diff options
Diffstat (limited to 'pkgs/applications/science')
52 files changed, 495 insertions, 159 deletions
diff --git a/pkgs/applications/science/astronomy/gprojector/default.nix b/pkgs/applications/science/astronomy/gprojector/default.nix index 3864058828f..26e8fe11a32 100644 --- a/pkgs/applications/science/astronomy/gprojector/default.nix +++ b/pkgs/applications/science/astronomy/gprojector/default.nix @@ -22,8 +22,8 @@ stdenvNoCC.mkDerivation rec { exec = "gprojector"; desktopName = "G.Projector"; comment = meta.description; - categories = "Science;"; - extraEntries = "StartupWMClass = gov-nasa-giss-projector-GProjector"; + categories = [ "Science" ]; + startupWMClass = "gov-nasa-giss-projector-GProjector"; }) ]; buildInputs = [ jre ]; diff --git a/pkgs/applications/science/biology/bcftools/default.nix b/pkgs/applications/science/biology/bcftools/default.nix index f6aa5e8892a..c04d6af080e 100644 --- a/pkgs/applications/science/biology/bcftools/default.nix +++ b/pkgs/applications/science/biology/bcftools/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "bcftools"; - version = "1.14"; + version = "1.15"; src = fetchurl { url = "https://github.com/samtools/bcftools/releases/download/${version}/${pname}-${version}.tar.bz2"; - sha256 = "sha256-t++Iron8tVZYxb6i6MuOdWsFXhOGADbWvhN1Z4KqGcs="; + sha256 = "sha256-GIXMtFCobpegCqkF1zgcqeB72JZ8BXBaYdAAfS4iKW4="; }; nativeBuildInputs = [ diff --git a/pkgs/applications/science/biology/febio-studio/default.nix b/pkgs/applications/science/biology/febio-studio/default.nix new file mode 100644 index 00000000000..e334637f243 --- /dev/null +++ b/pkgs/applications/science/biology/febio-studio/default.nix @@ -0,0 +1,61 @@ +{ lib, stdenv, fetchFromGitHub, cmake, zlib, libglvnd, libGLU, wrapQtAppsHook +, sshSupport ? true, openssl, libssh +, tetgenSupport ? true, tetgen +, ffmpegSupport ? true, ffmpeg +, dicomSupport ? false, dcmtk +, withModelRepo ? true +, withCadFeatures ? false +}: + +stdenv.mkDerivation rec { + pname = "febio-studio"; + version = "1.6.1"; + + src = fetchFromGitHub { + owner = "febiosoftware"; + repo = "FEBioStudio"; + rev = "v${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 + ++ lib.optional dicomSupport dcmtk + ; + + meta = with lib; { + description = "FEBio Suite Solver"; + 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 new file mode 100644 index 00000000000..e694f6c3b89 --- /dev/null +++ b/pkgs/applications/science/biology/febio-studio/febio-studio-cmake.patch @@ -0,0 +1,38 @@ +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/neuron/default.nix b/pkgs/applications/science/biology/neuron/default.nix index 804407968e1..4dc850f5062 100644 --- a/pkgs/applications/science/biology/neuron/default.nix +++ b/pkgs/applications/science/biology/neuron/default.nix @@ -14,7 +14,7 @@ }: stdenv.mkDerivation rec { - pname = "neuron"; + pname = "neuron${lib.optionalString useMpi "-mpi"}"; version = "7.5"; nativeBuildInputs = [ which pkg-config automake autoconf libtool ]; diff --git a/pkgs/applications/science/biology/picard-tools/default.nix b/pkgs/applications/science/biology/picard-tools/default.nix index 33d581ffd01..526a5b3ed33 100644 --- a/pkgs/applications/science/biology/picard-tools/default.nix +++ b/pkgs/applications/science/biology/picard-tools/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "picard-tools"; - version = "2.26.10"; + version = "2.26.11"; src = fetchurl { url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar"; - sha256 = "sha256-hKBWRmzyMVXiEmsz/eYbVIUhezZdSJnBvcgv6ShPI5U="; + sha256 = "sha256-0swggo1a5gExpj3VgaWKT/TYd7rfSFBcqRrAURnTPjM="; }; nativeBuildInputs = [ makeWrapper ]; diff --git a/pkgs/applications/science/biology/raxml/default.nix b/pkgs/applications/science/biology/raxml/default.nix index 6e747e318f5..d02d4726629 100644 --- a/pkgs/applications/science/biology/raxml/default.nix +++ b/pkgs/applications/science/biology/raxml/default.nix @@ -5,12 +5,12 @@ }: stdenv.mkDerivation rec { - pname = "RAxML"; + pname = "RAxML${lib.optionalString useMpi "-mpi"}"; version = "8.2.12"; src = fetchFromGitHub { owner = "stamatak"; - repo = "standard-${pname}"; + repo = "standard-RAxML"; rev = "v${version}"; sha256 = "1jqjzhch0rips0vp04prvb8vmc20c5pdmsqn8knadcf91yy859fh"; }; diff --git a/pkgs/applications/science/biology/spades/default.nix b/pkgs/applications/science/biology/spades/default.nix index b41d266dbab..5302b43bb02 100644 --- a/pkgs/applications/science/biology/spades/default.nix +++ b/pkgs/applications/science/biology/spades/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "SPAdes"; - version = "3.15.3"; + version = "3.15.4"; src = fetchurl { url = "http://cab.spbu.ru/files/release${version}/${pname}-${version}.tar.gz"; - sha256 = "sha256-suWp/XplruWriGIi1q9Pe3vH91XaegOUFXH6vWueFJk="; + sha256 = "sha256-OyQcUopCqL398j5b+PAISDR5BZDQhJHezqnw8AnYWJ8="; }; nativeBuildInputs = [ cmake ]; diff --git a/pkgs/applications/science/chemistry/chemtool/default.nix b/pkgs/applications/science/chemistry/chemtool/default.nix index 3b5d144ba22..bf78aeb825d 100644 --- a/pkgs/applications/science/chemistry/chemtool/default.nix +++ b/pkgs/applications/science/chemistry/chemtool/default.nix @@ -46,5 +46,6 @@ stdenv.mkDerivation rec { ''; license = licenses.mit; maintainers = with maintainers; [ AndersonTorres ]; + platforms = platforms.linux; }; } diff --git a/pkgs/applications/science/chemistry/d-seams/default.nix b/pkgs/applications/science/chemistry/d-seams/default.nix index f5e21db4b55..74260bacabc 100644 --- a/pkgs/applications/science/chemistry/d-seams/default.nix +++ b/pkgs/applications/science/chemistry/d-seams/default.nix @@ -2,13 +2,13 @@ , eigen, lua, luaPackages, liblapack, blas, lib, boost, gsl }: clangStdenv.mkDerivation rec { - version = "v1.0.1"; + version = "1.0.1"; pname = "d-SEAMS"; src = fetchFromGitHub { owner = "d-SEAMS"; repo = "seams-core"; - rev = "v1.0.1"; + rev = "v${version}"; sha256 = "03zhhl9vhi3rhc3qz1g3zb89jksgpdlrk15fcr8xcz8pkj6r5b1i"; }; diff --git a/pkgs/applications/science/chemistry/jmol/default.nix b/pkgs/applications/science/chemistry/jmol/default.nix index 20b665792ac..cc983e24618 100644 --- a/pkgs/applications/science/chemistry/jmol/default.nix +++ b/pkgs/applications/science/chemistry/jmol/default.nix @@ -12,19 +12,27 @@ let exec = "jmol"; desktopName = "JMol"; genericName = "Molecular Modeler"; - mimeType = "chemical/x-pdb;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;"; - categories = "Graphics;Education;Science;Chemistry;"; + mimeTypes = [ + "chemical/x-pdb" + "chemical/x-mdl-molfile" + "chemical/x-mol2" + "chemical/seq-aa-fasta" + "chemical/seq-na-fasta" + "chemical/x-xyz" + "chemical/x-mdl-sdf" + ]; + categories = [ "Graphics" "Education" "Science" "Chemistry" ]; }; in stdenv.mkDerivation rec { - version = "14.32.6"; + version = "14.32.24"; 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-${version}-binary.tar.gz"; - sha256 = "sha256-b9E/IJfqeA8rBSQogb/ZVBMW3y9bc2dBj/BIl0HWFR8="; + sha256 = "sha256-YxYNb2fS7KiUkZDSRx4FN+ZeMMNpfTaElitRE4RtD0g="; }; patchPhase = '' diff --git a/pkgs/applications/science/chemistry/marvin/default.nix b/pkgs/applications/science/chemistry/marvin/default.nix index 72958898428..3c2b11c0e29 100644 --- a/pkgs/applications/science/chemistry/marvin/default.nix +++ b/pkgs/applications/science/chemistry/marvin/default.nix @@ -4,12 +4,12 @@ with lib; stdenv.mkDerivation rec { pname = "marvin"; - version = "21.20.0"; + version = "22.3.0"; src = fetchurl { name = "marvin-${version}.deb"; url = "http://dl.chemaxon.com/marvin/${version}/marvin_linux_${versions.majorMinor version}.deb"; - sha256 = "sha256-xOtlJSUY7QLyggFXW0Ay3+6KNHIqljyDpyk0CP8jxWs="; + sha256 = "sha256-ASnweoVBYSnO/FjE9tpLgaOAgiPQeUnw7CzwkKRXnAg="; }; nativeBuildInputs = [ dpkg makeWrapper ]; diff --git a/pkgs/applications/science/chemistry/pymol/default.nix b/pkgs/applications/science/chemistry/pymol/default.nix index 39bbae77a66..5f7c0c1f6be 100644 --- a/pkgs/applications/science/chemistry/pymol/default.nix +++ b/pkgs/applications/science/chemistry/pymol/default.nix @@ -24,8 +24,16 @@ let genericName = "Molecular Modeler"; comment = description; icon = pname; - mimeType = "chemical/x-pdb;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;"; - categories = "Graphics;Education;Science;Chemistry;"; + mimeTypes = [ + "chemical/x-pdb" + "chemical/x-mdl-molfile" + "chemical/x-mol2" + "chemical/seq-aa-fasta" + "chemical/seq-na-fasta" + "chemical/x-xyz" + "chemical/x-mdl-sdf" + ]; + categories = [ "Graphics" "Education" "Science" "Chemistry" ]; }; in python3Packages.buildPythonApplication rec { diff --git a/pkgs/applications/science/electronics/diylc/default.nix b/pkgs/applications/science/electronics/diylc/default.nix index 987f6156b4b..ff4e3809fc2 100644 --- a/pkgs/applications/science/electronics/diylc/default.nix +++ b/pkgs/applications/science/electronics/diylc/default.nix @@ -27,7 +27,7 @@ let comment = "Multi platform circuit layout and schematic drawing tool"; exec = "diylc"; icon = "diylc_icon"; - categories = "Development;Electronics;"; + categories = [ "Development" "Electronics" ]; }; in stdenv.mkDerivation rec { diff --git a/pkgs/applications/science/electronics/eagle/eagle.nix b/pkgs/applications/science/electronics/eagle/eagle.nix index 2fb3b8c8b18..5b4c8eb790f 100644 --- a/pkgs/applications/science/electronics/eagle/eagle.nix +++ b/pkgs/applications/science/electronics/eagle/eagle.nix @@ -27,7 +27,7 @@ let comment = "Schematic capture and PCB layout"; desktopName = "Eagle"; genericName = "Schematic editor"; - categories = "Development;"; + categories = [ "Development" ]; }; buildInputs = diff --git a/pkgs/applications/science/electronics/eagle/eagle7.nix b/pkgs/applications/science/electronics/eagle/eagle7.nix index 94457c81ce9..f48d08d4079 100644 --- a/pkgs/applications/science/electronics/eagle/eagle7.nix +++ b/pkgs/applications/science/electronics/eagle/eagle7.nix @@ -37,7 +37,7 @@ stdenv.mkDerivation rec { comment = "Schematic capture and PCB layout"; desktopName = "Eagle"; genericName = "Schematic editor"; - categories = "Development;"; + categories = [ "Development" ]; }; buildInputs = diff --git a/pkgs/applications/science/geometry/tetgen/default.nix b/pkgs/applications/science/geometry/tetgen/default.nix index 1e3c96ae8c6..ff2b211b34d 100644 --- a/pkgs/applications/science/geometry/tetgen/default.nix +++ b/pkgs/applications/science/geometry/tetgen/default.nix @@ -1,18 +1,25 @@ -{lib, stdenv, fetchurl}: +{ lib, stdenv, fetchurl, cmake }: -let version = "1.6.0"; in -stdenv.mkDerivation { +stdenv.mkDerivation rec { pname = "tetgen"; - inherit version; + version = "1.6.0"; src = fetchurl { url = "http://wias-berlin.de/software/tetgen/1.5/src/tetgen${version}.tar.gz"; sha256 = "sha256-h7XmHr06Rx/E8s3XEkwrEd1mOfT+sflBpdL1EQ0Fzjk="; }; + nativeBuildInputs = [ cmake ]; + installPhase = '' - mkdir -p $out/bin + runHook preInstall + + mkdir -p $out/{bin,lib,include} cp tetgen $out/bin + cp libtet.a $out/lib + cp ../tetgen.{cxx,h} $out/include + + runHook postInstall ''; meta = { diff --git a/pkgs/applications/science/logic/alt-ergo/default.nix b/pkgs/applications/science/logic/alt-ergo/default.nix index 837f25e320f..096a648b4dd 100644 --- a/pkgs/applications/science/logic/alt-ergo/default.nix +++ b/pkgs/applications/science/logic/alt-ergo/default.nix @@ -12,36 +12,33 @@ let }; useDune2 = true; - - nativeBuildInputs = [ which ]; - in let alt-ergo-lib = ocamlPackages.buildDunePackage rec { pname = "alt-ergo-lib"; - inherit version src useDune2 nativeBuildInputs; + inherit version src useDune2; configureFlags = pname; + nativeBuildInputs = [ which ]; buildInputs = with ocamlPackages; [ dune-configurator ]; propagatedBuildInputs = with ocamlPackages; [ num ocplib-simplex stdlib-shims zarith ]; }; in let alt-ergo-parsers = ocamlPackages.buildDunePackage rec { pname = "alt-ergo-parsers"; - inherit version src useDune2 nativeBuildInputs; + inherit version src useDune2; configureFlags = pname; - buildInputs = with ocamlPackages; [ menhir ]; + nativeBuildInputs = [ which ocamlPackages.menhir ]; propagatedBuildInputs = [ alt-ergo-lib ] ++ (with ocamlPackages; [ camlzip psmt2-frontend ]); }; in ocamlPackages.buildDunePackage { - inherit pname version src useDune2 nativeBuildInputs; + inherit pname version src useDune2; configureFlags = pname; - buildInputs = [ alt-ergo-parsers ] ++ (with ocamlPackages; [ - cmdliner menhir ]) - ; + nativeBuildInputs = [ which ocamlPackages.menhir ]; + buildInputs = [ alt-ergo-parsers ocamlPackages.cmdliner ]; meta = { description = "High-performance theorem prover and SMT solver"; diff --git a/pkgs/applications/science/logic/anders/default.nix b/pkgs/applications/science/logic/anders/default.nix index 72e412fc3bd..bb60b2b8321 100644 --- a/pkgs/applications/science/logic/anders/default.nix +++ b/pkgs/applications/science/logic/anders/default.nix @@ -13,7 +13,10 @@ ocamlPackages.buildDunePackage rec { sha256 = "sha256-JUiZoo2rNLfgs94TlJqUNzul/7ODisCjSFAzhgSp1z4="; }; - buildInputs = with ocamlPackages; [ zarith menhir ]; + strictDeps = true; + + nativeBuildInputs = [ ocamlPackages.menhir ]; + buildInputs = [ ocamlPackages.zarith ]; meta = with lib; { description = "Modal Homotopy Type System"; diff --git a/pkgs/applications/science/logic/coq/default.nix b/pkgs/applications/science/logic/coq/default.nix index fe99b045512..29959be2fa9 100644 --- a/pkgs/applications/science/logic/coq/default.nix +++ b/pkgs/applications/science/logic/coq/default.nix @@ -69,7 +69,9 @@ let { case = range "8.7" "8.10"; out = ocamlPackages_4_09; } { case = range "8.5" "8.6"; out = ocamlPackages_4_05; } ] ocamlPackages_4_12; - ocamlBuildInputs = [ ocamlPackages.ocaml ocamlPackages.findlib ] + ocamlNativeBuildInputs = [ ocamlPackages.ocaml ocamlPackages.findlib ] + ++ optional (versionAtLeast "8.14") ocamlPackages.dune_2; + ocamlBuildInputs = [] ++ optional (!versionAtLeast "8.10") ocamlPackages.camlp5 ++ optional (!versionAtLeast "8.13") ocamlPackages.num ++ optional (versionAtLeast "8.13") ocamlPackages.zarith; @@ -79,7 +81,7 @@ self = stdenv.mkDerivation { passthru = { inherit coq-version; - inherit ocamlPackages ocamlBuildInputs; + inherit ocamlPackages ocamlBuildInputs ocamlNativeBuildInputs; # For compatibility inherit (ocamlPackages) ocaml camlp5 findlib num ; emacsBufferSetup = pkgs: '' @@ -129,14 +131,15 @@ self = stdenv.mkDerivation { }; nativeBuildInputs = [ pkg-config ] + ++ ocamlNativeBuildInputs ++ optional buildIde copyDesktopItems + ++ optional (buildIde && versionAtLeast "8.10") wrapGAppsHook ++ optional (!versionAtLeast "8.6") gnumake42; buildInputs = [ ncurses ] ++ ocamlBuildInputs ++ optionals buildIde (if versionAtLeast "8.10" - then [ ocamlPackages.lablgtk3-sourceview3 glib gnome.adwaita-icon-theme wrapGAppsHook ] + then [ ocamlPackages.lablgtk3-sourceview3 glib gnome.adwaita-icon-theme ] else [ ocamlPackages.lablgtk ]) - ++ optional (versionAtLeast "8.14") ocamlPackages.dune_2 ; postPatch = '' @@ -167,7 +170,7 @@ self = stdenv.mkDerivation { prefixKey = "-prefix "; - buildFlags = [ "revision" "coq" "coqide" ] ++ optional (!versionAtLeast "8.14") "bin/votour"; + buildFlags = [ "revision" "coq" ] ++ optional buildIde "coqide" ++ optional (!versionAtLeast "8.14") "bin/votour"; enableParallelBuilding = true; createFindlibDestdir = true; @@ -178,7 +181,7 @@ self = stdenv.mkDerivation { icon = "coq"; desktopName = "CoqIDE"; comment = "Graphical interface for the Coq proof assistant"; - categories = "Development;Science;Math;IDE;GTK"; + categories = [ "Development" "Science" "Math" "IDE" "GTK" ]; }); postInstall = let suffix = if versionAtLeast "8.14" then "-core" else ""; in '' diff --git a/pkgs/applications/science/logic/formula/default.nix b/pkgs/applications/science/logic/formula/default.nix new file mode 100644 index 00000000000..13c13713a72 --- /dev/null +++ b/pkgs/applications/science/logic/formula/default.nix @@ -0,0 +1,32 @@ +{ lib, stdenv, fetchFromGitHub, buildDotnetModule, dotnetCorePackages }: + +buildDotnetModule rec { + pname = "formula-dotnet"; + version = "2.0"; + + src = fetchFromGitHub { + owner = "VUISIS"; + repo = "formula-dotnet"; + rev = "e962438022350dca64335c0603c00d44cb10b528"; + sha256 = "sha256-hVtwV1MdsXaN6ZrGW4RG2HcNcv/hys/5VxGjH9vFdRE="; + }; + + nugetDeps = ./nuget.nix; + projectFile = "Src/CommandLine/CommandLine.csproj"; + + postFixup = if stdenv.isLinux then '' + mv $out/bin/CommandLine $out/bin/formula + '' else lib.optionalString stdenv.isDarwin '' + makeWrapper ${dotnetCorePackages.runtime_5_0}/bin/dotnet $out/bin/formula \ + --add-flags "$out/lib/formula-dotnet/CommandLine.dll" \ + --prefix DYLD_LIBRARY_PATH : $out/lib/formula-dotnet/runtimes/macos/native + ''; + + meta = with lib; { + description = "Formal Specifications for Verification and Synthesis"; + homepage = "https://github.com/VUISIS/formula-dotnet"; + license = licenses.mspl; + maintainers = with maintainers; [ siraben ]; + platforms = platforms.unix; + }; +} diff --git a/pkgs/applications/science/logic/formula/nuget.nix b/pkgs/applications/science/logic/formula/nuget.nix new file mode 100644 index 00000000000..e7ee3005e97 --- /dev/null +++ b/pkgs/applications/science/logic/formula/nuget.nix @@ -0,0 +1,77 @@ +{ fetchNuGet }: [ + (fetchNuGet { pname = "Antlr4.Runtime.Standard"; version = "4.7.2"; sha256 = "1pmrpsgqjfj0nzr1zqzk1m2fm0ynd4nklwq3dhvww08yjg5s0586"; }) + (fetchNuGet { pname = "Microsoft.NETCore.Platforms"; version = "1.1.0"; sha256 = "08vh1r12g6ykjygq5d3vq09zylgb84l63k49jc4v8faw9g93iqqm"; }) + (fetchNuGet { pname = "Microsoft.NETCore.Targets"; version = "1.1.0"; sha256 = "193xwf33fbm0ni3idxzbr5fdq3i2dlfgihsac9jj7whj0gd902nh"; }) + (fetchNuGet { pname = "Microsoft.Win32.Primitives"; version = "4.3.0"; sha256 = "0j0c1wj4ndj21zsgivsc24whiya605603kxrbiw6wkfdync464wq"; }) + (fetchNuGet { pname = "Microsoft.Z3.x64"; version = "4.8.7"; sha256 = "1wxlw29xm5x8vwji2s7gwk39wb88dkbpg76l9s9gq0hqpghwlmdz"; }) + (fetchNuGet { pname = "NETStandard.Library"; version = "1.6.1"; sha256 = "1z70wvsx2d847a2cjfii7b83pjfs34q05gb037fdjikv5kbagml8"; }) + (fetchNuGet { pname = "runtime.debian.8-x64.runtime.native.System.Security.Cryptography.OpenSsl"; version = "4.3.0"; sha256 = "16rnxzpk5dpbbl1x354yrlsbvwylrq456xzpsha1n9y3glnhyx9d"; }) + (fetchNuGet { pname = "runtime.fedora.23-x64.runtime.native.System.Security.Cryptography.OpenSsl"; 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version = "4.3.0"; sha256 = "1xxcx2xh8jin360yjwm4x4cf5y3a2bwpn2ygkfkwkicz7zk50s2z"; }) + (fetchNuGet { pname = "System.Threading.Tasks"; version = "4.3.0"; sha256 = "134z3v9abw3a6jsw17xl3f6hqjpak5l682k2vz39spj4kmydg6k7"; }) + (fetchNuGet { pname = "System.Threading.Timer"; version = "4.3.0"; sha256 = "1nx773nsx6z5whv8kaa1wjh037id2f1cxhb69pvgv12hd2b6qs56"; }) + (fetchNuGet { pname = "System.Threading"; version = "4.3.0"; sha256 = "0rw9wfamvhayp5zh3j7p1yfmx9b5khbf4q50d8k5rk993rskfd34"; }) + (fetchNuGet { pname = "System.Xml.ReaderWriter"; version = "4.3.0"; sha256 = "0c47yllxifzmh8gq6rq6l36zzvw4kjvlszkqa9wq3fr59n0hl3s1"; }) + (fetchNuGet { pname = "System.Xml.XDocument"; version = "4.3.0"; sha256 = "08h8fm4l77n0nd4i4fk2386y809bfbwqb7ih9d7564ifcxr5ssxd"; }) +] diff --git a/pkgs/applications/science/logic/isabelle/default.nix b/pkgs/applications/science/logic/isabelle/default.nix index bdfe881c1c3..aaac288b615 100644 --- a/pkgs/applications/science/logic/isabelle/default.nix +++ b/pkgs/applications/science/logic/isabelle/default.nix @@ -136,7 +136,7 @@ stdenv.mkDerivation rec { icon = "isabelle"; desktopName = "Isabelle"; comment = meta.description; - categories = "Education;Science;Math;"; + categories = [ "Education" "Science" "Math" ]; }; meta = with lib; { diff --git a/pkgs/applications/science/logic/key/default.nix b/pkgs/applications/science/logic/key/default.nix index 769fe6aff23..85a7ecb08c3 100644 --- a/pkgs/applications/science/logic/key/default.nix +++ b/pkgs/applications/science/logic/key/default.nix @@ -38,7 +38,8 @@ let | sh ''; outputHashMode = "recursive"; - outputHash = "sha256-1TWySkS8w7L6Q+V946kcLOnM4hL3fieFvLrF5BZAlh4="; + outputHashAlgo = "sha256"; + outputHash = "sha256-GjBUwJxeyJA6vGrPQVtNpcHb4CJlNlY4kHt1PT21xjo="; }; in stdenv.mkDerivation rec { inherit pname version src sourceRoot; @@ -60,7 +61,7 @@ in stdenv.mkDerivation rec { comment = meta.description; desktopName = "KeY"; genericName = "KeY"; - categories = "Science;"; + categories = [ "Science" ]; }) ]; diff --git a/pkgs/applications/science/logic/lean/default.nix b/pkgs/applications/science/logic/lean/default.nix index 806a3c34df1..22e755bd852 100644 --- a/pkgs/applications/science/logic/lean/default.nix +++ b/pkgs/applications/science/logic/lean/default.nix @@ -2,7 +2,7 @@ stdenv.mkDerivation rec { pname = "lean"; - version = "3.39.1"; + version = "3.39.2"; src = fetchFromGitHub { owner = "leanprover-community"; @@ -11,8 +11,8 @@ stdenv.mkDerivation rec { # from. this is then used to check whether an olean file should be # rebuilt. don't use a tag as rev because this will get replaced into # src/githash.h.in in preConfigure. - rev = "1781ded0d0062f40a7eaf3ead8dcbef4429c6321"; - sha256 = "0xdpbfjfa1q4cnf87nl7l760ivr4agpqmy3i1f2b132sgbjzm1xx"; + rev = "402f41cdedbd46a368fb7807bebe83550d887631"; + sha256 = "0jddakr07ixspw19xblpj1882vxxaljg3fflhn4myvigwzkav334"; }; nativeBuildInputs = [ cmake ]; diff --git a/pkgs/applications/science/logic/logisim-evolution/default.nix b/pkgs/applications/science/logic/logisim-evolution/default.nix index 688c8c319bd..67e699bc63f 100644 --- a/pkgs/applications/science/logic/logisim-evolution/default.nix +++ b/pkgs/applications/science/logic/logisim-evolution/default.nix @@ -20,7 +20,7 @@ stdenv.mkDerivation rec { exec = "logisim-evolution"; icon = "logisim-evolution"; comment = meta.description; - categories = "Education;"; + categories = [ "Education" ]; }) ]; diff --git a/pkgs/applications/science/logic/logisim/default.nix b/pkgs/applications/science/logic/logisim/default.nix index b4741aaed86..06dc024e6d2 100644 --- a/pkgs/applications/science/logic/logisim/default.nix +++ b/pkgs/applications/science/logic/logisim/default.nix @@ -20,7 +20,7 @@ stdenv.mkDerivation rec { exec = "logisim"; icon = "logisim"; comment = meta.description; - categories = "Education;"; + categories = [ "Education" ]; }) ]; diff --git a/pkgs/applications/science/logic/tlaplus/default.nix b/pkgs/applications/science/logic/tlaplus/default.nix index 7d447745a23..8b9f64a8f5b 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 = "1.7.1"; + version = "1.7.2"; src = fetchurl { url = "https://github.com/tlaplus/tlaplus/releases/download/v${version}/tla2tools.jar"; - sha256 = "d532ba31aafe17afba1130f92410d9257454ff7393d1eb2fe032f0c07f352da5"; + sha256 = "sha256-+hhUPkTtWXSoW9LGDA3BZiCuEXaA6o5pPSaRmZ7ZCyI="; }; nativeBuildInputs = [ makeWrapper ]; diff --git a/pkgs/applications/science/logic/tlaplus/tlaps.nix b/pkgs/applications/science/logic/tlaplus/tlaps.nix index 90a4aeb4f8a..14b3055ab36 100644 --- a/pkgs/applications/science/logic/tlaplus/tlaps.nix +++ b/pkgs/applications/science/logic/tlaplus/tlaps.nix @@ -11,10 +11,10 @@ stdenv.mkDerivation rec { pname = "tlaps"; - version = "1.4.3"; + version = "1.4.5"; src = fetchurl { - url = "https://tla.msr-inria.inria.fr/tlaps/dist/current/tlaps-${version}.tar.gz"; - sha256 = "1w5z3ns5xxmhmp8r4x2kjmy3clqam935gmvx82imyxrr1bamx6gf"; + url = "https://tla.msr-inria.inria.fr/tlaps/dist/${version}/tlaps-${version}.tar.gz"; + sha256 = "c296998acd14d5b93a8d5be7ee178007ef179957465966576bda26944b1b7fca"; }; buildInputs = [ ocaml isabelle cvc3 perl wget which ]; @@ -52,7 +52,7 @@ stdenv.mkDerivation rec { homepage = "https://tla.msr-inria.inria.fr/tlaps/content/Home.html"; license = lib.licenses.bsd2; platforms = lib.platforms.unix; - maintainers = [ ]; + maintainers = with lib.maintainers; [ florentc ]; }; } diff --git a/pkgs/applications/science/logic/tlaplus/toolbox.nix b/pkgs/applications/science/logic/tlaplus/toolbox.nix index 21c60d03ac1..7b1ee4384c9 100644 --- a/pkgs/applications/science/logic/tlaplus/toolbox.nix +++ b/pkgs/applications/science/logic/tlaplus/toolbox.nix @@ -18,10 +18,8 @@ let comment = "IDE for TLA+"; desktopName = name; genericName = comment; - categories = "Development"; - extraEntries = '' - StartupWMClass=TLA+ Toolbox - ''; + categories = [ "Development" ]; + startupWMClass = "TLA+ Toolbox"; }; diff --git a/pkgs/applications/science/logic/why3/default.nix b/pkgs/applications/science/logic/why3/default.nix index 78631486554..0f3dab8038e 100644 --- a/pkgs/applications/science/logic/why3/default.nix +++ b/pkgs/applications/science/logic/why3/default.nix @@ -3,15 +3,15 @@ stdenv.mkDerivation rec { pname = "why3"; - version = "1.4.0"; + version = "1.4.1"; src = fetchurl { - url = "https://gforge.inria.fr/frs/download.php/file/38425/why3-${version}.tar.gz"; - sha256 = "0lw0cpx347zz9vvwqibmbxgs80fsd16scgk3isscvwxnajpc3rv8"; + url = "https://why3.gitlabpages.inria.fr/releases/${pname}-${version}.tar.gz"; + sha256 = "sha256:1rqyypzlvagrn43ykl0c5wxyvnry5fl1ykn3xcvlzgghk96yq3jq"; }; buildInputs = with ocamlPackages; [ - ocaml findlib ocamlgraph zarith menhir menhirLib + ocaml findlib ocamlgraph zarith menhir # Emacs compilation of why3.el emacs # Documentation @@ -26,7 +26,7 @@ stdenv.mkDerivation rec { coqPackages.coq coqPackages.flocq ]; - propagatedBuildInputs = with ocamlPackages; [ camlzip num re sexplib ]; + propagatedBuildInputs = with ocamlPackages; [ camlzip menhirLib num re sexplib ]; enableParallelBuilding = true; diff --git a/pkgs/applications/science/logic/workcraft/default.nix b/pkgs/applications/science/logic/workcraft/default.nix index 2829cb59340..0c20faceb54 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 = "3.3.5"; + version = "3.3.6"; src = fetchurl { url = "https://github.com/workcraft/workcraft/releases/download/v${version}/workcraft-v${version}-linux.tar.gz"; - sha256 = "sha256-KErKYK3mmjp5uNdGQnjzUUIEwXT5fqbAPUunH72Mtig="; + sha256 = "sha256-5J4HOTz92ALUcZZr15jJ6vplc3KDwbFCXqjEhlOV4kE="; }; nativeBuildInputs = [ makeWrapper ]; diff --git a/pkgs/applications/science/math/geogebra/default.nix b/pkgs/applications/science/math/geogebra/default.nix index 7ebfe2030d4..8ab498c61d9 100644 --- a/pkgs/applications/science/math/geogebra/default.nix +++ b/pkgs/applications/science/math/geogebra/default.nix @@ -15,8 +15,8 @@ let desktopName = "Geogebra"; genericName = "Geogebra"; comment = meta.description; - categories = "Education;Science;Math;"; - mimeType = "application/vnd.geogebra.file;application/vnd.geogebra.tool;"; + categories = [ "Education" "Science" "Math" ]; + mimeTypes = [ "application/vnd.geogebra.file" "application/vnd.geogebra.tool" ]; }; meta = with lib; { diff --git a/pkgs/applications/science/math/getdp/default.nix b/pkgs/applications/science/math/getdp/default.nix index 5ea3550d08a..5713f84a866 100644 --- a/pkgs/applications/science/math/getdp/default.nix +++ b/pkgs/applications/science/math/getdp/default.nix @@ -2,10 +2,10 @@ stdenv.mkDerivation rec { pname = "getdp"; - version = "3.3.0"; + version = "3.4.0"; src = fetchurl { url = "http://getdp.info/src/getdp-${version}-source.tgz"; - sha256 = "1pfviy2bw8z5y6c15czvlvyjjg9pvpgrj9fr54xfi2gmvs7zkgpf"; + sha256 = "sha256-d5YxJgtMf94PD6EHvIXpPBFPKC+skI/2v1K5Sad51hA="; }; inherit (petsc) mpiSupport; @@ -26,7 +26,7 @@ stdenv.mkDerivation rec { ''; homepage = "http://getdp.info/"; license = licenses.gpl2Plus; - maintainers = with maintainers; [ wucke13 ]; + maintainers = with maintainers; [ ]; platforms = platforms.linux; }; } diff --git a/pkgs/applications/science/math/gmsh/default.nix b/pkgs/applications/science/math/gmsh/default.nix index 76fc20c4b04..4306ae09151 100644 --- a/pkgs/applications/science/math/gmsh/default.nix +++ b/pkgs/applications/science/math/gmsh/default.nix @@ -5,11 +5,11 @@ assert (!blas.isILP64) && (!lapack.isILP64); stdenv.mkDerivation rec { pname = "gmsh"; - version = "4.9.4"; + version = "4.9.5"; src = fetchurl { url = "https://gmsh.info/src/gmsh-${version}-source.tgz"; - sha256 = "sha256-rP8zQtGQfEKaS+PkWW7UT2zUP9WpSrdWZ/SGPNzy92k="; + sha256 = "sha256-/9ZJAIRCCHGciNkaZsKBiJAjEyt6nigsUVSMufbzrUQ="; }; buildInputs = [ diff --git a/pkgs/applications/science/math/gurobi/default.nix b/pkgs/applications/science/math/gurobi/default.nix index 91ee7c1c65e..dc947a94001 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 = "9.1.2"; + version = "9.5.0"; src = fetchurl { url = "https://packages.gurobi.com/${lib.versions.majorMinor version}/gurobi${version}_linux64.tar.gz"; - sha256 = "7f60bd675f79476bb2b32cd632aa1d470f8246f2b033b7652d8de86f6e7e429b"; + sha256 = "sha256-u1QuWl0WhfbjZOrwXqbFVySF/8N6IkUWnPPLQCiLwp4="; }; sourceRoot = "gurobi${builtins.replaceStrings ["."] [""] version}/linux64"; diff --git a/pkgs/applications/science/math/mathematica/l10ns.nix b/pkgs/applications/science/math/mathematica/l10ns.nix index 474c8d1ea06..60841eaa3ee 100644 --- a/pkgs/applications/science/math/mathematica/l10ns.nix +++ b/pkgs/applications/science/math/mathematica/l10ns.nix @@ -8,6 +8,13 @@ let allVersions = with lib; flip map # N.B. Versions in this list should be ordered from newest to oldest. [ { + version = "13.0.1"; + lang = "en"; + language = "English"; + sha256 = "3672a920c1b4af1afd480733f6d67665baf8258757dfe59a6ed6d7440cf26dba"; + installer = "Mathematica_13.0.1_BNDL_LINUX.sh"; + } + { version = "13.0.0"; lang = "en"; language = "English"; diff --git a/pkgs/applications/science/math/polymake/default.nix b/pkgs/applications/science/math/polymake/default.nix index f4f6366465b..d132a98dcb9 100644 --- a/pkgs/applications/science/math/polymake/default.nix +++ b/pkgs/applications/science/math/polymake/default.nix @@ -12,13 +12,13 @@ stdenv.mkDerivation rec { pname = "polymake"; - version = "4.5"; + version = "4.6"; src = fetchurl { # "The minimal version is a packager friendly version which omits # the bundled sources of cdd, lrs, libnormaliz, nauty and jReality." url = "https://polymake.org/lib/exe/fetch.php/download/polymake-${version}-minimal.tar.bz2"; - sha256 = "sha256-6UPUuzHBEvrYUjQONZW8WRwgcGkqFtUBg6OxBFZteZY="; + sha256 = "sha256-QjpE3e8R6uqEV6sV3V2G3beovMbJuxF3b54pWNfc+dA="; }; buildInputs = [ diff --git a/pkgs/applications/science/math/qalculate-gtk/default.nix b/pkgs/applications/science/math/qalculate-gtk/default.nix index 03f4b223803..7ba5838faba 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 rec { pname = "qalculate-gtk"; - version = "3.22.0"; + version = "4.0.0"; src = fetchFromGitHub { owner = "qalculate"; repo = "qalculate-gtk"; rev = "v${version}"; - sha256 = "sha256-BarbO25c103YImOOnjVgwgqpa3mUVvndgJeUHRf2I60="; + sha256 = "sha256-l9lR5MVHWiRz5RG/I/nXRY4GQSSaXXP7PlRNoAu9+yo="; }; hardeningDisable = [ "format" ]; diff --git a/pkgs/applications/science/math/sage/default.nix b/pkgs/applications/science/math/sage/default.nix index 2066087692a..70e24e2608d 100644 --- a/pkgs/applications/science/math/sage/default.nix +++ b/pkgs/applications/science/math/sage/default.nix @@ -1,5 +1,7 @@ { pkgs , withDoc ? false +, requireSageTests ? true +, extraPythonPackages ? ps: [] }: # Here sage and its dependencies are put together. Some dependencies may be pinned @@ -109,7 +111,7 @@ let rpy2 sphinx pillow - ]; + ] ++ extraPythonPackages python3.pkgs; pythonEnv = python3.buildEnv.override { extraLibs = pythonRuntimeDeps; @@ -166,5 +168,5 @@ in # A wrapper around sage that makes sure sage finds its docs (if they were build). callPackage ./sage.nix { inherit sage-tests sage-with-env sagedoc jupyter-kernel-definition; - inherit withDoc; + inherit withDoc requireSageTests; } diff --git a/pkgs/applications/science/math/sage/patches/no-cython-sources-in-tracebacks-on-ipython8.patch b/pkgs/applications/science/math/sage/patches/no-cython-sources-in-tracebacks-on-ipython8.patch new file mode 100644 index 00000000000..871e494c362 --- /dev/null +++ b/pkgs/applications/science/math/sage/patches/no-cython-sources-in-tracebacks-on-ipython8.patch @@ -0,0 +1,52 @@ +diff --git a/src/sage/repl/interface_magic.py b/src/sage/repl/interface_magic.py +index 8a455b69b0..a93e1c9e04 100644 +--- a/src/sage/repl/interface_magic.py ++++ b/src/sage/repl/interface_magic.py +@@ -260,7 +260,7 @@ class InterfaceMagic(object): + 2 + 120 + sage: shell.run_cell('%%gap foo\n1+1;\n') +- ...File "<string>", line unknown ++ ...File...<string>... + SyntaxError: Interface magics have no options, got "foo" + <BLANKLINE> + sage: shell.run_cell('%%gap?') +diff --git a/src/sage/repl/interpreter.py b/src/sage/repl/interpreter.py +index 71dbe429fd..36b1d986d6 100644 +--- a/src/sage/repl/interpreter.py ++++ b/src/sage/repl/interpreter.py +@@ -70,25 +70,6 @@ that shell. The bulk of this functionality is provided through + + TESTS: + +-Check that Cython source code appears in tracebacks:: +- +- sage: from sage.repl.interpreter import get_test_shell +- sage: shell = get_test_shell() +- sage: print("dummy line"); shell.run_cell('1/0') # see #25320 for the reason of the `...` and the dummy line in this test +- dummy line +- ... +- ZeroDivisionError...Traceback (most recent call last) +- <ipython-input-...> in <module>... +- ----> 1 Integer(1)/Integer(0) +- .../sage/rings/integer.pyx in sage.rings.integer.Integer...div... +- ... +- -> ... raise ZeroDivisionError("rational division by zero") +- ....: x = <Rational> Rational.__new__(Rational) +- ....: mpq_div_zz(x.value, ....value, (<Integer>right).value) +- <BLANKLINE> +- ZeroDivisionError: rational division by zero +- sage: shell.quit() +- + Test prompt transformer:: + + sage: from sage.repl.interpreter import SagePromptTransformer +@@ -423,7 +404,7 @@ def SagePreparseTransformer(lines): + sage: from sage.repl.interpreter import get_test_shell + sage: shell = get_test_shell() + sage: shell.run_cell(bad_syntax) +- File "<string>", line unknown ++ File...<string>... + SyntaxError: Mismatched ']' + <BLANKLINE> + sage: shell.quit() diff --git a/pkgs/applications/science/math/sage/sage-src.nix b/pkgs/applications/science/math/sage/sage-src.nix index 019694fd265..73a5881d214 100644 --- a/pkgs/applications/science/math/sage/sage-src.nix +++ b/pkgs/applications/science/math/sage/sage-src.nix @@ -119,6 +119,16 @@ stdenv.mkDerivation rec { # https://trac.sagemath.org/ticket/32959 ./patches/linbox-1.7-upgrade.patch + # To emit better tracebacks, IPython 8 parses Python files using the ast + # module (via the stack_data package). Since Cython is a superset of Python, + # this results in no Cython code being printed in tracebacks. Fixing this + # properly is tracked in https://github.com/alexmojaki/stack_data/issues/21, + # but for now we just disable the corresponding test. An alternative would + # be to revert IPython's IPython/core/ultratb.py, but this would need to be + # Sage-specific (since it would worsen tracebacks for pure Python code). + # Sage tracks this at https://trac.sagemath.org/ticket/33170 + ./patches/no-cython-sources-in-tracebacks-on-ipython8.patch + # https://trac.sagemath.org/ticket/32968 (fetchSageDiff { base = "9.5"; @@ -134,6 +144,17 @@ stdenv.mkDerivation rec { rev = "53532ddd4e2dc92469c1590ebf0c40f8f69bf579"; sha256 = "sha256-6SoSBvIlqvNwZV3jTB6uPdUtaWIOeNmddi2poK/WvGs="; }) + + # TODO: This will not be necessary when Sphinx 4.4.1 is released, + # since some warnings introduced in 4.4.0 will be disabled by then + # (https://github.com/sphinx-doc/sphinx/pull/10126). + # https://trac.sagemath.org/ticket/33272 + (fetchSageDiff { + base = "9.5"; + name = "sphinx-4.4-warnings.patch"; + rev = "97d7958bed441cf2ccc714d88f83d3a8426bc085"; + sha256 = "sha256-y1STE0oxswnijGCsBw8eHWWqpmT1XMznIfA0vvX9pFA="; + }) ]; patches = nixPatches ++ bugfixPatches ++ packageUpgradePatches; diff --git a/pkgs/applications/science/math/sage/sage.nix b/pkgs/applications/science/math/sage/sage.nix index 5805a5c7b0c..96122fba5ab 100644 --- a/pkgs/applications/science/math/sage/sage.nix +++ b/pkgs/applications/science/math/sage/sage.nix @@ -6,6 +6,7 @@ , jupyter-kernel , sagedoc , withDoc +, requireSageTests }: # A wrapper that makes sure sage finds its docs (if they were build) and the @@ -26,7 +27,7 @@ stdenv.mkDerivation rec { buildInputs = [ makeWrapper - + ] ++ lib.optionals requireSageTests [ # This is a hack to make sure sage-tests is evaluated. It doesn't acutally # produce anything of value, it just decouples the tests from the build. sage-tests diff --git a/pkgs/applications/science/misc/bada-bib/default.nix b/pkgs/applications/science/misc/bada-bib/default.nix index 356630329bb..bd2f94ac4a7 100644 --- a/pkgs/applications/science/misc/bada-bib/default.nix +++ b/pkgs/applications/science/misc/bada-bib/default.nix @@ -9,15 +9,15 @@ , glib , gnome , gobject-introspection -, gtk3 +, gtk4 , libxml2 , pkg-config , python3Packages -, wrapGAppsHook }: +, wrapGAppsHook4 }: python3Packages.buildPythonApplication rec { pname = "bada-bib"; - version = "0.4.1"; + version = "0.5.1"; format = "other"; strictDeps = false; # https://github.com/NixOS/nixpkgs/issues/56943 @@ -25,7 +25,7 @@ python3Packages.buildPythonApplication rec { owner = "RogerCrocker"; repo = "BadaBib"; rev = "v${version}"; - sha256 = "sha256-kub2lLauru2RrinzxMDyBVC0htPx0Niv/M6bbmTS7Hk="; + sha256 = "sha256-tb/720WPqcO4w1EMmidjtEidsjZ0dEhe+/vnJPM6kxo="; }; nativeBuildInputs = [ @@ -35,13 +35,13 @@ python3Packages.buildPythonApplication rec { meson ninja pkg-config - wrapGAppsHook + wrapGAppsHook4 ]; buildInputs = [ gdk-pixbuf glib - gtk3 + gtk4 ]; checkInputs = [ diff --git a/pkgs/applications/science/misc/colmap/default.nix b/pkgs/applications/science/misc/colmap/default.nix index 60f9810dfb6..c41c8593a5c 100644 --- a/pkgs/applications/science/misc/colmap/default.nix +++ b/pkgs/applications/science/misc/colmap/default.nix @@ -7,13 +7,13 @@ assert !cudaSupport || cudatoolkit != null; let boost_static = boost17x.override { enableStatic = true; }; in mkDerivation rec { - version = "3.6"; + version = "3.7"; pname = "colmap"; src = fetchFromGitHub { owner = "colmap"; repo = "colmap"; rev = version; - sha256 = "1kfivdmhpmdxjjf30rr57y2iy7xmdpg4h8aw3qgacv8ckfpgda3n"; + sha256 = "sha256-uVAw6qwhpgIpHkXgxttKupU9zU+vD0Za0maw2Iv4x+I="; }; buildInputs = [ @@ -30,7 +30,7 @@ mkDerivation rec { with a graphical and command-line interface. ''; homepage = "https://colmap.github.io/index.html"; - license = licenses.bsd2; + license = licenses.bsd3; platforms = platforms.linux; maintainers = with maintainers; [ lebastr ]; }; diff --git a/pkgs/applications/science/misc/cwltool/default.nix b/pkgs/applications/science/misc/cwltool/default.nix index 86cab93fa20..b3647e0f1b6 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 = "3.1.20220210171524"; + version = "3.1.20220221074232"; format = "setuptools"; src = fetchFromGitHub { owner = "common-workflow-language"; repo = pname; rev = version; - sha256 = "sha256-Z0Btg2NklOwwv9c9lIwE6ONpfwCqZfraNWZd3qxzpGs="; + sha256 = "sha256-hUdwtqYHcfyJ68LzwwCXAxr7YIkJm64brb+kA/WJqU8="; }; postPatch = '' diff --git a/pkgs/applications/science/misc/netlogo/default.nix b/pkgs/applications/science/misc/netlogo/default.nix index b22c6294fba..ed92dfb90da 100644 --- a/pkgs/applications/science/misc/netlogo/default.nix +++ b/pkgs/applications/science/misc/netlogo/default.nix @@ -8,7 +8,7 @@ let icon = name; comment = "A multi-agent programmable modeling environment"; desktopName = "NetLogo"; - categories = "Science;"; + categories = [ "Science" ]; }; in diff --git a/pkgs/applications/science/misc/simgrid/default.nix b/pkgs/applications/science/misc/simgrid/default.nix index 23815442da7..888419fbc86 100644 --- a/pkgs/applications/science/misc/simgrid/default.nix +++ b/pkgs/applications/science/misc/simgrid/default.nix @@ -1,13 +1,14 @@ -{ lib, stdenv, fetchFromGitLab, fetchpatch, cmake, perl, python3, boost, valgrind -# Optional requirements -# Lua 5.3 needed and not available now -#, luaSupport ? false, lua5 +{ stdenv, lib, fetchFromGitLab, cmake, perl, python3, boost , fortranSupport ? false, gfortran -, buildDocumentation ? false, transfig, ghostscript, doxygen +, buildDocumentation ? false, fig2dev, ghostscript, doxygen , buildJavaBindings ? false, openjdk +, buildPythonBindings ? true, python3Packages , modelCheckingSupport ? false, libunwind, libevent, elfutils # Inside elfutils: libelf and libdw +, minimalBindings ? false , debug ? false +, optimize ? (!debug) , moreTests ? false +, withoutBin ? false }: with lib; @@ -18,54 +19,35 @@ in stdenv.mkDerivation rec { pname = "simgrid"; - version = "3.28"; + version = "3.30"; src = fetchFromGitLab { domain = "framagit.org"; owner = pname; repo = pname; rev = "v${version}"; - sha256 = "0vylwgd4i89bvhbgfay0wq953324dwfmmr8jp9b4vvlc9m0017r9"; + sha256 = "1dg8ywqif20g0fs8dnd6364n080nvwx7f444zcfwqwz6iax61qv1"; }; - patches = [ - (fetchpatch { - name = "fix-smpi-dirs-absolute.patch"; - url = "https://framagit.org/simgrid/simgrid/-/commit/71f01e667577be1076646eb841e0a57bd5388545.patch"; - sha256 = "0x3y324b6269687zfy43ilc48bwrs4nb7svh2mpg88lrz53rky15"; - }) - ]; - propagatedBuildInputs = [ boost ]; - nativeBuildInputs = [ cmake perl python3 valgrind ] - ++ optionals fortranSupport [ gfortran ] - ++ optionals buildJavaBindings [ openjdk ] - ++ optionals buildDocumentation [ transfig ghostscript doxygen ] - ++ optionals modelCheckingSupport [ libunwind libevent elfutils ]; + nativeBuildInputs = [ cmake perl python3 ] + ++ optionals fortranSupport [ gfortran ] + ++ optionals buildJavaBindings [ openjdk ] + ++ optionals buildPythonBindings [ python3Packages.pybind11 ] + ++ optionals buildDocumentation [ fig2dev ghostscript doxygen ] + ++ optionals modelCheckingSupport [ libunwind libevent elfutils ]; - #buildInputs = optional luaSupport lua5; - - # Make it so that libsimgrid.so will be found when running programs from - # the build dir. - preConfigure = '' - export LD_LIBRARY_PATH="$PWD/build/lib" - ''; + outputs = [ "out" ] + ++ optionals buildPythonBindings [ "python" ]; - # Release mode is not supported in SimGrid + # "Release" does not work. non-debug mode is Debug compiled with optimization cmakeBuildType = "Debug"; - - # Disable/Enable functionality - # Note: those packages are not packaged in Nixpkgs yet so some options - # are disabled: - # - papi: for enable_smpi_papi - # - ns3: for enable_ns3 - # - lua53: for enable_lua - # - # For more information see: - # https://simgrid.org/doc/3.22/Installing_SimGrid.html#simgrid-compilation-options) 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" @@ -75,27 +57,28 @@ stdenv.mkDerivation rec { "-Denable_mallocators=on" "-Denable_debug=on" "-Denable_smpi=on" + "-Dminimal-bindings=${optionOnOff minimalBindings}" "-Denable_smpi_ISP_testsuite=${optionOnOff moreTests}" "-Denable_smpi_MPICH3_testsuite=${optionOnOff moreTests}" - "-Denable_compile_warnings=${optionOnOff debug}" - "-Denable_compile_optimizations=${optionOnOff (!debug)}" - "-Denable_lto=${optionOnOff (!debug)}" - # "-Denable_lua=${optionOnOff luaSupport}" - # "-Denable_smpi_papi=${optionOnOff moreTests}" + "-Denable_compile_warnings=off" + "-Denable_compile_optimizations=${optionOnOff optimize}" + "-Denable_lto=${optionOnOff optimize}" ]; - makeFlags = optional debug "VERBOSE=1"; - # Some Perl scripts are called to generate test during build which - # is before the fixupPhase, so do this manualy here: + # needed to run tests and to ensure correct shabangs in output scripts preBuild = '' patchShebangs .. ''; - doCheck = true; + # needed by tests (so libsimgrid.so is found) + preConfigure = '' + export LD_LIBRARY_PATH="$PWD/build/lib" + ''; - # Prevent the execution of tests known to fail. + doCheck = true; preCheck = '' + # prevent the execution of tests known to fail cat <<EOW >CTestCustom.cmake SET(CTEST_CUSTOM_TESTS_IGNORE smpi-replay-multiple) EOW @@ -104,6 +87,20 @@ stdenv.mkDerivation rec { make tests -j $NIX_BUILD_CORES ''; + postInstall = lib.optionalString withoutBin '' + # remove bin from output if requested. + # having a specific bin output would be cleaner but it does not work currently (circular references) + rm -rf $out/bin + '' + lib.optionalString buildPythonBindings '' + # manually install the python binding if requested. + mkdir -p $python/lib/python${lib.versions.majorMinor python3.version}/site-packages/ + cp ./lib/simgrid.cpython*.so $python/lib/python${lib.versions.majorMinor python3.version}/site-packages/ + ''; + + # improve debuggability if requested + hardeningDisable = lib.optionals debug [ "fortify" ]; + dontStrip = debug; + meta = { description = "Framework for the simulation of distributed applications"; longDescription = '' @@ -118,5 +115,6 @@ stdenv.mkDerivation rec { license = licenses.lgpl2Plus; maintainers = with maintainers; [ mickours mpoquet ]; platforms = platforms.all; + broken = stdenv.isDarwin; }; } diff --git a/pkgs/applications/science/misc/snakemake/default.nix b/pkgs/applications/science/misc/snakemake/default.nix index 40c102fc682..f4a3da9711d 100644 --- a/pkgs/applications/science/misc/snakemake/default.nix +++ b/pkgs/applications/science/misc/snakemake/default.nix @@ -1,8 +1,8 @@ -{ lib, python3Packages }: +{ lib, python3Packages, fetchFromGitHub }: python3Packages.buildPythonApplication rec { pname = "snakemake"; - version = "6.10.0"; + version = "6.15.5"; propagatedBuildInputs = with python3Packages; [ appdirs @@ -29,12 +29,31 @@ python3Packages.buildPythonApplication rec { wrapt ]; - src = python3Packages.fetchPypi { - inherit pname version; - sha256 = "199a86c8d1fcfdb88c4271a1507b0ab371a15bc407f2dad9b0ab8c43438adff8"; + src = fetchFromGitHub { + owner = "snakemake"; + repo = pname; + rev = "v${version}"; + sha256 = "sha256-i8C7gPLzUzSxNH9xwpr+fUKI1SvpYFsFBlspS74LoWU="; }; - doCheck = false; # Tests depend on Google Cloud credentials at ${HOME}/gcloud-service-key.json + # See + # https://github.com/snakemake/snakemake/blob/main/.github/workflows/main.yml#L99 + # for the current basic test suite. Tibanna and Tes require extra + # setup. + + checkInputs = with python3Packages; [ + pandas + pytestCheckHook + requests-mock + ]; + + disabledTestPaths = [ + "tests/test_tes.py" + "tests/test_tibanna.py" + "tests/test_linting.py" + ]; + + pythonImportsCheck = [ "snakemake" ]; meta = with lib; { homepage = "https://snakemake.github.io"; diff --git a/pkgs/applications/science/molecular-dynamics/gromacs/default.nix b/pkgs/applications/science/molecular-dynamics/gromacs/default.nix index dd4bb6ef142..69810f95b84 100644 --- a/pkgs/applications/science/molecular-dynamics/gromacs/default.nix +++ b/pkgs/applications/science/molecular-dynamics/gromacs/default.nix @@ -19,11 +19,11 @@ let in stdenv.mkDerivation rec { pname = "gromacs"; - version = "2021.5"; + version = "2022"; src = fetchurl { url = "ftp://ftp.gromacs.org/pub/gromacs/gromacs-${version}.tar.gz"; - sha256 = "1dh9l2gcv61h1r6qsg8vr3k1xp8jgd27czzg24kzf4k823k3z9pb"; + sha256 = "0s1bv8nvmdpiyk2yhcmzq8q936hm5jgnqb393101drh2dih0vmps"; }; nativeBuildInputs = [ cmake ]; diff --git a/pkgs/applications/science/programming/groove/default.nix b/pkgs/applications/science/programming/groove/default.nix index 86d77072ee8..f4c323defd6 100644 --- a/pkgs/applications/science/programming/groove/default.nix +++ b/pkgs/applications/science/programming/groove/default.nix @@ -7,7 +7,7 @@ let icon = "groove"; desktopName = "GROOVE Simulator"; comment = "GRaphs for Object-Oriented VErification"; - categories = "Science;ComputerScience;"; + categories = [ "Science" "ComputerScience" ]; }; in stdenv.mkDerivation rec { diff --git a/pkgs/applications/science/robotics/qgroundcontrol/default.nix b/pkgs/applications/science/robotics/qgroundcontrol/default.nix index 76d2318cead..afd05c3e8f7 100644 --- a/pkgs/applications/science/robotics/qgroundcontrol/default.nix +++ b/pkgs/applications/science/robotics/qgroundcontrol/default.nix @@ -6,7 +6,7 @@ mkDerivation rec { pname = "qgroundcontrol"; - version = "4.1.4"; + version = "4.2.0"; qtInputs = [ qtbase qtcharts qtlocation qtserialport qtsvg qtquickcontrols2 @@ -29,6 +29,8 @@ mkDerivation rec { "CONFIG+=StableBuild" # Default install tries to copy Qt files into package "CONFIG+=QGC_DISABLE_BUILD_SETUP" + # Tries to download x86_64-only prebuilt binaries + "DEFINES+=DISABLE_AIRMAP" "../qgroundcontrol.pro" ]; @@ -62,13 +64,13 @@ mkDerivation rec { owner = "mavlink"; repo = pname; rev = "v${version}"; - sha256 = "0lhc36jpy7a5bnysqi574nk5izglj557mf8n9lcsgvzwxlkb2rbf"; + sha256 = "sha256-TBnJQKO9cwxP9q+bIB1CaGnm9npymJ3iEAD9kPJi9JA="; fetchSubmodules = true; }; meta = with lib; { description = "Provides full ground station support and configuration for the PX4 and APM Flight Stacks"; - homepage = "http://qgroundcontrol.org/"; + homepage = "http://qgroundcontrol.com/"; license = licenses.gpl3Plus; platforms = platforms.linux; maintainers = with maintainers; [ lopsided98 ]; |