Merge master into staging-next
This commit is contained in:
commit
58ecfa2997
@ -5,6 +5,8 @@ with lib;
|
|||||||
let
|
let
|
||||||
cfg = config.services.kanata;
|
cfg = config.services.kanata;
|
||||||
|
|
||||||
|
upstreamDoc = "See [the upstream documentation](https://github.com/jtroo/kanata/blob/main/docs/config.adoc) and [example config files](https://github.com/jtroo/kanata/tree/main/cfg_samples) for more information.";
|
||||||
|
|
||||||
keyboard = {
|
keyboard = {
|
||||||
options = {
|
options = {
|
||||||
devices = mkOption {
|
devices = mkOption {
|
||||||
@ -22,28 +24,16 @@ let
|
|||||||
type = types.lines;
|
type = types.lines;
|
||||||
example = ''
|
example = ''
|
||||||
(defsrc
|
(defsrc
|
||||||
grv 1 2 3 4 5 6 7 8 9 0 - = bspc
|
caps)
|
||||||
tab q w e r t y u i o p [ ] \
|
|
||||||
caps a s d f g h j k l ; ' ret
|
|
||||||
lsft z x c v b n m , . / rsft
|
|
||||||
lctl lmet lalt spc ralt rmet rctl)
|
|
||||||
|
|
||||||
(deflayer qwerty
|
(deflayermap (default-layer)
|
||||||
grv 1 2 3 4 5 6 7 8 9 0 - = bspc
|
;; tap caps lock as caps lock, hold caps lock as left control
|
||||||
tab q w e r t y u i o p [ ] \
|
caps (tap-hold 100 100 caps lctl))
|
||||||
@cap a s d f g h j k l ; ' ret
|
|
||||||
lsft z x c v b n m , . / rsft
|
|
||||||
lctl lmet lalt spc ralt rmet rctl)
|
|
||||||
|
|
||||||
(defalias
|
|
||||||
;; tap within 100ms for capslk, hold more than 100ms for lctl
|
|
||||||
cap (tap-hold 100 100 caps lctl))
|
|
||||||
'';
|
'';
|
||||||
description = ''
|
description = ''
|
||||||
Configuration other than `defcfg`.
|
Configuration other than `defcfg`.
|
||||||
|
|
||||||
See [example config files](https://github.com/jtroo/kanata)
|
${upstreamDoc}
|
||||||
for more information.
|
|
||||||
'';
|
'';
|
||||||
};
|
};
|
||||||
extraDefCfg = mkOption {
|
extraDefCfg = mkOption {
|
||||||
@ -55,8 +45,7 @@ let
|
|||||||
from the devices option) and
|
from the devices option) and
|
||||||
`linux-continue-if-no-devs-found` (hardcoded to be yes).
|
`linux-continue-if-no-devs-found` (hardcoded to be yes).
|
||||||
|
|
||||||
See [example config files](https://github.com/jtroo/kanata)
|
${upstreamDoc}
|
||||||
for more information.
|
|
||||||
'';
|
'';
|
||||||
};
|
};
|
||||||
extraArgs = mkOption {
|
extraArgs = mkOption {
|
||||||
@ -153,7 +142,7 @@ in
|
|||||||
options.services.kanata = {
|
options.services.kanata = {
|
||||||
enable = mkEnableOption "kanata, a tool to improve keyboard comfort and usability with advanced customization";
|
enable = mkEnableOption "kanata, a tool to improve keyboard comfort and usability with advanced customization";
|
||||||
package = mkPackageOption pkgs "kanata" {
|
package = mkPackageOption pkgs "kanata" {
|
||||||
example = "kanata-with-cmd";
|
example = [ "kanata-with-cmd" ];
|
||||||
extraDescription = ''
|
extraDescription = ''
|
||||||
::: {.note}
|
::: {.note}
|
||||||
If {option}`danger-enable-cmd` is enabled in any of the keyboards, the
|
If {option}`danger-enable-cmd` is enabled in any of the keyboards, the
|
||||||
|
@ -1,59 +0,0 @@
|
|||||||
{ lib, stdenv, fetchFromGitLab, meson, ninja
|
|
||||||
, wrapGAppsHook3, pkg-config, desktop-file-utils
|
|
||||||
, appstream-glib, pythonPackages, glib, gobject-introspection
|
|
||||||
, gtk3, webkitgtk, glib-networking, gnome, gspell, texliveMedium
|
|
||||||
, shared-mime-info, libhandy, fira, sassc
|
|
||||||
}:
|
|
||||||
|
|
||||||
let
|
|
||||||
pythonEnv = pythonPackages.python.withPackages(p: with p; [
|
|
||||||
regex setuptools levenshtein pyenchant
|
|
||||||
pygobject3 pycairo pypandoc chardet
|
|
||||||
]);
|
|
||||||
|
|
||||||
in stdenv.mkDerivation rec {
|
|
||||||
pname = "apostrophe";
|
|
||||||
version = "2.6.3";
|
|
||||||
|
|
||||||
src = fetchFromGitLab {
|
|
||||||
owner = "World";
|
|
||||||
repo = pname;
|
|
||||||
domain = "gitlab.gnome.org";
|
|
||||||
rev = "v${version}";
|
|
||||||
sha256 = "sha256-RBrrG1TO810LidIelYGNaK7PjDq84D0cA8VcMojAW3M=";
|
|
||||||
};
|
|
||||||
|
|
||||||
nativeBuildInputs = [ meson ninja pkg-config desktop-file-utils
|
|
||||||
appstream-glib wrapGAppsHook3 sassc gobject-introspection ];
|
|
||||||
|
|
||||||
buildInputs = [ glib pythonEnv gtk3
|
|
||||||
gnome.adwaita-icon-theme webkitgtk gspell texliveMedium
|
|
||||||
glib-networking libhandy ];
|
|
||||||
|
|
||||||
postPatch = ''
|
|
||||||
substituteInPlace data/media/css/web/base.css \
|
|
||||||
--replace 'url("/app/share/fonts/FiraSans-Regular.ttf") format("ttf")' \
|
|
||||||
'url("${fira}/share/fonts/opentype/FiraSans-Regular.otf") format("otf")' \
|
|
||||||
--replace 'url("/app/share/fonts/FiraMono-Regular.ttf") format("ttf")' \
|
|
||||||
'url("${fira}/share/fonts/opentype/FiraMono-Regular.otf") format("otf")'
|
|
||||||
|
|
||||||
patchShebangs --build build-aux/meson_post_install.py
|
|
||||||
'';
|
|
||||||
|
|
||||||
preFixup = ''
|
|
||||||
gappsWrapperArgs+=(
|
|
||||||
--prefix PYTHONPATH : "$out/lib/python${pythonEnv.pythonVersion}/site-packages/"
|
|
||||||
--prefix PATH : "${texliveMedium}/bin"
|
|
||||||
--prefix XDG_DATA_DIRS : "${shared-mime-info}/share"
|
|
||||||
)
|
|
||||||
'';
|
|
||||||
|
|
||||||
meta = with lib; {
|
|
||||||
homepage = "https://gitlab.gnome.org/World/apostrophe";
|
|
||||||
description = "A distraction free Markdown editor for GNU/Linux";
|
|
||||||
license = licenses.gpl3;
|
|
||||||
platforms = platforms.linux;
|
|
||||||
maintainers = [ maintainers.sternenseemann ];
|
|
||||||
mainProgram = "apostrophe";
|
|
||||||
};
|
|
||||||
}
|
|
@ -1,6 +1,9 @@
|
|||||||
{ lib, stdenv
|
{ lib, stdenv
|
||||||
, fetchFromBitbucket
|
, fetchFromBitbucket
|
||||||
, autoreconfHook
|
, autoreconfHook
|
||||||
|
|
||||||
|
# Reverse dependency
|
||||||
|
, sage
|
||||||
}:
|
}:
|
||||||
|
|
||||||
stdenv.mkDerivation rec {
|
stdenv.mkDerivation rec {
|
||||||
@ -20,6 +23,8 @@ stdenv.mkDerivation rec {
|
|||||||
autoreconfHook
|
autoreconfHook
|
||||||
];
|
];
|
||||||
|
|
||||||
|
passthru.tests = { inherit sage; };
|
||||||
|
|
||||||
meta = with lib; {
|
meta = with lib; {
|
||||||
description = "Littlewood-Richardson calculator";
|
description = "Littlewood-Richardson calculator";
|
||||||
homepage = "http://math.rutgers.edu/~asbuch/lrcalc/";
|
homepage = "http://math.rutgers.edu/~asbuch/lrcalc/";
|
||||||
|
@ -2,13 +2,13 @@
|
|||||||
|
|
||||||
stdenv.mkDerivation (finalAttrs: {
|
stdenv.mkDerivation (finalAttrs: {
|
||||||
pname = "qalculate-gtk";
|
pname = "qalculate-gtk";
|
||||||
version = "5.0.0";
|
version = "5.1.0";
|
||||||
|
|
||||||
src = fetchFromGitHub {
|
src = fetchFromGitHub {
|
||||||
owner = "qalculate";
|
owner = "qalculate";
|
||||||
repo = "qalculate-gtk";
|
repo = "qalculate-gtk";
|
||||||
rev = "v${finalAttrs.version}";
|
rev = "v${finalAttrs.version}";
|
||||||
hash = "sha256-hlGNL7aMzxBxtATWJBqJTFEQqMv10oC3sRCdtRLHOww=";
|
hash = "sha256-yI+8TrNZJt4eJnDX5mk6RozBe2ZeP7sTyAjsgiYQPck=";
|
||||||
};
|
};
|
||||||
|
|
||||||
hardeningDisable = [ "format" ];
|
hardeningDisable = [ "format" ];
|
||||||
|
@ -2,13 +2,13 @@
|
|||||||
|
|
||||||
stdenv.mkDerivation (finalAttrs: {
|
stdenv.mkDerivation (finalAttrs: {
|
||||||
pname = "qalculate-qt";
|
pname = "qalculate-qt";
|
||||||
version = "5.0.0";
|
version = "5.1.0";
|
||||||
|
|
||||||
src = fetchFromGitHub {
|
src = fetchFromGitHub {
|
||||||
owner = "qalculate";
|
owner = "qalculate";
|
||||||
repo = "qalculate-qt";
|
repo = "qalculate-qt";
|
||||||
rev = "v${finalAttrs.version}";
|
rev = "v${finalAttrs.version}";
|
||||||
hash = "sha256-X7IY2yXpZiyE+T2dl0G4tWpJ5O6MVCy/sOY3v9inma0=";
|
hash = "sha256-gJfIC5HdA10gb/Dh/yhJbkCZfhUnN0zihqyfDjPv6ow=";
|
||||||
};
|
};
|
||||||
|
|
||||||
nativeBuildInputs = [ qmake intltool pkg-config qttools wrapQtAppsHook ];
|
nativeBuildInputs = [ qmake intltool pkg-config qttools wrapQtAppsHook ];
|
||||||
|
118
pkgs/by-name/ap/apostrophe/package.nix
Normal file
118
pkgs/by-name/ap/apostrophe/package.nix
Normal file
@ -0,0 +1,118 @@
|
|||||||
|
{
|
||||||
|
lib,
|
||||||
|
fetchFromGitLab,
|
||||||
|
gtksourceview5,
|
||||||
|
libspelling,
|
||||||
|
fetchFromGitHub,
|
||||||
|
python3Packages,
|
||||||
|
meson,
|
||||||
|
ninja,
|
||||||
|
pkg-config,
|
||||||
|
wrapGAppsHook4,
|
||||||
|
desktop-file-utils,
|
||||||
|
gobject-introspection,
|
||||||
|
libadwaita,
|
||||||
|
webkitgtk_6_0,
|
||||||
|
texliveMedium,
|
||||||
|
shared-mime-info,
|
||||||
|
}:
|
||||||
|
|
||||||
|
let
|
||||||
|
version = "3.0";
|
||||||
|
|
||||||
|
src = fetchFromGitLab {
|
||||||
|
owner = "World";
|
||||||
|
repo = "apostrophe";
|
||||||
|
domain = "gitlab.gnome.org";
|
||||||
|
rev = "v${version}";
|
||||||
|
sha256 = "sha256-wKxRCU00nSk7F8IZNWoLRtGs3m6ol3UBnArtppUOz/g=";
|
||||||
|
};
|
||||||
|
|
||||||
|
# Patches are required by upstream. Without the patches
|
||||||
|
# typing `- aaa`, newline, `- bbb` the program crashes
|
||||||
|
gtksourceview5-patched = gtksourceview5.overrideAttrs (prev: {
|
||||||
|
patches = (prev.patches or [ ]) ++ [ "${src}/build-aux/flatpak/sourceview_text_commits.patch" ];
|
||||||
|
});
|
||||||
|
|
||||||
|
libspelling-patched =
|
||||||
|
(libspelling.override { gtksourceview5 = gtksourceview5-patched; }).overrideAttrs
|
||||||
|
(prev: {
|
||||||
|
patches = (prev.patches or [ ]) ++ [ "${src}/build-aux/flatpak/libspelling_text_commits.patch" ];
|
||||||
|
});
|
||||||
|
|
||||||
|
reveal-js = fetchFromGitHub {
|
||||||
|
owner = "hakimel";
|
||||||
|
repo = "reveal.js";
|
||||||
|
|
||||||
|
# keep in sync with upstream shipped version
|
||||||
|
# in build-aux/flatpak/org.gnome.gitlab.somas.Apostrophe.json
|
||||||
|
rev = "4.6.0";
|
||||||
|
hash = "sha256-a+J+GasFmRvu5cJ1GLXscoJ+owzFXsLhCbeDbYChkyQ=";
|
||||||
|
};
|
||||||
|
in
|
||||||
|
python3Packages.buildPythonApplication rec {
|
||||||
|
inherit version src;
|
||||||
|
pname = "apostrophe";
|
||||||
|
pyproject = false;
|
||||||
|
|
||||||
|
postPatch =
|
||||||
|
''
|
||||||
|
substituteInPlace build-aux/meson_post_install.py \
|
||||||
|
--replace-fail 'gtk-update-icon-cache' 'gtk4-update-icon-cache'
|
||||||
|
|
||||||
|
patchShebangs --build build-aux/meson_post_install.py
|
||||||
|
''
|
||||||
|
# Should be done in postInstall, but meson checks this eagerly before build
|
||||||
|
+ ''
|
||||||
|
install -d $out/share/apostrophe/libs
|
||||||
|
cp -r ${reveal-js} $out/share/apostrophe/libs/reveal.js
|
||||||
|
'';
|
||||||
|
|
||||||
|
nativeBuildInputs = [
|
||||||
|
meson
|
||||||
|
ninja
|
||||||
|
pkg-config
|
||||||
|
wrapGAppsHook4
|
||||||
|
desktop-file-utils
|
||||||
|
gobject-introspection
|
||||||
|
];
|
||||||
|
|
||||||
|
buildInputs = [
|
||||||
|
libadwaita
|
||||||
|
gtksourceview5-patched
|
||||||
|
libspelling-patched
|
||||||
|
webkitgtk_6_0
|
||||||
|
];
|
||||||
|
|
||||||
|
propagatedBuildInputs = with python3Packages; [
|
||||||
|
pygobject3
|
||||||
|
pypandoc
|
||||||
|
chardet
|
||||||
|
];
|
||||||
|
|
||||||
|
dontWrapGApps = true;
|
||||||
|
|
||||||
|
preFixup = ''
|
||||||
|
makeWrapperArgs+=(
|
||||||
|
''${gappsWrapperArgs[@]}
|
||||||
|
--prefix PATH : "${texliveMedium}/bin"
|
||||||
|
--prefix XDG_DATA_DIRS : "${shared-mime-info}/share"
|
||||||
|
)
|
||||||
|
'';
|
||||||
|
|
||||||
|
passthru = {
|
||||||
|
inherit gtksourceview5-patched libspelling-patched reveal-js;
|
||||||
|
};
|
||||||
|
|
||||||
|
meta = {
|
||||||
|
homepage = "https://gitlab.gnome.org/World/apostrophe";
|
||||||
|
description = "A distraction free Markdown editor for GNU/Linux";
|
||||||
|
license = lib.licenses.gpl3Plus;
|
||||||
|
platforms = lib.platforms.linux;
|
||||||
|
maintainers = with lib.maintainers; [
|
||||||
|
sternenseemann
|
||||||
|
aleksana
|
||||||
|
];
|
||||||
|
mainProgram = "apostrophe";
|
||||||
|
};
|
||||||
|
}
|
@ -5,16 +5,16 @@
|
|||||||
|
|
||||||
rustPlatform.buildRustPackage rec {
|
rustPlatform.buildRustPackage rec {
|
||||||
pname = "cargo-expand";
|
pname = "cargo-expand";
|
||||||
version = "1.0.85";
|
version = "1.0.86";
|
||||||
|
|
||||||
src = fetchFromGitHub {
|
src = fetchFromGitHub {
|
||||||
owner = "dtolnay";
|
owner = "dtolnay";
|
||||||
repo = pname;
|
repo = pname;
|
||||||
rev = version;
|
rev = version;
|
||||||
hash = "sha256-2i9FAWF9b1tNdDbTwCzQY8Mh/h85uigR5IT9kzPft00=";
|
hash = "sha256-wp4JYuAHtZrHer4db0vBCchf8mQIt6jXWqjqpGKws4o=";
|
||||||
};
|
};
|
||||||
|
|
||||||
cargoHash = "sha256-Vl0zC9TPhiFv2SiZtzIUV7GftB1y9K1gLy1ajisP8Y0=";
|
cargoHash = "sha256-QNH3G34yTEecZyVgw2a1RJnd1CMfV4aw1OJqes/cK2s=";
|
||||||
|
|
||||||
meta = with lib; {
|
meta = with lib; {
|
||||||
description = "Cargo subcommand to show result of macro expansion";
|
description = "Cargo subcommand to show result of macro expansion";
|
||||||
|
@ -47,13 +47,13 @@ let
|
|||||||
in
|
in
|
||||||
stdenv'.mkDerivation (finalAttrs: {
|
stdenv'.mkDerivation (finalAttrs: {
|
||||||
pname = "fastfetch";
|
pname = "fastfetch";
|
||||||
version = "2.11.3";
|
version = "2.11.5";
|
||||||
|
|
||||||
src = fetchFromGitHub {
|
src = fetchFromGitHub {
|
||||||
owner = "fastfetch-cli";
|
owner = "fastfetch-cli";
|
||||||
repo = "fastfetch";
|
repo = "fastfetch";
|
||||||
rev = finalAttrs.version;
|
rev = finalAttrs.version;
|
||||||
hash = "sha256-kKtJvGnPncosmwjfTKa14G5jQiSkzkURBATvBmavdys=";
|
hash = "sha256-5Chyw4+U2n935YP/Msw8PJ+5iLMES71O+uABn6nVtiI=";
|
||||||
};
|
};
|
||||||
|
|
||||||
outputs = [ "out" "man" ];
|
outputs = [ "out" "man" ];
|
||||||
|
28
pkgs/by-name/go/go-cover-treemap/package.nix
Normal file
28
pkgs/by-name/go/go-cover-treemap/package.nix
Normal file
@ -0,0 +1,28 @@
|
|||||||
|
{ lib
|
||||||
|
, buildGoModule
|
||||||
|
, fetchFromGitHub
|
||||||
|
}:
|
||||||
|
|
||||||
|
buildGoModule rec {
|
||||||
|
pname = "go-cover-treemap";
|
||||||
|
version = "1.4.2";
|
||||||
|
|
||||||
|
src = fetchFromGitHub {
|
||||||
|
owner = "nikolaydubina";
|
||||||
|
repo = "go-cover-treemap";
|
||||||
|
rev = "v${version}";
|
||||||
|
hash = "sha256-MSkPot8uYcr8pxsIkJh2FThVK9xpzkN9Y69KeiQnQlA=";
|
||||||
|
};
|
||||||
|
|
||||||
|
vendorHash = "sha256-k/k+EGkuBnZFHrcWxnzLG8efWgb2i35Agf/sWbgTc4g=";
|
||||||
|
|
||||||
|
ldflags = [ "-s" "-w" ];
|
||||||
|
|
||||||
|
meta = with lib; {
|
||||||
|
description = "Go code coverage to SVG treemap";
|
||||||
|
homepage = "https://github.com/nikolaydubina/go-cover-treemap";
|
||||||
|
license = licenses.mit;
|
||||||
|
maintainers = with maintainers; [ doronbehar ];
|
||||||
|
mainProgram = "go-cover-treemap";
|
||||||
|
};
|
||||||
|
}
|
@ -18,13 +18,13 @@
|
|||||||
|
|
||||||
stdenv.mkDerivation (finalAttrs: {
|
stdenv.mkDerivation (finalAttrs: {
|
||||||
pname = "libqalculate";
|
pname = "libqalculate";
|
||||||
version = "5.0.0";
|
version = "5.1.0";
|
||||||
|
|
||||||
src = fetchFromGitHub {
|
src = fetchFromGitHub {
|
||||||
owner = "qalculate";
|
owner = "qalculate";
|
||||||
repo = "libqalculate";
|
repo = "libqalculate";
|
||||||
rev = "v${finalAttrs.version}";
|
rev = "v${finalAttrs.version}";
|
||||||
hash = "sha256-VhaGgtSU6+7eMY7ksQMpybmt2JBI80Nwgu7PCKrTorA=";
|
hash = "sha256-74P8jIeg0Pge+/U0cQsrEfE+P8upBAr8xSyLhB4zOVU=";
|
||||||
};
|
};
|
||||||
|
|
||||||
outputs = [ "out" "dev" "doc" ];
|
outputs = [ "out" "dev" "doc" ];
|
||||||
|
@ -12,6 +12,7 @@
|
|||||||
, python3
|
, python3
|
||||||
, qtbase
|
, qtbase
|
||||||
, qtdeclarative
|
, qtdeclarative
|
||||||
|
, gobject-introspection
|
||||||
}:
|
}:
|
||||||
|
|
||||||
stdenv.mkDerivation (finalAttrs: {
|
stdenv.mkDerivation (finalAttrs: {
|
||||||
@ -55,6 +56,7 @@ stdenv.mkDerivation (finalAttrs: {
|
|||||||
nativeCheckInputs = [
|
nativeCheckInputs = [
|
||||||
dbus
|
dbus
|
||||||
dbus-test-runner
|
dbus-test-runner
|
||||||
|
gobject-introspection
|
||||||
(python3.withPackages (ps: with ps; [
|
(python3.withPackages (ps: with ps; [
|
||||||
dbus-python
|
dbus-python
|
||||||
pygobject3
|
pygobject3
|
||||||
|
71
pkgs/development/python-modules/biom-format/default.nix
Normal file
71
pkgs/development/python-modules/biom-format/default.nix
Normal file
@ -0,0 +1,71 @@
|
|||||||
|
{
|
||||||
|
lib,
|
||||||
|
buildPythonPackage,
|
||||||
|
fetchFromGitHub,
|
||||||
|
fetchpatch,
|
||||||
|
setuptools,
|
||||||
|
cython,
|
||||||
|
click,
|
||||||
|
numpy,
|
||||||
|
scipy,
|
||||||
|
pandas,
|
||||||
|
h5py,
|
||||||
|
pytestCheckHook,
|
||||||
|
}:
|
||||||
|
|
||||||
|
buildPythonPackage rec {
|
||||||
|
pname = "biom-format";
|
||||||
|
version = "2.1.15";
|
||||||
|
pyproject = true;
|
||||||
|
|
||||||
|
src = fetchFromGitHub {
|
||||||
|
owner = "biocore";
|
||||||
|
repo = "biom-format";
|
||||||
|
rev = "refs/tags/${version}";
|
||||||
|
hash = "sha256-WRBc+C/UWme7wYogy4gH4KTIdIqU3KmBm2jWzGNxGQg=";
|
||||||
|
};
|
||||||
|
|
||||||
|
patches = [
|
||||||
|
# fixes a test, can be removed in next version after 2.1.15
|
||||||
|
(fetchpatch {
|
||||||
|
name = "fix-dataframe-comparison.patch";
|
||||||
|
url = "https://github.com/biocore/biom-format/commit/5d1c921ca2cde5d7332508503ce990a7209d1fdc.patch";
|
||||||
|
hash = "sha256-nyHi469ivjJSQ01yIk/6ZMXFdoo9wVuazJHnFdy2nBg=";
|
||||||
|
})
|
||||||
|
];
|
||||||
|
|
||||||
|
build-system = [
|
||||||
|
setuptools
|
||||||
|
cython
|
||||||
|
numpy
|
||||||
|
];
|
||||||
|
|
||||||
|
dependencies = [
|
||||||
|
click
|
||||||
|
numpy
|
||||||
|
scipy
|
||||||
|
pandas
|
||||||
|
h5py
|
||||||
|
];
|
||||||
|
|
||||||
|
# make pytest resolve the package from $out
|
||||||
|
# some tests don't work if we change the level of directory nesting
|
||||||
|
preCheck = ''
|
||||||
|
mkdir biom_tests
|
||||||
|
mv biom/tests biom_tests/tests
|
||||||
|
rm -r biom
|
||||||
|
'';
|
||||||
|
|
||||||
|
nativeCheckInputs = [ pytestCheckHook ];
|
||||||
|
|
||||||
|
pytestFlagsArray = [ "biom_tests/tests" ];
|
||||||
|
|
||||||
|
pythonImportsCheck = [ "biom" ];
|
||||||
|
|
||||||
|
meta = {
|
||||||
|
homepage = "http://biom-format.org/";
|
||||||
|
description = "Biological Observation Matrix (BIOM) format";
|
||||||
|
license = lib.licenses.bsd3;
|
||||||
|
maintainers = with lib.maintainers; [ tomasajt ];
|
||||||
|
};
|
||||||
|
}
|
@ -7,6 +7,9 @@
|
|||||||
, gmp
|
, gmp
|
||||||
, cython
|
, cython
|
||||||
, cysignals
|
, cysignals
|
||||||
|
|
||||||
|
# Reverse dependency
|
||||||
|
, sage
|
||||||
}:
|
}:
|
||||||
|
|
||||||
buildPythonPackage rec {
|
buildPythonPackage rec {
|
||||||
@ -53,6 +56,8 @@ buildPythonPackage rec {
|
|||||||
make check
|
make check
|
||||||
'';
|
'';
|
||||||
|
|
||||||
|
passthru.tests = { inherit sage; };
|
||||||
|
|
||||||
meta = with lib; {
|
meta = with lib; {
|
||||||
description = "Cython bindings for PARI";
|
description = "Cython bindings for PARI";
|
||||||
license = licenses.gpl2Plus;
|
license = licenses.gpl2Plus;
|
||||||
|
@ -4,6 +4,9 @@
|
|||||||
, buildPythonPackage
|
, buildPythonPackage
|
||||||
, cython
|
, cython
|
||||||
, pariSupport ? true, pari # for interfacing with the PARI/GP signal handler
|
, pariSupport ? true, pari # for interfacing with the PARI/GP signal handler
|
||||||
|
|
||||||
|
# Reverse dependency
|
||||||
|
, sage
|
||||||
}:
|
}:
|
||||||
|
|
||||||
assert pariSupport -> pari != null;
|
assert pariSupport -> pari != null;
|
||||||
@ -46,6 +49,8 @@ buildPythonPackage rec {
|
|||||||
|
|
||||||
enableParallelBuilding = true;
|
enableParallelBuilding = true;
|
||||||
|
|
||||||
|
passthru.tests = { inherit sage; };
|
||||||
|
|
||||||
meta = with lib; {
|
meta = with lib; {
|
||||||
description = "Interrupt and signal handling for Cython";
|
description = "Interrupt and signal handling for Cython";
|
||||||
mainProgram = "cysignals-CSI";
|
mainProgram = "cysignals-CSI";
|
||||||
|
@ -8,6 +8,9 @@
|
|||||||
, gdb
|
, gdb
|
||||||
, numpy
|
, numpy
|
||||||
, ncurses
|
, ncurses
|
||||||
|
|
||||||
|
# Reverse dependency
|
||||||
|
, sage
|
||||||
}:
|
}:
|
||||||
|
|
||||||
let
|
let
|
||||||
@ -57,6 +60,8 @@ in buildPythonPackage rec {
|
|||||||
doCheck = false;
|
doCheck = false;
|
||||||
# doCheck = !stdenv.isDarwin;
|
# doCheck = !stdenv.isDarwin;
|
||||||
|
|
||||||
|
passthru.tests = { inherit sage; };
|
||||||
|
|
||||||
# force regeneration of generated code in source distributions
|
# force regeneration of generated code in source distributions
|
||||||
# https://github.com/cython/cython/issues/5089
|
# https://github.com/cython/cython/issues/5089
|
||||||
setupHook = ./setup-hook.sh;
|
setupHook = ./setup-hook.sh;
|
||||||
|
@ -15,6 +15,9 @@
|
|||||||
, fplll
|
, fplll
|
||||||
, numpy
|
, numpy
|
||||||
|
|
||||||
|
# Reverse dependency
|
||||||
|
, sage
|
||||||
|
|
||||||
# tests
|
# tests
|
||||||
, pytestCheckHook
|
, pytestCheckHook
|
||||||
}:
|
}:
|
||||||
@ -72,6 +75,8 @@ buildPythonPackage rec {
|
|||||||
export PY_IGNORE_IMPORTMISMATCH=1
|
export PY_IGNORE_IMPORTMISMATCH=1
|
||||||
'';
|
'';
|
||||||
|
|
||||||
|
passthru.tests = { inherit sage; };
|
||||||
|
|
||||||
meta = with lib; {
|
meta = with lib; {
|
||||||
description = "A Python interface for fplll";
|
description = "A Python interface for fplll";
|
||||||
changelog = "https://github.com/fplll/fpylll/releases/tag/${version}";
|
changelog = "https://github.com/fplll/fpylll/releases/tag/${version}";
|
||||||
|
@ -5,6 +5,9 @@
|
|||||||
, gmp
|
, gmp
|
||||||
, mpfr
|
, mpfr
|
||||||
, libmpc
|
, libmpc
|
||||||
|
|
||||||
|
# Reverse dependency
|
||||||
|
, sage
|
||||||
}:
|
}:
|
||||||
|
|
||||||
let
|
let
|
||||||
@ -29,6 +32,8 @@ buildPythonPackage {
|
|||||||
|
|
||||||
pythonImportsCheck = [ "gmpy2" ];
|
pythonImportsCheck = [ "gmpy2" ];
|
||||||
|
|
||||||
|
passthru.tests = { inherit sage; };
|
||||||
|
|
||||||
meta = with lib; {
|
meta = with lib; {
|
||||||
description = "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x";
|
description = "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x";
|
||||||
homepage = "https://github.com/aleaxit/gmpy/";
|
homepage = "https://github.com/aleaxit/gmpy/";
|
||||||
|
@ -7,6 +7,9 @@
|
|||||||
, typing-extensions
|
, typing-extensions
|
||||||
, toml
|
, toml
|
||||||
, zipp
|
, zipp
|
||||||
|
|
||||||
|
# Reverse dependency
|
||||||
|
, sage
|
||||||
}:
|
}:
|
||||||
|
|
||||||
buildPythonPackage rec {
|
buildPythonPackage rec {
|
||||||
@ -41,6 +44,8 @@ buildPythonPackage rec {
|
|||||||
"importlib_metadata"
|
"importlib_metadata"
|
||||||
];
|
];
|
||||||
|
|
||||||
|
passthru.tests = { inherit sage; };
|
||||||
|
|
||||||
meta = with lib; {
|
meta = with lib; {
|
||||||
description = "Read metadata from Python packages";
|
description = "Read metadata from Python packages";
|
||||||
homepage = "https://importlib-metadata.readthedocs.io/";
|
homepage = "https://importlib-metadata.readthedocs.io/";
|
||||||
|
@ -10,6 +10,9 @@
|
|||||||
# dependencies
|
# dependencies
|
||||||
, importlib-metadata
|
, importlib-metadata
|
||||||
|
|
||||||
|
# Reverse dependency
|
||||||
|
, sage
|
||||||
|
|
||||||
# tests
|
# tests
|
||||||
, jaraco-collections
|
, jaraco-collections
|
||||||
, pytestCheckHook
|
, pytestCheckHook
|
||||||
@ -46,6 +49,8 @@ buildPythonPackage rec {
|
|||||||
"importlib_resources"
|
"importlib_resources"
|
||||||
];
|
];
|
||||||
|
|
||||||
|
passthru.tests = { inherit sage; };
|
||||||
|
|
||||||
meta = with lib; {
|
meta = with lib; {
|
||||||
description = "Read resources from Python packages";
|
description = "Read resources from Python packages";
|
||||||
homepage = "https://importlib-resources.readthedocs.io/";
|
homepage = "https://importlib-resources.readthedocs.io/";
|
||||||
|
@ -18,6 +18,9 @@
|
|||||||
, pyzmq
|
, pyzmq
|
||||||
, tornado
|
, tornado
|
||||||
, traitlets
|
, traitlets
|
||||||
|
|
||||||
|
# Reverse dependency
|
||||||
|
, sage
|
||||||
}:
|
}:
|
||||||
|
|
||||||
buildPythonPackage rec {
|
buildPythonPackage rec {
|
||||||
@ -63,6 +66,7 @@ buildPythonPackage rec {
|
|||||||
|
|
||||||
passthru.tests = {
|
passthru.tests = {
|
||||||
pytest = callPackage ./tests.nix { };
|
pytest = callPackage ./tests.nix { };
|
||||||
|
inherit sage;
|
||||||
};
|
};
|
||||||
|
|
||||||
meta = {
|
meta = {
|
||||||
|
@ -29,6 +29,9 @@
|
|||||||
, notebook
|
, notebook
|
||||||
, qtconsole
|
, qtconsole
|
||||||
|
|
||||||
|
# Reverse dependency
|
||||||
|
, sage
|
||||||
|
|
||||||
# Test dependencies
|
# Test dependencies
|
||||||
, pickleshare
|
, pickleshare
|
||||||
, pytest-asyncio
|
, pytest-asyncio
|
||||||
@ -106,6 +109,8 @@ buildPythonPackage rec {
|
|||||||
"test_clipboard_get"
|
"test_clipboard_get"
|
||||||
];
|
];
|
||||||
|
|
||||||
|
passthru.tests = { inherit sage; };
|
||||||
|
|
||||||
meta = with lib; {
|
meta = with lib; {
|
||||||
description = "IPython: Productive Interactive Computing";
|
description = "IPython: Productive Interactive Computing";
|
||||||
downloadPage = "https://github.com/ipython/ipython/";
|
downloadPage = "https://github.com/ipython/ipython/";
|
||||||
|
@ -12,6 +12,9 @@
|
|||||||
, pallets-sphinx-themes
|
, pallets-sphinx-themes
|
||||||
, sphinxcontrib-log-cabinet
|
, sphinxcontrib-log-cabinet
|
||||||
, sphinx-issues
|
, sphinx-issues
|
||||||
|
|
||||||
|
# Reverse dependency
|
||||||
|
, sage
|
||||||
}:
|
}:
|
||||||
|
|
||||||
buildPythonPackage rec {
|
buildPythonPackage rec {
|
||||||
@ -75,6 +78,8 @@ buildPythonPackage rec {
|
|||||||
inherit meta;
|
inherit meta;
|
||||||
};
|
};
|
||||||
|
|
||||||
|
passthru.tests = { inherit sage; };
|
||||||
|
|
||||||
meta = with lib; {
|
meta = with lib; {
|
||||||
changelog = "https://github.com/pallets/jinja/blob/${version}/CHANGES.rst";
|
changelog = "https://github.com/pallets/jinja/blob/${version}/CHANGES.rst";
|
||||||
description = "Very fast and expressive template engine";
|
description = "Very fast and expressive template engine";
|
||||||
|
@ -7,6 +7,9 @@
|
|||||||
, traitlets
|
, traitlets
|
||||||
, pip
|
, pip
|
||||||
, pytestCheckHook
|
, pytestCheckHook
|
||||||
|
|
||||||
|
# Reverse dependency
|
||||||
|
, sage
|
||||||
}:
|
}:
|
||||||
|
|
||||||
buildPythonPackage rec {
|
buildPythonPackage rec {
|
||||||
@ -61,6 +64,8 @@ buildPythonPackage rec {
|
|||||||
|
|
||||||
pythonImportsCheck = [ "jupyter_core" ];
|
pythonImportsCheck = [ "jupyter_core" ];
|
||||||
|
|
||||||
|
passthru.tests = { inherit sage; };
|
||||||
|
|
||||||
meta = with lib; {
|
meta = with lib; {
|
||||||
description = "Base package on which Jupyter projects rely";
|
description = "Base package on which Jupyter projects rely";
|
||||||
homepage = "https://jupyter.org/";
|
homepage = "https://jupyter.org/";
|
||||||
|
@ -69,6 +69,9 @@
|
|||||||
# required for headless detection
|
# required for headless detection
|
||||||
, libX11
|
, libX11
|
||||||
, wayland
|
, wayland
|
||||||
|
|
||||||
|
# Reverse dependency
|
||||||
|
, sage
|
||||||
}:
|
}:
|
||||||
|
|
||||||
let
|
let
|
||||||
@ -183,6 +186,8 @@ buildPythonPackage rec {
|
|||||||
};
|
};
|
||||||
};
|
};
|
||||||
|
|
||||||
|
passthru.tests = { inherit sage; };
|
||||||
|
|
||||||
env.MPLSETUPCFG = writeText "mplsetup.cfg" (lib.generators.toINI {} passthru.config);
|
env.MPLSETUPCFG = writeText "mplsetup.cfg" (lib.generators.toINI {} passthru.config);
|
||||||
|
|
||||||
# Encountering a ModuleNotFoundError, as describved and investigated at:
|
# Encountering a ModuleNotFoundError, as describved and investigated at:
|
||||||
|
@ -2,6 +2,9 @@
|
|||||||
, fetchPypi
|
, fetchPypi
|
||||||
, buildPythonPackage
|
, buildPythonPackage
|
||||||
, cython
|
, cython
|
||||||
|
|
||||||
|
# Reverse dependency
|
||||||
|
, sage
|
||||||
}:
|
}:
|
||||||
|
|
||||||
buildPythonPackage rec {
|
buildPythonPackage rec {
|
||||||
@ -19,6 +22,8 @@ buildPythonPackage rec {
|
|||||||
|
|
||||||
pythonImportsCheck = [ "memory_allocator" ];
|
pythonImportsCheck = [ "memory_allocator" ];
|
||||||
|
|
||||||
|
passthru.tests = { inherit sage; };
|
||||||
|
|
||||||
meta = with lib; {
|
meta = with lib; {
|
||||||
description = "An extension class to allocate memory easily with cython";
|
description = "An extension class to allocate memory easily with cython";
|
||||||
homepage = "https://github.com/sagemath/memory_allocator/";
|
homepage = "https://github.com/sagemath/memory_allocator/";
|
||||||
|
@ -5,6 +5,9 @@
|
|||||||
, isPyPy
|
, isPyPy
|
||||||
, setuptools
|
, setuptools
|
||||||
, pytestCheckHook
|
, pytestCheckHook
|
||||||
|
|
||||||
|
# Reverse dependency
|
||||||
|
, sage
|
||||||
}:
|
}:
|
||||||
|
|
||||||
buildPythonPackage rec {
|
buildPythonPackage rec {
|
||||||
@ -29,6 +32,8 @@ buildPythonPackage rec {
|
|||||||
];
|
];
|
||||||
};
|
};
|
||||||
|
|
||||||
|
passthru.tests = { inherit sage; };
|
||||||
|
|
||||||
nativeCheckInputs = [
|
nativeCheckInputs = [
|
||||||
pytestCheckHook
|
pytestCheckHook
|
||||||
];
|
];
|
||||||
|
@ -19,6 +19,9 @@
|
|||||||
# tests
|
# tests
|
||||||
, pytest-xdist
|
, pytest-xdist
|
||||||
, pytestCheckHook
|
, pytestCheckHook
|
||||||
|
|
||||||
|
# reverse dependency
|
||||||
|
, sage
|
||||||
}:
|
}:
|
||||||
|
|
||||||
buildPythonPackage rec {
|
buildPythonPackage rec {
|
||||||
@ -53,6 +56,8 @@ buildPythonPackage rec {
|
|||||||
];
|
];
|
||||||
};
|
};
|
||||||
|
|
||||||
|
passthru.tests = { inherit sage; };
|
||||||
|
|
||||||
nativeCheckInputs = [
|
nativeCheckInputs = [
|
||||||
pytest-xdist
|
pytest-xdist
|
||||||
pytestCheckHook
|
pytestCheckHook
|
||||||
|
@ -19,6 +19,9 @@
|
|||||||
, blas
|
, blas
|
||||||
, lapack
|
, lapack
|
||||||
|
|
||||||
|
# Reverse dependency
|
||||||
|
, sage
|
||||||
|
|
||||||
# tests
|
# tests
|
||||||
, hypothesis
|
, hypothesis
|
||||||
, pytest-xdist
|
, pytest-xdist
|
||||||
@ -177,6 +180,7 @@ in buildPythonPackage rec {
|
|||||||
blas = blas.provider;
|
blas = blas.provider;
|
||||||
blasImplementation = blas.implementation;
|
blasImplementation = blas.implementation;
|
||||||
inherit cfg;
|
inherit cfg;
|
||||||
|
tests = { inherit sage; };
|
||||||
};
|
};
|
||||||
|
|
||||||
# Disable test
|
# Disable test
|
||||||
|
@ -3,6 +3,9 @@
|
|||||||
, fetchPypi
|
, fetchPypi
|
||||||
, setuptools
|
, setuptools
|
||||||
, ptyprocess
|
, ptyprocess
|
||||||
|
|
||||||
|
# Reverse dependency
|
||||||
|
, sage
|
||||||
}:
|
}:
|
||||||
|
|
||||||
buildPythonPackage (rec {
|
buildPythonPackage (rec {
|
||||||
@ -24,6 +27,8 @@ buildPythonPackage (rec {
|
|||||||
|
|
||||||
propagatedBuildInputs = [ ptyprocess ];
|
propagatedBuildInputs = [ ptyprocess ];
|
||||||
|
|
||||||
|
passthru.tests = { inherit sage; };
|
||||||
|
|
||||||
meta = with lib; {
|
meta = with lib; {
|
||||||
homepage = "http://www.noah.org/wiki/Pexpect";
|
homepage = "http://www.noah.org/wiki/Pexpect";
|
||||||
description = "Automate interactive console applications such as ssh, ftp, etc";
|
description = "Automate interactive console applications such as ssh, ftp, etc";
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
, defusedxml, olefile, freetype, libjpeg, zlib, libtiff, libwebp, libxcrypt, tcl, lcms2, tk, libX11
|
, defusedxml, olefile, freetype, libjpeg, zlib, libtiff, libwebp, libxcrypt, tcl, lcms2, tk, libX11
|
||||||
, libxcb, openjpeg, libimagequant, numpy, pytestCheckHook, setuptools
|
, libxcb, openjpeg, libimagequant, numpy, pytestCheckHook, setuptools
|
||||||
# for passthru.tests
|
# for passthru.tests
|
||||||
, imageio, matplotlib, pilkit, pydicom, reportlab
|
, imageio, matplotlib, pilkit, pydicom, reportlab, sage
|
||||||
}@args:
|
}@args:
|
||||||
|
|
||||||
import ./generic.nix (rec {
|
import ./generic.nix (rec {
|
||||||
@ -24,7 +24,7 @@ import ./generic.nix (rec {
|
|||||||
};
|
};
|
||||||
|
|
||||||
passthru.tests = {
|
passthru.tests = {
|
||||||
inherit imageio matplotlib pilkit pydicom reportlab;
|
inherit imageio matplotlib pilkit pydicom reportlab sage;
|
||||||
};
|
};
|
||||||
|
|
||||||
meta = with lib; {
|
meta = with lib; {
|
||||||
|
@ -9,6 +9,9 @@
|
|||||||
, cysignals
|
, cysignals
|
||||||
, gmpy2
|
, gmpy2
|
||||||
, sphinx
|
, sphinx
|
||||||
|
|
||||||
|
# Reverse dependency
|
||||||
|
, sage
|
||||||
}:
|
}:
|
||||||
|
|
||||||
buildPythonPackage rec {
|
buildPythonPackage rec {
|
||||||
@ -54,6 +57,8 @@ buildPythonPackage rec {
|
|||||||
mv docs/build/html "$doc/share/doc/pplpy"
|
mv docs/build/html "$doc/share/doc/pplpy"
|
||||||
'';
|
'';
|
||||||
|
|
||||||
|
passthru.tests = { inherit sage; };
|
||||||
|
|
||||||
meta = with lib; {
|
meta = with lib; {
|
||||||
description = "A Python wrapper for ppl";
|
description = "A Python wrapper for ppl";
|
||||||
homepage = "https://gitlab.com/videlec/pplpy";
|
homepage = "https://gitlab.com/videlec/pplpy";
|
||||||
|
@ -4,6 +4,9 @@
|
|||||||
, primecount
|
, primecount
|
||||||
, cython
|
, cython
|
||||||
, cysignals
|
, cysignals
|
||||||
|
|
||||||
|
# Reverse dependency
|
||||||
|
, sage
|
||||||
}:
|
}:
|
||||||
|
|
||||||
buildPythonPackage rec {
|
buildPythonPackage rec {
|
||||||
@ -25,6 +28,8 @@ buildPythonPackage rec {
|
|||||||
|
|
||||||
pythonImportsCheck = [ "primecountpy" ];
|
pythonImportsCheck = [ "primecountpy" ];
|
||||||
|
|
||||||
|
passthru.tests = { inherit sage; };
|
||||||
|
|
||||||
meta = with lib; {
|
meta = with lib; {
|
||||||
description = "Cython interface for C++ primecount library";
|
description = "Cython interface for C++ primecount library";
|
||||||
homepage = "https://github.com/dimpase/primecountpy/";
|
homepage = "https://github.com/dimpase/primecountpy/";
|
||||||
|
@ -1,4 +1,4 @@
|
|||||||
{ lib, buildPythonPackage, fetchPypi, unittestCheckHook }:
|
{ lib, buildPythonPackage, fetchPypi, unittestCheckHook, pythonOlder }:
|
||||||
|
|
||||||
buildPythonPackage rec {
|
buildPythonPackage rec {
|
||||||
pname = "pycparser";
|
pname = "pycparser";
|
||||||
@ -11,6 +11,7 @@ buildPythonPackage rec {
|
|||||||
};
|
};
|
||||||
|
|
||||||
nativeCheckInputs = [ unittestCheckHook ];
|
nativeCheckInputs = [ unittestCheckHook ];
|
||||||
|
disabled = pythonOlder "3.8";
|
||||||
|
|
||||||
unittestFlagsArray = [ "-s" "tests" ];
|
unittestFlagsArray = [ "-s" "tests" ];
|
||||||
|
|
||||||
|
@ -1,53 +1,64 @@
|
|||||||
{ lib
|
{
|
||||||
, buildPythonPackage
|
lib,
|
||||||
, fetchPypi
|
buildPythonPackage,
|
||||||
, cython
|
fetchFromGitHub,
|
||||||
, lockfile
|
setuptools,
|
||||||
, cachecontrol
|
cython,
|
||||||
, decorator
|
oldest-supported-numpy,
|
||||||
, h5py
|
requests,
|
||||||
, ipython
|
decorator,
|
||||||
, matplotlib
|
natsort,
|
||||||
, natsort
|
numpy,
|
||||||
, numpy
|
pandas,
|
||||||
, pandas
|
scipy,
|
||||||
, scipy
|
h5py,
|
||||||
, hdmedians
|
hdmedians,
|
||||||
, scikit-learn
|
biom-format,
|
||||||
, coverage
|
python,
|
||||||
, python
|
pytestCheckHook,
|
||||||
, isPy3k
|
|
||||||
}:
|
}:
|
||||||
|
|
||||||
buildPythonPackage rec {
|
buildPythonPackage rec {
|
||||||
version = "0.6.0";
|
|
||||||
format = "setuptools";
|
|
||||||
pname = "scikit-bio";
|
pname = "scikit-bio";
|
||||||
disabled = !isPy3k;
|
version = "0.6.0";
|
||||||
|
pyproject = true;
|
||||||
|
|
||||||
src = fetchPypi {
|
src = fetchFromGitHub {
|
||||||
inherit pname version;
|
owner = "scikit-bio";
|
||||||
hash = "sha256-EBBafDwVrlkQJEkn8punqjUjSxnr5lE7hIRUc0OywQ8=";
|
repo = "scikit-bio";
|
||||||
|
rev = "refs/tags/${version}";
|
||||||
|
hash = "sha256-v8/r52pJpMi34SekPQBf7CqRbs+ZEyPR3WO5RBB7uKg=";
|
||||||
};
|
};
|
||||||
|
|
||||||
nativeBuildInputs = [ cython ];
|
build-system = [
|
||||||
nativeCheckInputs = [ coverage ];
|
setuptools
|
||||||
propagatedBuildInputs = [ lockfile cachecontrol decorator ipython matplotlib natsort numpy pandas scipy h5py hdmedians scikit-learn ];
|
cython
|
||||||
|
oldest-supported-numpy
|
||||||
|
];
|
||||||
|
|
||||||
# cython package not included for tests
|
dependencies = [
|
||||||
doCheck = false;
|
requests
|
||||||
|
decorator
|
||||||
|
natsort
|
||||||
|
numpy
|
||||||
|
pandas
|
||||||
|
scipy
|
||||||
|
h5py
|
||||||
|
hdmedians
|
||||||
|
biom-format
|
||||||
|
];
|
||||||
|
|
||||||
checkPhase = ''
|
nativeCheckInputs = [ pytestCheckHook ];
|
||||||
${python.interpreter} -m skbio.test
|
|
||||||
'';
|
# only the $out dir contains the built cython extensions, so we run the tests inside there
|
||||||
|
pytestFlagsArray = [ "${placeholder "out"}/${python.sitePackages}/skbio" ];
|
||||||
|
|
||||||
pythonImportsCheck = [ "skbio" ];
|
pythonImportsCheck = [ "skbio" ];
|
||||||
|
|
||||||
meta = with lib; {
|
meta = {
|
||||||
homepage = "http://scikit-bio.org/";
|
homepage = "http://scikit-bio.org/";
|
||||||
description = "Data structures, algorithms and educational resources for bioinformatics";
|
description = "Data structures, algorithms and educational resources for bioinformatics";
|
||||||
license = licenses.bsd3;
|
license = lib.licenses.bsd3;
|
||||||
platforms = [ "x86_64-linux" "x86_64-darwin" ];
|
maintainers = with lib.maintainers; [ tomasajt ];
|
||||||
maintainers = [ ];
|
|
||||||
};
|
};
|
||||||
}
|
}
|
||||||
|
@ -25,6 +25,9 @@
|
|||||||
, xsimd
|
, xsimd
|
||||||
, blas
|
, blas
|
||||||
, lapack
|
, lapack
|
||||||
|
|
||||||
|
# Reverse dependency
|
||||||
|
, sage
|
||||||
}:
|
}:
|
||||||
|
|
||||||
let
|
let
|
||||||
@ -193,6 +196,7 @@ in buildPythonPackage {
|
|||||||
# Pass it the names of the datasets to update their hashes
|
# Pass it the names of the datasets to update their hashes
|
||||||
++ (builtins.attrNames datasetsHashes)
|
++ (builtins.attrNames datasetsHashes)
|
||||||
;
|
;
|
||||||
|
tests = { inherit sage; };
|
||||||
};
|
};
|
||||||
|
|
||||||
SCIPY_USE_G77_ABI_WRAPPER = 1;
|
SCIPY_USE_G77_ABI_WRAPPER = 1;
|
||||||
|
@ -3,6 +3,9 @@
|
|||||||
, fetchPypi
|
, fetchPypi
|
||||||
, glibcLocales
|
, glibcLocales
|
||||||
, mpmath
|
, mpmath
|
||||||
|
|
||||||
|
# Reverse dependency
|
||||||
|
, sage
|
||||||
}:
|
}:
|
||||||
|
|
||||||
buildPythonPackage rec {
|
buildPythonPackage rec {
|
||||||
@ -27,6 +30,8 @@ buildPythonPackage rec {
|
|||||||
export LANG="en_US.UTF-8"
|
export LANG="en_US.UTF-8"
|
||||||
'';
|
'';
|
||||||
|
|
||||||
|
passthru.tests = { inherit sage; };
|
||||||
|
|
||||||
meta = with lib; {
|
meta = with lib; {
|
||||||
description = "A Python library for symbolic mathematics";
|
description = "A Python library for symbolic mathematics";
|
||||||
mainProgram = "isympy";
|
mainProgram = "isympy";
|
||||||
|
@ -10,7 +10,7 @@ buildPythonPackage {
|
|||||||
pyproject = true;
|
pyproject = true;
|
||||||
|
|
||||||
postPatch = ''
|
postPatch = ''
|
||||||
substituteInPlace "py/src/nftables.py" \
|
substituteInPlace "src/nftables.py" \
|
||||||
--replace-fail "libnftables.so.1" "${nftables}/lib/libnftables.so.1"
|
--replace-fail "libnftables.so.1" "${nftables}/lib/libnftables.so.1"
|
||||||
'';
|
'';
|
||||||
|
|
||||||
|
@ -29712,10 +29712,6 @@ with pkgs;
|
|||||||
|
|
||||||
appgate-sdp = callPackage ../applications/networking/appgate-sdp { };
|
appgate-sdp = callPackage ../applications/networking/appgate-sdp { };
|
||||||
|
|
||||||
apostrophe = callPackage ../applications/editors/apostrophe {
|
|
||||||
pythonPackages = python3Packages;
|
|
||||||
};
|
|
||||||
|
|
||||||
ardour = callPackage ../applications/audio/ardour { };
|
ardour = callPackage ../applications/audio/ardour { };
|
||||||
ardour_7 = callPackage ../applications/audio/ardour/7.nix { };
|
ardour_7 = callPackage ../applications/audio/ardour/7.nix { };
|
||||||
|
|
||||||
|
@ -1531,6 +1531,8 @@ self: super: with self; {
|
|||||||
|
|
||||||
binwalk-full = self.binwalk.override { visualizationSupport = true; };
|
binwalk-full = self.binwalk.override { visualizationSupport = true; };
|
||||||
|
|
||||||
|
biom-format = callPackage ../development/python-modules/biom-format { };
|
||||||
|
|
||||||
biopandas = callPackage ../development/python-modules/biopandas { };
|
biopandas = callPackage ../development/python-modules/biopandas { };
|
||||||
|
|
||||||
biopython = callPackage ../development/python-modules/biopython { };
|
biopython = callPackage ../development/python-modules/biopython { };
|
||||||
|
Loading…
Reference in New Issue
Block a user