Merge commit '83cbad92d73216bb0d9187c56cce0b91f9121d5a' into main

author: Mx Kookie <kookie@spacekookie.de> 2020-12-09 18:55:19 +0000
committer: Mx Kookie <kookie@spacekookie.de> 2020-12-09 18:55:19 +0000
commit: 80d90d9b204f7c17912740f9f414fe5d59f293ba (patch)
tree: 5f2065a06e724270610760d59d01c6888b375a46 /infra/libkookie/nixpkgs/pkgs/applications/science
parent: 3a31a84c7d3e589035ad08499206aac44a81f424 (diff)
parent: 83cbad92d73216bb0d9187c56cce0b91f9121d5a (diff)
103 files changed, 910 insertions, 581 deletions
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/astronomy/astrolabe-generator/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/astronomy/astrolabe-generator/default.nix
index cb3f3131ea14..4a6bdd9d1e9c 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/astronomy/astrolabe-generator/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/astronomy/astrolabe-generator/default.nix
@@ -25,7 +25,7 @@ stdenv.mkDerivation rec {
     homepage = "https://www.astrolabeproject.com";
     description = "A Java-based tool for generating EPS files for constructing astrolabes and related tools";
     license = licenses.gpl3;
-    maintainers = [ maintainers.genesis ];
+    maintainers = [ ];
     platforms = platforms.all;
   };
 }
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/astronomy/kstars/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/astronomy/kstars/default.nix
index 0b53e3e85ac3..fde8df610485 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/astronomy/kstars/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/astronomy/kstars/default.nix
@@ -1,27 +1,30 @@
 {
-  mkDerivation, lib, fetchgit,
-  extra-cmake-modules,
+  stdenv, extra-cmake-modules, fetchurl,
 
   kconfig, kdoctools, kguiaddons, ki18n, kinit, kiconthemes, kio,
-  knewstuff, kplotting, kwidgetsaddons, kxmlgui,
+  knewstuff, kplotting, kwidgetsaddons, kxmlgui, wrapQtAppsHook,
 
   qtx11extras, qtwebsockets,
 
   eigen, zlib,
 
-  cfitsio, indilib, xplanet
+  cfitsio, indilib, xplanet, libnova, gsl
 }:
 
-mkDerivation {
-  name = "kstars";
-  
-  src = fetchgit {
-    url = "https://anongit.kde.org/kstars.git";
-    rev = "7acc527939280edd22823371dc4e22494c6c626a";
-    sha256 = "1n1lgi7p3dj893fdnzjbnrha40p4apl0dy8zppcabxwrb1khb84v";
+stdenv.mkDerivation rec {
+  pname = "kstars";
+  version = "3.4.3";
+
+  src = fetchurl {
+    url = "https://mirrors.mit.edu/kde/stable/kstars/kstars-${version}.tar.xz";
+    sha256 = "0j5yxg6ay6sic194skz6vjzg6yvrpb3gvypvs0frjrcjbsl1j4f8";
   };
-  
-  nativeBuildInputs = [ extra-cmake-modules kdoctools ];
+
+  patches = [
+    ./indi-fix.patch
+  ];
+
+  nativeBuildInputs = [ extra-cmake-modules kdoctools wrapQtAppsHook ];
   buildInputs = [
     kconfig kdoctools kguiaddons ki18n kinit kiconthemes kio
     knewstuff kplotting kwidgetsaddons kxmlgui
@@ -30,10 +33,14 @@ mkDerivation {
 
     eigen zlib
 
-    cfitsio indilib xplanet
+    cfitsio indilib xplanet libnova gsl
+  ];
+
+  cmakeFlags = [
+    "-DINDI_NIX_ROOT=${indilib}"
   ];
 
-  meta = with lib; {
+  meta = with stdenv.lib; {
     description = "Virtual planetarium astronomy software";
     homepage = "https://kde.org/applications/education/org.kde.kstars";
     longDescription = ''
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/astronomy/kstars/indi-fix.patch b/infra/libkookie/nixpkgs/pkgs/applications/science/astronomy/kstars/indi-fix.patch
new file mode 100644
index 000000000000..9ff9f8a31dd3
--- /dev/null
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/astronomy/kstars/indi-fix.patch
@@ -0,0 +1,50 @@
+--- CMakeLists.txt	2020-11-02 13:58:06.119743710 -0600
++++ kstars-3.4.3/CMakeLists.txt	2020-11-02 14:05:01.707799274 -0600
+@@ -4,5 +4,7 @@
+ set (KStars_VERSION_REVISION 3)
+ set (CMAKE_CXX_STANDARD 11)
+ 
++add_definitions(-DINDI_NIX_ROOT=${INDI_NIX_ROOT})
++
+ # Build KStars Lite with -DBUILD_KSTARS_LITE=ON
+ option(BUILD_KSTARS_LITE "Build KStars Lite" OFF)
+
+--- ksutils.cpp	2020-11-02 13:47:44.883596916 -0600
++++ kstars-3.4.3/kstars/auxiliary/ksutils.cpp	2020-11-02 17:41:44.961937090 -0600
+@@ -1076,6 +1076,9 @@
+ {
+     QString snap = QProcessEnvironment::systemEnvironment().value("SNAP");
+     QString flat = QProcessEnvironment::systemEnvironment().value("FLATPAK_DEST");
++#define STR_EXPAND(x) #x
++#define STR(x) STR_EXPAND(x)
++    QString nix = QString(STR(INDI_NIX_ROOT));
+ 
+     if (option == "fitsDir")
+     {
+@@ -1089,7 +1091,7 @@
+         if (flat.isEmpty() == false)
+             return flat + "/bin/indiserver";
+         else
+-            return snap + "/usr/bin/indiserver";
++            return nix + "/bin/indiserver";
+     }
+     else if (option == "INDIHubAgent")
+     {
+@@ -1099,7 +1101,7 @@
+         if (flat.isEmpty() == false)
+             return flat + "/bin/indihub-agent";
+         else
+-            return snap + "/usr/bin/indihub-agent";
++            return nix + "/bin/indihub-agent";
+     }
+     else if (option == "indiDriversDir")
+     {
+@@ -1109,7 +1111,7 @@
+         if (flat.isEmpty() == false)
+             return flat + "/share/indi";
+         else
+-            return snap + "/usr/share/indi";
++            return nix + "/share/indi";
+ #else
+         return QStandardPaths::locate(QStandardPaths::GenericDataLocation, "indi", QStandardPaths::LocateDirectory);
+ #endif
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/astronomy/phd2/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/astronomy/phd2/default.nix
new file mode 100644
index 000000000000..98afba77c4f0
--- /dev/null
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/astronomy/phd2/default.nix
@@ -0,0 +1,29 @@
+{ stdenv, fetchFromGitHub, pkg-config, cmake, gtk3,
+  wxGTK30-gtk3, curl, gettext, glib, indilib, libnova }:
+
+stdenv.mkDerivation rec {
+  pname = "phd2";
+  version = "2.6.9dev1";
+
+  src = fetchFromGitHub {
+    owner = "OpenPHDGuiding";
+    repo = "phd2";
+    rev = "v${version}";
+    sha256 = "1ih7m9lilh12xbhmwm9kkicaqy72mi3firl6df7m5x38n2zj3zm4";
+  };
+
+  nativeBuildInputs = [ cmake pkg-config ];
+  buildInputs = [ gtk3 wxGTK30-gtk3 curl gettext glib indilib libnova ];
+
+  cmakeFlags = [
+    "-DOPENSOURCE_ONLY=1"
+  ];
+
+  meta = with stdenv.lib; {
+    homepage = "https://openphdguiding.org/";
+    description = "Telescope auto-guidance application";
+    license = licenses.bsd3;
+    maintainers = with maintainers; [ hjones2199 ];
+    platforms = [ "x86_64-linux" ];
+  };
+}
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/ants/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/ants/default.nix
index cb88e92fe1cb..ece218eea37d 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/ants/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/ants/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, fetchFromGitHub, fetchpatch, cmake, makeWrapper, itk4, vtk_7 }:
+{ stdenv, fetchFromGitHub, fetchpatch, cmake, makeWrapper, itk4, vtk_7, Cocoa }:
 
 stdenv.mkDerivation rec {
   pname    = "ANTs";
@@ -20,7 +20,7 @@ stdenv.mkDerivation rec {
   ];
 
   nativeBuildInputs = [ cmake makeWrapper ];
-  buildInputs = [ itk4 vtk_7 ];
+  buildInputs = [ itk4 vtk_7 ] ++ stdenv.lib.optional stdenv.isDarwin [ Cocoa ];
 
   cmakeFlags = [ "-DANTS_SUPERBUILD=FALSE" "-DUSE_VTK=TRUE" ];
 
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/bwa/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/bwa/default.nix
index 7212b42198c4..10859d9e8c13 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/bwa/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/bwa/default.nix
@@ -11,6 +11,12 @@ stdenv.mkDerivation rec {
 
   buildInputs = [ zlib ];
 
+  # Avoid hardcoding gcc to allow environments with a different
+  # C compiler to build
+  preConfigure = ''
+    sed -i '/^CC/d' Makefile
+  '';
+
   # it's unclear which headers are intended to be part of the public interface
   # so we may find ourselves having to add more here over time
   installPhase = ''
@@ -27,6 +33,6 @@ stdenv.mkDerivation rec {
     license     = licenses.gpl3;
     homepage    = "http://bio-bwa.sourceforge.net/";
     maintainers = with maintainers; [ luispedro ];
-    platforms = [ "x86_64-linux" ];
+    platforms = platforms.x86_64;
   };
 }
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/dcm2niix/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/dcm2niix/default.nix
index 59b173ac98cd..cfd1206f2314 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/dcm2niix/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/dcm2niix/default.nix
@@ -21,7 +21,7 @@ stdenv.mkDerivation rec {
   buildInputs = [ libyamlcpp ];
 
   meta = with stdenv.lib; {
-    description = "dcm2niix DICOM to NIfTI converter";
+    description = "DICOM to NIfTI converter";
     longDescription = ''
       dcm2niix is a designed to convert neuroimaging data from the
       DICOM format to the NIfTI format.
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/deeptools/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/deeptools/default.nix
index efa246a277fe..2621c5bbf037 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/deeptools/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/deeptools/default.nix
@@ -1,14 +1,14 @@
-{ lib
-, python
-}:
+{ lib, python, fetchFromGitHub }:
 with python.pkgs;
 buildPythonApplication rec {
   pname = "deepTools";
   version = "3.5.0";
 
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "1a14a29e60be13eac11bd204dab9aef73cd72fe56a94c587333f21087584c0d8";
+  src = fetchFromGitHub {
+    owner = "deeptools";
+    repo = "deepTools";
+    rev = version;
+    sha256 = "1bz8ln32mfc9k8l9wgp034vw80dxh6f92dfqxhcrpggk4akwj6ml";
   };
 
   propagatedBuildInputs = [
@@ -23,7 +23,7 @@ buildPythonApplication rec {
     deeptoolsintervals
   ];
 
-  checkInputs = [ pytest ];
+  checkInputs = [ nose ];
 
   meta = with lib; {
     homepage = "https://deeptools.readthedocs.io/en/develop";
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/hmmer/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/hmmer/default.nix
index 6ee7cd609c42..3b1420a18819 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/hmmer/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/hmmer/default.nix
@@ -1,12 +1,12 @@
 { stdenv, fetchurl }:
 
 stdenv.mkDerivation rec {
-  version = "3.3.1";
+  version = "3.3.2";
   pname = "hmmer";
 
   src = fetchurl {
     url = "http://eddylab.org/software/hmmer/${pname}-${version}.tar.gz";
-    sha256 = "1mcvr74w6ffd5z0p8v3jss473mbgard9lz5whjnk95c661lnmrlc";
+    sha256 = "0s9wf6n0qanbx8qs6igfl3vyjikwbrvh4d9d6mv54yp3xysykzlj";
   };
 
   meta = with stdenv.lib; {
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/igv/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/igv/default.nix
index bc4f1677fc98..3f9cb1a288b3 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/igv/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/igv/default.nix
@@ -2,10 +2,10 @@
 
 stdenv.mkDerivation rec {
   pname = "igv";
-  version = "2.8.9";
+  version = "2.8.13";
   src = fetchzip {
     url = "https://data.broadinstitute.org/igv/projects/downloads/2.8/IGV_${version}.zip";
-    sha256 = "1874w1xprv91caz1ymfxilq6inhj36xzx8j9m0mcyp0qfvfvyjp7";
+    sha256 = "0sab478jq96iw3fv0560hrrj8qbh40r8m4ncypdb7991j9haxl09";
   };
 
   installPhase = ''
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/kallisto/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/kallisto/default.nix
index 5a1bb187886b..014ae14cc794 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/kallisto/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/kallisto/default.nix
@@ -21,7 +21,7 @@ stdenv.mkDerivation rec {
   enableParallelBuilding = false;
 
   meta = with stdenv.lib; {
-    description = "Kallisto is a program for quantifying abundances of transcripts from RNA-Seq data";
+    description = "Program for quantifying abundances of transcripts from RNA-Seq data";
     homepage = "https://pachterlab.github.io/kallisto";
     license = licenses.bsd2;
     platforms = platforms.linux;
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/last/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/last/default.nix
index 13f6a23913fc..0976e5a10802 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/last/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/last/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "last";
-  version = "1066";
+  version = "1145";
 
   src = fetchurl {
     url = "http://last.cbrc.jp/last-${version}.zip";
-    sha256 = "098j3f3a80rmhd01ds7rnb9y1xykmll2yh5ivpnvskssd8z2vc4r";
+    sha256 = "0g54nmxxrirgid1i1k5i6rf7vnjpk9548sy06yqb4fj7vdzqgq99";
   };
 
   nativeBuildInputs = [ unzip ];
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/lumpy/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/lumpy/default.nix
index 04512e8e372e..f6267a2e017f 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/lumpy/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/lumpy/default.nix
@@ -7,13 +7,14 @@ let
 
 in stdenv.mkDerivation rec {
   pname = "lumpy";
-  version = "0.3.0";
+  version = "0.3.1";
 
   src = fetchFromGitHub {
     owner = "arq5x";
     repo = "lumpy-sv";
-    rev = version;
-    sha256 = "0azhzvmh9az9jcq0xprlzdz6w16azgszv4kshb903bwbnqirmk18";
+    rev = "v${version}";
+    sha256 = "0r71sg7qch8r6p6dw995znrqdj6q49hjdylhzbib2qmv8nvglhs9";
+    fetchSubmodules = true;
   };
 
   nativeBuildInputs = [ which ];
@@ -26,6 +27,8 @@ in stdenv.mkDerivation rec {
     # Use Nix htslib over bundled version
     sed -i 's/lumpy_filter: htslib/lumpy_filter:/' Makefile
     sed -i 's|../../lib/htslib/libhts.a|-lhts|' src/filter/Makefile
+    # Also make sure we use the includes from Nix's htslib
+    sed -i 's|../../lib/htslib/|${htslib}|' src/filter/Makefile
   '';
 
   # Upstream's makefile doesn't have an install target
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix
index d0f98719fa1a..d2b05943f7ce 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix
@@ -17,13 +17,13 @@ let
 
 in stdenv.mkDerivation rec {
   pname = "mosdepth";
-  version = "0.2.9";
+  version = "0.3.1";
 
   src = fetchFromGitHub {
     owner = "brentp";
     repo = "mosdepth";
     rev = "v${version}";
-    sha256 = "01gm9gj2x2zs4yx6wk761fi1papi7qr3gp4ln1kkn8n2f9y9h849";
+    sha256 = "1kcrvamrafz1m0s7mlbhaay8jyg97l1w37p6syl36r2m1plmwxjd";
   };
 
   nativeBuildInputs = [ nim ];
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix
index d496e78748d9..0353f2e7cebd 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "picard-tools";
-  version = "2.23.4";
+  version = "2.23.8";
 
   src = fetchurl {
     url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar";
-    sha256 = "0xg4nbx02a2kckr6p8pqjpv5rmp95bkmglgm1bma6f77s7hkab7q";
+    sha256 = "0aflbsxzc2pcp195bbgwk6zqabq0pszc41s1pw17khn8ywl2jjr2";
   };
 
   nativeBuildInputs = [ makeWrapper ];
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/plink/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/plink/default.nix
deleted file mode 100644
index 009e12aa02f0..000000000000
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/plink/default.nix
+++ /dev/null
@@ -1,25 +0,0 @@
-{ stdenv, fetchurl, zlib, unzip }:
-
-stdenv.mkDerivation {
-  name = "plink-1.07";
-
-  src = fetchurl {
-    url = "http://pngu.mgh.harvard.edu/~purcell/plink/dist/plink-1.07-src.zip";
-    sha256 = "4af56348443d0c6a1db64950a071b1fcb49cc74154875a7b43cccb4b6a7f482b";
-  };
-
-  buildInputs = [ zlib unzip ] ;
-
-  installPhase = ''
-    mkdir -p $out/bin
-    cp plink $out/bin
-  '';
-  
-  meta = {
-    description = "Whole genome association toolkit";
-    homepage = "http://pngu.mgh.harvard.edu/~purcell/plink/";
-    license = stdenv.lib.licenses.gpl2;
-    platforms = stdenv.lib.platforms.all;
-    broken = true;
-  };
-}
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/samblaster/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/samblaster/default.nix
index 7795ba237367..6846e3c84fae 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/samblaster/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/samblaster/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "samblaster";
-  version = "0.1.24";
+  version = "0.1.26";
 
   src = fetchFromGitHub {
     owner = "GregoryFaust";
     repo = "samblaster";
     rev = "v.${version}";
-    sha256 = "0iv2ddfw8363vb2x8gr3p8g88whb6mb9m0pf71i2cqsbv6jghap7";
+    sha256 = "0g24fq5hplnfgqkh3xqpg3lgx3wmxwnh9c7m6yw7pbi40lmgl1jv";
   };
 
   installPhase = ''
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/samtools/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/samtools/default.nix
index e750eea89ac9..27ed79a1f6ca 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/samtools/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/samtools/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "samtools";
-  version = "1.10";
+  version = "1.11";
 
   src = fetchurl {
     url = "https://github.com/samtools/samtools/releases/download/${version}/${pname}-${version}.tar.bz2";
-    sha256 = "119ms0dpydw8dkh3zc4yyw9zhdzgv12px4l2kayigv31bpqcb7kv";
+    sha256 = "1dp5wknak4arnw5ghhif9mmljlfnw5bgm91wib7z0j8wdjywx0z2";
   };
 
   nativeBuildInputs = [ perl ];
@@ -29,6 +29,6 @@ stdenv.mkDerivation rec {
     license = licenses.mit;
     homepage = "http://www.htslib.org/";
     platforms = platforms.unix;
-    maintainers = [ maintainers.mimame ];
+    maintainers = with maintainers; [ mimame unode ];
   };
 }
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/star/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/star/default.nix
index c331acbfe705..f2e1a2a8fee5 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/star/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/star/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "star";
-  version = "2.7.5c";
+  version = "2.7.6a";
 
   src = fetchFromGitHub {
     repo = "STAR";
     owner = "alexdobin";
     rev = version;
-    sha256 = "1plx9akrzwjk7f2j94l9ss0apg0asqmrf2bp0728d4bvlhnzmjyy";
+    sha256 = "1zw9f4jbhz0y51namnmid42pa7pviviy94q9db8w0774nksdf8is";
   };
 
   sourceRoot = "source/source";
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/tebreak/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/tebreak/default.nix
index 07669d097a44..82c624ba7cd9 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/tebreak/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/tebreak/default.nix
@@ -1,5 +1,5 @@
 { stdenv, fetchFromGitHub, last, exonerate, minia, python3Packages, bwa
-, samtools, findutils }:
+, samtools, findutils, python }:
 
 python3Packages.buildPythonApplication rec {
   pname = "tebreak";
@@ -32,6 +32,12 @@ python3Packages.buildPythonApplication rec {
     done
   '';
 
+  checkPhase = ''
+    $out/bin/tebreak -b test/data/example.ins.bam  -r test/data/Homo_sapiens_chr4_50000000-60000000_assembly19.fasta -p 4 --pickle test/example.pickle --detail_out test/example.tebreak.detail.out -i lib/teref.human.fa
+    pushd test
+    ${python.interpreter} checktest.py
+  '';
+
   meta = with stdenv.lib; {
     description = "Find and characterise transposable element insertions";
     homepage = "https://github.com/adamewing/tebreak";
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix
index 6545472a5295..e09abccad121 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix
@@ -17,14 +17,14 @@ let
   };
 in
 stdenv.mkDerivation rec {
-  version = "14.31.3";
+  version = "14.31.18";
   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 = "067051wp9kgkgcy3mvqwxhim0h1qfcf4jk8vrbzd3y9pwmjismzy";
+    sha256 = "0hkc7c08azbw3k91ygwz6r5y4yw6k8l7h4gcq5p71knd5k1fa5jd";
   };
 
   patchPhase = ''
@@ -48,6 +48,6 @@ stdenv.mkDerivation rec {
      homepage = "https://sourceforge.net/projects/jmol";
      license = licenses.lgpl2;
      platforms = platforms.all;
-     maintainers = with maintainers; [ timokau mounium ];
+     maintainers = with maintainers; [ mounium ] ++ teams.sage.members;
   };
 }
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/chemistry/marvin/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/chemistry/marvin/default.nix
index e8cd077afd20..ddab526ebe79 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/chemistry/marvin/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/chemistry/marvin/default.nix
@@ -4,12 +4,12 @@ with stdenv.lib;
 
 stdenv.mkDerivation rec {
   pname = "marvin";
-  version = "20.17.0";
+  version = "20.20.0";
 
   src = fetchurl {
     name = "marvin-${version}.deb";
     url = "http://dl.chemaxon.com/marvin/${version}/marvin_linux_${versions.majorMinor version}.deb";
-    sha256 = "0ip6ma9ivk5b74s9najn2rrkiha7hya1rjhgyrc71kwsj5gqgli0";
+    sha256 = "1a8b0drb0c95c8arm3aa0z0sbdm9ilj4h1g90i0qyn4g2wk2xsal";
   };
 
   nativeBuildInputs = [ dpkg makeWrapper ];
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/chemistry/openmolcas/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/chemistry/openmolcas/default.nix
index 0d74e784d772..d432e66a19f1 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/chemistry/openmolcas/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/chemistry/openmolcas/default.nix
@@ -7,7 +7,7 @@
 assert blas.implementation == "openblas" && lapack.implementation == "openblas";
 
 let
-  version = "19.11";
+  version = "20.10";
   gitLabRev = "v${version}";
 
   python = python3.withPackages (ps : with ps; [ six pyparsing ]);
@@ -20,18 +20,13 @@ in stdenv.mkDerivation {
     owner = "Molcas";
     repo = "OpenMolcas";
     rev = gitLabRev;
-    sha256 = "1wwqhkyyi7pw5x1ghnp83ir17zl5jsj7phhqxapybyi3bmg0i00q";
+    sha256 = "0xr9plgb0cfmxxqmd3wrhvl0hv2jqqfqzxwzs1jysq2m9cxl314v";
   };
 
-  patches = [ (fetchpatch {
-    name = "Fix-MPI-INT-size"; # upstream patch, fixes a Fortran compiler error
-    url = "https://gitlab.com/Molcas/OpenMolcas/commit/860e3350523f05ab18e49a428febac8a4297b6e4.patch";
-    sha256 = "0h96h5ikbi5l6ky41nkxmxfhjiykkiifq7vc2s3fdy1r1siv09sb";
-  }) (fetchpatch {
-    name = "fix-cisandbox"; # upstream patch, fixes a Fortran compiler error
-    url = "https://gitlab.com/Molcas/OpenMolcas/commit/d871590c8ce4689cd94cdbbc618954c65589393d.patch";
-    sha256 = "0dgz1w2rkglnis76spai3m51qa72j4bz6ppnk5zmzrr6ql7gwpgg";
-  })];
+  patches = [
+    # Required to handle openblas multiple outputs
+    ./openblasPath.patch
+];
 
   nativeBuildInputs = [ perl cmake texlive.combined.scheme-minimal makeWrapper ];
   buildInputs = [
@@ -55,7 +50,7 @@ in stdenv.mkDerivation {
     "-DTOOLS=ON"
     "-DHDF5=ON"
     "-DFDE=ON"
-    "-DOPENBLASROOT=${openblas}"
+    "-DOPENBLASROOT=${openblas.dev}"
   ];
 
   GAROOT=globalarrays;
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/chemistry/openmolcas/openblasPath.patch b/infra/libkookie/nixpkgs/pkgs/applications/science/chemistry/openmolcas/openblasPath.patch
new file mode 100644
index 000000000000..e47adcc3e9a3
--- /dev/null
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/chemistry/openmolcas/openblasPath.patch
@@ -0,0 +1,12 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 276ae4e2..db13e6e3 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -1507,7 +1507,6 @@ if (LINALG STREQUAL "OpenBLAS")
+     NAMES openblas
+     PATHS ${OPENBLASROOT}
+     PATH_SUFFIXES lib
+-    NO_DEFAULT_PATH
+   )
+ 
+   if (NOT LIBOPENBLAS)
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/appcsxcad/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/appcsxcad/default.nix
index d2b7c0d66a15..c2d7cefec9b8 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/appcsxcad/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/appcsxcad/default.nix
@@ -27,7 +27,6 @@ mkDerivation {
 
   nativeBuildInputs = [
     cmake
-    wrapQtAppsHook
   ];
 
   buildInputs = [
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/dsview/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/dsview/default.nix
index 4d3acb331d5d..e61017ea330d 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/dsview/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/dsview/default.nix
@@ -1,42 +1,46 @@
-{ stdenv, fetchFromGitHub, pkgconfig, cmake,
-libzip, boost, fftw, qtbase,
-libusb1, wrapQtAppsHook, libsigrok4dsl, libsigrokdecode4dsl
+{ lib, mkDerivation, fetchFromGitHub, pkgconfig, cmake
+, libzip, boost, fftw, qtbase, libusb1, libsigrok4dsl
+, libsigrokdecode4dsl, python3, fetchpatch
 }:
 
-stdenv.mkDerivation rec {
+mkDerivation rec {
   pname = "dsview";
 
-  version = "0.99";
+  version = "1.12";
 
   src = fetchFromGitHub {
       owner = "DreamSourceLab";
       repo = "DSView";
-      rev = version;
-      sha256 = "189i3baqgn8k3aypalayss0g489xi0an9hmvyggvxmgg1cvcwka2";
+      rev = "v${version}";
+      sha256 = "q7F4FuK/moKkouXTNPZDVon/W/ZmgtNHJka4MiTxA0U=";
   };
 
-  postUnpack = ''
-    export sourceRoot=$sourceRoot/DSView
-  '';
+  sourceRoot = "source/DSView";
 
   patches = [
     # Fix absolute install paths
     ./install.patch
+
+    # Fix buld with Qt5.15 already merged upstream for future release
+    # Using local file instead of content of commit #33e3d896a47 because
+    # sourceRoot make it unappliable
+    ./qt515.patch
   ];
 
-  nativeBuildInputs = [ cmake pkgconfig wrapQtAppsHook ];
+  nativeBuildInputs = [ cmake pkgconfig ];
 
   buildInputs = [
-   boost fftw qtbase libusb1 libzip libsigrokdecode4dsl libsigrok4dsl
+    boost fftw qtbase libusb1 libzip libsigrokdecode4dsl libsigrok4dsl
+    python3
   ];
 
   enableParallelBuilding = true;
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     description = "A GUI program for supporting various instruments from DreamSourceLab, including logic analyzer, oscilloscope, etc";
     homepage = "https://www.dreamsourcelab.com/";
     license = licenses.gpl3Plus;
     platforms = platforms.linux;
-    maintainers = [ maintainers.bachp ];
+    maintainers = with maintainers; [ bachp ];
   };
 }
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/dsview/install.patch b/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/dsview/install.patch
index e30a28d80fa3..75c3e9628656 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/dsview/install.patch
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/dsview/install.patch
@@ -2,10 +2,10 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt
 index c1c33e1..208a184 100644
 --- a/CMakeLists.txt
 +++ b/CMakeLists.txt
-@@ -403,8 +403,8 @@ install(DIRECTORY res DESTINATION share/${PROJECT_NAME})
- install(FILES icons/logo.png DESTINATION share/${PROJECT_NAME} RENAME logo.png)
- install(FILES ../NEWS DESTINATION share/${PROJECT_NAME} RENAME NEWS)
- install(FILES ../ug.pdf DESTINATION share/${PROJECT_NAME} RENAME ug.pdf)
+@@ -427,8 +427,8 @@
+ install(FILES ../NEWS31 DESTINATION share/${PROJECT_NAME} RENAME NEWS31)
+ install(FILES ../ug25.pdf DESTINATION share/${PROJECT_NAME} RENAME ug25.pdf)
+ install(FILES ../ug31.pdf DESTINATION share/${PROJECT_NAME} RENAME ug31.pdf)
 -install(FILES DreamSourceLab.rules DESTINATION /etc/udev/rules.d/)
 -install(FILES DSView.desktop DESTINATION /usr/share/applications/)
 +install(FILES DreamSourceLab.rules DESTINATION etc/udev/rules.d/)
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/dsview/qt515.patch b/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/dsview/qt515.patch
new file mode 100644
index 000000000000..552f2062ec57
--- /dev/null
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/dsview/qt515.patch
@@ -0,0 +1,13 @@
+diff --git a/pv/view/viewport.cpp b/pv/view/viewport.cpp
+index 921d3db..16cdce9 100755
+--- a/pv/view/viewport.cpp
++++ b/pv/view/viewport.cpp
+@@ -37,7 +37,7 @@
+ 
+ #include <QMouseEvent>
+ #include <QStyleOption>
+-
++#include <QPainterPath>
+ 
+ #include <math.h>
+ 
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/flatcam/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/flatcam/default.nix
index 360c6df7fe60..b8a80c5e9c11 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/flatcam/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/flatcam/default.nix
@@ -10,7 +10,7 @@ python3Packages.buildPythonApplication rec {
 
   src = fetchFromBitbucket {
     owner = "jpcgt";
-    repo = "${pname}";
+    repo = pname;
     rev = "533afd6a1772857cb633c011b5e0a15b60b1e92e"; # 8.5 with Red Hat packaging.
     sha256 = "199kiiml18k34z1zhk2hbhibphmnv0kb11kxiajq52alps0mjb3m";
   };
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/gtkwave/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/gtkwave/default.nix
index 36cc19142d19..ad5e9e55c575 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/gtkwave/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/gtkwave/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "gtkwave";
-  version = "3.3.106";
+  version = "3.3.107";
 
   src = fetchurl {
     url    = "mirror://sourceforge/gtkwave/${pname}-gtk3-${version}.tar.gz";
-    sha256 = "0ma53s27735x16dq5qi91kvlypkiwkxh2jhw0gziyccnk1mkdsji";
+    sha256 = "0ma30jyc94iid3v3m8aw4i2lyiqfxkpsdvdmmaibynk400cbzivl";
   };
 
   nativeBuildInputs = [ pkgconfig wrapGAppsHook ];
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/horizon-eda/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/horizon-eda/default.nix
index 3b6a4c7b7383..6b9f07ee68f1 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/horizon-eda/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/horizon-eda/default.nix
@@ -23,13 +23,13 @@
 
 stdenv.mkDerivation rec {
   pname = "horizon-eda";
-  version = "1.2.1";
+  version = "1.3.0";
 
   src = fetchFromGitHub {
     owner = "horizon-eda";
     repo = "horizon";
     rev = "v${version}";
-    sha256 = "0b1bi99xdhbkb2vdb9y6kyqm0h8y0q168jf2xi8kd0z7kww8li2p";
+    sha256 = "13c4p60vrmwmnrv2jcr2gc1cxnimy7j8yp1p6434pbbk2py9k8mx";
   };
 
   buildInputs = [
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/kicad/base.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/kicad/base.nix
index 3d83e905103b..7f11f483a9d0 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/kicad/base.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/kicad/base.nix
@@ -55,17 +55,6 @@ stdenv.mkDerivation rec {
 
   src = kicadSrc;
 
-  # quick fix for #72248
-  # should be removed if a a more permanent fix is published
-  patches = [
-    (
-      fetchpatch {
-        url = "https://github.com/johnbeard/kicad/commit/dfb1318a3989e3d6f9f2ac33c924ca5030ea273b.patch";
-        sha256 = "00ifd3fas8lid8svzh1w67xc8kyx89qidp7gm633r014j3kjkgcd";
-      }
-    )
-  ];
-
   # tagged releases don't have "unknown"
   # kicad nightlies use git describe --dirty
   # nix removes .git, so its approximated here
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/kicad/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/kicad/default.nix
index 7290503311d3..48a5779d207a 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/kicad/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/kicad/default.nix
@@ -212,11 +212,10 @@ stdenv.mkDerivation rec {
 
   # why does $makeWrapperArgs have to be added explicitly?
   # $out and $program_PYTHONPATH don't exist when makeWrapperArgs gets set?
-  # kicad-ogltest's source seems to indicate that crashing is expected behaviour...
   installPhase =
     let
       tools = [ "kicad" "pcbnew" "eeschema" "gerbview" "pcb_calculator" "pl_editor" "bitmap2component" ];
-      utils = [ "dxf2idf" "idf2vrml" "idfcyl" "idfrect" "kicad2step" "kicad-ogltest" ];
+      utils = [ "dxf2idf" "idf2vrml" "idfcyl" "idfrect" "kicad2step" ];
     in
     (concatStringsSep "\n"
       (flatten [
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/kicad/update.sh b/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/kicad/update.sh
index 8c154c302c84..cfd78323b77a 100755
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/kicad/update.sh
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/kicad/update.sh
@@ -110,7 +110,7 @@ for version in "${all_versions[@]}"; do
     echo "Checking src" >&2
     src_rev="$(${get_rev} "${gitlab}"/code/kicad.git "${version}" | cut -f1)"
     has_rev="$(grep -sm 1 "\"${pname}\"" -A 4 "${file}" | grep -sm 1 "${src_rev}" || true)"
-    has_hash="$(grep -sm 1 "\"${pname}\"" -A 5 "${file}" | grep -sm 1 "sha256")"
+    has_hash="$(grep -sm 1 "\"${pname}\"" -A 5 "${file}" | grep -sm 1 "sha256" || true)"
     if [[ -n ${has_rev} && -n ${has_hash} && -z ${clean} ]]; then
       echo "Reusing old ${pname}.src.sha256, already latest .rev" >&2
       grep -sm 1 "\"${pname}\"" -A 5 "${file}" | grep -sm 1 "rev" -A 1
@@ -130,7 +130,7 @@ for version in "${all_versions[@]}"; do
         echo "Checking i18n" >&2
         i18n_rev="$(${get_rev} "${i18n}" "${version}" | cut -f1)"
         has_rev="$(grep -sm 1 "\"${pname}\"" -A 11 "${file}" | grep -sm 1 "${i18n_rev}" || true)"
-        has_hash="$(grep -sm 1 "\"${pname}\"" -A 12 "${file}" | grep -sm 1 "i18n.sha256")"
+        has_hash="$(grep -sm 1 "\"${pname}\"" -A 12 "${file}" | grep -sm 1 "i18n.sha256" || true)"
         if [[ -n ${has_rev} && -n ${has_hash} && -z ${clean} ]]; then
           echo "Reusing old kicad-i18n-${today}.src.sha256, already latest .rev" >&2
           grep -sm 1 "\"${pname}\"" -A 12 "${file}" | grep -sm 1 "i18n" -A 1
@@ -146,7 +146,7 @@ for version in "${all_versions[@]}"; do
             url="${gitlab}/libraries/kicad-${lib}.git"
             lib_rev="$(${get_rev} "${url}" "${version}" | cut -f1 | head -n1)"
             has_rev="$(grep -sm 1 "\"${pname}\"" -A 19 "${file}" | grep -sm 1 "${lib_rev}" || true)"
-            has_hash="$(grep -sm 1 "\"${pname}\"" -A 20 "${file}" | grep -sm 1 "${lib}.sha256")"
+            has_hash="$(grep -sm 1 "\"${pname}\"" -A 20 "${file}" | grep -sm 1 "${lib}.sha256" || true)"
             if [[ -n ${has_rev} && -n ${has_hash} && -z ${clean} ]]; then
               echo "Reusing old kicad-${lib}-${today}.src.sha256, already latest .rev" >&2
               grep -sm 1 "\"${pname}\"" -A 20 "${file}" | grep -sm 1 "${lib}" -A 1
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/kicad/versions.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/kicad/versions.nix
index 1afb33b6fbd8..9f00f3fa8ba8 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/kicad/versions.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/kicad/versions.nix
@@ -3,49 +3,49 @@
 {
   "kicad" = {
     kicadVersion = {
-      version = "5.1.6";
+      version =			"5.1.8";
       src = {
-        rev = "c6e7f7de7df655fd59b57823499efc443009de6b";
-        sha256 = "1pa3z0h0679jmgxlzc833h6q85b5paxdp69kf2h93vkaryj58622";
+        rev =			"db9833491010954bc27fac92c83d2864bd95c23c";
+        sha256 =		"08ni9j2lw2hjc1csk6rkydcxwdal6da17ch60zkjij5vfsif2hix";
       };
     };
     libVersion = {
-      version = "5.1.6";
+      version =			"5.1.8";
       libSources = {
-        i18n.rev = "5ad171ce5c8d90f4740517c2adecb310d8be51bd";
-        i18n.sha256 = "0qryi8xjm23ka363zfl7bbga0v5c31fr3d4nyxp3m168vkv9zhha";
-        symbols.rev = "5150eaa2a7d15cfc6bb1459c527c4ebaa66d7708";
-        symbols.sha256 = "12w3rdy085drlikkpb27n9ni7cyg9l0pqy7hnr86cxjcw3l5wcx6";
-        templates.rev = "9213d439f757e6049b7e54f3ea08272a0d0f44a9";
-        templates.sha256 = "1hppcsrkn4dk6ggby6ckh0q65qxkywrbyxa4lwpaf7pxjyv498xg";
-        footprints.rev = "a61b4e49762fb355f654e65a1c7db1aaf7bb2332";
-        footprints.sha256 = "1kmf91a5mmvj9izrv40mkaw1w36yjgn8daczd9rq2wlmd0rdp1zx";
-        packages3d.rev = "150ff1caf0b01dc04c84f4f966f4f88fedfa8f8c";
-        packages3d.sha256 = "0b9jglf77fy0n0r8xs4yqkv6zvipyfvp0z5dnqlzp32csy5aqpi1";
+        i18n.rev =		"78adcd19e7ed53f4889d6db65a33dd8ec2d323e9";
+        i18n.sha256 =		"0x0w2m6d3xfm22y4anp5j2j67iwzby149ynj6qjlw2kcsi8kwk1j";
+        symbols.rev =		"bf475af94877e8fd9cf80e667578ff61835e02bb";
+        symbols.sha256 =	"1ii3r813653ng2ycggnknqx4g3ja7dbm4qyxrf9aq48ws0xkvhx3";
+        templates.rev =		"1ccbaf3704e8ff4030d0915f71e051af621ef7d7";
+        templates.sha256 =	"1a8xfcbdbb4ylrb5m7n2jjk9kwvgmlx1pmnn2cwj327a2b3m4jjs";
+        footprints.rev =	"302ac78bac21825532f970fb92714fa5973ad79b";
+        footprints.sha256 =	"0gyqxryda273hjn2rv8dha461j9bjh054y5dlpiw1wiha65lrf9i";
+        packages3d.rev =	"7abe02f30fd79b8f4f66c01589861df7f8f72f04";
+        packages3d.sha256 =	"1szcin52fcsyb55bj7xq7lz6ig187dpz3lk7blwab7b9c4dn3c3y";
       };
     };
   };
   "kicad-unstable" = {
     kicadVersion = {
-      version =			"2020-10-09";
+      version =			"2020-12-01";
       src = {
-        rev =			"560428a70f0196fb4ade620042c5ddefc1685ebe";
-        sha256 =		"0rzn83bpl06v1d49lcvwfg93nirn684bqqq536zxhmjm0ayx29ka";
+        rev =			"3c521942ed52e83482c82d426170b4fbf327f846";
+        sha256 =		"sha256:09qab69sy3n44kjlzxxx7gbksyr1kg8n14kz0zf8n71zfcqagci4";
       };
     };
     libVersion = {
-      version =			"2020-10-09";
+      version =			"2020-12-01";
       libSources = {
-        i18n.rev =		"d24af2da8cab4ce1081c401909a4a880514e5549";
-        i18n.sha256 =		"0r0sv52k84sw4jxf10lrmzwmn58d2fv5h57fdrspnmvnh10q63xf";
-        symbols.rev =		"9c50f4333bafc5a1abf7786436db5ffb6a66758d";
-        symbols.sha256 =	"06ic59svz0256isy93863i5ay4k8wshvp1kspnqrc776wmq03l3k";
-        templates.rev =		"41eae4ccd3ac02fdb969e3aa272c07ab51dcf5af";
-        templates.sha256 =	"0xxfkpsgbnafmpaxpz1747zn7fhqp0kfl32rzjrx4vzxyp25q805";
-        footprints.rev =	"50015af7e603cc499199c7e1c6daa7c85dd732ae";
-        footprints.sha256 =	"16bic67klbj7sgj7cab8ha2fg3ypp9ap82gxkn6ijvpl7dka8bhb";
-        packages3d.rev =	"df0dc0074491bb665b2c3ce569cbd4aa16118ad6";
-        packages3d.sha256 =	"027jlcp9fpryldjkcxhb1b5bpwqna9kl6r0lnkd86x238kj3rd8v";
+        i18n.rev =		"e89d9a89bec59199c1ade56ee2556591412ab7b0";
+        i18n.sha256 =		"sha256:04zaqyhj3qr4ymyd3k5vjpcna64j8klpsygcgjcv29s3rdi8glfl";
+        symbols.rev =		"e538abb015b4f289910a6f26b2f1b9cb8bf2efdb";
+        symbols.sha256 =	"sha256:117y4cm46anlrnw6y6mdjgl1a5gab6h6m7cwx3q7qb284m9bs5gi";
+        templates.rev =		"32a4f6fab863976fdcfa232e3e08fdcf3323a954";
+        templates.sha256 =	"sha256:13r94dghrh9slpj7nkzv0zqv5hk49s6pxm4q5ndqx0y8037ivmhk";
+        footprints.rev =	"15ffd67e01257d4d8134dbd6708cb58977eeccbe";
+        footprints.sha256 =	"sha256:1ad5k3wh2zqfibrar7pd3g363jk2q51dvraxnq3zlxa2x4znh7mw";
+        packages3d.rev =	"d8b7e8c56d535f4d7e46373bf24c754a8403da1f";
+        packages3d.sha256 =	"sha256:0dh8ixg0w43wzj5h3164dz6l1vl4llwxhi3qcdgj1lgvrs28aywd";
       };
     };
   };
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/librepcb/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/librepcb/default.nix
index de01b095e381..4b0a4108ab22 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/librepcb/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/librepcb/default.nix
@@ -1,39 +1,47 @@
-{ lib, mkDerivation, fetchFromGitHub, qtbase, qttools, qmake, wrapQtAppsHook }:
+{ stdenv, lib, fetchFromGitHub
+, qtbase, qttools, qmake, wrapQtAppsHook
+}:
 
-mkDerivation {
+stdenv.mkDerivation rec {
   pname = "librepcb";
-  version = "0.1.4";
+  version = "0.1.5";
 
   src = fetchFromGitHub {
-    owner = "LibrePCB";
-    repo = "LibrePCB";
+    owner  = pname;
+    repo   = pname;
+    rev    = version;
+    sha256 = "0ag8h3id2c1k9ds22rfrvyhf2vjhkv82xnrdrz4n1hnlr9566vcx";
     fetchSubmodules = true;
-    rev = "ae04eef5a71b5ba66ae2cee6b631c1c933ace535";
-    sha256 = "0wk5qny1jb6n4mwyyrs7syir3hmwxlwazcd80bpxharmsj7p0rzc";
   };
 
-  enableParallelBuilding = true;
-
   nativeBuildInputs = [ qmake qttools wrapQtAppsHook ];
-
   buildInputs = [ qtbase ];
 
   qmakeFlags = ["-r"];
+  enableParallelBuilding = true;
 
   postInstall = ''
-      mkdir -p $out/share/librepcb/fontobene
-      cp share/librepcb/fontobene/newstroke.bene $out/share/librepcb/fontobene/
-    '';
+    mkdir -p $out/share/librepcb/fontobene
+    cp share/librepcb/fontobene/newstroke.bene $out/share/librepcb/fontobene/
+  '';
+
+  # the build system tries to use 'git' at build time to find the HEAD hash.
+  # that's a no-no, so replace it with a quick hack. NOTE: the # adds a comment
+  # at the end of the line to remove the git call.
+  patchPhase = ''
+    substituteInPlace ./libs/librepcb/common/common.pro \
+      --replace 'GIT_COMMIT_SHA' 'GIT_COMMIT_SHA="\\\"${src.rev}\\\"" # '
+  '';
 
   preFixup = ''
     wrapQtApp $out/bin/librepcb
   '';
 
-  meta = with lib; {
+  meta = with stdenv.lib; {
     description = "A free EDA software to develop printed circuit boards";
-    homepage = "https://librepcb.org/";
-    maintainers = with maintainers; [ luz ];
-    license = licenses.gpl3;
-    platforms = platforms.linux;
+    homepage    = "https://librepcb.org/";
+    maintainers = with maintainers; [ luz thoughtpolice ];
+    license     = licenses.gpl3;
+    platforms   = platforms.linux;
   };
 }
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/magic-vlsi/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/magic-vlsi/default.nix
index 96849c300298..6667f2be9c3d 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/magic-vlsi/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/magic-vlsi/default.nix
@@ -1,16 +1,20 @@
-{ stdenv, fetchurl, m4, tcsh, libX11, tcl, tk, cairo, ncurses, mesa_glu, python3 }:
+{ stdenv, fetchurl
+, m4, tcsh, libX11, tcl, tk
+, cairo, ncurses, mesa_glu, python3
+}:
 
-stdenv.mkDerivation {
+stdenv.mkDerivation rec {
   pname = "magic-vlsi";
-  version = "8.3.5";
+  version = "8.3.80";
 
   src = fetchurl {
-    url = "http://opencircuitdesign.com/magic/archive/magic-8.3.5.tgz";
-    sha256 = "0wv4zmxlqjfaakgp802icn0cd9f8ylkz2sppix83axq8p5cg90yq";
+    url    = "http://opencircuitdesign.com/magic/archive/magic-${version}.tgz";
+    sha256 = "0a5x4sh5xsr79pqbgv6221jc4fvaxkg2pvrdhy1cs4bmsc1sbm9j";
   };
 
   buildInputs = [ m4 tcsh libX11 tcl tk cairo ncurses mesa_glu ];
   nativeBuildInputs = [ python3 ];
+  enableParallelBuilding = true;
 
   configureFlags = [
     "--with-tcl=${tcl}"
@@ -22,6 +26,8 @@ stdenv.mkDerivation {
     patchShebangs scripts/*
   '';
 
+  NIX_CFLAGS_COMPILE = "-Wno-implicit-function-declaration";
+
   patches = [
     ./0001-strip-bin-prefix.patch
     ./0002-fix-format-security.patch
@@ -29,8 +35,8 @@ stdenv.mkDerivation {
 
   meta = with stdenv.lib; {
     description = "VLSI layout tool written in Tcl";
-    homepage = "http://opencircuitdesign.com/magic/";
-    license = licenses.mit;
-    maintainers = [ maintainers.anna328p ];
+    homepage    = "http://opencircuitdesign.com/magic/";
+    license     = licenses.mit;
+    maintainers = with maintainers; [ anna328p thoughtpolice ];
   };
 }
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/nanovna-saver/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/nanovna-saver/default.nix
new file mode 100644
index 000000000000..62bda91e5008
--- /dev/null
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/nanovna-saver/default.nix
@@ -0,0 +1,51 @@
+{ lib, mkDerivationWith, wrapQtAppsHook, python3Packages, fetchFromGitHub
+, qtbase }:
+
+let
+  version = "0.3.7";
+  pname = "nanovna-saver";
+
+in mkDerivationWith python3Packages.buildPythonApplication {
+  inherit pname version;
+
+  src = fetchFromGitHub {
+    owner = "NanoVNA-Saver";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "0c22ckyypg91gfb2sdc684msw28nnb6r8cq3b362gafvv00a35mi";
+  };
+
+  nativeBuildInputs = [ wrapQtAppsHook ];
+
+  propagatedBuildInputs = with python3Packages; [
+    cython
+    scipy_1_4
+    pyqt5
+    pyserial
+    numpy
+  ];
+
+  doCheck = false;
+
+  dontWrapGApps = true;
+  dontWrapQtApps = true;
+
+  postFixup = ''
+    wrapProgram $out/bin/NanoVNASaver \
+      "''${gappsWrapperArgs[@]}" \
+      "''${qtWrapperArgs[@]}"
+  '';
+
+  meta = with lib; {
+    homepage = "https://github.com/NanoVNA-Saver/nanovna-saver";
+    description =
+      "A tool for reading, displaying and saving data from the NanoVNA";
+    longDescription = ''
+      A multiplatform tool to save Touchstone files from the NanoVNA, sweep
+      frequency spans in segments to gain more than 101 data points, and
+      generally display and analyze the resulting data.
+    '';
+    license = licenses.gpl3Only;
+    maintainers = with maintainers; [ zaninime ];
+  };
+}
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/ngspice/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/ngspice/default.nix
index ab2861d53f20..5113dc778f62 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/ngspice/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/ngspice/default.nix
@@ -14,11 +14,11 @@
 
 stdenv.mkDerivation rec {
   pname = "ngspice";
-  version = "32";
+  version = "33";
 
   src = fetchurl {
     url = "mirror://sourceforge/ngspice/ngspice-${version}.tar.gz";
-    sha256 = "1wiys30c9mqzxr7iv1sws0jnn4xi0mj3lanhnk2qfvaiji70rn9w";
+    sha256 = "1wa1hmpn13spmxqgbb1m7vgy32mwvjqwrxhymzll8z65q5nbd7dr";
   };
 
   nativeBuildInputs = [ flex bison ];
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/openhantek6022/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/openhantek6022/default.nix
index ad8fa3c7a7ae..acdac346fd3b 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/openhantek6022/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/openhantek6022/default.nix
@@ -2,13 +2,13 @@
 
 mkDerivation rec {
   pname = "openhantek6022";
-  version = "3.1.2";
+  version = "3.1.3";
 
   src = fetchFromGitHub {
     owner = "OpenHantek";
     repo = "OpenHantek6022";
     rev = version;
-    sha256 = "104j7d3i5y6jd20c2z3l10sr6sgdy8iki3g9mlwhddnr8x6nzc03";
+    sha256 = "1n4l8ks5808d99zj1vj0ck0v1lb9s7iv3ahww7ximbf9iha39pbm";
   };
 
   nativeBuildInputs = [ cmake makeWrapper ];
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/qcsxcad/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/qcsxcad/default.nix
deleted file mode 100644
index c12678c0047d..000000000000
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/qcsxcad/default.nix
+++ /dev/null
@@ -1,50 +0,0 @@
-{ stdenv
-, mkDerivation
-, fetchFromGitHub
-, cmake
-, csxcad
-, tinyxml
-, vtkWithQt5
-, wrapQtAppsHook
-, qtbase
-}:
-
-mkDerivation {
-  pname = "qcsxcad";
-  version = "unstable-2020-01-04";
-
-  src = fetchFromGitHub {
-    owner = "thliebig";
-    repo = "QCSXCAD";
-    rev = "0dabbaf2bc1190adec300871cf309791af842c8e";
-    sha256 = "11kbh0mxbdfh7s5azqin3i2alic5ihmdfj0jwgnrhlpjk4cbf9rn";
-  };
-
-  nativeBuildInputs = [
-    cmake
-    wrapQtAppsHook
-  ];
-
-  cmakeFlags = [
-    "-DCMAKE_INSTALL_PREFIX=${placeholder "out"}"
-    "-DCSXCAD_ROOT_DIR=${csxcad}"
-    "-DENABLE_RPATH=OFF"
-  ];
-
-  buildInputs = [
-    csxcad
-    tinyxml
-    vtkWithQt5
-    qtbase
-  ];
-
-  enableParallelBuilding = true;
-
-  meta = with stdenv.lib; {
-    description = "Qt library for CSXCAD";
-    homepage = "https://github.com/thliebig/QCSXCAD";
-    license = licenses.gpl3;
-    maintainers = with maintainers; [ matthuszagh ];
-    platforms = platforms.linux;
-  };
-}
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/verilog/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/verilog/default.nix
index df1ce7b7235f..6217df2db8f8 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/verilog/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/verilog/default.nix
@@ -1,43 +1,45 @@
-{ stdenv, fetchFromGitHub, autoconf, gperf, flex, bison, readline, ncurses
-, bzip2, zlib
-# Test inputs
+{ stdenv
+, fetchFromGitHub
+, autoconf
+, bison
+, bzip2
+, flex
+, gperf
+, ncurses
 , perl
+, readline
+, zlib
 }:
 
 let
   iverilog-test = fetchFromGitHub {
-    owner = "steveicarus";
-    repo = "ivtest";
-    rev = "6882cb8ec08926c4e356c6092f0c5f8c23328d5c";
-    sha256 = "04sj5nqzwls1y760kgnd9c2whkcrr8kvj9lisd5rvk0w580kjb2x";
+    owner  = "steveicarus";
+    repo   = "ivtest";
+    rev    = "253609b89576355b3bef2f91e90db62223ecf2be";
+    sha256 = "18i7jlr2csp7mplcrwjhllwvb6w3v7x7mnx7vdw48nd3g5scrydx";
   };
 in
 stdenv.mkDerivation rec {
-  pname = "iverilog";
-  version = "unstable-2020-08-24";
+  pname   = "iverilog";
+  version = "11.0";
 
   src = fetchFromGitHub {
-    owner = "steveicarus";
-    repo = pname;
-    rev = "d8556e4c86e1465b68bdc8d5ba2056ba95a42dfd";
-    sha256 = "sha256-sT9j/0Q2FD5MOGpH/quMGvAuM7t7QavRHKD9lX7Elfs=";
+    owner  = "steveicarus";
+    repo   = pname;
+    rev    = "v${stdenv.lib.replaceStrings ["."] ["_"] version}";
+    sha256 = "0nzcyi6l2zv9wxzsv9i963p3igyjds0n55x0ph561mc3pfbc7aqp";
   };
 
-  enableParallelBuilding = true;
+  nativeBuildInputs = [ autoconf bison flex gperf ];
 
-  preConfigure = ''
-    chmod +x $PWD/autoconf.sh
-    $PWD/autoconf.sh
-  '';
+  buildInputs = [ bzip2 ncurses readline zlib ];
 
-  nativeBuildInputs = [ autoconf gperf flex bison ];
+  preConfigure = "sh autoconf.sh";
+
+  enableParallelBuilding = true;
 
-  buildInputs = [ readline ncurses bzip2 zlib ];
+  doCheck = true;
 
-  # tests from .travis.yml
-  doCheck = true; # runs ``make check``
-  # most tests pass, but some that rely on exact text of floating-point numbers fail on aarch64.
-  doInstallCheck = !stdenv.isAarch64;
   installCheckInputs = [ perl ];
 
   installCheckPhase = ''
@@ -58,9 +60,9 @@ stdenv.mkDerivation rec {
 
   meta = with stdenv.lib; {
     description = "Icarus Verilog compiler";
-    homepage = "http://iverilog.icarus.com/";
-    license = with licenses; [ gpl2Plus lgpl21Plus] ;
-    maintainers = with maintainers; [ winden ];
-    platforms = platforms.all;
+    homepage    = "http://iverilog.icarus.com/";  # https does not work
+    license     = with licenses; [ gpl2Plus lgpl21Plus ];
+    maintainers = with maintainers; [ winden thoughtpolice ];
+    platforms   = platforms.all;
   };
 }
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/vhd2vl/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/vhd2vl/default.nix
index 43dfdcabd02f..be9e890fc8d5 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/vhd2vl/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/electronics/vhd2vl/default.nix
@@ -1,5 +1,6 @@
 { stdenv
 , fetchFromGitHub
+, fetchpatch
 , bison
 , flex
 , verilog
@@ -16,6 +17,15 @@ stdenv.mkDerivation rec {
     sha256 = "17va2pil4938j8c93anhy45zzgnvq3k71a7glj02synfrsv6fs8n";
   };
 
+  patches = stdenv.lib.optionals (!stdenv.isAarch64) [
+    # fix build with verilog 11.0 - https://github.com/ldoolitt/vhd2vl/pull/15
+    # for some strange reason, this is not needed for aarch64
+    (fetchpatch {
+      url = "https://github.com/ldoolitt/vhd2vl/commit/ce9b8343ffd004dfe8779a309f4b5a594dbec45e.patch";
+      sha256 = "1qaqhm2mk66spb2dir9n91b385rarglc067js1g6pcg8mg5v3hhf";
+    })
+  ];
+
   nativeBuildInputs = [
     bison
     flex
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/geometry/antiprism/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/geometry/antiprism/default.nix
new file mode 100644
index 000000000000..4691291a4257
--- /dev/null
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/geometry/antiprism/default.nix
@@ -0,0 +1,29 @@
+{ stdenv
+, fetchFromGitHub
+, autoreconfHook
+, libX11
+, libGL
+, libGLU
+, freeglut }:
+
+stdenv.mkDerivation rec {
+  pname = "antiprism";
+  version = "0.26";
+
+  src = fetchFromGitHub {
+    owner = "antiprism";
+    repo = pname;
+    rev = version;
+    sha256 = "sha256-5FE6IbYKk7eMT985R9NCX3GDXE8SrdVHFcCpKeJvKtQ=";
+  };
+
+  nativeBuildInputs = [ autoreconfHook ];
+  buildInputs = [ libX11 libGLU libGL.dev freeglut.dev ];
+
+  meta = with stdenv.lib; {
+    homepage = "https://www.antiprism.com";
+    description = "A collection of programs for generating, manipulating, transforming and viewing polyhedra";
+    license = with licenses; [ mit ];
+    maintainers = with maintainers; [ AndersonTorres ];
+  };
+}
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/logic/abc/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/logic/abc/default.nix
index 29d727d988e7..426c5a9df323 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/logic/abc/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/logic/abc/default.nix
@@ -4,13 +4,13 @@
 
 stdenv.mkDerivation rec {
   pname   = "abc-verifier";
-  version = "2020.06.22";
+  version = "2020.11.24";
 
   src = fetchFromGitHub {
-    owner  = "berkeley-abc";
+    owner  = "yosyshq";
     repo   = "abc";
-    rev    = "341db25668f3054c87aa3372c794e180f629af5d";
-    sha256 = "14cgv34vz5ljkcms6nrv19vqws2hs8bgjgffk5q03cbxnm2jxv5s";
+    rev    = "4f5f73d18b137930fb3048c0b385c82fa078db38";
+    sha256 = "0z1kp223kix7i4r7mbj2bzawkdzc55nsgc41m85dmbajl9fsj1m0";
   };
 
   nativeBuildInputs = [ cmake ];
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/logic/boolector/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/logic/boolector/default.nix
index aedc8e3484a9..0364a76639aa 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/logic/boolector/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/logic/boolector/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, fetchFromGitHub, lib, python3
+{ stdenv, fetchFromGitHub, fetchpatch, lib, python3
 , cmake, lingeling, btor2tools, gtest, gmp
 }:
 
@@ -13,6 +13,14 @@ stdenv.mkDerivation rec {
     sha256 = "0jkmaw678njqgkflzj9g374yk1mci8yqvsxkrqzlifn6bwhwb7ci";
   };
 
+  # excludes development artifacts from install, will be included in next release
+  patches = [
+    (fetchpatch {
+      url = "https://github.com/Boolector/boolector/commit/4d240436e34e65096671099766344dd9126145b1.patch";
+      sha256 = "1girsbvlhkkl1hldl2gsjynwc3m92jskn798qhx0ydg6whrfgcgw";
+    })
+  ];
+
   postPatch = ''
     sed s@REPLACEME@file://${gtest.src}@ ${./cmake-gtest.patch} | patch -p1
   '';
@@ -23,39 +31,39 @@ stdenv.mkDerivation rec {
   cmakeFlags =
     [ "-DBUILD_SHARED_LIBS=ON"
       "-DUSE_LINGELING=YES"
-      "-DBtor2Tools_INCLUDE_DIR=${btor2tools.dev}/include"
-      "-DBtor2Tools_LIBRARIES=${btor2tools.lib}/lib/libbtor2parser.so"
     ] ++ (lib.optional (gmp != null) "-DUSE_GMP=YES");
 
-  installPhase = ''
-    mkdir -p $out/bin $lib/lib $dev/include
-
-    cp -vr bin/* $out/bin
-    cp -vr lib/* $lib/lib
-
-    rm -rf $out/bin/{examples,tests}
-    # we don't care about gtest related libs
-    rm -rf $lib/lib/libg*
-
-    cd ../src
-    find . -iname '*.h' -exec cp --parents '{}' $dev/include \;
-    rm -rf $dev/include/tests
-  '';
-
   checkInputs = [ python3 ];
   doCheck = true;
-  preCheck = ''
-    export LD_LIBRARY_PATH=$(readlink -f lib)
-    patchShebangs ..
+  preCheck =
+    let var = if stdenv.isDarwin then "DYLD_LIBRARY_PATH" else "LD_LIBRARY_PATH";
+    in
+      # tests modelgen and modelgensmt2 spawn boolector in another processes and
+      # macOS strips DYLD_LIBRARY_PATH, hardcode it for testing
+      stdenv.lib.optionalString stdenv.isDarwin ''
+        cp -r bin bin.back
+        install_name_tool -change libboolector.dylib $(pwd)/lib/libboolector.dylib bin/boolector
+      '' + ''
+        export ${var}=$(readlink -f lib)
+        patchShebangs ..
+      '';
+
+  postCheck = stdenv.lib.optionalString stdenv.isDarwin ''
+    rm -rf bin
+    mv bin.back bin
   '';
 
-  outputs = [ "out" "dev" "lib" ];
+  # this is what haskellPackages.boolector expects
+  postInstall = ''
+    cp $out/include/boolector/boolector.h $out/include/boolector.h
+    cp $out/include/boolector/btortypes.h $out/include/btortypes.h
+  '';
 
   meta = with stdenv.lib; {
     description = "An extremely fast SMT solver for bit-vectors and arrays";
     homepage    = "https://boolector.github.io";
     license     = licenses.mit;
-    platforms   = platforms.linux;
+    platforms   = with platforms; linux ++ darwin;
     maintainers = with maintainers; [ thoughtpolice ];
   };
 }
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/logic/btor2tools/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/logic/btor2tools/default.nix
index 714ab49524b0..7d2aed7596e8 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/logic/btor2tools/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/logic/btor2tools/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, cmake, fetchFromGitHub }:
+{ stdenv, cmake, fetchFromGitHub, fixDarwinDylibNames }:
 
 stdenv.mkDerivation rec {
   pname = "btor2tools";
@@ -11,7 +11,7 @@ stdenv.mkDerivation rec {
     sha256 = "0mfqmkgvyw8fa2c09kww107dmk180ch1hp98r5kv41vnc04iqb0s";
   };
 
-  nativeBuildInputs = [ cmake ];
+  nativeBuildInputs = [ cmake ] ++ stdenv.lib.optional stdenv.isDarwin fixDarwinDylibNames;
 
   installPhase = ''
     mkdir -p $out $dev/include/btor2parser/ $lib/lib
@@ -27,7 +27,7 @@ stdenv.mkDerivation rec {
     description = "A generic parser and tool package for the BTOR2 format";
     homepage    = "https://github.com/Boolector/btor2tools";
     license     = licenses.mit;
-    platforms   = platforms.linux;
+    platforms   = platforms.unix;
     maintainers = with maintainers; [ thoughtpolice ];
   };
 }
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/logic/coq/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/logic/coq/default.nix
index 946cba41b143..dc9e40912d53 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/logic/coq/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/logic/coq/default.nix
@@ -35,6 +35,7 @@ let
    "8.11.1" = "0qriy9dy36dajsv5qmli8gd6v55mah02ya334nw49ky19v7518m0";
    "8.11.2" = "0f77ccyxdgbf1nrj5fa8qvrk1cyfy06fv8gj9kzfvlcgn0cf48sa";
    "8.12.0" = "18dc7k0piv6v064zgdadpw6mkkxk7j663hb3svgj5236fihjr0cz";
+   "8.12.1" = "1rkcyjjrzcqw9xk93hsq0vvji4f8r5iq0f739mghk60bghkpnb7q";
   }.${version};
   coq-version = stdenv.lib.versions.majorMinor version;
   versionAtLeast = stdenv.lib.versionAtLeast coq-version;
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/logic/coq2html/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/logic/coq2html/default.nix
index 2e56eda893e9..e53e8e7392c0 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/logic/coq2html/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/logic/coq2html/default.nix
@@ -1,6 +1,6 @@
 { stdenv, fetchgit, ocaml }:
 
-let 
+let
   version = "20170720";
 in
 
@@ -22,7 +22,7 @@ stdenv.mkDerivation {
   '';
 
   meta = with stdenv.lib; {
-    description = "coq2html is an HTML documentation generator for Coq source files";
+    description = "HTML documentation generator for Coq source files";
     longDescription = ''
       coq2html is an HTML documentation generator for Coq source files. It is
       an alternative to the standard coqdoc documentation generator
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/logic/cryptoverif/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/logic/cryptoverif/default.nix
index 6877060d36d6..28295ea28922 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/logic/cryptoverif/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/logic/cryptoverif/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "cryptoverif";
-  version = "2.01pl1";
+  version = "2.03pl1";
 
   src = fetchurl {
     url    = "http://prosecco.gforge.inria.fr/personal/bblanche/cryptoverif/cryptoverif${version}.tar.gz";
-    sha256 = "1bkmrv3wsy8mwhrxd3z3br9zgv37c2w6443rm4s9jl0aphcgnbiw";
+    sha256 = "0q7qa1qm7mbky3m36445gdmgmkb9mrhrdsk7mmwn8fzw0rfc6z00";
   };
 
   buildInputs = [ ocaml ];
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/logic/key/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/logic/key/default.nix
new file mode 100644
index 000000000000..b08c4d84d1fc
--- /dev/null
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/logic/key/default.nix
@@ -0,0 +1,74 @@
+{ stdenv
+, fetchurl
+, unzip
+, jdk
+, ant
+, jre
+, makeWrapper
+, runCommand
+, key
+}:
+
+# get this from the download URL when changing version
+let gitRevision = "7d3deab0763c88edee4f7a08e604661e0dbdd450";
+
+in stdenv.mkDerivation rec {
+  pname = "key";
+  version = "2.6.3";
+
+  src = fetchurl {
+    url = "https://formal.iti.kit.edu/key/releases/${version}/key-src-${version}_${gitRevision}.zip";
+    sha256 = "1dr5jmrqs0iy76wdsfiv5hx929i24yzm1xypzqqvx7afc7apyawy";
+  };
+
+  sourceRoot = "key";
+
+  nativeBuildInputs = [
+    unzip
+    jdk
+    ant
+    makeWrapper
+  ];
+
+  buildPhase = ''
+    ant -buildfile scripts/build.xml \
+      -Dgit.revision=${gitRevision} \
+      compileAll deployAll
+  '';
+
+  postCheck = ''
+    ant -buildfile scripts/build.xml \
+      -Dgit.revision=${gitRevision} \
+      compileAllTests runAllTests test-deploy-all
+  '';
+
+  installPhase = ''
+    mkdir -p $out/share/java
+    # Wrong version in the code. On next version change 2.5 to ${version}:
+    unzip deployment/key-2.5_${gitRevision}.zip -d $out/share/java
+    mkdir -p $out/bin
+    makeWrapper ${jre}/bin/java $out/bin/KeY \
+      --add-flags "-cp $out/share/java/KeY.jar de.uka.ilkd.key.core.Main"
+  '';
+
+  passthru.tests.check-version = runCommand "key-help" {} ''
+    ${key}/bin/KeY --help | grep 2.5 # Wrong version in the code. On next version change to ${version}
+    touch $out
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Java formal verification tool";
+    homepage = "https://www.key-project.org"; # also https://formal.iti.kit.edu/key/
+    longDescription = ''
+      The KeY System is a formal software development tool that aims to
+      integrate design, implementation, formal specification, and formal
+      verification of object-oriented software as seamlessly as possible.
+      At the core of the system is a novel theorem prover for the first-order
+      Dynamic Logic for Java with a user-friendly graphical interface.
+    '';
+    license = licenses.gpl2;
+    maintainers = with maintainers; [ fgaz ];
+    platforms = platforms.all;
+  };
+}
+
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/logic/lean/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/logic/lean/default.nix
index 32a75cabc13f..88e1b4fbc0e1 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/logic/lean/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/logic/lean/default.nix
@@ -2,22 +2,26 @@
 
 stdenv.mkDerivation rec {
   pname = "lean";
-  version = "3.19.0";
+  version = "3.23.0";
 
   src = fetchFromGitHub {
     owner  = "leanprover-community";
     repo   = "lean";
     rev    = "v${version}";
-    sha256 = "1dybq6104vc62x620izgblfd8dqc4ynaiw8ml07km78lq38anm6v";
+    sha256 = "09mklc1p6ms1jayg2f89hqfmhca3h5744lli936l38ypn1d00sxx";
   };
 
   nativeBuildInputs = [ cmake ];
   buildInputs = [ gmp ];
   enableParallelBuilding = true;
 
-  preConfigure = ''
-    cd src
-  '';
+  cmakeDir = "../src";
+
+  # Running the tests is required to build the *.olean files for the core
+  # library.
+  doCheck = true;
+
+  postPatch = "patchShebangs .";
 
   postInstall = stdenv.lib.optionalString stdenv.isDarwin ''
     substituteInPlace $out/bin/leanpkg \
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/logic/ott/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/logic/ott/default.nix
index ecc253a64d98..48ad63eaa993 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/logic/ott/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/logic/ott/default.nix
@@ -19,7 +19,7 @@ stdenv.mkDerivation rec {
   postInstall = "opaline -prefix $out";
 
   meta = {
-    description = "Ott: tool for the working semanticist";
+    description = "A tool for the working semanticist";
     longDescription = ''
       Ott is a tool for writing definitions of programming languages and
       calculi. It takes as input a definition of a language syntax and
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/logic/potassco/clingcon.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/logic/potassco/clingcon.nix
index 1203822d86e9..b74583ca1a2c 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/logic/potassco/clingcon.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/logic/potassco/clingcon.nix
@@ -11,7 +11,7 @@ stdenv.mkDerivation rec {
 
   src = fetchFromGitHub {
     owner = "potassco";
-    repo = "${pname}";
+    repo = pname;
     rev = "v${version}";
     fetchSubmodules = true;
     sha256 = "1q7517h10jfvjdk2czq8d6y57r8kr1j1jj2k2ip2qxkpyfigk4rs";
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/logic/proverif/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/logic/proverif/default.nix
index 6acae2bcb766..4242bb0599e9 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/logic/proverif/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/logic/proverif/default.nix
@@ -16,6 +16,7 @@ stdenv.mkDerivation rec {
     mkdir -p $out/bin
     cp ./proverif      $out/bin
     cp ./proveriftotex $out/bin
+    install -D -t $out/share/emacs/site-lisp/ emacs/proverif.el
   '';
 
   meta = {
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/logic/tlaplus/toolbox.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/logic/tlaplus/toolbox.nix
index 5c445459a36a..c9e97375b6c7 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/logic/tlaplus/toolbox.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/logic/tlaplus/toolbox.nix
@@ -3,7 +3,7 @@
 }:
 
 let
-  version = "1.6.0";
+  version = "1.7.0";
   arch = "x86_64";
 
   desktopItem = makeDesktopItem rec {
@@ -25,7 +25,7 @@ in stdenv.mkDerivation {
   inherit version;
   src = fetchzip {
     url = "https://tla.msr-inria.inria.fr/tlatoolbox/products/TLAToolbox-${version}-linux.gtk.${arch}.zip";
-    sha256 = "1mgx4p5qykf9q0p4cp6kcpc7fx8g5f2w1g40kdgas24hqwrgs3cm";
+    sha256 = "0v15wscawair5bghr5ixb4i062kmh9by1m0hnz2r1sawlqyafz02";
   };
 
   buildInputs = [ makeWrapper  ];
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/logic/workcraft/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/logic/workcraft/default.nix
index 4038db17f938..9ce6592d9989 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/logic/workcraft/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/logic/workcraft/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "workcraft";
-  version = "3.3.0";
+  version = "3.3.2";
 
   src = fetchurl {
     url = "https://github.com/workcraft/workcraft/releases/download/v${version}/workcraft-v${version}-linux.tar.gz";
-    sha256 = "072i7kan2c9f4s9jxwqr4ccsi9979c12xhwr385sbq06rwyrna85";
+    sha256 = "0v71x3fph2j3xrnysvkm7zsgnbxisfbdfgxzvzxxfdg59a6l3xid";
   };
 
   buildInputs = [ makeWrapper ];
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/logic/z3/4.4.0.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/logic/z3/4.4.0.nix
index 1e3bcea42ef7..a5388572db61 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/logic/z3/4.4.0.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/logic/z3/4.4.0.nix
@@ -33,7 +33,7 @@ stdenv.mkDerivation rec {
 
   meta = {
     description = "A high-performance theorem prover and SMT solver";
-    homepage    = "http://github.com/Z3Prover/z3";
+    homepage    = "https://github.com/Z3Prover/z3";
     license     = stdenv.lib.licenses.mit;
     platforms   = stdenv.lib.platforms.x86_64;
     maintainers = with stdenv.lib.maintainers; [ thoughtpolice ttuegel ];
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/logic/z3/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/logic/z3/default.nix
index 88aafcdae222..48512eff5300 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/logic/z3/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/logic/z3/default.nix
@@ -22,7 +22,8 @@ stdenv.mkDerivation rec {
     sha256 = "1hnbzq10d23drd7ksm3c1n2611c3kd0q0yxgz8y78zaafwczvwxx";
   };
 
-  buildInputs = [ python fixDarwinDylibNames ]
+  nativeBuildInputs = optional stdenv.hostPlatform.isDarwin fixDarwinDylibNames;
+  buildInputs = [ python ]
   ++ optional javaBindings jdk
   ++ optionals ocamlBindings [ ocaml findlib zarith ]
   ;
@@ -59,7 +60,7 @@ stdenv.mkDerivation rec {
     description = "A high-performance theorem prover and SMT solver";
     homepage    = "https://github.com/Z3Prover/z3";
     license     = stdenv.lib.licenses.mit;
-    platforms   = stdenv.lib.platforms.x86_64;
+    platforms   = stdenv.lib.platforms.unix;
     maintainers = with stdenv.lib.maintainers; [ thoughtpolice ttuegel ];
   };
 }
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/machine-learning/labelimg/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/machine-learning/labelimg/default.nix
index 05c56b0b0958..18c304e83165 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/machine-learning/labelimg/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/machine-learning/labelimg/default.nix
@@ -28,7 +28,7 @@
       makeWrapperArgs+=("''${qtWrapperArgs[@]}")
     '';
     meta = with stdenv.lib; {
-      description = "LabelImg is a graphical image annotation tool and label object bounding boxes in images";
+      description = "A graphical image annotation tool and label object bounding boxes in images";
       homepage = "https://github.com/tzutalin/labelImg";
       license = licenses.mit;
       platforms = platforms.linux;
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/math/R/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/math/R/default.nix
index 717b240c1cce..e4fbe8a7f2de 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/math/R/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/math/R/default.nix
@@ -12,11 +12,11 @@
 assert (!blas.isILP64) && (!lapack.isILP64);
 
 stdenv.mkDerivation rec {
-  name = "R-4.0.2";
+  name = "R-4.0.3";
 
   src = fetchurl {
     url = "https://cran.r-project.org/src/base/R-4/${name}.tar.gz";
-    sha256 = "0xdy3dy2bzdiba8z94hjykyra8si8a5q15s0bri7c26scjrymg6k";
+    sha256 = "03cypg2qf7v9mq9mr9alz9w5y9m5kdgwbc97bp26pyymg253m609";
   };
 
   dontUseImakeConfigure = true;
@@ -113,6 +113,6 @@ stdenv.mkDerivation rec {
     platforms = platforms.all;
     hydraPlatforms = platforms.linux;
 
-    maintainers = with maintainers; [ peti timokau ];
+    maintainers = with maintainers; [ peti ] ++ teams.sage.members;
   };
 }
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/math/bliss/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/math/bliss/default.nix
index 52b05646a70d..9ab90134aad4 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/math/bliss/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/math/bliss/default.nix
@@ -29,7 +29,7 @@ stdenv.mkDerivation rec {
   '';
 
   meta = with stdenv.lib; {
-    description = "bliss is an open source tool for computing automorphism groups and canonical forms of graphs. It has both a command line user interface as well as C++ and C programming language APIs";
+    description = "An open source tool for computing automorphism groups and canonical forms of graphs. It has both a command line user interface as well as C++ and C programming language APIs";
     homepage = "http://www.tcs.hut.fi/Software/bliss/";
     license = licenses.lgpl3;
     platforms = [ "i686-linux" "x86_64-linux" ];
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/math/calc/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/math/calc/default.nix
index 8e50f48b286b..e770cff2da9c 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/math/calc/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/math/calc/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, lib, fetchurl, utillinux, makeWrapper
+{ stdenv, lib, fetchurl, util-linux, makeWrapper
 , enableReadline ? true, readline, ncurses }:
 
 stdenv.mkDerivation rec {
@@ -19,7 +19,7 @@ stdenv.mkDerivation rec {
       --replace '-install_name ''${LIBDIR}/libcustcalc''${LIB_EXT_VERSION}' '-install_name ''${T}''${LIBDIR}/libcustcalc''${LIB_EXT_VERSION}'
   '';
 
-  buildInputs = [ utillinux makeWrapper ]
+  buildInputs = [ util-linux makeWrapper ]
              ++ lib.optionals enableReadline [ readline ncurses ];
 
   makeFlags = [
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/math/geogebra/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/math/geogebra/default.nix
index 5cebef83a4a9..a6950ad3451c 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/math/geogebra/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/math/geogebra/default.nix
@@ -1,18 +1,7 @@
-{ stdenv, fetchurl, jre, makeDesktopItem, makeWrapper, language ? "en_US" }:
-
-stdenv.mkDerivation rec {
+{ stdenv, fetchurl, jre, makeDesktopItem, makeWrapper, unzip, language ? "en_US" }:
+let
   pname = "geogebra";
-  version = "5-0-593-0";
-
-  preferLocalBuild = true;
-
-  src = fetchurl {
-    urls = [
-      "https://download.geogebra.org/installers/5.0/GeoGebra-Linux-Portable-${version}.tar.bz2"
-      "http://web.archive.org/https://download.geogebra.org/installers/5.0/GeoGebra-Linux-Portable-${version}.tar.bz2"
-    ];
-    sha256 = "d84c27a3299e6df08881733d22215a18decedcba4c2d97a9e5424c39cd57db35";
-  };
+  version = "5-0-609-0";
 
   srcIcon = fetchurl {
     url = "http://static.geogebra.org/images/geogebra-logo.svg";
@@ -30,23 +19,6 @@ stdenv.mkDerivation rec {
     mimeType = "application/vnd.geogebra.file;application/vnd.geogebra.tool;";
   };
 
-  buildInputs = [ makeWrapper ];
-
-  installPhase = ''
-    install -D geogebra/* -t "$out/libexec/geogebra/"
-
-    makeWrapper "$out/libexec/geogebra/geogebra" "$out/bin/geogebra" \
-      --set JAVACMD "${jre}/bin/java" \
-      --set GG_PATH "$out/libexec/geogebra" \
-      --add-flags "--language=${language}"
-
-    install -Dm644 "${desktopItem}/share/applications/"* \
-      -t $out/share/applications/
-
-    install -Dm644 "${srcIcon}" \
-      "$out/share/icons/hicolor/scalable/apps/geogebra.svg"
-  '';
-
   meta = with stdenv.lib; {
     description = "Dynamic mathematics software with graphics, algebra and spreadsheets";
     longDescription = ''
@@ -57,7 +29,61 @@ stdenv.mkDerivation rec {
     homepage = "https://www.geogebra.org/";
     maintainers = with maintainers; [ ma27 ];
     license = with licenses; [ gpl3 cc-by-nc-sa-30 geogebra ];
-    platforms = platforms.all;
+    platforms = with platforms; linux ++ darwin;
     hydraPlatforms = [];
   };
-}
+
+  linuxPkg = stdenv.mkDerivation {
+    inherit pname version meta srcIcon desktopItem;
+
+    preferLocalBuild = true;
+
+    src = fetchurl {
+      urls = [
+        "https://download.geogebra.org/installers/5.0/GeoGebra-Linux-Portable-${version}.tar.bz2"
+        "http://web.archive.org/web/20201022200454/https://download.geogebra.org/installers/5.0/GeoGebra-Linux-Portable-${version}.tar.bz2"
+      ];
+      sha256 = "0xbhg8hm3dqm3qkraj48pqwslrnjyxpq9mcgylr2m8i1gmqw7xwf";
+    };
+
+    nativeBuildInputs = [ makeWrapper ];
+
+    installPhase = ''
+      install -D geogebra/* -t "$out/libexec/geogebra/"
+
+      makeWrapper "$out/libexec/geogebra/geogebra" "$out/bin/geogebra" \
+        --set JAVACMD "${jre}/bin/java" \
+        --set GG_PATH "$out/libexec/geogebra" \
+        --add-flags "--language=${language}"
+
+      install -Dm644 "${desktopItem}/share/applications/"* \
+        -t $out/share/applications/
+
+      install -Dm644 "${srcIcon}" \
+        "$out/share/icons/hicolor/scalable/apps/geogebra.svg"
+    '';
+  };
+
+  darwinPkg = stdenv.mkDerivation {
+    inherit pname version meta;
+
+    preferLocalBuild = true;
+
+    src = fetchurl {
+      url = "https://download.geogebra.org/installers/5.0/GeoGebra-MacOS-Installer-withJava-${version}.zip";
+      sha256 = "16fgqwxz31cfmia0pyzpk05aqzrqr11sjbw37q9zb3xfh3p1r4gz";
+    };
+
+    dontUnpack = true;
+
+    nativeBuildInputs = [ unzip ];
+
+    installPhase = ''
+      install -dm755 $out/Applications
+      unzip $src -d $out/Applications
+    '';
+  };
+in
+if stdenv.isDarwin
+then darwinPkg
+else linuxPkg
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/math/geogebra/geogebra6.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/math/geogebra/geogebra6.nix
index 65caff82ead1..7bd582648937 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/math/geogebra/geogebra6.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/math/geogebra/geogebra6.nix
@@ -1,46 +1,70 @@
 { stdenv, unzip, fetchurl, electron_6, makeWrapper, geogebra }:
-stdenv.mkDerivation rec{
+let
+  pname = "geogebra";
+  version = "6-0-609-0";
 
-  name = "geogebra-${version}";
-  version = "6-0-600-0";
+  srcIcon = geogebra.srcIcon;
+  desktopItem = geogebra.desktopItem;
 
-  src = fetchurl {
-    urls = [
-        "https://download.geogebra.org/installers/6.0/GeoGebra-Linux64-Portable-${version}.zip"
-        "https://web.archive.org/web/20200904093945/https://download.geogebra.org/installers/6.0/GeoGebra-Linux64-Portable-${version}.zip"
-      ];
-    sha256 = "1l49rvfkil2cz6r7sa2mi0p6hvb6p66jv3x6xj8hjqls4l3sfhkm";
+  meta = with stdenv.lib; geogebra.meta // {
+    license = licenses.geogebra;
+    maintainers = with maintainers; [ voidless ];
+    platforms = with platforms; linux ++ darwin;
   };
 
-  dontConfigure = true;
-  dontBuild = true;
+  linuxPkg = stdenv.mkDerivation {
+    inherit pname version meta;
 
-  nativeBuildInputs = [
-    unzip
-    makeWrapper
-  ];
+    src = fetchurl {
+      urls = [
+          "https://download.geogebra.org/installers/6.0/GeoGebra-Linux64-Portable-${version}.zip"
+          "https://web.archive.org/web/20201022200156/https://download.geogebra.org/installers/6.0/GeoGebra-Linux64-Portable-${version}.zip"
+        ];
+      sha256 = "0rzcbq587x8827g9v03awa9hz27vyfjc0cz45ymbchqp31lsx49b";
+    };
 
-  unpackPhase = ''
-    unzip $src
-  '';
+    dontConfigure = true;
+    dontBuild = true;
 
-  installPhase = ''
-    mkdir -p $out/libexec/geogebra/ $out/bin
-    cp -r GeoGebra-linux-x64/{resources,locales} "$out/"
-    makeWrapper ${stdenv.lib.getBin electron_6}/bin/electron $out/bin/geogebra --add-flags "$out/resources/app"
-    install -Dm644 "${desktopItem}/share/applications/"* \
-      -t $out/share/applications/
+    nativeBuildInputs = [
+      unzip
+      makeWrapper
+    ];
 
-    install -Dm644 "${srcIcon}" \
-      "$out/share/icons/hicolor/scalable/apps/geogebra.svg"
-  '';
+    unpackPhase = ''
+      unzip $src
+    '';
 
-  srcIcon = geogebra.srcIcon;
+    installPhase = ''
+      mkdir -p $out/libexec/geogebra/ $out/bin
+      cp -r GeoGebra-linux-x64/{resources,locales} "$out/"
+      makeWrapper ${stdenv.lib.getBin electron_6}/bin/electron $out/bin/geogebra --add-flags "$out/resources/app"
+      install -Dm644 "${desktopItem}/share/applications/"* \
+        -t $out/share/applications/
 
-  desktopItem = geogebra.desktopItem;
-  meta = with stdenv.lib; geogebra.meta // {
-    license = licenses.geogebra;
-    maintainers = with maintainers; [ voidless ];
-    platforms = platforms.linux;
+      install -Dm644 "${srcIcon}" \
+        "$out/share/icons/hicolor/scalable/apps/geogebra.svg"
+    '';
+  };
+
+  darwinPkg = stdenv.mkDerivation {
+    inherit pname version meta;
+
+    src = fetchurl {
+      url = "https://download.geogebra.org/installers/6.0/GeoGebra-Classic-6-MacOS-Portable-${version}.zip";
+      sha256 = "0275869zgwbl1qjj593q6629hnxbwk9c15rkm29a3lh10pinb099";
+    };
+
+    dontUnpack = true;
+
+    nativeBuildInputs = [ unzip ];
+
+    installPhase = ''
+      install -dm755 $out/Applications
+      unzip $src -d $out/Applications
+    '';
   };
-}
+in
+if stdenv.isDarwin
+then darwinPkg
+else linuxPkg
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/math/gfan/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/math/gfan/default.nix
index adac92f376c8..7e2a4625d301 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/math/gfan/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/math/gfan/default.nix
@@ -8,11 +8,15 @@ stdenv.mkDerivation rec {
     sha256 = "02pihqb1lb76a0xbfwjzs1cd6ay3ldfxsm8dvsbl6qs3vkjxax56";
   };
 
-  patchPhase = stdenv.lib.optionalString stdenv.cc.isClang ''
+  patches = [
+    ./gfan-0.6.2-cddlib-prefix.patch
+  ];
+
+  postPatch = stdenv.lib.optionalString stdenv.cc.isClang ''
     substituteInPlace Makefile --replace "-fno-guess-branch-probability" ""
   '';
 
-  buildFlags = [ "CC=cc" "CXX=c++" "cddnoprefix=1" ];
+  buildFlags = [ "CC=cc" "CXX=c++" ];
   installFlags = [ ''PREFIX=$(out)'' ];
   buildInputs = [ gmp mpir cddlib ];
 
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/math/gfan/gfan-0.6.2-cddlib-prefix.patch b/infra/libkookie/nixpkgs/pkgs/applications/science/math/gfan/gfan-0.6.2-cddlib-prefix.patch
new file mode 100644
index 000000000000..8a96a991cf75
--- /dev/null
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/math/gfan/gfan-0.6.2-cddlib-prefix.patch
@@ -0,0 +1,55 @@
+diff -ru gfan0.6.2.orig/src/app_librarytest.cpp gfan0.6.2/src/app_librarytest.cpp
+--- gfan0.6.2.orig/src/app_librarytest.cpp	2020-10-19 08:41:27.981863500 +0900
++++ gfan0.6.2/src/app_librarytest.cpp	2020-10-19 08:42:44.551863500 +0900
+@@ -12,8 +12,8 @@
+ #include "setoper.h"
+ #include "cdd.h"
+ #else
+-#include "cdd/setoper.h"
+-#include "cdd/cdd.h"
++#include "cddlib/setoper.h"
++#include "cddlib/cdd.h"
+ #endif
+ #include <iostream>
+ #include <fstream>
+diff -ru gfan0.6.2.orig/src/gfanlib_zcone.cpp gfan0.6.2/src/gfanlib_zcone.cpp
+--- gfan0.6.2.orig/src/gfanlib_zcone.cpp	2020-10-19 08:41:27.981863500 +0900
++++ gfan0.6.2/src/gfanlib_zcone.cpp	2020-10-19 08:42:44.571863500 +0900
+@@ -16,8 +16,8 @@
+ #include "setoper.h"
+ #include "cdd.h"
+ #else
+-#include "cdd/setoper.h"
+-#include "cdd/cdd.h"
++#include "cddlib/setoper.h"
++#include "cddlib/cdd.h"
+ #endif
+ //}
+ 
+@@ -52,8 +52,8 @@
+ 				  "dd_free_global_constants()\n"
+ 				  "in your deinitialisation code (only available for cddlib version>=094d).\n"
+ 				  "This requires the header includes:\n"
+-				  "#include \"cdd/setoper.h\"\n"
+-				  "#include \"cdd/cdd.h\"\n"
++				  "#include \"cddlib/setoper.h\"\n"
++				  "#include \"cddlib/cdd.h\"\n"
+ 				  "\n"
+ 				  "Alternatively, you may call gfan:initializeCddlibIfRequired() and deinitializeCddlibIfRequired()\n"
+ 				  "if gfanlib is the only code using cddlib. If at some point cddlib is no longer required by gfanlib\n"
+diff -ru gfan0.6.2.orig/src/lp_cdd.cpp gfan0.6.2/src/lp_cdd.cpp
+--- gfan0.6.2.orig/src/lp_cdd.cpp	2020-10-19 08:41:27.991863500 +0900
++++ gfan0.6.2/src/lp_cdd.cpp	2020-10-19 08:42:44.571863500 +0900
+@@ -5,9 +5,9 @@
+ #include "cdd.h"
+ #include "cdd_f.h"
+ #else
+-#include "cdd/setoper.h"
+-#include "cdd/cdd.h"
+-#include "cdd/cdd_f.h"
++#include "cddlib/setoper.h"
++#include "cddlib/cdd.h"
++#include "cddlib/cdd_f.h"
+ #endif
+ //}
+ #include "termorder.h"
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/math/ginac/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/math/ginac/default.nix
index 701445f90100..3c129e8033bd 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/math/ginac/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/math/ginac/default.nix
@@ -1,11 +1,11 @@
 { stdenv, fetchurl, cln, pkgconfig, readline, gmp, python }:
 
 stdenv.mkDerivation rec {
-  name = "ginac-1.7.9";
+  name = "ginac-1.8.0";
 
   src = fetchurl {
     url    = "${meta.homepage}/${name}.tar.bz2";
-    sha256 = "08cqc87qq4w6z3l053x5gfqsa4zkgkicq8skxsbsj39nli1zzkb7";
+    sha256 = "0l9byzfxq3f9az5pcdldnl95ws8mpirkqky46f973mvxi5541d24";
   };
 
   propagatedBuildInputs = [ cln ];
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/math/gmsh/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/math/gmsh/default.nix
index db7e238e8ded..1b6dc2ae0076 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/math/gmsh/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/math/gmsh/default.nix
@@ -5,11 +5,11 @@ assert (!blas.isILP64) && (!lapack.isILP64);
 
 stdenv.mkDerivation rec {
   pname = "gmsh";
-  version = "4.6.0";
+  version = "4.7.1";
 
   src = fetchurl {
     url = "http://gmsh.info/src/gmsh-${version}-source.tgz";
-    sha256 = "075dyblmlfdlhgbb1dwk6jzlqx93q90n6zwpr3mpii5n1zjmab0g";
+    sha256 = "0shwi41van3k0z6rnpl3sz5nh46xbyyljwfpcp8pwxbc26aw5169";
   };
 
   buildInputs = [ blas lapack gmm fltk libjpeg zlib libGLU libGL
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/math/gretl/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/math/gretl/default.nix
new file mode 100644
index 000000000000..7d77453cbab0
--- /dev/null
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/math/gretl/default.nix
@@ -0,0 +1,43 @@
+{ stdenv, fetchurl, curl, fftw, gmp, gnuplot, gtk3, gtksourceview3, json-glib
+, lapack, libxml2, mpfr, openblas, pkg-config, readline }:
+
+stdenv.mkDerivation rec {
+  pname = "gretl";
+  version = "2020e";
+
+  src = fetchurl {
+    url = "mirror://sourceforge/gretl/${pname}-${version}.tar.xz";
+    sha256 = "105y5hkzgyvad6wc3y7nn327bvrsch6jp03ckkn0w0hpnhiywzx7";
+  };
+
+  buildInputs = [
+    curl
+    fftw
+    gmp
+    gnuplot
+    gtk3
+    gtksourceview3
+    json-glib
+    lapack
+    libxml2
+    mpfr
+    openblas
+    readline
+  ];
+
+  nativeBuildInputs = [ pkg-config ];
+
+  enableParallelBuilding = true;
+
+  meta = with stdenv.lib; {
+    description = "A software package for econometric analysis";
+    longDescription = ''
+      gretl is a cross-platform software package for econometric analysis,
+      written in the C programming language.
+    '';
+    homepage = "http://gretl.sourceforge.net";
+    license = licenses.gpl3;
+    maintainers = with maintainers; [ dmrauh ];
+    platforms = with platforms; all;
+  };
+}
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/math/lrcalc/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/math/lrcalc/default.nix
index 438a84c0e0be..ddd470e621a0 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/math/lrcalc/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/math/lrcalc/default.nix
@@ -34,7 +34,7 @@ stdenv.mkDerivation rec {
     description = "Littlewood-Richardson calculator";
     homepage = "http://math.rutgers.edu/~asbuch/lrcalc/";
     license = licenses.gpl2Plus;
-    maintainers = with maintainers; [ timokau ];
+    maintainers = teams.sage.members;
     platforms = platforms.unix;
   };
 }
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/math/mathematica/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/math/mathematica/default.nix
index ace5ee55d7b1..d04a89bd8842 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/math/mathematica/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/math/mathematica/default.nix
@@ -144,6 +144,9 @@ stdenv.mkDerivation rec {
   '';
 
   dontBuild = true;
+  
+  # This is primarily an IO bound build; there's little benefit to building remotely.
+  preferLocalBuild = true;
 
   # all binaries are already stripped
   dontStrip = true;
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/math/maxima/5.41.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/math/maxima/5.41.nix
deleted file mode 100644
index 829dffc6116e..000000000000
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/math/maxima/5.41.nix
+++ /dev/null
@@ -1,102 +0,0 @@
-{ stdenv, fetchurl, fetchpatch, sbcl, texinfo, perl, python, makeWrapper, rlwrap ? null
-, tk ? null, gnuplot ? null, ecl ? null, ecl-fasl ? false
-}:
-
-let
-  name    = "maxima";
-  # old version temporarily kept for sage, see discussion at
-  # https://github.com/NixOS/nixpkgs/commit/82254747af35f3e0e0d6f78023ded3a81e25331b
-  version = "5.41.0";
-
-  searchPath =
-    stdenv.lib.makeBinPath
-      (stdenv.lib.filter (x: x != null) [ sbcl ecl rlwrap tk gnuplot ]);
-in
-stdenv.mkDerivation ({
-  inherit version;
-  name = "${name}-${version}";
-
-  src = fetchurl {
-    url = "mirror://sourceforge/${name}/${name}-${version}.tar.gz";
-    sha256 = "0x0n81z0s4pl8nwpf7ivlsbvsdphm9w42250g7qdkizl0132by6s";
-  };
-
-  buildInputs = stdenv.lib.filter (x: x != null) [
-    sbcl ecl texinfo perl python makeWrapper
-  ];
-
-  postInstall = ''
-    # Make sure that maxima can find its runtime dependencies.
-    for prog in "$out/bin/"*; do
-      wrapProgram "$prog" --prefix PATH ":" "$out/bin:${searchPath}"
-    done
-    # Move emacs modules and documentation into the right place.
-    mkdir -p $out/share/emacs $out/share/doc
-    ln -s ../maxima/${version}/emacs $out/share/emacs/site-lisp
-    ln -s ../maxima/${version}/doc $out/share/doc/maxima
-  ''
-   + (stdenv.lib.optionalString ecl-fasl ''
-     cp src/binary-ecl/maxima.fas* "$out/lib/maxima/${version}/binary-ecl/"
-   '')
-  ;
-
-  patches = [
-    # fix path to info dir (see https://trac.sagemath.org/ticket/11348)
-    (fetchpatch {
-      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/maxima/patches/infodir.patch?id=07d6c37d18811e2b377a9689790a7c5e24da16ba";
-      sha256 = "09v64n60f7i6frzryrj0zd056lvdpms3ajky4f9p6kankhbiv21x";
-    })
-
-    # fix https://sourceforge.net/p/maxima/bugs/2596/
-    (fetchpatch {
-      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/maxima/patches/matrixexp.patch?id=07d6c37d18811e2b377a9689790a7c5e24da16ba";
-      sha256 = "06961hn66rhjijfvyym21h39wk98sfxhp051da6gz0n9byhwc6zg";
-    })
-
-    # undo https://sourceforge.net/p/maxima/code/ci/f5e9b0f7eb122c4e48ea9df144dd57221e5ea0ca, see see https://trac.sagemath.org/ticket/13364#comment:93
-    (fetchpatch {
-      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/maxima/patches/undoing_true_false_printing_patch.patch?id=07d6c37d18811e2b377a9689790a7c5e24da16ba";
-      sha256 = "0fvi3rcjv6743sqsbgdzazy9jb6r1p1yq63zyj9fx42wd1hgf7yx";
-    })
-
-    # upstream bug https://sourceforge.net/p/maxima/bugs/2520/ (not fixed)
-    # introduced in https://trac.sagemath.org/ticket/13364
-    (fetchpatch {
-      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/maxima/patches/0001-taylor2-Avoid-blowing-the-stack-when-diff-expand-isn.patch?id=07d6c37d18811e2b377a9689790a7c5e24da16ba";
-      sha256 = "0xa0b6cr458zp7lc7qi0flv5ar0r3ivsqhjl0c3clv86di2y522d";
-    })
-  ] ++ stdenv.lib.optionals ecl-fasl [
-    # build fasl, needed for ECL support
-    (fetchpatch {
-      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/maxima/patches/maxima.system.patch?id=07d6c37d18811e2b377a9689790a7c5e24da16ba";
-      sha256 = "18zafig8vflhkr80jq2ivk46k92dkszqlyq8cfmj0b2vcfjwwbar";
-    })
-    # There are some transient test failures. I hope this disables all those tests.
-    # If those test failures ever happen in the non-ecl version, that should be
-    # reportetd upstream.
-    ./known-ecl-failures.patch
-  ];
-
-  # Failures in the regression test suite won't abort the build process. We run
-  # the suite only so that potential errors show up in the build log. See also:
-  # https://sourceforge.net/tracker/?func=detail&aid=3365831&group_id=4933&atid=104933.
-  doCheck = true;
-
-  enableParallelBuilding = true;
-
-  meta = {
-    description = "Computer algebra system";
-    homepage = "http://maxima.sourceforge.net";
-    license = stdenv.lib.licenses.gpl2;
-
-    longDescription = ''
-      Maxima is a fairly complete computer algebra system written in
-      lisp with an emphasis on symbolic computation. It is based on
-      DOE-MACSYMA and licensed under the GPL. Its abilities include
-      symbolic integration, 3D plotting, and an ODE solver.
-    '';
-
-    platforms = stdenv.lib.platforms.unix;
-    maintainers = [ stdenv.lib.maintainers.peti ];
-  };
-})
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/math/maxima/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/math/maxima/default.nix
index 49ff0d5d5a05..1bf7d16f2904 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/math/maxima/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/math/maxima/default.nix
@@ -1,10 +1,10 @@
-{ stdenv, fetchurl, fetchpatch, sbcl, texinfo, perl, python, makeWrapper, rlwrap ? null
-, tk ? null, gnuplot ? null, ecl ? null, ecl-fasl ? false
+{ stdenv, fetchurl, fetchpatch, sbcl, texinfo, perl, python, makeWrapper, autoreconfHook
+, rlwrap ? null, tk ? null, gnuplot ? null, ecl ? null, ecl-fasl ? false
 }:
 
 let
   name    = "maxima";
-  version = "5.42.2";
+  version = "5.44.0";
 
   searchPath =
     stdenv.lib.makeBinPath
@@ -16,14 +16,20 @@ stdenv.mkDerivation ({
 
   src = fetchurl {
     url = "mirror://sourceforge/${name}/${name}-${version}.tar.gz";
-    sha256 = "0kdncy6137sg3rradirxzj10mkcvafxd892zlclwhr9sa7b12zhn";
+    sha256 = "1v6jr5s6hhj6r18gfk6hgxk2qd6z1dxkrjq9ss2z1y6sqi45wgyr";
   };
 
+  nativeBuildInputs = [ autoreconfHook ];
+
   buildInputs = stdenv.lib.filter (x: x != null) [
     sbcl ecl texinfo perl python makeWrapper
     gnuplot   # required in the test suite
   ];
 
+  postPatch = ''
+    substituteInPlace doc/info/Makefile.am --replace "/usr/bin/env perl" "${perl}/bin/perl"
+  '';
+
   postInstall = ''
     # Make sure that maxima can find its runtime dependencies.
     for prog in "$out/bin/"*; do
@@ -57,13 +63,6 @@ stdenv.mkDerivation ({
       url = "https://git.sagemath.org/sage.git/plain/build/pkgs/maxima/patches/undoing_true_false_printing_patch.patch?id=07d6c37d18811e2b377a9689790a7c5e24da16ba";
       sha256 = "0fvi3rcjv6743sqsbgdzazy9jb6r1p1yq63zyj9fx42wd1hgf7yx";
     })
-
-    # upstream bug https://sourceforge.net/p/maxima/bugs/2520/ (not fixed)
-    # introduced in https://trac.sagemath.org/ticket/13364
-    (fetchpatch {
-      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/maxima/patches/0001-taylor2-Avoid-blowing-the-stack-when-diff-expand-isn.patch?id=07d6c37d18811e2b377a9689790a7c5e24da16ba";
-      sha256 = "0xa0b6cr458zp7lc7qi0flv5ar0r3ivsqhjl0c3clv86di2y522d";
-    })
   ] ++ stdenv.lib.optionals ecl-fasl [
     # build fasl, needed for ECL support
     (fetchpatch {
@@ -74,11 +73,13 @@ stdenv.mkDerivation ({
 
   # The test suite is disabled since 5.42.2 because of the following issues:
   #
-  #   Errors found in /build/maxima-5.42.2/share/linearalgebra/rtest_matrixexp.mac, problems:
+  #   Error(s) found:
+  #   /build/maxima-5.44.0/share/linearalgebra/rtest_matrixexp.mac problems:
   #   (20 21 22)
-  #   Error found in rtest_arag, problem:
-  #   (error break)
-  #   3 tests failed out of 3,881 total tests.
+  #   Tests that were expected to fail but passed:
+  #   /build/maxima-5.44.0/share/vector/rtest_vect.mac problem:
+  #   (19)
+  #   3 tests failed out of 16,184 total tests.
   #
   # These failures don't look serious. It would be nice to fix them, but I
   # don't know how and probably won't have the time to find out.
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/math/maxima/known-ecl-failures.patch b/infra/libkookie/nixpkgs/pkgs/applications/science/math/maxima/known-ecl-failures.patch
deleted file mode 100644
index f1d612d993e6..000000000000
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/math/maxima/known-ecl-failures.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-diff --git a/tests/testsuite.lisp b/tests/testsuite.lisp
-index 45a81f4..36c35b8 100644
---- a/tests/testsuite.lisp
-+++ b/tests/testsuite.lisp
-@@ -25,13 +25,14 @@
-         ((mlist simp) "rtest10" 24 25)
-         ((mlist) "rtest11" #+(or gcl cmucl ccl64) 158 #+(or gcl cmucl ccl64) 174 #+gcl 175)
-         "rtest13" "rtest13s"
--        "rtest14"
-+        ;; "rtest14" ;; some tests sometimes fail with ecl, hard to reproduce. Observed failing: 250, 267, 297, 307, 310, 312, 315, 319
-         "rtest15"
- 	;; ccl versions 1.11 and earlier fail test 50.  Mark it as a
- 	;; known failure.  Presumably 1.12 will have this fixed.
-         ((mlist simp) "rtest16" #+ccl 50)
-         "rtestode" "rtestode_zp"
--        "rtest3" "rtest8"
-+        "rtest3"
-+        ((mlist simp) "rtest8" 104) ;; fails with ecl
-         ((mlist simp) "rtest12" 76 78)
-         "rexamples"
-         ((mlist simp) "rtesthyp" 105 112 113 123 124 128)
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/math/nauty/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/math/nauty/default.nix
index d75fc9731cdf..76e7c796a138 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/math/nauty/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/math/nauty/default.nix
@@ -33,7 +33,7 @@ stdenv.mkDerivation rec {
     inherit version;
     description = ''Programs for computing automorphism groups of graphs and digraphs'';
     license = licenses.asl20;
-    maintainers = with maintainers; [ raskin timokau ];
+    maintainers = teams.sage.members;
     platforms = platforms.unix;
     # I'm not sure if the filename will remain the same for future changelog or
     # if it will track changes to minor releases. Lets see. Better than nothing
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/math/palp/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/math/palp/default.nix
index c383438002f4..9ae4fe1ba920 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/math/palp/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/math/palp/default.nix
@@ -84,7 +84,7 @@ stdenv.mkDerivation rec {
     # version was released that pointed to gplv2 however, so thats probably
     # the right license.
     license = licenses.gpl2;
-    maintainers = with maintainers; [ timokau ];
+    maintainers = teams.sage.members;
     platforms = platforms.unix;
   };
 }
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/math/pari/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/math/pari/default.nix
index bd730a1eaaaa..a3e2f99ab274 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/math/pari/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/math/pari/default.nix
@@ -74,7 +74,7 @@ stdenv.mkDerivation rec {
     homepage = "http://pari.math.u-bordeaux.fr";
     downloadPage = "http://pari.math.u-bordeaux.fr/download.html";
     license = licenses.gpl2Plus;
-    maintainers = with maintainers; [ ertes raskin AndersonTorres timokau ];
+    maintainers = with maintainers; [ ertes AndersonTorres ] ++ teams.sage.members;
     platforms = platforms.linux ++ platforms.darwin;
     updateWalker = true;
   };
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/math/pari/gp2c.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/math/pari/gp2c.nix
index 7726a0d789e9..082ff60c3e8d 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/math/pari/gp2c.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/math/pari/gp2c.nix
@@ -5,11 +5,11 @@
 
 stdenv.mkDerivation rec {
   pname = "gp2c";
-  version = "0.0.11pl4";
+  version = "0.0.12";
 
   src = fetchurl {
     url = "https://pari.math.u-bordeaux.fr/pub/pari/GP2C/${pname}-${version}.tar.gz";
-    sha256 = "sha256-QGocEXxTahB5fHhlWtHXgMEl6brQ34LNwScxHNuB1rI=";
+    sha256 = "039ip7qkwwv46wrcdrz7y12m30kazzkjr44kqbc0h137g4wzd7zf";
   };
 
   buildInputs = [ pari perl ];
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/math/pspp/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/math/pspp/default.nix
index 95c2c3931b3c..d6c5b58f0d56 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/math/pspp/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/math/pspp/default.nix
@@ -1,19 +1,19 @@
 { stdenv, fetchurl, libxml2, readline, zlib, perl, cairo, gtk3, gsl
 , pkgconfig, gtksourceview, pango, gettext, dconf
 , makeWrapper, gsettings-desktop-schemas, hicolor-icon-theme
-, texinfo, ssw
+, texinfo, ssw, python3
 }:
 
 stdenv.mkDerivation rec {
   pname = "pspp";
-  version = "1.2.0";
+  version = "1.4.1";
 
   src = fetchurl {
     url = "mirror://gnu/pspp/${pname}-${version}.tar.gz";
-    sha256 = "07pp27zycrb5x927jwaj9r3q7hy915jh51xs85zxby6gfiwl63m5";
+    sha256 = "0lqrash677b09zxdlxp89z6k02y4i23mbqg83956dwl69wc53dan";
   };
 
-  nativeBuildInputs = [ pkgconfig texinfo ];
+  nativeBuildInputs = [ pkgconfig texinfo python3 ];
   buildInputs = [ libxml2 readline zlib perl cairo gtk3 gsl
     gtksourceview pango gettext
     makeWrapper gsettings-desktop-schemas hicolor-icon-theme ssw
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/math/pynac/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/math/pynac/default.nix
index 82e331216712..87fb205174bf 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/math/pynac/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/math/pynac/default.nix
@@ -4,8 +4,9 @@
 , pkgconfig
 , flint
 , gmp
-, python2
+, python3
 , singular
+, ncurses
 }:
 
 stdenv.mkDerivation rec {
@@ -23,8 +24,8 @@ stdenv.mkDerivation rec {
     flint
     gmp
     singular
-    singular
-    python2
+    python3
+    ncurses
   ];
 
   nativeBuildInputs = [
@@ -42,7 +43,7 @@ stdenv.mkDerivation rec {
     '';
     homepage    = "http://pynac.org";
     license = licenses.gpl3;
-    maintainers = with maintainers; [ timokau ];
+    maintainers = teams.sage.members;
     platforms   = platforms.unix;
   };
 }
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix
index 133df7c75ac5..09ead07dc09d 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "qalculate-gtk";
-  version = "3.13.0";
+  version = "3.15.0";
 
   src = fetchFromGitHub {
     owner = "qalculate";
     repo = "qalculate-gtk";
     rev = "v${version}";
-    sha256 = "0yrzvsii84r9d2i2hrs4f65wzv3yj24l9d9yqfv3j85881h8wkm2";
+    sha256 = "1w0r9vv1h3zbfdvk8965g5plfkz5clf81riil5b394ms9vsw0bx5";
   };
 
   hardeningDisable = [ "format" ];
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/math/rofi-calc/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/math/rofi-calc/default.nix
index 40b2711ff65a..ebf2d2f0475d 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/math/rofi-calc/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/math/rofi-calc/default.nix
@@ -12,13 +12,13 @@
 
 stdenv.mkDerivation rec {
   pname = "rofi-calc";
-  version = "1.8";
+  version = "1.9";
 
   src = fetchFromGitHub {
     owner = "svenstaro";
     repo = pname;
     rev = "v${version}";
-    sha256 = "0vwb9c3xvd2cms6cw8j8parg7w4bsxvvrd1wgggr8sz2p8rrvy5p";
+    sha256 = "ZGY4ZtAG/ZnEnC80modZBV4RdRQElbkjeoKCEFVrncE=";
   };
 
   nativeBuildInputs = [
@@ -48,7 +48,7 @@ stdenv.mkDerivation rec {
     homepage = "https://github.com/svenstaro/rofi-calc";
     license = licenses.mit;
     maintainers = with maintainers; [ luc65r albakham ];
-    platforms = [ "x86_64-linux" "x86_64-darwin" ];
+    platforms = with platforms; linux;
   };
 }
 
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/math/sage/flask-oldsessions.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/math/sage/flask-oldsessions.nix
index 403dc8708fab..86fe9912c19e 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/math/sage/flask-oldsessions.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/math/sage/flask-oldsessions.nix
@@ -30,7 +30,7 @@ buildPythonPackage rec {
   meta = with stdenv.lib; {
     description = "Provides a session class that works like the one in Flask before 0.10.";
     license = licenses.bsd2;
-    maintainers = with maintainers; [ timokau ];
+    maintainers = teams.sage.members;
     homepage = "https://github.com/mitsuhiko/flask-oldsessions";
   };
 }
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/math/sage/flask-openid.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/math/sage/flask-openid.nix
index 527173dec80a..900b033429ef 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/math/sage/flask-openid.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/math/sage/flask-openid.nix
@@ -22,7 +22,7 @@ buildPythonPackage rec {
   meta = with stdenv.lib; {
     description = "Adds openid support to flask applications";
     license = licenses.bsd2;
-    maintainers = with maintainers; [ timokau ];
+    maintainers = teams.sage.members;
     homepage = "https://pythonhosted.org/Flask-OpenID/";
   };
 }
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/math/sage/pybrial.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/math/sage/pybrial.nix
index 718414126ae8..5fc8a4aa6f48 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/math/sage/pybrial.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/math/sage/pybrial.nix
@@ -20,6 +20,6 @@ buildPythonPackage rec {
     meta = with stdenv.lib; {
       description = "python implementation of BRiAl";
       license = licenses.gpl2;
-      maintainers = with maintainers; [ timokau ];
+      maintainers = teams.sage.members;
     };
 }
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/math/sage/python-openid.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/math/sage/python-openid.nix
index 4c7fdadadaf0..1e8a908ac79a 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/math/sage/python-openid.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/math/sage/python-openid.nix
@@ -34,7 +34,7 @@ buildPythonPackage rec {
   meta = with stdenv.lib; {
     description = "OpenID library for Python";
     license = licenses.asl20;
-    maintainers = with maintainers; [ timokau ];
+    maintainers = teams.sage.members;
     homepage = "https://github.com/openid/python-openid/";
   };
 }
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/math/sage/sage.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/math/sage/sage.nix
index 4fa8ae6270ba..a21bffea14cd 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/math/sage/sage.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/math/sage/sage.nix
@@ -61,8 +61,9 @@ stdenv.mkDerivation rec {
   };
 
   meta = with stdenv.lib; {
+    broken = true;
     description = "Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab";
     license = licenses.gpl2;
-    maintainers = with maintainers; [ timokau ];
+    maintainers = teams.sage.members;
   };
 }
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/math/sage/sagenb.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/math/sage/sagenb.nix
index 77b2168ad974..ad5c53b6c118 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/math/sage/sagenb.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/math/sage/sagenb.nix
@@ -46,7 +46,7 @@ buildPythonPackage rec {
   meta = with stdenv.lib; {
     description = "Sage Notebook";
     license = licenses.gpl3Plus;
-    maintainers = with maintainers; [ timokau ];
+    maintainers = teams.sage.members;
   };
 
   # let sagenb use mathjax
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/math/singular/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/math/singular/default.nix
index a8c4f6bb9a09..8c5eac2c06d2 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/math/singular/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/math/singular/default.nix
@@ -108,7 +108,7 @@ stdenv.mkDerivation rec {
 
   meta = with lib; {
     description = "A CAS for polynomial computations";
-    maintainers = with maintainers; [ raskin timokau ];
+    maintainers = teams.sage.members;
     # 32 bit x86 fails with some link error: `undefined reference to `__divmoddi4@GCC_7.0.0'`
     platforms = subtractLists platforms.i686 platforms.unix;
     license = licenses.gpl3; # Or GPLv2 at your option - but not GPLv4
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/math/symmetrica/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/math/symmetrica/default.nix
index b363137fb99c..ca752259797f 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/math/symmetrica/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/math/symmetrica/default.nix
@@ -29,7 +29,7 @@ stdenv.mkDerivation rec {
   meta = with lib; {
     description = ''A collection of routines for representation theory and combinatorics'';
     license = licenses.isc;
-    maintainers = with maintainers; [raskin timokau];
+    maintainers = teams.sage.members;
     platforms = platforms.unix;
     homepage = "https://gitlab.com/sagemath/symmetrica";
   };
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/misc/convertall/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/misc/convertall/default.nix
new file mode 100644
index 000000000000..63ed18c89b2f
--- /dev/null
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/misc/convertall/default.nix
@@ -0,0 +1,37 @@
+{ stdenv, fetchFromGitHub, python3, wrapQtAppsHook }:
+
+let
+  inherit (python3.pkgs) wrapPython pyqt5;
+in stdenv.mkDerivation rec {
+  pname = "convertall";
+  version = "0.8.0";
+
+  src = fetchFromGitHub {
+    owner = "doug-101";
+    repo = "ConvertAll";
+    rev = "v${version}";
+    sha256 = "02xxasgbjbivsbhyfpn3cpv52lscdx5kc95s6ns1dvnmdg0fpng0";
+  };
+
+  nativeBuildInputs = [ python3 wrapPython wrapQtAppsHook ];
+
+  propagatedBuildInputs = [ pyqt5 ];
+
+  installPhase = ''
+    python3 install.py -p $out -x
+  '';
+
+  postFixup = ''
+    buildPythonPath $out
+    patchPythonScript $out/share/convertall/convertall.py
+    makeQtWrapper $out/share/convertall/convertall.py $out/bin/convertall
+  '';
+
+  meta = with stdenv.lib; {
+    homepage = "https://convertall.bellz.org/";
+    description = "Graphical unit converter";
+    license = licenses.gpl2Plus;
+    maintainers = with maintainers; [ orivej ];
+    platforms = pyqt5.meta.platforms;
+  };
+}
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/misc/cytoscape/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/misc/cytoscape/default.nix
index 12cdeb453d7a..647492bbe318 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/misc/cytoscape/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/misc/cytoscape/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "cytoscape";
-  version = "3.8.1";
+  version = "3.8.2";
 
   src = fetchurl {
     url = "https://github.com/cytoscape/cytoscape/releases/download/${version}/${pname}-unix-${version}.tar.gz";
-    sha256 = "006g0w29sccg5h0zlrxdp3lx4vx1bfdhx2cms6aah85r5b82wgkf";
+    sha256 = "0zgsq9qnyvmq96pgf7372r16rm034fd0r4qa72xi9zbd4f2r7z8w";
   };
 
   patches = [
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/misc/foldingathome/control.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/misc/foldingathome/control.nix
index 91c3b8c779cd..85be61f6686d 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/misc/foldingathome/control.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/misc/foldingathome/control.nix
@@ -8,7 +8,7 @@
 }:
 let
   majMin = stdenv.lib.versions.majorMinor version;
-  version = "7.6.13";
+  version = "7.6.21";
 
   python = python2.withPackages
     (
@@ -25,7 +25,7 @@ stdenv.mkDerivation rec {
 
   src = fetchurl {
     url = "https://download.foldingathome.org/releases/public/release/fahcontrol/debian-stable-64bit/v${majMin}/fahcontrol_${version}-1_all.deb";
-    sha256 = "0qfvhwc29cgqkwf2bkhq4gr2d1c4jgccfs58916ss03n4rwz9gng";
+    sha256 = "1vfrdqkrvdlyxaw3f6z92w5dllrv6810lmf8yhcmjcwmphipvf71";
   };
 
   nativeBuildInputs = [
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/misc/foldingathome/viewer.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/misc/foldingathome/viewer.nix
index cdeed6536efa..a383de621f29 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/misc/foldingathome/viewer.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/misc/foldingathome/viewer.nix
@@ -11,7 +11,7 @@
 }:
 let
   majMin = stdenv.lib.versions.majorMinor version;
-  version = "7.6.13";
+  version = "7.6.21";
 in
 stdenv.mkDerivation rec {
   inherit version;
@@ -19,7 +19,7 @@ stdenv.mkDerivation rec {
 
   src = fetchurl {
     url = "https://download.foldingathome.org/releases/public/release/fahviewer/debian-stable-64bit/v${majMin}/fahviewer_${version}_amd64.deb";
-    sha256 = "09yfvk16j1iwx8h1xg678ks3bc8760gfdn7n32j8r893kd32cwyk";
+    sha256 = "00fd00pf6fcpplcaahvy9ir60mk69d9rcmwsyq3jrv9mxqm9aq7p";
   };
 
   nativeBuildInputs = [
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/misc/nextinspace/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/misc/nextinspace/default.nix
new file mode 100644
index 000000000000..390b2c58ca68
--- /dev/null
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/misc/nextinspace/default.nix
@@ -0,0 +1,24 @@
+{ lib, fetchPypi, python3Packages }:
+
+python3Packages.buildPythonPackage rec {
+  pname = "nextinspace";
+  version = "1.0.6";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1h3dksxyy5gq071fa7i2p73s50918y1bkk38hgfwr4226c3wipvg";
+  };
+
+  pythonPath = with python3Packages; [
+    requests
+    tzlocal
+    colorama
+  ];
+
+  meta = with lib; {
+    description = "Print upcoming space-related events in your terminal";
+    homepage = "https://github.com/The-Kid-Gid/nextinspace";
+    license = licenses.gpl3;
+    maintainers = with maintainers; [ penguwin ];
+  };
+}
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/misc/openmodelica/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/misc/openmodelica/default.nix
index 50d4dcc1a9ff..268ae53401f5 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/misc/openmodelica/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/misc/openmodelica/default.nix
@@ -45,7 +45,7 @@ stdenv.mkDerivation {
   '';
 
   meta = with stdenv.lib; {
-    description = "OpenModelica is an open-source Modelica-based modeling and simulation environment";
+    description = "An open-source Modelica-based modeling and simulation environment";
     homepage    = "https://openmodelica.org";
     license     = licenses.gpl3;
     maintainers = with maintainers; [ smironov ];
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/misc/rink/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/misc/rink/default.nix
index b868706a05f9..0b1ef2b16ea9 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/misc/rink/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/misc/rink/default.nix
@@ -23,6 +23,6 @@ rustPlatform.buildRustPackage rec {
     description = "Unit-aware calculator";
     homepage = "https://rinkcalc.app";
     license = with licenses; [ mpl20 gpl3 ];
-    maintainers = with maintainers; [ sb0 filalex77 ];
+    maintainers = with maintainers; [ sb0 Br1ght0ne ];
   };
 }
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/misc/snakemake/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/misc/snakemake/default.nix
index 2b7532a93454..a03f7682a51c 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/misc/snakemake/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/misc/snakemake/default.nix
@@ -2,7 +2,7 @@
 
 python3Packages.buildPythonApplication rec {
   pname = "snakemake";
-  version = "5.19.3";
+  version = "5.28.0";
 
   propagatedBuildInputs = with python3Packages; [
     appdirs
@@ -13,6 +13,7 @@ python3Packages.buildPythonApplication rec {
     jsonschema
     nbformat
     psutil
+    pulp
     pyyaml
     ratelimiter
     requests
@@ -22,7 +23,7 @@ python3Packages.buildPythonApplication rec {
 
   src = python3Packages.fetchPypi {
     inherit pname version;
-    sha256 = "b83f3ef73e25dafcb39b3565030e33fa2f7e80ed70256c535dc7e58ea762305d";
+    sha256 = "2367ce91baf7f8fa7738d33aff9670ffdf5410bbac49aeb209f73b45a3425046";
   };
 
   doCheck = false; # Tests depend on Google Cloud credentials at ${HOME}/gcloud-service-key.json
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/molecular-dynamics/gromacs/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/molecular-dynamics/gromacs/default.nix
index 151abb099f5b..bfa4a1f43391 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/molecular-dynamics/gromacs/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/molecular-dynamics/gromacs/default.nix
@@ -9,11 +9,11 @@
 }:
 
 stdenv.mkDerivation {
-  name = "gromacs-2020.3";
+  name = "gromacs-2020.4";
 
   src = fetchurl {
-    url = "ftp://ftp.gromacs.org/pub/gromacs/gromacs-2020.3.tar.gz";
-    sha256 = "1acjrhcfzpqy2dncblhj97602jbg9gdha4q1bgji9nrj25lq6cch";
+    url = "ftp://ftp.gromacs.org/pub/gromacs/gromacs-2020.4.tar.gz";
+    sha256 = "1rplvgna60nqyb8nspaz3bfkwb044kv3zxdaa5whql5m441nj6am";
   };
 
   nativeBuildInputs = [ cmake ];
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/physics/xflr5/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/physics/xflr5/default.nix
index 85838b04cbf1..5ae56528f964 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/physics/xflr5/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/physics/xflr5/default.nix
@@ -1,6 +1,6 @@
-{ stdenv, lib, fetchurl, wrapQtAppsHook, qmake }:
+{ mkDerivation, lib, fetchurl, qmake }:
 
-stdenv.mkDerivation rec {
+mkDerivation rec {
   pname = "xflr5";
   version = "6.47";
 
@@ -11,13 +11,13 @@ stdenv.mkDerivation rec {
 
   enableParallelBuilding = true;
 
-  nativeBuildInputs = [ qmake wrapQtAppsHook ];
+  nativeBuildInputs = [ qmake ];
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     description = "An analysis tool for airfoils, wings and planes";
     homepage = https://sourceforge.net/projects/xflr5/;
     license = licenses.gpl3;
     maintainers = [ maintainers.esclear ];
     platforms = platforms.linux;
   };
-}
-\ No newline at end of file
+}
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/programming/scyther/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/programming/scyther/default.nix
index d1e948fe187b..ca6b57de611d 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/programming/scyther/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/programming/scyther/default.nix
@@ -13,7 +13,7 @@ let
   };
 
   meta = with lib; {
-    description = "Scyther is a tool for the automatic verification of security protocols";
+    description = "A tool for the automatic verification of security protocols";
     homepage = "https://www.cs.ox.ac.uk/people/cas.cremers/scyther/";
     license = licenses.gpl2;
     maintainers = with maintainers; [ infinisil ];
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/robotics/mavproxy/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/robotics/mavproxy/default.nix
index 9c7166afc2a9..a71ddc874c9d 100644
--- a/infra/libkookie/nixpkgs/pkgs/applications/science/robotics/mavproxy/default.nix
+++ b/infra/libkookie/nixpkgs/pkgs/applications/science/robotics/mavproxy/default.nix
@@ -3,11 +3,11 @@
 
 buildPythonApplication rec {
   pname = "MAVProxy";
-  version = "1.8.22";
+  version = "1.8.29";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "87d7f9c0b8f4f1db3ce3521f67cd244fe3b89ffead797e92f35a7f71bbe8b958";
+    sha256 = "8f5900dc0a404ab9cf5a00155f83e9aaeab18161ce21a352dfdcf2d7abf5d78e";
   };
 
   propagatedBuildInputs = [
author	Mx Kookie <kookie@spacekookie.de>	2020-12-09 18:55:19 +0000
committer	Mx Kookie <kookie@spacekookie.de>	2020-12-09 18:55:19 +0000
commit	80d90d9b204f7c17912740f9f414fe5d59f293ba (patch)
tree	5f2065a06e724270610760d59d01c6888b375a46 /infra/libkookie/nixpkgs/pkgs/applications/science
parent	3a31a84c7d3e589035ad08499206aac44a81f424 (diff)
parent	83cbad92d73216bb0d9187c56cce0b91f9121d5a (diff)