mirror of
https://github.com/NixOS/nixpkgs.git
synced 2024-09-29 15:43:00 +00:00
Merge staging-next into staging
This commit is contained in:
github-actions[bot]
GitHub
commit
c67f226431
@ -902,6 +902,17 @@ in mkLicense lset) ({
|
||||
free = false;
|
||||
};
|
||||
|
||||
ncbiPd = {
|
||||
spdxId = "NCBI-PD";
|
||||
fullname = "NCBI Public Domain Notice";
|
||||
# Due to United States copyright law, anything with this "license" does not have a copyright in the
|
||||
# jurisdiction of the United States. However, other jurisdictions may assign the United States
|
||||
# government copyright to the work, and the license explicitly states that in such a case, no license
|
||||
# is granted. This is nonfree and nonredistributable in most jurisdictions other than the United States.
|
||||
free = false;
|
||||
redistributable = false;
|
||||
};
|
||||
|
||||
ncsa = {
|
||||
spdxId = "NCSA";
|
||||
fullName = "University of Illinois/NCSA Open Source License";
|
||||
|
||||
@ -3814,6 +3814,15 @@
|
||||
githubId = 199180;
|
||||
name = "Claes Wallin";
|
||||
};
|
||||
clebs = {
|
||||
email = "borja.clemente@gmail.com";
|
||||
github = "clebs";
|
||||
githubId = 1059661;
|
||||
name = "Borja Clemente";
|
||||
keys = [{
|
||||
fingerprint = "C4E1 58BD FD33 3C77 B6C7 178E 2539 757E F64C 60DD";
|
||||
}];
|
||||
};
|
||||
cleeyv = {
|
||||
email = "cleeyv@riseup.net";
|
||||
github = "cleeyv";
|
||||
|
||||
@ -12,6 +12,8 @@
|
||||
|
||||
## Backward Incompatibilities {#sec-release-24.11-incompatibilities}
|
||||
|
||||
- `nginx` package no longer includes `gd` and `geoip` dependencies. For enabling it, override `nginx` package with the optionals `withImageFilter` and `withGeoIP`.
|
||||
|
||||
- `nvimpager` was updated to version 0.13.0, which changes the order of user and
|
||||
nvimpager settings: user commands in `-c` and `--cmd` now override the
|
||||
respective default settings because they are executed later.
|
||||
|
||||
@ -12,7 +12,7 @@ let
|
||||
${lib.concatLines (lib.mapAttrsToList
|
||||
(username: opts:
|
||||
let
|
||||
uid = if opts.uid == null then "-" else toString opts.uid;
|
||||
uid = if opts.uid == null then "/var/lib/nixos/uid/${username}" else toString opts.uid;
|
||||
in
|
||||
''u ${username} ${uid}:${opts.group} "${opts.description}" ${opts.home} ${utils.toShellPath opts.shell}''
|
||||
)
|
||||
@ -21,7 +21,7 @@ let
|
||||
|
||||
# Groups
|
||||
${lib.concatLines (lib.mapAttrsToList
|
||||
(groupname: opts: ''g ${groupname} ${if opts.gid == null then "-" else toString opts.gid}'') userCfg.groups)
|
||||
(groupname: opts: ''g ${groupname} ${if opts.gid == null then "/var/lib/nixos/gid/${groupname}" else toString opts.gid}'') userCfg.groups)
|
||||
}
|
||||
|
||||
# Group membership
|
||||
@ -106,6 +106,23 @@ in
|
||||
};
|
||||
})
|
||||
(lib.filterAttrs (_username: opts: opts.home != "/var/empty") userCfg.users);
|
||||
|
||||
# Create uid/gid marker files for those without an explicit id
|
||||
tmpfiles.settings.nixos-uid = lib.mapAttrs'
|
||||
(username: opts: lib.nameValuePair "/var/lib/nixos/uid/${username}" {
|
||||
f = {
|
||||
user = username;
|
||||
};
|
||||
})
|
||||
(lib.filterAttrs (_username: opts: opts.uid == null) userCfg.users);
|
||||
|
||||
tmpfiles.settings.nixos-gid = lib.mapAttrs'
|
||||
(groupname: opts: lib.nameValuePair "/var/lib/nixos/gid/${groupname}" {
|
||||
f = {
|
||||
group = groupname;
|
||||
};
|
||||
})
|
||||
(lib.filterAttrs (_groupname: opts: opts.gid == null) userCfg.groups);
|
||||
})
|
||||
|
||||
(lib.mkIf config.users.mutableUsers {
|
||||
|
||||
@ -15,6 +15,7 @@
|
||||
, gnome-desktop
|
||||
, gspell
|
||||
, gtk4
|
||||
, gtksourceview5
|
||||
, gst_all_1
|
||||
, json-glib
|
||||
, libgcrypt
|
||||
@ -28,17 +29,17 @@
|
||||
, plugins ? [ ]
|
||||
}:
|
||||
|
||||
stdenv.mkDerivation rec {
|
||||
stdenv.mkDerivation (finalAttrs: {
|
||||
pname = "chatty";
|
||||
version = "0.8.2";
|
||||
version = "0.8.3";
|
||||
|
||||
src = fetchFromGitLab {
|
||||
domain = "gitlab.gnome.org";
|
||||
owner = "World";
|
||||
repo = "Chatty";
|
||||
rev = "v${version}";
|
||||
rev = "v${finalAttrs.version}";
|
||||
fetchSubmodules = true;
|
||||
hash = "sha256-7SdoN9JjGwELOdISJwS1Afcydp/rE2uq/tHO/UrFKNU=";
|
||||
hash = "sha256-Ywed/8PhOgmzcka+5dyxjmWTcDBPF90LW+C2eeQmyLo=";
|
||||
};
|
||||
|
||||
nativeBuildInputs = [
|
||||
@ -59,6 +60,7 @@ stdenv.mkDerivation rec {
|
||||
gnome-desktop
|
||||
gspell
|
||||
gtk4
|
||||
gtksourceview5
|
||||
gst_all_1.gstreamer
|
||||
json-glib
|
||||
libgcrypt
|
||||
@ -82,9 +84,9 @@ stdenv.mkDerivation rec {
|
||||
description = "XMPP and SMS messaging via libpurple and ModemManager";
|
||||
mainProgram = "chatty";
|
||||
homepage = "https://gitlab.gnome.org/World/Chatty";
|
||||
changelog = "https://gitlab.gnome.org/World/Chatty/-/blob/${src.rev}/NEWS";
|
||||
changelog = "https://gitlab.gnome.org/World/Chatty/-/blob/${finalAttrs.src.rev}/NEWS";
|
||||
license = licenses.gpl3Plus;
|
||||
maintainers = with maintainers; [ dotlambda ];
|
||||
platforms = platforms.linux;
|
||||
};
|
||||
}
|
||||
})
|
||||
|
||||
@ -49,7 +49,7 @@ stdenv.mkDerivation rec {
|
||||
meta = with lib; {
|
||||
homepage = "https://github.com/ncbi/sra-tools";
|
||||
description = "The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.";
|
||||
license = licenses.publicDomain;
|
||||
license = licenses.ncbiPd;
|
||||
maintainers = with maintainers; [ thyol ];
|
||||
platforms = [ "x86_64-linux" ];
|
||||
};
|
||||
|
||||
@ -13,7 +13,7 @@ let
|
||||
in
|
||||
stdenv.mkDerivation (args // {
|
||||
name = "${name}-source";
|
||||
installPhase = "cp -pr --reflink=auto -- . $out";
|
||||
installPhase = "cp -r . $out";
|
||||
outputs = [ "out" ];
|
||||
separateDebugInfo = false;
|
||||
dontUnpack = false;
|
||||
|
||||
@ -10,18 +10,18 @@
|
||||
|
||||
buildNpmPackage rec {
|
||||
pname = "bitwarden-cli";
|
||||
version = "2024.3.1";
|
||||
version = "2024.4.1";
|
||||
|
||||
src = fetchFromGitHub {
|
||||
owner = "bitwarden";
|
||||
repo = "clients";
|
||||
rev = "cli-v${version}";
|
||||
hash = "sha256-JBEP4dNGL4rYKl2qNyhB2y/wZunikaGFltGVXLxgMWI=";
|
||||
hash = "sha256-Dz7EActqXd97kNxEaNINj2O6TLZWEgHHg1lOIa2+Lt4=";
|
||||
};
|
||||
|
||||
nodejs = nodejs_18;
|
||||
|
||||
npmDepsHash = "sha256-vNudSHIMmF7oXGz+ZymQahyHebs/CBDc6Oy1g0A5nqA=";
|
||||
npmDepsHash = "sha256-fjYez3nSDsG5kYtrun3CkDCz1GNAjNlwPzEL+/9qQRU=";
|
||||
|
||||
nativeBuildInputs = [
|
||||
python3
|
||||
|
||||
@ -17,7 +17,7 @@
|
||||
}:
|
||||
python3Packages.buildPythonApplication rec {
|
||||
pname = "errands";
|
||||
version = "46.2";
|
||||
version = "46.2.2";
|
||||
|
||||
pyproject = false;
|
||||
|
||||
@ -25,7 +25,7 @@ python3Packages.buildPythonApplication rec {
|
||||
owner = "mrvladus";
|
||||
repo = "Errands";
|
||||
rev = "refs/tags/${version}";
|
||||
hash = "sha256-p/2dHLWSdDAe0+xTvOgmGscTUPLG+0ddIVHMcHY86xg=";
|
||||
hash = "sha256-lX0exxZMbq/iC41bByMfT478vhOQadPJAN72PHiznKc=";
|
||||
};
|
||||
|
||||
nativeBuildInputs = [
|
||||
@ -59,12 +59,13 @@ python3Packages.buildPythonApplication rec {
|
||||
makeWrapperArgs+=("''${gappsWrapperArgs[@]}")
|
||||
'';
|
||||
|
||||
meta = with lib; {
|
||||
meta = {
|
||||
description = "Manage your tasks";
|
||||
changelog = "https://github.com/mrvladus/Errands/releases/tag/${version}";
|
||||
homepage = "https://github.com/mrvladus/Errands";
|
||||
license = licenses.mit;
|
||||
license = lib.licenses.mit;
|
||||
mainProgram = "errands";
|
||||
maintainers = with maintainers; [
|
||||
maintainers = with lib.maintainers; [
|
||||
luftmensch-luftmensch
|
||||
sund3RRR
|
||||
];
|
||||
|
||||
55
pkgs/by-name/li/libideviceactivation/package.nix
Normal file
55
pkgs/by-name/li/libideviceactivation/package.nix
Normal file
@ -0,0 +1,55 @@
|
||||
{
|
||||
stdenv,
|
||||
fetchFromGitHub,
|
||||
lib,
|
||||
pkg-config,
|
||||
automake,
|
||||
autoreconfHook,
|
||||
libtool,
|
||||
libplist,
|
||||
libimobiledevice,
|
||||
libxml2,
|
||||
curl,
|
||||
usbmuxd,
|
||||
}:
|
||||
|
||||
stdenv.mkDerivation (finalAttrs: {
|
||||
pname = "libideviceactivation";
|
||||
version = "1.1.1";
|
||||
|
||||
src = fetchFromGitHub {
|
||||
owner = "libimobiledevice";
|
||||
repo = "libideviceactivation";
|
||||
rev = "refs/tags/${finalAttrs.version}";
|
||||
hash = "sha256-owcQpCN4+A785oy9pCboJIyfpgZ6X+8PRzqGtWpYl2w=";
|
||||
};
|
||||
|
||||
nativeBuildInputs = [
|
||||
pkg-config
|
||||
automake
|
||||
autoreconfHook
|
||||
];
|
||||
|
||||
buildInputs = [
|
||||
libtool
|
||||
libplist
|
||||
libimobiledevice
|
||||
libxml2
|
||||
curl
|
||||
usbmuxd
|
||||
];
|
||||
|
||||
installFlags = [ "PREFIX=$(out)" ];
|
||||
|
||||
meta = {
|
||||
description = "A library to manage the activation process of Apple iOS devices.";
|
||||
homepage = "https://libimobiledevice.org";
|
||||
license = with lib.licenses; [
|
||||
lgpl21
|
||||
gpl3
|
||||
];
|
||||
mainProgram = "ideviceactivation";
|
||||
platforms = lib.platforms.linux;
|
||||
maintainers = with lib.maintainers; [ clebs ];
|
||||
};
|
||||
})
|
||||
@ -1,4 +1,10 @@
|
||||
{ lib, stdenv, fetchurl }:
|
||||
{
|
||||
lib,
|
||||
stdenv,
|
||||
fetchurl,
|
||||
testers,
|
||||
mpack,
|
||||
}:
|
||||
|
||||
stdenv.mkDerivation rec {
|
||||
pname = "mpack";
|
||||
@ -9,7 +15,11 @@ stdenv.mkDerivation rec {
|
||||
sha256 = "0k590z96509k96zxmhv72gkwhrlf55jkmyqlzi72m61r7axhhh97";
|
||||
};
|
||||
|
||||
patches = [ ./build-fix.patch ./sendmail-via-execvp.diff ./CVE-2011-4919.patch ];
|
||||
patches = [
|
||||
./build-fix.patch
|
||||
./sendmail-via-execvp.diff
|
||||
./CVE-2011-4919.patch
|
||||
];
|
||||
|
||||
postPatch = ''
|
||||
for f in *.{c,man,pl,unix} ; do
|
||||
@ -28,9 +38,20 @@ stdenv.mkDerivation rec {
|
||||
|
||||
enableParallelBuilding = true;
|
||||
|
||||
passthru.tests = {
|
||||
version = testers.testVersion {
|
||||
command = ''
|
||||
mpack 2>&1 || echo "mpack exited with error code $?"
|
||||
'';
|
||||
package = mpack;
|
||||
version = "mpack version ${version}";
|
||||
};
|
||||
};
|
||||
|
||||
meta = with lib; {
|
||||
description = "Utilities for encoding and decoding binary files in MIME";
|
||||
license = licenses.free;
|
||||
platforms = platforms.linux;
|
||||
maintainers = with maintainers; [ tomodachi94 ];
|
||||
};
|
||||
}
|
||||
@ -7,10 +7,12 @@
|
||||
inherit version;
|
||||
|
||||
defaultVersion = with lib.versions; lib.switch [ coq.version mathcomp-analysis.version] [
|
||||
{ cases = [ (isGe "8.17") (isGe "1.0") ]; out = "0.7.1"; }
|
||||
{ cases = [ (isGe "8.17") (range "0.6.6" "0.7.0") ]; out = "0.6.1"; }
|
||||
{ cases = [ (range "8.17" "8.18") (range "0.6.0" "0.6.7") ]; out = "0.5.2"; }
|
||||
{ cases = [ (range "8.15" "8.16") (range "0.5.4" "0.6.5") ]; out = "0.5.1"; }
|
||||
] null;
|
||||
release."0.7.1".sha256 = "sha256-/4Elb35SmscG6EjEcHYDo+AmWrpBUlygZL0WhaD+fcY=";
|
||||
release."0.6.1".sha256 = "sha256-tFB5lrwRPIlHkP+ebgcJwu03Cc9yVaOINOAo8Bf2LT4=";
|
||||
release."0.5.1".sha256 = "sha256-yBBl5l+V+dggsg5KM59Yo9CULKog/xxE8vrW+ZRnX7Y=";
|
||||
release."0.5.2".sha256 = "sha256-8WAnAV53c0pMTdwj8XcUDUkLZbpUgIQbEOgOb63uHQA=";
|
||||
|
||||
@ -57,6 +57,7 @@ stdenv.mkDerivation rec {
|
||||
] ++ (lib.optional (stdenv.buildPlatform != stdenv.hostPlatform)
|
||||
(if stdenv.hostPlatform.isAarch64 then "arch=arm64"
|
||||
else if stdenv.hostPlatform.isx86_64 then "arch=intel64"
|
||||
else if stdenv.hostPlatform.isi686 then "arch=ia32"
|
||||
else throw "Unsupported cross architecture"));
|
||||
|
||||
enableParallelBuilding = true;
|
||||
|
||||
@ -2,6 +2,7 @@
|
||||
lib,
|
||||
buildPythonPackage,
|
||||
fetchFromGitHub,
|
||||
apricot-select,
|
||||
numba,
|
||||
numpy,
|
||||
pynose,
|
||||
@ -37,15 +38,15 @@ buildPythonPackage rec {
|
||||
dependencies = [
|
||||
numba
|
||||
numpy
|
||||
scikit-learn
|
||||
scipy
|
||||
torchvision
|
||||
tqdm
|
||||
];
|
||||
|
||||
nativeCheckInputs = [
|
||||
pynose
|
||||
pytestCheckHook
|
||||
scikit-learn
|
||||
torchvision
|
||||
];
|
||||
|
||||
pythonImportsCheck = [ "apricot" ];
|
||||
@ -56,6 +57,21 @@ buildPythonPackage rec {
|
||||
"tests/test_optimizers/test_knapsack_feature_based.py"
|
||||
];
|
||||
|
||||
# NOTE: These tests seem to be flaky.
|
||||
disabledTests = [
|
||||
"test_digits_modular"
|
||||
"test_digits_modular_object"
|
||||
"test_digits_modular_sparse"
|
||||
"test_digits_sqrt_modular"
|
||||
"test_digits_sqrt_modular_object"
|
||||
"test_digits_sqrt_modular_sparse"
|
||||
];
|
||||
|
||||
# NOTE: Tests are disabled by default because they can run for hours and timeout on Hydra.
|
||||
doCheck = false;
|
||||
|
||||
passthru.tests.check = apricot-select.overridePythonAttrs { doCheck = true; };
|
||||
|
||||
meta = with lib; {
|
||||
description = "Module for submodular optimization for the purpose of selecting subsets of massive data sets";
|
||||
homepage = "https://github.com/jmschrei/apricot";
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
{
|
||||
lib,
|
||||
buildPythonPackage,
|
||||
fetchFromGitHub,
|
||||
fetchPypi,
|
||||
fetchpatch,
|
||||
pytestCheckHook,
|
||||
astunparse,
|
||||
@ -9,25 +9,17 @@
|
||||
}:
|
||||
buildPythonPackage rec {
|
||||
pname = "import-expression";
|
||||
version = "1.1.4";
|
||||
version = "1.1.5";
|
||||
pyproject = true;
|
||||
|
||||
src = fetchFromGitHub {
|
||||
owner = "ioistired";
|
||||
repo = "import-expression-parser";
|
||||
rev = "refs/tags/v${version}";
|
||||
hash = "sha256-mll2NePB7fthzltLOk6D9BgaDpH6GaW4psqcGun/0qM=";
|
||||
src = fetchPypi {
|
||||
inherit version;
|
||||
pname = "import_expression";
|
||||
hash = "sha256-mVlYj8/I3LFEoHJRds/vbCjH2x/C1oNiUCXmh1FtQME=";
|
||||
};
|
||||
|
||||
patches = [
|
||||
(fetchpatch {
|
||||
url = "https://github.com/ioistired/import-expression-parser/commit/3daf968c3163b64685aa529740e132f0df5ab262.patch";
|
||||
hash = "sha256-2Ubv3onor2D26udZbDDMb3iNLopEIRnIcO/X6WUVmJU=";
|
||||
})
|
||||
];
|
||||
|
||||
nativeBuildInputs = [ setuptools ];
|
||||
propagatedBuildInputs = [ astunparse ];
|
||||
build-system = [ setuptools ];
|
||||
dependencies = [ astunparse ];
|
||||
nativeCheckInputs = [ pytestCheckHook ];
|
||||
pytestFlagsArray = [ "tests.py" ];
|
||||
|
||||
|
||||
@ -3,7 +3,6 @@
|
||||
buildPythonPackage,
|
||||
deprecated,
|
||||
fetchFromGitHub,
|
||||
importlib-metadata,
|
||||
ipython,
|
||||
lark,
|
||||
matplotlib-inline,
|
||||
@ -12,7 +11,6 @@
|
||||
numpy,
|
||||
packaging,
|
||||
poetry-core,
|
||||
pydantic,
|
||||
pytest-asyncio,
|
||||
pytest-mock,
|
||||
pytestCheckHook,
|
||||
@ -27,20 +25,21 @@
|
||||
types-deprecated,
|
||||
types-python-dateutil,
|
||||
types-retry,
|
||||
typing-extensions,
|
||||
}:
|
||||
|
||||
buildPythonPackage rec {
|
||||
pname = "pyquil";
|
||||
version = "4.8.0";
|
||||
version = "4.9.2";
|
||||
pyproject = true;
|
||||
|
||||
disabled = pythonOlder "3.7";
|
||||
disabled = pythonOlder "3.8";
|
||||
|
||||
src = fetchFromGitHub {
|
||||
owner = "rigetti";
|
||||
repo = "pyquil";
|
||||
rev = "refs/tags/v${version}";
|
||||
hash = "sha256-MGI+R3oteqDWsXP+SlAGSRGiQiAj44YG6V7o90A4Krc=";
|
||||
hash = "sha256-TxmQ9QXTTr4Xv37WmgArfK8Q5H1zAu8qx8wRsvK+vVM=";
|
||||
};
|
||||
|
||||
pythonRelaxDeps = [
|
||||
@ -61,7 +60,6 @@ buildPythonPackage rec {
|
||||
networkx
|
||||
numpy
|
||||
packaging
|
||||
pydantic
|
||||
qcs-sdk-python
|
||||
rpcq
|
||||
scipy
|
||||
@ -69,7 +67,8 @@ buildPythonPackage rec {
|
||||
types-deprecated
|
||||
types-python-dateutil
|
||||
types-retry
|
||||
] ++ lib.optionals (pythonOlder "3.8") [ importlib-metadata ];
|
||||
typing-extensions
|
||||
];
|
||||
|
||||
nativeCheckInputs = [
|
||||
nest-asyncio
|
||||
|
||||
@ -24,16 +24,16 @@
|
||||
|
||||
buildPythonPackage rec {
|
||||
pname = "qcs-api-client";
|
||||
version = "0.25.0";
|
||||
version = "0.25.1";
|
||||
pyproject = true;
|
||||
|
||||
disabled = pythonOlder "3.7";
|
||||
disabled = pythonOlder "3.8";
|
||||
|
||||
src = fetchFromGitHub {
|
||||
owner = "rigetti";
|
||||
repo = "qcs-api-client-python";
|
||||
rev = "refs/tags/v${version}";
|
||||
hash = "sha256-dKjiicrPLRlaIwHwSqpY5dBMTzrZD4xfw3h54IN3rh0=";
|
||||
hash = "sha256-GtHAV4BvBdexjJxlT1jcNklSogYor2aWoQI2QNs/dOQ=";
|
||||
};
|
||||
|
||||
patches = [
|
||||
|
||||
@ -912,7 +912,7 @@ dependencies = [
|
||||
"futures-sink",
|
||||
"futures-util",
|
||||
"http",
|
||||
"indexmap 2.2.5",
|
||||
"indexmap 2.2.6",
|
||||
"slab",
|
||||
"tokio",
|
||||
"tokio-util",
|
||||
@ -1180,9 +1180,9 @@ dependencies = [
|
||||
|
||||
[[package]]
|
||||
name = "indexmap"
|
||||
version = "2.2.5"
|
||||
version = "2.2.6"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "7b0b929d511467233429c45a44ac1dcaa21ba0f5ba11e4879e6ed28ddb4f9df4"
|
||||
checksum = "168fb715dda47215e360912c096649d23d58bf392ac62f73919e831745e40f26"
|
||||
dependencies = [
|
||||
"equivalent",
|
||||
"hashbrown 0.14.3",
|
||||
@ -1901,7 +1901,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "e1d3afd2628e69da2be385eb6f2fd57c8ac7977ceeff6dc166ff1657b0e386a9"
|
||||
dependencies = [
|
||||
"fixedbitset",
|
||||
"indexmap 2.2.5",
|
||||
"indexmap 2.2.6",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
@ -2124,7 +2124,7 @@ dependencies = [
|
||||
|
||||
[[package]]
|
||||
name = "qcs"
|
||||
version = "0.21.4"
|
||||
version = "0.21.7"
|
||||
dependencies = [
|
||||
"assert2",
|
||||
"async-trait",
|
||||
@ -2136,7 +2136,7 @@ dependencies = [
|
||||
"float-cmp",
|
||||
"futures",
|
||||
"hex",
|
||||
"indexmap 1.9.3",
|
||||
"indexmap 2.2.6",
|
||||
"insta",
|
||||
"itertools 0.11.0",
|
||||
"lazy_static",
|
||||
@ -2260,7 +2260,7 @@ dependencies = [
|
||||
|
||||
[[package]]
|
||||
name = "qcs-sdk-python"
|
||||
version = "0.17.4"
|
||||
version = "0.17.7"
|
||||
dependencies = [
|
||||
"async-trait",
|
||||
"numpy",
|
||||
@ -2290,11 +2290,11 @@ checksum = "a1d01941d82fa2ab50be1e79e6714289dd7cde78eba4c074bc5a4374f650dfe0"
|
||||
|
||||
[[package]]
|
||||
name = "quil-rs"
|
||||
version = "0.23.0"
|
||||
source = "git+https://github.com/rigetti/quil-rs?tag=quil-py/v0.7.0#3bb618124c2165b7329c58c0f217d8ee9d816e67"
|
||||
version = "0.25.1"
|
||||
source = "git+https://github.com/rigetti/quil-rs?tag=quil-py/v0.9.1#4179fb03feff6b83edfb7a0448b0b3967ed28212"
|
||||
dependencies = [
|
||||
"approx",
|
||||
"indexmap 2.2.5",
|
||||
"indexmap 2.2.6",
|
||||
"itertools 0.12.1",
|
||||
"lexical",
|
||||
"ndarray",
|
||||
@ -3381,7 +3381,7 @@ version = "0.19.15"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "1b5bb770da30e5cbfde35a2d7b9b8a2c4b8ef89548a7a6aeab5c9a576e3e7421"
|
||||
dependencies = [
|
||||
"indexmap 2.2.5",
|
||||
"indexmap 2.2.6",
|
||||
"serde",
|
||||
"serde_spanned",
|
||||
"toml_datetime",
|
||||
@ -3394,7 +3394,7 @@ version = "0.22.8"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "c12219811e0c1ba077867254e5ad62ee2c9c190b0d957110750ac0cda1ae96cd"
|
||||
dependencies = [
|
||||
"indexmap 2.2.5",
|
||||
"indexmap 2.2.6",
|
||||
"serde",
|
||||
"serde_spanned",
|
||||
"toml_datetime",
|
||||
|
||||
@ -15,7 +15,7 @@
|
||||
|
||||
buildPythonPackage rec {
|
||||
pname = "qcs-sdk-python";
|
||||
version = "0.17.4";
|
||||
version = "0.17.7";
|
||||
pyproject = true;
|
||||
|
||||
disabled = pythonOlder "3.8";
|
||||
@ -24,13 +24,13 @@ buildPythonPackage rec {
|
||||
owner = "rigetti";
|
||||
repo = "qcs-sdk-rust";
|
||||
rev = "python/v${version}";
|
||||
hash = "sha256-Z/NK+xnugFieJqAbvGaVvxUaz9RC1vpWb4ydZTVbZeU=";
|
||||
hash = "sha256-6Rh5gQH+ObpWGR9rYJfkXnGfG1GjKLn+ckiR7RhKzoE=";
|
||||
};
|
||||
|
||||
cargoDeps = rustPlatform.importCargoLock {
|
||||
lockFile = ./Cargo.lock;
|
||||
outputHashes = {
|
||||
"quil-rs-0.23.0" = "sha256-l9wj1j7PJ5L497dPlkEpJ4ctAfjUIada5Vbn2h5ioVE=";
|
||||
"quil-rs-0.25.1" = "sha256-zC4DEjCN6y9XeZlzmXHSTbVTpFQ4Srozix89IHDhHXc=";
|
||||
};
|
||||
};
|
||||
|
||||
|
||||
@ -13,7 +13,7 @@
|
||||
|
||||
buildPythonPackage rec {
|
||||
pname = "quil";
|
||||
version = "0.7.1";
|
||||
version = "0.9.1";
|
||||
pyproject = true;
|
||||
|
||||
disabled = pythonOlder "3.8";
|
||||
@ -22,13 +22,13 @@ buildPythonPackage rec {
|
||||
owner = "rigetti";
|
||||
repo = "quil-rs";
|
||||
rev = "quil-py/v${version}";
|
||||
hash = "sha256-GFePbCJnVbzL4cpQ7fy1tk2l7NhAyTVW63lVYTv0/Oo=";
|
||||
hash = "sha256-c9nFF74Mr6S2b7NthRVUnarwxFZ9s5RUaoxYruE6QvI=";
|
||||
};
|
||||
|
||||
cargoDeps = rustPlatform.fetchCargoTarball {
|
||||
name = "${pname}-${version}";
|
||||
inherit src;
|
||||
hash = "sha256-catUGCFbkvov1z52f6eyxogflu61VcjIItgEVEWzkpY=";
|
||||
hash = "sha256-FNkXdBLfKnrD9aUe25uJHi+TtApgFSCryYCY1r8ebho=";
|
||||
};
|
||||
|
||||
buildAndTestSubdir = "quil-py";
|
||||
|
||||
@ -1498,6 +1498,43 @@ let
|
||||
buildInputs = [ cacert ] ++ attrs.buildInputs;
|
||||
});
|
||||
|
||||
|
||||
immunotation = let
|
||||
MHC41alleleList = fetchurl {
|
||||
url = "https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/allele.list";
|
||||
hash = "sha256-CRZ+0uHzcq5zK5eONucAChXIXO8tnq5sSEAS80Z7jhg=";
|
||||
};
|
||||
|
||||
MHCII40alleleList = fetchurl {
|
||||
url = "https://services.healthtech.dtu.dk/services/NetMHCIIpan-4.0/alleles_name.list";
|
||||
hash = "sha256-K4Ic2NUs3P4IkvOODwZ0c4Yh8caex5Ih0uO5jXRHp40=";
|
||||
};
|
||||
|
||||
# List of valid countries, regions and ethnic groups
|
||||
# The original page is changing a bit every day, but the relevant
|
||||
# content does not. Use archive.org to get a stable snapshot.
|
||||
# It can be updated from time to time, or when the package becomes
|
||||
# deficient. This may be difficult to know.
|
||||
# Update the snapshot date, and add id_ after it, as described here:
|
||||
# https://web.archive.org/web/20130806040521/http://faq.web.archive.org/page-without-wayback-code/
|
||||
validGeographics = fetchurl {
|
||||
url = "https://web.archive.org/web/20240418194005id_/http://www.allelefrequencies.net/hla6006a.asp";
|
||||
hash = "sha256-m7Wkmh/cPxeqn94LwoznIh+fcFXskmSGErUYj6kTqak=";
|
||||
};
|
||||
in old.immunotation.overrideAttrs (attrs: {
|
||||
patches = [ ./patches/immunotation.patch ];
|
||||
postPatch = ''
|
||||
substituteInPlace "R/external_resources_input.R" --replace-fail \
|
||||
"nix-NetMHCpan-4.1-allele-list" ${MHC41alleleList}
|
||||
|
||||
substituteInPlace "R/external_resources_input.R" --replace-fail \
|
||||
"nix-NETMHCIIpan-4.0-alleles-name-list" ${MHCII40alleleList}
|
||||
|
||||
substituteInPlace "R/AFND_interface.R" --replace-fail \
|
||||
"nix-valid-geographics" ${validGeographics}
|
||||
'';
|
||||
});
|
||||
|
||||
rstan = old.rstan.overrideAttrs (attrs: {
|
||||
env = (attrs.env or { }) // {
|
||||
NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION";
|
||||
|
||||
47
pkgs/development/r-modules/patches/immunotation.patch
Normal file
47
pkgs/development/r-modules/patches/immunotation.patch
Normal file
@ -0,0 +1,47 @@
|
||||
diff --git a/R/AFND_interface.R b/R/AFND_interface.R
|
||||
index b62e8e0..0f22d85 100644
|
||||
--- a/R/AFND_interface.R
|
||||
+++ b/R/AFND_interface.R
|
||||
@@ -244,9 +244,9 @@ check_population <- function(hla_population) {
|
||||
#' @return list of valid countries, regions and ethnic origin
|
||||
#' @keywords internal
|
||||
get_valid_geographics <- function() {
|
||||
- url <- "http://www.allelefrequencies.net/hla6006a.asp?"
|
||||
- html_input <- getURL(url, read_method = "html")
|
||||
-
|
||||
+ # http://www.allelefrequencies.net/hla6006a.asp?
|
||||
+ html_input <- xml2::read_html("nix-valid-geographics")
|
||||
+
|
||||
rvest_tables <- rvest::html_table(html_input, fill = TRUE)
|
||||
|
||||
# country
|
||||
diff --git a/R/external_resources_input.R b/R/external_resources_input.R
|
||||
index c4b1dc1..8fc5881 100644
|
||||
--- a/R/external_resources_input.R
|
||||
+++ b/R/external_resources_input.R
|
||||
@@ -74,16 +74,17 @@ getURL <- function(URL, N.TRIES=2L,
|
||||
# MHC I
|
||||
# netmhcI_input_template is an internal variable containing list of valid
|
||||
# NetMHCpan input alleles
|
||||
-netmhcI_input_template <- getURL(
|
||||
- URL="https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/allele.list",
|
||||
- read_method = "delim", delim = "\t",
|
||||
- col_names = c("netmhc_input", "hla_chain_name", "HLA_gene"))
|
||||
+netmhcI_input_template <- readr::read_delim(
|
||||
+ # https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/allele.list
|
||||
+ "nix-NetMHCpan-4.1-allele-list",
|
||||
+ delim = "\t",
|
||||
+ skip = 0,
|
||||
+ col_names = c("netmhc_input", "hla_chain_name", "HLA_gene")
|
||||
+ )
|
||||
|
||||
# MHC II
|
||||
-lines <- getURL(
|
||||
- URL = paste0("https://services.healthtech.dtu.dk/services/",
|
||||
- "NetMHCIIpan-4.0/alleles_name.list"),
|
||||
- read_method = "lines")
|
||||
+# https://services.healthtech.dtu.dk/services/NetMHCIIpan-4.0/alleles_name.list
|
||||
+lines <- readr::read_lines("nix-NETMHCIIpan-4.0-alleles-name-list")
|
||||
lines_rep <- stringr::str_replace_all(lines, "\t+|\\s\\s+", "\t")
|
||||
netmhcII_input_template <- suppressWarnings(
|
||||
suppressMessages(read.delim(textConnection(lines_rep), sep = "\t")))
|
||||
@ -5,16 +5,16 @@
|
||||
|
||||
rustPlatform.buildRustPackage rec {
|
||||
pname = "neocmakelsp";
|
||||
version = "0.6.25";
|
||||
version = "0.6.26";
|
||||
|
||||
src = fetchFromGitHub {
|
||||
owner = "Decodetalkers";
|
||||
repo = "neocmakelsp";
|
||||
rev = "v${version}";
|
||||
hash = "sha256-2eZ1f0oxCNf0hJEQ8hkvsTwCaAWJrIYCyIY5PNfaxI4=";
|
||||
hash = "sha256-9pCi7bevgE2tO0n1LvhLIcFV8sVpAagkVB8l5WWdIbM=";
|
||||
};
|
||||
|
||||
cargoHash = "sha256-mo/d99Y41/pxMzVvI6LkjnhotGV5j0ee4GItly0aqpY=";
|
||||
cargoHash = "sha256-xm+8IDLvPDOFJ6FyeQdpbWgQ9XE6bW5i29W0S9JSQzc=";
|
||||
|
||||
meta = with lib; {
|
||||
description = "A cmake lsp based on tower-lsp and treesitter";
|
||||
|
||||
@ -5,18 +5,18 @@
|
||||
|
||||
buildNpmPackage rec {
|
||||
pname = "android-tv-card";
|
||||
version = "3.7.3";
|
||||
version = "3.7.4";
|
||||
|
||||
src = fetchFromGitHub {
|
||||
owner = "Nerwyn";
|
||||
repo = "android-tv-card";
|
||||
rev = version;
|
||||
hash = "sha256-uhdo4K5JqKogQGKr0dkFl579YeAQNbhOwHAFTLpqY6Y=";
|
||||
hash = "sha256-5GdN6zCE24kGLM4ka8vHdpIEWTQAzve/1l3+5OV95i0=";
|
||||
};
|
||||
|
||||
patches = [ ./dont-call-git.patch ];
|
||||
|
||||
npmDepsHash = "sha256-wrmj4lewxBnWVlpkb/AP3lfuGNcvYGf+HWBQw7bcr1Q=";
|
||||
npmDepsHash = "sha256-fVnqGe/ao0Ilk/mWbHGscYQlIIk3K0mpm1wS4F8Lio4=";
|
||||
|
||||
installPhase = ''
|
||||
runHook preInstall
|
||||
|
||||
@ -4,6 +4,8 @@ outer@{ lib, stdenv, fetchurl, fetchpatch, openssl, zlib, pcre, libxml2, libxslt
|
||||
, nixosTests
|
||||
, installShellFiles, substituteAll, removeReferencesTo, gd, geoip, perl
|
||||
, withDebug ? false
|
||||
, withGeoIP ? false
|
||||
, withImageFilter ? false
|
||||
, withKTLS ? true
|
||||
, withStream ? true
|
||||
, withMail ? false
|
||||
@ -64,9 +66,11 @@ stdenv.mkDerivation {
|
||||
removeReferencesTo
|
||||
] ++ nativeBuildInputs;
|
||||
|
||||
buildInputs = [ openssl zlib pcre libxml2 libxslt gd geoip perl ]
|
||||
buildInputs = [ openssl zlib pcre libxml2 libxslt perl ]
|
||||
++ buildInputs
|
||||
++ mapModules "inputs";
|
||||
++ mapModules "inputs"
|
||||
++ lib.optional withGeoIP geoip
|
||||
++ lib.optional withImageFilter gd;
|
||||
|
||||
configureFlags = [
|
||||
"--sbin-path=bin/nginx"
|
||||
@ -112,10 +116,9 @@ stdenv.mkDerivation {
|
||||
"--with-http_perl_module"
|
||||
"--with-perl=${perl}/bin/perl"
|
||||
"--with-perl_modules_path=lib/perl5"
|
||||
] ++ lib.optional withSlice "--with-http_slice_module"
|
||||
++ lib.optional (gd != null) "--with-http_image_filter_module"
|
||||
++ lib.optional (geoip != null) "--with-http_geoip_module"
|
||||
++ lib.optional (withStream && geoip != null) "--with-stream_geoip_module"
|
||||
] ++ lib.optional withImageFilter "--with-http_image_filter_module"
|
||||
++ lib.optional withSlice "--with-http_slice_module"
|
||||
++ lib.optionals withGeoIP ([ "--with-http_geoip_module" ] ++ lib.optional withStream "--with-stream_geoip_module")
|
||||
++ lib.optional (with stdenv.hostPlatform; isLinux || isFreeBSD) "--with-file-aio"
|
||||
++ configureFlags
|
||||
++ map (mod: "--add-module=${mod.src}") modules;
|
||||
|
||||
@ -10995,8 +10995,6 @@ with pkgs;
|
||||
|
||||
mkgmap-splitter = callPackage ../applications/misc/mkgmap/splitter { };
|
||||
|
||||
mpack = callPackage ../tools/networking/mpack { };
|
||||
|
||||
mtm = callPackage ../tools/misc/mtm { };
|
||||
|
||||
op-geth = callPackage ../applications/blockchains/optimism/geth.nix {
|
||||
|
||||
Loading…
Reference in New Issue
Block a user