@ -75,7 +75,7 @@ buildPythonPackage rec {
meta = {
description = "Statistical and novel interactive HTML plots for Python";
homepage = "http://github.com/bokeh/bokeh";
homepage = https://github.com/bokeh/bokeh;
license = lib.licenses.bsd3;
maintainers = with lib.maintainers; [ orivej ];
};

View File

@@ -1,4 +1,11 @@
{ stdenv, fetchPypi, buildPythonPackage, persistent, zope_interface, transaction }:
{ stdenv
, fetchPypi
, buildPythonPackage
, persistent
, zope_interface
, transaction
, zope_testrunner
}:
buildPythonPackage rec {
pname = "BTrees";
@@ -6,6 +13,7 @@ buildPythonPackage rec {
buildInputs = [ transaction ];
propagatedBuildInputs = [ persistent zope_interface ];
checkInputs = [ zope_testrunner ];
src = fetchPypi {
inherit pname version;

View File

@@ -1,7 +1,8 @@
{ stdenv, fetchPypi, buildPythonPackage
, more-itertools, six
, pytest, pytestcov, portend
, backports_unittest-mock, setuptools_scm }:
, backports_unittest-mock
, backports_functools_lru_cache }:
buildPythonPackage rec {
pname = "cheroot";
@@ -14,9 +15,16 @@ buildPythonPackage rec {
propagatedBuildInputs = [ more-itertools six ];
buildInputs = [ setuptools_scm ];
checkInputs = [ pytest pytestcov portend backports_unittest-mock backports_functools_lru_cache ];
checkInputs = [ pytest pytestcov portend backports_unittest-mock ];
# Disable testmon, it needs pytest-testmon, which we do not currently have in nikpkgs,
# and is only used to skip some tests that are already known to work.
postPatch = ''
substituteInPlace "./pytest.ini" --replace "--testmon" ""
substituteInPlace setup.py --replace "use_scm_version=True" "version=\"${version}\"" \
--replace "'setuptools_scm>=1.15.0'," "" \
--replace "'setuptools_scm_git_archive>=1.0'," "" \
'';
checkPhase = ''
py.test cheroot

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@@ -2,6 +2,7 @@
, cheroot, portend, routes, six
, setuptools_scm
, backports_unittest-mock, objgraph, pathpy, pytest, pytestcov
, backports_functools_lru_cache, requests_toolbelt
}:
buildPythonPackage rec {
@@ -17,7 +18,7 @@ buildPythonPackage rec {
buildInputs = [ setuptools_scm ];
checkInputs = [ backports_unittest-mock objgraph pathpy pytest pytestcov ];
checkInputs = [ backports_unittest-mock objgraph pathpy pytest pytestcov backports_functools_lru_cache requests_toolbelt ];
checkPhase = ''
LANG=en_US.UTF-8 pytest

View File

@@ -6,12 +6,12 @@
, enum34, functools32,
}:
buildPythonApplication rec {
version = "1.20.1";
version = "1.21.2";
pname = "docker-compose";
src = fetchPypi {
inherit pname version;
sha256 = "34c043ebd4c23e4b864812c16b41dad25cec6b675557b180ced52d372e1a9e66";
sha256 = "0b0wihlyk89y6n0mly2vbljzqai1hhs6yzplskwdah2lfn9p3c38";
};
# lots of networking and other fails

View File

@@ -23,7 +23,7 @@ buildPythonPackage rec {
meta = with stdenv.lib; {
description = "Simple Python implementation of the Git file formats and protocols";
homepage = http://samba.org/~jelmer/dulwich/;
homepage = https://samba.org/~jelmer/dulwich/;
license = licenses.gpl2Plus;
maintainers = with maintainers; [ koral ];
};

View File

@@ -39,6 +39,6 @@ buildPythonPackage rec {
'';
license = licenses.bsd2;
maintainers = with maintainers; [ timokau ];
homepage = http://pythonhosted.org/Flask-AutoIndex/;
homepage = https://pythonhosted.org/Flask-AutoIndex/;
};
}

View File

@@ -0,0 +1,28 @@
{ lib, buildPythonPackage, fetchPypi, flask, pytest, pytestcov }:
buildPythonPackage rec {
pname = "Flask-Caching";
version = "1.4.0";
src = fetchPypi {
inherit pname version;
sha256 = "e34f24631ba240e09fe6241e1bf652863e0cff06a1a94598e23be526bc2e4985";
};
propagatedBuildInputs = [ flask ];
checkInputs = [ pytest pytestcov ];
checkPhase = ''
py.test
'';
# https://github.com/sh4nks/flask-caching/pull/74
doCheck = false;
meta = with lib; {
description = "Adds caching support to your Flask application";
homepage = https://github.com/sh4nks/flask-caching;
license = licenses.bsd3;
};
}

View File

@@ -1,5 +1,5 @@
{ stdenv, fetchPypi, buildPythonPackage
, crayons, flask, flask_cache, gunicorn, maya, meinheld, whitenoise }:
, crayons, flask, flask-caching, gunicorn, maya, meinheld, whitenoise }:
buildPythonPackage rec {
pname = "Flask-Common";
@@ -10,7 +10,7 @@ buildPythonPackage rec {
sha256 = "13d99f2dbc0a332b8bc4b2cc394d3e48f89672c266868e372cd9d7b433d921a9";
};
propagatedBuildInputs = [ crayons flask flask_cache gunicorn maya meinheld whitenoise ];
propagatedBuildInputs = [ crayons flask flask-caching gunicorn maya meinheld whitenoise ];
meta = with stdenv.lib; {
description = "Flask extension with lots of common time-savers";

View File

@@ -16,6 +16,10 @@ buildPythonPackage rec {
patchPhase = if isPy3k then ''
rm tests/test_crypto.py tests/test_paging.py
'' else null;
# Disable test broken with aniso > 3.0.0, can be removed when updating to a flask-restful version with commit 54979f0
preCheck = ''
substituteInPlace "./tests/test_inputs.py" --replace "test_bad_isointervals" "disabled_bad_isointervals"
'';
buildInputs = [ nose mock blinker ];
propagatedBuildInputs = [ flask six pytz aniso8601 pycrypto ];
PYTHON_EGG_CACHE = "`pwd`/.egg-cache";

View File

@@ -23,7 +23,7 @@ buildPythonPackage rec {
meta = with lib; {
description = "Hierarchical Density-Based Spatial Clustering of Applications with Noise, a clustering algorithm with a scikit-learn compatible API";
homepage = http://github.com/scikit-learn-contrib/hdbscan;
homepage = https://github.com/scikit-learn-contrib/hdbscan;
license = licenses.bsd3;
maintainers = with maintainers; [ ixxie ];
};

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@@ -26,7 +26,7 @@ buildPythonPackage rec {
meta = {
description = "Lightweight pipelining: using Python functions as pipeline jobs";
homepage = http://pythonhosted.org/joblib/;
homepage = https://pythonhosted.org/joblib/;
license = lib.licenses.bsd3;
};
}

View File

@@ -29,7 +29,7 @@ buildPythonPackage rec {
meta = with stdenv.lib; {
description = "A library to parse MT940 files and returns smart Python collections for statistics and manipulation";
homepage = "http://pythonhosted.org/mt-940/";
homepage = https://pythonhosted.org/mt-940/;
license = licenses.bsd3;
};
}

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@@ -0,0 +1,24 @@
{ lib, buildPythonPackage, fetchPypi, requests, pytest }:
buildPythonPackage rec {
version = "2.3.0";
pname = "plaid-python";
src = fetchPypi {
inherit pname version;
sha256 = "0kp0crzjginmga6qvwwppar5b2pbdvwryf6vdpxgx7kkwzv33w97";
};
checkInputs = [ pytest ];
# Integration tests require API keys and internet access
checkPhase = "py.test -rxs ./tests/unit";
propagatedBuildInputs = [ requests ];
meta = {
description = "Python client library for the Plaid API and Link";
homepage = https://github.com/plaid/plaid-python;
license = lib.licenses.mit;
maintainers = with lib.maintainers; [ bhipple ];
};
}

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@@ -32,7 +32,7 @@ buildPythonPackage rec {
'';
meta = with stdenv.lib; {
homepage = http://www.logilab.org/project/pylint;
homepage = https://www.logilab.org/project/pylint;
description = "A bug and style checker for Python";
platforms = platforms.all;
license = licenses.gpl1Plus;

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@@ -13,7 +13,7 @@ buildPythonPackage rec {
doCheck = false;
meta = with stdenv.lib; {
homepage = "http://github.com/mongodb/mongo-python-driver";
homepage = https://github.com/mongodb/mongo-python-driver;
license = licenses.asl20;
description = "Python driver for MongoDB ";
};

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@@ -14,7 +14,7 @@ buildPythonPackage rec {
meta = with stdenv.lib; {
description = "Distributed object middleware for Python (IPC/RPC)";
homepage = http://pythonhosted.org/Pyro/;
homepage = https://pythonhosted.org/Pyro/;
license = licenses.mit;
platforms = platforms.unix;
maintainers = with maintainers; [ bjornfor ];

View File

@@ -2,18 +2,21 @@
buildPythonPackage rec {
pname = "pyslurm";
version = "20180427";
version = "20180604";
src = fetchFromGitHub {
repo = "pyslurm";
owner = "PySlurm";
rev = "3900e1afac9ffd13c80c57d8c39933d42eb7bad7";
sha256 = "1a183ig4sdbc70rx2yyaslyq61wkbsf8cbim1jj0kzrp65nf0vls";
rev = "9dd4817e785fee138a9e29c3d71d2ea44898eedc";
sha256 = "14ivwc27sjnk0z0jpfgyy9bd91m2bhcz11lzp1kk9xn4495i7wvj";
};
buildInputs = [ cython slurm ];
setupPyBuildFlags = [ "--slurm-lib=${slurm}/lib" "--slurm-inc=${slurm.dev}/include" ];
# Test cases need /etc/slurm/slurm.conf and require a working slurm installation
doCheck = false;
meta = with lib; {
homepage = https://github.com/PySlurm/pyslurm;
description = "Python bindings to Slurm";

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@@ -2,11 +2,11 @@
buildPythonPackage rec {
pname = "pytest-mock";
version = "1.8.0";
version = "1.10.0";
src = fetchPypi {
inherit pname version;
sha256 = "2dd545496af6a0559432b11de79f1fd4fa4a541ae2e01892d5ba6041f85f0994";
sha256 = "d89a8209d722b8307b5e351496830d5cc5e192336003a485443ae9adeb7dd4c0";
};
propagatedBuildInputs = [ pytest ] ++ lib.optional (!isPy3k) mock;

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@@ -19,7 +19,7 @@ buildPythonPackage rec {
meta = with lib;{
description = "py.test plugin to abort hanging tests";
homepage = http://bitbucket.org/pytest-dev/pytest-timeout/;
homepage = https://bitbucket.org/pytest-dev/pytest-timeout/;
license = licenses.mit;
maintainers = with maintainers; [ makefu ];
};

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@@ -0,0 +1,31 @@
{ buildPythonPackage, stdenv, fetchPypi
, requests
, nose
, responses
}:
buildPythonPackage rec {
pname = "python-forecastio";
version = "1.4.0";
src = fetchPypi {
inherit pname version;
sha256 = "0m6lf4a46pnwm5xg9dnmwslwzrpnj6d9agw570grciivbvb1ji0l";
};
checkInputs = [ nose ];
propagatedBuildInputs = [ requests responses ];
checkPhase = ''
nosetests
'';
meta = with stdenv.lib; {
homepage = https://zeevgilovitz.com/python-forecast.io/;
description = "A thin Python Wrapper for the Dark Sky (formerly forecast.io) weather API";
license = licenses.bsd2;
maintainers = with maintainers; [ makefu ];
};
}

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@@ -13,7 +13,7 @@ buildPythonPackage rec {
meta = with stdenv.lib; {
description = "OpenID support for modern servers and consumers";
homepage = http://github.com/openid/python-openid;
homepage = https://github.com/openid/python-openid;
license = licenses.asl20;
};
}

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@@ -10,7 +10,7 @@ buildPythonPackage rec {
sha256 = "d587a520182f9d8aef7659cca429f4382881589c8883a0a55322b2f94970bdb3";
};
meta = {
homepage = http://arthurdejong.org/python-stdnum/;
homepage = https://arthurdejong.org/python-stdnum/;
description = "Python module to handle standardized numbers and codes";
maintainers = with lib.maintainers; [ johbo ];
license = lib.licenses.lgpl2Plus;

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@@ -61,7 +61,7 @@ in buildPythonPackage rec {
meta = {
description = "Tensors and Dynamic neural networks in Python with strong GPU acceleration.";
homepage = http://pytorch.org/;
homepage = https://pytorch.org/;
license = lib.licenses.bsd3;
platforms = lib.platforms.linux;
maintainers = with lib.maintainers; [ teh ];

View File

@@ -1,19 +1,21 @@
--- a/setup.py
+++ b/setup.py
@@ -28,11 +28,11 @@ from setuptools.dist import Distribution
@@ -18,13 +18,13 @@ from setuptools.dist import Distribution
requirements = [
"IBMQuantumExperience>=1.8.29",
"IBMQuantumExperience>=1.9.2",
- "matplotlib>=2.1,<2.2",
- "networkx>=2.0,<2.1",
- "numpy>=1.13,<1.15",
- "ply==3.10",
- "scipy>=0.19,<1.1",
- "scipy>=0.19,<1.2",
- "sympy>=1.0,<1.2",
- "pillow>=4.2.1,<5.2"
+ "matplotlib>=2.1",
+ "networkx>=2.0",
+ "numpy>=1.13",
+ "ply>=3.10",
+ "scipy>=0.19",
"sympy>=1.0",
"pillow>=4.2.1"
+ "sympy>=1.0",
+ "pillow>=4.2.1"
]

View File

@@ -26,8 +26,8 @@ buildPythonPackage rec {
meta = {
description = "ReStructuredText viewer";
homepage = http://mg.pov.lt/restview/;
homepage = https://mg.pov.lt/restview/;
license = lib.licenses.gpl2;
maintainers = with lib.maintainers; [ koral ];
};
}
}

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@@ -1,15 +1,15 @@
{ lib, fetchPypi, buildPythonPackage, pytest, hypothesis }:
{ lib, fetchPypi, buildPythonPackage, pytest }:
buildPythonPackage rec {
pname = "rlp";
version = "1.0.1";
version = "0.6.0";
src = fetchPypi {
inherit pname version;
sha256 = "492c11b18e89af42f98e96bca7671ffee4ad4cf5e69ea23b4d2221157d81b512";
sha256 = "0d3gx4mp8q4z369s5yk1n9c55sgfw9fidbwqxq67d6s7l45rm1w7";
};
checkInputs = [ pytest hypothesis ];
checkInputs = [ pytest ];
propagatedBuildInputs = [ ];
meta = {
@@ -17,6 +17,5 @@ buildPythonPackage rec {
homepage = "https://github.com/ethereum/pyrlp";
license = lib.licenses.mit;
maintainers = with lib.maintainers; [ gebner ];
broken = true; # Requires a chain of unpackaged dependencies.
};
}

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@@ -2,6 +2,7 @@
, buildPythonPackage
, fetchPypi
, isPyPy
, isPy27
, readline
, R
, pcre
@@ -16,12 +17,18 @@
}:
buildPythonPackage rec {
version = "2.9.3";
version = if isPy27 then
"2.8.6" # python2 support dropped in 2.9.x
else
"2.9.3";
pname = "rpy2";
disabled = isPyPy;
src = fetchPypi {
inherit version pname;
sha256 = "1b72958e683339ea0c3bd9f73738e9ece2da8da8008a10e2e0c68fc7864e9361";
sha256 = if isPy27 then
"162zki5c1apgv6qbafi7n66y4hgpgp43xag7q75qb6kv99ri6k80" # 2.8.x
else
"1b72958e683339ea0c3bd9f73738e9ece2da8da8008a10e2e0c68fc7864e9361"; # 2.9.x
};
buildInputs = [
readline

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@@ -19,7 +19,7 @@ buildPythonPackage rec {
meta = with stdenv.lib; {
description = "S3FS builds on boto3 to provide a convenient Python filesystem interface for S3.";
homepage = http://github.com/dask/s3fs/;
homepage = https://github.com/dask/s3fs/;
license = licenses.bsd3;
maintainers = with maintainers; [ teh ];
};

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@@ -13,6 +13,12 @@ buildPythonPackage rec {
checkInputs = [ nose jinja2 mock ];
propagatedBuildInputs = [ chardet dnspython lmtpd pythondaemon six ];
# The tests use salmon executable installed by salmon itself so we need to add
# that to PATH
checkPhase = ''
PATH=$out/bin:$PATH nosetests .
'';
meta = with stdenv.lib; {
homepage = http://salmon-mail.readthedocs.org/;
description = "Pythonic mail application server";

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@@ -50,7 +50,7 @@ buildPythonPackage rec {
meta = {
description = "SciPy (pronounced 'Sigh Pie') is open-source software for mathematics, science, and engineering. ";
homepage = http://www.scipy.org/;
homepage = https://www.scipy.org/;
maintainers = with lib.maintainers; [ fridh ];
};
}

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@@ -31,7 +31,7 @@ buildPythonPackage rec {
meta = with lib; {
description = "A fast high-level web crawling and web scraping framework, used to crawl websites and extract structured data from their pages";
homepage = http://scrapy.org/;
homepage = https://scrapy.org/;
license = licenses.bsd3;
maintainers = with maintainers; [ drewkett ];
platforms = platforms.unix;

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@@ -0,0 +1,28 @@
{ stdenv, buildPythonPackage, fetchFromGitHub, numpy, scipy, deap, scikitlearn, python }:
buildPythonPackage rec {
pname = "sklearn-deap";
version = "0.2.2";
# No tests in Pypi
src = fetchFromGitHub {
owner = "rsteca";
repo = pname;
rev = "${version}";
sha256 = "01ynmzxg181xhv2d7bs53zjvk9x2qpxix32sspq54mpigxh13ava";
};
propagatedBuildInputs = [ numpy scipy deap scikitlearn ];
checkPhase = ''
${python.interpreter} test.py
'';
meta = with stdenv.lib; {
description = "Use evolutionary algorithms instead of gridsearch in scikit-learn";
homepage = https://github.com/rsteca/sklearn-deap;
license = licenses.lgpl3;
maintainers = with maintainers; [ psyanticy ];
};
}

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@@ -12,7 +12,7 @@ buildPythonPackage rec {
propagatedBuildInputs = [ tornado ];
meta = with lib; {
homepage = http://github.com/mrjoes/sockjs-tornado/;
homepage = https://github.com/mrjoes/sockjs-tornado/;
description = "SockJS python server implementation on top of Tornado framework";
license = licenses.mit;
maintainers = with maintainers; [ abbradar ];

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@@ -19,7 +19,7 @@ buildPythonPackage rec {
meta = with lib; {
description = "SPAKE2 password-authenticated key exchange library";
homepage = "http://github.com/warner/python-spake2";
homepage = https://github.com/warner/python-spake2;
license = licenses.mit;
};
}

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@@ -22,9 +22,9 @@ buildPythonPackage rec{
'';
meta = {
homepage = "http://github.com/pytoolz/toolz/";
homepage = https://github.com/pytoolz/toolz/;
description = "List processing tools and functional utilities";
license = lib.licenses.bsd3;
maintainers = with lib.maintainers; [ fridh ];
};
}
}

View File

@@ -24,7 +24,7 @@ buildPythonPackage rec {
meta = {
description = "PyTorch vision library";
homepage = http://pytorch.org/;
homepage = https://pytorch.org/;
license = lib.licenses.bsd3;
maintainers = with lib.maintainers; [ ericsagnes ];
};

View File

@@ -44,7 +44,7 @@ buildPythonPackage rec {
doCheck = false;
meta = with stdenv.lib; {
homepage = http://twistedmatrix.com/;
homepage = https://twistedmatrix.com/;
description = "Twisted, an event-driven networking engine written in Python";
longDescription = ''
Twisted is an event-driven networking engine written in Python

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@@ -4,7 +4,7 @@
buildPythonPackage rec {
pname = "txtorcon";
version = "0.20.0";
version = "18.0.0";
checkInputs = [ pytest mock lsof GeoIP ];
propagatedBuildInputs = [
@@ -15,7 +15,7 @@ buildPythonPackage rec {
src = fetchPypi {
inherit pname version;
sha256 = "dc80cb76b3ddacef6d671c0a088cb1a45274c0858554c32ce55d0f41421c740e";
sha256 = "0z2gsyp9msxrzsm7vq2vq8231a678g4g563xni6cnq4xdb4nx3w1";
};
# Skip a failing test until fixed upstream:

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@@ -15,7 +15,7 @@ buildPythonPackage rec {
doCheck = false;
meta = with stdenv.lib; {
homepage = http://pythonhosted.org/uncertainties/;
homepage = https://pythonhosted.org/uncertainties/;
description = "Transparent calculations with uncertainties on the quantities involved (aka error propagation)";
maintainers = with maintainers; [ rnhmjoj ];
license = licenses.bsd3;

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@@ -18,7 +18,7 @@ buildPythonPackage rec {
meta = with lib; {
description = "Media asset management for Python, with glue code for various web frameworks";
homepage = http://github.com/miracle2k/webassets/;
homepage = https://github.com/miracle2k/webassets/;
license = licenses.bsd2;
maintainers = with maintainers; [ abbradar ];
};

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@@ -21,7 +21,7 @@ buildPythonPackage rec {
meta = with stdenv.lib; {
description = "Fast, pure-Python full text indexing, search, and spell
checking library.";
homepage = "http://bitbucket.org/mchaput/whoosh";
homepage = https://bitbucket.org/mchaput/whoosh;
license = licenses.bsd2;
maintainers = with maintainers; [ nand0p ];
platforms = platforms.all;

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@@ -16,7 +16,7 @@ buildPythonPackage rec {
doCheck = false;
meta = with lib;{
homepage = http://jquery.org;
homepage = https://jquery.org;
description = "jquery packaged static files for python";
license = licenses.mit;
maintainers = with maintainers; [ makefu ];

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@@ -19,7 +19,7 @@ buildPythonPackage rec {
meta = with stdenv.lib; {
description = "Inter-process locks";
homepage = http://www.python.org/pypi/zc.lockfile;
homepage = https://www.python.org/pypi/zc.lockfile;
license = licenses.zpl20;
maintainers = with maintainers; [ goibhniu ];
};