diff options
Diffstat (limited to 'pkgs/applications/science')
30 files changed, 161 insertions, 184 deletions
diff --git a/pkgs/applications/science/astronomy/siril/default.nix b/pkgs/applications/science/astronomy/siril/default.nix index 569d537172542..2f572350bae02 100644 --- a/pkgs/applications/science/astronomy/siril/default.nix +++ b/pkgs/applications/science/astronomy/siril/default.nix @@ -7,13 +7,13 @@ stdenv.mkDerivation rec { pname = "siril"; - version = "1.2.1"; + version = "1.2.3"; src = fetchFromGitLab { owner = "free-astro"; repo = "siril"; rev = version; - hash = "sha256-njvByA8nbG3qHKfv8eX20TrIhngVI0nzIHmhYIN6htE="; + hash = "sha256-JUMk2XHMOeocSpeeI+k3s9TsEQCdqz3oigTzuwRHbT4="; }; nativeBuildInputs = [ diff --git a/pkgs/applications/science/astronomy/stellarium/default.nix b/pkgs/applications/science/astronomy/stellarium/default.nix index 687c0b3a2dda2..426a7f18dff3f 100644 --- a/pkgs/applications/science/astronomy/stellarium/default.nix +++ b/pkgs/applications/science/astronomy/stellarium/default.nix @@ -24,13 +24,13 @@ stdenv.mkDerivation (finalAttrs: { pname = "stellarium"; - version = "24.1"; + version = "24.2"; src = fetchFromGitHub { owner = "Stellarium"; repo = "stellarium"; rev = "v${finalAttrs.version}"; - hash = "sha256-t3eFmiG9X2cmnjc/PQwZ2bw1SCHaNRA83wiT1cPbKJc="; + hash = "sha256-tqyLwlf8hugixZSsFCZPTtchO3VXk3m/nX1kuDoLOAY="; }; patches = [ diff --git a/pkgs/applications/science/biology/gatk/default.nix b/pkgs/applications/science/biology/gatk/default.nix index 41623bf640dda..50dc0613c743f 100644 --- a/pkgs/applications/science/biology/gatk/default.nix +++ b/pkgs/applications/science/biology/gatk/default.nix @@ -2,10 +2,10 @@ stdenv.mkDerivation rec { pname = "gatk"; - version = "4.5.0.0"; + version = "4.6.0.0"; src = fetchzip { url = "https://github.com/broadinstitute/gatk/releases/download/${version}/gatk-${version}.zip"; - sha256 = "sha256-c3YZsSCjZY75jooiqtc8x/xsWTvYm9labUcOydDlSRQ="; + sha256 = "sha256-AwGRkgVbG2gA4K1JG0WPr4v18JHG5YzYUKdJ2EJZX+Y="; }; nativeBuildInputs = [ makeWrapper ]; diff --git a/pkgs/applications/science/biology/iqtree/default.nix b/pkgs/applications/science/biology/iqtree/default.nix index 4dfbaa25b36a4..60827b8e3a685 100644 --- a/pkgs/applications/science/biology/iqtree/default.nix +++ b/pkgs/applications/science/biology/iqtree/default.nix @@ -10,13 +10,13 @@ stdenv.mkDerivation rec { pname = "iqtree"; - version = "2.3.4"; + version = "2.3.5"; src = fetchFromGitHub { owner = "iqtree"; repo = "iqtree2"; rev = "v${version}"; - hash = "sha256-dnUFllqcABB3JDYoCwPGtIYD/h5lzX2XKOroDpijPpU="; + hash = "sha256-ld+9vPJRVHMEe5/igqRr6RkISY2ipfGkJFHDOSZuAmg="; fetchSubmodules = true; }; diff --git a/pkgs/applications/science/biology/jbrowse/default.nix b/pkgs/applications/science/biology/jbrowse/default.nix index 395e5b5dcd9ab..3a7e009cc1561 100644 --- a/pkgs/applications/science/biology/jbrowse/default.nix +++ b/pkgs/applications/science/biology/jbrowse/default.nix @@ -2,11 +2,11 @@ let pname = "jbrowse"; - version = "2.11.2"; + version = "2.12.2"; src = fetchurl { url = "https://github.com/GMOD/jbrowse-components/releases/download/v${version}/jbrowse-desktop-v${version}-linux.AppImage"; - sha256 = "sha256-7kZsK3vYgxubgtoIG1dByHgEBOlh9GUq+i3u/1eo0/o="; + sha256 = "sha256-dnvs+niNo8VPuOk9uODezLxdghwutLuhgG5Jyxi8mW0="; }; appimageContents = appimageTools.extractType2 { diff --git a/pkgs/applications/science/biology/kent/default.nix b/pkgs/applications/science/biology/kent/default.nix index 400e073f69057..f30a6725bb474 100644 --- a/pkgs/applications/science/biology/kent/default.nix +++ b/pkgs/applications/science/biology/kent/default.nix @@ -13,13 +13,13 @@ }: stdenv.mkDerivation rec { pname = "kent"; - version = "465"; + version = "467"; src = fetchFromGitHub { owner = "ucscGenomeBrowser"; repo = pname; rev = "v${version}_base"; - hash = "sha256-QeHqXSbad5LCmQ8DfLxl2pyXJvKV4G7uLXBtRd7LME0="; + hash = "sha256-Y8iHSo70nsPZwVy8ZiiqjU3mGrPOyPQkW0VpLS+ulGE="; }; buildInputs = [ libpng libuuid zlib bzip2 xz openssl curl libmysqlclient ]; diff --git a/pkgs/applications/science/biology/last/default.nix b/pkgs/applications/science/biology/last/default.nix index 700b2cf3b4548..7cfdb674c6e49 100644 --- a/pkgs/applications/science/biology/last/default.nix +++ b/pkgs/applications/science/biology/last/default.nix @@ -9,13 +9,13 @@ stdenv.mkDerivation rec { pname = "last"; - version = "1544"; + version = "1548"; src = fetchFromGitLab { owner = "mcfrith"; repo = "last"; rev = "refs/tags/${version}"; - hash = "sha256-jxNudfUvSqV1QUzdvG8LWtL977oho9QuOQImmwbQiIM="; + hash = "sha256-6mLPnyEAuRvCeV8pv3avsm6CKDrBPgX8xSxGO2kvTrM="; }; nativeBuildInputs = [ diff --git a/pkgs/applications/science/biology/picard-tools/default.nix b/pkgs/applications/science/biology/picard-tools/default.nix index 880ea77e9d245..e8786fe4b9c0e 100644 --- a/pkgs/applications/science/biology/picard-tools/default.nix +++ b/pkgs/applications/science/biology/picard-tools/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "picard-tools"; - version = "3.1.1"; + version = "3.2.0"; src = fetchurl { url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar"; - sha256 = "sha256-FcefUf0KwAEEn53XubrB2991ncsCMKicf20fJG6LurQ="; + sha256 = "sha256-4lj6Lj9fphzWeZ7I4HP0mpX73OrxY9imCXGyYZuG+kE="; }; nativeBuildInputs = [ makeWrapper ]; diff --git a/pkgs/applications/science/biology/poretools/default.nix b/pkgs/applications/science/biology/poretools/default.nix deleted file mode 100644 index 27a1b7ed38416..0000000000000 --- a/pkgs/applications/science/biology/poretools/default.nix +++ /dev/null @@ -1,23 +0,0 @@ -{ lib, python2Packages, fetchFromGitHub }: - -python2Packages.buildPythonPackage rec { - pname = "poretools"; - version = "unstable-2016-07-10"; - - src = fetchFromGitHub { - repo = pname; - owner = "arq5x"; - rev = "e426b1f09e86ac259a00c261c79df91510777407"; - sha256 = "0bglj833wxpp3cq430p1d3xp085ls221js2y90w7ir2x5ay8l7am"; - }; - - propagatedBuildInputs = [ python2Packages.h5py python2Packages.matplotlib python2Packages.seaborn python2Packages.pandas ]; - - meta = { - description = "Toolkit for working with nanopore sequencing data from Oxford Nanopore"; - license = lib.licenses.mit; - homepage = "https://poretools.readthedocs.io/en/latest/"; - maintainers = [ lib.maintainers.rybern ]; - broken = true; # Build error: h5py-3.9.0 not supported for interpreter python2.7 - }; -} diff --git a/pkgs/applications/science/biology/spades/default.nix b/pkgs/applications/science/biology/spades/default.nix deleted file mode 100644 index 0b0491a71aaef..0000000000000 --- a/pkgs/applications/science/biology/spades/default.nix +++ /dev/null @@ -1,32 +0,0 @@ -{ lib, stdenv, fetchurl, zlib, bzip2, cmake, python3 }: - -stdenv.mkDerivation rec { - pname = "SPAdes"; - version = "3.15.5"; - - src = fetchurl { - url = "http://cab.spbu.ru/files/release${version}/${pname}-${version}.tar.gz"; - sha256 = "sha256-FVw2QNVx8uexmgUDHR/Q0ZvYLfeF04hw+5O9JBsSu/o="; - }; - - nativeBuildInputs = [ cmake ]; - - buildInputs = [ zlib bzip2 python3 ]; - - doCheck = true; - - sourceRoot = "${pname}-${version}/src"; - - env.CXXFLAGS = toString [ - # GCC 13: error: 'uint32_t' does not name a type - "-include cstdint" - ]; - - meta = with lib; { - description = "St. Petersburg genome assembler: assembly toolkit containing various assembly pipelines"; - license = licenses.gpl2Only; - homepage = "http://cab.spbu.ru/software/spades/"; - platforms = [ "x86_64-linux" "x86_64-darwin" ]; - maintainers = [ maintainers.bzizou ]; - }; -} diff --git a/pkgs/applications/science/chemistry/openmolcas/default.nix b/pkgs/applications/science/chemistry/openmolcas/default.nix index 8ad9794739559..d500e78b24820 100644 --- a/pkgs/applications/science/chemistry/openmolcas/default.nix +++ b/pkgs/applications/science/chemistry/openmolcas/default.nix @@ -43,13 +43,13 @@ let in stdenv.mkDerivation rec { pname = "openmolcas"; - version = "24.02"; + version = "24.06"; src = fetchFromGitLab { owner = "Molcas"; repo = "OpenMolcas"; rev = "v${version}"; - hash = "sha256-4Ek0cnaRfLEbj1Nj31rRp9b2sois4rIFTcpOUq9h2mw="; + hash = "sha256-/y6vEvA1Zf+p7Z0WpcN4P5voLN8MmfbKz1FuthgVQp0="; }; patches = [ diff --git a/pkgs/applications/science/electronics/dsview/default.nix b/pkgs/applications/science/electronics/dsview/default.nix index b7950bfbb8d95..5d6c83f5dfaa1 100644 --- a/pkgs/applications/science/electronics/dsview/default.nix +++ b/pkgs/applications/science/electronics/dsview/default.nix @@ -1,18 +1,18 @@ { stdenv, lib, fetchFromGitHub, pkg-config, cmake, wrapQtAppsHook -, libzip, boost, fftw, qtbase, qtwayland, qtsvg, libusb1 +, libzip, boost, fftw, libusb1, qtbase, qtsvg, qtwayland , python3, desktopToDarwinBundle }: stdenv.mkDerivation rec { pname = "dsview"; - version = "1.3.1"; + version = "1.3.2"; src = fetchFromGitHub { owner = "DreamSourceLab"; repo = "DSView"; rev = "v${version}"; - sha256 = "sha256-LwrlB+Nwq34YjwGmnbUWS3W//ZHr8Do2Wf2te+2oBeI="; + sha256 = "sha256-d/TfCuJzAM0WObOiBhgfsTirlvdROrlCm+oL1cqUrIs="; }; patches = [ diff --git a/pkgs/applications/science/electronics/gtkwave/default.nix b/pkgs/applications/science/electronics/gtkwave/default.nix index 3e0f3613ba903..d28a5cf809065 100644 --- a/pkgs/applications/science/electronics/gtkwave/default.nix +++ b/pkgs/applications/science/electronics/gtkwave/default.nix @@ -16,11 +16,11 @@ stdenv.mkDerivation rec { pname = "gtkwave"; - version = "3.3.119"; + version = "3.3.120"; src = fetchurl { url = "mirror://sourceforge/gtkwave/${pname}-gtk3-${version}.tar.gz"; - sha256 = "sha256-6rPgnnZBEVwHhIv7MPfdDDu+K4y+RQF+leB327pqwDg="; + sha256 = "sha256-XalIY/suXYjMAZ4r/cZ2AiOYETiUtYXYZOEcqDQbJNg="; }; nativeBuildInputs = [ pkg-config wrapGAppsHook3 ]; diff --git a/pkgs/applications/science/electronics/kicad/versions.nix b/pkgs/applications/science/electronics/kicad/versions.nix index 4c55703edccf4..b3ddbd5b604fe 100644 --- a/pkgs/applications/science/electronics/kicad/versions.nix +++ b/pkgs/applications/science/electronics/kicad/versions.nix @@ -3,23 +3,23 @@ { "kicad" = { kicadVersion = { - version = "8.0.2"; + version = "8.0.3"; src = { - rev = "55a4d4f5e2f54be6ccf74a8919d04684c9df4c50"; - sha256 = "069ycii9zvdxwxd73afd6bp975r1555yvifi9zdb77qyvn0d9nr9"; + rev = "8ba5ba46af8502ea7a7d2a9754363167c2742399"; + sha256 = "0hafvcjjwylgcpgyyasmb2q210k82wvcswvgjvwwh76bwshwcpwa"; }; }; libVersion = { - version = "8.0.2"; + version = "8.0.3"; libSources = { - symbols.rev = "099ac0c8ac402a685fde00b1369e34a116e29661"; - symbols.sha256 = "0w333f89yw2m0zlpkg0k6hfwlj10snm8laihdjnsb22asyz4pbhn"; - templates.rev = "2e2da58e02707d327d59d4101c401a82dc9a26f6"; - templates.sha256 = "073a6cyvzzy0vmkj3ip4ziq7b7pcizs70nm5acw838dxghjfyv3v"; - footprints.rev = "e8c30550cde4945cbe1bf30cccf0b3c1e2bda6c6"; - footprints.sha256 = "10j8qjljc1fv8k4zp3zn0da33g57hn6pgrgmbgp18dsa539xvxcz"; - packages3d.rev = "249f7947587529026e1676cd70c8d7493a8d8162"; - packages3d.sha256 = "04gvfb54jhnww2qwrxc27wpyrvmjasdc4xhr0ridl7dglh4qcp35"; + symbols.rev = "2bc103c46a8daacbba2cded8b9f095b330ba928d"; + symbols.sha256 = "1za0spq09bbj7xwfwr1abmwjnqfd3zx0crayaz7915ja0ifi75hd"; + templates.rev = "0f57b59d365d1f8b8fdd0745e10beb035e88ba37"; + templates.sha256 = "03idwrk3vj9h2az8j8lqpbdbnfxdbkzh4db68kq3644yj3cnlcza"; + footprints.rev = "539ffd8c0898ad8c8c51c2ab85ba56bfd77271c7"; + footprints.sha256 = "0ik4hjl5m65wnpaymg58zbvsfvchhyq5x3psvj6005mgv2hrican"; + packages3d.rev = "3172a1cc0931c1734efad68623374d5277f8ab60"; + packages3d.sha256 = "1yjlg7cxwhlzcdbxjqyqamr140sz8gvzi63k2401mhdbh88c9kii"; }; }; }; diff --git a/pkgs/applications/science/logic/cbmc/default.nix b/pkgs/applications/science/logic/cbmc/default.nix index dcf5b5bb37fa2..c980e84f9d9f6 100644 --- a/pkgs/applications/science/logic/cbmc/default.nix +++ b/pkgs/applications/science/logic/cbmc/default.nix @@ -13,13 +13,13 @@ stdenv.mkDerivation rec { pname = "cbmc"; - version = "5.95.1"; + version = "6.0.1"; src = fetchFromGitHub { owner = "diffblue"; repo = pname; rev = "${pname}-${version}"; - sha256 = "sha256-fDLSo5EeHyPTliAqFp+5mfaB0iZXIMXeMyF21fjl5k4="; + sha256 = "sha256-7syRpCNL7TRZoJaNrmAdahNy7IyovyniYyOwD/lzhuw="; }; nativeBuildInputs = [ diff --git a/pkgs/applications/science/logic/coq/default.nix b/pkgs/applications/science/logic/coq/default.nix index 68b424b32fb4a..8f0f88461e653 100644 --- a/pkgs/applications/science/logic/coq/default.nix +++ b/pkgs/applications/science/logic/coq/default.nix @@ -58,6 +58,8 @@ let "8.18.0".sha256 = "sha256-WhiBs4nzPHQ0R24xAdM49kmxSCPOxiOVMA1iiMYunz4="; "8.19.0".sha256 = "sha256-ixsYCvCXpBHqJ71hLQklphlwoOO3i/6w2PJjllKqf9k="; "8.19.1".sha256 = "sha256-kmZ8Uk8jpzjOd67aAPp3C+vU2oNaBw9pr7+Uixcgg94="; + "8.19.2".sha256 = "sha256-q+i07JsMZp83Gqav6v1jxsgPLN7sPvp5/oszVnavmz0="; + "8.20+rc1".sha256 = "sha256-OLGPMvvA3hc42zdgWSOnOkN0/WwzBpneUcUVRNcNVms="; }; releaseRev = v: "V${v}"; fetched = import ../../../../build-support/coq/meta-fetch/default.nix diff --git a/pkgs/applications/science/logic/dafny/default.nix b/pkgs/applications/science/logic/dafny/default.nix index f85e6cf22879d..93ae5c92b32fe 100644 --- a/pkgs/applications/science/logic/dafny/default.nix +++ b/pkgs/applications/science/logic/dafny/default.nix @@ -8,32 +8,37 @@ buildDotnetModule rec { pname = "Dafny"; - version = "4.6.0"; + version = "4.7.0"; src = fetchFromGitHub { owner = "dafny-lang"; repo = "dafny"; rev = "v${version}"; - hash = "sha256-3t0drxM7PZzrLbxBKYa6Gja2u6GK6Pc+ejoswag3P3k="; + hash = "sha256-XoSk08TVv17YyuTsRJ25e6bwSwKIF2+HjF5nFaul8+M="; }; - postPatch = '' - cp ${ - writeScript "fake-gradlew-for-dafny" '' - mkdir -p build/libs/ - javac $(find -name "*.java" | grep "^./src/main") -d classes - jar cf build/libs/DafnyRuntime-${version}.jar -C classes dafny - ''} Source/DafnyRuntime/DafnyRuntimeJava/gradlew + postPatch = + let + # This file wasn't updated between 4.6.0 and 4.7.0. + runtimeJarVersion = "4.6.0"; + in + '' + cp ${ + writeScript "fake-gradlew-for-dafny" '' + mkdir -p build/libs/ + javac $(find -name "*.java" | grep "^./src/main") -d classes + jar cf build/libs/DafnyRuntime-${runtimeJarVersion}.jar -C classes dafny + ''} Source/DafnyRuntime/DafnyRuntimeJava/gradlew - # Needed to fix - # "error NETSDK1129: The 'Publish' target is not supported without - # specifying a target framework. The current project targets multiple - # frameworks, you must specify the framework for the published - # application." - substituteInPlace Source/DafnyRuntime/DafnyRuntime.csproj \ - --replace TargetFrameworks TargetFramework \ - --replace "netstandard2.0;net452" net6.0 - ''; + # Needed to fix + # "error NETSDK1129: The 'Publish' target is not supported without + # specifying a target framework. The current project targets multiple + # frameworks, you must specify the framework for the published + # application." + substituteInPlace Source/DafnyRuntime/DafnyRuntime.csproj \ + --replace-warn TargetFrameworks TargetFramework \ + --replace-warn "netstandard2.0;net452" net6.0 + ''; buildInputs = [ jdk11 ]; nugetDeps = ./deps.nix; diff --git a/pkgs/applications/science/logic/dafny/deps.nix b/pkgs/applications/science/logic/dafny/deps.nix index 91fe5624ac7f7..0c96fca4ec539 100644 --- a/pkgs/applications/science/logic/dafny/deps.nix +++ b/pkgs/applications/science/logic/dafny/deps.nix @@ -3,18 +3,19 @@ { fetchNuGet }: [ (fetchNuGet { pname = "Boogie"; version = "3.1.3"; sha256 = "0xzc7s0rjb8dhdkdf71g6pdsnyhbl534xpwd8gbx6g16a87iqx6i"; }) - (fetchNuGet { pname = "Boogie.AbstractInterpretation"; version = "3.1.3"; sha256 = "0a7v2jkkbh59pyc5nz4avszm3dbmp4amkmr6lvn0gyc3hxgn8d3k"; }) - (fetchNuGet { pname = "Boogie.BaseTypes"; version = "3.1.3"; sha256 = "1h94yl4ymhd2g14i5w8lnnh2zw7gx65qydzvv8cm8d5yn64gch63"; }) - (fetchNuGet { pname = "Boogie.CodeContractsExtender"; version = "3.1.3"; sha256 = "0b1h1lz997lgyq34bx3ngnhgcrw8j4qvsa6iygb6bydxz7rirrf4"; }) - (fetchNuGet { pname = "Boogie.Concurrency"; version = "3.1.3"; sha256 = "1aq0gdz1xkmp82c67vrmyvkncfbbj5zxrsg78lsmmi22h9qbkzm3"; }) - (fetchNuGet { pname = "Boogie.Core"; version = "3.1.3"; sha256 = "0yhl272lv9lncjval2z7zl9wavlxx8bivj467zl2zzbrxw2k5wz8"; }) - (fetchNuGet { pname = "Boogie.ExecutionEngine"; version = "3.1.3"; sha256 = "0p0zp329h6mddbswm3pdcyvy03y69vyznv11ph6bkpya21lsxqy7"; }) - (fetchNuGet { pname = "Boogie.Graph"; version = "3.1.3"; sha256 = "1p8vb4x4iy7f0ycwb8f71j9a2ci8irwg3rvad2hg3rgbihbwp1qj"; }) - (fetchNuGet { pname = "Boogie.Houdini"; version = "3.1.3"; sha256 = "06qlgi9f70r2w7w6h9qw3lx9dd4pbddpdplqjxi090rpry6dhrbz"; }) - (fetchNuGet { pname = "Boogie.Model"; version = "3.1.3"; sha256 = "0fbvnrghaq17fdpjx12axxrrjp1mh99skaznmvxd1ylsqqnn4cbk"; }) - (fetchNuGet { pname = "Boogie.Provers.SMTLib"; version = "3.1.3"; sha256 = "0x7gpc7m04in2gzdn4jgjphd2xjqrdfmh84wzwnwpvi5wyn869jc"; }) - (fetchNuGet { pname = "Boogie.VCExpr"; version = "3.1.3"; sha256 = "0dyndhqz1yf9qnq9mw73g53rnz0xfbdbi3yk6pg7fdm1m3363h5p"; }) - (fetchNuGet { pname = "Boogie.VCGeneration"; version = "3.1.3"; sha256 = "1bl83727zc1rhskx548p5pa27804n3f5i9n233jvcz6n6bfjn74k"; }) + (fetchNuGet { pname = "Boogie.AbstractInterpretation"; version = "3.1.6"; sha256 = "1c6z13dz0sbkmk4ay64aihy7s7xlfdvhpcknxhw1m1b0yly5qj6b"; }) + (fetchNuGet { pname = "Boogie.BaseTypes"; version = "3.1.6"; sha256 = "1hxcpc45f32g3jpaw7mg6k9qsppcb3p20wxv4d4dc3nz0r52lrmr"; }) + (fetchNuGet { pname = "Boogie.CodeContractsExtender"; version = "3.1.6"; sha256 = "1qk7w7c40fpkvvarbgi1bkdcxpn12r0lqngpwwjw8i7nk84ni5gl"; }) + (fetchNuGet { pname = "Boogie.Concurrency"; version = "3.1.6"; sha256 = "11981gfa0n4s214yilnxqhh1clr4l78iqlws6gv01z1n6rxgbyla"; }) + (fetchNuGet { pname = "Boogie.Core"; version = "3.1.6"; sha256 = "0sgj6i1hvp90g2zfqs1aly500xnv3fq9d4cfgii5kpza8vgm7w4g"; }) + (fetchNuGet { pname = "Boogie.ExecutionEngine"; version = "3.1.6"; sha256 = "08vxxwcnkykcngihkp0bvfwkgwxb3nnqjp5f1vz4bnw708xs0ydg"; }) + (fetchNuGet { pname = "Boogie.Graph"; version = "3.1.6"; sha256 = "0fzj65pnky8i83jj2h9nszij25a46z68fy2sm3pxwlg678nmx2jz"; }) + (fetchNuGet { pname = "Boogie.Houdini"; version = "3.1.6"; sha256 = "0lfljb9brnr79hp1f0ff6fcy51ml66pjj102jk4pqpmsjwvcjx43"; }) + (fetchNuGet { pname = "Boogie.Model"; version = "3.1.6"; sha256 = "0546b27mxv97v7qilb1carbwip0q7sz9zz7sxizpww6yc3j8w8if"; }) + (fetchNuGet { pname = "Boogie.Provers.LeanAuto"; version = "3.1.6"; sha256 = "1x1f35g0kxzhxvw4icmbvkik16py47j6h04gj0ckwbny9qmglaby"; }) + (fetchNuGet { pname = "Boogie.Provers.SMTLib"; version = "3.1.6"; sha256 = "0mqlpwfxgv9dd773254rrbgbjb5mpa3xkvlq32ml752h36j8m2r9"; }) + (fetchNuGet { pname = "Boogie.VCExpr"; version = "3.1.6"; sha256 = "0p7axpjn4qg191bs7b33zf9l336bdznvxp3305z2ssnkakjx247h"; }) + (fetchNuGet { pname = "Boogie.VCGeneration"; version = "3.1.6"; sha256 = "05z2lr92hbllikv65gh7m3i879fnn6pjn2acf133sijx9b1jixdb"; }) (fetchNuGet { pname = "CocoR"; version = "2014.12.24"; sha256 = "0ps8h7aawkcc1910qnh13llzb01pvgsjmg862pxp0p4wca2dn7a2"; }) (fetchNuGet { pname = "JetBrains.Annotations"; version = "2021.1.0"; sha256 = "07pnhxxlgx8spmwmakz37nmbvgyb6yjrbrhad5rrn6y767z5r1gb"; }) (fetchNuGet { pname = "MediatR"; version = "8.1.0"; sha256 = "0cqx7yfh998xhsfk5pr6229lcjcs1jxxyqz7dwskc9jddl6a2akp"; }) diff --git a/pkgs/applications/science/logic/klee/default.nix b/pkgs/applications/science/logic/klee/default.nix index b610ce558605d..fb02c6d40b9dc 100644 --- a/pkgs/applications/science/logic/klee/default.nix +++ b/pkgs/applications/science/logic/klee/default.nix @@ -1,10 +1,8 @@ { lib -, stdenv +, llvmPackages , callPackage , fetchFromGitHub , cmake -, clang -, llvm , python3 , z3 , stp @@ -13,6 +11,7 @@ , sqlite , gtest , lit +, nix-update-script # Build KLEE in debug mode. Defaults to false. , debug ? false @@ -30,19 +29,35 @@ # Enable runtime asserts. Default false. , runtimeAsserts ? false -# Extra klee-uclibc config. +# Klee uclibc. Defaults to the bundled version. +, kleeuClibc ? null + +# Extra klee-uclibc config for the default klee-uclibc. , extraKleeuClibcConfig ? {} }: +# Klee supports these LLVM versions. +let + llvmVersion = llvmPackages.llvm.version; + inherit (lib.strings) versionAtLeast versionOlder; +in +assert versionAtLeast llvmVersion "11" && versionOlder llvmVersion "17"; + let + # The chosen version of klee-uclibc. + chosenKleeuClibc = + if kleeuClibc == null then + callPackage ./klee-uclibc.nix { + llvmPackages = llvmPackages; + inherit extraKleeuClibcConfig debugRuntime runtimeAsserts; + } + else + kleeuClibc; + # Python used for KLEE tests. kleePython = python3.withPackages (ps: with ps; [ tabulate ]); - - # The klee-uclibc derivation. - kleeuClibc = callPackage ./klee-uclibc.nix { - inherit stdenv clang llvm extraKleeuClibcConfig debugRuntime runtimeAsserts; - }; -in stdenv.mkDerivation rec { +in +llvmPackages.stdenv.mkDerivation rec { pname = "klee"; version = "3.1"; @@ -54,14 +69,16 @@ in stdenv.mkDerivation rec { }; nativeBuildInputs = [ cmake ]; + buildInputs = [ + llvmPackages.llvm cryptominisat gperftools - llvm sqlite stp z3 ]; + nativeCheckInputs = [ gtest @@ -77,10 +94,10 @@ in stdenv.mkDerivation rec { onOff = val: if val then "ON" else "OFF"; in [ "-DKLEE_RUNTIME_BUILD_TYPE=${if debugRuntime then "Debug" else "Release"}" - "-DLLVMCC=${clang}/bin/clang" - "-DLLVMCXX=${clang}/bin/clang++" + "-DLLVMCC=${llvmPackages.clang}/bin/clang" + "-DLLVMCXX=${llvmPackages.clang}/bin/clang++" "-DKLEE_ENABLE_TIMESTAMP=${onOff false}" - "-DKLEE_UCLIBC_PATH=${kleeuClibc}" + "-DKLEE_UCLIBC_PATH=${chosenKleeuClibc}" "-DENABLE_KLEE_ASSERTS=${onOff asserts}" "-DENABLE_POSIX_RUNTIME=${onOff true}" "-DENABLE_UNIT_TESTS=${onOff true}" @@ -94,20 +111,25 @@ in stdenv.mkDerivation rec { env.NIX_CFLAGS_COMPILE = toString ["-Wno-macro-redefined"]; prePatch = '' - patchShebangs . + patchShebangs --build . ''; # https://github.com/klee/klee/issues/1690 hardeningDisable = [ "fortify" ]; + enableParallelBuilding = true; doCheck = true; passthru = { - # Let the user depend on `klee.uclibc` for klee-uclibc - uclibc = kleeuClibc; + updateScript = nix-update-script { + extraArgs = [ "--version-regex" "v(\d\.\d)" ]; + }; + # Let the user access the chosen uClibc outside the derivation. + uclibc = chosenKleeuClibc; }; meta = with lib; { + mainProgram = "klee"; description = "Symbolic virtual machine built on top of LLVM"; longDescription = '' KLEE is a symbolic virtual machine built on top of the LLVM compiler @@ -128,7 +150,7 @@ in stdenv.mkDerivation rec { that matches a computed test input, including setting up files, pipes, environment variables, and passing command line arguments. ''; - homepage = "https://klee.github.io/"; + homepage = "https://klee.github.io"; license = licenses.ncsa; platforms = [ "x86_64-linux" ]; maintainers = with maintainers; [ numinit ]; diff --git a/pkgs/applications/science/logic/klee/klee-uclibc.nix b/pkgs/applications/science/logic/klee/klee-uclibc.nix index 5bbd8e69a46fa..c87a881e75336 100644 --- a/pkgs/applications/science/logic/klee/klee-uclibc.nix +++ b/pkgs/applications/science/logic/klee/klee-uclibc.nix @@ -1,13 +1,12 @@ { lib -, stdenv +, llvmPackages , fetchurl , fetchFromGitHub -, which , linuxHeaders -, clang -, llvm , python3 , curl +, which +, nix-update-script , debugRuntime ? true , runtimeAsserts ? false , extraKleeuClibcConfig ? {} @@ -24,21 +23,22 @@ let "RUNTIME_PREFIX" = "/"; "DEVEL_PREFIX" = "/"; }); -in stdenv.mkDerivation rec { +in +llvmPackages.stdenv.mkDerivation rec { pname = "klee-uclibc"; version = "1.4"; src = fetchFromGitHub { owner = "klee"; repo = "klee-uclibc"; rev = "klee_uclibc_v${version}"; - sha256 = "sha256-sogQK5Ed0k5tf4rrYwCKT4YRKyEovgT25p0BhGvJ1ok="; + hash = "sha256-sogQK5Ed0k5tf4rrYwCKT4YRKyEovgT25p0BhGvJ1ok="; }; nativeBuildInputs = [ - clang - curl - llvm + llvmPackages.clang + llvmPackages.llvm python3 + curl which ]; @@ -47,11 +47,11 @@ in stdenv.mkDerivation rec { # HACK: needed for cross-compile. # See https://www.mail-archive.com/klee-dev@imperial.ac.uk/msg03141.html - KLEE_CFLAGS = "-idirafter ${clang}/resource-root/include"; + KLEE_CFLAGS = "-idirafter ${llvmPackages.clang}/resource-root/include"; prePatch = '' - patchShebangs ./configure - patchShebangs ./extra + patchShebangs --build ./configure + patchShebangs --build ./extra ''; # klee-uclibc configure does not support --prefix, so we override configurePhase entirely @@ -88,13 +88,19 @@ in stdenv.mkDerivation rec { makeFlags = ["HAVE_DOT_CONFIG=y"]; + enableParallelBuilding = true; + + passthru.updateScript = nix-update-script { + extraArgs = [ "--version-regex" "v(\d\.\d)" ]; + }; + meta = with lib; { description = "Modified version of uClibc for KLEE"; longDescription = '' klee-uclibc is a bitcode build of uClibc meant for compatibility with the KLEE symbolic virtual machine. ''; - homepage = "https://klee.github.io/"; + homepage = "https://github.com/klee/klee-uclibc"; license = licenses.lgpl3; maintainers = with maintainers; [ numinit ]; }; diff --git a/pkgs/applications/science/logic/lean4/default.nix b/pkgs/applications/science/logic/lean4/default.nix index ac41b03643dc7..2ec05098f4078 100644 --- a/pkgs/applications/science/logic/lean4/default.nix +++ b/pkgs/applications/science/logic/lean4/default.nix @@ -10,13 +10,13 @@ stdenv.mkDerivation (finalAttrs: { pname = "lean4"; - version = "4.7.0"; + version = "4.8.0"; src = fetchFromGitHub { owner = "leanprover"; repo = "lean4"; rev = "v${finalAttrs.version}"; - hash = "sha256-jHY8BhDotfGcMS0Xzl5iawqCaug3dDEKuD5Y1WcM06I="; + hash = "sha256-R75RrAQb/tRTtMvy/ddLl1KQaA7V71nocvjIS9geMrg="; }; postPatch = '' diff --git a/pkgs/applications/science/math/R/default.nix b/pkgs/applications/science/math/R/default.nix index 5ceb413a24211..b6fac3cca9e5a 100644 --- a/pkgs/applications/science/math/R/default.nix +++ b/pkgs/applications/science/math/R/default.nix @@ -1,4 +1,4 @@ -{ lib, stdenv, fetchurl, fetchpatch, bzip2, gfortran, libX11, libXmu, libXt, libjpeg, libpng +{ lib, stdenv, fetchurl, bzip2, gfortran, libX11, libXmu, libXt, libjpeg, libpng , libtiff, ncurses, pango, pcre2, perl, readline, tcl, texlive, texliveSmall, tk, xz, zlib , less, texinfo, graphviz, icu, pkg-config, bison, imake, which, jdk, blas, lapack , curl, Cocoa, Foundation, libobjc, libcxx, tzdata @@ -15,13 +15,13 @@ assert (!blas.isILP64) && (!lapack.isILP64); stdenv.mkDerivation (finalAttrs: { pname = "R"; - version = "4.3.3"; + version = "4.4.1"; src = let inherit (finalAttrs) pname version; in fetchurl { url = "https://cran.r-project.org/src/base/R-${lib.versions.major version}/${pname}-${version}.tar.gz"; - sha256 = "sha256-gIUSMTk7hb84d+6eObKC51Dthkxexgy9aObhOfBSAzA="; + sha256 = "sha256-tMtnXequtymdOyZdIYzeQ/GSlRzluJt7saUUijay2U0="; }; outputs = [ "out" "tex" ]; @@ -37,12 +37,6 @@ stdenv.mkDerivation (finalAttrs: { patches = [ ./no-usr-local-search-paths.patch - (fetchpatch { - # https://hiddenlayer.com/research/r-bitrary-code-execution/ - name = "CVE-2024-27322.patch"; - url = "https://github.com/r-devel/r-svn/commit/f7c46500f455eb4edfc3656c3fa20af61b16abb7.patch"; - hash = "sha256-CH2mMmie9E96JeGSC7UGm7/roUNhK5xv6HO53N2ixEI="; - }) ]; # Test of the examples for package 'tcltk' fails in Darwin sandbox. See: diff --git a/pkgs/applications/science/math/eigenmath/default.nix b/pkgs/applications/science/math/eigenmath/default.nix index cb6748ec37796..a120de87b9ff1 100644 --- a/pkgs/applications/science/math/eigenmath/default.nix +++ b/pkgs/applications/science/math/eigenmath/default.nix @@ -7,13 +7,13 @@ stdenv.mkDerivation rec { pname = "eigenmath"; - version = "3.26-unstable-2024-06-09"; + version = "3.27-unstable-2024-06-20"; src = fetchFromGitHub { owner = "georgeweigt"; repo = pname; - rev = "285fc0133f0e7bb5e1e220b75246ce542ae50269"; - hash = "sha256-ddED3PaHSSupe/QqMYj88GCmh9IrRvpAd4/WEpRTN00="; + rev = "c3e3da104dbef888c3e52659134d5e9bdc12764d"; + hash = "sha256-fqCphnRQw79v7ZTCZU9ucm/R7BKY7yCZYDSnxD7uRS8="; }; checkPhase = let emulator = stdenv.hostPlatform.emulator buildPackages; in '' diff --git a/pkgs/applications/science/math/fricas/default.nix b/pkgs/applications/science/math/fricas/default.nix index 9f0b87f011a10..43a00a5e1fbac 100644 --- a/pkgs/applications/science/math/fricas/default.nix +++ b/pkgs/applications/science/math/fricas/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "fricas"; - version = "1.3.10"; + version = "1.3.11"; src = fetchFromGitHub { owner = "fricas"; repo = "fricas"; rev = version; - sha256 = "sha256-T1xDndDnHq/hmhTWWO3Eu0733u8+C8sJMCF6pbLU2GI="; + sha256 = "sha256-EX/boSs6rK4RrJ5W6Rd0TSHsbQsNiFI1evFuNPBMeu8="; }; buildInputs = [ sbcl libX11 libXpm libICE libSM libXt libXau libXdmcp ]; diff --git a/pkgs/applications/science/math/qalculate-gtk/default.nix b/pkgs/applications/science/math/qalculate-gtk/default.nix index e4fc506516fdd..a27d7c1ffdb6f 100644 --- a/pkgs/applications/science/math/qalculate-gtk/default.nix +++ b/pkgs/applications/science/math/qalculate-gtk/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation (finalAttrs: { pname = "qalculate-gtk"; - version = "5.1.0"; + version = "5.2.0"; src = fetchFromGitHub { owner = "qalculate"; repo = "qalculate-gtk"; rev = "v${finalAttrs.version}"; - hash = "sha256-yI+8TrNZJt4eJnDX5mk6RozBe2ZeP7sTyAjsgiYQPck="; + hash = "sha256-vH4GZaeQ6Ji9aWh8R5B6PE2fBBW7KTyCsFkpgHu6yg8="; }; hardeningDisable = [ "format" ]; diff --git a/pkgs/applications/science/math/qalculate-qt/default.nix b/pkgs/applications/science/math/qalculate-qt/default.nix index 3c4e19d56ebd7..5b56fe7581a3a 100644 --- a/pkgs/applications/science/math/qalculate-qt/default.nix +++ b/pkgs/applications/science/math/qalculate-qt/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation (finalAttrs: { pname = "qalculate-qt"; - version = "5.1.0"; + version = "5.2.0"; src = fetchFromGitHub { owner = "qalculate"; repo = "qalculate-qt"; rev = "v${finalAttrs.version}"; - hash = "sha256-gJfIC5HdA10gb/Dh/yhJbkCZfhUnN0zihqyfDjPv6ow="; + hash = "sha256-jlzuLLEFi72ElVBJSRikrMMaHIVWKRUAWGyeqzuj7xw="; }; nativeBuildInputs = [ qmake intltool pkg-config qttools wrapQtAppsHook ]; diff --git a/pkgs/applications/science/misc/root/default.nix b/pkgs/applications/science/misc/root/default.nix index ded47a661a21a..5d01a33e5dcc4 100644 --- a/pkgs/applications/science/misc/root/default.nix +++ b/pkgs/applications/science/misc/root/default.nix @@ -56,7 +56,7 @@ stdenv.mkDerivation rec { pname = "root"; - version = "6.32.00"; + version = "6.32.02"; passthru = { tests = import ./tests { inherit callPackage; }; @@ -64,12 +64,14 @@ stdenv.mkDerivation rec { src = fetchurl { url = "https://root.cern.ch/download/root_v${version}.source.tar.gz"; - hash = "sha256-EvIDaBpZBBxHTOlSN2Hm8OiGGzvueN9feZqNtVGJ5dI="; + hash = "sha256-PQ92vwWFfhgHzPssngFPUlvLYl+UojcLRV9LFklhYC0="; }; clad_src = fetchgit { url = "https://github.com/vgvassilev/clad"; - rev = "refs/tags/v1.5"; # Make sure that this is the same tag as in the ROOT build files! + # Make sure that this is the same tag as in the ROOT build files! + # https://github.com/root-project/root/blob/master/interpreter/cling/tools/plugins/clad/CMakeLists.txt#L76 + rev = "refs/tags/v1.5"; hash = "sha256-s0DbHfLthv51ZICnTd30O4qG/DyZPk5tADeu3bBRoOw="; }; @@ -166,7 +168,6 @@ stdenv.mkDerivation rec { "-Dmysql=OFF" "-Dpgsql=OFF" "-Dsqlite=OFF" - "-Dtmva-pymva=OFF" "-Dvdt=OFF" ] ++ lib.optional (stdenv.cc.libc != null) "-DC_INCLUDE_DIRS=${lib.getDev stdenv.cc.libc}/include" @@ -222,6 +223,9 @@ stdenv.mkDerivation rec { ]}" ''; + # error: aligned allocation function of type 'void *(std::size_t, std::align_val_t)' is only available on macOS 10.13 or newer + CXXFLAGS = lib.optional (stdenv.hostPlatform.system == "x86_64-darwin") "-faligned-allocation"; + # To use the debug information on the fly (without installation) # add the outPath of root.debug into NIX_DEBUG_INFO_DIRS (in PATH-like format) # and make sure that gdb from Nixpkgs can be found in PATH. diff --git a/pkgs/applications/science/misc/snakemake/default.nix b/pkgs/applications/science/misc/snakemake/default.nix index ade5239762518..7f0e70c642134 100644 --- a/pkgs/applications/science/misc/snakemake/default.nix +++ b/pkgs/applications/science/misc/snakemake/default.nix @@ -6,14 +6,14 @@ python3.pkgs.buildPythonApplication rec { pname = "snakemake"; - version = "8.13.0"; + version = "8.14.0"; format = "setuptools"; src = fetchFromGitHub { owner = "snakemake"; repo = pname; rev = "refs/tags/v${version}"; - hash = "sha256-Xd8mZ8tsemJ53hAMED2biRyDlEw/gG/Hh1iZSwSB1vY="; + hash = "sha256-6oguN4u4OUDXpDsbueSBNwtWgLCaKmgq3w/d/MsMh7Y="; # https://github.com/python-versioneer/python-versioneer/issues/217 postFetch = '' sed -i "$out"/snakemake/_version.py -e 's#git_refnames = ".*"#git_refnames = " (tag: v${version})"#' diff --git a/pkgs/applications/science/molecular-dynamics/gromacs/default.nix b/pkgs/applications/science/molecular-dynamics/gromacs/default.nix index bf2fd1dbf3504..6531002ceb31b 100644 --- a/pkgs/applications/science/molecular-dynamics/gromacs/default.nix +++ b/pkgs/applications/science/molecular-dynamics/gromacs/default.nix @@ -24,7 +24,7 @@ assert enableCuda -> singlePrec; let - inherit (cudaPackages.cudaFlags) cudaCapabilities dropDot; + inherit (cudaPackages.flags) cmakeCudaArchitecturesString; # Select reasonable defaults for all major platforms # The possible values are defined in CMakeLists.txt: @@ -111,10 +111,10 @@ in stdenv.mkDerivation rec { ] ) ++ lib.optionals enableCuda [ "-DGMX_GPU=CUDA" - (lib.cmakeFeature "CMAKE_CUDA_ARCHITECTURES" (builtins.concatStringsSep ";" (map dropDot cudaCapabilities))) + (lib.cmakeFeature "CMAKE_CUDA_ARCHITECTURES" cmakeCudaArchitecturesString) # Gromacs seems to ignore and override the normal variables, so we add this ad hoc: - (lib.cmakeFeature "GMX_CUDA_TARGET_COMPUTE" (builtins.concatStringsSep ";" (map dropDot cudaCapabilities))) + (lib.cmakeFeature "GMX_CUDA_TARGET_COMPUTE" cmakeCudaArchitecturesString) ]; postInstall = '' diff --git a/pkgs/applications/science/physics/nnpdf/default.nix b/pkgs/applications/science/physics/nnpdf/default.nix index a4762323dcf95..c1de306e6bf05 100644 --- a/pkgs/applications/science/physics/nnpdf/default.nix +++ b/pkgs/applications/science/physics/nnpdf/default.nix @@ -60,7 +60,5 @@ stdenv.mkDerivation rec { license = licenses.gpl3Only; maintainers = [ maintainers.veprbl ]; platforms = platforms.unix; - # never built on aarch64-darwin since first introduction in nixpkgs - broken = (stdenv.isDarwin && stdenv.isAarch64) || (stdenv.isLinux && stdenv.isAarch64); }; } |