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Merge branch 'staging-next'

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The failure diff seems good-enough on Hydra now.
This commit is contained in:
Vladimír Čunát 2018-09-01 17:02:05 +02:00
parent cdb244a3d4 355f19653c
commit 342d3db703
No known key found for this signature in database
GPG key ID: E747DF1F9575A3AA
212 changed files with 1082 additions and 661 deletions
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8
pkgs/applications/misc/octoprint/default.nix
View file

@ -62,6 +62,14 @@ let
# No tests included
doCheck = false;
};
pylru = super.pylru.overridePythonAttrs (oldAttrs: rec {
version = "1.0.9";
src = oldAttrs.src.override {
inherit version;
sha256 = "71376192671f0ad1690b2a7427d39a29b1df994c8469a9b46b03ed7e28c0172c";
};
});
};
};

8
pkgs/applications/networking/newsreaders/pan/default.nix
View file

@ -2,7 +2,7 @@
, stdenv, fetchurl, pkgconfig, gtk3, gtkspell3 ? null
, perl, gmime2, gettext, intltool, itstool, libxml2, dbus-glib, libnotify, gnutls
, makeWrapper, gnupg
, gnomeSupport ? true, libgnome-keyring3
, gnomeSupport ? true, gnome3, libsecret
}:
assert spellChecking -> gtkspell3 != null;
@ -17,10 +17,10 @@ stdenv.mkDerivation {
sha256 = "1b4wamv33hprghcjk903bpvnd233yxyrm18qnh13alc8h1553nk8";
};
nativeBuildInputs = [ pkgconfig makeWrapper ];
buildInputs = [ gtk3 perl gmime2 gettext intltool itstool libxml2 dbus-glib libnotify gnutls ]
nativeBuildInputs = [ pkgconfig gettext intltool itstool libxml2 makeWrapper ];
buildInputs = [ gtk3 gmime2 libnotify gnutls ]
++ stdenv.lib.optional spellChecking gtkspell3
++ stdenv.lib.optional gnomeSupport libgnome-keyring3;
++ stdenv.lib.optionals gnomeSupport [ libsecret gnome3.gcr ];
configureFlags = [
"--with-dbus"

10
pkgs/applications/science/math/sage/default.nix
View file

@ -21,7 +21,7 @@ let
sagelib = self.callPackage ./sagelib.nix {
inherit flint ecl arb;
inherit sage-src openblas-blas-pc openblas-cblas-pc openblas-lapack-pc pynac singular;
inherit sage-src pynac singular;
linbox = nixpkgs.linbox.override { withSage = true; };
};
@ -41,13 +41,13 @@ let
};
sage-env = self.callPackage ./sage-env.nix {
inherit sage-src python rWrapper openblas-cblas-pc ecl singular palp flint pynac pythonEnv;
inherit sage-src python rWrapper ecl singular palp flint pynac pythonEnv;
pkg-config = nixpkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig
};
sage-with-env = self.callPackage ./sage-with-env.nix {
inherit pythonEnv;
inherit sage-src openblas-blas-pc openblas-cblas-pc openblas-lapack-pc pynac singular;
inherit sage-src pynac singular;
pkg-config = nixpkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig
three = nodePackages_8_x.three;
};
@ -60,10 +60,6 @@ let
};
};
openblas-blas-pc = callPackage ./openblas-pc.nix { name = "blas"; };
openblas-cblas-pc = callPackage ./openblas-pc.nix { name = "cblas"; };
openblas-lapack-pc = callPackage ./openblas-pc.nix { name = "lapack"; };
sage-src = callPackage ./sage-src.nix {};
pythonRuntimeDeps = with python.pkgs; [

17
pkgs/applications/science/math/sage/openblas-pc.nix
View file

@ -1,17 +0,0 @@
{ openblasCompat
, writeTextFile
, name
}:
writeTextFile {
name = "openblas-${name}-pc-${openblasCompat.version}";
destination = "/lib/pkgconfig/${name}.pc";
text = ''
Name: ${name}
Version: ${openblasCompat.version}
Description: ${name} for SageMath, provided by the OpenBLAS package.
Cflags: -I${openblasCompat}/include
Libs: -L${openblasCompat}/lib -lopenblas
'';
}

6
pkgs/applications/science/math/sage/sage-env.nix
View file

@ -37,7 +37,7 @@
, lcalc
, rubiks
, flintqs
, openblas-cblas-pc
, openblasCompat
, flint
, gmp
, mpfr
@ -98,9 +98,9 @@ writeTextFile rec {
export PKG_CONFIG_PATH='${lib.concatStringsSep ":" (map (pkg: "${pkg}/lib/pkgconfig") [
# This is only needed in the src/sage/misc/cython.py test and I'm not sure if there's really a use-case
# for it outside of the tests. However since singular and openblas are runtime dependencies anyways
# and openblas-cblas-pc is tiny, it doesn't really hurt to include.
# it doesn't really hurt to include.
singular
openblas-cblas-pc
openblasCompat
])
}'
export SAGE_ROOT='${sage-src}'

6
pkgs/applications/science/math/sage/sage-with-env.nix
View file

@ -4,9 +4,6 @@
, sage-env
, sage-src
, openblasCompat
, openblas-blas-pc
, openblas-cblas-pc
, openblas-lapack-pc
, pkg-config
, three
, singular
@ -32,9 +29,6 @@ let
makeWrapper
pkg-config
openblasCompat # lots of segfaults with regular (64 bit) openblas
openblas-blas-pc
openblas-cblas-pc
openblas-lapack-pc
singular
three
pynac

7
pkgs/applications/science/math/sage/sagelib.nix
View file

@ -3,9 +3,6 @@
, buildPythonPackage
, arb
, openblasCompat
, openblas-blas-pc
, openblas-cblas-pc
, openblas-lapack-pc
, brial
, cliquer
, cypari2
@ -59,9 +56,7 @@ buildPythonPackage rec {
nativeBuildInputs = [
iml
perl
openblas-blas-pc
openblas-cblas-pc
openblas-lapack-pc
openblasCompat
jupyter_core
];

45
pkgs/applications/science/molecular-dynamics/lammps/default.nix
View file

@ -1,25 +1,37 @@
{ stdenv, writeText, fetchurl,
libpng, fftw,
mpiSupport ? false, mpi ? null
{ lib
, bash
, stdenv
, writeText
, fetchFromGitHub
, libpng
, gzip
, fftw
, openblas
, mpiSupport ? false, mpi ? null
}:
assert mpiSupport -> mpi != null;
stdenv.mkDerivation rec {
# LAMMPS has weird versioning converted to ISO 8601 format
version = "2016-02-16";
version = "patch_2Aug2018";
name = "lammps-${version}";
src = fetchurl {
url = "mirror://sourceforge/lammps/lammps-16Feb16.tar.gz";
sha256 = "1yzfbkxma3xa1288rnn66h4w0smbmjkwq1fx1y60pjiw0prmk105";
lammps_packages = "asphere body class2 colloid compress coreshell dipole granular kspace manybody mc misc molecule opt peri qeq replica rigid shock snap srd user-reaxc";
lammps_includes = "-DLAMMPS_EXCEPTIONS -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64";
src = fetchFromGitHub {
owner = "lammps";
repo = "lammps";
rev = "${version}";
sha256 = "1ph9pr7s11wgmspmnhxa55bh1pq2cyl8iimfi62lbpbpl9pr1ilc";
};
passthru = {
inherit mpi;
};
buildInputs = [ fftw libpng ]
buildInputs = [ fftw libpng openblas gzip bash ]
++ (stdenv.lib.optionals mpiSupport [ mpi ]);
# Must do manual build due to LAMMPS requiring a seperate build for
@ -27,13 +39,19 @@ stdenv.mkDerivation rec {
builder = writeText "builder.sh" ''
source $stdenv/setup
tar xzf $src
cd lammps-*/src
make mode=exe ${if mpiSupport then "mpi" else "serial"} SHELL=$SHELL LMP_INC="-DLAMMPS_GZIP -DLAMMPS_PNG" FFT_PATH=-DFFT_FFTW3 FFT_LIB=-lfftw3 JPG_LIB=-lpng
make mode=shlib ${if mpiSupport then "mpi" else "serial"} SHELL=$SHELL LMP_INC="-DLAMMPS_GZIP -DLAMMPS_PNG" FFT_PATH=-DFFT_FFTW3 FFT_LIB=-lfftw3 JPG_LIB=-lpng
mkdir lammps
cp -r $src/lib $src/src lammps
chmod -R 755 lammps/src/
cd lammps/src
for pack in ${lammps_packages}; do make "yes-$pack" SHELL=$SHELL; done
make mode=exe ${if mpiSupport then "mpi" else "serial"} SHELL=$SHELL LMP_INC="${lammps_includes}" FFT_PATH=-DFFT_FFTW3 FFT_LIB=-lfftw3 JPG_LIB=-lpng
make mode=shlib ${if mpiSupport then "mpi" else "serial"} SHELL=$SHELL LMP_INC="${lammps_includes}" FFT_PATH=-DFFT_FFTW3 FFT_LIB=-lfftw3 JPG_LIB=-lpng
mkdir -p $out/bin
cp -v lmp_* $out/bin/lammps
cp -v lmp_* $out/bin/
mkdir -p $out/include
cp -v *.h $out/include/
mkdir -p $out/lib
cp -v liblammps* $out/lib/
@ -51,5 +69,6 @@ stdenv.mkDerivation rec {
homepage = http://lammps.sandia.gov;
license = stdenv.lib.licenses.gpl2;
platforms = stdenv.lib.platforms.linux;
maintainers = with lib.maintainers; [ costrouc ];
};
}

12
pkgs/desktops/gnome-3/core/gnome-desktop/default.nix
View file

@ -1,4 +1,4 @@
{ stdenv, fetchurl, pkgconfig, libxslt, which, libX11, gnome3, gtk3, glib
{ stdenv, fetchurl, substituteAll, pkgconfig, libxslt, which, libX11, gnome3, gtk3, glib
, intltool, libxml2, xkeyboard_config, isocodes, itstool, wayland
, libseccomp, bubblewrap, gobjectIntrospection, gtk-doc, docbook_xsl }:
@ -30,18 +30,16 @@ stdenv.mkDerivation rec {
propagatedBuildInputs = [ gnome3.gsettings-desktop-schemas ];
patches = [
./bubblewrap-paths.patch
(substituteAll {
src = ./bubblewrap-paths.patch;
BUBBLEWRAP_BIN = "${bubblewrap}/bin/bwrap";
})
];
configureFlags = [
"--enable-gtk-doc"
];
postPatch = ''
substituteInPlace libgnome-desktop/gnome-desktop-thumbnail-script.c --subst-var-by \
BUBBLEWRAP_BIN "${bubblewrap}/bin/bwrap"
'';
passthru = {
updateScript = gnome3.updateScript {
packageName = "gnome-desktop";

27
pkgs/desktops/gnome-3/core/gnome-keyring/default.nix
View file

@ -1,6 +1,6 @@
{ stdenv, fetchurl, pkgconfig, dbus, libgcrypt, libtasn1, pam, python2, glib, libxslt
, intltool, pango, gcr, gdk_pixbuf, atk, p11-kit, openssh, wrapGAppsHook
, docbook_xsl, docbook_xml_dtd_42, gnome3 }:
{ stdenv, fetchurl, pkgconfig, dbus, libgcrypt, pam, python2, glib, libxslt
, gettext, gcr, libcap_ng, libselinux, p11-kit, openssh, wrapGAppsHook
, docbook_xsl, docbook_xml_dtd_43, gnome3 }:
stdenv.mkDerivation rec {
name = "gnome-keyring-${version}";
@ -11,21 +11,15 @@ stdenv.mkDerivation rec {
sha256 = "0sk4las4ji8wv9nx8mldzqccmpmkvvr9pdwv9imj26r10xyin5w1";
};
passthru = {
updateScript = gnome3.updateScript { packageName = "gnome-keyring"; attrPath = "gnome3.gnome-keyring"; };
};
outputs = [ "out" "dev" ];
buildInputs = with gnome3; [
dbus libgcrypt pam gtk3 libgnome-keyring openssh
pango gcr gdk_pixbuf atk p11-kit
buildInputs = [
glib libgcrypt pam openssh libcap_ng libselinux
gcr p11-kit
];
propagatedBuildInputs = [ glib libtasn1 libxslt ];
nativeBuildInputs = [
pkgconfig intltool docbook_xsl docbook_xml_dtd_42 wrapGAppsHook
pkgconfig gettext libxslt docbook_xsl docbook_xml_dtd_43 wrapGAppsHook
];
configureFlags = [
@ -48,6 +42,13 @@ stdenv.mkDerivation rec {
make check
'';
passthru = {
updateScript = gnome3.updateScript {
packageName = "gnome-keyring";
attrPath = "gnome3.gnome-keyring";
};
};
meta = with stdenv.lib; {
description = "Collection of components in GNOME that store secrets, passwords, keys, certificates and make them available to applications";
homepage = https://wiki.gnome.org/Projects/GnomeKeyring;

4
pkgs/desktops/gnome-3/core/gnome-shell/default.nix
View file

@ -2,7 +2,7 @@
, python3Packages, libsoup, polkit, clutter, networkmanager, docbook_xsl , docbook_xsl_ns, at-spi2-core
, libstartup_notification, telepathy-glib, telepathy-logger, libXtst, unzip, glibcLocales, shared-mime-info
, libgweather, libcanberra-gtk3, librsvg, geoclue2, perl, docbook_xml_dtd_42, desktop-file-utils
, libpulseaudio, libical, gobjectIntrospection, gstreamer, wrapGAppsHook
, libpulseaudio, libical, gobjectIntrospection, gstreamer, wrapGAppsHook, libxslt
, accountsservice, gdk_pixbuf, gdm, upower, ibus, networkmanagerapplet
, sassc, systemd, gst_all_1 }:
@ -27,7 +27,7 @@ in stdenv.mkDerivation rec {
nativeBuildInputs = [
meson ninja pkgconfig gettext docbook_xsl docbook_xsl_ns docbook_xml_dtd_42 perl wrapGAppsHook glibcLocales
sassc desktop-file-utils
sassc desktop-file-utils libxslt.bin
];
buildInputs = with gnome3; [
systemd caribou

3
pkgs/desktops/xfce4-13/xfce4-settings/default.nix
View file

@ -1,4 +1,4 @@
{ mkXfceDerivation, automakeAddFlags, dbus-glib, exo, garcon, gtk3
{ mkXfceDerivation, automakeAddFlags, exo, garcon, gtk3
, libnotify ? null, libxfce4ui, libxfce4util, libxklavier ? null
, upower ? null, xfconf, xf86inputlibinput ? null }:
@ -19,7 +19,6 @@ mkXfceDerivation rec {
nativeBuildInputs = [ automakeAddFlags ];
buildInputs = [
dbus-glib
exo
garcon
gtk3

5
pkgs/development/libraries/mesa/default.nix
View file

@ -63,7 +63,7 @@ let
in
let
version = "18.1.5";
version = "18.1.7";
branch = head (splitString "." version);
in
@ -77,7 +77,7 @@ let self = stdenv.mkDerivation {
"ftp://ftp.freedesktop.org/pub/mesa/older-versions/${branch}.x/${version}/mesa-${version}.tar.xz"
"https://mesa.freedesktop.org/archive/mesa-${version}.tar.xz"
];
sha256 = "69dbe6f1a6660386f5beb85d4fcf003ee23023ed7b9a603de84e9a37e8d98dea";
sha256 = "655e3b32ce3bdddd5e6e8768596e5d4bdef82d0dd37067c324cc4b2daa207306";
};
prePatch = "patchShebangs .";
@ -100,6 +100,7 @@ let self = stdenv.mkDerivation {
"--with-dri-driverdir=$(drivers)/lib/dri"
"--with-dri-searchpath=${libglvnd.driverLink}/lib/dri"
"--with-platforms=x11,wayland,drm"
"--enable-texture-float"
]
++ (optional (galliumDrivers != [])
("--with-gallium-drivers=" +

46
pkgs/development/libraries/pagmo2/default.nix Normal file
View file

@ -0,0 +1,46 @@
{ lib
, fetchFromGitHub
, stdenv
, cmake
, eigen
, nlopt
, ipopt
, boost
, writeText
}:
stdenv.mkDerivation rec {
name = "pagmo2-${version}";
version = "2.8";
src = fetchFromGitHub {
owner = "esa";
repo = "pagmo2";
rev = "v${version}";
sha256 = "1xwxamcn3fkwr62jn6bkanrwy0cvsksf75hfwx4fvl56awnbz41z";
};
buildInputs = [ cmake eigen nlopt ipopt boost ];
preBuild = ''
cp -r $src/* .
'';
cmakeFlags = [ "-DPAGMO_BUILD_TESTS=no"
"-DPAGMO_WITH_EIGEN3=yes" "-DPAGMO_WITH_NLOPT=yes"
"-DNLOPT_LIBRARY=${nlopt}/lib/libnlopt_cxx.so" "-DPAGMO_WITH_IPOPT=yes"
"-DCMAKE_CXX_FLAGS='-fuse-ld=gold'" ];
checkPhase = ''
ctest
'';
# All but one test pass skip for now (tests also take about 30 min to compile)
doCheck = false;
meta = {
homepage = https://esa.github.io/pagmo2/;
description = "Scientific library for massively parallel optimization";
license = stdenv.lib.licenses.gpl3Plus;
};
}

14
pkgs/development/libraries/science/math/openblas/default.nix
View file

@ -136,6 +136,20 @@ stdenv.mkDerivation rec {
doCheck = true;
checkTarget = "tests";
postInstall = ''
# Write pkgconfig aliases. Upstream report:
# https://github.com/xianyi/OpenBLAS/issues/1740
for alias in blas cblas lapack; do
cat <<EOF > $out/lib/pkgconfig/openblas-$alias.pc
Name: $alias
Version: ${version}
Description: $alias provided by the OpenBLAS package.
Cflags: -I$out/include
Libs: -L$out/lib -lopenblas
EOF
done
'';
meta = with stdenv.lib; {
description = "Basic Linear Algebra Subprograms";
license = licenses.bsd3;

6
pkgs/development/libraries/umockdev/default.nix
View file

@ -1,10 +1,12 @@
{ stdenv, fetchFromGitHub, autoreconfHook, libtool
{ stdenv, fetchFromGitHub, autoreconfHook, umockdev, gobjectIntrospection
, pkgconfig, glib, systemd, libgudev, vala }:
stdenv.mkDerivation rec {
name = "umockdev-${version}";
version = "0.12";
outputs = [ "bin" "out" "dev" "doc" ];
src = fetchFromGitHub {
owner = "martinpitt";
repo = "umockdev";
@ -19,7 +21,7 @@ stdenv.mkDerivation rec {
buildInputs = [ glib systemd libgudev ];
nativeBuildInputs = [ autoreconfHook libtool pkgconfig vala ];
nativeBuildInputs = [ autoreconfHook pkgconfig vala gobjectIntrospection ];
enableParallelBuilding = true;

4
pkgs/development/perl-modules/DB_File/default.nix
View file

@ -1,11 +1,11 @@
{fetchurl, buildPerlPackage, db}:
buildPerlPackage rec {
name = "DB_File-1.841";
name = "DB_File-1.842";
src = fetchurl {
url = "mirror://cpan/authors/id/P/PM/PMQS/${name}.tar.gz";
sha256 = "11fks42kgscpia0mxx4lc9krm7q4gv6w7m5h3m2jr3dl7viv36hn";
sha256 = "0w2d99vs9qarng2f9fpg3gchfdzy6an13507jhclcl8wv183h5hg";
};
preConfigure = ''

4
pkgs/development/python-modules/APScheduler/default.nix
View file

@ -20,11 +20,11 @@
buildPythonPackage rec {
pname = "APScheduler";
version = "3.5.1";
version = "3.5.3";
src = fetchPypi {
inherit pname version;
sha256 = "952c8f46a11f32b9d5bfbe3e347dac2cdf0680d8b4799590dc9c3a9865b73b65";
sha256 = "6599bc78901ee7e9be85cbd073d9cc155c42d2bc867c5cde4d4d1cc339ebfbeb";
};
buildInputs = [

4
pkgs/development/python-modules/Flask-PyMongo/default.nix
View file

@ -8,11 +8,11 @@
buildPythonPackage rec {
pname = "Flask-PyMongo";
version = "2.0.1";
version = "2.1.0";
src = fetchPypi {
inherit pname version;
sha256 = "6a02add52ac245064720c2bb8b02074b9a5a0d9498279510ea2a537512fd3fa5";
sha256 = "0b99dd99985660ebbc4b34bb44550f88a527cbc573faa01febccce3c4ab28347";
};
checkInputs = [ pytest ];

4
pkgs/development/python-modules/XlsxWriter/default.nix
View file

@ -2,11 +2,11 @@
buildPythonPackage rec {
pname = "XlsxWriter";
version = "1.0.5";
version = "1.0.9";
src = fetchPypi {
inherit pname version;
sha256 = "bd4661c04a68621cb2ebc07c38b8b2e98e30bf213a16e1cf3675b61e26ca9bf2";
sha256 = "98a94b32d4929d3e34595b4654b8e7f951182f540056b9cb734c88899912f729";
};
meta = {

4
pkgs/development/python-modules/absl-py/default.nix
View file

@ -6,11 +6,11 @@
buildPythonPackage rec {
pname = "absl-py";
version = "0.2.2";
version = "0.4.1";
src = fetchPypi {
inherit pname version;
sha256 = "e0eb8358b549552b1cc5972350bc3e41dd0a926c15b3ff95ce60f3c78c80824c";
sha256 = "1e6e70506fb4d867cf269af7bcc27b744c36bbc4c516f0f8ccf2039956deea72";
};
propagatedBuildInputs = [ six ];

4
pkgs/development/python-modules/aiofiles/default.nix
View file

@ -9,11 +9,11 @@
buildPythonPackage rec {
pname = "aiofiles";
version = "0.3.2";
version = "0.4.0";
src = fetchPypi {
inherit pname version;
sha256 = "852a493a877b73e11823bfd4e8e5ef2610d70d12c9eaed961bcd9124d8de8c10";
sha256 = "021ea0ba314a86027c166ecc4b4c07f2d40fc0f4b3a950d1868a0f2571c2bbee";
};
disabled = pythonOlder "3.3";

4
pkgs/development/python-modules/aiohue/default.nix
View file

@ -2,11 +2,11 @@
buildPythonPackage rec {
pname = "aiohue";
version = "1.6.0";
version = "1.7.0";
src = fetchPypi {
inherit pname version;
sha256 = "87f0f86865e88ea715ab358b1e5f2838b79ee7cdc0bdf762e9ed60aaf4c8bd4a";
sha256 = "26989babdc3f38575164b60b9536309271d58db005a03045b6e9cca4fc5201d8";
};
propagatedBuildInputs = [ aiohttp ];

4
pkgs/development/python-modules/allpairspy/default.nix
View file

@ -2,11 +2,11 @@
buildPythonPackage rec {
pname = "allpairspy";
version = "2.4.0";
version = "2.4.1";
src = fetchPypi {
inherit pname version;
sha256 = "9fb7962ee523bd96c5098cd3c97ac1b8eb73021d3df9314657ee9de00f52e034";
sha256 = "e8b35751f91692bf0318091b3f44cdf9bbbe3f37a2ff4786eaffc09dc7114fb3";
};
propagatedBuildInputs = [ six ];

4
pkgs/development/python-modules/argon2_cffi/default.nix
View file

@ -9,12 +9,12 @@
buildPythonPackage rec {
pname = "argon2_cffi";
version = "18.1.0";
version = "18.3.0";
name = "${pname}-${version}";
src = fetchPypi {
inherit pname version;
sha256 = "7e4b75611b73f53012117ad21cdde7a17b32d1e99ff6799f22d827eb83a2a59b";
sha256 = "003f588de43a817af6ecc1c06103fa0801de63849db3cb0f37576bb2da29043d";
};
propagatedBuildInputs = [ cffi six ];

36
pkgs/development/python-modules/ase/default.nix Normal file
View file

@ -0,0 +1,36 @@
{ lib
, fetchurl
, buildPythonPackage
, numpy
, scipy
, matplotlib
, flask
, pillow
, psycopg2
}:
buildPythonPackage rec {
version = "3.16.2";
pname = "ase";
src = fetchurl {
url = "https://gitlab.com/${pname}/${pname}/-/archive/${version}/${pname}-${version}.tar.gz";
sha256 = "171j3f4a261cfnqjq98px5fldxql65i3jgf60wc945xvh0mbc8ds";
};
propagatedBuildInputs = [ numpy scipy matplotlib flask pillow psycopg2 ];
checkPhase = ''
$out/bin/ase test
'';
# tests just hang most likely due to something with subprocesses and cli
doCheck = false;
meta = {
description = "Atomic Simulation Environment";
homepage = https://wiki.fysik.dtu.dk/ase/;
license = lib.licenses.lgpl21Plus;
maintainers = with lib.maintainers; [ costrouc ];
};
}

4
pkgs/development/python-modules/astroid/default.nix
View file

@ -5,13 +5,13 @@
buildPythonPackage rec {
pname = "astroid";
version = "2.0.1";
version = "2.0.4";
disabled = pythonOlder "3.4";
src = fetchPypi {
inherit pname version;
sha256 = "218e36cf8d98a42f16214e8670819ce307fa707d1dcf7f9af84c7aede1febc7f";
sha256 = "c7013d119ec95eb626f7a2011f0b63d0c9a095df9ad06d8507b37084eada1a8d";
};
# From astroid/__pkginfo__.py

4
pkgs/development/python-modules/astropy/default.nix
View file

@ -7,7 +7,7 @@
buildPythonPackage rec {
pname = "astropy";
version = "3.0.3";
version = "3.0.4";
disabled = !isPy3k; # according to setup.py
@ -15,7 +15,7 @@ buildPythonPackage rec {
src = fetchPypi {
inherit pname version;
sha256 = "6af07abe5e263820a3dec93832a6ad74005013071490e125afbc6514411721da";
sha256 = "f5d37d20632ba74bd0b12a85179c12f64a9ea037ffc916d8a2de3be4f4656c76";
};
propagatedBuildInputs = [ pytest numpy ]; # yes it really has pytest in install_requires

4
pkgs/development/python-modules/async_generator/default.nix
View file

@ -2,13 +2,13 @@
buildPythonPackage rec {
pname = "async_generator";
version = "1.9";
version = "1.10";
disabled = pythonOlder "3.5";
src = fetchPypi {
inherit pname version;
sha256 = "b7d5465c6174fe86dba498ececb175f93a6097ffb7cc91946405e1f05b848371";
sha256 = "6ebb3d106c12920aaae42ccb6f787ef5eefdcdd166ea3d628fa8476abe712144";
};
checkInputs = [ pytest pytest-asyncio ];

11
pkgs/development/python-modules/autobahn/default.nix
View file

@ -1,22 +1,22 @@
{ stdenv, buildPythonPackage, fetchPypi, isPy3k, isPy33,
unittest2, mock, pytest, trollius, asyncio,
pytest-asyncio, futures,
pytest-asyncio, futures, cffi,
six, twisted, txaio, zope_interface
}:
buildPythonPackage rec {
pname = "autobahn";
version = "18.6.1";
version = "18.8.1";
src = fetchPypi {
inherit pname version;
sha256 = "2f41bfc512ec482044fa8cfa74182118dedd87e03b3494472d9ff1b5a1e27d24";
sha256 = "b69858e0be4bff8437b0bd82a0db1cbef7405e16bd9354ba587c043d6d5e1ad9";
};
# Upstream claim python2 support, but tests require pytest-asyncio which
# is pythn3 only. Therefore, tests are skipped for python2.
doCheck = isPy3k;
buildInputs = stdenv.lib.optionals isPy3k [ unittest2 mock pytest pytest-asyncio ];
propagatedBuildInputs = [ six twisted zope_interface txaio ] ++
checkInputs = stdenv.lib.optionals isPy3k [ unittest2 mock pytest pytest-asyncio ];
propagatedBuildInputs = [ cffi six twisted zope_interface txaio ] ++
(stdenv.lib.optional isPy33 asyncio) ++
(stdenv.lib.optionals (!isPy3k) [ trollius futures ]);
@ -29,6 +29,5 @@ buildPythonPackage rec {
homepage = "https://crossbar.io/autobahn";
license = licenses.mit;
maintainers = with maintainers; [ nand0p ];
platforms = platforms.all;
};
}

4
pkgs/development/python-modules/aws-adfs/default.nix
View file

@ -2,12 +2,12 @@
, pytest, pytestrunner, pytestcov, mock, glibcLocales, lxml, boto3, requests, click, configparser }:
buildPythonPackage rec {
version = "0.12.0";
version = "0.12.1";
pname = "aws-adfs";
src = fetchPypi {
inherit pname version;
sha256 = "1cjrm61k6905dmhgrqyc5caxx5hbhj3sr6cx4r6sbdyz453i7pc6";
sha256 = "72725d7005252b96ccfa9719fe4beec2b86301bff894d4d97a50fc1d05393fd8";
};
# Relax version constraint

3
pkgs/development/python-modules/backports_lzma/default.nix
View file

@ -24,6 +24,9 @@ if !(pythonOlder "3.3") then null else buildPythonPackage rec {
${python.interpreter} test/test_lzma.py
'';
# Relative import does not seem to function.
doCheck = false;
meta = {
description = "Backport of Python 3.3's 'lzma' module for XZ/LZMA compressed files";
homepage = https://github.com/peterjc/backports.lzma;

4
pkgs/development/python-modules/beautifulsoup4/default.nix
View file

@ -2,11 +2,11 @@
buildPythonPackage rec {
pname = "beautifulsoup4";
version = "4.6.0";
version = "4.6.3";
src = fetchPypi {
inherit pname version;
sha256 = "12cf0ygpz9srpfh9gx2f9ba0swa1rzypv3sm4r0hmjyw6b4nm2w0";
sha256 = "90f8e61121d6ae58362ce3bed8cd997efb00c914eae0ff3d363c32f9a9822d10";
};
buildInputs = [ nose ];

4
pkgs/development/python-modules/bitmath/default.nix
View file

@ -2,11 +2,11 @@
buildPythonPackage rec {
pname = "bitmath";
version = "1.3.1.2";
version = "1.3.3.1";
src = fetchPypi {
inherit pname version;
sha256 = "1k8d1wmxqjc8cqzaixpxf45k6dl1kqhblr0g4wyjl0qa18q8wasd";
sha256 = "293325f01e65defe966853111df11d39215eb705a967cb115851da8c4cfa3eb8";
};
checkInputs = [ (if isPy3k then progressbar33 else progressbar231) mock ];

4
pkgs/development/python-modules/bleach/default.nix
View file

@ -9,11 +9,11 @@
buildPythonPackage rec {
pname = "bleach";
version = "2.1.3";
version = "2.1.4";
src = fetchPypi {
inherit pname version;
sha256 = "eb7386f632349d10d9ce9d4a838b134d4731571851149f9cc2c05a9a837a9a44";
sha256 = "0ee95f6167129859c5dce9b1ca291ebdb5d8cd7e382ca0e237dfd0dad63f63d8";
};
checkInputs = [ pytest pytestrunner ];

4
pkgs/development/python-modules/bootstrapped-pip/default.nix
View file

@ -9,9 +9,9 @@ let
};
setuptools_source = fetchPypi {
pname = "setuptools";
version = "40.0.0";
version = "40.2.0";
format = "wheel";
sha256 = "d68abee4eed409fbe8c302ac4d8429a1ffef912cd047a903b5701c024048dd49";
sha256 = "ea3796a48a207b46ea36a9d26de4d0cc87c953a683a7b314ea65d666930ea8e6";
};
in stdenv.mkDerivation rec {

4
pkgs/development/python-modules/boto3/default.nix
View file

@ -13,13 +13,13 @@
buildPythonPackage rec {
pname = "boto3";
version = "1.7.57";
version = "1.7.84";
src = fetchFromGitHub {
owner = "boto";
repo = "boto3";
rev = version;
sha256 = "0rp3vclx7mvfl6isa47m7dzlrf33qb9vj53p0gj4cw3mgl14cnbl";
sha256 = "0d9kqjqmnn53p1xpmdbbjxcxv2482yx3vjhxw8izp0mpq58i5c14";
};
propagatedBuildInputs = [ botocore jmespath s3transfer ] ++ lib.optionals (!isPy3k) [ futures ];

4
pkgs/development/python-modules/botocore/default.nix
View file

@ -11,11 +11,11 @@
buildPythonPackage rec {
pname = "botocore";
version = "1.10.65";
version = "1.10.84";
src = fetchPypi {
inherit pname version;
sha256 = "35f626029a6b17bfd503ce3379b121606e3f965edcab2612bc75ce8603fdf08c";
sha256 = "d3e4b5a2c903ea30d19d41ea2f65d0e51dce54f4f4c4dfd6ecd7b04f240844a8";
};
propagatedBuildInputs = [

5
pkgs/development/python-modules/bottleneck/default.nix
View file

@ -1,6 +1,7 @@
{ buildPythonPackage
, fetchPypi
, nose
, pytest
, numpy
, python
}:
@ -15,10 +16,10 @@ buildPythonPackage rec {
sha256 = "6efcde5f830aed64feafca0359b51db0e184c72af8ba6675b4a99f263922eb36";
};
checkInputs = [ nose ];
checkInputs = [ pytest nose ];
propagatedBuildInputs = [ numpy ];
checkPhase = ''
nosetests -v $out/${python.sitePackages}
py.test -p no:warnings $out/${python.sitePackages}
'';
postPatch = ''
substituteInPlace setup.py --replace "__builtins__.__NUMPY_SETUP__ = False" ""

4
pkgs/development/python-modules/breathe/default.nix
View file

@ -1,12 +1,12 @@
{ lib, fetchPypi, buildPythonPackage, docutils, six, sphinx, isPy3k }:
buildPythonPackage rec {
version = "4.9.1";
version = "4.10.0";
pname = "breathe";
src = fetchPypi {
inherit pname version;
sha256 = "76e1f3706efeda2610d9a8e7b421d2877ff0654a3fe6d3190a8686536111a684";
sha256 = "e94370b8b607a32d9611ed8246e635f02c21dc6847f04e888a00f66a12694eff";
};
propagatedBuildInputs = [ docutils six sphinx ];

4
pkgs/development/python-modules/btrees/default.nix
View file

@ -9,7 +9,7 @@
buildPythonPackage rec {
pname = "BTrees";
version = "4.5.0";
version = "4.5.1";
buildInputs = [ transaction ];
propagatedBuildInputs = [ persistent zope_interface ];
@ -17,7 +17,7 @@ buildPythonPackage rec {
src = fetchPypi {
inherit pname version;
sha256 = "46b02cb69b26a5238db771ea1955b503df73ecf254bb8063af4c61999fc75b5c";
sha256 = "dcc096c3cf92efd6b9365951f89118fd30bc209c9af83bf050a28151a9992786";
};
meta = with stdenv.lib; {

4
pkgs/development/python-modules/bugwarrior/default.nix
View file

@ -5,11 +5,11 @@
buildPythonPackage rec {
pname = "bugwarrior";
version = "1.5.1";
version = "1.6.0";
src = fetchPypi {
inherit pname version;
sha256 = "0kxknjbw5kchd88i577vlzibg8j60r7zzdhbnragj9wg5s3w60xb";
sha256 = "cfa4fac19b4f4638928347b8fe192315f72813c3e8ed668867e5891338c7e4ec";
};
buildInputs = [ mock unittest2 nose /* jira megaplan */ ];

4
pkgs/development/python-modules/buildout/default.nix
View file

@ -2,11 +2,11 @@
buildPythonPackage rec {
pname = "zc.buildout";
version = "2.2.5";
version = "2.12.1";
src = fetchPypi {
inherit pname version;
sha256 = "fb08f24f9e51e647e29d714f6e9ad51a4ea28673dddeed831315617bb5a805d0";
sha256 = "1e180b62fd129a68cb3a9ec8eb0ef457e18921269a93e87ef2cc34519415332d";
};
meta = with stdenv.lib; {

24
pkgs/development/python-modules/cairocffi/cairocffi-0.8.1-cairo-1.15.12.patch
View file

@ -1,24 +0,0 @@
diff --git a/cairocffi/test_cairo.py b/cairocffi/test_cairo.py
index 1588349..5452910 100644
--- a/cairocffi/test_cairo.py
+++ b/cairocffi/test_cairo.py
@@ -292,7 +292,8 @@ def test_pdf_surface():
pdf_bytes = file_obj.getvalue()
assert pdf_bytes.startswith(b'%PDF')
assert b'/MediaBox [ 0 0 123 432 ]' in pdf_bytes
- assert pdf_bytes.count(b'/Type /Page\n') == 1
+ assert pdf_bytes.count(b'/Type /Pages') == 1
+ assert pdf_bytes.count(b'/Type /Page') == 2
file_obj = io.BytesIO()
surface = PDFSurface(file_obj, 1, 1)
@@ -306,7 +307,8 @@ def test_pdf_surface():
assert b'/MediaBox [ 0 0 1 1 ]' not in pdf_bytes
assert b'/MediaBox [ 0 0 12 100 ]' in pdf_bytes
assert b'/MediaBox [ 0 0 42 700 ]' in pdf_bytes
- assert pdf_bytes.count(b'/Type /Page\n') == 2
+ assert pdf_bytes.count(b'/Type /Pages') == 1
+ assert pdf_bytes.count(b'/Type /Page') == 3
def test_svg_surface():

5
pkgs/development/python-modules/cairocffi/default.nix
View file

@ -17,11 +17,11 @@
buildPythonPackage rec {
pname = "cairocffi";
version = "0.8.1";
version = "0.9.0";
src = fetchPypi {
inherit pname version;
sha256 = "0y373vafv7q35msg7gqdn7niifr3j4j4n070hflxshahs59irss7";
sha256 = "15386c3a9e08823d6826c4491eaccc7b7254b1dc587a3b9ce60c350c3f990337";
};
LC_ALL = "en_US.UTF-8";
@ -49,7 +49,6 @@ buildPythonPackage rec {
gdk_pixbuf = gdk_pixbuf.out;
})
./fix_test_scaled_font.patch
./cairocffi-0.8.1-cairo-1.15.12.patch
];
meta = with lib; {

15
pkgs/development/python-modules/celery/default.nix
View file

@ -2,7 +2,18 @@
pytest, case, kombu, billiard, pytz, anyjson, amqp, eventlet
}:
buildPythonPackage rec {
let
# Needed for celery
pytest_32 = pytest.overridePythonAttrs( oldAttrs: rec {
version = "3.2.5";
src = oldAttrs.src.override {
inherit version;
sha256 = "6d5bd4f7113b444c55a3bbb5c738a3dd80d43563d063fc42dcb0aaefbdd78b81";
};
});
in buildPythonPackage rec {
pname = "celery";
version = "4.2.0";
@ -27,7 +38,7 @@ buildPythonPackage rec {
unset NIX_REDIRECTS LD_PRELOAD
'';
buildInputs = [ pytest case ];
checkInputs = [ pytest_32 case ];
propagatedBuildInputs = [ kombu billiard pytz anyjson amqp eventlet ];
meta = with stdenv.lib; {

8
pkgs/development/python-modules/cement/default.nix
View file

@ -1,18 +1,20 @@
{ stdenv, buildPythonPackage, fetchPypi }:
{ stdenv, buildPythonPackage, fetchPypi, isPy3k }:
buildPythonPackage rec {
pname = "cement";
version = "2.10.12";
version = "3.0.0";
src = fetchPypi {
inherit pname version;
sha256 = "58efb4eacd9ec977ce797a364a13851de6e42392bbde5287d44294f06c5a2f70";
sha256 = "e50e1033d61d18b36787a60d52cad0d3fe20780e7e2f78f0204bde32000645f9";
};
# Disable test tests since they depend on a memcached server running on
# 127.0.0.1:11211.
doCheck = false;
disabled = !isPy3k;
meta = with stdenv.lib; {
homepage = http://builtoncement.com/;
description = "A CLI Application Framework for Python.";

4
pkgs/development/python-modules/certifi/default.nix
View file

@ -5,11 +5,11 @@
buildPythonPackage rec {
pname = "certifi";
version = "2018.4.16";
version = "2018.8.24";
src = fetchPypi {
inherit pname version;
sha256 = "13e698f54293db9f89122b0581843a782ad0934a4fe0172d2a980ba77fc61bb7";
sha256 = "376690d6f16d32f9d1fe8932551d80b23e9d393a8578c5633a2ed39a64861638";
};
meta = {

4
pkgs/development/python-modules/cftime/default.nix
View file

@ -9,11 +9,11 @@
buildPythonPackage rec {
pname = "cftime";
version = "1.0.0";
version = "1.0.1";
src = fetchPypi {
inherit pname version;
sha256 = "f62fe79ed2ad38f4211477e59f6f045c91278351f4ce7578e33ddf52fb121ea8";
sha256 = "20556931f546838d09be5d589482dfae6164e0d403f0aab2163c006b680d3b92";
};
checkInputs = [ pytest coveralls pytestcov ];

4
pkgs/development/python-modules/chainer/default.nix
View file

@ -6,11 +6,11 @@
buildPythonPackage rec {
pname = "chainer";
version = "4.3.0";
version = "4.4.0";
src = fetchPypi {
inherit pname version;
sha256 = "a83044256edb1946c47cb9ae687d195c2aa0deaef46ab85a8ffc4a01f7001683";
sha256 = "9cc4d43e1ea3e0766e211e4e755dbb879f2cf27a805cfa52e32b99fd1e5f24dd";
};
checkInputs = [

4
pkgs/development/python-modules/channels/default.nix
View file

@ -3,11 +3,11 @@
}:
buildPythonPackage rec {
pname = "channels";
version = "2.1.2";
version = "2.1.3";
src = fetchPypi {
inherit pname version;
sha256 = "173441ccf2ac3a93c3b4f86135db301cbe95be58f5815c1e071f2e7154c192a2";
sha256 = "8d503d18b92cef488ba68808a2205e055d29a6a1abae92d277f8f7a9c8752f13";
};
# Files are missing in the distribution

10
pkgs/development/python-modules/cherrypy/default.nix
View file

@ -1,20 +1,20 @@
{ lib, buildPythonPackage, fetchPypi
, cheroot, portend, routes, six
, setuptools_scm
, cheroot, contextlib2, portend, routes, six
, setuptools_scm, zc_lockfile
, backports_unittest-mock, objgraph, pathpy, pytest, pytestcov
, backports_functools_lru_cache, requests_toolbelt
}:
buildPythonPackage rec {
pname = "CherryPy";
version = "17.0.0";
version = "17.3.0";
src = fetchPypi {
inherit pname version;
sha256 = "3cdb5fbae183db49ab1f1a90643d521aa060c93f90001cc99c19d8d15b7a3fb7";
sha256 = "c3e4d76232ade4c47666b9008f92556465df517b8dca833ece3bed027028ae7d";
};
propagatedBuildInputs = [ cheroot portend routes six ];
propagatedBuildInputs = [ cheroot contextlib2 portend routes six zc_lockfile ];
buildInputs = [ setuptools_scm ];

4
pkgs/development/python-modules/cloudpickle/default.nix
View file

@ -2,11 +2,11 @@
buildPythonPackage rec {
pname = "cloudpickle";
version = "0.5.3";
version = "0.5.5";
src = fetchPypi {
inherit pname version;
sha256 = "54858c7b7dc763ed894ff91059c1d0b017d593fe23850d3d8d75f47d98398197";
sha256 = "6ea4b548f61a4f616b065182716318c7dced8c053517f35ac59cec22802daf3d";
};
buildInputs = [ pytest mock ];

10
pkgs/development/python-modules/cmd2/default.nix
View file

@ -1,15 +1,15 @@
{ stdenv, fetchPypi, buildPythonPackage, pythonOlder, isPy3k
, pyperclip, six, pyparsing, vim, wcwidth, colorama
, contextlib2 ? null
, contextlib2 ? null, setuptools_scm
, pytest, mock, which, glibcLocales
}:
buildPythonPackage rec {
pname = "cmd2";
version = "0.9.3";
version = "0.9.4";
src = fetchPypi {
inherit pname version;
sha256 = "cffc94ad46425f80dfb243f53f456b11cea3f45e683504a60b64618a6d28b417";
sha256 = "0037dcf92331c63ae43e7e644536e646fff8be2fd5a83da06b3482f910f929c6";
};
LC_ALL="en_US.UTF-8";
@ -31,6 +31,10 @@ buildPythonPackage rec {
doCheck = !stdenv.isDarwin;
disabled = !isPy3k;
buildInputs = [
setuptools_scm
];
propagatedBuildInputs = [
colorama
pyperclip

4
pkgs/development/python-modules/coveralls/default.nix
View file

@ -16,12 +16,12 @@
buildPythonPackage rec {
pname = "coveralls";
name = "${pname}-python-${version}";
version = "1.3.0";
version = "1.4.0";
# wanted by tests
src = fetchPypi {
inherit pname version;
sha256 = "664794748d2e5673e347ec476159a9d87f43e0d2d44950e98ed0e27b98da8346";
sha256 = "7ddb2e3114db9604a7cb1fcc68a7dcca32dce346f5ba568c99979b38e166f5a6";
};
checkInputs = [

4
pkgs/development/python-modules/cryptography/default.nix
View file

@ -23,11 +23,11 @@
buildPythonPackage rec {
# also bump cryptography_vectors
pname = "cryptography";
version = "2.3";
version = "2.3.1";
src = fetchPypi {
inherit pname version;
sha256 = "c132bab45d4bd0fff1d3fe294d92b0a6eb8404e93337b3127bdec9f21de117e6";
sha256 = "8d10113ca826a4c29d5b85b2c4e045ffa8bad74fb525ee0eceb1d38d4c70dfd6";
};
outputs = [ "out" "dev" ];

4
pkgs/development/python-modules/cryptography_vectors/default.nix
View file

@ -5,11 +5,11 @@
buildPythonPackage rec {
# also bump cryptography
pname = "cryptography_vectors";
version = "2.3";
version = "2.3.1";
src = fetchPypi {
inherit pname version;
sha256 = "356a2ded84ae379e556515eec9b68dd74957651a38465d10605bb9fbae280f15";
sha256 = "bf4d9b61dce69c49e830950aa36fad194706463b0b6dfe81425b9e0bc6644d46";
};
# No tests included

4
pkgs/development/python-modules/cupy/default.nix
View file

@ -6,11 +6,11 @@
buildPythonPackage rec {
pname = "cupy";
version = "4.3.0";
version = "4.4.0";
src = fetchPypi {
inherit pname version;
sha256 = "ea818ff7f36cf6e5b3d3faef5af36a501c8bdeb78805820afa2999789ed698d5";
sha256 = "fca0e3d3fdad4c825197ea421bed0d253224b44daf738d82af5cba856c1c0b3e";
};
checkInputs = [

14
pkgs/development/python-modules/debian/default.nix
View file

@ -1,14 +1,22 @@
{ buildPythonPackage, fetchPypi
{ lib, buildPythonPackage, fetchPypi
, chardet, six}:
buildPythonPackage rec {
pname = "python-debian";
version = "0.1.32";
version = "0.1.33";
src = fetchPypi {
inherit pname version;
sha256 = "143887ac647ad30819f289f5a4ca13b77e56df27b686b84c34669447f7591280";
sha256 = "06e91d45019fe5f2e111ba827ea77730d6ce2fea698ada4e5b0b70b5fdbc18c5";
};
propagatedBuildInputs = [ chardet six ];
# No tests in archive
doCheck = false;
meta = {
description = "Debian package related modules";
license = lib.licenses.gpl2;
};
}

4
pkgs/development/python-modules/deform/default.nix
View file

@ -4,11 +4,11 @@
buildPythonPackage rec {
pname = "deform";
version = "2.0.5";
version = "2.0.6";
src = fetchPypi {
inherit pname version;
sha256 = "874d3346a02c500432efdcc73b1a7174aa0ea69cd52a99bb9a812967f54f6f79";
sha256 = "bda0b809c8a668e105e30650a6766103207eafdd12c313acd59274ccd2c4d297";
};
postPatch = ''

4
pkgs/development/python-modules/detox/default.nix
View file

@ -3,11 +3,11 @@
buildPythonPackage rec {
pname = "detox";
version = "0.12";
version = "0.13";
src = fetchPypi {
inherit pname version;
sha256 = "06svvkszg6xlg0fr471smn4rmpfga960d6qqsyhyiwa48k59n4gk";
sha256 = "f0c2af9c29f8e200a50b561ccc531df3087c80e7d3de6cfa9828f5fea3c8f56c";
};
buildInputs = [ pytest ];

47
pkgs/development/python-modules/dftfit/default.nix Normal file
View file

@ -0,0 +1,47 @@
{ lib
, fetchPypi
, buildPythonPackage
, pymatgen
, marshmallow
, pyyaml
, pygmo
, pandas
, scipy
, numpy
, scikitlearn
, lammps-cython
, pymatgen-lammps
, pytestrunner
, pytest
, pytestcov
, pytest-benchmark
, isPy3k
, openssh
}:
buildPythonPackage rec {
pname = "dftfit";
version = "0.4.22";
disabled = (!isPy3k);
src = fetchPypi {
inherit pname version;
sha256 = "06dbdc21cf9ed199bfceae5301172bee2164a3b9ef6f0814a089530c320ebb3a";
};
buildInputs = [ pytestrunner ];
checkInputs = [ pytest pytestcov pytest-benchmark openssh ];
propagatedBuildInputs = [ pymatgen marshmallow pyyaml pygmo
pandas scipy numpy scikitlearn
lammps-cython pymatgen-lammps ];
# tests require git lfs download. and is quite large so skip tests
doCheck = false;
meta = {
description = "Ab-Initio Molecular Dynamics Potential Development";
homepage = https://gitlab.com/costrouc/dftfit;
license = lib.licenses.mit;
maintainers = with lib.maintainers; [ costrouc ];
};
}

4
pkgs/development/python-modules/docker/default.nix
View file

@ -3,12 +3,12 @@
, ipaddress, backports_ssl_match_hostname, docker_pycreds
}:
buildPythonPackage rec {
version = "3.4.1";
version = "3.5.0";
pname = "docker";
src = fetchPypi {
inherit pname version;
sha256 = "ad077b49660b711d20f50f344f70cfae014d635ef094bf21b0d7df5f0aeedf99";
sha256 = "bc693be5a84b3b9e5aaf156068c5c0a445ee5138c638c3fbc857133bf67ebe07";
};
propagatedBuildInputs = [

35
pkgs/development/python-modules/docutils/default.nix Normal file
View file

@ -0,0 +1,35 @@
{ lib
, fetchurl
, buildPythonPackage
, isPy3k
, python
}:
buildPythonPackage rec {
pname = "docutils";
version = "0.14";
src = fetchurl {
url = "mirror://sourceforge/docutils/${pname}.tar.gz";
sha256 = "0x22fs3pdmr42kvz6c654756wja305qv6cx1zbhwlagvxgr4xrji";
};
checkPhase = if isPy3k then ''
${python.interpreter} test3/alltests.py
'' else ''
${python.interpreter} test/alltests.py
'';
# Create symlinks lacking a ".py" suffix, many programs depend on these names
postFixup = ''
(cd $out/bin && for f in *.py; do
ln -s $f $(echo $f | sed -e 's/\.py$//')
done)
'';
meta = {
description = "Docutils -- Python Documentation Utilities";
homepage = http://docutils.sourceforge.net/;
maintainers = with lib.maintainers; [ garbas AndersonTorres ];
};
}

4
pkgs/development/python-modules/dogpile.cache/default.nix
View file

@ -4,11 +4,11 @@
buildPythonPackage rec {
pname = "dogpile.cache";
version = "0.6.6";
version = "0.6.7";
src = fetchPypi {
inherit pname version;
sha256 = "044d4ea0a0abc72491044f3d3df8e1fc9e8fa7a436c6e9a0da5850d23a0d16c1";
sha256 = "fca7deb7c276b879b01c15c5d39b3c05701dc43b263ec3fef1e52cb851cf88ab";
};
# Disable concurrency tests that often fail,

4
pkgs/development/python-modules/dulwich/default.nix
View file

@ -4,12 +4,12 @@
, git, glibcLocales }:
buildPythonPackage rec {
version = "0.19.5";
version = "0.19.6";
pname = "dulwich";
src = fetchPypi {
inherit pname version;
sha256 = "34f99e575fe1f1e89cca92cec1ddd50b4991199cb00609203b28df9eb83ce259";
sha256 = "9a7dc5c5759f3d3b7a9ac0a684aa2c47f099e1722d9caab5b043cef1d73ff4a2";
};
LC_ALL = "en_US.UTF-8";

4
pkgs/development/python-modules/easydict/default.nix
View file

@ -2,11 +2,11 @@
buildPythonPackage rec {
pname = "easydict";
version = "1.7";
version = "1.8";
src = fetchPypi {
inherit pname version;
sha256 = "1xpnwjdw4x5kficjgcajqcal6bxcb0ax8l6hdkww9fp6lrh28x8v";
sha256 = "f1ec91110737a62fe28d14970ffa7a7c7b441a32e35a6f3da6a6082ffb7f9432";
};
docheck = false; # No tests in archive

4
pkgs/development/python-modules/elasticsearch/default.nix
View file

@ -7,11 +7,11 @@
buildPythonPackage (rec {
pname = "elasticsearch";
version = "6.3.0";
version = "6.3.1";
src = fetchPypi {
inherit pname version;
sha256 = "80ff7a1a56920535a9987da333c7e385b2ded27595b6de33860707dab758efbe";
sha256 = "aada5cfdc4a543c47098eb3aca6663848ef5d04b4324935ced441debc11ec98b";
};
# Check is disabled because running them destroy the content of the local cluster!

4
pkgs/development/python-modules/faker/default.nix
View file

@ -8,11 +8,11 @@ assert pythonOlder "3.3" -> ipaddress != null;
buildPythonPackage rec {
pname = "Faker";
version = "0.8.17";
version = "0.8.18";
src = fetchPypi {
inherit pname version;
sha256 = "0e9a1227a3a0f3297a485715e72ee6eb77081b17b629367042b586e38c03c867";
sha256 = "0184fa252f86214308bb6bed344f96294f2e3528fbffafc727890cf2a86d6027";
};
checkInputs = [

4
pkgs/development/python-modules/fastrlock/default.nix
View file

@ -2,11 +2,11 @@
buildPythonPackage rec {
pname = "fastrlock";
version = "0.3";
version = "0.4";
src = fetchPypi {
inherit pname version;
sha256 = "00mr9b15d539z89ng5nf89s2ryhk90xwx95jal77ma0wslixrk5d";
sha256 = "6abdbb35205792e2d2a8c441aaa41a613d43ee2d88b3af4fd9735ae7a5f7db6b";
};
meta = with stdenv.lib; {

4
pkgs/development/python-modules/filelock/default.nix
View file

@ -2,11 +2,11 @@
buildPythonPackage rec {
pname = "filelock";
version = "3.0.4";
version = "3.0.6";
src = fetchPypi {
inherit pname version;
sha256 = "011327d4ed939693a5b28c0fdf2fd9bda1f68614c1d6d0643a89382ce9843a71";
sha256 = "59ccab92fe118da7e5ce5a9fcd95506ade58d9d5f606db4922192524edfac820";
};
meta = with stdenv.lib; {

4
pkgs/development/python-modules/folium/default.nix
View file

@ -18,10 +18,10 @@ buildPythonPackage rec {
src = fetchPypi {
inherit pname version;
sha256 = "0yfb8ygq67m149n72bb8h7dk9mx8d3ivc5ygqwdj4q8qggj1ns08";
sha256 = "08681be47b1861221bc7cf17b6e368a8d734db81682d716c22a11e839f47cb79";
};
checkInputs = [ pytest numpy nbconvert pandas mock ];
checkInputs = [ pytest nbconvert pandas mock ];
propagatedBuildInputs = [ jinja2 branca six requests numpy ];
# No tests in archive

4
pkgs/development/python-modules/fonttools/default.nix
View file

@ -8,11 +8,11 @@
buildPythonPackage rec {
pname = "fonttools";
version = "3.28.0";
version = "3.29.0";
src = fetchPypi {
inherit pname version;
sha256 = "ebf2ee25a6060e8551880a3b05d6ecadcdcfbd1b32fc272ff7b3acdb22945b6f";
sha256 = "aab38c8c131670684321437d4857dcb4de1c775efd152a9ca9c4d81f1cb97fe7";
extension = "zip";
};

4
pkgs/development/python-modules/gevent/default.nix
View file

@ -2,11 +2,11 @@
buildPythonPackage rec {
pname = "gevent";
version = "1.3.5";
version = "1.3.6";
src = fetchPypi {
inherit pname version;
sha256 = "7f15861f3cc92f49663ca88c4774d26d8044783a65fbc28071a2bd1c7bf36ff0";
sha256 = "7b413c391e8ad6607b7f7540d698a94349abd64e4935184c595f7cdcc69904c6";
};
buildInputs = [ libev ];

4
pkgs/development/python-modules/google_api_core/default.nix
View file

@ -3,11 +3,11 @@
buildPythonPackage rec {
pname = "google-api-core";
version = "1.2.1";
version = "1.3.0";
src = fetchPypi {
inherit pname version;
sha256 = "e24e391054ed6e925ff6d03f225d9f66f3da97d0ab6f61e59274fb918fbe3ef1";
sha256 = "ac85fc7f6687bb0271f2f70ca298da90f35789f9de1fe3a11e8caeb571332b77";
};
propagatedBuildInputs = [

4
pkgs/development/python-modules/google_auth/default.nix
View file

@ -3,11 +3,11 @@
buildPythonPackage rec {
pname = "google-auth";
version = "1.5.0";
version = "1.5.1";
src = fetchPypi {
inherit pname version;
sha256 = "1745c9066f698eac3da99cef082914495fb71bc09597ba7626efbbb64c4acc57";
sha256 = "9ca363facbf2622d9ba828017536ccca2e0f58bd15e659b52f312172f8815530";
};
checkInputs = [ pytest mock oauth2client flask requests urllib3 pytest-localserver ];

4
pkgs/development/python-modules/gphoto2/default.nix
View file

@ -4,11 +4,11 @@
buildPythonPackage rec {
pname = "gphoto2";
version = "1.8.2";
version = "1.8.3";
src = fetchPypi {
inherit pname version;
sha256 = "1806bdjc18qh0wyayxymgjnqqqlxs2iwvgk594anxw9y69hrxqni";
sha256 = "0257f90f0d8342b8bc996ff1b45b2cd3219a29f8123aa21a6da159ee3566e49f";
};
nativeBuildInputs = [ pkgconfig ];

4
pkgs/development/python-modules/grpcio-tools/default.nix
View file

@ -2,11 +2,11 @@
buildPythonPackage rec {
pname = "grpcio-tools";
version = "1.13.0";
version = "1.14.1";
src = fetchPypi {
inherit pname version;
sha256 = "1ck6818kb4nb6skm9lqg492brqs7kfk65f4hh2c7h7c8pkbrpcw1";
sha256 = "4ce5aa660d7884f23aac1eafa93b97a4c3e2b512edff871e91fdb6ee86ebd5ea";
};
enableParallelBuilding = true;

4
pkgs/development/python-modules/grpcio/default.nix
View file

@ -4,11 +4,11 @@
with stdenv.lib;
buildPythonPackage rec {
pname = "grpcio";
version = "1.13.0";
version = "1.14.1";
src = fetchPypi {
inherit pname version;
sha256 = "6324581e215157f0fbe335dff2e21a65b4406db98ac7cca05f1e23b4f510b426";
sha256 = "4bf23666e763ca7ff6010465864e9f088f4ac7ecc1e11abd6f85b250e66b2c05";
};
nativeBuildInputs = [ pkgconfig ] ++ optional stdenv.isDarwin darwin.cctools;

3
pkgs/development/python-modules/h5py/default.nix
View file

@ -37,6 +37,9 @@ in buildPythonPackage rec {
propagatedBuildInputs = [ numpy six]
++ optionals mpiSupport [ mpi4py openssh ];
# https://github.com/h5py/h5py/issues/1088
doCheck = false;
meta = {
description =
"Pythonic interface to the HDF5 binary data format";

4
pkgs/development/python-modules/hvac/default.nix
View file

@ -2,11 +2,11 @@
buildPythonPackage rec {
pname = "hvac";
version = "0.6.2";
version = "0.6.3";
src = fetchPypi {
inherit pname version;
sha256 = "4bc80744df5f09882b1cc91755b03b7b62b093fc63c8c4abb26fbfb9c9e878dd";
sha256 = "54672a93f75453a7de13c7c10c6d8a51630e2559a8e2a563d8e272e9e188443f";
};
propagatedBuildInputs = [ requests ];

4
pkgs/development/python-modules/ibmquantumexperience/default.nix
View file

@ -7,11 +7,11 @@
buildPythonPackage rec {
pname = "IBMQuantumExperience";
version = "1.9.8";
version = "2.0.2";
src = fetchPypi {
inherit pname version;
sha256 = "78a7d9770fa2884d79d3c8b18f374644866e4d22ec151cf703053f7530bb7b7c";
sha256 = "f2a5662d7457c297af0751985979e64a88569beb07cfedad0ce1dfa5a7237842";
};
propagatedBuildInputs = [

4
pkgs/development/python-modules/invoke/default.nix
View file

@ -5,11 +5,11 @@
buildPythonPackage rec {
pname = "invoke";
version = "1.1.0";
version = "1.1.1";
src = fetchPypi {
inherit pname version;
sha256 = "0aiy1xvk1f91246zxd1zqrm679vdvd10h843a2na41cqr3cflpi6";
sha256 = "1c2cf54c9b9af973ad9704d8ba81b225117cab612568cacbfb3fc42958cc20a9";
};
# errors with vendored libs

4
pkgs/development/python-modules/ipython/default.nix
View file

@ -23,11 +23,11 @@
buildPythonPackage rec {
pname = "ipython";
version = "6.4.0";
version = "6.5.0";
src = fetchPypi {
inherit pname version;
sha256 = "eca537aa61592aca2fef4adea12af8e42f5c335004dfa80c78caf80e8b525e5c";
sha256 = "b0f2ef9eada4a68ef63ee10b6dde4f35c840035c50fd24265f8052c98947d5a4";
};
prePatch = lib.optionalString stdenv.isDarwin ''

4
pkgs/development/python-modules/ipywidgets/default.nix
View file

@ -14,11 +14,11 @@
buildPythonPackage rec {
pname = "ipywidgets";
version = "7.3.0";
version = "7.4.0";
src = fetchPypi {
inherit pname version;
sha256 = "3ce93db970a94f06f38121da70757cdbcce884ecd14f79a4dd9bc49a47e0f33b";
sha256 = "fd24a66d82f2ea49e281da7714a7c656340d3ec24dff376b17590fa59469b817";
};
# Tests are not distributed

4
pkgs/development/python-modules/jdatetime/default.nix
View file

@ -2,11 +2,11 @@
buildPythonPackage rec {
pname = "jdatetime";
version = "2.2.1";
version = "3.0.0";
src = fetchPypi {
inherit pname version;
sha256 = "030a47ad3acbde45cb03872e2c6415c675dbb4a82462302971e93076145b5096";
sha256 = "07cdb02e8d6610c38e8ae7746b12cbc39068cc5d54fb2baa915579b60d781b5b";
};
propagatedBuildInputs = [ six ];

5
pkgs/development/python-modules/jinja2/default.nix
View file

@ -14,9 +14,12 @@ buildPythonPackage rec {
propagatedBuildInputs = [ markupsafe ];
checkPhase = ''
pytest -v
pytest -v tests
'';
# RecursionError: maximum recursion depth exceeded
doCheck = false;
meta = with stdenv.lib; {
homepage = http://jinja.pocoo.org/;
description = "Stand-alone template engine";

4
pkgs/development/python-modules/jira/default.nix
View file

@ -6,13 +6,13 @@
buildPythonPackage rec {
pname = "jira";
version = "1.0.15";
version = "2.0.0";
PBR_VERSION = version;
src = fetchPypi {
inherit pname version;
sha256 = "20108a1d5b0dd058d5d4e0047f2d09ee06aaa413b22ca4d5c249e86167417fe8";
sha256 = "e2a94adff98e45b29ded030adc76103eab34fa7d4d57303f211f572bedba0e93";
};
buildInputs = [ glibcLocales pytest pytestcov pytestrunner pbr ];

4
pkgs/development/python-modules/joblib/default.nix
View file

@ -9,10 +9,10 @@
buildPythonPackage rec {
pname = "joblib";
version = "0.12.1";
version = "0.12.3";
src = fetchPypi {
inherit pname version;
sha256 = "68e6128e4734196616a39e2d48830ec7d61551c7f5748849e4c91478d2444524";
sha256 = "333b9bf16ff015d6b56bf80b9831afdd243443cb84c7ff7b6e342f117e354c42";
};
checkInputs = [ sphinx numpydoc pytest ];

4
pkgs/development/python-modules/jsonrpc-async/default.nix
View file

@ -3,11 +3,11 @@
buildPythonPackage rec {
pname = "jsonrpc-async";
version = "1.0.0";
version = "1.0.1";
src = fetchPypi {
inherit pname version;
sha256 = "6241a221b52e18265fe6bb59c60633acebb6fb5ef8c04de9a076b757aa133b86";
sha256 = "adda3ff6e122b1932b6e20cf583666ea65db4248bc19b04811a4ccc0f0b03d95";
};
propagatedBuildInputs = [ aiohttp jsonrpc-base ];

4
pkgs/development/python-modules/jsonrpc-base/default.nix
View file

@ -2,11 +2,11 @@
buildPythonPackage rec {
pname = "jsonrpc-base";
version = "1.0.1";
version = "1.0.2";
src = fetchPypi {
inherit pname version;
sha256 = "21f860c915617f6475aa1ac5a1ec11de03cce6b279741f25ad97d8a4c5b76c3c";
sha256 = "f9baac32aa51c3052d03b86ff30a9856900b8b4a4eb175f7bf2c8722520b8637";
};
propagatedBuildInputs = [ ];

4
pkgs/development/python-modules/jsonrpc-websocket/default.nix
View file

@ -3,11 +3,11 @@
buildPythonPackage rec {
pname = "jsonrpc-websocket";
version = "1.0.0";
version = "1.0.1";
src = fetchPypi {
inherit pname version;
sha256 = "40949836996c0a8104e7878997d3f68bda4561e9d3af64e5cd178127ec3c2778";
sha256 = "e74e490fefa3b8f33620fca98f7cd9a53fb765b9ed6f78360482a3f364230885";
};
propagatedBuildInputs = [ aiohttp jsonrpc-base ];

4
pkgs/development/python-modules/junos-eznc/default.nix
View file

@ -15,11 +15,11 @@
buildPythonPackage rec {
pname = "junos-eznc";
version = "2.1.8";
version = "2.1.9";
src = fetchPypi {
inherit pname version;
sha256 = "daa62e5abfc66ef12e4fb43a1c264673e662e6f2d937cd10666c1c6dcf2ac6ac";
sha256 = "a6729c35efd764e1f22457b72898bba554986466306ad29ad2d0bb071e997093";
};

4
pkgs/development/python-modules/jupyterlab/default.nix
View file

@ -1,12 +1,12 @@
{ lib, buildPythonPackage, isPy3k, fetchPypi, ipython_genutils, jupyterlab_launcher, notebook }:
buildPythonPackage rec {
pname = "jupyterlab";
version = "0.33.7";
version = "0.34.6";
disabled = !isPy3k;
src = fetchPypi {
inherit pname version;
sha256 = "ab9f7bcbc3b4e107897f368aa0527cdc1b4ccf0c370e218ae03ac1d75fac261c";
sha256 = "d6e5a3855a0d55e6aa4ab704379da5da3db2e652442e79acfa2e9d14ef50ccb3";
};
propagatedBuildInputs = [

4
pkgs/development/python-modules/jupyterlab_launcher/default.nix
View file

@ -1,11 +1,11 @@
{ lib, buildPythonPackage, fetchPypi, jsonschema, notebook }:
buildPythonPackage rec {
pname = "jupyterlab_launcher";
version = "0.11.2";
version = "0.13.1";
src = fetchPypi {
inherit pname version;
sha256 = "236a647f4c3f8417413643a918a893a5f662fb5d2fdccce2fd101e3cca2e7fd1";
sha256 = "f880eada0b8b1f524d5951dc6fcae0d13b169897fc8a247d75fb5beadd69c5f0";
};
propagatedBuildInputs = [

4
pkgs/development/python-modules/keras-applications/default.nix
View file

@ -2,11 +2,11 @@
buildPythonPackage rec {
pname = "Keras_Applications";
version = "1.0.4";
version = "1.0.5";
src = fetchPypi {
inherit pname version;
sha256 = "8c95300328630ae74fb0828b6fa38269a25c0228a02f1e5181753bfd48961f49";
sha256 = "26a7318b9d8d5be80d75ab08a1284aaf4b94125dd8271b18ca89791e16eb2cfc";
};
# Cyclic dependency: keras-applications requires keras, which requires keras-applications

4
pkgs/development/python-modules/keras-preprocessing/default.nix
View file

@ -2,11 +2,11 @@
buildPythonPackage rec {
pname = "Keras_Preprocessing";
version = "1.0.2";
version = "1.0.3";
src = fetchPypi {
inherit pname version;
sha256 = "f5306554d2b454d825b36f35e327744f5477bd2ae21017f1a93b2097bed6757e";
sha256 = "02ba0a3b31ed89c4b0c21d55ba7d87529097d56f394e3850b6d3c9e6c63ce7ae";
};
# Cyclic dependency: keras-preprocessing requires keras, which requires keras-preprocessing

9
pkgs/development/python-modules/keyrings-alt/default.nix
View file

@ -11,12 +11,15 @@ buildPythonPackage rec {
sha256 = "0nnva8g03dv6gdhjk1ihn2qw7g15232fyj8shipah9whgfv8d75m";
};
postPatch = ''
substituteInPlace pytest.ini \
--replace "--flake8" ""
'';
nativeBuildInputs = [ setuptools_scm ];
propagatedBuildInputs = [ six ];
# Fails with "ImportError: cannot import name mock"
#doCheck = false;
checkInputs = [ pytest pytest-flake8 keyring ] ++ stdenv.lib.optional (pythonOlder "3.3") backports_unittest-mock;
checkInputs = [ pytest keyring ] ++ stdenv.lib.optional (pythonOlder "3.3") backports_unittest-mock;
checkPhase = ''
py.test

4
pkgs/development/python-modules/kubernetes/default.nix
View file

@ -4,7 +4,7 @@
buildPythonPackage rec {
pname = "kubernetes";
version = "6.0.0";
version = "7.0.0";
prePatch = ''
sed -e 's/sphinx>=1.2.1,!=1.3b1,<1.4 # BSD/sphinx/' -i test-requirements.txt
@ -23,7 +23,7 @@ buildPythonPackage rec {
src = fetchPypi {
inherit pname version;
sha256 = "b370ab4abd925309db69a14a4723487948e9a83de60ca92782ec14992b741c89";
sha256 = "84dfb4319afac189e8327b71b9332b5329d2a78074f58958c5f06a870edf32ba";
};
checkInputs = [ isort coverage pytest mock sphinx autopep8 pep8 codecov recommonmark nose ];

53
pkgs/development/python-modules/lammps-cython/default.nix Normal file
View file

@ -0,0 +1,53 @@
{ lib
, fetchurl
, buildPythonPackage
, lammps-mpi
, mpi
, mpi4py
, numpy
, cython
, pymatgen
, ase
, pytestrunner
, pytest
, pytestcov
, isPy3k
, openssh
}:
buildPythonPackage rec {
pname = "lammps-cython";
version = "0.5.7";
disabled = (!isPy3k);
src = fetchurl {
url = "https://gitlab.com/costrouc/${pname}/-/archive/v${version}/${pname}-v${version}.tar.gz";
sha256 = "1wj9scmjdl00af13b5ihfccrjpikrdgkzd88ialam1nkxvxi42bl";
};
buildInputs = [ cython pytestrunner ];
checkInputs = [ pytest pytestcov openssh ];
propagatedBuildInputs = [ mpi4py pymatgen ase numpy ];
preBuild = ''
echo "Creating lammps.cfg file..."
cat << EOF > lammps.cfg
[lammps]
lammps_include_dir = ${lammps-mpi}/include
lammps_library_dir = ${lammps-mpi}/lib
lammps_library = lammps_mpi
[mpi]
mpi_include_dir = ${mpi}/include
mpi_library_dir = ${mpi}/lib
mpi_library = mpi
EOF
'';
meta = {
description = "Pythonic Wrapper to LAMMPS using cython";
homepage = https://gitlab.com/costrouc/lammps-cython;
license = lib.licenses.mit;
maintainers = with lib.maintainers; [ costrouc ];
};
}

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