diff options
Diffstat (limited to 'pkgs/applications/science')
32 files changed, 172 insertions, 418 deletions
diff --git a/pkgs/applications/science/astronomy/kstars/default.nix b/pkgs/applications/science/astronomy/kstars/default.nix index 3769948fd3eff..c4721c490cce2 100644 --- a/pkgs/applications/science/astronomy/kstars/default.nix +++ b/pkgs/applications/science/astronomy/kstars/default.nix @@ -14,11 +14,11 @@ mkDerivation rec { pname = "kstars"; - version = "3.6.3"; + version = "3.6.4"; src = fetchurl { url = "mirror://kde/stable/kstars/kstars-${version}.tar.xz"; - sha256 = "sha256-sve9q4iM/Y8+K64Ceby/KGx5Un5G0o5cCnIxJkXTgug="; + sha256 = "sha256-9MJqJVgSZVBzlLv08Z6i8yO4YV1exsD5+yLJjqIGD20="; }; nativeBuildInputs = [ extra-cmake-modules kdoctools ]; diff --git a/pkgs/applications/science/astronomy/stellarium/default.nix b/pkgs/applications/science/astronomy/stellarium/default.nix index c3880b0b1d2be..2b8d292eada0b 100644 --- a/pkgs/applications/science/astronomy/stellarium/default.nix +++ b/pkgs/applications/science/astronomy/stellarium/default.nix @@ -30,6 +30,14 @@ stdenv.mkDerivation rec { hash = "sha256-7jzS3pRklPsCTgCr3nrywfHCNlBDHuyuGGvrVoI9+A0="; }; + postPatch = lib.optionalString stdenv.isDarwin '' + substituteInPlace CMakeLists.txt \ + --replace 'SET(CMAKE_INSTALL_PREFIX "''${PROJECT_BINARY_DIR}/Stellarium.app/Contents")' \ + 'SET(CMAKE_INSTALL_PREFIX "${placeholder "out"}/Applications/Stellarium.app/Contents")' + substituteInPlace src/CMakeLists.txt \ + --replace "\''${_qt_bin_dir}/../" "${qtmultimedia}/lib/qt-6/" + ''; + nativeBuildInputs = [ cmake perl @@ -44,22 +52,28 @@ stdenv.mkDerivation rec { qtmultimedia qtserialport qttranslations - qtwayland qtwebengine calcmysky qxlsx indilib libnova + ] ++ lib.optionals stdenv.isLinux [ + qtwayland ]; preConfigure = lib.optionalString stdenv.isDarwin '' - substituteInPlace CMakeLists.txt \ - --replace 'SET(CMAKE_INSTALL_PREFIX "''${PROJECT_BINARY_DIR}/Stellarium.app/Contents")' \ - 'SET(CMAKE_INSTALL_PREFIX "${placeholder "out"}/Applications/Stellarium.app/Contents")' + export LC_ALL=en_US.UTF-8 ''; + # fatal error: 'QtSerialPort/QSerialPortInfo' file not found + env.NIX_CFLAGS_COMPILE = lib.optionalString stdenv.isDarwin "-F${qtserialport}/lib"; + dontWrapGApps = true; + postInstall = lib.optionalString stdenv.isDarwin '' + makeWrapper $out/Applications/Stellarium.app/Contents/MacOS/Stellarium $out/bin/stellarium + ''; + preFixup = '' qtWrapperArgs+=("''${gappsWrapperArgs[@]}") ''; diff --git a/pkgs/applications/science/biology/blast/bin.nix b/pkgs/applications/science/biology/blast/bin.nix index 03e61bdcbe867..daae9c096144a 100644 --- a/pkgs/applications/science/biology/blast/bin.nix +++ b/pkgs/applications/science/biology/blast/bin.nix @@ -35,7 +35,7 @@ in stdenv.mkDerivation { inherit pname version src; - nativeBuildInputs = lib.optional stdenv.isLinux [ autoPatchelfHook ]; + nativeBuildInputs = lib.optionals stdenv.isLinux [ autoPatchelfHook ]; buildInputs = [ python3 perl ] ++ lib.optionals stdenv.isLinux [ zlib bzip2 glib libxml2 ]; diff --git a/pkgs/applications/science/biology/dssp/default.nix b/pkgs/applications/science/biology/dssp/default.nix index 762b0515e85c2..59da360d1b6df 100644 --- a/pkgs/applications/science/biology/dssp/default.nix +++ b/pkgs/applications/science/biology/dssp/default.nix @@ -1,19 +1,30 @@ -{ lib, stdenv, fetchFromGitHub, boost, cmake, libcifpp, zlib, }: +{ lib, stdenv, fetchFromGitHub, cmake, libcifpp, libmcfp, zlib }: +let + libcifpp' = libcifpp.overrideAttrs (oldAttrs: rec { + # dssp 4.2.2.1 requires specific version "5.0.8" of libcifpp + version = "5.0.8"; + src = fetchFromGitHub { + inherit (oldAttrs.src) owner repo; + rev = "v${version}"; + sha256 = "sha256-KJGcopGhCWSl+ElG3BPJjBf/kvYJowOHxto6Ci1IMco="; + }; + }); +in stdenv.mkDerivation rec { pname = "dssp"; - version = "4.0.5"; + version = "4.2.2.1"; src = fetchFromGitHub { owner = "PDB-REDO"; repo = pname; rev = "v${version}"; - sha256 = "1x35rdcm4fch66pjbmy73lv0gdb6g9y3v023a66512a6nzsqjsir"; + sha256 = "sha256-vmGvC5d8LTo+pcY9sxwj0d6JvH8Lyk+QSOZo5raBci4="; }; nativeBuildInputs = [ cmake ]; - buildInputs = [ boost libcifpp zlib ]; + buildInputs = [ libcifpp' libmcfp zlib ]; meta = with lib; { description = "Calculate the most likely secondary structure assignment given the 3D structure of a protein"; diff --git a/pkgs/applications/science/biology/subread/default.nix b/pkgs/applications/science/biology/subread/default.nix index d083e202a9ffe..45f0a1d7f4626 100644 --- a/pkgs/applications/science/biology/subread/default.nix +++ b/pkgs/applications/science/biology/subread/default.nix @@ -6,11 +6,11 @@ stdenv.mkDerivation rec { pname = "subread"; - version = "2.0.4"; + version = "2.0.5"; src = fetchurl { url = "mirror://sourceforge/subread/subread-${version}/subread-${version}-source.tar.gz"; - sha256 = "sha256-xUs37YOzQxjY8Rm1wC+50KZcgRGVvMnhdF322vdMots="; + sha256 = "sha256-frZzd+IV4IxfPK44PWOgV9yPRPoUB3smPbxoDchbaSc="; }; buildInputs = [ diff --git a/pkgs/applications/science/biology/tandem-aligner/default.nix b/pkgs/applications/science/biology/tandem-aligner/default.nix index 53daffbe0677e..5f197bd7f79cd 100644 --- a/pkgs/applications/science/biology/tandem-aligner/default.nix +++ b/pkgs/applications/science/biology/tandem-aligner/default.nix @@ -6,14 +6,14 @@ , zlib }: -stdenv.mkDerivation { +stdenv.mkDerivation (finalAttrs: { pname = "TandemAligner"; - version = "unstable-2022-09-17"; + version = "0.1"; src = fetchFromGitHub { owner = "seryrzu"; repo = "tandem_aligner"; - rev = "ac6004f108ad20477045f4d0b037d96051a9df70"; + rev = "v${finalAttrs.version}"; hash = "sha256-iMDj1HZ8LzmZckuAM3lbG3eSJSd/5JGVA6SBs7+AgX8="; }; @@ -58,9 +58,10 @@ stdenv.mkDerivation { meta = { description = "A parameter-free algorithm for sequence alignment"; homepage = "https://github.com/seryrzu/tandem_aligner"; + changelog = "https://github.com/seryrzu/tandem_aligner/releases/tag/v${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/truvari/default.nix b/pkgs/applications/science/biology/truvari/default.nix index 412642f523f2d..cf64070d782f2 100644 --- a/pkgs/applications/science/biology/truvari/default.nix +++ b/pkgs/applications/science/biology/truvari/default.nix @@ -1,47 +1,76 @@ { lib , fetchFromGitHub , python3Packages +, runtimeShell +, bcftools +, htslib }: -python3Packages.buildPythonApplication rec { +let + ssshtest = fetchFromGitHub { + owner = "ryanlayer"; + repo = "ssshtest"; + rev = "d21f7f928a167fca6e2eb31616673444d15e6fd0"; + hash = "sha256-zecZHEnfhDtT44VMbHLHOhRtNsIMWeaBASupVXtmrks="; + }; +in python3Packages.buildPythonApplication rec { pname = "truvari"; - version = "2.1.1"; + version = "4.0.0"; src = fetchFromGitHub { - owner = "spiralgenetics"; + owner = "ACEnglish"; repo = "truvari"; rev = "v${version}"; - sha256 = "14nsdbj063qm175xxixs34cihvsiskc9gym8pg7gbwsh13k5a00h"; + hash = "sha256-UJNMKEV5m2jFqnWvkVAtymkcE2TjPIXp7JqRZpMSqsE="; }; postPatch = '' substituteInPlace setup.py \ - --replace 'python-Levenshtein==0.12.1' 'python-Levenshtein>=0.12.1' + --replace "rich==" "rich>=" + substituteInPlace truvari/utils.py \ + --replace "/bin/bash" "${runtimeShell}" + patchShebangs repo_utils/test_files ''; propagatedBuildInputs = with python3Packages; [ - pyvcf - levenshtein - progressbar2 + rich + edlib pysam - pyfaidx intervaltree + joblib + numpy pytabix - acebinf bwapy - joblib pandas ]; - # no tests - doCheck = false; + makeWrapperArgs = [ + "--prefix" "PATH" ":" (lib.makeBinPath [ bcftools htslib ]) + ]; + pythonImportsCheck = [ "truvari" ]; + nativeCheckInputs = [ + bcftools + htslib + ] ++ (with python3Packages; [ + coverage + ]); + + checkPhase = '' + runHook preCheck + + ln -s ${ssshtest}/ssshtest . + bash repo_utils/truvari_ssshtests.sh + + runHook postCheck + ''; + meta = with lib; { description = "Structural variant comparison tool for VCFs"; - homepage = "https://github.com/spiralgenetics/truvari"; + homepage = "https://github.com/ACEnglish/truvari"; license = licenses.mit; - maintainers = with maintainers; [ scalavision ]; + maintainers = with maintainers; [ natsukium scalavision ]; longDescription = '' Truvari is a benchmarking tool for comparison sets of SVs. It can calculate the recall, precision, and f-measure of a diff --git a/pkgs/applications/science/chemistry/jmol/default.nix b/pkgs/applications/science/chemistry/jmol/default.nix index 98f7ccbfee02a..5ad4ce884ce72 100644 --- a/pkgs/applications/science/chemistry/jmol/default.nix +++ b/pkgs/applications/science/chemistry/jmol/default.nix @@ -25,14 +25,14 @@ let }; in stdenv.mkDerivation rec { - version = "16.1.3"; + version = "16.1.9"; pname = "jmol"; src = let baseVersion = "${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-k1F4OaER9vg8GIi4eqppeh2f0MtlcBSfd4zkewFp2As="; + hash = "sha256-QGduoUKWNUjNlMEYO0wD5+igjuF03V5SVlgq44d2HDs="; }; patchPhase = '' diff --git a/pkgs/applications/science/electronics/bitscope/common.nix b/pkgs/applications/science/electronics/bitscope/common.nix index 1cd23d0f414d7..6a024748daf28 100644 --- a/pkgs/applications/science/electronics/bitscope/common.nix +++ b/pkgs/applications/science/electronics/bitscope/common.nix @@ -1,5 +1,5 @@ { atk -, buildFHSUserEnv +, buildFHSEnv , cairo , dpkg , gdk-pixbuf @@ -56,7 +56,7 @@ let ${(wrapBinary libs) attrs.toolName} ''; }); -in buildFHSUserEnv { +in buildFHSEnv { name = "${attrs.toolName}-${attrs.version}"; runScript = "${pkg.outPath}/bin/${attrs.toolName}"; } // { inherit (pkg) meta name; } diff --git a/pkgs/applications/science/electronics/dataexplorer/default.nix b/pkgs/applications/science/electronics/dataexplorer/default.nix index 535871e4edba8..94d24283990a0 100644 --- a/pkgs/applications/science/electronics/dataexplorer/default.nix +++ b/pkgs/applications/science/electronics/dataexplorer/default.nix @@ -8,11 +8,11 @@ stdenv.mkDerivation rec { pname = "dataexplorer"; - version = "3.7.4"; + version = "3.7.6"; src = fetchurl { url = "mirror://savannah/dataexplorer/dataexplorer-${version}-src.tar.gz"; - sha256 = "sha256-bghI7Hun7ZKUVEj7T58K0oaclnhUGd4z+eIqZF3eXHQ="; + sha256 = "sha256-mwz4o1m2ldjyD4pbwMQxeaI8a8JXzis+s0I+6GW8WaY="; }; nativeBuildInputs = [ ant makeWrapper ]; @@ -45,8 +45,8 @@ stdenv.mkDerivation rec { --set SWT_GTK3 0 \ --set LIBOVERLAY_SCROLLBAR 0 - install -Dvm644 build/misc/GNU_LINUX_JUNSI_ICHARER_DUO_UDEV_RULE/50-Junsi-iCharger-DUO.rules \ - $out/etc/udev/rules.d/50-Junsi-iCharger-DUO.rules + 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 \ $out/etc/udev/rules.d/50-SkyRC-Charger.rules ''; diff --git a/pkgs/applications/science/electronics/gerbv/default.nix b/pkgs/applications/science/electronics/gerbv/default.nix index f83cfa1bf04e1..0c45184e31c74 100644 --- a/pkgs/applications/science/electronics/gerbv/default.nix +++ b/pkgs/applications/science/electronics/gerbv/default.nix @@ -1,13 +1,12 @@ -{ lib, stdenv, fetchgit, fetchpatch, pkg-config, gettext, libtool, automake, autoconf, cairo, gtk2, autoreconfHook }: +{ lib, stdenv, fetchurl, fetchpatch, pkg-config, gettext, libtool, automake, autoconf, cairo, gtk2-x11, autoreconfHook }: -stdenv.mkDerivation { +stdenv.mkDerivation rec { pname = "gerbv"; - version = "2015-10-08"; + version = "2.7.0"; - src = fetchgit { - url = "git://git.geda-project.org/gerbv.git"; - rev = "76b8b67bfa10823ce98f1c4c3b49a2afcadf7659"; - sha256 = "00jn1xhf6kblxc5gac1wvk8zm12fy6sk81nj3jwdag0z6wk3z446"; + src = fetchurl { + url = "mirror://sourceforge/gerbv/${pname}-${version}.tar.gz"; + sha256 = "sha256-xe6AjEIwzmvjrRCrY8VHCYOG1DAicE3iXduTeOYgU7Q="; }; patches = [ @@ -21,15 +20,17 @@ stdenv.mkDerivation { ]; nativeBuildInputs = [ autoreconfHook pkg-config automake autoconf ]; - buildInputs = [ gettext libtool cairo gtk2 ]; + buildInputs = [ gettext libtool cairo gtk2-x11 ]; configureFlags = ["--disable-update-desktop-database"]; + env.NIX_CFLAGS_COMPILE = "-Wno-format-security"; + meta = with lib; { description = "A Gerber (RS-274X) viewer"; homepage = "http://gerbv.geda-project.org/"; maintainers = with maintainers; [ mog ]; - platforms = platforms.linux; + platforms = platforms.unix; license = licenses.gpl2; }; } diff --git a/pkgs/applications/science/electronics/gtkwave/default.nix b/pkgs/applications/science/electronics/gtkwave/default.nix index cc03a2e8c8196..276c59aee7d55 100644 --- a/pkgs/applications/science/electronics/gtkwave/default.nix +++ b/pkgs/applications/science/electronics/gtkwave/default.nix @@ -16,11 +16,11 @@ stdenv.mkDerivation rec { pname = "gtkwave"; - version = "3.3.114"; + version = "3.3.115"; src = fetchurl { url = "mirror://sourceforge/gtkwave/${pname}-gtk3-${version}.tar.gz"; - sha256 = "sha256-zzpfyrs3qWckzeLkp0A73ye1HpFGzmenlNvkcBfPhKw="; + sha256 = "sha256-rbenwCsYygg1oGS2cvbNxR+HXEVLAYmnQ/LOi5HmSqU="; }; nativeBuildInputs = [ pkg-config wrapGAppsHook ]; diff --git a/pkgs/applications/science/electronics/kicad/base.nix b/pkgs/applications/science/electronics/kicad/base.nix index eb65b6881ae20..1b0bdc3ae49ca 100644 --- a/pkgs/applications/science/electronics/kicad/base.nix +++ b/pkgs/applications/science/electronics/kicad/base.nix @@ -94,9 +94,6 @@ stdenv.mkDerivation rec { # should be resolved in the next release "-DCMAKE_CTEST_ARGUMENTS='--exclude-regex;qa_eeschema'" ] - ++ optionals (!stable) [ # workaround for https://gitlab.com/kicad/code/kicad/-/issues/14346 - "-DPYTHON_SITE_PACKAGE_PATH=${placeholder "out"}/${python.sitePackages}/" - ] ++ optional (stable && !withNgspice) "-DKICAD_SPICE=OFF" ++ optionals (!withScripting) [ "-DKICAD_SCRIPTING_WXPYTHON=OFF" diff --git a/pkgs/applications/science/electronics/kicad/versions.nix b/pkgs/applications/science/electronics/kicad/versions.nix index b102da24a3d40..2c81611888196 100644 --- a/pkgs/applications/science/electronics/kicad/versions.nix +++ b/pkgs/applications/science/electronics/kicad/versions.nix @@ -3,45 +3,45 @@ { "kicad" = { kicadVersion = { - version = "7.0.1"; + version = "7.0.2"; src = { - rev = "3b83917a115be1ce2f33a73039f59f8784b5c2e7"; - sha256 = "021safxvyq9qzs08jy3jvpazmhvix4kyl05s9y9hwmyzdmdl2smn"; + rev = "6a45011f421d65a241e1df4a2dc720819922f343"; + sha256 = "0san7pjgvd8niwrki722qb6y46r71rlyspqp43pmkiz55dmz52zx"; }; }; libVersion = { - version = "7.0.1"; + version = "7.0.2"; libSources = { - symbols.rev = "adfe3c06b5750d81580ed44e669b578f49c205eb"; - symbols.sha256 = "14c5gci13m30xv0cmic5jxsmfx9lq3fnd8hyq3mmgkrw7443zy30"; - templates.rev = "66d76556d9e81f8a5be74457686d211c666ed200"; - templates.sha256 = "02i279269mhq7wjhb1yqk90820ncssxl9n7b20qr2r4fmm7jpvxv"; - footprints.rev = "1cf5a1d979cffebd62464c1bb0d7b09c5ee3b8c3"; - footprints.sha256 = "0k0z40wmaq665hjxb6kp1yl3v7clxz49r6ki0chyphsxv1cnixmy"; - packages3d.rev = "e54b5b6368d03f396098448bcce37f2e432dac33"; - packages3d.sha256 = "0nzi7ijfb3rjm98kaa9va2mkh0nfzpq4vfhxkq8j18qhx24h5c8v"; + symbols.rev = "22ed11504c140fded542eeb104cdb02e0a65672e"; + symbols.sha256 = "0aah92rb8yx00z0xwx9z7xn5rrw4cc3z35gr7c0bnb49hiak01jc"; + templates.rev = "331068741c80fee8195646d3dee40f3b840495e7"; + templates.sha256 = "1qi20mrsfn4fxmr1fyphmil2i9p2nzmwk5rlfchc5aq2194nj3lq"; + footprints.rev = "e187e2dfa9bd04d91cad0d875049ab56780b6e32"; + footprints.sha256 = "1qrdznfd4a6kzwd4aaijkpyjy0xnrmi66isq9z52652a8s6ja48v"; + packages3d.rev = "6374ae3db8b43a4d779185b7017fcfe0e1f32590"; + packages3d.sha256 = "1nkk4325jh89vh52ykfnf9pz1k3jk5017gz6r2cia2v4b3jadi31"; }; }; }; "kicad-unstable" = { kicadVersion = { - version = "2023-03-29"; + version = "2023-04-14"; src = { - rev = "d5bc223ff2cd1fbf4e923e23b5bb442bb54faa95"; - sha256 = "0pbzmv9vh4bzhsxj46gjkgh7kk6a0v8gijvkmb56fy5i8xv2ixkn"; + rev = "4a3f77cd9dac9dc5921eb9beaa63d0d3c9c051e5"; + sha256 = "06dsiyvr7zn3cp13w0y63d1qmjlhzsqlvajkximg3pw5mmiljxrr"; }; }; libVersion = { - version = "2023-03-29"; + version = "2023-04-14"; libSources = { - symbols.rev = "36fc1c88921bf32ebf667e027dfe63cca649fd95"; - symbols.sha256 = "177mqvjf3knldnl7pf1abv4pmlgi5cg02ggfwbc655jq4x6x8fkz"; + symbols.rev = "38d4e7e1ab6a9b5d9eee85f687e60467753b2135"; + symbols.sha256 = "0df6fx9b19v6sxrfyggbisw72y66kiwqi05k8mldsgiw6q55gbkc"; templates.rev = "867eef383a0f61015cb69677d5c632d78a2ea01a"; templates.sha256 = "1qi20mrsfn4fxmr1fyphmil2i9p2nzmwk5rlfchc5aq2194nj3lq"; - footprints.rev = "dc4574eb65136d95a7775d09412d5159f8d7832c"; - footprints.sha256 = "1iz4wyiysdii378c3pjgkgwh1cssxbh5jkbhvj7rmi2vmgngl6nc"; - packages3d.rev = "e54b5b6368d03f396098448bcce37f2e432dac33"; - packages3d.sha256 = "0nzi7ijfb3rjm98kaa9va2mkh0nfzpq4vfhxkq8j18qhx24h5c8v"; + footprints.rev = "4da055a2d572ff87e7ecea97cf358ed8c1d46dfc"; + footprints.sha256 = "1xb84284dmcb7mbvzlrxb4v4km3ih7gq856h8cglf9jn8wzlnvrk"; + packages3d.rev = "0f43a0962437feb53bd2083e9f39efffb5a5dd90"; + packages3d.sha256 = "1nkk4325jh89vh52ykfnf9pz1k3jk5017gz6r2cia2v4b3jadi31"; }; }; }; diff --git a/pkgs/applications/science/electronics/nvc/default.nix b/pkgs/applications/science/electronics/nvc/default.nix index 5ec866ea9c490..cb7be33429780 100644 --- a/pkgs/applications/science/electronics/nvc/default.nix +++ b/pkgs/applications/science/electronics/nvc/default.nix @@ -16,28 +16,15 @@ stdenv.mkDerivation rec { pname = "nvc"; - version = "1.9.0"; + version = "1.9.1"; src = fetchFromGitHub { owner = "nickg"; repo = pname; rev = "r${version}"; - hash = "sha256-hsoEAFSXI2bvzZV33jdg1849fipPQlUu3MZVvht54fI="; + hash = "sha256-UeA+6RKZMttLThyAf80ONximXRJNw5mUNM+cyCDTcGM="; }; - patches = [ - # TODO: remove me on next release - (fetchpatch { - url = "https://github.com/nickg/nvc/commit/c857e16c33851f8a5386b97bc0dada2836b5db83.patch"; - hash = "sha256-rvZHI1iQXT9zLpCugg5mGmMZBRbTe9PSHtDG7FVZ67Q="; - }) - ]; - - # TODO: recheck me on next release - postPatch = lib.optionalString stdenv.isLinux '' - sed -i "/vhpi4/d" test/regress/testlist.txt - ''; - nativeBuildInputs = [ autoreconfHook check diff --git a/pkgs/applications/science/logic/sad/default.nix b/pkgs/applications/science/logic/sad/default.nix deleted file mode 100644 index a509d70ed4624..0000000000000 --- a/pkgs/applications/science/logic/sad/default.nix +++ /dev/null @@ -1,41 +0,0 @@ -{ lib, stdenv, fetchurl, haskell, spass }: - -stdenv.mkDerivation rec { - pname = "system-for-automated-deduction"; - version = "2.3.25"; - src = fetchurl { - url = "http://nevidal.org/download/sad-${version}.tar.gz"; - sha256 = "10jd93xgarik7xwys5lq7fx4vqp7c0yg1gfin9cqfch1k1v8ap4b"; - }; - buildInputs = [ haskell.compiler.ghc844 spass ]; - patches = [ - ./patch.patch - # Since the LTS 12.0 update, <> is an operator in Prelude, colliding with - # the <> operator with a different meaning defined by this package - ./monoid.patch - ]; - postPatch = '' - substituteInPlace Alice/Main.hs --replace init.opt $out/init.opt - ''; - installPhase = '' - mkdir -p $out/{bin,provers} - install alice $out/bin - install provers/moses $out/provers - substituteAll provers/provers.dat $out/provers/provers.dat - substituteAll init.opt $out/init.opt - cp -r examples $out - ''; - inherit spass; - meta = { - description = "A program for automated proving of mathematical texts"; - longDescription = '' - The system for automated deduction is intended for automated processing of formal mathematical texts - written in a special language called ForTheL (FORmal THEory Language) or in a traditional first-order language - ''; - license = lib.licenses.gpl3Plus; - maintainers = [ lib.maintainers.schmitthenner ]; - homepage = "http://nevidal.org/sad.en.html"; - platforms = lib.platforms.linux; - broken = true; # ghc-8.4.4 is gone from Nixpkgs - }; -} diff --git a/pkgs/applications/science/logic/sad/monoid.patch b/pkgs/applications/science/logic/sad/monoid.patch deleted file mode 100644 index da9c21bcae918..0000000000000 --- a/pkgs/applications/science/logic/sad/monoid.patch +++ /dev/null @@ -1,51 +0,0 @@ -diff --git a/Alice/Core/Check.hs b/Alice/Core/Check.hs -index 0700fa0388f..69815864710 100644 ---- a/Alice/Core/Check.hs -+++ b/Alice/Core/Check.hs -@@ -18,8 +18,12 @@ - - along with this program. If not, see <http://www.gnu.org/licenses/>. - -} - -+{-# LANGUAGE NoImplicitPrelude #-} -+ - module Alice.Core.Check (fillDef) where - -+import Prelude hiding ((<>)) -+ - import Control.Monad - import Data.Maybe - -diff --git a/Alice/Core/Reason.hs b/Alice/Core/Reason.hs -index c361bcf220d..4e493d8c91b 100644 ---- a/Alice/Core/Reason.hs -+++ b/Alice/Core/Reason.hs -@@ -17,9 +17,12 @@ - - You should have received a copy of the GNU General Public License - - along with this program. If not, see <http://www.gnu.org/licenses/>. - -} -+{-# LANGUAGE NoImplicitPrelude #-} - - module Alice.Core.Reason where - -+import Prelude hiding ((<>)) -+ - import Control.Monad - - import Alice.Core.Base -diff --git a/Alice/Core/Verify.hs b/Alice/Core/Verify.hs -index 4f8550bdf11..0f59d135b16 100644 ---- a/Alice/Core/Verify.hs -+++ b/Alice/Core/Verify.hs -@@ -18,8 +18,12 @@ - - along with this program. If not, see <http://www.gnu.org/licenses/>. - -} - -+{-# LANGUAGE NoImplicitPrelude #-} -+ - module Alice.Core.Verify (verify) where - -+import Prelude hiding ((<>)) -+ - import Control.Monad - import Data.IORef - import Data.Maybe diff --git a/pkgs/applications/science/logic/sad/patch.patch b/pkgs/applications/science/logic/sad/patch.patch deleted file mode 100644 index a5b1d61770837..0000000000000 --- a/pkgs/applications/science/logic/sad/patch.patch +++ /dev/null @@ -1,200 +0,0 @@ -diff -aur serious/sad-2.3-25/Alice/Core/Base.hs sad-2.3-25/Alice/Core/Base.hs ---- serious/sad-2.3-25/Alice/Core/Base.hs 2008-03-29 18:24:12.000000000 +0000 -+++ sad-2.3-25/Alice/Core/Base.hs 2015-11-27 06:38:28.740840823 +0000 -@@ -21,6 +21,7 @@ - module Alice.Core.Base where - - import Control.Monad -+import Control.Applicative - import Data.IORef - import Data.List - import Data.Time -@@ -61,10 +62,21 @@ - type CRMC a b = IORef RState -> IO a -> (b -> IO a) -> IO a - newtype CRM b = CRM { runCRM :: forall a . CRMC a b } - -+instance Functor CRM where -+ fmap = liftM -+ -+instance Applicative CRM where -+ pure = return -+ (<*>) = ap -+ - instance Monad CRM where - return r = CRM $ \ _ _ k -> k r - m >>= n = CRM $ \ s z k -> runCRM m s z (\ r -> runCRM (n r) s z k) - -+instance Alternative CRM where -+ (<|>) = mplus -+ empty = mzero -+ - instance MonadPlus CRM where - mzero = CRM $ \ _ z _ -> z - mplus m n = CRM $ \ s z k -> runCRM m s (runCRM n s z k) k -diff -aur serious/sad-2.3-25/Alice/Core/Thesis.hs sad-2.3-25/Alice/Core/Thesis.hs ---- serious/sad-2.3-25/Alice/Core/Thesis.hs 2008-03-05 13:10:50.000000000 +0000 -+++ sad-2.3-25/Alice/Core/Thesis.hs 2015-11-27 06:35:08.311015166 +0000 -@@ -21,6 +21,7 @@ - module Alice.Core.Thesis (thesis) where - - import Control.Monad -+import Control.Applicative - import Data.List - import Data.Maybe - -@@ -126,11 +127,22 @@ - - newtype TM res = TM { runTM :: [String] -> [([String], res)] } - -+instance Functor TM where -+ fmap = liftM -+ -+instance Applicative TM where -+ pure = return -+ (<*>) = ap -+ - instance Monad TM where - return r = TM $ \ s -> [(s, r)] - m >>= k = TM $ \ s -> concatMap apply (runTM m s) - where apply (s, r) = runTM (k r) s - -+instance Alternative TM where -+ (<|>) = mplus -+ empty = mzero -+ - instance MonadPlus TM where - mzero = TM $ \ _ -> [] - mplus m k = TM $ \ s -> runTM m s ++ runTM k s -diff -aur serious/sad-2.3-25/Alice/Export/Base.hs sad-2.3-25/Alice/Export/Base.hs ---- serious/sad-2.3-25/Alice/Export/Base.hs 2008-03-09 09:36:39.000000000 +0000 -+++ sad-2.3-25/Alice/Export/Base.hs 2015-11-27 06:32:47.782738005 +0000 -@@ -39,7 +39,7 @@ - -- Database reader - - readPrDB :: String -> IO [Prover] --readPrDB file = do inp <- catch (readFile file) $ die . ioeGetErrorString -+readPrDB file = do inp <- catchIOError (readFile file) $ die . ioeGetErrorString - - let dws = dropWhile isSpace - cln = reverse . dws . reverse . dws -diff -aur serious/sad-2.3-25/Alice/Export/Prover.hs sad-2.3-25/Alice/Export/Prover.hs ---- serious/sad-2.3-25/Alice/Export/Prover.hs 2008-03-09 09:36:39.000000000 +0000 -+++ sad-2.3-25/Alice/Export/Prover.hs 2015-11-27 06:36:47.632919161 +0000 -@@ -60,7 +60,7 @@ - when (askIB IBPdmp False ins) $ putStrLn tsk - - seq (length tsk) $ return $ -- do (wh,rh,eh,ph) <- catch run -+ do (wh,rh,eh,ph) <- catchIOError run - $ \ e -> die $ "run error: " ++ ioeGetErrorString e - - hPutStrLn wh tsk ; hClose wh -diff -aur serious/sad-2.3-25/Alice/ForTheL/Base.hs sad-2.3-25/Alice/ForTheL/Base.hs ---- serious/sad-2.3-25/Alice/ForTheL/Base.hs 2008-03-09 09:36:39.000000000 +0000 -+++ sad-2.3-25/Alice/ForTheL/Base.hs 2015-11-27 06:31:51.921230428 +0000 -@@ -226,7 +226,7 @@ - varlist = do vs <- chainEx (char ',') var - nodups vs ; return vs - --nodups vs = unless (null $ dups vs) $ -+nodups vs = unless ((null :: [a] -> Bool) $ dups vs) $ - fail $ "duplicate names: " ++ show vs - - hidden = askPS psOffs >>= \ n -> return ('h':show n) -diff -aur serious/sad-2.3-25/Alice/Import/Reader.hs sad-2.3-25/Alice/Import/Reader.hs ---- serious/sad-2.3-25/Alice/Import/Reader.hs 2008-03-09 09:36:39.000000000 +0000 -+++ sad-2.3-25/Alice/Import/Reader.hs 2015-11-27 06:36:41.818866167 +0000 -@@ -24,7 +24,7 @@ - import Control.Monad - import System.IO - import System.IO.Error --import System.Exit -+import System.Exit hiding (die) - - import Alice.Data.Text - import Alice.Data.Instr -@@ -44,7 +44,7 @@ - readInit "" = return [] - - readInit file = -- do input <- catch (readFile file) $ die file . ioeGetErrorString -+ do input <- catchIOError (readFile file) $ die file . ioeGetErrorString - let tkn = tokenize input ; ips = initPS () - inp = ips { psRest = tkn, psFile = file, psLang = "Init" } - liftM fst $ fireLPM instf inp -@@ -74,7 +74,7 @@ - reader lb fs (ps:ss) [TI (InStr ISfile file)] = - do let gfl = if null file then hGetContents stdin - else readFile file -- input <- catch gfl $ die file . ioeGetErrorString -+ input <- catchIOError gfl $ die file . ioeGetErrorString - let tkn = tokenize input - ips = initPS $ (psProp ps) { tvr_expr = [] } - sps = ips { psRest = tkn, psFile = file, psOffs = psOffs ps } -diff -aur serious/sad-2.3-25/Alice/Parser/Base.hs sad-2.3-25/Alice/Parser/Base.hs ---- serious/sad-2.3-25/Alice/Parser/Base.hs 2008-03-09 09:36:40.000000000 +0000 -+++ sad-2.3-25/Alice/Parser/Base.hs 2015-11-27 06:14:28.616734527 +0000 -@@ -20,6 +20,7 @@ - - module Alice.Parser.Base where - -+import Control.Applicative - import Control.Monad - import Data.List - -@@ -45,11 +46,22 @@ - type CPMC a b c = (c -> CPMS a b) -> (String -> CPMS a b) -> CPMS a b - newtype CPM a c = CPM { runCPM :: forall b . CPMC a b c } - -+instance Functor (CPM a) where -+ fmap = liftM -+ -+instance Applicative (CPM a) where -+ pure = return -+ (<*>) = ap -+ - instance Monad (CPM a) where - return r = CPM $ \ k _ -> k r - m >>= n = CPM $ \ k l -> runCPM m (\ b -> runCPM (n b) k l) l - fail e = CPM $ \ _ l -> l e - -+instance Alternative (CPM a) where -+ (<|>) = mplus -+ empty = mzero -+ - instance MonadPlus (CPM a) where - mzero = CPM $ \ _ _ _ z -> z - mplus m n = CPM $ \ k l s -> runCPM m k l s . runCPM n k l s -diff -aur serious/sad-2.3-25/init.opt sad-2.3-25/init.opt ---- serious/sad-2.3-25/init.opt 2007-10-11 15:25:45.000000000 +0000 -+++ sad-2.3-25/init.opt 2015-11-27 07:23:41.372816854 +0000 -@@ -1,6 +1,6 @@ - # Alice init options --[library examples] --[provers provers/provers.dat] -+[library @out@/examples] -+[provers @out@/provers/provers.dat] - [prover spass] - [timelimit 3] - [depthlimit 7] -diff -aur serious/sad-2.3-25/provers/provers.dat sad-2.3-25/provers/provers.dat ---- serious/sad-2.3-25/provers/provers.dat 2008-08-26 21:20:25.000000000 +0000 -+++ sad-2.3-25/provers/provers.dat 2015-11-27 07:24:18.878169702 +0000 -@@ -3,7 +3,7 @@ - Pmoses - LMoses - Fmoses --Cprovers/moses -+C@out@/provers/moses - Yproved in - Nfound unprovable in - Utimeout in -@@ -12,7 +12,7 @@ - Pspass - LSPASS - Fdfg --Cprovers/SPASS -CNFOptSkolem=0 -PProblem=0 -PGiven=0 -Stdin -TimeLimit=%d -+C@spass@/bin/SPASS -CNFOptSkolem=0 -PProblem=0 -PGiven=0 -Stdin -TimeLimit=%d - YSPASS beiseite: Proof found. - NSPASS beiseite: Completion found. - USPASS beiseite: Ran out of time. diff --git a/pkgs/applications/science/logic/tlaplus/default.nix b/pkgs/applications/science/logic/tlaplus/default.nix index 4572a06d63378..abbcd417693e4 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 = "1.7.2"; + version = "1.7.3"; src = fetchurl { url = "https://github.com/tlaplus/tlaplus/releases/download/v${version}/tla2tools.jar"; - sha256 = "sha256-+hhUPkTtWXSoW9LGDA3BZiCuEXaA6o5pPSaRmZ7ZCyI="; + sha256 = "sha256-5P8V6oH05voSXAgwBDclSxdxdMalrfaNpElkar4IUZ0="; }; nativeBuildInputs = [ makeWrapper ]; diff --git a/pkgs/applications/science/logic/z3/default.nix b/pkgs/applications/science/logic/z3/default.nix index f810a5a56739a..e2842d9d15a4f 100644 --- a/pkgs/applications/science/logic/z3/default.nix +++ b/pkgs/applications/science/logic/z3/default.nix @@ -92,8 +92,8 @@ in sha256 = "sha256-ItmtZHDhCeLAVtN7K80dqyAh20o7TM4xk2sTb9QgHvk="; }; z3_4_8 = common { - version = "4.8.15"; - sha256 = "0xkwqz0y5d1lfb6kfqy8wn8n2dqalzf4c8ghmjsajc1bpdl70yc5"; + version = "4.8.17"; + sha256 = "sha256-BSwjgOU9EgCcm18Zx0P9mnoPc9ZeYsJwEu0ffnACa+8="; }; z3_4_8_5 = common { tag = "Z3"; diff --git a/pkgs/applications/science/machine-learning/streamlit/default.nix b/pkgs/applications/science/machine-learning/streamlit/default.nix index ad22d57882ed6..3db5356b49643 100755 --- a/pkgs/applications/science/machine-learning/streamlit/default.nix +++ b/pkgs/applications/science/machine-learning/streamlit/default.nix @@ -26,12 +26,12 @@ buildPythonApplication rec { pname = "streamlit"; - version = "1.18.1"; + version = "1.21.0"; format = "wheel"; # source currently requires pipenv src = fetchPypi { inherit pname version format; - hash = "sha256-lO2QfM/G+4M55f8JCZBwk10SkMp4gXb68KncHm90k7g="; + hash = "sha256-BYYlmJUqkSbhZlLKpbyI7u6nsnc68lLi2szxyEzqrvQ="; }; propagatedBuildInputs = [ diff --git a/pkgs/applications/science/math/form/default.nix b/pkgs/applications/science/math/form/default.nix index 73fe0cfb5dc36..c56ee432bdae0 100644 --- a/pkgs/applications/science/math/form/default.nix +++ b/pkgs/applications/science/math/form/default.nix @@ -1,13 +1,13 @@ { lib, stdenv, fetchurl, gmp, zlib }: stdenv.mkDerivation { - version = "4.3.0"; + version = "4.3.1"; pname = "form"; # This tarball is released by author, it is not downloaded from tag, so can't use fetchFromGitHub src = fetchurl { - url = "https://github.com/vermaseren/form/releases/download/v4.3.0/form-4.3.0.tar.gz"; - sha256 = "sha256-sjTg0JX3PssJBM3DsNjYMjqfp/RncKUvsiJnxiSq+/Y="; + url = "https://github.com/vermaseren/form/releases/download/v4.3.1/form-4.3.1.tar.gz"; + sha256 = "sha256-8fUS3DT+m71rGfLf7wX8uZEt+0PINop1t5bsRy7ou84="; }; buildInputs = [ gmp zlib ]; diff --git a/pkgs/applications/science/math/glsurf/default.nix b/pkgs/applications/science/math/glsurf/default.nix index ec3bb4c795b32..b4e8c6fb23db0 100644 --- a/pkgs/applications/science/math/glsurf/default.nix +++ b/pkgs/applications/science/math/glsurf/default.nix @@ -67,5 +67,6 @@ stdenv.mkDerivation rec { homepage = "https://raffalli.eu/~christophe/glsurf/"; description = "A program to draw implicit surfaces and curves"; license = lib.licenses.gpl2Plus; + platforms = lib.platforms.all; }; } diff --git a/pkgs/applications/science/math/jags/default.nix b/pkgs/applications/science/math/jags/default.nix index 1acc6a287ca50..0878070136943 100644 --- a/pkgs/applications/science/math/jags/default.nix +++ b/pkgs/applications/science/math/jags/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "JAGS"; - version = "4.3.1"; + version = "4.3.2"; src = fetchurl { url = "mirror://sourceforge/mcmc-jags/JAGS-${version}.tar.gz"; - sha256 = "sha256-+SWDVbXp6xO9M8X6cg8MvrrOp9CkpCtxsPsUUB7hQik="; + sha256 = "sha256-hx9VavQDp8LOag8C8Vz4WlcnY+CT0mZY66xVxKtHL8g="; }; nativeBuildInputs = [ gfortran ]; diff --git a/pkgs/applications/science/math/nasc/default.nix b/pkgs/applications/science/math/nasc/default.nix index f420c940f35c6..d25f0ad344966 100644 --- a/pkgs/applications/science/math/nasc/default.nix +++ b/pkgs/applications/science/math/nasc/default.nix @@ -60,6 +60,8 @@ stdenv.mkDerivation rec { substituteInPlace subprojects/libqalculate/libqalculate/Calculator-plot.cc \ --replace 'commandline = "gnuplot"' 'commandline = "${gnuplot}/bin/gnuplot"' \ --replace '"gnuplot - ' '"${gnuplot}/bin/gnuplot - ' + substituteInPlace subprojects/libqalculate/libqalculate/meson.build \ + --replace "link_with: 'libqalculate_lib_static'" "link_with: libqalculate_lib_static" ''; passthru = { @@ -80,6 +82,5 @@ stdenv.mkDerivation rec { platforms = platforms.linux; license = licenses.gpl3Plus; mainProgram = "com.github.parnold_x.nasc"; - broken = true; # at 2022-09-23 }; } diff --git a/pkgs/applications/science/math/qalculate-gtk/default.nix b/pkgs/applications/science/math/qalculate-gtk/default.nix index 0c82e7ebf376b..573b42c39f622 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 = "4.6.0"; + version = "4.6.1"; src = fetchFromGitHub { owner = "qalculate"; repo = "qalculate-gtk"; rev = "v${version}"; - sha256 = "sha256-RdvoBs/QeBR032nMh79TLMGU6U7dsY6Ep+QKq4IKRTk="; + sha256 = "sha256-eBclDq9Uiu5rA74tlBkOiP3fRwAZn84F3LPA2cKkuw8="; }; hardeningDisable = [ "format" ]; diff --git a/pkgs/applications/science/math/qalculate-qt/default.nix b/pkgs/applications/science/math/qalculate-qt/default.nix index 67c7f6fb4a61e..21ab877b7a0ce 100644 --- a/pkgs/applications/science/math/qalculate-qt/default.nix +++ b/pkgs/applications/science/math/qalculate-qt/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "qalculate-qt"; - version = "4.6.0"; + version = "4.6.1"; src = fetchFromGitHub { owner = "qalculate"; repo = "qalculate-qt"; rev = "v${version}"; - hash = "sha256-/TDzjlB8rW/TorndcLbxY9pc3q7vY3M6eLxBRfnBs9Y="; + hash = "sha256-9DT1U0iKj5C/Tc9MggEr/RwHhVr4GSOJQVhTiLFk9NY="; }; nativeBuildInputs = [ qmake intltool pkg-config wrapQtAppsHook ]; diff --git a/pkgs/applications/science/math/sage/patches/ipywidgets-on_submit-deprecationwarning.patch b/pkgs/applications/science/math/sage/patches/ipywidgets-on_submit-deprecationwarning.patch deleted file mode 100644 index b0f3634340f53..0000000000000 --- a/pkgs/applications/science/math/sage/patches/ipywidgets-on_submit-deprecationwarning.patch +++ /dev/null @@ -1,13 +0,0 @@ -diff --git a/src/sage/interacts/library.py b/src/sage/interacts/library.py -index 06d680109a..139b00bfd1 100644 ---- a/src/sage/interacts/library.py -+++ b/src/sage/interacts/library.py -@@ -1434,6 +1434,8 @@ def riemann_sum( - creates the mathlet:: - - sage: interacts.calculus.riemann_sum() -+ ... -+ DeprecationWarning: on_submit is deprecated. Instead, set the .continuous_update attribute to False and observe the value changing with: mywidget.observe(callback, 'value'). - Manual interactive function <function riemann_sum at ...> with 9 widgets - title: HTMLText(value='<h2>Riemann integral with random sampling</h2>') - f: EvalText(value='x^2+1', description='$f(x)=$', layout=Layout(max_width='41em')) diff --git a/pkgs/applications/science/math/sage/sage-src.nix b/pkgs/applications/science/math/sage/sage-src.nix index 8913d636fae98..f2e02685416cd 100644 --- a/pkgs/applications/science/math/sage/sage-src.nix +++ b/pkgs/applications/science/math/sage/sage-src.nix @@ -141,12 +141,23 @@ stdenv.mkDerivation rec { sha256 = "sha256-YdPnMsjXBm9ZRm6a8hH8rSynkrABjLoIzqwp3F/rKAw="; }) + # https://github.com/sagemath/sage/pull/35336, merged in 10.0.beta8 + (fetchpatch { + name = "ipywidgets-8.0.5-upgrade.patch"; + url = "https://github.com/sagemath/sage/commit/7ab3e3aa81d47a35d09161b965bba8ab16fd5c9e.diff"; + sha256 = "sha256-WjdsPTui6uv92RerlV0mqltmLaxADvz+3aqSvxBFmfU="; + }) + + # https://github.com/sagemath/sage/pull/35499 + (fetchpatch { + name = "ipywidgets-8.0.5-upgrade-part-deux.patch"; + url = "https://github.com/sagemath/sage/pull/35499.diff"; + sha256 = "sha256-uNCjLs9qrARTQNsq1+kTdvuV2A1M4xx5b1gWh5c55X0="; + }) + # rebased from https://github.com/sagemath/sage/pull/34994, merged in sage 10.0.beta2 ./patches/numpy-1.24-upgrade.patch - # temporarily paper over https://github.com/jupyter-widgets/ipywidgets/issues/3669 - ./patches/ipywidgets-on_submit-deprecationwarning.patch - # Sage uses mixed integer programs (MIPs) to find edge disjoint # spanning trees. For some reason, aarch64 glpk takes much longer # than x86_64 glpk to solve such MIPs. Since the MIP formulation diff --git a/pkgs/applications/science/misc/foldingathome/client.nix b/pkgs/applications/science/misc/foldingathome/client.nix index 47a86fa2aeaf1..c927df9a54916 100644 --- a/pkgs/applications/science/misc/foldingathome/client.nix +++ b/pkgs/applications/science/misc/foldingathome/client.nix @@ -1,6 +1,6 @@ { lib, stdenv , autoPatchelfHook -, buildFHSUserEnv +, buildFHSEnv , dpkg , fetchurl , gcc-unwrapped @@ -35,7 +35,7 @@ let installPhase = "cp -ar usr $out"; }; in -buildFHSUserEnv { +buildFHSEnv { name = fahclient.name; targetPkgs = pkgs': [ diff --git a/pkgs/applications/science/misc/root/default.nix b/pkgs/applications/science/misc/root/default.nix index 037b8dfa09c75..2ebfd4a1a87a7 100644 --- a/pkgs/applications/science/misc/root/default.nix +++ b/pkgs/applications/science/misc/root/default.nix @@ -191,7 +191,7 @@ stdenv.mkDerivation rec { "-Dpythia6=OFF" "-Dpythia8=OFF" "-Drfio=OFF" - "-Droot7=OFF" + "-Droot7=ON" "-Dsqlite=OFF" "-Dssl=ON" "-Dtmva=ON" diff --git a/pkgs/applications/science/misc/sasview/default.nix b/pkgs/applications/science/misc/sasview/default.nix index ca94be96d64e3..ddc0cdfa4e5b8 100644 --- a/pkgs/applications/science/misc/sasview/default.nix +++ b/pkgs/applications/science/misc/sasview/default.nix @@ -25,6 +25,12 @@ python3.pkgs.buildPythonApplication rec { }) ]; + # AttributeError: module 'numpy' has no attribute 'float'. + postPatch = '' + substituteInPlace src/sas/sascalc/pr/p_invertor.py \ + --replace "dtype=np.float)" "dtype=float)" + ''; + nativeBuildInputs = [ python3.pkgs.pyqt5 wrapQtAppsHook |