diff options
Diffstat (limited to 'pkgs/applications/science')
141 files changed, 1144 insertions, 1349 deletions
diff --git a/pkgs/applications/science/astronomy/celestia/default.nix b/pkgs/applications/science/astronomy/celestia/default.nix index 8b40196fdbff5..2d227389d4298 100644 --- a/pkgs/applications/science/astronomy/celestia/default.nix +++ b/pkgs/applications/science/astronomy/celestia/default.nix @@ -1,4 +1,4 @@ -{ lib, stdenv, fetchFromGitHub, pkg-config, freeglut, gtk2, gtkglext +{ lib, stdenv, fetchFromGitHub, pkg-config, libglut, gtk2, gtkglext , libjpeg_turbo, libtheora, libXmu, lua, libGLU, libGL, perl, autoreconfHook }: @@ -15,7 +15,7 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ pkg-config autoreconfHook ]; buildInputs = [ - freeglut gtk2 gtkglext lua perl + libglut gtk2 gtkglext lua perl libjpeg_turbo libtheora libXmu libGLU libGL ]; @@ -27,7 +27,7 @@ stdenv.mkDerivation rec { enableParallelBuilding = true; meta = with lib; { - homepage = "https://celestia.space/"; + homepage = "https://celestiaproject.space/"; description = "Real-time 3D simulation of space"; mainProgram = "celestia"; changelog = "https://github.com/CelestiaProject/Celestia/releases/tag/${version}"; diff --git a/pkgs/applications/science/astronomy/gnuastro/default.nix b/pkgs/applications/science/astronomy/gnuastro/default.nix deleted file mode 100644 index d1c40d3fefb3e..0000000000000 --- a/pkgs/applications/science/astronomy/gnuastro/default.nix +++ /dev/null @@ -1,37 +0,0 @@ -{ lib, stdenv, fetchurl, libtool -, cfitsio, curl, ghostscript, gsl, libgit2, libjpeg, libtiff, lzlib, wcslib }: - -stdenv.mkDerivation rec { - pname = "gnuastro"; - version = "0.22"; - - src = fetchurl { - url = "mirror://gnu/gnuastro/gnuastro-${version}.tar.gz"; - sha256 = "sha256-f9fxaga95VrtliggkM2SITW+6pAjaeWvgUOJ6rnMcwg="; - }; - - nativeBuildInputs = [ libtool ]; - - buildInputs = [ - cfitsio - curl - ghostscript - gsl - libgit2 - libjpeg - libtiff - lzlib - wcslib - ]; - - enableParallelBuilding = true; - - meta = with lib; { - description = "GNU astronomy utilities and library"; - homepage = "https://www.gnu.org/software/gnuastro/"; - changelog = "https://git.savannah.gnu.org/cgit/gnuastro.git/plain/NEWS?id=gnuastro_v${version}"; - license = licenses.gpl3Plus; - platforms = platforms.unix; - maintainers = with maintainers; [ sikmir ]; - }; -} diff --git a/pkgs/applications/science/astronomy/stellarium/default.nix b/pkgs/applications/science/astronomy/stellarium/default.nix index 426a7f18dff3f..87118beec99f0 100644 --- a/pkgs/applications/science/astronomy/stellarium/default.nix +++ b/pkgs/applications/science/astronomy/stellarium/default.nix @@ -20,6 +20,8 @@ , qttools , exiv2 , nlopt +, testers +, xvfb-run }: stdenv.mkDerivation (finalAttrs: { @@ -93,6 +95,18 @@ stdenv.mkDerivation (finalAttrs: { qtWrapperArgs+=("''${gappsWrapperArgs[@]}") ''; + passthru.tests.version = testers.testVersion { + package = finalAttrs.finalPackage; + command = '' + # Create a temporary home directory because stellarium aborts with an + # error if it can't write some configuration files. + tmpdir=$(mktemp -d) + + # stellarium can't be run in headless mode, therefore we need xvfb-run. + HOME="$tmpdir" ${xvfb-run}/bin/xvfb-run stellarium --version + ''; + }; + meta = { description = "Free open-source planetarium"; mainProgram = "stellarium"; diff --git a/pkgs/applications/science/biology/ants/default.nix b/pkgs/applications/science/biology/ants/default.nix index c4b932f6dbae8..21dbf69407f21 100644 --- a/pkgs/applications/science/biology/ants/default.nix +++ b/pkgs/applications/science/biology/ants/default.nix @@ -10,13 +10,13 @@ stdenv.mkDerivation (finalAttrs: { pname = "ANTs"; - version = "2.5.2"; + version = "2.5.3"; src = fetchFromGitHub { owner = "ANTsX"; repo = "ANTs"; rev = "refs/tags/v${finalAttrs.version}"; - hash = "sha256-crvLxUP/uM0u1oakxcpsiULAKUo+86hGATs/kHNseaw="; + hash = "sha256-DZzuHMC0XymFCnDn+H1pRFx9jUt+s03PaN88R4ZBRwY="; }; nativeBuildInputs = [ diff --git a/pkgs/applications/science/biology/dcm2niix/default.nix b/pkgs/applications/science/biology/dcm2niix/default.nix index a7f30dbc075df..acf43e52764da 100644 --- a/pkgs/applications/science/biology/dcm2niix/default.nix +++ b/pkgs/applications/science/biology/dcm2niix/default.nix @@ -21,15 +21,15 @@ let sha256 = "sha256-8HNFUGx2uuEb8UrGUiqkN+uVDX83YIisT2uO1Z7GCxc="; }; in -stdenv.mkDerivation rec { - version = "1.0.20230411"; +stdenv.mkDerivation (finalAttrs: { + version = "1.0.20240202"; pname = "dcm2niix"; src = fetchFromGitHub { owner = "rordenlab"; repo = "dcm2niix"; - rev = "v${version}"; - sha256 = "sha256-kOVEoqrk4l6sH8iDVx1QmOYP5tCufxsWnCnn9BibZ08="; + rev = "v${finalAttrs.version}"; + sha256 = "sha256-vJUPv/6KNCsU8UjwfktHdTlsweG7+UGgAEZeESfBkD8="; }; patches = lib.optionals withCloudflareZlib [ @@ -55,15 +55,16 @@ stdenv.mkDerivation rec { "-DZLIB_IMPLEMENTATION=Cloudflare" ]; - meta = with lib; { + meta = { description = "DICOM to NIfTI converter"; mainProgram = "dcm2niix"; longDescription = '' dcm2niix is designed to convert neuroimaging data from the DICOM format to the NIfTI format. ''; homepage = "https://www.nitrc.org/projects/dcm2nii"; - license = licenses.bsd3; - maintainers = with maintainers; [ ashgillman rbreslow ]; - platforms = platforms.all; + changelog = "https://github.com/rordenlab/dcm2niix/releases/tag/v${finalAttrs.version}"; + license = lib.licenses.bsd3; + maintainers = with lib.maintainers; [ ashgillman rbreslow ]; + platforms = lib.platforms.all; }; -} +}) diff --git a/pkgs/applications/science/biology/febio-studio/default.nix b/pkgs/applications/science/biology/febio-studio/default.nix deleted file mode 100644 index 708bd0f4305a4..0000000000000 --- a/pkgs/applications/science/biology/febio-studio/default.nix +++ /dev/null @@ -1,62 +0,0 @@ -{ lib, stdenv, fetchFromGitHub, cmake, zlib, libglvnd, libGLU, wrapQtAppsHook -, sshSupport ? true, openssl, libssh -, tetgenSupport ? true, tetgen -, ffmpegSupport ? true, ffmpeg_4 -, dicomSupport ? false, dcmtk -, withModelRepo ? true -, withCadFeatures ? false -}: - -stdenv.mkDerivation rec { - pname = "febio-studio"; - version = "1.6.1"; - - src = fetchFromGitHub { - owner = "febiosoftware"; - repo = "FEBioStudio"; - rev = "v${version}"; - sha256 = "0r6pg49i0q9idp7pjymj7mlxd63qjvmfvg0l7fmx87y1yd2hfw4h"; - }; - - patches = [ - ./febio-studio-cmake.patch # Fix Errors that appear with certain Cmake flags - ]; - - cmakeFlags = [ - "-DQt_Ver=5" - "-DNOT_FIRST=On" - "-DOpenGL_GL_PREFERENCE=GLVND" - ] - ++ lib.optional sshSupport "-DUSE_SSH=On" - ++ lib.optional tetgenSupport "-DUSE_TETGEN=On" - ++ lib.optional ffmpegSupport "-DUSE_FFMPEG=On" - ++ lib.optional dicomSupport "-DUSE_DICOM=On" - ++ lib.optional withModelRepo "-DMODEL_REPO=On" - ++ lib.optional withCadFeatures "-DCAD_FEATURES=On" - ; - - - installPhase = '' - runHook preInstall - mkdir -p $out/ - cp -R bin $out/ - runHook postInstall - ''; - - nativeBuildInputs = [ cmake wrapQtAppsHook ]; - buildInputs = [ zlib libglvnd libGLU openssl libssh ] - ++ lib.optional sshSupport openssl - ++ lib.optional tetgenSupport tetgen - ++ lib.optional ffmpegSupport ffmpeg_4 - ++ lib.optional dicomSupport dcmtk - ; - - meta = with lib; { - description = "FEBio Suite Solver"; - mainProgram = "FEBioStudio"; - license = with licenses; [ mit ]; - homepage = "https://febio.org/"; - platforms = platforms.unix; - maintainers = with maintainers; [ Scriptkiddi ]; - }; -} diff --git a/pkgs/applications/science/biology/febio-studio/febio-studio-cmake.patch b/pkgs/applications/science/biology/febio-studio/febio-studio-cmake.patch deleted file mode 100644 index e694f6c3b89f2..0000000000000 --- a/pkgs/applications/science/biology/febio-studio/febio-studio-cmake.patch +++ /dev/null @@ -1,38 +0,0 @@ -diff --git a/FEBioStudio/RepositoryPanel.cpp b/FEBioStudio/RepositoryPanel.cpp -index 382db303..314cdc68 100644 ---- a/FEBioStudio/RepositoryPanel.cpp -+++ b/FEBioStudio/RepositoryPanel.cpp -@@ -1364,10 +1364,10 @@ void CRepositoryPanel::loadingPageProgress(qint64 bytesSent, qint64 bytesTotal) - - #else - --CRepositoryPanel::CRepositoryPanel(CMainWindow* pwnd, QWidget* parent){} -+CRepositoryPanel::CRepositoryPanel(CMainWindow* pwnd, QDockWidget* parent){} - CRepositoryPanel::~CRepositoryPanel(){} - void CRepositoryPanel::OpenLink(const QString& link) {} --// void CRepositoryPanel::Raise() {} -+void CRepositoryPanel::Raise() {} - void CRepositoryPanel::SetModelList(){} - void CRepositoryPanel::ShowMessage(QString message) {} - void CRepositoryPanel::ShowWelcomeMessage(QByteArray messages) {} -@@ -1396,6 +1396,7 @@ void CRepositoryPanel::on_actionSearch_triggered() {} - void CRepositoryPanel::on_actionClearSearch_triggered() {} - void CRepositoryPanel::on_actionDeleteRemote_triggered() {} - void CRepositoryPanel::on_actionModify_triggered() {} -+void CRepositoryPanel::on_actionCopyPermalink_triggered() {} - void CRepositoryPanel::on_treeWidget_itemSelectionChanged() {} - void CRepositoryPanel::on_treeWidget_customContextMenuRequested(const QPoint &pos) {} - void CRepositoryPanel::DownloadItem(CustomTreeWidgetItem *item) {} -diff --git a/FEBioStudio/WzdUpload.cpp b/FEBioStudio/WzdUpload.cpp -index 5ce74346..20062e06 100644 ---- a/FEBioStudio/WzdUpload.cpp -+++ b/FEBioStudio/WzdUpload.cpp -@@ -1183,7 +1183,7 @@ void CWzdUpload::on_saveJson_triggered() - getProjectJson(&projectInfo); - - QFile file(filedlg.selectedFiles()[0]); -- file.open(QIODeviceBase::WriteOnly); -+ file.open(QIODevice::WriteOnly); - file.write(projectInfo); - file.close(); - } diff --git a/pkgs/applications/science/biology/genmap/default.nix b/pkgs/applications/science/biology/genmap/default.nix index 235135cb60506..772975fc6450b 100644 --- a/pkgs/applications/science/biology/genmap/default.nix +++ b/pkgs/applications/science/biology/genmap/default.nix @@ -15,7 +15,7 @@ stdenv.mkDerivation rec { repo = "genmap"; rev = "genmap-v${version}"; fetchSubmodules = true; - sha256 = "sha256-7sIKBRMNzyCrZ/c2nXkknb6a5YsXe6DRE2IFhp6AviY="; + hash = "sha256-7sIKBRMNzyCrZ/c2nXkknb6a5YsXe6DRE2IFhp6AviY="; }; nativeBuildInputs = [ cmake ]; 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${version}"; - hash = "sha256-dnUFllqcABB3JDYoCwPGtIYD/h5lzX2XKOroDpijPpU="; + hash = "sha256-ld+9vPJRVHMEe5/igqRr6RkISY2ipfGkJFHDOSZuAmg="; fetchSubmodules = true; }; diff --git a/pkgs/applications/science/biology/jbrowse/default.nix b/pkgs/applications/science/biology/jbrowse/default.nix index 3a7e009cc1561..ce39ca8f425ac 100644 --- a/pkgs/applications/science/biology/jbrowse/default.nix +++ b/pkgs/applications/science/biology/jbrowse/default.nix @@ -1,12 +1,12 @@ -{ lib, fetchurl, appimageTools, wrapGAppsHook3 }: +{ lib, fetchurl, appimageTools }: let pname = "jbrowse"; - version = "2.12.2"; + version = "2.13.1"; src = fetchurl { url = "https://github.com/GMOD/jbrowse-components/releases/download/v${version}/jbrowse-desktop-v${version}-linux.AppImage"; - sha256 = "sha256-dnvs+niNo8VPuOk9uODezLxdghwutLuhgG5Jyxi8mW0="; + sha256 = "sha256-JxV7ZxA3/YMG6ziYOA8QiBVth9UunVGJLTy1E110y6w="; }; appimageContents = appimageTools.extractType2 { diff --git a/pkgs/applications/science/biology/kallisto/default.nix b/pkgs/applications/science/biology/kallisto/default.nix index 55c555e387de7..5eb6d40d030c8 100644 --- a/pkgs/applications/science/biology/kallisto/default.nix +++ b/pkgs/applications/science/biology/kallisto/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "kallisto"; - version = "0.50.1"; + version = "0.51.0"; src = fetchFromGitHub { repo = "kallisto"; owner = "pachterlab"; rev = "v${version}"; - sha256 = "sha256-JJZJOl4u6FzngrrMuC2AfD5ry2LBOT8tdz2piH+9LFE="; + sha256 = "sha256-+tnuka6uzoNr5pLuE2yV97KmqdThIG0IwiO+SCYiCk8="; }; nativeBuildInputs = [ autoconf cmake ]; diff --git a/pkgs/applications/science/biology/kent/default.nix b/pkgs/applications/science/biology/kent/default.nix index f30a6725bb474..7d73ed90856dc 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 = "467"; + version = "468"; src = fetchFromGitHub { owner = "ucscGenomeBrowser"; repo = pname; rev = "v${version}_base"; - hash = "sha256-Y8iHSo70nsPZwVy8ZiiqjU3mGrPOyPQkW0VpLS+ulGE="; + hash = "sha256-OM/noraW2X8WV5wqWEFiI5/JPOBmsp0fTeDdcZoXxAA="; }; buildInputs = [ libpng libuuid zlib bzip2 xz openssl curl libmysqlclient ]; diff --git a/pkgs/applications/science/biology/last/default.nix b/pkgs/applications/science/biology/last/default.nix index 7cfdb674c6e49..9057e767c1759 100644 --- a/pkgs/applications/science/biology/last/default.nix +++ b/pkgs/applications/science/biology/last/default.nix @@ -9,13 +9,13 @@ stdenv.mkDerivation rec { pname = "last"; - version = "1548"; + version = "1550"; src = fetchFromGitLab { owner = "mcfrith"; repo = "last"; rev = "refs/tags/${version}"; - hash = "sha256-6mLPnyEAuRvCeV8pv3avsm6CKDrBPgX8xSxGO2kvTrM="; + hash = "sha256-kvI3m2FIPscU/a3GEH+O3yx5TgdNHdYP6OW3/mI2roM="; }; nativeBuildInputs = [ diff --git a/pkgs/applications/science/biology/macs2/default.nix b/pkgs/applications/science/biology/macs2/default.nix index 26ec138048f7e..153f85535f943 100644 --- a/pkgs/applications/science/biology/macs2/default.nix +++ b/pkgs/applications/science/biology/macs2/default.nix @@ -1,9 +1,11 @@ -{ lib, python3, fetchpatch, fetchPypi }: +{ lib, python311, fetchpatch, fetchPypi }: -python3.pkgs.buildPythonPackage rec { +# pin python311 because macs2 does not support python 3.12 +# https://github.com/macs3-project/MACS/issues/598#issuecomment-1812622572 +python311.pkgs.buildPythonPackage rec { pname = "macs2"; version = "2.2.9.1"; - format = "pyproject"; + pyproject = true; src = fetchPypi { pname = lib.toUpper pname; @@ -20,20 +22,19 @@ python3.pkgs.buildPythonPackage rec { }) ]; - nativeBuildInputs = with python3.pkgs; [ + build-system = with python311.pkgs; [ cython_0 numpy setuptools - wheel ]; - propagatedBuildInputs = with python3.pkgs; [ + dependencies = with python311.pkgs; [ numpy ]; __darwinAllowLocalNetworking = true; - nativeCheckInputs = with python3.pkgs; [ + nativeCheckInputs = with python311.pkgs; [ unittestCheckHook ]; diff --git a/pkgs/applications/science/biology/migrate/default.nix b/pkgs/applications/science/biology/migrate/default.nix index 7820f177bfb7b..53fc807776126 100644 --- a/pkgs/applications/science/biology/migrate/default.nix +++ b/pkgs/applications/science/biology/migrate/default.nix @@ -11,7 +11,7 @@ stdenv.mkDerivation (finalAttrs: { pname = "migrate"; src = fetchurl { - url = "https://peterbeerli.com/migrate-html5/download_version4/${finalAttrs.pname}-${finalAttrs.version}.src.tar.gz"; + url = "https://peterbeerli.com/migrate-html5/download_version4/migrate-${finalAttrs.version}.src.tar.gz"; hash = "sha256-twkoR9L6VPUye12OC0B5w0PxcxyKain6RkhCswLEdwg="; }; diff --git a/pkgs/applications/science/biology/mrbayes/default.nix b/pkgs/applications/science/biology/mrbayes/default.nix index 54f5b9bbb3703..88b402712016b 100644 --- a/pkgs/applications/science/biology/mrbayes/default.nix +++ b/pkgs/applications/science/biology/mrbayes/default.nix @@ -1,4 +1,4 @@ -{ lib, stdenv, fetchFromGitHub, readline }: +{ lib, stdenv, fetchFromGitHub }: stdenv.mkDerivation rec { pname = "mrbayes"; @@ -23,7 +23,7 @@ stdenv.mkDerivation rec { MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees. ''; - maintainers = with maintainers; [ ]; + maintainers = [ ]; license = licenses.gpl2Plus; homepage = "https://nbisweden.github.io/MrBayes/"; platforms = platforms.linux; diff --git a/pkgs/applications/science/biology/nest/default.nix b/pkgs/applications/science/biology/nest/default.nix index 807af7ce488ac..96418346eeb9e 100644 --- a/pkgs/applications/science/biology/nest/default.nix +++ b/pkgs/applications/science/biology/nest/default.nix @@ -13,20 +13,19 @@ , boost , python3 , readline -, autoPatchelfHook , withPython ? false , withMpi ? false }: stdenv.mkDerivation rec { pname = "nest"; - version = "3.7"; + version = "3.8"; src = fetchFromGitHub { owner = "nest"; repo = "nest-simulator"; rev = "v${version}"; - hash = "sha256-EwhpsfRmBLJnPiH6hXQXgG9jSNoC2oqq5lZ6t038VpI="; + hash = "sha256-hysOe1ZZpCClVOGo0+UeCP7imAakXrZlnJ4V95zfiyA="; }; postPatch = '' diff --git a/pkgs/applications/science/biology/neuron/default.nix b/pkgs/applications/science/biology/neuron/default.nix index ef79fb11a824d..e54d3c9ba7a12 100644 --- a/pkgs/applications/science/biology/neuron/default.nix +++ b/pkgs/applications/science/biology/neuron/default.nix @@ -23,7 +23,7 @@ let in stdenv.mkDerivation (finalAttrs: { pname = "neuron"; - version = "8.2.4"; + version = "8.2.6"; # format is for pythonModule conversion format = "other"; @@ -54,7 +54,7 @@ stdenv.mkDerivation (finalAttrs: { ] ++ optionals useMpi [ python3.pkgs.mpi4py ] ++ optionals useRx3d [ - python3.pkgs.cython_0 # NOTE: cython<3 is required as of 8.2.4 + python3.pkgs.cython_0 # NOTE: cython<3 is required as of 8.2.6 python3.pkgs.numpy ]; @@ -89,7 +89,7 @@ stdenv.mkDerivation (finalAttrs: { repo = "nrn"; rev = finalAttrs.version; fetchSubmodules = true; - hash = "sha256-KsULc+LHoWmrkGYebpoUot6DhStKidbLQf5a3S+pi4s="; + hash = "sha256-xASBpsF8rIzrb5G+4Qi6rvWC2wqL7nAGlSeMsBAI6WM="; }; meta = with lib; { diff --git a/pkgs/applications/science/biology/sambamba/default.nix b/pkgs/applications/science/biology/sambamba/default.nix index b6635f02aacdf..e62a5bb14aae4 100644 --- a/pkgs/applications/science/biology/sambamba/default.nix +++ b/pkgs/applications/science/biology/sambamba/default.nix @@ -16,7 +16,7 @@ stdenv.mkDerivation rec { owner = "biod"; repo = "sambamba"; rev = "v${version}"; - sha256 = "sha256-3O9bHGpMuCgdR2Wm7Dv1VUjMT1QTn8K1hdwgjvwhFDw="; + hash = "sha256-3O9bHGpMuCgdR2Wm7Dv1VUjMT1QTn8K1hdwgjvwhFDw="; fetchSubmodules = true; }; diff --git a/pkgs/applications/science/biology/sratoolkit/default.nix b/pkgs/applications/science/biology/sratoolkit/default.nix deleted file mode 100644 index 62c21a23eb66a..0000000000000 --- a/pkgs/applications/science/biology/sratoolkit/default.nix +++ /dev/null @@ -1,56 +0,0 @@ -{ stdenv -, lib -, fetchurl -, autoPatchelfHook -, libidn -, zlib -, bzip2 -}: - - -let - libidn11 = libidn.overrideAttrs (old: { - pname = "libidn"; - version = "1.34"; - src = fetchurl { - url = "mirror://gnu/libidn/libidn-1.34.tar.gz"; - sha256 = "0g3fzypp0xjcgr90c5cyj57apx1cmy0c6y9lvw2qdcigbyby469p"; - }; - }); - -in - -stdenv.mkDerivation rec { - pname = "sratoolkit"; - version = "2.11.3"; - - src = fetchurl { - url = "https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/${version}/sratoolkit.${version}-ubuntu64.tar.gz"; - sha256 = "1590lc4cplxr3lhjqci8fjncy67imn2h14qd2l87chmhjh243qvx"; - }; - - nativeBuildInputs = [ - autoPatchelfHook - ]; - - buildInputs = [ - libidn11 - zlib - bzip2 - stdenv.cc.cc.lib - ]; - - sourceRoot = "sratoolkit.${version}-ubuntu64/bin"; - - installPhase = '' - find -L . -executable -type f -! -name "*remote-fuser*" -exec install -m755 -D {} $out/bin/{} \; - ''; - - meta = with lib; { - homepage = "https://github.com/ncbi/sra-tools"; - description = "SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives"; - license = licenses.ncbiPd; - maintainers = with maintainers; [ thyol ]; - platforms = [ "x86_64-linux" ]; - }; -} diff --git a/pkgs/applications/science/biology/tandem-aligner/default.nix b/pkgs/applications/science/biology/tandem-aligner/default.nix deleted file mode 100644 index d44489debbb62..0000000000000 --- a/pkgs/applications/science/biology/tandem-aligner/default.nix +++ /dev/null @@ -1,67 +0,0 @@ -{ lib -, stdenv -, fetchFromGitHub -, fetchpatch -, cmake -, zlib -}: - -stdenv.mkDerivation (finalAttrs: { - pname = "TandemAligner"; - version = "0.1"; - - src = fetchFromGitHub { - owner = "seryrzu"; - repo = "tandem_aligner"; - rev = "v${finalAttrs.version}"; - hash = "sha256-iMDj1HZ8LzmZckuAM3lbG3eSJSd/5JGVA6SBs7+AgX8="; - }; - - patches = [ - (fetchpatch { - # https://github.com/seryrzu/tandem_aligner/pull/4 - url = "https://github.com/seryrzu/tandem_aligner/commit/8b516c94f90aaa9cb84278aa811285d4204b03a9.patch"; - hash = "sha256-kD46SykXklG/avK0+sc61YKFw9Bes8ZgFAjVXmcpN8k="; - stripLen = 1; - }) - ]; - - sourceRoot = "${finalAttrs.src.name}/tandem_aligner"; - - nativeBuildInputs = [ cmake ]; - - buildInputs = [ zlib ]; - - installPhase = '' - runHook preInstall - mkdir -p $out/bin - cp src/projects/tandem_aligner/tandem_aligner $out/bin - runHook postInstall - ''; - - doCheck = true; - - # adapted from target test_launch in Makefile - checkPhase = '' - runHook preCheck - mkdir -p $TMPDIR/test_launch - src/projects/tandem_aligner/tandem_aligner \ - --first $src/tandem_aligner/test_dataset/first.fasta \ - --second $src/tandem_aligner/test_dataset/second.fasta \ - -o $TMPDIR/test_launch \ - --debug - grep -q "Thank you for using TandemAligner!" $TMPDIR/test_launch/tandem_aligner.log - diff $TMPDIR/test_launch/cigar.txt $src/tandem_aligner/test_dataset/true_cigar.txt - runHook postCheck - ''; - - meta = { - description = "Parameter-free algorithm for sequence alignment"; - homepage = "https://github.com/seryrzu/tandem_aligner"; - changelog = "https://github.com/seryrzu/tandem_aligner/releases/tag/v${finalAttrs.version}"; - license = lib.licenses.bsd3; - maintainers = with lib.maintainers; [ amesgen ]; - platforms = lib.platforms.linux; - mainProgram = "tandem_aligner"; - }; -}) diff --git a/pkgs/applications/science/biology/trimal/default.nix b/pkgs/applications/science/biology/trimal/default.nix index b2ef121caa9a2..f822fe50b1648 100644 --- a/pkgs/applications/science/biology/trimal/default.nix +++ b/pkgs/applications/science/biology/trimal/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "trimal"; - version = "1.4.1"; + version = "1.5.0"; src = fetchFromGitHub { repo = pname; owner = "scapella"; rev = "v${version}"; - sha256 = "0isc7s3514di4z953xq53ncjkbi650sh4q9yyw5aag1n9hqnh7k0"; + sha256 = "sha256-6GXirih7nY0eD2XS8aplLcYf53EeLuae+ewdUgBiKQQ="; }; postUnpack = '' diff --git a/pkgs/applications/science/biology/truvari/default.nix b/pkgs/applications/science/biology/truvari/default.nix index 946f4be606326..3c523b21fc641 100644 --- a/pkgs/applications/science/biology/truvari/default.nix +++ b/pkgs/applications/science/biology/truvari/default.nix @@ -15,14 +15,14 @@ let }; in python3Packages.buildPythonApplication rec { pname = "truvari"; - version = "4.1.0"; + version = "4.2.2"; pyproject = true; src = fetchFromGitHub { owner = "ACEnglish"; repo = "truvari"; rev = "v${version}"; - hash = "sha256-HFVAv1TTL/nMjr62tQKhMdwh25P/y4nBGzSbxoJxMmo="; + hash = "sha256-SFBVatcVavBfQtFbBcXifBX3YnKsxJS669vCcyjsBA4="; }; postPatch = '' @@ -31,11 +31,11 @@ in python3Packages.buildPythonApplication rec { patchShebangs repo_utils/test_files ''; - nativeBuildInputs = [ + build-system = [ python3Packages.setuptools ]; - propagatedBuildInputs = with python3Packages; [ + dependencies = with python3Packages; [ pywfa rich edlib @@ -46,6 +46,7 @@ in python3Packages.buildPythonApplication rec { pytabix bwapy pandas + pyabpoa ]; makeWrapperArgs = [ diff --git a/pkgs/applications/science/chemistry/gwyddion/default.nix b/pkgs/applications/science/chemistry/gwyddion/default.nix index c379e432bdeb2..9e64ee7afe4db 100644 --- a/pkgs/applications/science/chemistry/gwyddion/default.nix +++ b/pkgs/applications/science/chemistry/gwyddion/default.nix @@ -24,19 +24,18 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ pkg-config file ]; - buildInputs = with lib; - [ gtk2 fftw ] ++ - optionals openglSupport [ gnome2.gtkglext libGL ] ++ - optional openexrSupport openexr ++ - optional libXmuSupport xorg.libXmu ++ - optional fitsSupport cfitsio ++ - optional libpngSupport libpng ++ - optional libxsltSupport libxslt ++ - optional libxml2Support libxml2 ++ - optional libwebpSupport libwebp ++ - optional zlibSupport zlib ++ - optional libuniqueSupport libunique ++ - optional libzipSupport libzip; + buildInputs = [ gtk2 fftw ] ++ + lib.optionals openglSupport [ gnome2.gtkglext libGL ] ++ + lib.optional openexrSupport openexr ++ + lib.optional libXmuSupport xorg.libXmu ++ + lib.optional fitsSupport cfitsio ++ + lib.optional libpngSupport libpng ++ + lib.optional libxsltSupport libxslt ++ + lib.optional libxml2Support libxml2 ++ + lib.optional libwebpSupport libwebp ++ + lib.optional zlibSupport zlib ++ + lib.optional libuniqueSupport libunique ++ + lib.optional libzipSupport libzip; # This patch corrects problems with python support, but should apply cleanly # regardless of whether python support is enabled, and have no effects if @@ -59,7 +58,7 @@ stdenv.mkDerivation rec { ''; license = lib.licenses.gpl2; platforms = with lib.platforms; linux ++ darwin; - maintainers = [ lib.maintainers.cge ]; + maintainers = [ ]; # never built on aarch64-darwin since first introduction in nixpkgs broken = stdenv.isDarwin && stdenv.isAarch64; }; diff --git a/pkgs/applications/science/chemistry/jmol/default.nix b/pkgs/applications/science/chemistry/jmol/default.nix index cba6a40b59923..a48019febb1de 100644 --- a/pkgs/applications/science/chemistry/jmol/default.nix +++ b/pkgs/applications/science/chemistry/jmol/default.nix @@ -25,14 +25,14 @@ let }; in stdenv.mkDerivation rec { - version = "16.2.17"; + version = "16.2.21"; pname = "jmol"; src = let baseVersion = "${lib.versions.major version}.${lib.versions.minor version}"; in fetchurl { url = "mirror://sourceforge/jmol/Jmol/Version%20${baseVersion}/Jmol%20${version}/Jmol-${version}-binary.tar.gz"; - hash = "sha256-1iBLLfaoztbphhrG3NVWH+PVSbCZd+HQqvCYF3H9S/E="; + hash = "sha256-9gIOrHoy0JyoPXaHOfBDHCL+ykmmHNam+Um12sHqZsE="; }; patchPhase = '' diff --git a/pkgs/applications/science/chemistry/marvin/default.nix b/pkgs/applications/science/chemistry/marvin/default.nix index 4228e818e4887..e1e911e2d4dfb 100644 --- a/pkgs/applications/science/chemistry/marvin/default.nix +++ b/pkgs/applications/science/chemistry/marvin/default.nix @@ -1,14 +1,12 @@ { lib, stdenv, fetchurl, dpkg, makeWrapper, coreutils, gawk, gnugrep, gnused, openjdk17 }: -with lib; - stdenv.mkDerivation rec { pname = "marvin"; version = "23.17.0"; src = fetchurl { name = "marvin-${version}.deb"; - url = "http://dl.chemaxon.com/marvin/${version}/marvin_linux_${versions.majorMinor version}.deb"; + url = "http://dl.chemaxon.com/marvin/${version}/marvin_linux_${lib.versions.majorMinor version}.deb"; hash = "sha256-zE/9EaOsNJwzE4Doasm9N8QG4t7wDOxqpV/Nhc4p7Ws="; }; @@ -22,7 +20,7 @@ stdenv.mkDerivation rec { wrapBin() { makeWrapper $1 $out/bin/$(basename $1) \ --set INSTALL4J_JAVA_HOME "${openjdk17}" \ - --prefix PATH : ${makeBinPath [ coreutils gawk gnugrep gnused ]} + --prefix PATH : ${lib.makeBinPath [ coreutils gawk gnugrep gnused ]} } cp -r opt $out mkdir -p $out/bin $out/share/pixmaps $out/share/applications @@ -33,12 +31,12 @@ stdenv.mkDerivation rec { for name in cxcalc cxtrain evaluate molconvert mview msketch; do wrapBin $out/opt/chemaxon/marvinsuite/bin/$name done - ${concatStrings (map (name: '' + ${lib.concatStrings (map (name: '' substitute ${./. + "/${name}.desktop"} $out/share/applications/${name}.desktop --subst-var out '') [ "LicenseManager" "MarvinSketch" "MarvinView" ])} ''; - meta = { + meta = with lib; { description = "Chemical modelling, analysis and structure drawing program"; homepage = "https://chemaxon.com/products/marvin"; maintainers = with maintainers; [ fusion809 ]; diff --git a/pkgs/applications/science/chemistry/nwchem/default.nix b/pkgs/applications/science/chemistry/nwchem/default.nix index 61266a9f02854..af63e2a77568b 100644 --- a/pkgs/applications/science/chemistry/nwchem/default.nix +++ b/pkgs/applications/science/chemistry/nwchem/default.nix @@ -1,6 +1,5 @@ { lib , stdenv -, pkgs , fetchFromGitHub , fetchurl , mpiCheckPhaseHook @@ -14,7 +13,6 @@ , lapack , python3 , tcsh -, bash , automake , autoconf , libtool diff --git a/pkgs/applications/science/chemistry/octopus/default.nix b/pkgs/applications/science/chemistry/octopus/default.nix index 2e87cf3db51aa..a9b881b2cdc01 100644 --- a/pkgs/applications/science/chemistry/octopus/default.nix +++ b/pkgs/applications/science/chemistry/octopus/default.nix @@ -36,7 +36,7 @@ stdenv.mkDerivation rec { owner = "octopus-code"; repo = "octopus"; rev = version; - sha256 = "sha256-8wZR+bYdxJFsUPMWbIGYxRdNzjLgHm+KFLjY7fSN7io="; + hash = "sha256-8wZR+bYdxJFsUPMWbIGYxRdNzjLgHm+KFLjY7fSN7io="; }; nativeBuildInputs = [ diff --git a/pkgs/applications/science/chemistry/pymol/default.nix b/pkgs/applications/science/chemistry/pymol/default.nix index 1733ba2f236c9..295ac7e14cb23 100644 --- a/pkgs/applications/science/chemistry/pymol/default.nix +++ b/pkgs/applications/science/chemistry/pymol/default.nix @@ -2,7 +2,6 @@ , lib , fetchFromGitHub , makeDesktopItem -, python3 , python3Packages , netcdf , glew @@ -50,7 +49,7 @@ python3Packages.buildPythonApplication rec { postPatch = '' substituteInPlace setup.py \ - --replace-fail "self.install_libbase" '"${placeholder "out"}/${python3.sitePackages}"' + --replace-fail "self.install_libbase" '"${placeholder "out"}/${python3Packages.python.sitePackages}"' ''; build-system = [ @@ -63,10 +62,10 @@ python3Packages.buildPythonApplication rec { postInstall = with python3Packages; '' wrapProgram $out/bin/pymol \ - --prefix PYTHONPATH : ${lib.makeSearchPathOutput "lib" python3.sitePackages [ pyqt5 pyqt5.pyqt5-sip ]} + --prefix PYTHONPATH : ${lib.makeSearchPathOutput "lib" python3Packages.python.sitePackages [ pyqt5 pyqt5.pyqt5-sip ]} mkdir -p "$out/share/icons/" - ln -s $out/${python3.sitePackages}/pymol/pymol_path/data/pymol/icons/icon2.svg "$out/share/icons/pymol.svg" + ln -s $out/${python3Packages.python.sitePackages}/pymol/pymol_path/data/pymol/icons/icon2.svg "$out/share/icons/pymol.svg" '' + lib.optionalString stdenv.hostPlatform.isLinux '' cp -r "${desktopItem}/share/applications/" "$out/share/" ''; diff --git a/pkgs/applications/science/chemistry/quantum-espresso/default.nix b/pkgs/applications/science/chemistry/quantum-espresso/default.nix index 2c565cb5db9f0..2156c1d269691 100644 --- a/pkgs/applications/science/chemistry/quantum-espresso/default.nix +++ b/pkgs/applications/science/chemistry/quantum-espresso/default.nix @@ -4,7 +4,6 @@ , fetchFromGitHub , git , cmake -, gnum4 , gfortran , pkg-config , fftw diff --git a/pkgs/applications/science/computer-architecture/accelergy/default.nix b/pkgs/applications/science/computer-architecture/accelergy/default.nix index 9eb6f341b714d..42609ada09a38 100644 --- a/pkgs/applications/science/computer-architecture/accelergy/default.nix +++ b/pkgs/applications/science/computer-architecture/accelergy/default.nix @@ -1,4 +1,4 @@ -{ lib, fetchFromGitHub, python3Packages, pkgs }: +{ lib, fetchFromGitHub, python3Packages }: python3Packages.buildPythonApplication rec { pname = "accelergy"; diff --git a/pkgs/applications/science/computer-architecture/timeloop/default.nix b/pkgs/applications/science/computer-architecture/timeloop/default.nix index ec8ec3ed8abc6..7fc5da8dfa89a 100644 --- a/pkgs/applications/science/computer-architecture/timeloop/default.nix +++ b/pkgs/applications/science/computer-architecture/timeloop/default.nix @@ -41,10 +41,6 @@ stdenv.mkDerivation rec { enableParallelBuilding = true; - #link-time optimization fails on darwin - #see https://github.com/NixOS/nixpkgs/issues/19098 - env.NIX_CFLAGS_COMPILE = lib.optionalString stdenv.isDarwin "-fno-lto"; - postPatch = '' # Fix gcc-13 build failure due to missing includes: sed -e '1i #include <cstdint>' -i \ diff --git a/pkgs/applications/science/electronics/caneda/default.nix b/pkgs/applications/science/electronics/caneda/default.nix index 4a4cf61c7f658..7eac675eca4e6 100644 --- a/pkgs/applications/science/electronics/caneda/default.nix +++ b/pkgs/applications/science/electronics/caneda/default.nix @@ -19,7 +19,7 @@ mkDerivation rec { mainProgram = "caneda"; homepage = "http://caneda.org"; license = lib.licenses.gpl2Plus; - maintainers = with lib.maintainers; [viric]; + maintainers = [ ]; platforms = with lib.platforms; linux; }; } diff --git a/pkgs/applications/science/electronics/dataexplorer/default.nix b/pkgs/applications/science/electronics/dataexplorer/default.nix deleted file mode 100644 index 224d804ee1f69..0000000000000 --- a/pkgs/applications/science/electronics/dataexplorer/default.nix +++ /dev/null @@ -1,82 +0,0 @@ -{ lib -, stdenv -, fetchurl -, ant -, jdk -, makeWrapper -, strip-nondeterminism -}: - -stdenv.mkDerivation (finalAttrs: { - pname = "dataexplorer"; - version = "3.8.5"; - - src = fetchurl { - url = "mirror://savannah/dataexplorer/dataexplorer-${finalAttrs.version}-src.tar.gz"; - hash = "sha256-b68xIZNbzHdPyZwLngcnjcoBtI6AeTdrblz/qx/HbGQ="; - }; - - nativeBuildInputs = [ - ant - jdk - makeWrapper - strip-nondeterminism - ]; - - buildPhase = '' - runHook preBuild - ant -f build/build.xml dist - runHook postBuild - ''; - - doCheck = false; - # Missing dependencies (e.g. junit). Does not work. - #checkPhase = '' - # ant -f build/build.xml check - #''; - - installPhase = '' - runHook preInstall - - ant -Dprefix=$out/share/ -f build/build.xml install - - # The sources contain a wrapper script in $out/share/DataExplorer/DataExplorer - # but it hardcodes bash shebang and does not pin the java path. - # So we create our own wrapper, using similar cmdline args as upstream. - mkdir -p $out/bin - makeWrapper ${jdk}/bin/java $out/bin/DataExplorer \ - --add-flags "-Xms64m -Xmx3092m -jar $out/share/DataExplorer/DataExplorer.jar" \ - --set SWT_GTK3 0 - - makeWrapper ${jdk}/bin/java $out/bin/DevicePropertiesEditor \ - --add-flags "-Xms32m -Xmx512m -classpath $out/share/DataExplorer/DataExplorer.jar gde.ui.dialog.edit.DevicePropertiesEditor" \ - --set SWT_GTK3 0 \ - --set LIBOVERLAY_SCROLLBAR 0 - - install -Dvm644 build/misc/GNU_LINUX_JUNSI_ICHARER_USB_UDEV_RULE/50-Junsi-iCharger-USB.rules \ - $out/etc/udev/rules.d/50-Junsi-iCharger-USB.rules - install -Dvm644 build/misc/GNU_LINUX_SKYRC_UDEV_RULE/50-SkyRC-Charger.rules \ - $out/etc/udev/rules.d/50-SkyRC-Charger.rules - - runHook postInstall - ''; - - # manually call strip-nondeterminism because using stripJavaArchivesHook takes - # too long to strip bundled jars - postFixup = '' - strip-nondeterminism --type jar $out/share/DataExplorer/{DataExplorer.jar,devices/*.jar} - ''; - - meta = with lib; { - description = "Graphical tool to analyze data, gathered from various hardware devices"; - homepage = "https://www.nongnu.org/dataexplorer/index.html"; - license = licenses.gpl3Plus; - maintainers = with maintainers; [ panicgh ]; - platforms = [ "x86_64-linux" ]; - sourceProvenance = with sourceTypes; [ - fromSource - binaryNativeCode # contains RXTXcomm (JNI library with *.so files) - binaryBytecode # contains thirdparty jar files, e.g. javax.json, org.glassfish.json - ]; - }; -}) diff --git a/pkgs/applications/science/electronics/diylc/default.nix b/pkgs/applications/science/electronics/diylc/default.nix index ced8c72d2155d..072faf3a8a5b9 100644 --- a/pkgs/applications/science/electronics/diylc/default.nix +++ b/pkgs/applications/science/electronics/diylc/default.nix @@ -73,6 +73,6 @@ stdenv.mkDerivation rec { license = licenses.gpl3Plus; sourceProvenance = with sourceTypes; [ binaryBytecode ]; platforms = platforms.linux; - maintainers = with maintainers; [ ]; + maintainers = [ ]; }; } diff --git a/pkgs/applications/science/electronics/dwfv/default.nix b/pkgs/applications/science/electronics/dwfv/default.nix deleted file mode 100644 index 415cc29812d3d..0000000000000 --- a/pkgs/applications/science/electronics/dwfv/default.nix +++ /dev/null @@ -1,21 +0,0 @@ -{ lib, rustPlatform, fetchCrate }: - -rustPlatform.buildRustPackage rec { - pname = "dwfv"; - version = "0.4.1"; - - src = fetchCrate { - inherit version pname; - sha256 = "0xxgwbbbzaldbl04k5ksk61wa6i4f9mc84q04ljg438z0k8q6cr7"; - }; - - cargoSha256 = "1z51yx3psdxdzmwny0rzlch5hjx2pssll73q79qij2bc7wgyjscy"; - - meta = with lib; { - description = "Simple digital waveform viewer with vi-like key bindings"; - mainProgram = "dwfv"; - homepage = "https://github.com/psurply/dwfv"; - license = licenses.mit; - maintainers = with maintainers; [ newam ]; - }; -} diff --git a/pkgs/applications/science/electronics/flopoco/default.nix b/pkgs/applications/science/electronics/flopoco/default.nix index 2da80512e2b2c..e15ef3277a664 100644 --- a/pkgs/applications/science/electronics/flopoco/default.nix +++ b/pkgs/applications/science/electronics/flopoco/default.nix @@ -25,7 +25,7 @@ stdenv.mkDerivation rec { repo = pname; # flopoco-4.1.3 is not tagged on GitLab rev = "67598298207c9f3261c35679c8a5966480c4343c"; - sha256 = "sha256-0jRjg4/qciqBcjsi6BTbKO4VJkcoEzpC98wFkUOIGbI="; + hash = "sha256-0jRjg4/qciqBcjsi6BTbKO4VJkcoEzpC98wFkUOIGbI="; }; patches = [ @@ -54,12 +54,12 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ bison cmake + flex installShellFiles ]; buildInputs = [ boost - flex gmp libxml2 mpfi diff --git a/pkgs/applications/science/electronics/fped/default.nix b/pkgs/applications/science/electronics/fped/default.nix index edfe34c0e25e8..e3984dba77d8d 100644 --- a/pkgs/applications/science/electronics/fped/default.nix +++ b/pkgs/applications/science/electronics/fped/default.nix @@ -3,7 +3,6 @@ , pkg-config }: -with lib; stdenv.mkDerivation { pname = "fped"; version = "unstable-2017-05-11"; @@ -39,7 +38,7 @@ stdenv.mkDerivation { gtk2 ]; - meta = { + meta = with lib; { description = "Editor that allows the interactive creation of footprints electronic components"; mainProgram = "fped"; homepage = "http://projects.qi-hardware.com/index.php/p/fped/"; diff --git a/pkgs/applications/science/electronics/kicad/default.nix b/pkgs/applications/science/electronics/kicad/default.nix index 1cec011fae33f..459523ea61690 100644 --- a/pkgs/applications/science/electronics/kicad/default.nix +++ b/pkgs/applications/science/electronics/kicad/default.nix @@ -7,7 +7,7 @@ , callPackage , callPackages -, gnome +, adwaita-icon-theme , dconf , gtk3 , wxGTK32 @@ -25,7 +25,7 @@ , withNgspice ? !stdenv.isDarwin , libngspice , withScripting ? true -, python3 +, python311 , addons ? [ ] , debug ? false , sanitizeAddress ? false @@ -122,10 +122,14 @@ let else versionsImport.${baseName}.libVersion.version; wxGTK = wxGTK32; - python = python3; + # KiCAD depends on wxWidgets, which uses distutils (removed in Python 3.12) + # See also: https://github.com/wxWidgets/Phoenix/issues/2104 + # Eventually, wxWidgets should support Python 3.12: https://github.com/wxWidgets/Phoenix/issues/2553 + # Until then, we use Python 3.11 which still includes distutils + python = python311; wxPython = python.pkgs.wxpython; addonPath = "addon.zip"; - addonsDrvs = map (pkg: pkg.override { inherit addonPath python3; }) addons; + addonsDrvs = map (pkg: pkg.override { inherit addonPath python; }) addons; addonsJoined = runCommand "addonsJoined" @@ -157,7 +161,7 @@ stdenv.mkDerivation rec { # Common libraries, referenced during runtime, via the wrapper. passthru.libraries = callPackages ./libraries.nix { inherit libSrc; }; - passthru.callPackage = newScope { inherit addonPath python3; }; + passthru.callPackage = newScope { inherit addonPath python; }; base = callPackage ./base.nix { inherit stable testing baseName; inherit kicadSrc kicadVersion; @@ -197,7 +201,7 @@ stdenv.mkDerivation rec { makeWrapperArgs = with passthru.libraries; [ "--prefix XDG_DATA_DIRS : ${base}/share" "--prefix XDG_DATA_DIRS : ${hicolor-icon-theme}/share" - "--prefix XDG_DATA_DIRS : ${gnome.adwaita-icon-theme}/share" + "--prefix XDG_DATA_DIRS : ${adwaita-icon-theme}/share" "--prefix XDG_DATA_DIRS : ${gtk3}/share/gsettings-schemas/${gtk3.name}" "--prefix XDG_DATA_DIRS : ${gsettings-desktop-schemas}/share/gsettings-schemas/${gsettings-desktop-schemas.name}" # wrapGAppsHook3 did these two as well, no idea if it matters... diff --git a/pkgs/applications/science/electronics/kicad/versions.nix b/pkgs/applications/science/electronics/kicad/versions.nix index b3ddbd5b604fe..3d66c909036e5 100644 --- a/pkgs/applications/science/electronics/kicad/versions.nix +++ b/pkgs/applications/science/electronics/kicad/versions.nix @@ -3,23 +3,23 @@ { "kicad" = { kicadVersion = { - version = "8.0.3"; + version = "8.0.4"; src = { - rev = "8ba5ba46af8502ea7a7d2a9754363167c2742399"; - sha256 = "0hafvcjjwylgcpgyyasmb2q210k82wvcswvgjvwwh76bwshwcpwa"; + rev = "5609722002776982320b6a8fbe6d096bbccf469b"; + sha256 = "03971przr1kzmkr302qzx30mmp92mkwg29dwjvzayc522iskxcbx"; }; }; libVersion = { - version = "8.0.3"; + version = "8.0.4"; libSources = { - symbols.rev = "2bc103c46a8daacbba2cded8b9f095b330ba928d"; - symbols.sha256 = "1za0spq09bbj7xwfwr1abmwjnqfd3zx0crayaz7915ja0ifi75hd"; - templates.rev = "0f57b59d365d1f8b8fdd0745e10beb035e88ba37"; + symbols.rev = "967a2828636d21f90ccc28dcfdc0e48508101c9d"; + symbols.sha256 = "1s8mkxb3ncb0w8z5q8jzhryb0yri7g51vx29qykqwv4ksra1f07i"; + templates.rev = "9c51a73b2e2fc4ea75d8b8be0a78bc9fb1785433"; templates.sha256 = "03idwrk3vj9h2az8j8lqpbdbnfxdbkzh4db68kq3644yj3cnlcza"; - footprints.rev = "539ffd8c0898ad8c8c51c2ab85ba56bfd77271c7"; - footprints.sha256 = "0ik4hjl5m65wnpaymg58zbvsfvchhyq5x3psvj6005mgv2hrican"; - packages3d.rev = "3172a1cc0931c1734efad68623374d5277f8ab60"; - packages3d.sha256 = "1yjlg7cxwhlzcdbxjqyqamr140sz8gvzi63k2401mhdbh88c9kii"; + footprints.rev = "a2aa9b5aea64c0efad9a31bc9ca88d48c0203752"; + footprints.sha256 = "1aqdb7mamz8xzz1qrw3qnvnaj97asb8z37w1cjz6y06sjcznlihn"; + packages3d.rev = "5430edd57b3a66fe69288aa8fda714f9732a7f52"; + packages3d.sha256 = "0vixdcldvnl8lr8bq3rc748q3vhx1lr2a0i071w914xyn983z9vz"; }; }; }; diff --git a/pkgs/applications/science/electronics/kingstvis/default.nix b/pkgs/applications/science/electronics/kingstvis/default.nix index 3699aebbbff0e..0a39c66bc662a 100644 --- a/pkgs/applications/science/electronics/kingstvis/default.nix +++ b/pkgs/applications/science/electronics/kingstvis/default.nix @@ -6,7 +6,6 @@ , glib , lib , libGL -, stdenv , xkeyboard_config , xorg , zlib diff --git a/pkgs/applications/science/electronics/librepcb/default.nix b/pkgs/applications/science/electronics/librepcb/default.nix index cff52d67dc477..061043a67d411 100644 --- a/pkgs/applications/science/electronics/librepcb/default.nix +++ b/pkgs/applications/science/electronics/librepcb/default.nix @@ -10,7 +10,7 @@ stdenv.mkDerivation rec { owner = pname; repo = pname; rev = version; - sha256 = "sha256-Vyp7asVqvKFkkEb67LXapMkT1AQSburN3+B2dXIPcEU="; + hash = "sha256-Vyp7asVqvKFkkEb67LXapMkT1AQSburN3+B2dXIPcEU="; fetchSubmodules = true; }; diff --git a/pkgs/applications/science/electronics/magic-vlsi/default.nix b/pkgs/applications/science/electronics/magic-vlsi/default.nix index 0be742f76e3c6..28b1b91ae1a24 100644 --- a/pkgs/applications/science/electronics/magic-vlsi/default.nix +++ b/pkgs/applications/science/electronics/magic-vlsi/default.nix @@ -13,11 +13,11 @@ stdenv.mkDerivation rec { pname = "magic-vlsi"; - version = "8.3.483"; + version = "8.3.486"; src = fetchurl { url = "http://opencircuitdesign.com/magic/archive/magic-${version}.tgz"; - sha256 = "sha256-JyawlH/zUTJ7fGf63zHvZ3q8AYRwFELwh+63RN9IkBA="; + sha256 = "sha256-RLAA97roY41imjxehEFzF+peLmrS+rTQkVua+8dxKDY="; }; nativeBuildInputs = [ python3 ]; diff --git a/pkgs/applications/science/electronics/nanovna-saver/default.nix b/pkgs/applications/science/electronics/nanovna-saver/default.nix index dd58794ed182c..d4c3c68991a22 100644 --- a/pkgs/applications/science/electronics/nanovna-saver/default.nix +++ b/pkgs/applications/science/electronics/nanovna-saver/default.nix @@ -1,25 +1,28 @@ { lib, + stdenv, python3, fetchFromGitHub, qt6, }: python3.pkgs.buildPythonApplication rec { pname = "nanovna-saver"; - version = "0.6.3"; + version = "0.6.4"; src = fetchFromGitHub { owner = "NanoVNA-Saver"; repo = pname; rev = "refs/tags/v${version}"; - sha256 = "sha256-lL6n3hcsIbLmrRKPi/ckWW2XUAtmBqvMSplkWOF4VKQ="; + sha256 = "sha256-fAVsjknhLhsrGdHu2Q6JWLoFoxZoc+wDCNja+ySCsR4="; }; - nativeBuildInputs = [ + nativeBuildInputs = [ qt6.wrapQtAppsHook qt6.qtbase ]; + buildInputs = lib.optional stdenv.isLinux qt6.qtwayland; + propagatedBuildInputs = with python3.pkgs; [ cython scipy diff --git a/pkgs/applications/science/electronics/nvc/default.nix b/pkgs/applications/science/electronics/nvc/default.nix index 62b62ff15faae..c05527234f70f 100644 --- a/pkgs/applications/science/electronics/nvc/default.nix +++ b/pkgs/applications/science/electronics/nvc/default.nix @@ -15,13 +15,13 @@ stdenv.mkDerivation rec { pname = "nvc"; - version = "1.12.2"; + version = "1.13.2"; src = fetchFromGitHub { owner = "nickg"; repo = "nvc"; rev = "r${version}"; - hash = "sha256-9nqho+iDqy8oQLSxBppXoafzEuS6AkcUuqEY3xxfFs4="; + hash = "sha256-ir4/zwGaIGMUP8kVqoXV1Kn2A8yJYVQHJpb1sVfhOSI="; }; nativeBuildInputs = [ diff --git a/pkgs/applications/science/electronics/openboardview/default.nix b/pkgs/applications/science/electronics/openboardview/default.nix index 4aa9ab2b66f29..60ee6cef77530 100644 --- a/pkgs/applications/science/electronics/openboardview/default.nix +++ b/pkgs/applications/science/electronics/openboardview/default.nix @@ -24,7 +24,7 @@ stdenv.mkDerivation rec { owner = "OpenBoardView"; repo = "OpenBoardView"; rev = version; - sha256 = "sha256-sKDDOPpCagk7rBRlMlZhx+RYYbtoLzJsrnL8qKZMKW8="; + hash = "sha256-sKDDOPpCagk7rBRlMlZhx+RYYbtoLzJsrnL8qKZMKW8="; fetchSubmodules = true; }; diff --git a/pkgs/applications/science/electronics/openroad/default.nix b/pkgs/applications/science/electronics/openroad/default.nix index 16659892a6ee7..0c929fe47c18e 100644 --- a/pkgs/applications/science/electronics/openroad/default.nix +++ b/pkgs/applications/science/electronics/openroad/default.nix @@ -15,7 +15,6 @@ , clp # for or-tools , eigen , glpk -, gtest , lcov , lemon-graph , libjpeg diff --git a/pkgs/applications/science/electronics/picoscope/default.nix b/pkgs/applications/science/electronics/picoscope/default.nix index 3aa5cb22aa52c..27e527a01d876 100644 --- a/pkgs/applications/science/electronics/picoscope/default.nix +++ b/pkgs/applications/science/electronics/picoscope/default.nix @@ -15,13 +15,12 @@ ] }: let - shared_meta = lib: - with lib; { - homepage = "https://www.picotech.com/downloads/linux"; - maintainers = with maintainers; [ expipiplus1 wirew0rm ] ++ teams.lumiguide.members; - platforms = [ "x86_64-linux" ]; - license = licenses.unfree; - }; + shared_meta = lib: { + homepage = "https://www.picotech.com/downloads/linux"; + maintainers = with lib.maintainers; [ expipiplus1 wirew0rm ] ++ lib.teams.lumiguide.members; + platforms = [ "x86_64-linux" ]; + license = lib.licenses.unfree; + }; libpicoipp = callPackage ({ stdenv, lib, fetchurl, autoPatchelfHook, dpkg }: stdenv.mkDerivation rec { @@ -39,11 +38,10 @@ let install -Dt $out/usr/share/doc/libpicoipp usr/share/doc/libpicoipp/copyright runHook postInstall ''; - meta = with lib; - shared_meta lib // { - sourceProvenance = with sourceTypes; [ binaryNativeCode ]; - description = "library for picotech oscilloscope software"; - }; + meta = shared_meta lib // { + sourceProvenance = with lib.sourceTypes; [ binaryNativeCode ]; + description = "library for picotech oscilloscope software"; + }; }) { }; # If we don't have a platform available, put a dummy version here, so at diff --git a/pkgs/applications/science/electronics/systemc/default.nix b/pkgs/applications/science/electronics/systemc/default.nix index 8e47ef9606566..089ccd85c0331 100644 --- a/pkgs/applications/science/electronics/systemc/default.nix +++ b/pkgs/applications/science/electronics/systemc/default.nix @@ -26,6 +26,6 @@ stdenv.mkDerivation rec { homepage = "https://systemc.org/"; license = licenses.asl20; platforms = platforms.unix; - maintainers = with maintainers; [ victormignot amiloradovsky ]; + maintainers = with maintainers; [ amiloradovsky ]; }; } diff --git a/pkgs/applications/science/electronics/verilator/default.nix b/pkgs/applications/science/electronics/verilator/default.nix index 92f8fa52b91f9..1bed876157569 100644 --- a/pkgs/applications/science/electronics/verilator/default.nix +++ b/pkgs/applications/science/electronics/verilator/default.nix @@ -1,31 +1,57 @@ -{ lib, stdenv, fetchFromGitHub, fetchpatch, perl, flex, bison, python3, autoconf, - which, cmake, ccache, help2man, makeWrapper, glibcLocales, - systemc, git, numactl }: +{ + lib, + stdenv, + fetchFromGitHub, + perl, + flex, + bison, + python3, + autoconf, + which, + help2man, + makeWrapper, + systemc, + git, + numactl, + coreutils, +}: stdenv.mkDerivation rec { pname = "verilator"; - version = "5.022"; + version = "5.026"; + + # Verilator gets the version from this environment variable + # if it can't do git describe while building. + VERILATOR_SRC_VERSION = "v${version}"; src = fetchFromGitHub { owner = pname; repo = pname; rev = "v${version}"; - hash = "sha256-Ya3lqK8BfvMVLZUrD2Et6OmptteWXp5VmZb2x2G/V/E="; + hash = "sha256-Ds6w95tqlKjIFnkq2kKyslprKCwMOtBOoy7LuTon3KM="; }; - patches = [ - (fetchpatch { - # Fix try-lock spuriously fail in V3ThreadPool destructor - # https://github.com/verilator/verilator/pull/4938 - url = "https://github.com/verilator/verilator/commit/4b9cce4369c78423779238e585ed693c456d464e.patch"; - hash = "sha256-sGrk/pxqZqUcmJdzQoPlzXMmYqHCOmd9Y2n6ieVNg1U="; - }) - ]; - enableParallelBuilding = true; - buildInputs = [ perl python3 systemc ]; # ccache - nativeBuildInputs = [ makeWrapper flex bison autoconf help2man git ]; - nativeCheckInputs = [ which numactl ]; # cmake + buildInputs = [ + perl + python3 + systemc + # ccache + ]; + nativeBuildInputs = [ + makeWrapper + flex + bison + autoconf + help2man + git + ]; + nativeCheckInputs = [ + which + numactl + coreutils + # cmake + ]; doCheck = stdenv.isLinux; # darwin tests are broken for now... checkTarget = "test"; @@ -36,16 +62,12 @@ stdenv.mkDerivation rec { patchShebangs bin/* src/* nodist/* docs/bin/* examples/xml_py/* \ test_regress/{driver.pl,t/*.{pl,pf}} \ ci/* ci/docker/run/* ci/docker/run/hooks/* ci/docker/buildenv/build.sh + # verilator --gdbbt uses /bin/echo to test if gdb works. + sed -i 's|/bin/echo|${coreutils}\/bin\/echo|' bin/verilator ''; # grep '^#!/' -R . | grep -v /nix/store | less # (in nix-shell after patchPhase) - postInstall = lib.optionalString stdenv.isLinux '' - for x in $(ls $out/bin/verilator*); do - wrapProgram "$x" --set LOCALE_ARCHIVE "${glibcLocales}/lib/locale/locale-archive" - done - ''; - env = { SYSTEMC_INCLUDE = "${lib.getDev systemc}/include"; SYSTEMC_LIBDIR = "${lib.getLib systemc}/lib"; @@ -53,9 +75,15 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Fast and robust (System)Verilog simulator/compiler and linter"; - homepage = "https://www.veripool.org/verilator"; - license = with licenses; [ lgpl3Only artistic2 ]; - platforms = platforms.unix; - maintainers = with maintainers; [ thoughtpolice amiloradovsky ]; + homepage = "https://www.veripool.org/verilator"; + license = with licenses; [ + lgpl3Only + artistic2 + ]; + platforms = platforms.unix; + maintainers = with maintainers; [ + thoughtpolice + amiloradovsky + ]; }; } diff --git a/pkgs/applications/science/electronics/verilog/default.nix b/pkgs/applications/science/electronics/verilog/default.nix deleted file mode 100644 index 06e8a94a4c537..0000000000000 --- a/pkgs/applications/science/electronics/verilog/default.nix +++ /dev/null @@ -1,80 +0,0 @@ -{ lib, stdenv -, fetchFromGitHub -, fetchpatch -, autoconf -, bison -, bzip2 -, flex -, gperf -, ncurses -, perl -, python3 -, readline -, zlib -}: - -stdenv.mkDerivation rec { - pname = "iverilog"; - version = "12.0"; - - src = fetchFromGitHub { - owner = "steveicarus"; - repo = pname; - rev = "v${lib.replaceStrings ["."] ["_"] version}"; - hash = "sha256-J9hedSmC6mFVcoDnXBtaTXigxrSCFa2AhhFd77ueo7I="; - }; - - nativeBuildInputs = [ autoconf bison flex gperf ]; - - CC_FOR_BUILD="${stdenv.cc}/bin/cc"; - CXX_FOR_BUILD="${stdenv.cc}/bin/c++"; - - patches = [ - # NOTE(jleightcap): `-Werror=format-security` warning patched shortly after release, backport the upstream fix - (fetchpatch { - name = "format-security"; - url = "https://github.com/steveicarus/iverilog/commit/23e51ef7a8e8e4ba42208936e0a6a25901f58c65.patch"; - hash = "sha256-fMWfBsCl2fuXe+6AR10ytb8QpC84bXlP5RSdrqsWzEk="; - }) - ]; - - buildInputs = [ bzip2 ncurses readline zlib ]; - - preConfigure = "sh autoconf.sh"; - - enableParallelBuilding = true; - - env = lib.optionalAttrs stdenv.isDarwin { - NIX_CFLAGS_COMPILE = "-Wno-error=implicit-function-declaration"; - }; - - # NOTE(jleightcap): the `make check` target only runs a "Hello, World"-esque sanity check. - # the tests in the doInstallCheck phase run a full regression test suite. - # however, these tests currently fail upstream on aarch64 - # (see https://github.com/steveicarus/iverilog/issues/917) - # so disable the full suite for now. - doCheck = true; - doInstallCheck = !stdenv.isAarch64; - - nativeInstallCheckInputs = [ - perl - (python3.withPackages (pp: with pp; [ - docopt - ])) - ]; - - installCheckPhase = '' - runHook preInstallCheck - export PATH="$PATH:$out/bin" - sh .github/test.sh - runHook postInstallCheck - ''; - - meta = with lib; { - description = "Icarus Verilog compiler"; - homepage = "http://iverilog.icarus.com/"; # https does not work - license = with licenses; [ gpl2Plus lgpl21Plus ]; - maintainers = with maintainers; [ thoughtpolice ]; - platforms = platforms.all; - }; -} diff --git a/pkgs/applications/science/electronics/vhd2vl/default.nix b/pkgs/applications/science/electronics/vhd2vl/default.nix index 078f5e9514047..28656fe6e1216 100644 --- a/pkgs/applications/science/electronics/vhd2vl/default.nix +++ b/pkgs/applications/science/electronics/vhd2vl/default.nix @@ -3,7 +3,7 @@ , fetchFromGitHub , bison , flex -, verilog +, iverilog , which }: @@ -25,7 +25,7 @@ stdenv.mkDerivation rec { ]; buildInputs = [ - verilog + iverilog ]; # the "translate" target both (a) builds the software and (b) runs diff --git a/pkgs/applications/science/electronics/xoscope/default.nix b/pkgs/applications/science/electronics/xoscope/default.nix index 0fa0c1bc79bfc..37b9076c01cc7 100644 --- a/pkgs/applications/science/electronics/xoscope/default.nix +++ b/pkgs/applications/science/electronics/xoscope/default.nix @@ -27,7 +27,7 @@ stdenv.mkDerivation rec { mainProgram = "xoscope"; homepage = "https://xoscope.sourceforge.net"; license = lib.licenses.gpl2Plus; - maintainers = with lib.maintainers; [viric]; + maintainers = [ ]; platforms = with lib.platforms; linux; }; } diff --git a/pkgs/applications/science/electronics/xyce/default.nix b/pkgs/applications/science/electronics/xyce/default.nix index 93c155038a22b..85cdafb660575 100644 --- a/pkgs/applications/science/electronics/xyce/default.nix +++ b/pkgs/applications/science/electronics/xyce/default.nix @@ -17,14 +17,12 @@ , withMPI ? false # for doc , texliveMedium -, pandoc , enableDocs ? true # for tests , bash , bc , openssh # required by MPI , perl -, perlPackages , python3 , enableTests ? true }: diff --git a/pkgs/applications/science/geometry/antiprism/default.nix b/pkgs/applications/science/geometry/antiprism/default.nix index 62ffc099dc6cd..9d4c6fc6a4091 100644 --- a/pkgs/applications/science/geometry/antiprism/default.nix +++ b/pkgs/applications/science/geometry/antiprism/default.nix @@ -4,7 +4,7 @@ , libX11 , libGL , libGLU -, freeglut }: +, libglut }: stdenv.mkDerivation rec { pname = "antiprism"; @@ -18,7 +18,7 @@ stdenv.mkDerivation rec { }; nativeBuildInputs = [ autoreconfHook ]; - buildInputs = [ libX11 libGLU libGL.dev freeglut.dev ]; + buildInputs = [ libX11 libGLU libGL libglut ]; meta = with lib; { homepage = "https://www.antiprism.com"; diff --git a/pkgs/applications/science/geometry/tetgen/default.nix b/pkgs/applications/science/geometry/tetgen/default.nix index dce56dc4e17d2..e64941f4243ad 100644 --- a/pkgs/applications/science/geometry/tetgen/default.nix +++ b/pkgs/applications/science/geometry/tetgen/default.nix @@ -27,6 +27,6 @@ stdenv.mkDerivation rec { mainProgram = "tetgen"; homepage = "http://tetgen.org/"; license = lib.licenses.agpl3Plus; - platforms = lib.platforms.linux; + platforms = lib.platforms.unix; }; } diff --git a/pkgs/applications/science/logic/beluga/default.nix b/pkgs/applications/science/logic/beluga/default.nix index b1497e2b1dcbe..d85f375f9f89d 100644 --- a/pkgs/applications/science/logic/beluga/default.nix +++ b/pkgs/applications/science/logic/beluga/default.nix @@ -2,13 +2,13 @@ ocamlPackages.buildDunePackage rec { pname = "beluga"; - version = "1.1.1"; + version = "1.1.2"; src = fetchFromGitHub { owner = "Beluga-lang"; repo = "Beluga"; rev = "refs/tags/v${version}"; - hash = "sha256-l/C77czLtlLnpadVx4d9ve9jv/e11jsOgzrbXt+Zo5s="; + hash = "sha256-QUZ3mmd0gBQ+hnAeo/TbvFsETnThAdAoQyfpz2F//4g="; }; duneVersion = "3"; diff --git a/pkgs/applications/science/logic/bitwuzla/default.nix b/pkgs/applications/science/logic/bitwuzla/default.nix index c1eb751fb1a57..f5a5296de9c47 100644 --- a/pkgs/applications/science/logic/bitwuzla/default.nix +++ b/pkgs/applications/science/logic/bitwuzla/default.nix @@ -43,7 +43,7 @@ stdenv.mkDerivation (finalAttrs: { # but setting it to shared works even in pkgsStatic "-Ddefault_library=shared" - (lib.strings.mesonEnable "testing" finalAttrs.doCheck) + (lib.strings.mesonEnable "testing" finalAttrs.finalPackage.doCheck) ]; nativeCheckInputs = [ python3 ]; diff --git a/pkgs/applications/science/logic/cadical/default.nix b/pkgs/applications/science/logic/cadical/default.nix index 12b01dea1a3dd..6d49ef0ab3f63 100644 --- a/pkgs/applications/science/logic/cadical/default.nix +++ b/pkgs/applications/science/logic/cadical/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "cadical"; - version = "1.9.5"; + version = "2.0.0"; src = fetchFromGitHub { owner = "arminbiere"; repo = "cadical"; rev = "rel-${version}"; - sha256 = "sha256-mAKuz8WjX+ywQ7Sw5hRMPftsbbilTlmQ9qZVowXxs28="; + sha256 = "sha256-qoeEM9SdpuFuBPeQlCzuhPLcJ+bMQkTUTGiT8QdU8rc="; }; outputs = [ "out" "dev" "lib" ]; diff --git a/pkgs/applications/science/logic/coq/default.nix b/pkgs/applications/science/logic/coq/default.nix index 8f0f88461e653..25531c6a33af0 100644 --- a/pkgs/applications/science/logic/coq/default.nix +++ b/pkgs/applications/science/logic/coq/default.nix @@ -11,14 +11,13 @@ , ocamlPackages_4_14 , ncurses , buildIde ? null # default is true for Coq < 8.14 and false for Coq >= 8.14 -, glib, gnome, wrapGAppsHook3, makeDesktopItem, copyDesktopItems +, glib, adwaita-icon-theme, wrapGAppsHook3, makeDesktopItem, copyDesktopItems , csdp ? null , version, coq-version ? null }@args: -let lib' = lib; in -let lib = import ../../../../build-support/coq/extra-lib.nix {lib = lib';}; in -with builtins; with lib; let + lib = import ../../../../build-support/coq/extra-lib.nix { inherit (args) lib; }; + release = { "8.5pl1".sha256 = "1976ki5xjg2r907xj9p7gs0kpdinywbwcqlgxqw75dgp0hkgi00n"; "8.5pl2".sha256 = "109rrcrx7mz0fj7725kjjghfg5ydwb24hjsa5hspa27b4caah7rh"; @@ -67,29 +66,29 @@ let { inherit release releaseRev; location = { owner = "coq"; repo = "coq";}; } args.version; version = fetched.version; - coq-version = args.coq-version or (if version != "dev" then versions.majorMinor version else "dev"); - coqAtLeast = v: coq-version == "dev" || versionAtLeast coq-version v; + coq-version = args.coq-version or (if version != "dev" then lib.versions.majorMinor version else "dev"); + coqAtLeast = v: coq-version == "dev" || lib.versionAtLeast coq-version v; buildIde = args.buildIde or (!coqAtLeast "8.14"); - ideFlags = optionalString (buildIde && !coqAtLeast "8.10") + ideFlags = lib.optionalString (buildIde && !coqAtLeast "8.10") "-lablgtkdir ${ocamlPackages.lablgtk}/lib/ocaml/*/site-lib/lablgtk2 -coqide opt"; csdpPatch = lib.optionalString (csdp != null) '' substituteInPlace plugins/micromega/sos.ml --replace "; csdp" "; ${csdp}/bin/csdp" substituteInPlace plugins/micromega/coq_micromega.ml --replace "System.is_in_system_path \"csdp\"" "true" ''; ocamlPackages = if customOCamlPackages != null then customOCamlPackages - else with versions; switch coq-version [ - { case = range "8.16" "8.18"; out = ocamlPackages_4_14; } - { case = range "8.14" "8.15"; out = ocamlPackages_4_12; } - { case = range "8.11" "8.13"; out = ocamlPackages_4_10; } - { case = range "8.7" "8.10"; out = ocamlPackages_4_09; } - { case = range "8.5" "8.6"; out = ocamlPackages_4_05; } + else lib.switch coq-version [ + { case = lib.versions.range "8.16" "8.18"; out = ocamlPackages_4_14; } + { case = lib.versions.range "8.14" "8.15"; out = ocamlPackages_4_12; } + { case = lib.versions.range "8.11" "8.13"; out = ocamlPackages_4_10; } + { case = lib.versions.range "8.7" "8.10"; out = ocamlPackages_4_09; } + { case = lib.versions.range "8.5" "8.6"; out = ocamlPackages_4_05; } ] ocamlPackages_4_14; - ocamlNativeBuildInputs = with ocamlPackages; [ ocaml findlib ] - ++ optional (coqAtLeast "8.14") dune_3; + ocamlNativeBuildInputs = [ ocamlPackages.ocaml ocamlPackages.findlib ] + ++ lib.optional (coqAtLeast "8.14") ocamlPackages.dune_3; ocamlPropagatedBuildInputs = [ ] - ++ optional (!coqAtLeast "8.10") ocamlPackages.camlp5 - ++ optional (!coqAtLeast "8.13") ocamlPackages.num - ++ optional (coqAtLeast "8.13") ocamlPackages.zarith; + ++ lib.optional (!coqAtLeast "8.10") ocamlPackages.camlp5 + ++ lib.optional (!coqAtLeast "8.13") ocamlPackages.num + ++ lib.optional (coqAtLeast "8.13") ocamlPackages.zarith; self = stdenv.mkDerivation { pname = "coq"; inherit (fetched) version src; @@ -111,7 +110,7 @@ self = stdenv.mkDerivation { (coq-prog-args)) (mapc (lambda (arg) (when (file-directory-p (concat arg "/lib/coq/${coq-version}/user-contrib")) - (setenv "COQPATH" (concat (getenv "COQPATH") ":" arg "/lib/coq/${coq-version}/user-contrib")))) '(${concatStringsSep " " (map (pkg: "\"${pkg}\"") pkgs)})) + (setenv "COQPATH" (concat (getenv "COQPATH") ":" arg "/lib/coq/${coq-version}/user-contrib")))) '(${lib.concatStringsSep " " (map (pkg: "\"${pkg}\"") pkgs)})) ; TODO Abstract this pattern from here and nixBufferBuilders.withPackages! (defvar nixpkgs--coq-buffer-count 0) (when (eq nixpkgs--coq-buffer-count 0) @@ -148,13 +147,13 @@ self = stdenv.mkDerivation { nativeBuildInputs = [ pkg-config ] ++ ocamlNativeBuildInputs - ++ optional buildIde copyDesktopItems - ++ optional (buildIde && coqAtLeast "8.10") wrapGAppsHook3 - ++ optional (!coqAtLeast "8.6") gnumake42; + ++ lib.optional buildIde copyDesktopItems + ++ lib.optional (buildIde && coqAtLeast "8.10") wrapGAppsHook3 + ++ lib.optional (!coqAtLeast "8.6") gnumake42; buildInputs = [ ncurses ] - ++ optionals buildIde + ++ lib.optionals buildIde (if coqAtLeast "8.10" - then [ ocamlPackages.lablgtk3-sourceview3 glib gnome.adwaita-icon-theme ] + then [ ocamlPackages.lablgtk3-sourceview3 glib adwaita-icon-theme ] else [ ocamlPackages.lablgtk ]) ; @@ -188,12 +187,12 @@ self = stdenv.mkDerivation { prefixKey = "-prefix "; - buildFlags = [ "revision" "coq" ] ++ optional buildIde "coqide" ++ optional (!coqAtLeast "8.14") "bin/votour"; + buildFlags = [ "revision" "coq" ] ++ lib.optional buildIde "coqide" ++ lib.optional (!coqAtLeast "8.14") "bin/votour"; enableParallelBuilding = true; createFindlibDestdir = true; - desktopItems = optional buildIde (makeDesktopItem { + desktopItems = lib.optional buildIde (makeDesktopItem { name = "coqide"; exec = "coqide"; icon = "coq"; @@ -202,18 +201,18 @@ self = stdenv.mkDerivation { categories = [ "Development" "Science" "Math" "IDE" "GTK" ]; }); - postInstall = let suffix = optionalString (coqAtLeast "8.14") "-core"; in optionalString (!coqAtLeast "8.17") '' + postInstall = let suffix = lib.optionalString (coqAtLeast "8.14") "-core"; in lib.optionalString (!coqAtLeast "8.17") '' cp bin/votour $out/bin/ '' + '' ln -s $out/lib/coq${suffix} $OCAMLFIND_DESTDIR/coq${suffix} - '' + optionalString (coqAtLeast "8.14") '' + '' + lib.optionalString (coqAtLeast "8.14") '' ln -s $out/lib/coqide-server $OCAMLFIND_DESTDIR/coqide-server - '' + optionalString buildIde '' + '' + lib.optionalString buildIde '' mkdir -p "$out/share/pixmaps" ln -s "$out/share/coq/coq.png" "$out/share/pixmaps/" ''; - meta = { + meta = with lib; { description = "Coq proof assistant"; longDescription = '' Coq is a formal proof management system. It provides a formal language diff --git a/pkgs/applications/science/logic/cvc5/default.nix b/pkgs/applications/science/logic/cvc5/default.nix index 93a05e97ff9e1..c3b9af935dd55 100644 --- a/pkgs/applications/science/logic/cvc5/default.nix +++ b/pkgs/applications/science/logic/cvc5/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "cvc5"; - version = "1.1.2"; + version = "1.2.0"; src = fetchFromGitHub { owner = "cvc5"; repo = "cvc5"; rev = "cvc5-${version}"; - hash = "sha256-v+3/2IUslQOySxFDYgTBWJIDnyjbU2RPdpfLcIkEtgQ="; + hash = "sha256-d5F4KwPQ1nwYJbEidQsvqyaGwEugo291SpsJE2rr558="; }; nativeBuildInputs = [ pkg-config cmake flex ]; diff --git a/pkgs/applications/science/logic/dafny/default.nix b/pkgs/applications/science/logic/dafny/default.nix index f85e6cf22879d..93ae5c92b32fe 100644 --- a/pkgs/applications/science/logic/dafny/default.nix +++ b/pkgs/applications/science/logic/dafny/default.nix @@ -8,32 +8,37 @@ buildDotnetModule rec { pname = "Dafny"; - version = "4.6.0"; + version = "4.7.0"; src = fetchFromGitHub { owner = "dafny-lang"; repo = "dafny"; rev = "v${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/hol/default.nix b/pkgs/applications/science/logic/hol/default.nix index de47df098da13..f23dce326dd57 100644 --- a/pkgs/applications/science/logic/hol/default.nix +++ b/pkgs/applications/science/logic/hol/default.nix @@ -4,16 +4,12 @@ let pname = "hol4"; vnum = "14"; -in -let version = "k.${vnum}"; longVersion = "kananaskis-${vnum}"; holsubdir = "hol-${longVersion}"; kernelFlag = if experimentalKernel then "--expk" else "--stdknl"; -in -let polymlEnableShared = with pkgs; lib.overrideDerivation polyml (attrs: { configureFlags = [ "--enable-shared" ]; }); diff --git a/pkgs/applications/science/logic/hol_light/0004-Fix-compilation-with-camlp5-7.11.patch b/pkgs/applications/science/logic/hol_light/0004-Fix-compilation-with-camlp5-7.11.patch new file mode 100644 index 0000000000000..2fc2b1544c442 --- /dev/null +++ b/pkgs/applications/science/logic/hol_light/0004-Fix-compilation-with-camlp5-7.11.patch @@ -0,0 +1,66 @@ +From: Stephane Glondu <steph@glondu.net> +Date: Wed, 12 Feb 2020 05:42:32 +0100 +Subject: Fix compilation with camlp5 7.11 + +--- + pa_j_4.xx_7.xx.ml | 17 +++++++++++------ + 1 file changed, 11 insertions(+), 6 deletions(-) + +diff --git a/pa_j_4.xx_7.xx.ml b/pa_j_4.xx_7.xx.ml +index 4f7ed60..e834058 100755 +--- a/pa_j/pa_j_4.xx_7.xx.ml ++++ b/pa_j/pa_j_4.xx_7.xx.ml +@@ -410,9 +410,10 @@ and reloc_module_type floc sh = + | MtApp loc x1 x2 → + let loc = floc loc in + MtApp loc (self x1) (self x2) +- | MtFun loc x1 x2 x3 → ++ | MtFun loc x x3 → + let loc = floc loc in +- MtFun loc x1 (self x2) (self x3) ++ let x = vala_map (option_map (fun (x1, x2) -> (x1, self x2))) x in ++ MtFun loc x (self x3) + | MtLid loc x1 → + let loc = floc loc in + MtLid loc x1 +@@ -507,9 +508,10 @@ and reloc_module_expr floc sh = + | MeApp loc x1 x2 → + let loc = floc loc in + MeApp loc (self x1) (self x2) +- | MeFun loc x1 x2 x3 → ++ | MeFun loc x x3 → + let loc = floc loc in +- MeFun loc x1 (reloc_module_type floc sh x2) (self x3) ++ let x = vala_map (option_map (fun (x1, x2) -> (x1, reloc_module_type floc sh x2))) x in ++ MeFun loc x (self x3) + | MeStr loc x1 → + let loc = floc loc in + MeStr loc (vala_map (List.map (reloc_str_item floc sh)) x1) +@@ -2007,7 +2009,7 @@ EXTEND + | -> <:vala< [] >> ] ] + ; + mod_binding: +- [ [ i = V UIDENT; me = mod_fun_binding -> (i, me) ] ] ++ [ [ i = V uidopt "uidopt"; me = mod_fun_binding -> (i, me) ] ] + ; + mod_fun_binding: + [ RIGHTA +@@ -2070,7 +2072,7 @@ EXTEND + <:sig_item< value $lid:i$ : $t$ >> ] ] + ; + mod_decl_binding: +- [ [ i = V UIDENT; mt = module_declaration -> (i, mt) ] ] ++ [ [ i = V uidopt "uidopt"; mt = module_declaration -> (i, mt) ] ] + ; + module_declaration: + [ RIGHTA +@@ -2092,6 +2094,9 @@ EXTEND + | "module"; i = V mod_ident ""; ":="; me = module_expr -> + <:with_constr< module $_:i$ := $me$ >> ] ] + ; ++ uidopt: ++ [ [ m = V UIDENT -> Some m ] ] ++ ; + (* Core expressions *) + expr: + [ "top" RIGHTA diff --git a/pkgs/applications/science/logic/hol_light/default.nix b/pkgs/applications/science/logic/hol_light/default.nix index 0e3dee4b0c0ad..59389f11a2828 100644 --- a/pkgs/applications/science/logic/hol_light/default.nix +++ b/pkgs/applications/science/logic/hol_light/default.nix @@ -1,4 +1,4 @@ -{ lib, stdenv, runtimeShell, fetchFromGitHub, fetchpatch, ocaml, findlib, num, zarith, camlp5, camlp-streams }: +{ lib, stdenv, runtimeShell, fetchFromGitHub, ocaml, findlib, num, zarith, camlp5, camlp-streams }: let use_zarith = lib.versionAtLeast ocaml.version "4.14"; @@ -28,21 +28,16 @@ in stdenv.mkDerivation { pname = "hol_light"; - version = "unstable-2024-05-10"; + version = "unstable-2024-07-07"; src = fetchFromGitHub { owner = "jrh13"; repo = "hol-light"; - rev = "d8366986e22555c4e4c8ff49667d646d15c35f14"; - hash = "sha256-dN9X7yQlFof759I5lxxL4DxDe8V3XAhCRaryO9NabY4="; + rev = "16b184e30e7e3fe9add7d1ee93242323ed2e1726"; + hash = "sha256-V0OtsmX5pa+CH3ZXmNG3juXwXZ5+A0k13eMCAfaRziQ="; }; - patches = [ - (fetchpatch { - url = "https://salsa.debian.org/ocaml-team/hol-light/-/raw/master/debian/patches/0004-Fix-compilation-with-camlp5-7.11.patch"; - sha256 = "180qmxbrk3vb1ix7j77hcs8vsar91rs11s5mm8ir5352rz7ylicr"; - }) - ]; + patches = [ ./0004-Fix-compilation-with-camlp5-7.11.patch ]; strictDeps = true; diff --git a/pkgs/applications/science/logic/isabelle/components/default.nix b/pkgs/applications/science/logic/isabelle/components/default.nix deleted file mode 100644 index dd7b605f56af0..0000000000000 --- a/pkgs/applications/science/logic/isabelle/components/default.nix +++ /dev/null @@ -1,5 +0,0 @@ -{ callPackage }: - -{ - isabelle-linter = callPackage ./isabelle-linter.nix {}; -} diff --git a/pkgs/applications/science/logic/isabelle/components/isabelle-linter.nix b/pkgs/applications/science/logic/isabelle/components/isabelle-linter.nix deleted file mode 100644 index 91bf5ba32b68e..0000000000000 --- a/pkgs/applications/science/logic/isabelle/components/isabelle-linter.nix +++ /dev/null @@ -1,35 +0,0 @@ -{ stdenv, lib, fetchFromGitHub, isabelle }: - -stdenv.mkDerivation rec { - pname = "isabelle-linter"; - version = "2023-1.0.0"; - - src = fetchFromGitHub { - owner = "isabelle-prover"; - repo = "isabelle-linter"; - rev = "Isabelle2023-v1.0.0"; - sha256 = "sha256-q9+qN94NaTzvhbcNQj7yH/VVfs1QgCH8OU8HW+5+s9U="; - }; - - nativeBuildInputs = [ isabelle ]; - - buildPhase = '' - export HOME=$TMP - isabelle components -u $(pwd) - isabelle scala_build - ''; - - installPhase = '' - dir=$out/Isabelle${isabelle.version}/contrib/${pname}-${version} - mkdir -p $dir - cp -r * $dir/ - ''; - - meta = with lib; { - description = "Linter component for Isabelle"; - homepage = "https://github.com/isabelle-prover/isabelle-linter"; - maintainers = with maintainers; [ jvanbruegge ]; - license = licenses.mit; - platforms = platforms.all; - }; -} diff --git a/pkgs/applications/science/logic/isabelle/default.nix b/pkgs/applications/science/logic/isabelle/default.nix deleted file mode 100644 index edc4483bcfa98..0000000000000 --- a/pkgs/applications/science/logic/isabelle/default.nix +++ /dev/null @@ -1,251 +0,0 @@ -{ lib -, stdenv -, fetchurl -, coreutils -, nettools -, java -, scala_3 -, polyml -, veriT -, vampire -, eprover-ho -, naproche -, rlwrap -, perl -, makeDesktopItem -, isabelle-components -, symlinkJoin -, fetchhg -}: - -let - sha1 = stdenv.mkDerivation { - pname = "isabelle-sha1"; - version = "2021-1"; - - src = fetchhg { - url = "https://isabelle.sketis.net/repos/sha1"; - rev = "e0239faa6f42"; - sha256 = "sha256-4sxHzU/ixMAkSo67FiE6/ZqWJq9Nb9OMNhMoXH2bEy4="; - }; - - buildPhase = (if stdenv.isDarwin then '' - LDFLAGS="-dynamic -undefined dynamic_lookup -lSystem" - '' else '' - LDFLAGS="-fPIC -shared" - '') + '' - CFLAGS="-fPIC -I." - $CC $CFLAGS -c sha1.c -o sha1.o - $LD $LDFLAGS sha1.o -o libsha1.so - ''; - - installPhase = '' - mkdir -p $out/lib - cp libsha1.so $out/lib/ - ''; - }; -in stdenv.mkDerivation (finalAttrs: rec { - pname = "isabelle"; - version = "2023"; - - dirname = "Isabelle${version}"; - - src = - if stdenv.isDarwin - then - fetchurl - { - url = "https://isabelle.in.tum.de/website-${dirname}/dist/${dirname}_macos.tar.gz"; - sha256 = "sha256-0VSW2SrHNI3/k4cCCZ724ruXaq7W1NCPsLrXFZ9l1/Q="; - } - else if stdenv.hostPlatform.isx86 - then - fetchurl { - url = "https://isabelle.in.tum.de/website-${dirname}/dist/${dirname}_linux.tar.gz"; - sha256 = "sha256-Go4ZCsDz5gJ7uWG5VLrNJOddMPX18G99FAadpX53Rqg="; - } - else - fetchurl { - url = "https://isabelle.in.tum.de/website-${dirname}/dist/${dirname}_linux_arm.tar.gz"; - hash = "sha256-Tzxxs0gKw6vymbaXIzH8tK5VgUrpOIp9vcWQ/zxnRCc="; - }; - - nativeBuildInputs = [ java ]; - - buildInputs = [ polyml veriT vampire eprover-ho nettools ] - ++ lib.optionals (!stdenv.isDarwin) [ java ]; - - sourceRoot = "${dirname}${lib.optionalString stdenv.isDarwin ".app"}"; - - doCheck = stdenv.hostPlatform.system != "aarch64-linux"; - checkPhase = "bin/isabelle build -v HOL-SMT_Examples"; - - postUnpack = lib.optionalString stdenv.isDarwin '' - mv $sourceRoot ${dirname} - sourceRoot=${dirname} - ''; - - postPatch = '' - patchShebangs lib/Tools/ bin/ - - cat >contrib/verit-*/etc/settings <<EOF - ISABELLE_VERIT=${veriT}/bin/veriT - EOF - - cat >contrib/e-*/etc/settings <<EOF - E_HOME=${eprover-ho}/bin - E_VERSION=${eprover-ho.version} - EOF - - cat >contrib/vampire-*/etc/settings <<EOF - VAMPIRE_HOME=${vampire}/bin - VAMPIRE_VERSION=${vampire.version} - VAMPIRE_EXTRA_OPTIONS="--mode casc" - EOF - - cat >contrib/polyml-*/etc/settings <<EOF - ML_SYSTEM_64=true - ML_SYSTEM=${polyml.name} - ML_PLATFORM=${stdenv.system} - ML_HOME=${polyml}/bin - ML_OPTIONS="--minheap 1000" - POLYML_HOME="\$COMPONENT" - ML_SOURCES="\$POLYML_HOME/src" - EOF - - cat >contrib/jdk*/etc/settings <<EOF - ISABELLE_JAVA_PLATFORM=${stdenv.system} - ISABELLE_JDK_HOME=${java} - EOF - - '' + lib.optionalString stdenv.hostPlatform.isx86 '' - rm contrib/naproche-*/x86*/Naproche-SAD - ln -s ${naproche}/bin/Naproche-SAD contrib/naproche-*/x86*/ - '' + '' - - echo ISABELLE_LINE_EDITOR=${rlwrap}/bin/rlwrap >>etc/settings - - for comp in contrib/jdk* contrib/polyml-* contrib/verit-* contrib/vampire-* contrib/e-*; do - rm -rf $comp/${if stdenv.hostPlatform.isx86 then "x86" else "arm"}* - done - - substituteInPlace lib/Tools/env \ - --replace /usr/bin/env ${coreutils}/bin/env - - substituteInPlace src/Tools/Setup/src/Environment.java \ - --replace 'cmd.add("/usr/bin/env");' "" \ - --replace 'cmd.add("bash");' "cmd.add(\"$SHELL\");" - - substituteInPlace src/Pure/General/sha1.ML \ - --replace '"$ML_HOME/" ^ (if ML_System.platform_is_windows then "sha1.dll" else "libsha1.so")' '"${sha1}/lib/libsha1.so"' - - rm -r heaps - '' + lib.optionalString (stdenv.hostPlatform.system == "x86_64-darwin") '' - substituteInPlace lib/scripts/isabelle-platform \ - --replace 'ISABELLE_APPLE_PLATFORM64=arm64-darwin' "" - '' + lib.optionalString stdenv.isLinux '' - arch=${if stdenv.hostPlatform.system == "x86_64-linux" then "x86_64-linux" - else if stdenv.hostPlatform.isx86 then "x86-linux" - else "arm64-linux"} - for f in contrib/*/$arch/{z3,epclextract,nunchaku,SPASS,zipperposition}; do - patchelf --set-interpreter $(cat ${stdenv.cc}/nix-support/dynamic-linker) "$f"${lib.optionalString stdenv.isAarch64 " || true"} - done - patchelf --set-interpreter $(cat ${stdenv.cc}/nix-support/dynamic-linker) contrib/bash_process-*/platform_$arch/bash_process - for d in contrib/kodkodi-*/jni/$arch; do - patchelf --set-rpath "${lib.concatStringsSep ":" [ "${java}/lib/openjdk/lib/server" "${stdenv.cc.cc.lib}/lib" ]}" $d/*.so - done - patchelf --set-rpath "${stdenv.cc.cc.lib}/lib" contrib/z3-*/$arch/z3 - ''; - - buildPhase = '' - export HOME=$TMP # The build fails if home is not set - setup_name=$(basename contrib/isabelle_setup*) - - #The following is adapted from https://isabelle.sketis.net/repos/isabelle/file/Isabelle2021-1/Admin/lib/Tools/build_setup - TARGET_DIR="contrib/$setup_name/lib" - rm -rf "$TARGET_DIR" - mkdir -p "$TARGET_DIR/isabelle/setup" - declare -a ARGS=("-Xlint:unchecked") - - SOURCES="$(${perl}/bin/perl -e 'while (<>) { if (m/(\S+\.java)/) { print "$1 "; } }' "src/Tools/Setup/etc/build.props")" - for SRC in $SOURCES - do - ARGS["''${#ARGS[@]}"]="src/Tools/Setup/$SRC" - done - echo "Building isabelle setup" - javac -d "$TARGET_DIR" -classpath "${scala_3.bare}/lib/scala3-interfaces-${scala_3.version}.jar:${scala_3.bare}/lib/scala3-compiler_3-${scala_3.version}.jar" "''${ARGS[@]}" - jar -c -f "$TARGET_DIR/isabelle_setup.jar" -e "isabelle.setup.Setup" -C "$TARGET_DIR" isabelle - rm -rf "$TARGET_DIR/isabelle" - - echo "Building HOL heap" - bin/isabelle build -v -o system_heaps -b HOL - ''; - - installPhase = '' - mkdir -p $out/bin - mv $TMP/$dirname $out - cd $out/$dirname - bin/isabelle install $out/bin - - # icon - mkdir -p "$out/share/icons/hicolor/isabelle/apps" - cp "$out/Isabelle${version}/lib/icons/isabelle.xpm" "$out/share/icons/hicolor/isabelle/apps/" - - # desktop item - mkdir -p "$out/share" - cp -r "${desktopItem}/share/applications" "$out/share/applications" - ''; - - desktopItem = makeDesktopItem { - name = "isabelle"; - exec = "isabelle jedit"; - icon = "isabelle"; - desktopName = "Isabelle"; - comment = meta.description; - categories = [ "Education" "Science" "Math" ]; - }; - - meta = with lib; { - description = "A generic proof assistant"; - - longDescription = '' - Isabelle is a generic proof assistant. It allows mathematical formulas - to be expressed in a formal language and provides tools for proving those - formulas in a logical calculus. - ''; - homepage = "https://isabelle.in.tum.de/"; - sourceProvenance = with sourceTypes; [ - fromSource - binaryNativeCode # source bundles binary dependencies - ]; - license = licenses.bsd3; - maintainers = [ maintainers.jwiegley maintainers.jvanbruegge ]; - platforms = platforms.unix; - }; - - passthru.withComponents = f: - let - isabelle = finalAttrs.finalPackage; - base = "$out/${isabelle.dirname}"; - components = f isabelle-components; - in symlinkJoin { - name = "isabelle-with-components-${isabelle.version}"; - paths = [ isabelle ] ++ (builtins.map (c: c.override { inherit isabelle; }) components); - - postBuild = '' - rm $out/bin/* - - cd ${base} - rm bin/* - cp ${isabelle}/${isabelle.dirname}/bin/* bin/ - rm etc/components - cat ${isabelle}/${isabelle.dirname}/etc/components > etc/components - - export HOME=$TMP - bin/isabelle install $out/bin - patchShebangs $out/bin - '' + lib.concatMapStringsSep "\n" (c: '' - echo contrib/${c.pname}-${c.version} >> ${base}/etc/components - '') components; - }; -}) diff --git a/pkgs/applications/science/logic/key/default.nix b/pkgs/applications/science/logic/key/default.nix index 5a48abfc4aa48..0cd5e90cbb504 100644 --- a/pkgs/applications/science/logic/key/default.nix +++ b/pkgs/applications/science/logic/key/default.nix @@ -2,7 +2,6 @@ , fetchurl , jdk , gradle_7 -, perl , jre , makeWrapper , makeDesktopItem @@ -12,6 +11,9 @@ }: let + gradle = gradle_7; + +in stdenv.mkDerivation rec { pname = "key"; version = "2.10.0"; src = fetchurl { @@ -20,30 +22,6 @@ let }; sourceRoot = "key-${version}/key"; - # fake build to pre-download deps into fixed-output derivation - deps = stdenv.mkDerivation { - pname = "${pname}-deps"; - inherit version src sourceRoot; - nativeBuildInputs = [ gradle_7 perl ]; - buildPhase = '' - export GRADLE_USER_HOME=$(mktemp -d) - # https://github.com/gradle/gradle/issues/4426 - ${lib.optionalString stdenv.isDarwin "export TERM=dumb"} - gradle --no-daemon classes testClasses - ''; - # perl code mavenizes pathes (com.squareup.okio/okio/1.13.0/a9283170b7305c8d92d25aff02a6ab7e45d06cbe/okio-1.13.0.jar -> com/squareup/okio/okio/1.13.0/okio-1.13.0.jar) - installPhase = '' - find $GRADLE_USER_HOME/caches/modules-2 -type f -regex '.*\.\(jar\|pom\)' \ - | perl -pe 's#(.*/([^/]+)/([^/]+)/([^/]+)/[0-9a-f]{30,40}/([^/\s]+))$# ($x = $2) =~ tr|\.|/|; "install -Dm444 $1 \$out/$x/$3/$4/$5" #e' \ - | sh - ''; - outputHashMode = "recursive"; - outputHashAlgo = "sha256"; - outputHash = "sha256-GjBUwJxeyJA6vGrPQVtNpcHb4CJlNlY4kHt1PT21xjo="; - }; -in stdenv.mkDerivation rec { - inherit pname version src sourceRoot; - nativeBuildInputs = [ jdk gradle_7 @@ -65,23 +43,15 @@ in stdenv.mkDerivation rec { }) ]; - # disable tests (broken on darwin) - gradleAction = if stdenv.isDarwin then "assemble" else "build"; - - buildPhase = '' - runHook preBuild + mitmCache = gradle.fetchDeps { + inherit pname; + data = ./deps.json; + }; - export GRADLE_USER_HOME=$(mktemp -d) - # https://github.com/gradle/gradle/issues/4426 - ${lib.optionalString stdenv.isDarwin "export TERM=dumb"} - # point to offline repo - sed -ie "s#repositories {#repositories { maven { url '${deps}' }#g" build.gradle - cat <(echo "pluginManagement { repositories { maven { url '${deps}' } } }") settings.gradle > settings_new.gradle - mv settings_new.gradle settings.gradle - gradle --offline --no-daemon ${gradleAction} + __darwinAllowLocalNetworking = true; - runHook postBuild - ''; + # tests are broken on darwin + doCheck = !stdenv.isDarwin; installPhase = '' runHook preInstall diff --git a/pkgs/applications/science/logic/key/deps.json b/pkgs/applications/science/logic/key/deps.json new file mode 100644 index 0000000000000..4d6dee8060f9d --- /dev/null +++ b/pkgs/applications/science/logic/key/deps.json @@ -0,0 +1,387 @@ +{ + "!comment": "This is a nixpkgs Gradle dependency lockfile. For more details, refer to the Gradle section in the nixpkgs manual.", + "!version": 1, + "https://plugins.gradle.org/m2": { + "ca/coglinc#javacc-gradle-plugin/2.4.0": { + "jar": "sha256-RsMHTru+ENUOzWkQpiYxCkE5FlZ5Ct0JF+kBp9afidw=", + "pom": "sha256-NTSsuHwtwH2hAqOP1wn1oANHgSkM+gcjPZTLXMOiyrA=" + }, + "ca/coglinc/javacc#ca.coglinc.javacc.gradle.plugin/2.4.0": { + "pom": "sha256-zmWjvt7VamHG21s6/cHApVuH6mvAewTxamaqn8DP2jw=" + }, + "com/github/hierynomus/license-base#com.github.hierynomus.license-base.gradle.plugin/0.15.0": { + "pom": "sha256-jWmQF6e7GyViPR4EGOKapRwtUYEHkgNaR8PG+hgMSXU=" + }, + "com/github/hierynomus/license-report#com.github.hierynomus.license-report.gradle.plugin/0.15.0": { + "pom": "sha256-OIRMJK0goaid41C254nDEz3FeeD51kZSyQi9uCgwAxM=" + }, + "com/github/johnrengelman/shadow#com.github.johnrengelman.shadow.gradle.plugin/7.1.0": { + "pom": "sha256-mh4hygODDXleq/uKbALOM4QuvCPGd+xqqZ50W1FPKt4=" + }, + "com/google/guava#guava-jdk5/17.0": { + "jar": "sha256-Wb9FZUe23aPO2WjLVvfy0+FEdOLeKWCjLEfjHB5FbGE=", + "pom": "sha256-+MFSYngT1FvE58wXrW7WpkmgIxroGf+44F0ZsgWj22Y=" + }, + "com/google/guava#guava-parent-jdk5/17.0": { + "pom": "sha256-WpYGvCdjKVazwR34h+mz54WFQGiqpOCAjtVmD2Cx+28=" + }, + "com/mycila#license-maven-plugin-parent/3.0": { + "pom": "sha256-DR8XPOud8hKSZ2Z8EMiR5eXXJm2C46hQcGaNtW2wy/o=" + }, + "com/mycila#license-maven-plugin/3.0": { + "jar": "sha256-Ul/o866FI9Be7ac2ZFxB6cMw8CV4K1s95u8Lqs8teMw=", + "pom": "sha256-kmJwjckIctcrvmfLFVITU6feJkgJzh6zLflfvqR2/IM=" + }, + "com/mycila#mycila-pom/3": { + "pom": "sha256-QCd6OyVlPuZDPEaFLacOlzbBmNlLyvbSw0cIqHOjGyY=" + }, + "com/mycila#mycila-xmltool/4.4.ga": { + "jar": "sha256-ddeyvpOBpl9vrDLzEIIhEvgFVm6fipekXY8Tz1UEnOA=", + "pom": "sha256-wMaee7roquvUQOFnjOn1AotD07ToHNQ26Y+BOkvDIrI=" + }, + "com/mycila/xmltool#xmltool/3.3": { + "jar": "sha256-hw+TlnieL0inuPso38BwwvjnSyAHJ0ziPmm2WBEP0pQ=", + "pom": "sha256-64P2FpRcjH37TYDm+QnnKG9SO7EQd4ArzSFr1w6ccXo=" + }, + "commons-io#commons-io/2.11.0": { + "jar": "sha256-lhsvbYfbrMXVSr9Fq3puJJX4m3VZiWLYxyPOqbwhCQg=", + "pom": "sha256-LgFv1+MkS18sIKytg02TqkeQSG7h5FZGQTYaPoMe71k=" + }, + "commons-io#commons-io/2.4": { + "jar": "sha256-zGpB3D6qzJ5ECmvQ0okLINNrTuQI/i1nEi8yi7bgFYE=", + "pom": "sha256-srXdRs+Zj6Ym62+KHBFPYWfI05JpQWTmJTPliY6bMfI=" + }, + "commons-logging#commons-logging/1.1.1": { + "jar": "sha256-zm+RPK0fDbOq1wGG1lxbx//Mmpnj/o4LE3MSgZ98Ni8=", + "pom": "sha256-0PLhbQVOi7l63ZyiZSXrI0b2koCfzSooeH2ozrPDXug=" + }, + "gradle/plugin/com/github/johnrengelman#shadow/7.1.0": { + "jar": "sha256-Bar4oiGwbGeS7hmZYZPolH7zv3Il6nWOUYsywoNxCJA=", + "pom": "sha256-q7tz6sHPSyR/wBbmyohafaFjNk/vyYDICvjTy+jRSQI=" + }, + "gradle/plugin/com/hierynomus/gradle/plugins#license-gradle-plugin/0.15.0": { + "jar": "sha256-gpLVOVy+k7lGe/p64JgC70z9316oNexy6jxKahfw9ZY=", + "pom": "sha256-IAmy13nhNo/tPGzHVwS58EVRv+3tFpk4F0ltrbtDyiw=" + }, + "org/apache#apache/10": { + "pom": "sha256-gC/uznKFLa/L0KQlpgNnxyxcubbqWq5ZSBEoVpGJ2vk=" + }, + "org/apache#apache/13": { + "pom": "sha256-/1E9sDYf1BI3vvR4SWi8FarkeNTsCpSW+BEHLMrzhB0=" + }, + "org/apache#apache/16": { + "pom": "sha256-n4X/L9fWyzCXqkf7QZ7n8OvoaRCfmKup9Oyj9J50pA4=" + }, + "org/apache#apache/23": { + "pom": "sha256-vBBiTgYj82V3+sVjnKKTbTJA7RUvttjVM6tNJwVDSRw=" + }, + "org/apache#apache/4": { + "pom": "sha256-npMjomuo6yOU7+8MltMbcN9XCAhjDcFHyrHnNUHMUZQ=" + }, + "org/apache#apache/9": { + "pom": "sha256-SUbmClR8jtpp87wjxbbw2tz4Rp6kmx0dp940rs/PGN0=" + }, + "org/apache/ant#ant-launcher/1.10.11": { + "jar": "sha256-2rUw33qYC1rI/X6NIIJDrg0+vW3gmxqiznVjYMwu0lY=", + "pom": "sha256-7SoGiCYb624I7FSzgxLx1ILM8aO4Y8R9KNW5CkRtHB4=" + }, + "org/apache/ant#ant-parent/1.10.11": { + "pom": "sha256-V6BTJoLzD6MHQWoiWSnVcQrNpy17Je4IyvmNyCzTXbY=" + }, + "org/apache/ant#ant/1.10.11": { + "jar": "sha256-iMC4m7uq4B4Nn8rpO+eS9au+NAkQb47uhY/fNl28B1Q=", + "pom": "sha256-wiiU2ctGq/XOv27rK8z+TXjhju6jEaDqat3VnftLH+M=" + }, + 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"sha256-tR+IZ8kranIkmVV/w6H96ne9+e9XRyL+kM5DailVlFQ=" + }, + "org/sonatype/oss#oss-parent/9": { + "pom": "sha256-+0AmX5glSCEv+C42LllzKyGH7G8NgBgohcFO8fmCgno=" + } + } +} diff --git a/pkgs/applications/science/logic/lean4/default.nix b/pkgs/applications/science/logic/lean4/default.nix index 2ec05098f4078..3e5398e2b7849 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 = "4.8.0"; + version = "4.9.0"; src = fetchFromGitHub { owner = "leanprover"; repo = "lean4"; rev = "v${finalAttrs.version}"; - hash = "sha256-R75RrAQb/tRTtMvy/ddLl1KQaA7V71nocvjIS9geMrg="; + hash = "sha256-wi7outnKpz60to6Z7MSGAKK6COxmpJo6iu6Re86jqlo="; }; postPatch = '' @@ -62,7 +62,7 @@ stdenv.mkDerivation (finalAttrs: { changelog = "https://github.com/leanprover/lean4/blob/${finalAttrs.src.rev}/RELEASES.md"; license = licenses.asl20; platforms = platforms.all; - maintainers = with maintainers; [ ]; + maintainers = with maintainers; [ danielbritten ]; mainProgram = "lean"; }; }) diff --git a/pkgs/applications/science/logic/monosat/default.nix b/pkgs/applications/science/logic/monosat/default.nix index 067ba8ceb1b33..1bd2d29d45059 100644 --- a/pkgs/applications/science/logic/monosat/default.nix +++ b/pkgs/applications/science/logic/monosat/default.nix @@ -3,8 +3,6 @@ # annoying and break the python library, so let's not bother for now includeJava ? !stdenv.hostPlatform.isDarwin, includeGplCode ? true }: -with lib; - let boolToCmake = x: if x then "ON" else "OFF"; @@ -52,14 +50,14 @@ let "-DCMAKE_SKIP_BUILD_RPATH=ON" ]; - postInstall = optionalString includeJava '' + postInstall = lib.optionalString includeJava '' mkdir -p $out/share/java cp monosat.jar $out/share/java ''; passthru = { inherit python; }; - meta = { + meta = with lib; { description = "SMT solver for Monotonic Theories"; mainProgram = "monosat"; platforms = platforms.unix; diff --git a/pkgs/applications/science/logic/msat/default.nix b/pkgs/applications/science/logic/msat/default.nix index 299fe95224eba..3c27493baff87 100644 --- a/pkgs/applications/science/logic/msat/default.nix +++ b/pkgs/applications/science/logic/msat/default.nix @@ -1,4 +1,4 @@ -{ lib, ocamlPackages }: +{ ocamlPackages }: with ocamlPackages; buildDunePackage { pname = "msat-bin"; diff --git a/pkgs/applications/science/logic/naproche/default.nix b/pkgs/applications/science/logic/naproche/default.nix deleted file mode 100644 index d2070ba8240ff..0000000000000 --- a/pkgs/applications/science/logic/naproche/default.nix +++ /dev/null @@ -1,35 +0,0 @@ -{ lib, fetchFromGitHub, haskellPackages, makeWrapper, eprover }: - -with haskellPackages; mkDerivation { - pname = "Naproche-SAD"; - version = "unstable-2024-01-18"; - - src = fetchFromGitHub { - owner = "naproche"; - repo = "naproche"; - rev = "bb3dbcbd2173e3334bc5bdcd04c07c6836a11387"; - hash = "sha256-DWcowUjy8/VBuhqvDYlVINHssF4KhuzT0L+m1YwUxoE="; - }; - - isExecutable = true; - - buildTools = [ hpack makeWrapper ]; - executableHaskellDepends = [ - base array bytestring containers ghc-prim megaparsec mtl network process - split temporary text threads time transformers uuid - ]; - - prePatch = "hpack"; - doCheck = false; # Tests are broken in upstream - - postInstall = '' - wrapProgram $out/bin/Naproche-SAD \ - --set-default NAPROCHE_EPROVER ${eprover}/bin/eprover - ''; - - homepage = "https://github.com/naproche/naproche#readme"; - description = "Write formal proofs in natural language and LaTeX"; - maintainers = with lib.maintainers; [ jvanbruegge ]; - license = lib.licenses.gpl3Only; - mainProgram = "Naproche-SAD"; -} diff --git a/pkgs/applications/science/logic/prover9/default.nix b/pkgs/applications/science/logic/prover9/default.nix index 5c476be06e4e7..a82e44c8a5109 100644 --- a/pkgs/applications/science/logic/prover9/default.nix +++ b/pkgs/applications/science/logic/prover9/default.nix @@ -41,6 +41,6 @@ stdenv.mkDerivation { the Otter Prover. This is the LADR command-line version. ''; platforms = platforms.linux; - maintainers = with maintainers; [ ]; + maintainers = [ ]; }; } diff --git a/pkgs/applications/science/logic/redprl/default.nix b/pkgs/applications/science/logic/redprl/default.nix index 03117d4e03285..a6354a091665e 100644 --- a/pkgs/applications/science/logic/redprl/default.nix +++ b/pkgs/applications/science/logic/redprl/default.nix @@ -9,7 +9,7 @@ stdenv.mkDerivation { repo = "sml-redprl"; rev = "c72190de76f7ed1cfbe1d2046c96e99ac5022b0c"; fetchSubmodules = true; - sha256 = "sha256-xrQT5o0bsIN+mCYUOz9iY4+j3HGROb1I6R2ADcLy8n4="; + hash = "sha256-xrQT5o0bsIN+mCYUOz9iY4+j3HGROb1I6R2ADcLy8n4="; }; buildInputs = [ mlton ]; diff --git a/pkgs/applications/science/logic/stp/default.nix b/pkgs/applications/science/logic/stp/default.nix index fb41ea07f5a15..1025663b1bd7c 100644 --- a/pkgs/applications/science/logic/stp/default.nix +++ b/pkgs/applications/science/logic/stp/default.nix @@ -1,5 +1,17 @@ -{ lib, stdenv, cmake, boost, bison, flex, fetchFromGitHub, perl -, python3, python3Packages, zlib, minisat, cryptominisat }: +{ lib +, stdenv +, cmake +, boost +, bison +, flex +, fetchFromGitHub +, fetchpatch +, perl +, python3 +, zlib +, minisat +, cryptominisat +}: stdenv.mkDerivation rec { pname = "stp"; @@ -8,14 +20,20 @@ stdenv.mkDerivation rec { src = fetchFromGitHub { owner = "stp"; repo = "stp"; - rev = version; - sha256 = "1yg2v4wmswh1sigk47drwsxyayr472mf4i47lqmlcgn9hhbx1q87"; + rev = version; + hash = "sha256-B+HQF4TJPkYrpodE4qo4JHvlu+a5HTJf1AFyXTnZ4vk="; }; patches = [ # Fix missing type declaration # due to undeterminisitic compilation # of circularly dependent headers ./stdint.patch + + # Python 3.12+ compatibility for build: https://github.com/stp/stp/pull/450 + (fetchpatch { + url = "https://github.com/stp/stp/commit/fb185479e760b6ff163512cb6c30ac9561aadc0e.patch"; + hash = "sha256-guFgeWOrxRrxkU7kMvd5+nmML0rwLYW196m1usE2qiA="; + }) ]; postPatch = '' @@ -26,10 +44,16 @@ stdenv.mkDerivation rec { sed -e '1i #include <cstdint>' -i include/stp/AST/ASTNode.h ''; - buildInputs = [ boost zlib minisat cryptominisat python3 ]; + buildInputs = [ + boost + zlib + minisat + cryptominisat + python3 + ]; nativeBuildInputs = [ cmake bison flex perl ]; preConfigure = '' - python_install_dir=$out/${python3Packages.python.sitePackages} + python_install_dir=$out/${python3.sitePackages} mkdir -p $python_install_dir cmakeFlagsArray=( $cmakeFlagsArray @@ -40,7 +64,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Simple Theorem Prover"; - maintainers = with maintainers; [ McSinyx ]; + maintainers = with maintainers; [ McSinyx numinit ]; platforms = platforms.linux; license = licenses.mit; }; diff --git a/pkgs/applications/science/logic/surelog/default.nix b/pkgs/applications/science/logic/surelog/default.nix index 7b4c85fe9b215..0d795611b95a8 100644 --- a/pkgs/applications/science/logic/surelog/default.nix +++ b/pkgs/applications/science/logic/surelog/default.nix @@ -16,13 +16,13 @@ stdenv.mkDerivation (finalAttrs: { pname = "surelog"; - version = "1.82"; + version = "1.83"; src = fetchFromGitHub { owner = "chipsalliance"; - repo = finalAttrs.pname; + repo = "surelog"; rev = "v${finalAttrs.version}"; - hash = "sha256-iW2mQPmKfbAWaiEURyVly5IjJ3YpXjVBkm/UbUuwb6k="; + hash = "sha256-V4LmW4ca6KfugOu0XnGwutRqWR/9K6ESokHOB2yAVag="; fetchSubmodules = false; # we use all dependencies from nix }; diff --git a/pkgs/applications/science/logic/tlaplus/default.nix b/pkgs/applications/science/logic/tlaplus/default.nix index f478bf204d4f3..f53da73e1e632 100644 --- a/pkgs/applications/science/logic/tlaplus/default.nix +++ b/pkgs/applications/science/logic/tlaplus/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "tlaplus"; - version = "1.7.3"; + version = "1.7.4"; src = fetchurl { url = "https://github.com/tlaplus/tlaplus/releases/download/v${version}/tla2tools.jar"; - sha256 = "sha256-5P8V6oH05voSXAgwBDclSxdxdMalrfaNpElkar4IUZ0="; + sha256 = "sha256-k2omIGHJFGlN/WaaVDviRXPEXVqg/yCouWsj0B4FDog="; }; nativeBuildInputs = [ makeWrapper ]; diff --git a/pkgs/applications/science/logic/uhdm/default.nix b/pkgs/applications/science/logic/uhdm/default.nix index 182f6eb81eeb2..72b55ffbcd7ab 100644 --- a/pkgs/applications/science/logic/uhdm/default.nix +++ b/pkgs/applications/science/logic/uhdm/default.nix @@ -10,13 +10,13 @@ stdenv.mkDerivation (finalAttrs: { pname = "UHDM"; # When updating this package, also consider updating science/logic/surelog - version = "1.82"; + version = "1.83"; src = fetchFromGitHub { owner = "chipsalliance"; - repo = finalAttrs.pname; + repo = "UHDM"; rev = "v${finalAttrs.version}"; - hash = "sha256-sl83l6nLN/bluED5bnFShviD1Vv8hmRazxIcLUg/ego="; + hash = "sha256-va8qAzsg589C6rLmG1uIMDr4X30qpBgRO1ZVKdEs5ok="; fetchSubmodules = false; # we use all dependencies from nix }; diff --git a/pkgs/applications/science/logic/workcraft/default.nix b/pkgs/applications/science/logic/workcraft/default.nix index cc512acad7937..ba95bc2239ab2 100644 --- a/pkgs/applications/science/logic/workcraft/default.nix +++ b/pkgs/applications/science/logic/workcraft/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "workcraft"; - version = "3.4.2"; + version = "3.5.0"; src = fetchurl { url = "https://github.com/workcraft/workcraft/releases/download/v${version}/workcraft-v${version}-linux.tar.gz"; - sha256 = "sha256-+O6fl/+D89L5xrrTaAnBTfw0tFz/CoKLaBa+OHtdnaA="; + sha256 = "sha256-ZOmc83OZVHIt/Sq6KQWuG4/xyeaETL8qJmmSjGcqL60="; }; nativeBuildInputs = [ makeWrapper ]; diff --git a/pkgs/applications/science/logic/yices/default.nix b/pkgs/applications/science/logic/yices/default.nix index de80cd725653f..f29a5e1f3f51f 100644 --- a/pkgs/applications/science/logic/yices/default.nix +++ b/pkgs/applications/science/logic/yices/default.nix @@ -2,20 +2,15 @@ stdenv.mkDerivation rec { pname = "yices"; - # We never want X.Y.${odd} versions as they are moving development tags. - version = "2.6.4"; + version = "2.6.5"; src = fetchFromGitHub { owner = "SRI-CSL"; repo = "yices2"; rev = "Yices-${version}"; - sha256 = "sha256-qdxh86CkKdm65oHcRgaafTG9GUOoIgTDjeWmRofIpNE="; + hash = "sha256-/sKyHkFW5I5kojNIRPEKojzTvfRZiyVIN5VlBIbAV7k="; }; - patches = [ - # musl has no ldconfig, create symlinks explicitly - ./linux-no-ldconfig.patch - ]; postPatch = "patchShebangs tests/regress/check.sh"; nativeBuildInputs = [ autoreconfHook ]; diff --git a/pkgs/applications/science/logic/yices/linux-no-ldconfig.patch b/pkgs/applications/science/logic/yices/linux-no-ldconfig.patch deleted file mode 100644 index bad3da6ad4a28..0000000000000 --- a/pkgs/applications/science/logic/yices/linux-no-ldconfig.patch +++ /dev/null @@ -1,13 +0,0 @@ ---- a/Makefile.build -+++ b/Makefile.build -@@ -474,8 +474,9 @@ install-darwin: install-default - install-solaris: install-default - $(LDCONFIG) -n $(DESTDIR)$(libdir) && (cd $(DESTDIR)$(libdir) && $(LN_S) -f libyices.so.$(YICES_VERSION) libyices.so) - -+# avoid ldconfig as it's not present on musl - install-linux install-unix: install-default -- $(LDCONFIG) -n $(DESTDIR)$(libdir) && (cd $(DESTDIR)$(libdir) && $(LN_S) -f libyices.so.$(YICES_VERSION) libyices.so) -+ (cd $(DESTDIR)$(libdir) && $(LN_S) -f libyices.so.$(YICES_VERSION) libyices.so.$(MAJOR).$(MINOR) && $(LN_S) -f libyices.so.$(MAJOR).$(MINOR) libyices.so) - - # on FreeBSD: the library file is libyices.so.X.Y and ldconfig does not take -n - # TODO: fix this. We must also create a symbolic link: libyices.so.X in libdir diff --git a/pkgs/applications/science/logic/z3/default.nix b/pkgs/applications/science/logic/z3/default.nix index 2db1fc95f7974..a17cc5561cf21 100644 --- a/pkgs/applications/science/logic/z3/default.nix +++ b/pkgs/applications/science/logic/z3/default.nix @@ -16,8 +16,6 @@ assert javaBindings -> jdk != null; assert ocamlBindings -> ocaml != null && findlib != null && zarith != null; -with lib; - let common = { version, sha256, patches ? [ ], tag ? "z3" }: stdenv.mkDerivation rec { pname = "z3"; @@ -32,25 +30,25 @@ let common = { version, sha256, patches ? [ ], tag ? "z3" }: strictDeps = true; nativeBuildInputs = [ python ] - ++ optional stdenv.hostPlatform.isDarwin fixDarwinDylibNames - ++ optional javaBindings jdk - ++ optionals ocamlBindings [ ocaml findlib ] + ++ lib.optional stdenv.hostPlatform.isDarwin fixDarwinDylibNames + ++ lib.optional javaBindings jdk + ++ lib.optionals ocamlBindings [ ocaml findlib ] ; propagatedBuildInputs = [ python.pkgs.setuptools ] - ++ optionals ocamlBindings [ zarith ]; + ++ lib.optionals ocamlBindings [ zarith ]; enableParallelBuilding = true; - postPatch = optionalString ocamlBindings '' + postPatch = lib.optionalString ocamlBindings '' export OCAMLFIND_DESTDIR=$ocaml/lib/ocaml/${ocaml.version}/site-lib mkdir -p $OCAMLFIND_DESTDIR/stublibs ''; - configurePhase = concatStringsSep " " + configurePhase = lib.concatStringsSep " " ( [ "${python.pythonOnBuildForHost.interpreter} scripts/mk_make.py --prefix=$out" ] - ++ optional javaBindings "--java" - ++ optional ocamlBindings "--ml" - ++ optional pythonBindings "--python --pypkgdir=$out/${python.sitePackages}" + ++ lib.optional javaBindings "--java" + ++ lib.optional ocamlBindings "--ml" + ++ lib.optional pythonBindings "--python --pypkgdir=$out/${python.sitePackages}" ) + "\n" + "cd build"; doCheck = true; @@ -63,19 +61,19 @@ let common = { version, sha256, patches ? [ ], tag ? "z3" }: mkdir -p $dev $lib mv $out/lib $lib/lib mv $out/include $dev/include - '' + optionalString pythonBindings '' + '' + lib.optionalString pythonBindings '' mkdir -p $python/lib mv $lib/lib/python* $python/lib/ ln -sf $lib/lib/libz3${stdenv.hostPlatform.extensions.sharedLibrary} $python/${python.sitePackages}/z3/lib/libz3${stdenv.hostPlatform.extensions.sharedLibrary} - '' + optionalString javaBindings '' + '' + lib.optionalString javaBindings '' mkdir -p $java/share/java mv com.microsoft.z3.jar $java/share/java moveToOutput "lib/libz3java.${stdenv.hostPlatform.extensions.sharedLibrary}" "$java" ''; outputs = [ "out" "lib" "dev" "python" ] - ++ optional javaBindings "java" - ++ optional ocamlBindings "ocaml"; + ++ lib.optional javaBindings "java" + ++ lib.optional ocamlBindings "ocaml"; meta = with lib; { description = "High-performance theorem prover and SMT solver"; diff --git a/pkgs/applications/science/machine-learning/finalfrontier/default.nix b/pkgs/applications/science/machine-learning/finalfrontier/default.nix index 1a6e9351d3a79..9dbbe8455d1b2 100644 --- a/pkgs/applications/science/machine-learning/finalfrontier/default.nix +++ b/pkgs/applications/science/machine-learning/finalfrontier/default.nix @@ -20,7 +20,7 @@ rustPlatform.buildRustPackage rec { sha256 = "sha256-bnRzXIYairlBjv2JxU16UXYc5BB3VeKZNiJ4+XDzub4="; }; - cargoSha256 = "sha256-C/D9EPfifyajrCyXE8w/qRuzWEoyJJIcj4xii94/9l4="; + cargoHash = "sha256-C/D9EPfifyajrCyXE8w/qRuzWEoyJJIcj4xii94/9l4="; nativeBuildInputs = [ installShellFiles @@ -47,6 +47,6 @@ rustPlatform.buildRustPackage rec { mainProgram = "finalfrontier"; homepage = "https://github.com/finalfusion/finalfrontier/"; license = licenses.asl20; - maintainers = with maintainers; [ ]; + maintainers = [ ]; }; } diff --git a/pkgs/applications/science/machine-learning/finalfusion-utils/default.nix b/pkgs/applications/science/machine-learning/finalfusion-utils/default.nix index 0df8a0525be51..b6fa984e7d5b0 100644 --- a/pkgs/applications/science/machine-learning/finalfusion-utils/default.nix +++ b/pkgs/applications/science/machine-learning/finalfusion-utils/default.nix @@ -21,7 +21,7 @@ rustPlatform.buildRustPackage rec { sha256 = "sha256-suzivynlgk4VvDOC2dQR40n5IJHoJ736+ObdrM9dIqE="; }; - cargoSha256 = "sha256-HekjmctuzOWs5k/ihhsV8vVkm6906jEnFf3yvhkrA5Y="; + cargoHash = "sha256-HekjmctuzOWs5k/ihhsV8vVkm6906jEnFf3yvhkrA5Y="; nativeBuildInputs = [ installShellFiles ]; @@ -49,7 +49,7 @@ rustPlatform.buildRustPackage rec { description = "Utility for converting, quantizing, and querying word embeddings"; homepage = "https://github.com/finalfusion/finalfusion-utils/"; license = licenses.asl20; - maintainers = with maintainers; [ ]; + maintainers = [ ]; mainProgram = "finalfusion"; }; } diff --git a/pkgs/applications/science/machine-learning/sc2-headless/default.nix b/pkgs/applications/science/machine-learning/sc2-headless/default.nix index d96d71695e757..37128ce67e39d 100644 --- a/pkgs/applications/science/machine-learning/sc2-headless/default.nix +++ b/pkgs/applications/science/machine-learning/sc2-headless/default.nix @@ -57,6 +57,6 @@ in stdenv.mkDerivation rec { url = "https://blzdistsc2-a.akamaihd.net/AI_AND_MACHINE_LEARNING_LICENSE.html"; free = false; }; - maintainers = with lib.maintainers; [ ]; + maintainers = [ ]; }; } diff --git a/pkgs/applications/science/machine-learning/shogun/default.nix b/pkgs/applications/science/machine-learning/shogun/default.nix index 1e317fdec03e3..75bd2278d6069 100644 --- a/pkgs/applications/science/machine-learning/shogun/default.nix +++ b/pkgs/applications/science/machine-learning/shogun/default.nix @@ -53,7 +53,7 @@ let owner = "shogun-toolbox"; repo = "shogun"; rev = "shogun_${version}"; - sha256 = "sha256-38aULxK50wQ2+/ERosSpRyBmssmYSGv5aaWfWSlrSRc="; + hash = "sha256-38aULxK50wQ2+/ERosSpRyBmssmYSGv5aaWfWSlrSRc="; fetchSubmodules = true; }; diff --git a/pkgs/applications/science/machine-learning/starspace/default.nix b/pkgs/applications/science/machine-learning/starspace/default.nix deleted file mode 100644 index f4ca74ef5bbf1..0000000000000 --- a/pkgs/applications/science/machine-learning/starspace/default.nix +++ /dev/null @@ -1,40 +0,0 @@ -{ lib, stdenv, fetchFromGitHub, boost, zlib }: - -stdenv.mkDerivation rec { - pname = "starspace"; - version = "unstable-2019-12-13"; - - src = fetchFromGitHub { - owner = "facebookresearch"; - repo = pname; - rev = "8aee0a950aa607c023e5c91cff518bec335b5df5"; - sha256 = "0sc7a37z1skb9377a1qs8ggwrkz0nmpybx7sms38xj05b702kbvj"; - }; - - buildInputs = [ boost zlib ]; - - makeFlags = [ - "CXX=${stdenv.cc.targetPrefix}c++" - "BOOST_DIR=${boost.dev}/include" - ]; - - preBuild = '' - cp makefile_compress makefile - ''; - - installPhase = '' - mkdir -p $out/bin - mv starspace $out/bin - ''; - - meta = with lib; { - # Does not build against gcc-13. No development activity upstream - # for past few years. - broken = true; - description = "General-purpose neural model for efficient learning of entity embeddings"; - homepage = "https://ai.facebook.com/tools/starspace/"; - license = licenses.mit; - platforms = platforms.unix; - maintainers = [ maintainers.mausch ]; - }; -} diff --git a/pkgs/applications/science/machine-learning/uarmsolver/default.nix b/pkgs/applications/science/machine-learning/uarmsolver/default.nix index 12bca5531364a..2f24f782927bc 100644 --- a/pkgs/applications/science/machine-learning/uarmsolver/default.nix +++ b/pkgs/applications/science/machine-learning/uarmsolver/default.nix @@ -6,13 +6,13 @@ stdenv.mkDerivation rec { pname = "uarmsolver"; - version = "0.2.6"; + version = "0.3.0"; src = fetchFromGitHub { owner = "firefly-cpp"; repo = "uARMSolver"; rev = version; - sha256 = "sha256-E8hc7qoIDaNERMUhVlh+iBvQX1odzd/szeMSh8TCNFo="; + sha256 = "sha256-IMlh6Y5iVouMZatR1uxw0gUNZBdh2qm56s+GEjcr1+M="; }; nativeBuildInputs = [ cmake ]; diff --git a/pkgs/applications/science/math/bcal/default.nix b/pkgs/applications/science/math/bcal/default.nix index 9ba028d1cb650..6e87136170c64 100644 --- a/pkgs/applications/science/math/bcal/default.nix +++ b/pkgs/applications/science/math/bcal/default.nix @@ -33,6 +33,6 @@ stdenv.mkDerivation rec { homepage = "https://github.com/jarun/bcal"; license = licenses.gpl3Only; platforms = platforms.unix; - maintainers = with maintainers; [ ]; + maintainers = [ ]; }; } diff --git a/pkgs/applications/science/math/caffe/default.nix b/pkgs/applications/science/math/caffe/default.nix index 2a84d4b27b141..0f36c4783df78 100644 --- a/pkgs/applications/science/math/caffe/default.nix +++ b/pkgs/applications/science/math/caffe/default.nix @@ -147,7 +147,7 @@ stdenv.mkDerivation rec { Center (BVLC) and by community contributors. ''; homepage = "http://caffe.berkeleyvision.org/"; - maintainers = with maintainers; [ ]; + maintainers = [ ]; broken = (pythonSupport && (python.isPy310)) || cudaSupport diff --git a/pkgs/applications/science/math/geogebra/geogebra6.nix b/pkgs/applications/science/math/geogebra/geogebra6.nix index 38b668804ad16..40169a72e4a6f 100644 --- a/pkgs/applications/science/math/geogebra/geogebra6.nix +++ b/pkgs/applications/science/math/geogebra/geogebra6.nix @@ -1,4 +1,12 @@ -{ lib, stdenv, unzip, fetchurl, electron, makeWrapper, geogebra }: +{ + lib, + stdenv, + unzip, + fetchurl, + electron, + makeWrapper, + geogebra, +}: let pname = "geogebra"; version = "6-0-794-0"; @@ -14,14 +22,17 @@ let calculus in one easy-to-use package. ''; homepage = "https://www.geogebra.org/"; - maintainers = with maintainers; [ voidless sikmir ]; + maintainers = with maintainers; [ + voidless + sikmir + ]; license = licenses.geogebra; sourceProvenance = with sourceTypes; [ binaryBytecode - binaryNativeCode # some jars include native binaries + binaryNativeCode # some jars include native binaries ]; platforms = with platforms; linux ++ darwin; - hydraPlatforms = []; + hydraPlatforms = [ ]; }; linuxPkg = stdenv.mkDerivation { @@ -50,7 +61,9 @@ let installPhase = '' mkdir -p $out/libexec/geogebra/ $out/bin cp -r GeoGebra-linux-x64/{resources,locales} "$out/" - makeWrapper ${lib.getBin electron}/bin/electron $out/bin/geogebra --add-flags "$out/resources/app" + makeWrapper ${lib.getBin electron}/bin/electron $out/bin/geogebra \ + --add-flags "$out/resources/app" \ + --add-flags "\''${NIXOS_OZONE_WL:+\''${WAYLAND_DISPLAY:+--ozone-platform-hint=auto --enable-features=WaylandWindowDecorations}}" install -Dm644 "${desktopItem}/share/applications/"* \ -t $out/share/applications/ @@ -84,6 +97,4 @@ let }; }; in -if stdenv.isDarwin -then darwinPkg -else linuxPkg +if stdenv.isDarwin then darwinPkg else linuxPkg diff --git a/pkgs/applications/science/math/getdp/default.nix b/pkgs/applications/science/math/getdp/default.nix index 8accf9d76725a..18000c147d87e 100644 --- a/pkgs/applications/science/math/getdp/default.nix +++ b/pkgs/applications/science/math/getdp/default.nix @@ -27,7 +27,7 @@ stdenv.mkDerivation rec { ''; homepage = "http://getdp.info/"; license = licenses.gpl2Plus; - maintainers = with maintainers; [ ]; + maintainers = [ ]; platforms = platforms.linux; }; } diff --git a/pkgs/applications/science/math/glsurf/default.nix b/pkgs/applications/science/math/glsurf/default.nix index 38caee5805b43..0edaa32babd70 100644 --- a/pkgs/applications/science/math/glsurf/default.nix +++ b/pkgs/applications/science/math/glsurf/default.nix @@ -5,7 +5,7 @@ , makeWrapper , libGLU , libGL -, freeglut +, libglut , mpfr , gmp , pkgsHostTarget @@ -32,7 +32,7 @@ stdenv.mkDerivation rec { ]); buildInputs = [ - freeglut + libglut libGL libGLU mpfr diff --git a/pkgs/applications/science/math/gurobi/default.nix b/pkgs/applications/science/math/gurobi/default.nix index e8f4794d4179d..eff61579a5f99 100644 --- a/pkgs/applications/science/math/gurobi/default.nix +++ b/pkgs/applications/science/math/gurobi/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "gurobi"; - version = "11.0.2"; + version = "11.0.3"; src = fetchurl { url = "https://packages.gurobi.com/${lib.versions.majorMinor version}/gurobi${version}_linux64.tar.gz"; - hash = "sha256-9DrIo+25h7mgphRSrNnY2+nrNzaMbafONuUkfLKho2g="; + hash = "sha256-gqLIZxwjS7qp3GTaIrGVGr9BxiBH/fdwBOZfJKkd/RM="; }; sourceRoot = "gurobi${builtins.replaceStrings ["."] [""] version}/linux64"; diff --git a/pkgs/applications/science/math/mathematica/generic.nix b/pkgs/applications/science/math/mathematica/generic.nix index 5a96bf1a26252..c1c10f8937ce0 100644 --- a/pkgs/applications/science/math/mathematica/generic.nix +++ b/pkgs/applications/science/math/mathematica/generic.nix @@ -1,4 +1,4 @@ -{ addOpenGLRunpath +{ addDriverRunpath , autoPatchelfHook , lib , makeWrapper @@ -57,7 +57,7 @@ let cudaEnv = symlinkJoin { ]; postBuild = '' if [ ! -e $out/lib/libcuda.so ]; then - ln -s ${addOpenGLRunpath.driverLink}/lib/libcuda.so $out/lib + ln -s ${addDriverRunpath.driverLink}/lib/libcuda.so $out/lib fi ln -s lib $out/lib64 ''; @@ -69,7 +69,7 @@ in stdenv.mkDerivation { nativeBuildInputs = [ autoPatchelfHook makeWrapper - ] ++ lib.optional cudaSupport addOpenGLRunpath; + ] ++ lib.optional cudaSupport addDriverRunpath; buildInputs = [ alsa-lib @@ -136,8 +136,8 @@ in stdenv.mkDerivation { "--set QT_QPA_PLATFORM wayland;xcb" ] ++ lib.optionals cudaSupport [ "--set CUDA_PATH ${cudaEnv}" - "--set NVIDIA_DRIVER_LIBRARY_PATH ${addOpenGLRunpath.driverLink}/lib/libnvidia-tls.so" - "--set CUDA_LIBRARY_PATH ${addOpenGLRunpath.driverLink}/lib/libcuda.so" + "--set NVIDIA_DRIVER_LIBRARY_PATH ${addDriverRunpath.driverLink}/lib/libnvidia-tls.so" + "--set CUDA_LIBRARY_PATH ${addDriverRunpath.driverLink}/lib/libcuda.so" ]; unpackPhase = '' diff --git a/pkgs/applications/science/math/maxima/5.47.0-CVE-2024-34490.patch b/pkgs/applications/science/math/maxima/5.47.0-CVE-2024-34490.patch new file mode 100644 index 0000000000000..008fe725fa895 --- /dev/null +++ b/pkgs/applications/science/math/maxima/5.47.0-CVE-2024-34490.patch @@ -0,0 +1,86 @@ +Based on upstream https://sourceforge.net/p/maxima/code/ci/51704ccb090f6f971b641e4e0b7c1c22c4828bf7/ +adjusted to apply to 5.47.0 + +diff --git a/src/gnuplot_def.lisp b/src/gnuplot_def.lisp +index 80c174bd5..6fdc8da6d 100644 +--- a/src/gnuplot_def.lisp ++++ b/src/gnuplot_def.lisp +@@ -286,7 +286,7 @@ + (format nil "set term postscript eps color solid lw 2 size 16.4 cm, 12.3 cm font \",24\" ~a" gstrings))) + (if (getf plot-options :gnuplot_out_file) + (setq out-file (getf plot-options :gnuplot_out_file)) +- (setq out-file "maxplot.ps"))) ++ (setq out-file (format nil "~a.ps" (random-name 16))))) + ((eq (getf plot-options :gnuplot_term) '$dumb) + (if (getf plot-options :gnuplot_dumb_term_command) + (setq terminal-command +@@ -294,7 +294,7 @@ + (setq terminal-command "set term dumb 79 22")) + (if (getf plot-options :gnuplot_out_file) + (setq out-file (getf plot-options :gnuplot_out_file)) +- (setq out-file "maxplot.txt"))) ++ (setq out-file (format nil "~a.txt" (random-name 16))))) + ((eq (getf plot-options :gnuplot_term) '$default) + (if (getf plot-options :gnuplot_default_term_command) + (setq terminal-command +diff --git a/src/plot.lisp b/src/plot.lisp +index fb2b3136b..8877f7025 100644 +--- a/src/plot.lisp ++++ b/src/plot.lisp +@@ -1755,16 +1755,24 @@ plot3d([cos(y)*(10.0+6*cos(x)), sin(y)*(10.0+6*cos(x)),-6*sin(x)], + + (defvar $xmaxima_plot_command "xmaxima") + ++;; random-file-name ++;; Creates a random word of 'count' alphanumeric characters ++(defun random-name (count) ++ (let ((chars "0123456789abcdefghijklmnopqrstuvwxyz") (name "")) ++ (setf *random-state* (make-random-state t)) ++ (dotimes (i count) ++ (setq name (format nil "~a~a" name (aref chars (random 36))))) ++ name)) ++ + (defun plot-set-gnuplot-script-file-name (options) + (let ((gnuplot-term (getf options :gnuplot_term)) + (gnuplot-out-file (getf options :gnuplot_out_file))) + (if (and (find (getf options :plot_format) '($gnuplot_pipes $gnuplot)) + (eq gnuplot-term '$default) gnuplot-out-file) + (plot-file-path gnuplot-out-file t options) +- (plot-file-path +- (format nil "maxout~d.~(~a~)" +- (getpid) +- (ensure-string (getf options :plot_format))) nil options)))) ++ (plot-file-path (format nil "~a.~a" (random-name 16) ++ (ensure-string (getf options :plot_format))) ++ nil options)))) + + (defun plot-temp-file0 (file &optional (preserve-file nil)) + (let ((filename +@@ -2577,9 +2585,13 @@ plot2d ( x^2+y^2 = 1, [x, -2, 2], [y, -2 ,2]); + (format dest "}~%")) + (format dest "}~%")) + ++; TODO: Check whether this function is still being used (villate 20240325) + (defun show-open-plot (ans file) + (cond ($show_openplot +- (with-open-file (st1 (plot-temp-file (format nil "maxout~d.xmaxima" (getpid))) :direction :output :if-exists :supersede) ++ (with-open-file ++ (st1 (plot-temp-file ++ (format nil "~a.xmaxima" (random-name 16))) ++ :direction :output :if-exists :supersede) + (princ ans st1)) + ($system (concatenate 'string *maxima-prefix* + (if (string= *autoconf-windows* "true") "\\bin\\" "/bin/") +diff --git a/src/xmaxima_def.lisp b/src/xmaxima_def.lisp +index b6513b564..5a13b6141 100644 +--- a/src/xmaxima_def.lisp ++++ b/src/xmaxima_def.lisp +@@ -431,7 +431,7 @@ + (format $pstream "}~%")))))) + + (defmethod plot-shipout ((plot xmaxima-plot) options &optional output-file) +- (let ((file (plot-file-path (format nil "maxout~d.xmaxima" (getpid))))) ++ (let ((file (plot-file-path (format nil "~a.xmaxima" (random-name 16))))) + (cond ($show_openplot + (with-open-file (fl + #+sbcl (sb-ext:native-namestring file) diff --git a/pkgs/applications/science/math/maxima/default.nix b/pkgs/applications/science/math/maxima/default.nix index e7ac178cd5d13..c1458186b2ae1 100644 --- a/pkgs/applications/science/math/maxima/default.nix +++ b/pkgs/applications/science/math/maxima/default.nix @@ -20,11 +20,11 @@ let in stdenv.mkDerivation (finalAttrs: { pname = "maxima"; - version = "5.46.0"; + version = "5.47.0"; src = fetchurl { - url = "mirror://sourceforge/${finalAttrs.pname}/${finalAttrs.pname}-${finalAttrs.version}.tar.gz"; - sha256 = "sha256-c5Dwa0jaZckDPosvYpuXi5AFZFSlQCLbfecOIiWqiwc="; + url = "mirror://sourceforge/maxima/maxima-${finalAttrs.version}.tar.gz"; + sha256 = "sha256-kQQCGyT9U+jAOpg1CctC6TepJejAyFwzXXcJoU/UD3o="; }; nativeBuildInputs = [ @@ -79,6 +79,8 @@ stdenv.mkDerivation (finalAttrs: { url = "https://raw.githubusercontent.com/sagemath/sage/07d6c37d18811e2b377a9689790a7c5e24da16ba/build/pkgs/maxima/patches/undoing_true_false_printing_patch.patch"; sha256 = "0fvi3rcjv6743sqsbgdzazy9jb6r1p1yq63zyj9fx42wd1hgf7yx"; }) + + ./5.47.0-CVE-2024-34490.patch ]; # The test suite is disabled since 5.42.2 because of the following issues: diff --git a/pkgs/applications/science/math/msieve/default.nix b/pkgs/applications/science/math/msieve/default.nix index bda3e5b3a040a..a5af9e844eca4 100644 --- a/pkgs/applications/science/math/msieve/default.nix +++ b/pkgs/applications/science/math/msieve/default.nix @@ -2,12 +2,12 @@ stdenv.mkDerivation rec { pname = "msieve"; - version = "r1050"; + version = "1056"; src = fetchsvn { url = "svn://svn.code.sf.net/p/msieve/code/trunk"; - rev = "1050"; - hash = "sha256-cn6OhE4zhrpB7BFrRdOnucjATbfo5mLkK7O0Usx1quE="; + rev = version; + hash = "sha256-6ErVn4pYPMG5VFjOQURLsHNpN0pGdp55+rjY8988onU="; }; buildInputs = [ zlib gmp ecm ]; diff --git a/pkgs/applications/science/math/mxnet/default.nix b/pkgs/applications/science/math/mxnet/default.nix index 839537438962b..880caaff5afb6 100644 --- a/pkgs/applications/science/math/mxnet/default.nix +++ b/pkgs/applications/science/math/mxnet/default.nix @@ -16,7 +16,7 @@ stdenv.mkDerivation rec { src = fetchurl { name = "apache-mxnet-src-${version}-incubating.tar.gz"; - url = "https://dlcdn.apache.org/incubator/mxnet/${version}/apache-mxnet-src-${version}-incubating.tar.gz"; + url = "mirror://apache/incubator/mxnet/${version}/apache-mxnet-src-${version}-incubating.tar.gz"; hash = "sha256-EephMoF02MKblvNBl34D3rC/Sww3rOZY+T442euMkyI="; }; diff --git a/pkgs/applications/science/math/nota/default.nix b/pkgs/applications/science/math/nota/default.nix index eae11806d7254..3a98eacd47171 100644 --- a/pkgs/applications/science/math/nota/default.nix +++ b/pkgs/applications/science/math/nota/default.nix @@ -36,6 +36,6 @@ mkDerivation rec { description = "Most beautiful command line calculator"; homepage = "https://kary.us/nota"; license = lib.licenses.mpl20; - maintainers = with lib.maintainers; [ dtzWill ]; + maintainers = [ ]; mainProgram = "nota"; } diff --git a/pkgs/applications/science/math/numworks-epsilon/default.nix b/pkgs/applications/science/math/numworks-epsilon/default.nix index 98d5d0d4560ad..71da675614da9 100644 --- a/pkgs/applications/science/math/numworks-epsilon/default.nix +++ b/pkgs/applications/science/math/numworks-epsilon/default.nix @@ -14,13 +14,13 @@ stdenv.mkDerivation rec { pname = "numworks-epsilon"; - version = "22.2.0"; + version = "23.2.3"; src = fetchFromGitHub { owner = "numworks"; repo = "epsilon"; rev = version; - hash = "sha256-E2WaXTn8+Ky9kdZxvQmEt63Ggo6Ns0fZ0Za+rQGIMSg="; + hash = "sha256-w9ddcULE1MrGnYcXA0qOg1elQv/eBhcXqhMSjWT3Bkk="; }; nativeBuildInputs = [ pkg-config ]; diff --git a/pkgs/applications/science/math/qalculate-gtk/default.nix b/pkgs/applications/science/math/qalculate-gtk/default.nix index e4fc506516fdd..a27d7c1ffdb6f 100644 --- a/pkgs/applications/science/math/qalculate-gtk/default.nix +++ b/pkgs/applications/science/math/qalculate-gtk/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation (finalAttrs: { pname = "qalculate-gtk"; - version = "5.1.0"; + version = "5.2.0"; src = fetchFromGitHub { owner = "qalculate"; repo = "qalculate-gtk"; rev = "v${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..b1db5ce31a791 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 = "5.2.0.1"; src = fetchFromGitHub { owner = "qalculate"; repo = "qalculate-qt"; rev = "v${finalAttrs.version}"; - hash = "sha256-gJfIC5HdA10gb/Dh/yhJbkCZfhUnN0zihqyfDjPv6ow="; + hash = "sha256-kzOxOCZmu4mYYgegRBU8SMAkTiE4p1AugVAeZa8yDDE="; }; nativeBuildInputs = [ qmake intltool pkg-config qttools wrapQtAppsHook ]; diff --git a/pkgs/applications/science/math/ripser/default.nix b/pkgs/applications/science/math/ripser/default.nix index 3f536f25aa115..38a00d504406b 100644 --- a/pkgs/applications/science/math/ripser/default.nix +++ b/pkgs/applications/science/math/ripser/default.nix @@ -5,14 +5,11 @@ , fileFormat ? "lowerTriangularCsv" }: -with lib; - -assert assertOneOf "fileFormat" fileFormat +assert lib.assertOneOf "fileFormat" fileFormat ["lowerTriangularCsv" "upperTriangularCsv" "dipha"]; assert useGoogleHashmap -> sparsehash != null; let - inherit (lib) optional; version = "1.2.1"; in stdenv.mkDerivation { @@ -26,19 +23,19 @@ stdenv.mkDerivation { sha256 = "sha256-BxmkPQ/nl5cF+xwQMTjXnLgkLgdmT/39y7Kzl2wDfpE="; }; - buildInputs = optional useGoogleHashmap sparsehash; + buildInputs = lib.optional useGoogleHashmap sparsehash; buildFlags = [ "-std=c++11" "-O3" "-D NDEBUG" ] - ++ optional useCoefficients "-D USE_COEFFICIENTS" - ++ optional indicateProgress "-D INDICATE_PROGRESS" - ++ optional useGoogleHashmap "-D USE_GOOGLE_HASHMAP" - ++ optional (fileFormat == "lowerTriangularCsv") "-D FILE_FORMAT_LOWER_TRIANGULAR_CSV" - ++ optional (fileFormat == "upperTriangularCsv") "-D FILE_FORMAT_UPPER_TRIANGULAR_CSV" - ++ optional (fileFormat == "dipha") "-D FILE_FORMAT_DIPHA" + ++ lib.optional useCoefficients "-D USE_COEFFICIENTS" + ++ lib.optional indicateProgress "-D INDICATE_PROGRESS" + ++ lib.optional useGoogleHashmap "-D USE_GOOGLE_HASHMAP" + ++ lib.optional (fileFormat == "lowerTriangularCsv") "-D FILE_FORMAT_LOWER_TRIANGULAR_CSV" + ++ lib.optional (fileFormat == "upperTriangularCsv") "-D FILE_FORMAT_UPPER_TRIANGULAR_CSV" + ++ lib.optional (fileFormat == "dipha") "-D FILE_FORMAT_DIPHA" ; buildPhase = "c++ ripser.cpp -o ripser $buildFlags"; diff --git a/pkgs/applications/science/math/sage/patches/gap-element-crash.patch b/pkgs/applications/science/math/sage/patches/gap-element-crash.patch new file mode 100644 index 0000000000000..b5396e2b78543 --- /dev/null +++ b/pkgs/applications/science/math/sage/patches/gap-element-crash.patch @@ -0,0 +1,18 @@ +diff --git a/src/sage/libs/gap/element.pyx b/src/sage/libs/gap/element.pyx +index b2b0681c052..b2e5807392c 100644 +--- a/src/sage/libs/gap/element.pyx ++++ b/src/sage/libs/gap/element.pyx +@@ -35,6 +35,13 @@ from sage.structure.coerce cimport coercion_model as cm + ### helper functions to construct lists and records ######################## + ############################################################################ + ++ ++cdef extern from *: ++ """ ++ #pragma GCC optimize("O1") ++ """ ++ ++ + cdef Obj make_gap_list(sage_list) except NULL: + """ + Convert Sage lists into Gap lists diff --git a/pkgs/applications/science/math/sage/sage-env.nix b/pkgs/applications/science/math/sage/sage-env.nix index f95e08c51ff4d..e886f6645468b 100644 --- a/pkgs/applications/science/math/sage/sage-env.nix +++ b/pkgs/applications/science/math/sage/sage-env.nix @@ -5,6 +5,7 @@ , sage-docbuild , env-locations , gfortran +, ninja , bash , coreutils , gnused @@ -63,6 +64,7 @@ let "@sage-local@/build" pythonEnv gfortran # for inline fortran + ninja # for inline fortran via numpy.f2py stdenv.cc # for cython bash coreutils diff --git a/pkgs/applications/science/math/sage/sage-src.nix b/pkgs/applications/science/math/sage/sage-src.nix index de0c2e3b1e20e..b21bb07e6a646 100644 --- a/pkgs/applications/science/math/sage/sage-src.nix +++ b/pkgs/applications/science/math/sage/sage-src.nix @@ -61,19 +61,9 @@ stdenv.mkDerivation rec { hash = "sha256-uCXchYx26DdxTjR1k2748KCEHPnekKS2fAM7SpyhNvM="; }) - # https://github.com/sagemath/sage/pull/37763, landed in 10.4.beta2 - (fetchpatch { - name = "scipy-fault-tolerance.patch"; - url = "https://github.com/sagemath/sage/commit/551139c09f26a5da96b1187c3f0dd17b8d80ef84.diff"; - hash = "sha256-PR4przrZ3ieHaW2nSY7l7VhNfrUupu9yCIrXpeyoAgg="; - }) - - # first two commits from https://github.com/sagemath/sage/pull/38100 - (fetchpatch { - name = "sphinx-7.3-update.patch"; - url = "https://github.com/sagemath/sage/compare/10.4.beta7...d2932e142991b442a3eee5dc4f8949e3f7e6fe5c.patch"; - hash = "sha256-g6w0ImE0d2ocKnbGMQikcz9eI9r3/gESlA1NrQfGimk="; - }) + # compile libs/gap/element.pyx with -O1 + # a more conservative version of https://github.com/sagemath/sage/pull/37951 + ./patches/gap-element-crash.patch ]; # Patches needed because of package updates. We could just pin the versions of @@ -83,12 +73,40 @@ stdenv.mkDerivation rec { # should come from or be proposed to upstream. This list will probably never # be empty since dependencies update all the time. packageUpgradePatches = [ - # https://github.com/sagemath/sage/pull/37492 + # https://github.com/sagemath/sage/pull/37763, landed in 10.4.beta2 + (fetchpatch { + name = "scipy-fault-tolerance.patch"; + url = "https://github.com/sagemath/sage/commit/551139c09f26a5da96b1187c3f0dd17b8d80ef84.diff"; + hash = "sha256-PR4przrZ3ieHaW2nSY7l7VhNfrUupu9yCIrXpeyoAgg="; + }) + + # https://github.com/sagemath/sage/pull/37492, landed in 10.4.beta5 (fetchpatch { name = "singular-4.3.2p14-upgrade.patch"; url = "https://github.com/sagemath/sage/commit/a0c56816b051e97da44ac0a4e4d4f6915cf7fa0f.diff"; sha256 = "sha256-WGMmPeBoj2LUC+2qxWuaJL89QUuGt6axGvxWkpM9LYg="; }) + + # https://github.com/sagemath/sage/pull/37949, landed in 10.4.beta6 + (fetchpatch { + name = "conway-polynomials-new-len.patch"; + url = "https://github.com/sagemath/sage/commit/c9f5b45179e92ea0de1e0dbe0f47464010902851.diff"; + hash = "sha256-DwN2UIX8dxfxjIiqVvMdGbIxJ7CR/Ag2XUmS5vUKFTs="; + }) + + # https://github.com/sagemath/sage/pull/37967, landed in 10.4.beta6 + (fetchpatch { + name = "conway-polynomials-ell-point.patch"; + url = "https://github.com/sagemath/sage/commit/4e0bbaf90262a42f8ea14d5bcfed65f9d1787f54.diff"; + hash = "sha256-9gXydi1A+n7+K8YpH0PB8l/OMexhgO2F5NccU0cK+ls="; + }) + + # https://github.com/sagemath/sage/pull/38100, landed in 10.4.beta8 + (fetchpatch { + name = "sphinx-7.3-update.patch"; + url = "https://github.com/sagemath/sage/commit/e1b22690db42885423be5049246eb71ff52bdfef.diff"; + hash = "sha256-04KAyz8+0pJbRV8Ld0bNX1OoEx/35gIh3Nff+6n8QUU="; + }) ]; patches = nixPatches ++ bugfixPatches ++ packageUpgradePatches; diff --git a/pkgs/applications/science/math/sage/sagelib.nix b/pkgs/applications/science/math/sage/sagelib.nix index 1552de773d014..1a138eea81d9e 100644 --- a/pkgs/applications/science/math/sage/sagelib.nix +++ b/pkgs/applications/science/math/sage/sagelib.nix @@ -6,7 +6,7 @@ , perl , pkg-config , sage-setup -, pythonRelaxDepsHook +, setuptools , gd , iml , libpng @@ -63,6 +63,7 @@ , lrcalc-python , matplotlib , memory-allocator +, meson-python , mpmath , networkx , numpy @@ -79,7 +80,6 @@ , sphinx , sympy , typing-extensions -, nbclassic }: assert (!blas.isILP64) && (!lapack.isILP64); @@ -103,7 +103,7 @@ buildPythonPackage rec { pip # needed to query installed packages pkg-config sage-setup - pythonRelaxDepsHook + setuptools ]; pythonRelaxDeps = [ @@ -173,6 +173,7 @@ buildPythonPackage rec { lrcalc-python matplotlib memory-allocator + meson-python mpmath networkx numpy @@ -189,8 +190,6 @@ buildPythonPackage rec { sphinx sympy typing-extensions - - nbclassic ]; preBuild = '' diff --git a/pkgs/applications/science/math/scalp/default.nix b/pkgs/applications/science/math/scalp/default.nix index fc230a11966fb..f6ec20faff594 100644 --- a/pkgs/applications/science/math/scalp/default.nix +++ b/pkgs/applications/science/math/scalp/default.nix @@ -18,7 +18,7 @@ stdenv.mkDerivation rec { url = "https://digidev.digi.e-technik.uni-kassel.de/git/scalp.git"; # mirrored at https://git.sr.ht/~weijia/scalp rev = "185b84e4ff967f42cf2de5db4db4e6fa0cc18fb8"; - sha256 = "sha256-NyMZdJwdD3FR6uweYCclJjfcf3Y24Bns1ViwsmJ5izg="; + hash = "sha256-NyMZdJwdD3FR6uweYCclJjfcf3Y24Bns1ViwsmJ5izg="; }; nativeBuildInputs = [ diff --git a/pkgs/applications/science/math/singular/default.nix b/pkgs/applications/science/math/singular/default.nix index d1b17eccee23b..ee84ae440b304 100644 --- a/pkgs/applications/science/math/singular/default.nix +++ b/pkgs/applications/science/math/singular/default.nix @@ -31,7 +31,7 @@ stdenv.mkDerivation rec { # if a release is tagged (which sometimes does not happen), it will # be in the format below. rev = "Release-${lib.replaceStrings ["."] ["-"] version}"; - sha256 = "sha256-5JZgI5lnfX4JlBSEAL7Wv6uao/57GBaMqwgslJt9Bjk="; + hash = "sha256-5JZgI5lnfX4JlBSEAL7Wv6uao/57GBaMqwgslJt9Bjk="; # the repository's .gitattributes file contains the lines "/Tst/ # export-ignore" and "/doc/ export-ignore" so some directories are diff --git a/pkgs/applications/science/math/wolfram-engine/default.nix b/pkgs/applications/science/math/wolfram-engine/default.nix index 685bc1bff3b18..4ce49e6cad4ca 100644 --- a/pkgs/applications/science/math/wolfram-engine/default.nix +++ b/pkgs/applications/science/math/wolfram-engine/default.nix @@ -2,8 +2,6 @@ , stdenv , autoPatchelfHook , requireFile -, callPackage -, makeWrapper , alsa-lib , dbus , fontconfig diff --git a/pkgs/applications/science/math/wolfram-engine/l10ns.nix b/pkgs/applications/science/math/wolfram-engine/l10ns.nix index ae1886bae1543..cfd296087d742 100644 --- a/pkgs/applications/science/math/wolfram-engine/l10ns.nix +++ b/pkgs/applications/science/math/wolfram-engine/l10ns.nix @@ -4,7 +4,7 @@ , majorVersion ? null }: -let allVersions = with lib; flip map +let allVersions = lib.flip map # N.B. Versions in this list should be ordered from newest to oldest. [ { @@ -45,7 +45,7 @@ let allVersions = with lib; flip map ] ({ version, lang, language, sha256, installer }: { inherit version lang; - name = "wolfram-engine-${version}" + optionalString (lang != "en") "-${lang}"; + name = "wolfram-engine-${version}" + lib.optionalString (lang != "en") "-${lang}"; src = requireFile { name = installer; message = '' @@ -58,14 +58,12 @@ let allVersions = with lib; flip map }; }); minVersion = - with lib; if majorVersion == null - then elemAt (builtins.splitVersion (elemAt allVersions 0).version) 0 + then lib.elemAt (builtins.splitVersion (lib.elemAt allVersions 0).version) 0 else majorVersion; maxVersion = toString (1 + builtins.fromJSON minVersion); in -with lib; -findFirst (l: (l.lang == lang +lib.findFirst (l: (l.lang == lang && l.version >= minVersion && l.version < maxVersion)) (throw "Version ${minVersion} in language ${lang} not supported") diff --git a/pkgs/applications/science/math/wolfram-engine/notebook.nix b/pkgs/applications/science/math/wolfram-engine/notebook.nix index 85570eeca7fbc..07cd0afa3099d 100644 --- a/pkgs/applications/science/math/wolfram-engine/notebook.nix +++ b/pkgs/applications/science/math/wolfram-engine/notebook.nix @@ -1,4 +1,4 @@ -{ lib, stdenv, writeScriptBin, jupyter, wolfram-for-jupyter-kernel }: +{ stdenv, writeScriptBin, jupyter, wolfram-for-jupyter-kernel }: let wolfram-jupyter = jupyter.override { definitions = { wolfram = wolfram-for-jupyter-kernel.definition; }; }; diff --git a/pkgs/applications/science/math/wxmaxima/default.nix b/pkgs/applications/science/math/wxmaxima/default.nix index db2ff0c4a8444..2a6225eab7653 100644 --- a/pkgs/applications/science/math/wxmaxima/default.nix +++ b/pkgs/applications/science/math/wxmaxima/default.nix @@ -6,7 +6,7 @@ , gettext , maxima , wxGTK -, gnome +, adwaita-icon-theme , glib }: @@ -25,7 +25,7 @@ stdenv.mkDerivation (finalAttrs:{ wxGTK maxima # So it won't embed svg files into headers. - gnome.adwaita-icon-theme + adwaita-icon-theme # So it won't crash under Sway. glib ]; diff --git a/pkgs/applications/science/math/yacas/default.nix b/pkgs/applications/science/math/yacas/default.nix index 7fa2fe1a6075e..ad4e3f37d07ff 100644 --- a/pkgs/applications/science/math/yacas/default.nix +++ b/pkgs/applications/science/math/yacas/default.nix @@ -80,7 +80,7 @@ stdenv.mkDerivation rec { description = "Easy to use, general purpose Computer Algebra System${lib.optionalString enableGui ", built with GUI."}"; homepage = "http://www.yacas.org/"; license = lib.licenses.gpl2Plus; - maintainers = with lib.maintainers; [ viric ]; + maintainers = [ ]; platforms = with lib.platforms; linux; }; } diff --git a/pkgs/applications/science/medicine/dcmtk/default.nix b/pkgs/applications/science/medicine/dcmtk/default.nix index 0fa41ba08760f..8dc85e2ee1077 100644 --- a/pkgs/applications/science/medicine/dcmtk/default.nix +++ b/pkgs/applications/science/medicine/dcmtk/default.nix @@ -1,7 +1,6 @@ { lib, stdenv, fetchFromGitHub, zlib, libtiff, libxml2, openssl, libiconv , libpng, cmake }: -with lib; stdenv.mkDerivation rec { pname = "dcmtk"; version = "3.6.8"; @@ -17,7 +16,7 @@ stdenv.mkDerivation rec { doCheck = true; - meta = { + meta = with lib; { description = "Collection of libraries and applications implementing large parts of the DICOM standard"; longDescription = '' diff --git a/pkgs/applications/science/medicine/xmedcon/default.nix b/pkgs/applications/science/medicine/xmedcon/default.nix index 1f0686cc0dad0..b4170dfa228a7 100644 --- a/pkgs/applications/science/medicine/xmedcon/default.nix +++ b/pkgs/applications/science/medicine/xmedcon/default.nix @@ -28,7 +28,7 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ pkg-config wrapGAppsHook3 ]; meta = with lib; { - description = "Open source toolkit for medical image conversion "; + description = "Open source toolkit for medical image conversion"; homepage = "https://xmedcon.sourceforge.net/"; license = licenses.lgpl2Plus; maintainers = with maintainers; [ arianvp flokli ]; diff --git a/pkgs/applications/science/misc/bada-bib/default.nix b/pkgs/applications/science/misc/bada-bib/default.nix index 83abd40030ee5..fba3726329094 100644 --- a/pkgs/applications/science/misc/bada-bib/default.nix +++ b/pkgs/applications/science/misc/bada-bib/default.nix @@ -7,7 +7,6 @@ , gdk-pixbuf , gettext , glib -, gnome , gobject-introspection , gtk4 , gtksourceview5 diff --git a/pkgs/applications/science/misc/boinc/default.nix b/pkgs/applications/science/misc/boinc/default.nix index 0c559a530e089..b8b57857c02aa 100644 --- a/pkgs/applications/science/misc/boinc/default.nix +++ b/pkgs/applications/science/misc/boinc/default.nix @@ -10,7 +10,7 @@ , libGL , libXmu , libXi -, freeglut +, libglut , libjpeg , libtool , wxGTK32 @@ -27,14 +27,14 @@ stdenv.mkDerivation rec { pname = "boinc"; - version = "8.0.2"; + version = "8.0.4"; src = fetchFromGitHub { name = "${pname}-${version}-src"; owner = "BOINC"; repo = "boinc"; rev = "client_release/${lib.versions.majorMinor version}/${version}"; - hash = "sha256-e0zEdiN3QQHj6MNGd1pfaZf3o9rOpCTmuNSJQb3sss4="; + hash = "sha256-dp0zRMIG0PGXhth+Cc8FDhzl5X/4ud3GFCdE7wqPL/c="; }; nativeBuildInputs = [ libtool automake autoconf m4 pkg-config ]; @@ -48,7 +48,7 @@ stdenv.mkDerivation rec { libGL libXmu libXi - freeglut + libglut libjpeg wxGTK32 gtk3 diff --git a/pkgs/applications/science/misc/colmap/default.nix b/pkgs/applications/science/misc/colmap/default.nix index d071c90562cd4..59e58351c0f6b 100644 --- a/pkgs/applications/science/misc/colmap/default.nix +++ b/pkgs/applications/science/misc/colmap/default.nix @@ -1,43 +1,62 @@ -{ mkDerivation, lib, fetchFromGitHub, cmake, boost179, ceres-solver, eigen, +{ lib, fetchFromGitHub, cmake, boost179, ceres-solver, eigen, freeimage, glog, libGLU, glew, qtbase, + flann, + cgal, + gmp, + mpfr, autoAddDriverRunpath, config, - cudaSupport ? config.cudaSupport, cudaPackages + stdenv, + qt5, + xorg, + cudaSupport ? config.cudaSupport, + cudaCapabilities ? cudaPackages.cudaFlags.cudaCapabilities, + cudaPackages }: assert cudaSupport -> cudaPackages != { }; let boost_static = boost179.override { enableStatic = true; }; + stdenv' = if cudaSupport then cudaPackages.backendStdenv else stdenv; # TODO: migrate to redist packages inherit (cudaPackages) cudatoolkit; in -mkDerivation rec { - version = "3.7"; +stdenv'.mkDerivation rec { + version = "3.9.1"; pname = "colmap"; src = fetchFromGitHub { owner = "colmap"; repo = "colmap"; rev = version; - hash = "sha256-uVAw6qwhpgIpHkXgxttKupU9zU+vD0Za0maw2Iv4x+I="; + hash = "sha256-Xb4JOttCMERwPYs5DyGKHw+f9Wik1/rdJQKbgVuygH8="; }; - # TODO: rm once the gcc11 issue is closed, https://github.com/colmap/colmap/issues/1418#issuecomment-1049305256 cmakeFlags = lib.optionals cudaSupport [ - "-DCUDA_ENABLED=ON" - "-DCUDA_NVCC_FLAGS=--std=c++14" + (lib.cmakeBool "CUDA_ENABLED" true) + (lib.cmakeFeature "CMAKE_CUDA_ARCHITECTURES" + (lib.strings.concatStringsSep ";" + (map cudaPackages.cudaFlags.dropDot + cudaCapabilities))) ]; buildInputs = [ boost_static ceres-solver eigen freeimage glog libGLU glew qtbase + flann + cgal + gmp + mpfr + xorg.libSM ] ++ lib.optionals cudaSupport [ cudatoolkit + cudaPackages.cuda_cudart.static ]; nativeBuildInputs = [ cmake + qt5.wrapQtAppsHook ] ++ lib.optionals cudaSupport [ autoAddDriverRunpath ]; diff --git a/pkgs/applications/science/misc/cwltool/default.nix b/pkgs/applications/science/misc/cwltool/default.nix index ab43eac8bffb0..1c616866a173d 100644 --- a/pkgs/applications/science/misc/cwltool/default.nix +++ b/pkgs/applications/science/misc/cwltool/default.nix @@ -7,14 +7,14 @@ python3.pkgs.buildPythonApplication rec { pname = "cwltool"; - version = "3.1.20240508115724"; + version = "3.1.20240708091337"; pyproject = true; src = fetchFromGitHub { owner = "common-workflow-language"; repo = "cwltool"; rev = "refs/tags/${version}"; - hash = "sha256-hBP/8PIqvs820UsxrRuyMVIWgQGFVcMHCUToxhcupTk="; + hash = "sha256-Umxh8sRBy7fC6+GrcN1q4iO0KVpmUhGPtnqZZK/6c9M="; }; postPatch = '' @@ -24,7 +24,8 @@ python3.pkgs.buildPythonApplication rec { --replace '"schema-salad >= 8.4.20230426093816, < 9",' "" \ --replace "PYTEST_RUNNER + " "" substituteInPlace pyproject.toml \ - --replace "ruamel.yaml>=0.16.0,<0.18" "ruamel.yaml" + --replace "ruamel.yaml>=0.16.0,<0.18" "ruamel.yaml" \ + --replace "mypy==1.10.0" "mypy==1.10.*" ''; nativeBuildInputs = [ diff --git a/pkgs/applications/science/misc/foldingathome/viewer.nix b/pkgs/applications/science/misc/foldingathome/viewer.nix index 7f28c8d1b1463..bb2c3c0abe30e 100644 --- a/pkgs/applications/science/misc/foldingathome/viewer.nix +++ b/pkgs/applications/science/misc/foldingathome/viewer.nix @@ -2,7 +2,7 @@ , autoPatchelfHook , dpkg , fetchurl -, freeglut +, libglut , gcc-unwrapped , libGL , libGLU @@ -29,7 +29,7 @@ stdenv.mkDerivation rec { ]; buildInputs = [ - freeglut + libglut gcc-unwrapped.lib libGL libGLU diff --git a/pkgs/applications/science/misc/gephi/default.nix b/pkgs/applications/science/misc/gephi/default.nix index 77b6584412a5a..fe638bde1ba46 100644 --- a/pkgs/applications/science/misc/gephi/default.nix +++ b/pkgs/applications/science/misc/gephi/default.nix @@ -1,11 +1,6 @@ { lib, fetchFromGitHub, jdk11, maven, jogl }: -let - mavenJdk11 = maven.override { - jdk = jdk11; - }; -in -mavenJdk11.buildMavenPackage rec { +maven.buildMavenPackage rec { pname = "gephi"; version = "0.10.1"; @@ -16,6 +11,7 @@ mavenJdk11.buildMavenPackage rec { hash = "sha256-ZNSEaiD32zFfF2ISKa1CmcT9Nq6r5i2rNHooQAcVbn4="; }; + mvnJdk = jdk11; mvnHash = "sha256-/2/Yb26Ry0NHQQ3j0LXnjwC0wQqJiztvTgWixyMJqvg="; nativeBuildInputs = [ jdk11 ]; diff --git a/pkgs/applications/science/misc/golly/default.nix b/pkgs/applications/science/misc/golly/default.nix index 52b05cbb7e9b2..b509387fe8838 100644 --- a/pkgs/applications/science/misc/golly/default.nix +++ b/pkgs/applications/science/misc/golly/default.nix @@ -12,6 +12,10 @@ stdenv.mkDerivation rec { wxGTK perl python3 zlib libGLU libGL libX11 SDL2 ]; + nativeBuildInputs = [ + (python3.withPackages (ps: [ps.setuptools])) + ]; + setSourceRoot = '' sourceRoot=$(echo */gui-wx) ''; diff --git a/pkgs/applications/science/misc/openmvs/default.nix b/pkgs/applications/science/misc/openmvs/default.nix index 35f46f7a4552b..57c4367d2a822 100644 --- a/pkgs/applications/science/misc/openmvs/default.nix +++ b/pkgs/applications/science/misc/openmvs/default.nix @@ -33,7 +33,7 @@ stdenv.mkDerivation rec { owner = "cdcseacave"; repo = "openmvs"; rev = "v${version}"; - sha256 = "sha256-j/tGkR73skZiU+bP4j6aZ5CxkbIcHtqKcaUTgNvj0C8="; + hash = "sha256-j/tGkR73skZiU+bP4j6aZ5CxkbIcHtqKcaUTgNvj0C8="; fetchSubmodules = true; }; diff --git a/pkgs/applications/science/misc/openrefine/default.nix b/pkgs/applications/science/misc/openrefine/default.nix index b94f23671024b..6d169db23b925 100644 --- a/pkgs/applications/science/misc/openrefine/default.nix +++ b/pkgs/applications/science/misc/openrefine/default.nix @@ -7,20 +7,15 @@ , jq , makeWrapper , maven -, writeText }: let - maven' = maven.override { - inherit jdk; - }; - - version = "3.8.1"; + version = "3.8.2"; src = fetchFromGitHub { owner = "openrefine"; repo = "openrefine"; rev = version; - hash = "sha256-MnFwFJdKIU7D8GQgnDvCO+P8r8h1Se/wmbt/Z3EX+3Q="; + hash = "sha256-3KCO9ooYN8PPVirU2wh7wu4feHqugc3JSXWR2aWIanE="; }; npmPkg = buildNpmPackage { @@ -47,7 +42,7 @@ let ''; }; -in maven'.buildMavenPackage { +in maven.buildMavenPackage { inherit src version; pname = "openrefine"; @@ -55,8 +50,10 @@ in maven'.buildMavenPackage { postPatch = '' cp -r ${npmPkg} main/webapp/modules/core/3rdparty ''; + + mvnJdk = jdk; mvnParameters = "-pl !packaging"; - mvnHash = "sha256-0qsKUMV9M0ZaddR5ust8VikSrsutdxVNNezKqR+F/6M="; + mvnHash = "sha256-AuZp+uq5bmb4gnzKvqXeTmBrsCT6qmJOrwtJq9iCkRQ="; nativeBuildInputs = [ makeWrapper ]; diff --git a/pkgs/applications/science/misc/rink/default.nix b/pkgs/applications/science/misc/rink/default.nix index 6b5917e163287..ae51d55168a9f 100644 --- a/pkgs/applications/science/misc/rink/default.nix +++ b/pkgs/applications/science/misc/rink/default.nix @@ -1,5 +1,5 @@ { lib, stdenv, fetchFromGitHub, rustPlatform, openssl, pkg-config, ncurses -, curl, libiconv, Security }: +, curl, installShellFiles, asciidoctor, libiconv, Security }: rustPlatform.buildRustPackage rec { version = "0.8.0"; @@ -14,13 +14,21 @@ rustPlatform.buildRustPackage rec { cargoHash = "sha256-j1pQfMjDNu57otOBTVBQEZIx80p4/beEUQdUkAJhvso="; - nativeBuildInputs = [ pkg-config ]; + nativeBuildInputs = [ pkg-config installShellFiles asciidoctor ]; buildInputs = [ ncurses ] ++ (if stdenv.isDarwin then [ curl libiconv Security ] else [ openssl ]); # Some tests fail and/or attempt to use internet servers. doCheck = false; + postBuild = '' + make man + ''; + + postInstall = '' + installManPage build/* + ''; + meta = with lib; { description = "Unit-aware calculator"; mainProgram = "rink"; diff --git a/pkgs/applications/science/misc/root/default.nix b/pkgs/applications/science/misc/root/default.nix index 5d01a33e5dcc4..fd998f7328182 100644 --- a/pkgs/applications/science/misc/root/default.nix +++ b/pkgs/applications/science/misc/root/default.nix @@ -56,7 +56,7 @@ stdenv.mkDerivation rec { pname = "root"; - version = "6.32.02"; + version = "6.32.04"; passthru = { tests = import ./tests { inherit callPackage; }; @@ -64,15 +64,15 @@ stdenv.mkDerivation rec { src = fetchurl { url = "https://root.cern.ch/download/root_v${version}.source.tar.gz"; - hash = "sha256-PQ92vwWFfhgHzPssngFPUlvLYl+UojcLRV9LFklhYC0="; + hash = "sha256-Ey8Saq59MO+8zX3NmRt62hiQrleYDvMAwWQh+dTQfqg="; }; clad_src = fetchgit { url = "https://github.com/vgvassilev/clad"; # 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="; + rev = "refs/tags/v1.6"; + hash = "sha256-Fv3i84lgoifxtyWKhQjj1c4bR9wSl5SPzUh0ZhZBxFI="; }; nativeBuildInputs = [ makeWrapper cmake pkg-config git ]; @@ -165,6 +165,7 @@ stdenv.mkDerivation rec { "-Dfail-on-missing=ON" "-Dfitsio=OFF" "-Dgnuinstall=ON" + "-Dmathmore=ON" "-Dmysql=OFF" "-Dpgsql=OFF" "-Dsqlite=OFF" diff --git a/pkgs/applications/science/misc/root/tests/test-thisroot.nix b/pkgs/applications/science/misc/root/tests/test-thisroot.nix index 3540dde8c9138..3610e23acbffb 100644 --- a/pkgs/applications/science/misc/root/tests/test-thisroot.nix +++ b/pkgs/applications/science/misc/root/tests/test-thisroot.nix @@ -3,7 +3,6 @@ , root , bash , fish -, ksh , tcsh , zsh }: runCommand "test-thisroot" diff --git a/pkgs/applications/science/misc/simgrid/default.nix b/pkgs/applications/science/misc/simgrid/default.nix index a2b04e1877f89..37c7fb3a2a054 100644 --- a/pkgs/applications/science/misc/simgrid/default.nix +++ b/pkgs/applications/science/misc/simgrid/default.nix @@ -12,12 +12,6 @@ , withoutBin ? false }: -with lib; - -let - optionOnOff = option: if option then "on" else "off"; -in - stdenv.mkDerivation rec { pname = "simgrid"; version = "3.35"; @@ -32,44 +26,45 @@ stdenv.mkDerivation rec { propagatedBuildInputs = [ boost ]; nativeBuildInputs = [ cmake perl python3 ] - ++ optionals fortranSupport [ gfortran ] - ++ optionals buildJavaBindings [ openjdk ] - ++ optionals buildPythonBindings [ python3Packages.pybind11 ] - ++ optionals buildDocumentation [ fig2dev ghostscript doxygen ] - ++ optionals bmfSupport [ eigen ] - ++ optionals modelCheckingSupport [ libunwind libevent elfutils ]; + ++ lib.optionals fortranSupport [ gfortran ] + ++ lib.optionals buildJavaBindings [ openjdk ] + ++ lib.optionals buildPythonBindings [ python3Packages.pybind11 ] + ++ lib.optionals buildDocumentation [ fig2dev ghostscript doxygen ] + ++ lib.optionals bmfSupport [ eigen ] + ++ lib.optionals modelCheckingSupport [ libunwind libevent elfutils ]; outputs = [ "out" ] - ++ optionals buildPythonBindings [ "python" ]; + ++ lib.optionals buildPythonBindings [ "python" ]; # "Release" does not work. non-debug mode is Debug compiled with optimization cmakeBuildType = "Debug"; - cmakeFlags = [ - "-Denable_documentation=${optionOnOff buildDocumentation}" - "-Denable_java=${optionOnOff buildJavaBindings}" - "-Denable_python=${optionOnOff buildPythonBindings}" - "-DSIMGRID_PYTHON_LIBDIR=./" # prevents CMake to install in ${python3} dir - "-Denable_msg=${optionOnOff buildJavaBindings}" - "-Denable_fortran=${optionOnOff fortranSupport}" - "-Denable_model-checking=${optionOnOff modelCheckingSupport}" - "-Denable_ns3=off" - "-Denable_lua=off" - "-Denable_lib_in_jar=off" - "-Denable_maintainer_mode=off" - "-Denable_mallocators=on" - "-Denable_debug=on" - "-Denable_smpi=on" - "-Dminimal-bindings=${optionOnOff minimalBindings}" - "-Denable_smpi_ISP_testsuite=${optionOnOff moreTests}" - "-Denable_smpi_MPICH3_testsuite=${optionOnOff moreTests}" - "-Denable_compile_warnings=off" - "-Denable_compile_optimizations=${optionOnOff optimize}" - "-Denable_lto=${optionOnOff optimize}" + cmakeFlags = [ + (lib.cmakeBool "enable_documentation" buildDocumentation) + (lib.cmakeBool "enable_java" buildJavaBindings) + (lib.cmakeBool "enable_python" buildPythonBindings) + (lib.cmakeFeature "SIMGRID_PYTHON_LIBDIR" "./") # prevents CMake to install in ${python3} dir + (lib.cmakeBool "enable_msg" buildJavaBindings) + (lib.cmakeBool "enable_fortran" fortranSupport) + (lib.cmakeBool "enable_model-checking" modelCheckingSupport) + (lib.cmakeBool "enable_ns3" false) + (lib.cmakeBool "enable_lua" false) + (lib.cmakeBool "enable_lib_in_jar" false) + (lib.cmakeBool "enable_maintainer_mode" false) + (lib.cmakeBool "enable_mallocators" true) + (lib.cmakeBool "enable_debug" true) + (lib.cmakeBool "enable_smpi" true) + (lib.cmakeBool "minimal-bindings" minimalBindings) + (lib.cmakeBool "enable_smpi_ISP_testsuite" moreTests) + (lib.cmakeBool "enable_smpi_MPICH3_testsuite" moreTests) + (lib.cmakeBool "enable_compile_warnings" false) + (lib.cmakeBool "enable_compile_optimizations" optimize) + (lib.cmakeBool "enable_lto" optimize) # RPATH of binary /nix/store/.../bin/... contains a forbidden reference to /build/ - "-DCMAKE_SKIP_BUILD_RPATH=ON" + (lib.cmakeBool "CMAKE_SKIP_BUILD_RPATH" optimize) ]; - makeFlags = optional debug "VERBOSE=1"; + + makeFlags = lib.optional debug "VERBOSE=1"; # needed to run tests and to ensure correct shabangs in output scripts preBuild = '' @@ -106,7 +101,7 @@ stdenv.mkDerivation rec { hardeningDisable = lib.optionals debug [ "fortify" ]; dontStrip = debug; - meta = { + meta = with lib; { description = "Framework for the simulation of distributed applications"; longDescription = '' SimGrid is a toolkit that provides core functionalities for the diff --git a/pkgs/applications/science/misc/vite/default.nix b/pkgs/applications/science/misc/vite/default.nix index f1c9329c94df9..8cf8ceb497a84 100644 --- a/pkgs/applications/science/misc/vite/default.nix +++ b/pkgs/applications/science/misc/vite/default.nix @@ -27,7 +27,7 @@ stdenv.mkDerivation rec { homepage = "http://vite.gforge.inria.fr/"; license = lib.licenses.cecill20; - maintainers = with lib.maintainers; [ ]; + maintainers = [ ]; platforms = lib.platforms.linux; }; } diff --git a/pkgs/applications/science/molecular-dynamics/lammps/default.nix b/pkgs/applications/science/molecular-dynamics/lammps/default.nix index b881d339300c4..2474998450cbf 100644 --- a/pkgs/applications/science/molecular-dynamics/lammps/default.nix +++ b/pkgs/applications/science/molecular-dynamics/lammps/default.nix @@ -75,8 +75,9 @@ stdenv.mkDerivation (finalAttrs: { inherit extraBuildInputs; }; cmakeFlags = [ + (lib.cmakeBool "BUILD_SHARED_LIBS" true) ] - ++ (builtins.map (p: "-DPKG_${p}=ON") (builtins.attrNames (lib.filterAttrs (n: v: v) packages))) + ++ (lib.mapAttrsToList (n: v: lib.cmakeBool "PKG_${n}" v) packages) ++ (lib.mapAttrsToList (n: v: "-D${n}=${v}") extraCmakeFlags) ; @@ -99,7 +100,7 @@ stdenv.mkDerivation (finalAttrs: { ln -s $out/share/vim-plugins/lammps $out/share/nvim/site ''; - meta = with lib; { + meta = { description = "Classical Molecular Dynamics simulation code"; longDescription = '' LAMMPS is a classical molecular dynamics simulation code designed to @@ -109,13 +110,16 @@ stdenv.mkDerivation (finalAttrs: { under the terms of the GNU Public License (GPL). ''; homepage = "https://www.lammps.org"; - license = licenses.gpl2Only; - platforms = platforms.linux; + license = lib.licenses.gpl2Only; + platforms = lib.platforms.linux; # compiling lammps with 64 bit support blas and lapack might cause runtime # segfaults. In anycase both blas and lapack should have the same #bits # support. broken = (blas.isILP64 && lapack.isILP64); - maintainers = [ maintainers.costrouc maintainers.doronbehar ]; + maintainers = with lib.maintainers; [ + costrouc + doronbehar + ]; mainProgram = "lmp"; }; }) diff --git a/pkgs/applications/science/networking/sumo/default.nix b/pkgs/applications/science/networking/sumo/default.nix index 6f5be3df816eb..ad50200c1a839 100644 --- a/pkgs/applications/science/networking/sumo/default.nix +++ b/pkgs/applications/science/networking/sumo/default.nix @@ -11,7 +11,7 @@ stdenv.mkDerivation rec { owner = "eclipse"; repo = "sumo"; rev = "v${lib.replaceStrings ["."] ["_"] version}"; - sha256 = "sha256-y/bkdDWrb1KB0EOVSJPfPVYHGp/zQ2+Shb6eLsFQRNQ="; + hash = "sha256-y/bkdDWrb1KB0EOVSJPfPVYHGp/zQ2+Shb6eLsFQRNQ="; fetchSubmodules = true; }; diff --git a/pkgs/applications/science/physics/elmerfem/default.nix b/pkgs/applications/science/physics/elmerfem/default.nix index 4b19bc4b17b48..309e81fad7463 100644 --- a/pkgs/applications/science/physics/elmerfem/default.nix +++ b/pkgs/applications/science/physics/elmerfem/default.nix @@ -2,7 +2,6 @@ , stdenv , fetchFromGitHub , cmake -, git , gfortran , mpi , blas diff --git a/pkgs/applications/science/programming/groove/default.nix b/pkgs/applications/science/programming/groove/default.nix index fb314cdff30ce..6350d0badee9f 100644 --- a/pkgs/applications/science/programming/groove/default.nix +++ b/pkgs/applications/science/programming/groove/default.nix @@ -50,6 +50,6 @@ in stdenv.mkDerivation rec { license = licenses.asl20; sourceProvenance = with sourceTypes; [ binaryBytecode ]; platforms = platforms.all; - maintainers = with maintainers; [ ]; + maintainers = [ ]; }; } diff --git a/pkgs/applications/science/robotics/emuflight-configurator/default.nix b/pkgs/applications/science/robotics/emuflight-configurator/default.nix index 9669d48e744e0..66b9cf0efa8ea 100644 --- a/pkgs/applications/science/robotics/emuflight-configurator/default.nix +++ b/pkgs/applications/science/robotics/emuflight-configurator/default.nix @@ -3,11 +3,11 @@ stdenv.mkDerivation rec { pname = "emuflight-configurator"; - version = "0.4.1"; + version = "0.4.3"; src = fetchurl { url = "https://github.com/emuflight/EmuConfigurator/releases/download/${version}/emuflight-configurator_${version}_linux64.zip"; - sha256 = "sha256-e4HNg5yr9V5LyT0hYP6gzw0tZm4dLidJg5MQtH3L3JI="; + sha256 = "sha256-7NcN1wF3BUClJBVm13VnV80N/+a2jAEIRqB/x9+GDEg="; }; nativeBuildInputs = [ wrapGAppsHook3 unzip copyDesktopItems ]; diff --git a/pkgs/applications/science/robotics/mujoco/default.nix b/pkgs/applications/science/robotics/mujoco/default.nix index d4a7a961d3984..f36d316164aac 100644 --- a/pkgs/applications/science/robotics/mujoco/default.nix +++ b/pkgs/applications/science/robotics/mujoco/default.nix @@ -16,14 +16,14 @@ let abseil-cpp = fetchFromGitHub { owner = "abseil"; repo = "abseil-cpp"; - rev = "d7aaad83b488fd62bd51c81ecf16cd938532cc0a"; - hash = "sha256-eA2/dZpNOlex1O5PNa3XSZhpMB3AmaIoHzVDI9TD/cg="; + rev = "4447c7562e3bc702ade25105912dce503f0c4010"; + hash = "sha256-51jpDhdZ0n+KLmxh8KVaTz53pZAB0dHjmILFX+OLud4="; }; benchmark = fetchFromGitHub { owner = "google"; repo = "benchmark"; - rev = "e45585a4b8e75c28479fa4107182c28172799640"; - hash = "sha256-pgHvmRpPd99ePUVRsi7WXLVSZngZ5q6r1vWW4mdGvxY="; + rev = "7c8ed6b082aa3c7a3402f18e50da4480421d08fd"; + hash = "sha256-xX3o4wX7RUvw1x2gOlT6sGhutDYLBZ/JzFnv68qN6E8="; }; ccd = fetchFromGitHub { owner = "danfis"; @@ -34,14 +34,14 @@ let eigen3 = fetchFromGitLab { owner = "libeigen"; repo = "eigen"; - rev = "2a9055b50ed22101da7d77e999b90ed50956fe0b"; - hash = "sha256-tx/XR7xJ7IMh5RMvL8wRo/g+dfD3xcjZkLPSY4D9HaY="; + rev = "33d0937c6bdf5ec999939fb17f2a553183d14a74"; + hash = "sha256-qmFsmFEQCDH+TRFc8+5BsYAG1ybL08fWhn8NpM6H6xY="; }; googletest = fetchFromGitHub { owner = "google"; repo = "googletest"; - rev = "f8d7d77c06936315286eb55f8de22cd23c188571"; - hash = "sha256-t0RchAHTJbuI5YW4uyBPykTvcjy90JW9AOPNjIhwh6U="; + rev = "b514bdc898e2951020cbdca1304b75f5950d1f59"; + hash = "sha256-1OJ2SeSscRBNr7zZ/a8bJGIqAnhkg45re0j3DtPfcXM="; }; lodepng = fetchFromGitHub { owner = "lvandeve"; @@ -129,7 +129,7 @@ let in stdenv.mkDerivation rec { pname = "mujoco"; - version = "3.1.6"; + version = "3.2.2"; # Bumping version? Make sure to look though the MuJoCo's commit # history for bumped dependency pins! @@ -137,7 +137,7 @@ in stdenv.mkDerivation rec { owner = "google-deepmind"; repo = "mujoco"; rev = "refs/tags/${version}"; - hash = "sha256-64zUplr1E5WSb5RpTW9La1zKVT67a1VrftiUqc2SHlU="; + hash = "sha256-UUPB7AY6OYWaK5uBu92kmoIE116AfFa34sYmF943AOU="; }; patches = [ ./mujoco-system-deps-dont-fetch.patch ]; diff --git a/pkgs/applications/science/robotics/qgroundcontrol/default.nix b/pkgs/applications/science/robotics/qgroundcontrol/default.nix index 25b1f4e5d5ce6..c2ee629d77ba9 100644 --- a/pkgs/applications/science/robotics/qgroundcontrol/default.nix +++ b/pkgs/applications/science/robotics/qgroundcontrol/default.nix @@ -4,7 +4,7 @@ stdenv.mkDerivation rec { pname = "qgroundcontrol"; - version = "4.3.0"; + version = "4.4.1"; propagatedBuildInputs = [ qtbase qtcharts qtlocation qtserialport qtsvg qtquickcontrols2 @@ -67,7 +67,7 @@ stdenv.mkDerivation rec { owner = "mavlink"; repo = pname; rev = "v${version}"; - sha256 = "sha256-a0+cpT413qi88PvaWQPxKABHfK7vbPE7B42n84n/SAk="; + hash = "sha256-FdF9QQYCF7HbmjvUQgV6HytJo2Aje2OEDPO2GSl1dqE="; fetchSubmodules = true; }; @@ -76,7 +76,7 @@ stdenv.mkDerivation rec { homepage = "http://qgroundcontrol.com/"; license = licenses.gpl3Plus; platforms = platforms.linux; - maintainers = with maintainers; [ lopsided98 ]; + maintainers = with maintainers; [ lopsided98 pandapip1 ]; mainProgram = "QGroundControl"; }; } |