diff options
Diffstat (limited to 'pkgs/applications/science')
11 files changed, 32 insertions, 116 deletions
diff --git a/pkgs/applications/science/astronomy/calcmysky/default.nix b/pkgs/applications/science/astronomy/calcmysky/default.nix index cf762d36de74..9b7f50415ecd 100644 --- a/pkgs/applications/science/astronomy/calcmysky/default.nix +++ b/pkgs/applications/science/astronomy/calcmysky/default.nix @@ -11,13 +11,13 @@ stdenv.mkDerivation rec { pname = "calcmysky"; - version = "0.3.1"; + version = "0.3.2"; src = fetchFromGitHub { owner = "10110111"; repo = "CalcMySky"; rev = "refs/tags/v${version}"; - hash = "sha256-oqYOXoIPVqCD3HL7ShNoF89W725hFHX0Ei/yVJNTS5I="; + hash = "sha256-AP6YkORbvH8PzF869s2OWbTwTfwMC+RLJx3V3BqVy88="; }; nativeBuildInputs = [ cmake wrapQtAppsHook ]; diff --git a/pkgs/applications/science/biology/igv/default.nix b/pkgs/applications/science/biology/igv/default.nix index 6959a14df250..0d8d87ac4109 100644 --- a/pkgs/applications/science/biology/igv/default.nix +++ b/pkgs/applications/science/biology/igv/default.nix @@ -2,10 +2,10 @@ stdenv.mkDerivation rec { pname = "igv"; - version = "2.17.2"; + version = "2.17.3"; src = fetchzip { url = "https://data.broadinstitute.org/igv/projects/downloads/${lib.versions.majorMinor version}/IGV_${version}.zip"; - sha256 = "sha256-KMLy+YxRT5EDZhfqkZRHrPR9BmBg6hFWLSNwJhZ2I+k="; + sha256 = "sha256-SGqkWBv4nol0+lnGN7wBHJvndcIqZ5+Wt1wAcXA42cU="; }; installPhase = '' diff --git a/pkgs/applications/science/biology/seqkit/default.nix b/pkgs/applications/science/biology/seqkit/default.nix index 9682265b9342..1c572ba56354 100644 --- a/pkgs/applications/science/biology/seqkit/default.nix +++ b/pkgs/applications/science/biology/seqkit/default.nix @@ -5,16 +5,16 @@ buildGoModule rec { pname = "seqkit"; - version = "2.7.0"; + version = "2.8.0"; src = fetchFromGitHub { owner = "shenwei356"; repo = "seqkit"; rev = "v${version}"; - sha256 = "sha256-tnVkFING9BH/iNOdKeCsSk4ln2fLUUpI5ASaQ7CCdrg="; + sha256 = "sha256-JsrmRUbSNCFJ58tIblKq+VRXCD1mBeCAcosDGiVb5Gs="; }; - vendorHash = "sha256-o7XGBI05BK7kOBagVV2eteJmkzLTmio41KOm46GdzDU="; + vendorHash = "sha256-0//kySYhNmfiwiys/Ku0/8RzKpnxO0+byD8pcIkvDY0="; meta = with lib; { description = "cross-platform and ultrafast toolkit for FASTA/Q file manipulation"; diff --git a/pkgs/applications/science/chemistry/autodock-vina/default.nix b/pkgs/applications/science/chemistry/autodock-vina/default.nix index 499bedb929ff..d56b8a02a20d 100644 --- a/pkgs/applications/science/chemistry/autodock-vina/default.nix +++ b/pkgs/applications/science/chemistry/autodock-vina/default.nix @@ -20,10 +20,10 @@ stdenv.mkDerivation (finalAttrs: { hash = "sha256-yguUMEX0tn75wKrPKyqlCYbBFaEwC5b1s3k9xept1Fw="; }; - sourceRoot = - if stdenv.isDarwin - then "source/build/mac/release" - else "source/build/linux/release"; + sourceRoot = "${finalAttrs.src.name}/build/${ + if stdenv.hostPlatform.isDarwin then "mac" + else "linux" + }/release"; buildInputs = [ boost' diff --git a/pkgs/applications/science/electronics/fritzing/default.nix b/pkgs/applications/science/electronics/fritzing/default.nix index efe70f125d04..955edb9b59ae 100644 --- a/pkgs/applications/science/electronics/fritzing/default.nix +++ b/pkgs/applications/science/electronics/fritzing/default.nix @@ -54,28 +54,29 @@ stdenv.mkDerivation { qtbase qtsvg qtserialport - qtwayland qt5compat boost libgit2 quazip libngspice clipper + ] ++ lib.optionals stdenv.isLinux [ + qtwayland ]; postPatch = '' # Use packaged quazip, libgit and ngspice sed -i "/pri\/quazipdetect.pri/d" phoenix.pro sed -i "/pri\/spicedetect.pri/d" phoenix.pro - substituteInPlace phoenix.pro \ - --replace 'LIBGIT_STATIC = true' 'LIBGIT_STATIC = false' + substituteInPlace pri/libgit2detect.pri \ + --replace-fail 'LIBGIT_STATIC = true' 'LIBGIT_STATIC = false' #TODO: Do not hardcode SHA. substituteInPlace src/fapplication.cpp \ - --replace 'PartsChecker::getSha(dir.absolutePath());' '"${partsSha}";' + --replace-fail 'PartsChecker::getSha(dir.absolutePath());' '"${partsSha}";' substituteInPlace phoenix.pro \ - --replace "6.5.10" "${qtbase.version}" + --replace-fail "6.5.10" "${qtbase.version}" mkdir parts cp -a ${parts}/* parts/ @@ -92,6 +93,13 @@ stdenv.mkDerivation { "phoenix.pro" ]; + postInstall = lib.optionalString stdenv.isDarwin '' + mkdir $out/Applications + mv $out/bin/Fritzing.app $out/Applications/Fritzing.app + cp FritzingInfo.plist $out/Applications/Fritzing.app/Contents/Info.plist + makeWrapper $out/Applications/Fritzing.app/Contents/MacOS/Fritzing $out/bin/Fritzing + ''; + postFixup = '' # generate the parts.db file QT_QPA_PLATFORM=offscreen "$out/bin/Fritzing" \ @@ -105,7 +113,7 @@ stdenv.mkDerivation { homepage = "https://fritzing.org/"; license = with licenses; [ gpl3 cc-by-sa-30 ]; maintainers = with maintainers; [ robberer muscaln ]; - platforms = platforms.linux; + platforms = platforms.unix; mainProgram = "Fritzing"; }; } diff --git a/pkgs/applications/science/electronics/magic-vlsi/default.nix b/pkgs/applications/science/electronics/magic-vlsi/default.nix index 15130deefc58..50be90716e09 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 = "8.3.463"; + version = "8.3.464"; src = fetchurl { url = "http://opencircuitdesign.com/magic/archive/magic-${version}.tgz"; - sha256 = "sha256-ba5kTz5ncsEPTh0a0/tbp37qFogUQ+W4p2rPNFLNIAY="; + sha256 = "sha256-ICXFskoB/mqKPgjWeIoJ81H2eg4dPSj0bHY7S5/A858="; }; nativeBuildInputs = [ python3 ]; diff --git a/pkgs/applications/science/logic/coq/default.nix b/pkgs/applications/science/logic/coq/default.nix index e52a51936180..37a8aba7d8c7 100644 --- a/pkgs/applications/science/logic/coq/default.nix +++ b/pkgs/applications/science/logic/coq/default.nix @@ -57,6 +57,7 @@ let "8.17.1".sha256 = "sha256-x+RwkbxMg9aR0L3WSCtpIz8jwA5cJA4tXAtHMZb20y4="; "8.18.0".sha256 = "sha256-WhiBs4nzPHQ0R24xAdM49kmxSCPOxiOVMA1iiMYunz4="; "8.19.0".sha256 = "sha256-ixsYCvCXpBHqJ71hLQklphlwoOO3i/6w2PJjllKqf9k="; + "8.19.1".sha256 = "sha256-kmZ8Uk8jpzjOd67aAPp3C+vU2oNaBw9pr7+Uixcgg94="; }; releaseRev = v: "V${v}"; fetched = import ../../../../build-support/coq/meta-fetch/default.nix diff --git a/pkgs/applications/science/math/eigenmath/default.nix b/pkgs/applications/science/math/eigenmath/default.nix index 49515a6601d4..674a5ea0d973 100644 --- a/pkgs/applications/science/math/eigenmath/default.nix +++ b/pkgs/applications/science/math/eigenmath/default.nix @@ -7,13 +7,13 @@ stdenv.mkDerivation rec { pname = "eigenmath"; - version = "unstable-2024-03-06"; + version = "unstable-2024-03-11"; src = fetchFromGitHub { owner = "georgeweigt"; repo = pname; - rev = "ff2a5f89969e106f57ad624ac3897e06f26692d7"; - hash = "sha256-54nw734EjICaac8PvdgiGeDWdJTCXnWVUJL2uE937E4="; + rev = "dfa24af6c747e1c90d79a462c2a5a0716b3a1dc0"; + hash = "sha256-kgC+E/ecgl27Hs+qCyqg8CjbEyB91AgN397DST/dPMI="; }; checkPhase = let emulator = stdenv.hostPlatform.emulator buildPackages; in '' diff --git a/pkgs/applications/science/math/primecount/default.nix b/pkgs/applications/science/math/primecount/default.nix deleted file mode 100644 index c3e2565989ed..000000000000 --- a/pkgs/applications/science/math/primecount/default.nix +++ /dev/null @@ -1,56 +0,0 @@ -{ lib -, stdenv -, fetchFromGitHub -, cmake -, primesieve -}: - -stdenv.mkDerivation rec { - pname = "primecount"; - version = "7.10"; - - src = fetchFromGitHub { - owner = "kimwalisch"; - repo = "primecount"; - rev = "v${version}"; - hash = "sha256-z7sHGR6zZSTV1PbL0WPGHf52CYQ572KC1yznCuIEJbQ="; - }; - - nativeBuildInputs = [ - cmake - ]; - - buildInputs = [ - primesieve - ]; - - cmakeFlags = [ - "-DBUILD_LIBPRIMESIEVE=ON" - "-DBUILD_PRIMECOUNT=ON" - "-DBUILD_SHARED_LIBS=ON" - "-DBUILD_STATIC_LIBS=OFF" - "-DBUILD_TESTS=ON" - ]; - - meta = with lib; { - homepage = "https://github.com/kimwalisch/primecount"; - changelog = "https://github.com/kimwalisch/primecount/blob/v${version}/ChangeLog"; - description = "Fast prime counting function implementations"; - longDescription = '' - primecount is a command-line program and C/C++ library that counts the - primes below an integer x ≤ 10^31 using highly optimized implementations - of the combinatorial prime counting algorithms. - - primecount includes implementations of all important combinatorial prime - counting algorithms known up to this date all of which have been - parallelized using OpenMP. primecount contains the first ever open source - implementations of the Deleglise-Rivat algorithm and Xavier Gourdon's - algorithm (that works). primecount also features a novel load balancer - that is shared amongst all implementations and that scales up to hundreds - of CPU cores. primecount has already been used to compute several prime - counting function world records. - ''; - license = licenses.bsd2; - inherit (primesieve.meta) maintainers platforms; - }; -} diff --git a/pkgs/applications/science/math/primesieve/default.nix b/pkgs/applications/science/math/primesieve/default.nix deleted file mode 100644 index 4d3c06bd9287..000000000000 --- a/pkgs/applications/science/math/primesieve/default.nix +++ /dev/null @@ -1,37 +0,0 @@ -{ lib -, stdenv -, fetchFromGitHub -, cmake -}: - -stdenv.mkDerivation rec { - pname = "primesieve"; - version = "12.1"; - - src = fetchFromGitHub { - owner = "kimwalisch"; - repo = "primesieve"; - rev = "v${version}"; - hash = "sha256-AHl2GfZ1oJ8ZyjJzvg10AqN7TA7HFZ+qa6N2v51Qa78="; - }; - - nativeBuildInputs = [ cmake ]; - - meta = with lib; { - homepage = "https://primesieve.org/"; - changelog = "https://github.com/kimwalisch/primesieve/blob/v${version}/ChangeLog"; - description = "Fast C/C++ prime number generator"; - longDescription = '' - primesieve is a command-line program and C/C++ library for quickly - generating prime numbers. It is very cache efficient, it detects your - CPU's L1 & L2 cache sizes and allocates its main data structures - accordingly. It is also multi-threaded by default, it uses all available - CPU cores whenever possible i.e. if sequential ordering is not - required. primesieve can generate primes and prime k-tuplets up to 264. - ''; - license = licenses.bsd2; - maintainers = teams.sage.members ++ - (with maintainers; [ abbradar AndersonTorres ]); - platforms = platforms.unix; - }; -} diff --git a/pkgs/applications/science/misc/openrefine/default.nix b/pkgs/applications/science/misc/openrefine/default.nix index 2ad67027ade4..9f2ef0f29b31 100644 --- a/pkgs/applications/science/misc/openrefine/default.nix +++ b/pkgs/applications/science/misc/openrefine/default.nix @@ -27,7 +27,7 @@ let inherit src version; pname = "openrefine-npm"; - sourceRoot = "source/main/webapp"; + sourceRoot = "${src.name}/main/webapp"; npmDepsHash = "sha256-8GhcL4tohQ5u2HeYN6JyTMMobUOqAL8ETCLiP1SoDSk="; |