Merge remote-tracking branch 'origin/master' into staging-next

Conflicts:
	pkgs/development/python-modules/pyarrow/default.nix

pkgs/applications/emulators/dosbox-staging/default.nix

@@ -1,10 +1,15 @@
-{ alsa-lib
-, copyDesktopItems
+{ lib
+, stdenv
 , fetchFromGitHub
+, SDL2
+, SDL2_image
+, SDL2_net
+, alsa-lib
+, copyDesktopItems
 , fluidsynth
 , glib
 , gtest
-, lib
+, irr1
 , libGL
 , libGLU
 , libjack2
@@ -20,22 +25,17 @@
 , ninja
 , opusfile
 , pkg-config
-, irr1
-, SDL2
-, SDL2_image
-, SDL2_net
 , speexdsp
-, stdenv
 }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation (self: {
   pname = "dosbox-staging";
   version = "0.80.1";
 
   src = fetchFromGitHub {
-    owner = pname;
-    repo = pname;
-    rev = "v${version}";
+    owner = "dosbox-staging";
+    repo = "dosbox-staging";
+    rev = "v${self.version}";
     hash = "sha256-I90poBeLSq1c8PXyjrx7/UcbfqFNnnNiXfJdWhLPGMc=";
   };
 
@@ -49,6 +49,9 @@ stdenv.mkDerivation rec {
   ];
 
   buildInputs = [
+    SDL2
+    SDL2_image
+    SDL2_net
     alsa-lib
     fluidsynth
     glib
@@ -63,9 +66,6 @@ stdenv.mkDerivation rec {
     libslirp
     libsndfile
     opusfile
-    SDL2
-    SDL2_image
-    SDL2_net
     speexdsp
   ];
 
@@ -91,17 +91,17 @@ stdenv.mkDerivation rec {
     # original dosbox. Doing it this way allows us to work with frontends and
     # launchers that expect the binary to be named dosbox, but get out of the
     # way of vanilla dosbox if the user desires to install that as well.
-    mv $out/bin/dosbox $out/bin/${pname}
+    mv $out/bin/dosbox $out/bin/${self.pname}
     makeWrapper $out/bin/dosbox-staging $out/bin/dosbox
 
     # Create a symlink to dosbox manual instead of merely copying it
     pushd $out/share/man/man1/
-    mv dosbox.1.gz ${pname}.1.gz
-    ln -s ${pname}.1.gz dosbox.1.gz
+    mv dosbox.1.gz ${self.pname}.1.gz
+    ln -s ${self.pname}.1.gz dosbox.1.gz
     popd
   '';
 
-  meta = with lib; {
+  meta = {
     homepage = "https://dosbox-staging.github.io/";
     description = "A modernized DOS emulator";
     longDescription = ''
@@ -110,10 +110,14 @@ stdenv.mkDerivation rec {
       existing DOSBox codebase while leveraging modern development tools and
       practices.
     '';
-    license = licenses.gpl2Plus;
-    maintainers = with maintainers; [ joshuafern AndersonTorres ];
-    platforms = platforms.unix;
+    changelog = "https://github.com/dosbox-staging/dosbox-staging/releases/tag/v${self.version}";
+    license = lib.licenses.gpl2Plus;
+    maintainers = [
+      lib.maintainers.joshuafern
+      lib.maintainers.AndersonTorres
+    ];
+    platforms = lib.platforms.unix;
     priority = 101;
   };
-}
-# TODO: report upstream about not finding SDL2_net
+})
+# TODO: report upstream about not finding extra SDL2 libraries

pkgs/applications/graphics/eyedropper/default.nix

@@ -50,7 +50,7 @@ stdenv.mkDerivation rec {
   ];
 
   meta = with lib; {
-    description = "An easy-to-use color picker and editor";
+    description = "A powerful color picker and formatter";
     homepage = "https://github.com/FineFindus/eyedropper";
     license = licenses.gpl3Plus;
     platforms = platforms.linux;

pkgs/applications/graphics/tesseract/tesseract3.nix

@@ -3,15 +3,23 @@
 
 stdenv.mkDerivation rec {
   pname = "tesseract";
-  version = "3.05.00";
+  version = "3.05.02";
 
   src = fetchFromGitHub {
     owner = "tesseract-ocr";
     repo = "tesseract";
     rev = version;
-    hash = "sha256-YHj00gG/3SW0ILTiQwphiCxuP9OCDya27hyFQB27mYc=";
+    hash = "sha256-28osuZnVwkJpNTYkU+5D5PI8xtViFzGCMScHzkS2H20=";
   };
 
+  # leptonica 1.83 made internal structures private. using internal headers isn't
+  # great, but tesseract3's days are numbered anyway
+  postPatch = ''
+    for f in textord/devanagari_processing.cpp cube/cube_line_object.h cube/cube_line_segmenter.h cube/cube_utils.h ; do
+      sed -i '/allheaders.h/a#include "pix_internal.h"' "$f"
+    done
+  '';
+
   enableParallelBuilding = true;
 
   nativeBuildInputs = [

pkgs/applications/graphics/tesseract/tesseract4.nix

@@ -3,26 +3,20 @@
 
 stdenv.mkDerivation rec {
   pname = "tesseract";
-  version = "4.1.1";
+  version = "4.1.3";
 
   src = fetchFromGitHub {
     owner = "tesseract-ocr";
     repo = "tesseract";
     rev = version;
-    hash = "sha256-lu/Y5mlCI8AajhiWaID0fGo5PghEQZdgt2X0K9c/QrE=";
+    hash = "sha256-sV3w53ky13ESc0dGPutMGQ4TcmOeWJkvUwBPIyzSTc8=";
   };
 
-  patches = [
-    # https://github.com/tesseract-ocr/tesseract/issues/3447
-    (fetchpatch {
-      url = "https://github.com/tesseract-ocr/tesseract/commit/dbc79b09d195490dfa3f7d338eadac07ad6683f7.patch";
-      sha256 = "sha256-lGlg0etuU4RXfdq1QH2bYObdeGrFHKf9O8zMUAbfNIQ=";
-    })
-    (fetchpatch {
-      url = "https://github.com/tesseract-ocr/tesseract/commit/6dc4b184b1ebf2e68461f6b63f63a033bc7245f7.patch";
-      sha256 = "sha256-DwIX3r5NmeajI6WgIVHDbkhLH/ygJIjPO5XrbzWQhSw=";
-    })
-  ];
+  # leptonica 1.83 made internal structures private. using internal headers isn't
+  # great, but tesseract4's days are numbered anyway
+  postPatch = ''
+    sed -i '/allheaders.h/a#include "pix_internal.h"' src/textord/devanagari_processing.cpp
+  '';
 
   enableParallelBuilding = true;
 

pkgs/applications/misc/qt-box-editor/default.nix

@@ -10,23 +10,25 @@
 
 mkDerivation {
   pname = "qt-box-editor";
-  version = "unstable-2019-07-12";
+  version = "unstable-2019-07-14";
 
   src = fetchFromGitHub {
     owner = "zdenop";
     repo = "qt-box-editor";
-    rev = "75a68b466868ba41ba2886caa796057403fe1901";
-    sha256 = "0zwsyy7cnbhy5aazwlkhd9y8bnzlgy1gffqa46abajn4809b95k3";
+    rev = "cba2929dabc6c715acd1a282ba161fee914c87f6";
+    hash = "sha256-3dWnAu0CLO3atjbC1zJEnL3vzsIEecDDDhW3INMfCv4=";
   };
 
   buildInputs = [ qtbase qtsvg leptonica tesseract ];
 
   nativeBuildInputs = [ qmake ];
 
-  # remove with next release
-  # https://github.com/zdenop/qt-box-editor/pull/78
+  # https://github.com/zdenop/qt-box-editor/issues/87
   postPatch = ''
-    printf "INSTALLS += target\ntarget.path = $out/bin" >>  qt-box-editor.pro
+    sed -i '/allheaders.h/a#include <leptonica/pix_internal.h>' src/TessTools.h
+
+    substituteInPlace qt-box-editor.pro \
+      --replace '-llept' '-lleptonica'
   '';
 
   meta = with lib; {

pkgs/applications/networking/go-graft/default.nix

@@ -2,19 +2,19 @@
 
 buildGoModule rec {
   pname = "go-graft";
-  version = "0.2.16";
+  version = "0.2.17";
 
   src = fetchFromGitHub {
     owner = "mzz2017";
     repo = "gg";
     rev = "v${version}";
-    sha256 = "sha256-zdOcQ/+WXS7pDfnvYdb/FDjMT3yJdwnS8DoH2MIDcDs=";
+    sha256 = "sha256-UhRsgUz9au7e47cS6yrIJXc/8ZxVDpMHWBjoAcw+oCM=";
   };
 
   CGO_ENABLED = 0;
 
   ldflags = [ "-X github.com/mzz2017/gg/cmd.Version=${version}" "-s" "-w" "-buildid=" ];
-  vendorHash = "sha256-kx94B1XIXWJOY9Y69lNb/sHWVjsuFuOXrdtJFJrUuAs=";
+  vendorHash = "sha256-EiBt2SxUQY05Wr7KJbK+fs3U3iSmqECJ0glS8B2Ox9Q=";
   subPackages = [ "." ];
 
   meta = with lib; {

pkgs/applications/networking/instant-messengers/discord/default.nix

@@ -3,7 +3,7 @@ let
   versions = if stdenv.isLinux then {
     stable = "0.0.24";
     ptb = "0.0.38";
-    canary = "0.0.146";
+    canary = "0.0.148";
   } else {
     stable = "0.0.264";
     ptb = "0.0.59";
@@ -22,7 +22,7 @@ let
       };
       canary = fetchurl {
         url = "https://dl-canary.discordapp.net/apps/linux/${version}/discord-canary-${version}.tar.gz";
-        sha256 = "sha256-5GiG+RGqwHUdIeSVWpbaIw3sTuZbvIQeetXSEvSqTls=";
+        sha256 = "sha256-2ZrSDyPj3AHriCWZ/bb303H3J97TTun//WjmInNEmwk=";
       };
     };
     x86_64-darwin = {

pkgs/applications/science/biology/last/default.nix

@@ -9,13 +9,13 @@
 
 stdenv.mkDerivation rec {
   pname = "last";
-  version = "1445";
+  version = "1447";
 
   src = fetchFromGitLab {
     owner = "mcfrith";
     repo = "last";
     rev = "refs/tags/${version}";
-    hash = "sha256-E3D9KmCIVcwXblwJ0wePk0wKoXwKA2UsSGqfMmRsw2A=";
+    hash = "sha256-zts1F2tFeBP7CQifpc2M4i6duK8FA7hQXTOizv8/kWM=";
   };
 
   nativeBuildInputs = [

pkgs/applications/science/math/gap/default.nix

@@ -134,8 +134,6 @@ stdenv.mkDerivation rec {
     # https://github.com/NixOS/nixpkgs/pull/192548#discussion_r992824942
     rm -r "$out/share/gap/pkg"
     cp -ar pkg tst "$out/share/gap"
-
-    makeWrapper "$out/lib/gap/gap" "$out/bin/gap" --add-flags "-l $out/share/gap"
   '';
 
   preFixup = ''

pkgs/applications/science/math/pari/default.nix

@@ -1,6 +1,7 @@
 { lib
 , stdenv
 , fetchurl
+, fetchpatch
 , gmp
 , libX11
 , libpthreadstubs
@@ -25,6 +26,15 @@ stdenv.mkDerivation rec {
     hash = "sha256-sEYoER7iKHZRmksc2vsy/rqjTq+iT56B9Y+NBX++4N0=";
   };
 
+  patches = [
+    # https://pari.math.u-bordeaux.fr/cgi-bin/bugreport.cgi?bug=2441
+    (fetchpatch {
+      name = "fix-find_isogenous_from_Atkin.patch";
+      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/pari/patches/bug2441.patch?id=9.8.rc0";
+      hash = "sha256-DvOUFlFDnopN+MJY6GYRPNabuoHPFch/nNn+49ygznc=";
+    })
+  ];
+
   buildInputs = [
     gmp
     libX11

pkgs/applications/science/math/sage/README.md

@@ -10,7 +10,7 @@ First you should find out which change to nixpkgs is at fault (if you don't alre
 
 If the build broke as a result of a package update, try those solutions in order:
 
-- search the [sage trac](https://trac.sagemath.org/) for keywords like "Upgrade <package>". Maybe somebody has already proposed a patch that fixes the issue. You can then add a `fetchpatch` to `sage-src.nix`.
+- search the [sage GitHub repo](https://github.com/sagemath/sage) for keywords like "Upgrade <package>". Maybe somebody has already proposed a patch that fixes the issue. You can then add a `fetchpatch` to `sage-src.nix`.
 
 - check if [gentoo](https://github.com/cschwan/sage-on-gentoo/tree/master/sci-mathematics/sage), [debian](https://salsa.debian.org/science-team/sagemath/tree/master/debian) or [arch linux](https://git.archlinux.org/svntogit/community.git/tree/trunk?h=packages/sagemath) already solved the problem. You can then again add a `fetchpatch` to `sage-src.nix`. If applicable you should also [propose the patch upstream](#proposing-a-sage-patch).
 
@@ -19,7 +19,7 @@ If the build broke as a result of a package update, try those solutions in order
 ```
 [user@localhost ~]$ git clone https://github.com/sagemath/sage.git
 [user@localhost ~]$ cd sage
-[user@localhost sage]$ git checkout 8.2 # substitute the relevant version here
+[user@localhost sage]$ git checkout 9.8 # substitute the relevant version here
 ```
 
 Then make the needed changes and generate a patch with `git diff`:
@@ -29,42 +29,10 @@ Then make the needed changes and generate a patch with `git diff`:
 [user@localhost ~]$ git diff -u > /path/to/nixpkgs/pkgs/applications/science/math/sage/patches/name-of-patch.patch
 ```
 
-Now just add the patch to `sage-src.nix` and test your changes. If they fix the problem, [propose them upstream](#proposing-a-sage-patch) and add a link to the trac ticket.
+Now just add the patch to `sage-src.nix` and test your changes. If they fix the problem, submit a PR upstream (refer to sages [Developer's Guide](http://doc.sagemath.org/html/en/developer/index.html) for further details).
 
 - pin the package version in `default.nix` and add a note that explains why that is necessary.
 
-
-## Proposing a sage patch
-
-You can [login the sage trac using GitHub](https://trac.sagemath.org/login). Your username will then be `gh-<your-github-name>`. The only other way is to request a trac account via email. After that refer to [git the hard way](http://doc.sagemath.org/html/en/developer/manual_git.html#chapter-manual-git) in the sage documentation. The "easy way" requires a non-GitHub account (requested via email) and a special tool. The "hard way" is really not all that hard if you're a bit familiar with git.
-
-Here's the gist, assuming you want to use ssh key authentication. First, [add your public ssh key](https://trac.sagemath.org/prefs/sshkeys). Then:
-
-```
-[user@localhost ~]$ git clone https://github.com/sagemath/sage.git
-[user@localhost ~]$ cd sage
-[user@localhost sage]$ git remote add trac git@trac.sagemath.org:sage.git -t master
-[user@localhost sage]$ git checkout -b u/gh-<your-github-username>/<your-branch-name> develop
-[user@localhost sage]$ <make changes>
-[user@localhost sage]$ git add .
-[user@localhost sage]$ git commit
-[user@localhost sage]$ git show # review your changes
-[user@localhost sage]$ git push --set-upstream trac u/gh-<your-github-username>/<your-branch-name>
-```
-
-You now created a branch on the trac server (you *must* follow the naming scheme as you only have push access to branches with the `u/gh-<your-github-username>/` prefix).
-Now you can [create a new trac ticket](https://trac.sagemath.org/newticket).
-- Write a description of the change
-- set the type and component as appropriate
-- write your real name in the "Authors" field
-- write `u/gh-<your-github-username>/<your-branch-name>` in the "Branch" field
-- click "Create ticket"
-- click "Modify" on the top right of your ticket (for some reason you can only change the ticket status after you have created it)
-- set the ticket status from `new` to `needs_review`
-- click "Save changes"
-
-Refer to sages [Developer's Guide](http://doc.sagemath.org/html/en/developer/index.html) for further details.
-
 ## I want to update sage
 
 You'll need to change the `version` field in `sage-src.nix`. Afterwards just try to build and let nix tell you which patches no longer apply (hopefully because they were adopted upstream). Remove those.
@@ -74,5 +42,5 @@ If the problem is not obvious, you can try to first update sage to an intermedia
 
 ## Well, that didn't help!
 
-If you couldn't fix the problem, create a GitHub issue on the nixpkgs repo and ping @timokau (or whoever is listed in the `maintainers` list of the sage package).
+If you couldn't fix the problem, create a GitHub issue on the nixpkgs repo and ping the sage maintainers (as listed in the sage package).
 Describe what you did and why it didn't work. Afterwards it would be great if you help the next guy out and improve this documentation!

pkgs/applications/science/math/sage/env-locations.nix

@@ -35,7 +35,8 @@ writeTextFile rec {
     export GRAPHS_DATA_DIR='${graphs}/share/graphs'
     export ELLCURVE_DATA_DIR='${elliptic_curves}/share/ellcurves'
     export POLYTOPE_DATA_DIR='${polytopes_db}/share/reflexive_polytopes'
-    export GAP_ROOT_DIR='${gap}/share/gap'
+    export GAP_LIB_DIR='${gap}/lib/gap'
+    export GAP_SHARE_DIR='${gap}/share/gap'
     export ECLDIR='${maxima.lisp-compiler}/lib/${maxima.lisp-compiler.pname}-${maxima.lisp-compiler.version}/'
     export COMBINATORIAL_DESIGN_DATA_DIR="${combinatorial_designs}/share/combinatorial_designs"
     export CREMONA_MINI_DATA_DIR="${elliptic_curves}/share/cremona"

pkgs/applications/science/math/sage/patches/pari-2.15.1-upgrade-rebased.patch

@@ -1,26 +0,0 @@
-diff --git a/src/sage/geometry/polyhedron/backend_normaliz.py b/src/sage/geometry/polyhedron/backend_normaliz.py
-index 86b89632a5..ca8a43b248 100644
---- a/src/sage/geometry/polyhedron/backend_normaliz.py
-+++ b/src/sage/geometry/polyhedron/backend_normaliz.py
-@@ -53,7 +53,7 @@ def _number_field_elements_from_algebraics_list_of_lists_of_lists(listss, **kwds
-         1.732050807568878?
-         sage: from sage.geometry.polyhedron.backend_normaliz import _number_field_elements_from_algebraics_list_of_lists_of_lists
-         sage: K, results, hom = _number_field_elements_from_algebraics_list_of_lists_of_lists([[[rt2], [1]], [[rt3]], [[1], []]]); results  # optional - sage.rings.number_field
--        [[[-a^3 + 3*a], [1]], [[-a^2 + 2]], [[1], []]]
-+        [[[-a^3 + 3*a], [1]], [[a^2 - 2]], [[1], []]]
-     """
-     from sage.rings.qqbar import number_field_elements_from_algebraics
-     numbers = []
-diff --git a/src/sage/lfunctions/pari.py b/src/sage/lfunctions/pari.py
-index d2b20f1891..6c31efe239 100644
---- a/src/sage/lfunctions/pari.py
-+++ b/src/sage/lfunctions/pari.py
-@@ -339,7 +339,7 @@ def lfun_eta_quotient(scalings, exponents):
-         0.0374412812685155
- 
-         sage: lfun_eta_quotient([6],[4])
--        [[Vecsmall([7]), [Vecsmall([6]), Vecsmall([4])]], 0, [0, 1], 2, 36, 1]
-+        [[Vecsmall([7]), [Vecsmall([6]), Vecsmall([4]), 0]], 0, [0, 1], 2, 36, 1]
- 
-         sage: lfun_eta_quotient([2,1,4], [5,-2,-2])
-         Traceback (most recent call last):

pkgs/applications/science/math/sage/sage-src.nix

@@ -57,14 +57,14 @@ let
   );
 in
 stdenv.mkDerivation rec {
-  version = "9.7";
+  version = "9.8";
   pname = "sage-src";
 
   src = fetchFromGitHub {
     owner = "sagemath";
     repo = "sage";
     rev = version;
-    sha256 = "sha256-MYpCp18wqKwCa+tcJ7He14p1FXDlVm1vubQqQS9g3LY=";
+    sha256 = "sha256-dDbrzJXsOBARYfJz0r7n3LbaoXHnx7Acz6HBa95NV9o=";
   };
 
   # Patches needed because of particularities of nix or the way this is packaged.
@@ -89,14 +89,6 @@ stdenv.mkDerivation rec {
     # To help debug the transient error in
     # https://trac.sagemath.org/ticket/23087 when it next occurs.
     ./patches/configurationpy-error-verbose.patch
-
-    # https://trac.sagemath.org/ticket/33907
-    (fetchSageDiff {
-      name = "interfaces-expectpy-intermittent.patch";
-      base = "9.8.beta6";
-      rev = "6f5c1c2fc8bcfb5e6555716d05ce70511795ffa1";
-      sha256 = "sha256-z8FQxtrk62MHzPjrUTad+fMAE6XV8GTsLWKgGOM3zBg=";
-    })
   ];
 
   # Patches needed because of package updates. We could just pin the versions of
@@ -119,28 +111,12 @@ stdenv.mkDerivation rec {
     # adapted from https://trac.sagemath.org/ticket/23712#comment:22
     ./patches/tachyon-renamed-focallength.patch
 
-    # https://trac.sagemath.org/ticket/34118
-    (fetchSageDiff {
-      name = "sympy-1.11-upgrade.patch";
-      base = "9.7";
-      rev = "52815744bde2b682245b6f985a112f7cb8666056";
-      sha256 = "sha256-gv6z6JkQ6S6oCJQNkVgcPVvzlplyvR1nC7pWmcUiSc0=";
-    })
-
-    # https://trac.sagemath.org/ticket/34460
-    (fetchSageDiff {
-      name = "ipywidgets-8-upgrade.patch";
-      base = "9.7";
-      rev = "2816dbacb342398a23bb3099e20c92c8020ab0fa";
-      sha256 = "sha256-tCOsMxXwPkRg3FJGVvTqDzlWdra78UfDY6nci0Nr9GI=";
-    })
-
     # https://trac.sagemath.org/ticket/34391
     (fetchSageDiff {
       name = "gap-4.12-upgrade.patch";
-      base = "9.8.beta2";
-      rev = "eb8cd42feb58963adba67599bf6e311e03424328";
-      sha256 = "sha256-0dKewOZe2n3PqSdxCJt18FkqwTdrD0VA5MXAMiTW8Tw=";
+      base = "9.8.beta7";
+      rev = "dd4a17281adcda74e11f998ef519b6bd0dafb043";
+      sha256 = "sha256-UQT9DO9xd5hh5RucvUkIm+rggPKu8bc1YaSI6LVYH98=";
     })
 
     # https://trac.sagemath.org/ticket/34701
@@ -151,46 +127,6 @@ stdenv.mkDerivation rec {
       sha256 = "sha256-9BhQLFB3wUhiXRQsK9L+I62lSjvTfrqMNi7QUIQvH4U=";
     })
 
-    # https://trac.sagemath.org/ticket/34537
-    (fetchSageDiff {
-      name = "pari-2.15.1-upgrade.patch";
-      squashed = true;
-      base = "54cd6fe6de52aee5a433e0569e8c370618cb2047"; # 9.8.beta1
-      rev = "1e86aa26790d84bf066eca67f98a60a8aa3d4d3a";
-      sha256 = "sha256-LUgcMqrKXWb72Kxl0n6MV5unLXlQSeG8ncN41F7TRSc=";
-      excludes = ["build/*"
-                  "src/sage/geometry/polyhedron/base_number_field.py"
-                  "src/sage/geometry/polyhedron/backend_normaliz.py"
-                  "src/sage/lfunctions/pari.py"];
-    })
-    # Some files were excluded from the above patch due to
-    # conflicts. The patch below contains rebased versions.
-    ./patches/pari-2.15.1-upgrade-rebased.patch
-
-    # https://trac.sagemath.org/ticket/34668
-    (fetchSageDiff {
-      name = "matplotlib-3.6-upgrade.patch";
-      base = "9.8.beta2";
-      rev = "5501e0de0dca1cff0355326dd42bd8c7e5749568";
-      sha256 = "sha256-ceJkVaecIsZewN8v/3gPQXFbFjv5Akz6zEFg/ToXdek=";
-    })
-
-    # https://trac.sagemath.org/ticket/34693
-    (fetchSageDiff {
-      name = "matplotlib-3.6-docbuilding.patch";
-      base = "9.8.beta4";
-      rev = "64589686c261d33e6b5aff2589bcae8af004bcc6";
-      sha256 = "sha256-j5AMY1TmhP+HBBBYaFZSkABJ5vtwe6iP2LRfGEgSm8Q=";
-    })
-
-    # https://trac.sagemath.org/ticket/34615
-    (fetchSageDiff {
-      name = "sphinx-5.2-upgrade.patch";
-      base = "9.8.beta1";
-      rev = "8f8af65e54d3a9962cfab40f15dc23f4e955b43f";
-      sha256 = "sha256-yhDdyxnXSSkqLcuOPBWSEBc26rk1Od3gLcWW8S2p8bY=";
-    })
-
     # temporarily paper over https://github.com/jupyter-widgets/ipywidgets/issues/3669
     ./patches/ipywidgets-on_submit-deprecationwarning.patch
 

pkgs/applications/terminal-emulators/foot/default.nix

@@ -18,7 +18,7 @@
 , wayland-scanner
 , pkg-config
 , utf8proc
-, allowPgo ? true
+, allowPgo ? !stdenv.hostPlatform.isMusl
 , python3  # for PGO
 # for clang stdenv check
 , foot

pkgs/applications/version-management/sapling/default.nix

@@ -88,111 +88,93 @@ let
       runHook postInstall
     '';
   };
-
-  # Builds the main `sl` binary and its Python extensions
-  sapling = python3Packages.buildPythonPackage {
-    pname = "sapling-main";
-    inherit src version;
-
-    sourceRoot = "source/eden/scm";
-
-    # Upstream does not commit Cargo.lock
-    cargoDeps = rustPlatform.importCargoLock {
-      lockFile = ./Cargo.lock;
-      outputHashes = {
-        "cloned-0.1.0" = "sha256-DYQTK722wgeDUJtOVXHLt42G6gpe6A62rET+JH+bPKU=";
-        "deltae-0.3.0" = "sha256-a9Skaqs+tVTw8x83jga+INBr+TdaMmo35Bf2wbfR6zs=";
-        "fb303_core-0.0.0" = "sha256-YEFNTYvtgp8nc/1O7AbdyxCD3Xx2xCjbS17fTTEsUL0=";
-        "fbthrift-0.0.1+unstable" = "sha256-mDoYhXOzQIDqP7XdmiBbmq5VmAKAgggTNH/kW2kHv4k=";
-        "reqwest-0.11.11" = "sha256-uhc8XhkGW22XDNo0qreWdXeFF2cslOOZHfTRQ30IBcE=";
-        "serde_bser-0.3.1" = "sha256-/zn1NfXWytXvnalkgPsg9BdujVV97PGkXwmPtQGVeCc=";
-      };
-    };
-    postPatch = ''
-      cp ${./Cargo.lock} Cargo.lock
-    '';
-
-    # Since the derivation builder doesn't have network access to remain pure,
-    # fetch the artifacts manually and link them. Then replace the hardcoded URLs
-    # with filesystem paths for the curl calls.
-    postUnpack = ''
-      mkdir $sourceRoot/hack_pydeps
-      ${lib.concatStrings (map (li: "ln -s ${fetchurl li} $sourceRoot/hack_pydeps/${baseNameOf li.url}\n") links)}
-      sed -i "s|https://files.pythonhosted.org/packages/[[:alnum:]]*/[[:alnum:]]*/[[:alnum:]]*/|file://$NIX_BUILD_TOP/$sourceRoot/hack_pydeps/|g" $sourceRoot/setup.py
-    '';
-
-    # Now, copy the "sl web" (aka edenscm-isl) results into the output of this
-    # package, so that the command can actually work. NOTES:
-    #
-    # 1) This applies on all systems (so no conditional a la postFixup)
-    # 2) This doesn't require any kind of fixup itself, so we leave it out
-    #    of postFixup for that reason, too
-    # 3) If asked, we optionally patch in a hardcoded path to the 'nodejs' package,
-    #    so that 'sl web' always works
-    # 4) 'sl web' will still work if 'nodejs' is in $PATH, just not OOTB
-    preFixup = ''
-      sitepackages=$out/lib/${python3Packages.python.libPrefix}/site-packages
-      chmod +w $sitepackages
-      cp -r ${isl} $sitepackages/edenscm-isl
-    '' + lib.optionalString (!enableMinimal) ''
-      chmod +w $sitepackages/edenscm-isl/run-isl
-      substituteInPlace $sitepackages/edenscm-isl/run-isl \
-        --replace 'NODE=node' 'NODE=${nodejs}/bin/node'
-    '';
-
-    postFixup = lib.optionalString stdenv.isLinux ''
-      wrapProgram $out/bin/sl \
-        --set LOCALE_ARCHIVE "${glibcLocales}/lib/locale/locale-archive"
-    '';
-
-    nativeBuildInputs = [
-      curl
-      pkg-config
-    ] ++ (with rustPlatform; [
-      myCargoSetupHook
-      rust.cargo
-      rust.rustc
-    ]);
-
-    buildInputs = [
-      openssl
-    ] ++ lib.optionals stdenv.isDarwin [
-      curl
-      libiconv
-      CoreFoundation
-      CoreServices
-      Security
-    ];
-
-    doCheck = false;
-
-    HGNAME = "sl";
-    SAPLING_OSS_BUILD = "true";
-    SAPLING_VERSION = version;
-    SAPLING_VERSION_HASH = versionHash;
-  };
 in
-stdenv.mkDerivation {
+# Builds the main `sl` binary and its Python extensions
+python3Packages.buildPythonApplication {
   pname = "sapling";
-  inherit version;
+  inherit src version;
 
-  dontUnpack = true;
+  sourceRoot = "source/eden/scm";
 
-  installPhase = ''
-    runHook preInstall
-
-    mkdir -p $out
-    cp -r ${sapling}/* $out
-
-    runHook postInstall
+  # Upstream does not commit Cargo.lock
+  cargoDeps = rustPlatform.importCargoLock {
+    lockFile = ./Cargo.lock;
+    outputHashes = {
+      "cloned-0.1.0" = "sha256-DYQTK722wgeDUJtOVXHLt42G6gpe6A62rET+JH+bPKU=";
+      "deltae-0.3.0" = "sha256-a9Skaqs+tVTw8x83jga+INBr+TdaMmo35Bf2wbfR6zs=";
+      "fb303_core-0.0.0" = "sha256-YEFNTYvtgp8nc/1O7AbdyxCD3Xx2xCjbS17fTTEsUL0=";
+      "fbthrift-0.0.1+unstable" = "sha256-mDoYhXOzQIDqP7XdmiBbmq5VmAKAgggTNH/kW2kHv4k=";
+      "reqwest-0.11.11" = "sha256-uhc8XhkGW22XDNo0qreWdXeFF2cslOOZHfTRQ30IBcE=";
+      "serde_bser-0.3.1" = "sha256-/zn1NfXWytXvnalkgPsg9BdujVV97PGkXwmPtQGVeCc=";
+    };
+  };
+  postPatch = ''
+    cp ${./Cargo.lock} Cargo.lock
   '';
 
+  # Since the derivation builder doesn't have network access to remain pure,
+  # fetch the artifacts manually and link them. Then replace the hardcoded URLs
+  # with filesystem paths for the curl calls.
+  postUnpack = ''
+    mkdir $sourceRoot/hack_pydeps
+    ${lib.concatStrings (map (li: "ln -s ${fetchurl li} $sourceRoot/hack_pydeps/${baseNameOf li.url}\n") links)}
+    sed -i "s|https://files.pythonhosted.org/packages/[[:alnum:]]*/[[:alnum:]]*/[[:alnum:]]*/|file://$NIX_BUILD_TOP/$sourceRoot/hack_pydeps/|g" $sourceRoot/setup.py
+  '';
+
+  # Now, copy the "sl web" (aka edenscm-isl) results into the output of this
+  # package, so that the command can actually work. NOTES:
+  #
+  # 1) This applies on all systems (so no conditional a la postFixup)
+  # 2) This doesn't require any kind of fixup itself, so we leave it out
+  #    of postFixup for that reason, too
+  # 3) If asked, we optionally patch in a hardcoded path to the 'nodejs' package,
+  #    so that 'sl web' always works
+  # 4) 'sl web' will still work if 'nodejs' is in $PATH, just not OOTB
+  preFixup = ''
+    sitepackages=$out/lib/${python3Packages.python.libPrefix}/site-packages
+    chmod +w $sitepackages
+    cp -r ${isl} $sitepackages/edenscm-isl
+  '' + lib.optionalString (!enableMinimal) ''
+    chmod +w $sitepackages/edenscm-isl/run-isl
+    substituteInPlace $sitepackages/edenscm-isl/run-isl \
+      --replace 'NODE=node' 'NODE=${nodejs}/bin/node'
+  '';
+
+  postFixup = lib.optionalString stdenv.isLinux ''
+    wrapProgram $out/bin/sl \
+      --set LOCALE_ARCHIVE "${glibcLocales}/lib/locale/locale-archive"
+  '';
+
+  nativeBuildInputs = [
+    curl
+    pkg-config
+  ] ++ (with rustPlatform; [
+    myCargoSetupHook
+    rust.cargo
+    rust.rustc
+  ]);
+
+  buildInputs = [
+    openssl
+  ] ++ lib.optionals stdenv.isDarwin [
+    curl
+    libiconv
+    CoreFoundation
+    CoreServices
+    Security
+  ];
+
+  HGNAME = "sl";
+  SAPLING_OSS_BUILD = "true";
+  SAPLING_VERSION = version;
+  SAPLING_VERSION_HASH = versionHash;
+
   # just a simple check phase, until we have a running test suite. this should
   # help catch issues like lack of a LOCALE_ARCHIVE setting (see GH PR #202760)
   doCheck = true;
-  checkPhase = ''
+  installCheckPhase = ''
     echo -n "testing sapling version; should be \"${version}\"... "
-    ${sapling}/bin/sl version | grep -qw "${version}"
+    $out/bin/sl version | grep -qw "${version}"
     echo "OK!"
   '';
 

pkgs/applications/video/ccextractor/default.nix

@@ -23,7 +23,10 @@ stdenv.mkDerivation rec {
     sha256 = "sha256-usVAKBkdd8uz9cD5eLd0hnwGonOJLscRdc+iWDlNXVc=";
   };
 
-  postPatch = lib.optionalString stdenv.isDarwin ''
+  postPatch = ''
+    # https://github.com/CCExtractor/ccextractor/issues/1467
+    sed -i '/allheaders.h/a#include <leptonica/pix_internal.h>' src/lib_ccx/ocr.c
+  '' + lib.optionalString stdenv.isDarwin ''
     substituteInPlace src/CMakeLists.txt \
     --replace 'add_definitions(-DGPAC_CONFIG_LINUX)' 'add_definitions(-DGPAC_CONFIG_DARWIN)'
   '';

pkgs/applications/video/mirakurun/default.nix

@@ -39,6 +39,9 @@ stdenvNoCC.mkDerivation rec {
     yarnLock = ./yarn.lock;
     packageJSON = ./package.json;
 
+    # workaround for https://github.com/webpack/webpack/issues/14532
+    NODE_OPTIONS = "--openssl-legacy-provider";
+
     patches = [
       # NOTE: fixes for hardcoded paths and assumptions about filesystem
       # permissions

pkgs/applications/video/openshot-qt/default.nix

@@ -7,6 +7,7 @@
 , gtk3
 , libopenshot
 , python3
+, qtbase
 , qtsvg
 , wrapGAppsHook
 }:
@@ -55,7 +56,7 @@ mkDerivationWith python3.pkgs.buildPythonApplication rec {
   ''
   # Fix toolbar icons on Darwin
   + lib.optionalString stdenv.isDarwin ''
-    --suffix QT_PLUGIN_PATH : "${lib.getBin qtsvg}/lib/qt-5.12.7/plugins" \
+    --suffix QT_PLUGIN_PATH : "${lib.getBin qtsvg}/${qtbase.qtPluginPrefix}" \
   '' + ''
     "''${gappsWrapperArgs[@]}" \
     "''${qtWrapperArgs[@]}"

pkgs/applications/video/openshot-qt/libopenshot.nix

@@ -31,8 +31,6 @@ stdenv.mkDerivation rec {
 
   postPatch = ''
     sed -i 's/{UNITTEST++_INCLUDE_DIR}/ENV{UNITTEST++_INCLUDE_DIR}/g' tests/CMakeLists.txt
-    sed -i 's/{_REL_PYTHON_MODULE_PATH}/ENV{_REL_PYTHON_MODULE_PATH}/g' bindings/python/CMakeLists.txt
-    export _REL_PYTHON_MODULE_PATH=$(toPythonPath $out)
   '';
 
   nativeBuildInputs = lib.optionals stdenv.isLinux [
@@ -62,7 +60,10 @@ stdenv.mkDerivation rec {
 
   doCheck = false;
 
-  cmakeFlags = [ "-DENABLE_RUBY=OFF" ];
+  cmakeFlags = [
+    "-DENABLE_RUBY=OFF"
+    "-DPYTHON_MODULE_PATH=${python3.sitePackages}"
+  ];
 
   meta = with lib; {
     homepage = "http://openshot.org/";

pkgs/applications/virtualization/singularity/packages.nix

@@ -7,16 +7,14 @@ let
   apptainer = callPackage
     (import ./generic.nix rec {
       pname = "apptainer";
-      # TODO: Upgrade to 1.1.4 only after https://github.com/apptainer/apptainer/pull/967 get merge
-      # and https://github.com/apptainer/apptainer/issues/958 get fixed
-      version = "1.1.3";
+      version = "1.1.5";
       projectName = "apptainer";
 
       src = fetchFromGitHub {
         owner = "apptainer";
         repo = "apptainer";
         rev = "v${version}";
-        hash = "sha256-QFg6RC77OE/a6Qlzn6Zi5I7Iaq/U3/m0eI9yLArzuNc=";
+        hash = "sha256-onJkpHJNsO0cQO2m+TmdMuMkuvH178mDhOeX41bYFic=";
       };
 
       # Update by running

pkgs/data/fonts/julia-mono/default.nix

@@ -2,12 +2,12 @@
 
 stdenvNoCC.mkDerivation rec {
   pname = "JuliaMono-ttf";
-  version = "0.047";
+  version = "0.048";
 
   src = fetchzip {
     url = "https://github.com/cormullion/juliamono/releases/download/v${version}/${pname}.tar.gz";
     stripRoot = false;
-    hash = "sha256-tCZo48SBGdhcsP1wgaWkfWr3L3Yz+p/iqesLmarSWbk=";
+    hash = "sha256-KSyJMlQclEj2CR+5uSYLmPtseWiDIUuahaPDx7Tn/bw=";
   };
 
   installPhase = ''

pkgs/development/compilers/zig/0.10.nix

@@ -47,6 +47,7 @@ stdenv.mkDerivation rec {
   cmakeFlags = [
     # file RPATH_CHANGE could not write new RPATH
     "-DCMAKE_SKIP_BUILD_RPATH=ON"
+    "-DZIG_TARGET_MCPU=baseline"
   ];
 
   doCheck = true;

pkgs/development/libraries/arrow-cpp/default.nix

@@ -43,7 +43,7 @@
   # non-existent in older versions
   # see https://github.com/boostorg/process/issues/55
 , enableS3 ? (!stdenv.isDarwin) || (lib.versionOlder boost.version "1.69" || lib.versionAtLeast boost.version "1.70")
-, enableGcs ? !stdenv.isDarwin # google-cloud-cpp is not supported on darwin
+, enableGcs ? (!stdenv.isDarwin) && (lib.versionAtLeast grpc.cxxStandard "17") # google-cloud-cpp is not supported on darwin, needs to support C++17
 }:
 
 assert lib.asserts.assertMsg
@@ -52,17 +52,19 @@ assert lib.asserts.assertMsg
 
 let
   arrow-testing = fetchFromGitHub {
+    name = "arrow-testing";
     owner = "apache";
     repo = "arrow-testing";
-    rev = "5bab2f264a23f5af68f69ea93d24ef1e8e77fc88";
-    hash = "sha256-Pxx8ohUpXb5u1995IvXmxQMqWiDJ+7LAll/AjQP7ph8=";
+    rev = "ecab1162cbec872e17d949ecc86181670aee045c";
+    hash = "sha256-w6rEuxfLTEO8DyXV44G6JOMeTfYtskFCOj9rHXNmj2Y=";
   };
 
   parquet-testing = fetchFromGitHub {
+    name = "parquet-testing";
     owner = "apache";
     repo = "parquet-testing";
-    rev = "aafd3fc9df431c2625a514fb46626e5614f1d199";
-    hash = "sha256-cO5t/mgsbBhbSefx8EMGTyxmgTjhZ8mFujkFQ3p/JS0=";
+    rev = "5b82793ef7196f7b3583e85669ced211cd8b5ff2";
+    hash = "sha256-gcOvk7qFHZgJWE9CpucC8zwayYw47VbC3lmSRu4JQFg=";
   };
 
   aws-sdk-cpp-arrow = aws-sdk-cpp.override {
@@ -79,11 +81,11 @@ let
 in
 stdenv.mkDerivation rec {
   pname = "arrow-cpp";
-  version = "9.0.0";
+  version = "11.0.0";
 
   src = fetchurl {
     url = "mirror://apache/arrow/arrow-${version}/apache-arrow-${version}.tar.gz";
-    hash = "sha256-qaAz8KNJAomZj0WGgNGVec8HkRcXumWv3my4AHD3qbU=";
+    hash = "sha256-Ldjw6ghIpYeFYo7jpXZ1VI1QnhchOi9dcrDZALQ/VDA=";
   };
   sourceRoot = "apache-arrow-${version}/cpp";
 
@@ -108,15 +110,15 @@ stdenv.mkDerivation rec {
   ARROW_XSIMD_URL = fetchFromGitHub {
     owner = "xtensor-stack";
     repo = "xsimd";
-    rev = "8.1.0";
-    hash = "sha256-Aqs6XJkGjAjGAp0PprabSM4m+32M/UXpSHppCHdzaZk=";
+    rev = "9.0.1";
+    hash = "sha256-onALN6agtrHWigtFlCeefD9CiRZI4Y690XTzy2UDnrk=";
   };
 
   ARROW_SUBSTRAIT_URL = fetchFromGitHub {
     owner = "substrait-io";
     repo = "substrait";
-    rev = "v0.6.0";
-    hash = "sha256-hxCBomL4Qg9cHLRg9ZiO9k+JVOZXn6f4ikPtK+V9tno=";
+    rev = "v0.20.0";
+    hash = "sha256-71hAwJ0cGvpwK/ibeeQt82e9uqxcu9sM1rPtPENMPfs=";
   };
 
   patches = [
@@ -148,18 +150,17 @@ stdenv.mkDerivation rec {
     utf8proc
     zlib
     zstd
-  ] ++ lib.optionals enableShared [
-    python3.pkgs.python
-    python3.pkgs.numpy
   ] ++ lib.optionals enableFlight [
     grpc
     openssl
     protobuf
+    sqlite
   ] ++ lib.optionals enableS3 [ aws-sdk-cpp-arrow openssl ]
   ++ lib.optionals enableGcs [
     crc32c
     curl
-    google-cloud-cpp grpc
+    google-cloud-cpp
+    grpc
     nlohmann_json
   ];
 
@@ -183,16 +184,12 @@ stdenv.mkDerivation rec {
     "-DARROW_COMPUTE=ON"
     "-DARROW_CSV=ON"
     "-DARROW_DATASET=ON"
-    "-DARROW_ENGINE=ON"
     "-DARROW_FILESYSTEM=ON"
     "-DARROW_FLIGHT_SQL=${if enableFlight then "ON" else "OFF"}"
     "-DARROW_HDFS=ON"
     "-DARROW_IPC=ON"
     "-DARROW_JEMALLOC=${if enableJemalloc then "ON" else "OFF"}"
     "-DARROW_JSON=ON"
-    "-DARROW_PLASMA=ON"
-    # Disable Python for static mode because openblas is currently broken there.
-    "-DARROW_PYTHON=${if enableShared then "ON" else "OFF"}"
     "-DARROW_USE_GLOG=ON"
     "-DARROW_WITH_BACKTRACE=ON"
     "-DARROW_WITH_BROTLI=ON"
@@ -203,21 +200,21 @@ stdenv.mkDerivation rec {
     "-DARROW_WITH_ZLIB=ON"
     "-DARROW_WITH_ZSTD=ON"
     "-DARROW_MIMALLOC=ON"
-    # Parquet options:
-    "-DARROW_PARQUET=ON"
     "-DARROW_SUBSTRAIT=ON"
-    "-DPARQUET_BUILD_EXECUTABLES=ON"
     "-DARROW_FLIGHT=${if enableFlight then "ON" else "OFF"}"
     "-DARROW_FLIGHT_TESTING=${if enableFlight then "ON" else "OFF"}"
     "-DARROW_S3=${if enableS3 then "ON" else "OFF"}"
     "-DARROW_GCS=${if enableGcs then "ON" else "OFF"}"
+    # Parquet options:
+    "-DARROW_PARQUET=ON"
+    "-DPARQUET_BUILD_EXECUTABLES=ON"
+    "-DPARQUET_REQUIRE_ENCRYPTION=ON"
   ] ++ lib.optionals (!enableShared) [
     "-DARROW_TEST_LINKAGE=static"
   ] ++ lib.optionals stdenv.isDarwin [
     "-DCMAKE_INSTALL_RPATH=@loader_path/../lib" # needed for tools executables
-  ] ++ lib.optional (!stdenv.isx86_64) "-DARROW_USE_SIMD=OFF"
-  ++ lib.optional enableS3 "-DAWSSDK_CORE_HEADER_FILE=${aws-sdk-cpp-arrow}/include/aws/core/Aws.h"
-  ++ lib.optionals enableGcs [ "-DCMAKE_CXX_STANDARD=${grpc.cxxStandard}" ];
+  ] ++ lib.optionals (!stdenv.isx86_64) [ "-DARROW_USE_SIMD=OFF" ]
+  ++ lib.optionals enableS3 [ "-DAWSSDK_CORE_HEADER_FILE=${aws-sdk-cpp-arrow}/include/aws/core/Aws.h" ];
 
   doInstallCheck = true;
   ARROW_TEST_DATA = lib.optionalString doInstallCheck "${arrow-testing}/data";
@@ -239,31 +236,33 @@ stdenv.mkDerivation rec {
         "TestS3FSGeneric.*"
       ];
     in
-    lib.optionalString doInstallCheck "-${builtins.concatStringsSep ":" filteredTests}";
+    lib.optionalString doInstallCheck "-${lib.concatStringsSep ":" filteredTests}";
+
   __darwinAllowLocalNetworking = true;
-  nativeInstallCheckInputs = [ perl which sqlite ] ++ lib.optional enableS3 minio;
-  installCheckPhase =
-    let
-      excludedTests = lib.optionals stdenv.isDarwin [
-        # Some plasma tests need to be patched to use a shorter AF_UNIX socket
-        # path on Darwin. See https://github.com/NixOS/nix/pull/1085
-        "plasma-external-store-tests"
-        "plasma-client-tests"
-      ] ++ [ "arrow-gcsfs-test" ];
-    in
-    ''
-      runHook preInstallCheck
 
-      ctest -L unittest \
-        --exclude-regex '^(${builtins.concatStringsSep "|" excludedTests})$'
+  nativeInstallCheckInputs = [ perl which sqlite ]
+    ++ lib.optionals enableS3 [ minio ]
+    ++ lib.optionals enableFlight [ python3 ];
 
-      runHook postInstallCheck
-    '';
+  disabledTests = [
+    # requires networking
+    "arrow-gcsfs-test"
+    "arrow-flight-integration-test"
+  ];
+
+  installCheckPhase = ''
+    runHook preInstallCheck
+
+    ctest -L unittest --exclude-regex '^(${lib.concatStringsSep "|" disabledTests})$'
+
+    runHook postInstallCheck
+  '';
 
   meta = with lib; {
     description = "A cross-language development platform for in-memory data";
     homepage = "https://arrow.apache.org/docs/cpp/";
     license = licenses.asl20;
+    broken = (stdenv.isLinux && stdenv.isAarch64) || stdenv.isDarwin; # waiting on gtest changes in staging
     platforms = platforms.unix;
     maintainers = with maintainers; [ tobim veprbl cpcloud ];
   };

pkgs/development/libraries/irr1/default.nix

@@ -4,25 +4,25 @@
 , cmake
 }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation (self: {
   pname = "irr1";
   version = "1.9.4";
 
   src = fetchFromGitHub {
     owner = "berndporr";
     repo = "iir1";
-    rev = version;
+    rev = self.version;
     hash = "sha256-T8gl51IkZIGq+6D5ge4Kb3wm5aw7Rhphmnf6TTGwHbs=";
   };
 
   nativeBuildInputs = [ cmake ];
 
   meta = {
-    description = "A DSP IIR realtime filter library written in C++";
-    downloadPage = "https://github.com/berndporr/iir1";
     homepage = "http://berndporr.github.io/iir1/";
+    description = "A DSP IIR realtime filter library written in C++";
+    changelog = "https://github.com/berndporr/iir1/releases/tag/${self.version}";
     license = lib.licenses.mit;
     maintainers = [ lib.maintainers.AndersonTorres ];
     platforms = lib.platforms.unix;
   };
-}
+})

pkgs/development/libraries/jbig2enc/default.nix

@@ -0,0 +1,60 @@
+{ lib
+, stdenv
+, fetchFromGitHub
+, fetchpatch
+, leptonica
+, zlib
+, libwebp
+, giflib
+, libjpeg
+, libpng
+, libtiff
+, autoreconfHook
+}:
+
+stdenv.mkDerivation rec {
+  pname = "jbig2enc";
+  version = "0.29";
+
+  src = fetchFromGitHub {
+    owner = "agl";
+    repo = "jbig2enc";
+    rev = version;
+    hash = "sha256-IAL4egXgaGmCilzcryjuvOoHhahyrfGWY68GBfXXgAM=";
+  };
+
+  buildInputs = [ autoreconfHook ];
+  propagatedBuildInputs = [
+    leptonica
+    zlib
+    libwebp
+    giflib
+    libjpeg
+    libpng
+    libtiff
+  ];
+
+  patches = [
+    (fetchpatch {
+      name = "fix-build-leptonica-1.83.patch";
+      url = "https://github.com/agl/jbig2enc/commit/ea050190466f5336c69c6a11baa1cb686677fcab.patch";
+      hash = "sha256-+kScjFgDEU9F7VOUNAhm2XBjGm49fzAH8hYhmTm8xv8=";
+    })
+  ];
+
+  # This is necessary, because the resulting library has
+  # /tmp/nix-build-jbig2enc/src/.libs before /nix/store/jbig2enc/lib
+  # in its rpath, which means that patchelf --shrink-rpath removes
+  # the /nix/store one.  By cleaning up before fixup, we ensure that
+  # the /tmp/nix-build-jbig2enc/src/.libs directory is gone.
+  preFixup = ''
+    make clean
+  '';
+
+  meta = {
+    description = "Encoder for the JBIG2 image compression format";
+    license = lib.licenses.asl20;
+    platforms = lib.platforms.all;
+    homepage = "https://github.com/agl/jbig2enc";
+  };
+}

pkgs/development/libraries/leptonica/default.nix

@@ -4,11 +4,11 @@
 
 stdenv.mkDerivation rec {
   pname = "leptonica";
-  version = "1.82.0";
+  version = "1.83.0";
 
   src = fetchurl {
     url = "http://www.leptonica.org/source/${pname}-${version}.tar.gz";
-    sha256 = "sha256-FVMC7pFGaMJ7b+PKn/LaY7JF9tYvMGHI8nVjd0uK4tY=";
+    sha256 = "sha256-IGWR3VjPhO84CDba0TO1jJ0a+SSR9amCXDRqFiBEvP4=";
   };
 
   nativeBuildInputs = [ autoreconfHook pkg-config ];

pkgs/development/libraries/s2n-tls/default.nix

@@ -8,13 +8,13 @@
 
 stdenv.mkDerivation rec {
   pname = "s2n-tls";
-  version = "1.3.34";
+  version = "1.3.36";
 
   src = fetchFromGitHub {
     owner = "aws";
     repo = pname;
     rev = "v${version}";
-    sha256 = "sha256-CaVo2OxfB7ImMOgPuyvKQFbTeEm3PqD8CV96jUEZ8U0=";
+    sha256 = "sha256-IL7+f+7Igvm7KeBpDwnIoIB8IUqg3JDEtLFQslBIENE=";
   };
 
   nativeBuildInputs = [ cmake ];

pkgs/development/libraries/science/math/sympow/default.nix

@@ -1,5 +1,6 @@
 { lib, stdenv
 , fetchFromGitLab
+, fetchpatch
 , makeWrapper
 , which
 , autoconf
@@ -20,7 +21,14 @@ stdenv.mkDerivation rec {
     sha256 = "132l0xv00ld1svvv9wh99wfra4zzjv2885h2sq0dsl98wiyvi5zl";
   };
 
-  patches = [ ./clean-extra-logfile-output-from-pari.patch ];
+  patches = [
+    ./clean-extra-logfile-output-from-pari.patch
+    (fetchpatch {
+      name = "null-terminate-dupdirname.patch";
+      url = "https://gitlab.com/rezozer/forks/sympow/-/merge_requests/5.diff";
+      sha256 = "sha256-yKjio+qN9teL8L+mb7WOBN/iv545vRIxW20FJU37oO4=";
+    })
+  ];
 
   postUnpack = ''
     patchShebangs .

pkgs/development/libraries/stfl/default.nix

@@ -9,6 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "1460d5lc780p3q38l3wc9jfr2a7zlyrcra0li65aynj738cam9yl";
   };
 
+  makeFlags = [ "CC=${stdenv.cc.targetPrefix}cc" ];
+
   buildInputs = [ ncurses libiconv ];
 
   preBuild = ''
@@ -16,12 +18,22 @@ stdenv.mkDerivation rec {
     sed -i s%ncursesw/ncurses.h%ncurses.h% stfl_internals.h
   '' + lib.optionalString stdenv.isDarwin ''
     sed -i s/-soname/-install_name/ Makefile
-  '';
+  ''
+  # upstream builds shared library unconditionally. Also, it has no
+  # support for cross-compilation.
+  + lib.optionalString stdenv.hostPlatform.isStatic ''
+    sed -i 's/all:.*/all: libstfl.a stfl.pc/' Makefile
+    sed -i 's/\tar /\t${stdenv.cc.targetPrefix}ar /' Makefile
+    sed -i 's/\tranlib /\t${stdenv.cc.targetPrefix}ranlib /' Makefile
+    sed -i '/install -m 644 libstfl.so./d' Makefile
+    sed -i '/ln -fs libstfl.so./d' Makefile
+  '' ;
 
   installPhase = ''
     DESTDIR=$out prefix=\"\" make install
-
-    # some programs rely on libstfl.so.0 to be present, so link it
+  ''
+  # some programs rely on libstfl.so.0 to be present, so link it
+  + lib.optionalString (!stdenv.hostPlatform.isStatic) ''
     ln -s $out/lib/libstfl.so.0.24 $out/lib/libstfl.so.0
   '';
 

pkgs/development/libraries/thrift/default.nix

@@ -36,11 +36,14 @@ stdenv.mkDerivation rec {
 
   buildInputs = [
     boost
+  ] ++ lib.optionals (!static) [
+    (python3.withPackages (ps: [ps.twisted]))
+  ];
+
+  propagatedBuildInputs = [
     libevent
     openssl
     zlib
-  ] ++ lib.optionals (!static) [
-    (python3.withPackages (ps: [ps.twisted]))
   ];
 
   postPatch = ''
@@ -66,6 +69,11 @@ stdenv.mkDerivation rec {
       url = "https://github.com/apache/thrift/commit/c41ad9d5119e9bdae1746167e77e224f390f2c42.diff";
       hash = "sha256-FkErrg/6vXTomS4AsCsld7t+Iccc55ZiDaNjJ3W1km0=";
     })
+    (fetchpatch {
+      name = "thrift-install-FindLibevent.patch"; # https://github.com/apache/thrift/pull/2726
+      url = "https://github.com/apache/thrift/commit/2ab850824f75d448f2ba14a468fb77d2594998df.diff";
+      hash = "sha256-ejMKFG/cJgoPlAFzVDPI4vIIL7URqaG06/IWdQ2NkhY=";
+    })
   ];
 
   cmakeFlags = [

pkgs/development/python-modules/awswrangler/default.nix

@@ -0,0 +1,88 @@
+{ backoff
+, SPARQLWrapper
+, boto3
+, buildPythonPackage
+, fetchFromGitHub
+, gremlinpython
+, jsonpath-ng
+, lib
+, moto
+, openpyxl
+, opensearch-py
+, pandas
+, pg8000
+, poetry-core
+, progressbar2
+, pyarrow
+, pymysql
+, pyodbc
+, pytestCheckHook
+, pythonOlder
+, pythonRelaxDepsHook
+, redshift-connector
+, requests-aws4auth
+}:
+
+buildPythonPackage rec {
+  pname = "awswrangler";
+  version = "2.19.0";
+  format = "pyproject";
+
+  disabled = pythonOlder "3.7.1";
+
+  src = fetchFromGitHub {
+    owner = "aws";
+    repo = "aws-sdk-pandas";
+    rev = "refs/tags/${version}";
+    hash = "sha256-xUEytEgr/djfnoOowLxAZmbPkMS+vU0fuPY7JxZXEe0=";
+  };
+
+  nativeBuildInputs = [ poetry-core pythonRelaxDepsHook ];
+
+  propagatedBuildInputs = [
+    backoff
+    boto3
+    gremlinpython
+    jsonpath-ng
+    openpyxl
+    opensearch-py
+    pandas
+    pg8000
+    progressbar2
+    pyarrow
+    pymysql
+    redshift-connector
+    requests-aws4auth
+  ];
+
+  pythonRelaxDeps = [
+    "gremlinpython"
+    "numpy"
+    "pandas"
+    "pg8000"
+  ];
+
+  nativeCheckInputs = [ moto pytestCheckHook ];
+
+  pytestFlagsArray = [
+    # Subset of tests that run in upstream CI (many others require credentials)
+    # https://github.com/aws/aws-sdk-pandas/blob/2b7c62ac0762b1303149bb3c03979791479ba4f9/.github/workflows/minimal-tests.yml
+    "tests/test_metadata.py"
+    "tests/test_session.py"
+    "tests/test_utils.py"
+    "tests/test_moto.py"
+  ];
+
+  passthru.optional-dependencies = {
+    sqlserver = [ pyodbc ];
+    sparql = [ SPARQLWrapper ];
+  };
+
+  meta = {
+    description = "Pandas on AWS";
+    homepage = "https://github.com/aws/aws-sdk-pandas";
+    changelog = "https://github.com/aws/aws-sdk-pandas/releases/tag/${version}";
+    license = lib.licenses.asl20;
+    maintainers = with lib.maintainers; [ mcwitt ];
+  };
+}

pkgs/development/python-modules/bundlewrap/default.nix

@@ -31,7 +31,7 @@ buildPythonPackage rec {
 
   nativeBuildInputs = [ setuptools ];
   propagatedBuildInputs = [
-    cryptography jinja2 Mako passlib pyyaml requests tomlkit librouteros
+    setuptools cryptography jinja2 Mako passlib pyyaml requests tomlkit librouteros
   ] ++ lib.optionals (pythonOlder "3.11") [ rtoml ];
 
   pythonImportsCheck = [ "bundlewrap" ];

pkgs/development/python-modules/dask/default.nix

@@ -1,5 +1,6 @@
 { lib
 , stdenv
+, arrow-cpp
 , bokeh
 , buildPythonPackage
 , click
@@ -70,13 +71,14 @@ buildPythonPackage rec {
   };
 
   nativeCheckInputs = [
-    fastparquet
-    pyarrow
     pytestCheckHook
     pytest-rerunfailures
     pytest-xdist
     scipy
     zarr
+  ] ++ lib.optionals (!arrow-cpp.meta.broken) [ # support is sparse on aarch64
+    fastparquet
+    pyarrow
   ];
 
   dontUseSetuptoolsCheck = true;

pkgs/development/python-modules/effect/default.nix

@@ -1,40 +1,52 @@
-{ buildPythonPackage
-, fetchPypi
-, lib
-, isPy3k
-, six
+{ lib
 , attrs
-, pytest
+, buildPythonPackage
+, fetchPypi
+, pytestCheckHook
+, pythonOlder
+, six
 , testtools
 }:
 
 buildPythonPackage rec {
-  version = "1.1.0";
   pname = "effect";
-  disabled = (!isPy3k);
+  version = "1.1.0";
+  format = "setuptools";
+
+  disabled = pythonOlder "3.7";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "7affb603707c648b07b11781ebb793a4b9aee8acf1ac5764c3ed2112adf0c9ea";
+    hash = "sha256-ev+2A3B8ZIsHsReB67eTpLmu6KzxrFdkw+0hEq3wyeo=";
   };
 
+  postPatch = ''
+    substituteInPlace effect/test_do.py \
+      --replace "py.test" "pytest"
+  '';
+
+  propagatedBuildInputs = [
+    attrs
+    six
+  ];
+
   nativeCheckInputs = [
-    pytest
+    pytestCheckHook
+  ];
+
+  checkInputs = [
     testtools
   ];
 
-  propagatedBuildInputs = [
-    six
-    attrs
+  pythonImportsCheck = [
+    "effect"
   ];
 
-  checkPhase = ''
-    pytest
-  '';
-
   meta = with lib; {
     description = "Pure effects for Python";
-    homepage = "https://github.com/python-effect/effect";
+    homepage = "https://effect.readthedocs.io/";
+    changelog = "https://github.com/python-effect/effect/releases/tag/${version}";
     license = licenses.mit;
+    maintainers = with maintainers; [ ];
   };
 }

pkgs/development/python-modules/fpylll/default.nix

@@ -1,7 +1,6 @@
 { stdenv
 , lib
 , fetchFromGitHub
-, fetchpatch
 , buildPythonPackage
 , pkgconfig
 , gmp
@@ -16,23 +15,15 @@
 
 buildPythonPackage rec {
   pname = "fpylll";
-  version = "0.5.7";
+  version = "0.5.9";
 
   src = fetchFromGitHub {
     owner = "fplll";
     repo = "fpylll";
     rev = version;
-    sha256 = "sha256-iUPreJ8BSB8LDisbJis0xn8ld6+Nf9Z4AP8SWJlCfZg=";
+    sha256 = "sha256-T6l6hKzRDevlLyLu5H+bnEdl0OhsPer1coCDiftbPAk=";
   };
 
-  patches = [
-   (fetchpatch {
-     name = "remove-strategies-doctest.patch";
-     url = "https://github.com/fplll/fpylll/commit/3edffcd189e9d827a322d83b0f84d32e5f067442.patch";
-     sha256 = "sha256-U7qOIbVzUNwYmjOPryjnE3J+MX/vMwm3T0UyOZ5ylLc=";
-   })
-  ];
-
   buildInputs = [
     gmp
     pari

pkgs/development/python-modules/mediapy/default.nix

@@ -21,6 +21,8 @@ buildPythonPackage rec {
 
   propagatedBuildInputs = [ ipython matplotlib numpy pillow ];
 
+  format = "flit";
+
   pythonImportsCheck = [ "mediapy" ];
 
   meta = with lib; {

pkgs/development/python-modules/pyarrow/default.nix

@@ -18,18 +18,15 @@
 , pkg-config
 , scipy
 , setuptools-scm
-, six
 }:
 
 let
   zero_or_one = cond: if cond then 1 else 0;
-
-  _arrow-cpp = arrow-cpp.override { python3 = python; };
 in
 
 buildPythonPackage rec {
   pname = "pyarrow";
-  inherit (_arrow-cpp) version src;
+  inherit (arrow-cpp) version src;
 
   disabled = pythonOlder "3.7";
 
@@ -42,13 +39,14 @@ buildPythonPackage rec {
     setuptools-scm
   ];
 
+  buildInputs = [ arrow-cpp ];
+
   propagatedBuildInputs = [
     cffi
     cloudpickle
     fsspec
     numpy
     scipy
-    six
   ];
 
   nativeCheckInputs = [
@@ -61,20 +59,24 @@ buildPythonPackage rec {
   PYARROW_BUILD_TYPE = "release";
 
   PYARROW_WITH_DATASET = zero_or_one true;
-  PYARROW_WITH_FLIGHT = zero_or_one _arrow-cpp.enableFlight;
+  PYARROW_WITH_FLIGHT = zero_or_one arrow-cpp.enableFlight;
   PYARROW_WITH_HDFS = zero_or_one true;
   PYARROW_WITH_PARQUET = zero_or_one true;
-  PYARROW_WITH_PLASMA = zero_or_one (!stdenv.isDarwin);
-  PYARROW_WITH_S3 = zero_or_one _arrow-cpp.enableS3;
+  PYARROW_WITH_PARQUET_ENCRYPTION = zero_or_one true;
+  # Plasma is deprecated since arrow 10.0.0
+  PYARROW_WITH_PLASMA = zero_or_one false;
+  PYARROW_WITH_S3 = zero_or_one arrow-cpp.enableS3;
+  PYARROW_WITH_GCS = zero_or_one arrow-cpp.enableGcs;
+  PYARROW_BUNDLE_ARROW_CPP_HEADERS = zero_or_one false;
 
   PYARROW_CMAKE_OPTIONS = [
     "-DCMAKE_INSTALL_RPATH=${ARROW_HOME}/lib"
   ];
 
-  ARROW_HOME = _arrow-cpp;
-  PARQUET_HOME = _arrow-cpp;
+  ARROW_HOME = arrow-cpp;
+  PARQUET_HOME = arrow-cpp;
 
-  ARROW_TEST_DATA = lib.optionalString doCheck _arrow-cpp.ARROW_TEST_DATA;
+  ARROW_TEST_DATA = lib.optionalString doCheck arrow-cpp.ARROW_TEST_DATA;
 
   doCheck = true;
 
@@ -86,6 +88,13 @@ buildPythonPackage rec {
     export PYARROW_PARALLEL=$NIX_BUILD_CORES
   '';
 
+  postInstall = ''
+    # copy the pyarrow C++ header files to the appropriate location
+    pyarrow_include="$out/${python.sitePackages}/pyarrow/include"
+    mkdir -p "$pyarrow_include/arrow/python"
+    find "$PWD/pyarrow/src/arrow" -type f -name '*.h' -exec cp {} "$pyarrow_include/arrow/python" \;
+  '';
+
   pytestFlagsArray = [
     # Deselect a single test because pyarrow prints a 2-line error message where
     # only a single line is expected. The additional line of output comes from
@@ -103,6 +112,8 @@ buildPythonPackage rec {
     "--deselect=pyarrow/tests/test_pandas.py::test_threaded_pandas_import"
     # Flaky test, works locally but not on Hydra
     "--deselect=pyarrow/tests/test_csv.py::TestThreadedCSVTableRead::test_cancellation"
+    # expects arrow-cpp headers to be bundled
+    "--deselect=pyarrow/tests/test_cpp_internals.py::test_pyarrow_include"
   ] ++ lib.optionals stdenv.isDarwin [
     # Requires loopback networking
     "--deselect=pyarrow/tests/test_ipc.py::test_socket_"
@@ -110,11 +121,18 @@ buildPythonPackage rec {
     "--deselect=pyarrow/tests/test_flight.py::test_large_descriptor"
     "--deselect=pyarrow/tests/test_flight.py::test_large_metadata_client"
     "--deselect=pyarrow/tests/test_flight.py::test_none_action_side_effect"
+    # fails to compile
+    "--deselect=pyarrow/tests/test_cython.py::test_cython_api"
   ] ++ lib.optionals (pythonAtLeast "3.11") [
     # Repr output is printing number instead of enum name so these tests fail
     "--deselect=pyarrow/tests/test_fs.py::test_get_file_info"
+  ] ++ lib.optionals stdenv.isLinux [
+    # this test requires local networking
+    "--deselect=pyarrow/tests/test_fs.py::test_filesystem_from_uri_gcs"
   ];
 
+  disabledTests = [ "GcsFileSystem" ];
+
   dontUseSetuptoolsCheck = true;
 
   preCheck = ''
@@ -129,7 +147,7 @@ buildPythonPackage rec {
 
   pythonImportsCheck = [
     "pyarrow"
-  ] ++ map (module: "pyarrow.${module}") ([
+  ] ++ map (module: "pyarrow.${module}") [
     "compute"
     "csv"
     "dataset"
@@ -139,9 +157,7 @@ buildPythonPackage rec {
     "hdfs"
     "json"
     "parquet"
-  ] ++ lib.optionals (!stdenv.isDarwin) [
-    "plasma"
-  ]);
+  ];
 
   meta = with lib; {
     description = "A cross-language development platform for in-memory data";

pkgs/development/python-modules/pyipma/default.nix

@@ -13,7 +13,7 @@
 
 buildPythonPackage rec {
   pname = "pyipma";
-  version = "3.0.5";
+  version = "3.0.6";
   format = "setuptools";
 
   disabled = pythonOlder "3.7";
@@ -22,7 +22,7 @@ buildPythonPackage rec {
     owner = "dgomes";
     repo = pname;
     rev = "refs/tags/${version}";
-    hash = "sha256-KyXHNkP/XJlTdVFdP91x3udMquQju8G2VUHLPvZymtk=";
+    hash = "sha256-BwW8gUFeinZ9Z/v1orJKRTqt2WxVMD+hQj+A3gU1LDI=";
   };
 
   propagatedBuildInputs = [
@@ -52,6 +52,7 @@ buildPythonPackage rec {
   meta = with lib; {
     description = "Library to retrieve information from Instituto Português do Mar e Atmosfera";
     homepage = "https://github.com/dgomes/pyipma";
+    changelog = "https://github.com/dgomes/pyipma/releases/tag/${version}";
     license = with licenses; [ mit ];
     maintainers = with maintainers; [ fab ];
   };

pkgs/development/python-modules/pyoutbreaksnearme/default.nix

@@ -1,7 +1,6 @@
 { lib
 , aiohttp
 , aresponses
-, aiocache
 , buildPythonPackage
 , fetchFromGitHub
 , poetry-core
@@ -9,39 +8,29 @@
 , pytest-aiohttp
 , pytestCheckHook
 , pythonOlder
-, pythonRelaxDepsHook
-, msgpack
 , ujson
 }:
 
 buildPythonPackage rec {
-  pname = "pyflunearyou";
-  version = "2021.10.0";
+  pname = "pyoutbreaksnearme";
+  version = "2022.10.0";
   format = "pyproject";
 
-  disabled = pythonOlder "3.6";
+  disabled = pythonOlder "3.9";
 
   src = fetchFromGitHub {
     owner = "bachya";
     repo = pname;
-    rev = version;
-    sha256 = "sha256-Q65OSE4qckpvaIvZULBR434i7hwuVM97eSq1Blb1oIU=";
+    rev = "refs/tags/${version}";
+    sha256 = "sha256-D7oXkKDSg+yF+j1WyG/VVY12hLU6oyhEtxLrF6IkMSA=";
   };
 
-  pythonRelaxDeps = [
-    "aiocache"
-    "ujson"
-  ];
-
   nativeBuildInputs = [
     poetry-core
-    pythonRelaxDepsHook
   ];
 
   propagatedBuildInputs = [
     aiohttp
-    aiocache
-    msgpack
     ujson
   ];
 
@@ -58,12 +47,13 @@ buildPythonPackage rec {
   ];
 
   pythonImportsCheck = [
-    "pyflunearyou"
+    "pyoutbreaksnearme"
   ];
 
   meta = with lib; {
-    description = "Python library for retrieving UV-related information from Flu Near You";
-    homepage = "https://github.com/bachya/pyflunearyou";
+    description = "Library for retrieving data from for Outbreaks Near Me";
+    homepage = "https://github.com/bachya/pyoutbreaksnearme";
+    changelog = "https://github.com/bachya/pyoutbreaksnearme/releases/tag/${version}";
     license = with licenses; [ mit ];
     maintainers = with maintainers; [ fab ];
   };

pkgs/development/python-modules/scmrepo/default.nix

@@ -11,11 +11,12 @@
 , pygtrie
 , pythonOlder
 , setuptools
+, shortuuid
 }:
 
 buildPythonPackage rec {
   pname = "scmrepo";
-  version = "0.1.7";
+  version = "0.1.9";
   format = "pyproject";
 
   disabled = pythonOlder "3.7";
@@ -24,7 +25,7 @@ buildPythonPackage rec {
     owner = "iterative";
     repo = pname;
     rev = "refs/tags/${version}";
-    hash = "sha256-F+t/3Nfcw+LG9Kh0Je2JwPWUWBNsZXTEaQOKaTT5ig0=";
+    hash = "sha256-WXePQMHCAmcGUHNNHBaqNQisewMUR87iJC0K2ltYVBE=";
   };
 
   postPatch = ''
@@ -46,6 +47,7 @@ buildPythonPackage rec {
     pathspec
     pygit2
     pygtrie
+    shortuuid
   ];
 
   # Requires a running Docker instance

pkgs/development/python-modules/shortuuid/default.nix

@@ -28,6 +28,7 @@ buildPythonPackage rec {
   meta = with lib; {
     description = "Library to generate concise, unambiguous and URL-safe UUIDs";
     homepage = "https://github.com/stochastic-technologies/shortuuid/";
+    changelog = "https://github.com/skorokithakis/shortuuid/blob/v${version}/CHANGELOG.md";
     license = licenses.bsd3;
     maintainers = with maintainers; [ zagy ];
   };

pkgs/development/python-modules/tesserocr/default.nix

@@ -24,6 +24,11 @@ buildPythonPackage rec {
     sha256 = "1bmj76gi8401lcqdaaznfmz9yf11myy1bzivqwwq08z3dwzxswck";
   };
 
+  # https://github.com/sirfz/tesserocr/issues/314
+  postPatch = ''
+    sed -i '/allheaders.h/a\    pass\n\ncdef extern from "leptonica/pix_internal.h" nogil:' tesseract.pxd
+  '';
+
   nativeBuildInputs = [
     cython
     pkg-config

pkgs/development/python-modules/xmlschema/default.nix

@@ -10,7 +10,7 @@
 
 buildPythonPackage rec {
   pname = "xmlschema";
-  version = "2.2.0";
+  version = "2.2.1";
   format = "setuptools";
 
   disabled = pythonOlder "3.7";
@@ -19,7 +19,7 @@ buildPythonPackage rec {
     owner = "sissaschool";
     repo = "xmlschema";
     rev = "refs/tags/v${version}";
-    hash = "sha256-KK1F8OVK+19ZWwu+2UtTMiVNyPPoPOv3V1qJFZAu2h4=";
+    hash = "sha256-yF2L5VxUkqJjen5JeCQis4Q1o1KCJtRJ+S52wnS5VQg=";
   };
 
   propagatedBuildInputs = [

pkgs/development/tools/bpf-linker/default.nix

@@ -2,7 +2,7 @@
 , stdenv
 , rustPlatform
 , fetchFromGitHub
-, llvmPackages_14
+, llvmPackages_15
 , zlib
 , ncurses
 , libxml2
@@ -10,21 +10,21 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "bpf-linker";
-  version = "0.9.4";
+  version = "0.9.5";
 
   src = fetchFromGitHub {
     owner = "aya-rs";
     repo = pname;
     rev = "v${version}";
-    hash = "sha256-jYuBk78aGQLUeNF6d6kjGPuMxEF22XJquHcs23WVGm0=";
+    hash = "sha256-LEZ2to1bzJ/H/XYytuh/7NT7+04aI8chpKIFxxVzM+4=";
   };
 
-  cargoHash = "sha256-X8EVpOxDHwE/wj/gly/wdZ6tsrMrz3kkDe9gEPbk6iw=";
+  cargoHash = "sha256-s8cW7lXtvgemuQueTtAywewnDVJ/WDcz8SBqsC/tO80=";
 
   buildNoDefaultFeatures = true;
   buildFeatures = [ "system-llvm" ];
 
-  nativeBuildInputs = [ llvmPackages_14.llvm ];
+  nativeBuildInputs = [ llvmPackages_15.llvm ];
   buildInputs = [ zlib ncurses libxml2 ];
 
   # fails with: couldn't find crate `core` with expected target triple bpfel-unknown-none

pkgs/development/tools/misc/circleci-cli/default.nix

@@ -2,16 +2,16 @@
 
 buildGoModule rec {
   pname = "circleci-cli";
-  version = "0.1.23334";
+  version = "0.1.23391";
 
   src = fetchFromGitHub {
     owner = "CircleCI-Public";
     repo = pname;
     rev = "v${version}";
-    sha256 = "sha256-1+PcjameB9/1MoyM0RAxrhuE649INyLlhgxA5xJQ9Pw=";
+    sha256 = "sha256-mTqrckoYbxtlwonXp6mtbXSpmVB3WfSXaOkyycBVjx0=";
   };
 
-  vendorHash = "sha256-E24b8PUA1Hy+OepQe2n6TecCMKKicdr5KUdiJ663Td0=";
+  vendorHash = "sha256-7k5jmXvNtxezialavNz8NM7esl2vpXcjRW2n/9GAycs=";
 
   nativeBuildInputs = [ installShellFiles ];
 

pkgs/development/tools/misc/saleae-logic-2/default.nix

@@ -1,10 +1,10 @@
 { lib, fetchurl, makeDesktopItem, appimageTools }:
 let
   name = "saleae-logic-2";
-  version = "2.4.3";
+  version = "2.4.6";
   src = fetchurl {
     url = "https://downloads.saleae.com/logic2/Logic-${version}-master.AppImage";
-    hash = "sha256-xF87Q1K25/9pUYt660RY2RCIC6u2m2ArBQb2nWhiKvw=";
+    hash = "sha256-FYLjg4lzr8M22r4yoKfMIAx2HKGi2fcD28AaV1ChkLk=";
   };
   desktopItem = makeDesktopItem {
     inherit name;

pkgs/os-specific/linux/dracut/default.nix

@@ -10,24 +10,17 @@
 , bash
 , kmod
 , binutils
-, busybox
 , bzip2
 , coreutils
 , cpio
 , findutils
-, glibc
 , gnugrep
 , gnused
 , gnutar
 , gzip
-, kbd
-, lvm2
 , lz4
 , lzop
-, procps
-, rng-tools
 , squashfsTools
-, systemd
 , util-linux
 , xz
 , zstd
@@ -76,23 +69,16 @@ stdenv.mkDerivation rec {
     wrapProgram $out/bin/dracut --prefix PATH : ${lib.makeBinPath [
       coreutils
       util-linux
-    ]} --prefix DRACUT_PATH : ${lib.makeBinPath [
+    ]} --suffix DRACUT_PATH : ${lib.makeBinPath [
       bash
       binutils
       coreutils
       findutils
-      glibc
       gnugrep
       gnused
       gnutar
-      kbd
-      lvm2
-      procps
-      rng-tools
-      squashfsTools
-      systemd
+      stdenv.cc.libc  # for ldd command
       util-linux
-      busybox
     ]}
     wrapProgram $out/bin/dracut-catimages --set PATH ${lib.makeBinPath [
       coreutils

pkgs/servers/http/nginx/modules.nix

@@ -351,8 +351,8 @@ let self = {
     name = "njs";
     src = fetchhg {
       url = "https://hg.nginx.org/njs";
-      rev = "0.7.8";
-      sha256 = "sha256-jsR8EOeW8tAo2utKznuUaCG4hK0oU0ZJSnnGmI5HUDk=";
+      rev = "0.7.10";
+      sha256 = "sha256-/yKzY+BUFxLk8bWo+mqKfRVRsC2moe+WvhaRYIGdr6Y=";
       name = "nginx-njs";
     };
 

pkgs/tools/admin/eksctl/default.nix

@@ -2,16 +2,16 @@
 
 buildGoModule rec {
   pname = "eksctl";
-  version = "0.128.0";
+  version = "0.129.0";
 
   src = fetchFromGitHub {
     owner = "weaveworks";
     repo = pname;
     rev = version;
-    sha256 = "sha256-CKtDj9Ht81i8EcpjHqluWfwkEU15a/TZd6N+jCSzIc8=";
+    sha256 = "sha256-p9haEozDc1ZTGar89Clm7eEFFLJCYcw+gBN40Zg5vi8=";
   };
 
-  vendorHash = "sha256-aSXj21JNqX/cc62oFqyedmvczmudcV7RhLyWrKsdOMQ=";
+  vendorHash = "sha256-Vb0sgOOIQI0rTJDITFoMbXJcnN7BondbFTm3AF1JTLo=";
 
   doCheck = false;
 

pkgs/tools/admin/trivy/default.nix

@@ -5,17 +5,17 @@
 
 buildGoModule rec {
   pname = "trivy";
-  version = "0.37.1";
+  version = "0.37.2";
 
   src = fetchFromGitHub {
     owner = "aquasecurity";
     repo = pname;
     rev = "v${version}";
-    sha256 = "sha256-4kjsNaiXnmJk88ivVnpTemOOc/asKrcZLGpO8gtV0J8=";
+    sha256 = "sha256-k5S0ttOhI+vjiGJpIPVi9ro6n3f2Cxe7HiADvs14Zuo=";
   };
   # hash missmatch on across linux and darwin
   proxyVendor = true;
-  vendorSha256 = "sha256-qI29Qb8im9Xii83ayG1jZtZsrsAT0JQOcuKOM7VYro0=";
+  vendorSha256 = "sha256-EJw5DxiBF+gw5X+vqrnZsNCm2umOHEq6GeQ5V/Z0DrE=";
 
   excludedPackages = "misc";
 

pkgs/tools/cd-dvd/vobsub2srt/default.nix

@@ -11,6 +11,8 @@ stdenv.mkDerivation rec {
     sha256 = "sha256-i6V2Owb8GcTcWowgb/BmdupOSFsYiCF2SbC9hXa26uY=";
   };
 
+  NIX_CFLAGS_COMPILE = lib.optionals stdenv.cc.isGNU [ "-std=c++11" ];
+
   nativeBuildInputs = [ cmake pkg-config ];
   buildInputs = [ libtiff ];
   propagatedBuildInputs = [ tesseract ];

pkgs/tools/graphics/jbig2enc/53ce5fe7e73d7ed95c9e12b52dd4984723f865fa.patch

@@ -1,47 +0,0 @@
-From 53ce5fe7e73d7ed95c9e12b52dd4984723f865fa Mon Sep 17 00:00:00 2001
-From: =?UTF-8?q?Zdenko=20Podobn=C3=BD?= <zdenop@gmail.com>
-Date: Sun, 6 Apr 2014 21:25:27 +0200
-Subject: [PATCH] fix build with leptonica 1.70
-
----
- configure.ac |  1 +
- src/jbig2.cc | 13 +++++++++----
- 2 files changed, 10 insertions(+), 4 deletions(-)
-
-diff --git a/configure.ac b/configure.ac
-index fe37c22..753a607 100644
---- a/configure.ac
-+++ b/configure.ac
-@@ -55,6 +55,7 @@ AC_CHECK_LIB([lept], [findFileFormatStream], [], [
-			echo "Error! Leptonica not detected."
-			exit -1
-			])
-+AC_CHECK_FUNCS(expandBinaryPower2Low,,)
- # test for function - it should detect leptonica dependecies
-
- # Check for possible dependancies of leptonica.
-diff --git a/src/jbig2.cc b/src/jbig2.cc
-index e10f042..515c1ef 100644
---- a/src/jbig2.cc
-+++ b/src/jbig2.cc
-@@ -130,11 +130,16 @@ segment_image(PIX *pixb, PIX *piximg) {
-   // input color image, so we have to do it this way...
-   // is there a better way?
-   // PIX *pixd = pixExpandBinary(pixd4, 4);
--  PIX *pixd = pixCreate(piximg->w, piximg->h, 1);
--  pixCopyResolution(pixd, piximg);
--  if (verbose) pixInfo(pixd, "mask image: ");
--  expandBinaryPower2Low(pixd->data, pixd->w, pixd->h, pixd->wpl,
-+  PIX *pixd;
-+#ifdef HAVE_EXPANDBINARYPOWER2LOW
-+    pixd = pixCreate(piximg->w, piximg->h, 1);
-+    pixCopyResolution(pixd, piximg);
-+    expandBinaryPower2Low(pixd->data, pixd->w, pixd->h, pixd->wpl,
-                         pixd4->data, pixd4->w, pixd4->h, pixd4->wpl, 4);
-+#else
-+    pixd = pixExpandBinaryPower2(pixd4, 4);
-+#endif
-+  if (verbose) pixInfo(pixd, "mask image: ");
-
-   pixDestroy(&pixd4);
-   pixDestroy(&pixsf4);

pkgs/tools/graphics/jbig2enc/default.nix

@@ -1,35 +0,0 @@
-{ lib, stdenv, fetchFromGitHub, leptonica, zlib, libwebp, giflib, libjpeg, libpng, libtiff }:
-
-stdenv.mkDerivation rec {
-  pname = "jbig2enc";
-  version = "0.28";
-
-  src = fetchFromGitHub {
-    owner = "agl";
-    repo = "jbig2enc";
-    rev = "${version}-dist";
-    hash = "sha256-Y3IVTjvO5tqn/O076y/llnTyenKpbx1WyT/JFZ/s0VY=";
-  };
-
-  propagatedBuildInputs = [ leptonica zlib libwebp giflib libjpeg libpng libtiff ];
-
-  patches = [
-    # https://github.com/agl/jbig2enc/commit/53ce5fe7e73d7ed95c9e12b52dd4984723f865fa
-    ./53ce5fe7e73d7ed95c9e12b52dd4984723f865fa.patch
-  ];
-
-  # This is necessary, because the resulting library has
-  # /tmp/nix-build-jbig2enc/src/.libs before /nix/store/jbig2enc/lib
-  # in its rpath, which means that patchelf --shrink-rpath removes
-  # the /nix/store one.  By cleaning up before fixup, we ensure that
-  # the /tmp/nix-build-jbig2enc/src/.libs directory is gone.
-  preFixup = ''
-    make clean
-  '';
-
-  meta = {
-    description = "Encoder for the JBIG2 image compression format";
-    license = lib.licenses.asl20;
-    platforms = lib.platforms.all;
-  };
-}

pkgs/tools/misc/boxxy/default.nix

@@ -0,0 +1,26 @@
+{ lib
+, rustPlatform
+, fetchFromGitHub
+}:
+
+rustPlatform.buildRustPackage rec {
+  pname = "boxxy";
+  version = "0.2.7";
+
+  src = fetchFromGitHub {
+    owner = "queer";
+    repo = "boxxy";
+    rev = "v${version}";
+    hash = "sha256-mvSarA0rZuOQvgf2NJXWIWoeZtvb+D/GofAHPKQDH6U=";
+  };
+
+  cargoHash = "sha256-Psc9qErqi3aangNowXxhkEXphFCR7pp+DKTKtk6tMo0=";
+
+  meta = with lib; {
+    description = "Puts bad Linux applications in a box with only their files";
+    homepage = "https://github.com/queer/boxxy";
+    license = licenses.mit;
+    maintainers = with maintainers; [ dit7ya ];
+    platforms = platforms.linux;
+  };
+}

pkgs/tools/networking/snowflake/default.nix

@@ -2,7 +2,7 @@
 
 buildGoModule rec {
   pname = "snowflake";
-  version = "2.5.0";
+  version = "2.5.1";
 
   src = fetchFromGitLab {
     domain = "gitlab.torproject.org";
@@ -10,10 +10,10 @@ buildGoModule rec {
     owner = "anti-censorship/pluggable-transports";
     repo = "snowflake";
     rev = "v${version}";
-    sha256 = "sha256-7iwRbik3hUj6Zv3tqLKqhGUIag6OnWRhpWqW6NTI+FU=";
+    sha256 = "sha256-r2NRIb6qbA1B5HlVNRqa9ongQpyiyPskhembPHX3Lgc=";
   };
 
-  vendorHash = "sha256-wHLYVf8QurMbmdLNkTFGgmncOJlJHZF8PwYTUniXOGY=";
+  vendorHash = "sha256-dnfm4KiVD89bnHV7bfw5aXWHGdcH9JBdrtvuS6s8N5w=";
 
   meta = with lib; {
     description = "System to defeat internet censorship";

pkgs/tools/package-management/nfpm/default.nix

@@ -2,16 +2,16 @@
 
 buildGoModule rec {
   pname = "nfpm";
-  version = "2.25.0";
+  version = "2.25.1";
 
   src = fetchFromGitHub {
     owner = "goreleaser";
     repo = pname;
     rev = "v${version}";
-    sha256 = "sha256-Mu0/mWkdrhaybI0iAB/MuD7UTbDDC73ZMxr8kU7R23I=";
+    sha256 = "sha256-J5vAvF22NKMvvaftfVugWYAP6uM6pcyKEPqRDf+J9A4=";
   };
 
-  vendorHash = "sha256-YDV816jTLAqbSjiKXvbkwPbPCLPplH+NFN1SCVjWcbk=";
+  vendorHash = "sha256-GaESwr7rvDvjQ7zi/LbndiB2lQGmIELTx7wAJitj5kw=";
 
   ldflags = [ "-s" "-w" "-X main.version=${version}" ];
 

pkgs/tools/security/erosmb/default.nix

@@ -5,14 +5,14 @@
 
 python3.pkgs.buildPythonApplication rec {
   pname = "erosmb";
-  version = "0.1.4";
+  version = "0.1.5";
   format = "pyproject";
 
   src = fetchFromGitHub {
     owner = "viktor02";
     repo = "EroSmb";
     rev = "refs/tags/v${version}";
-    hash = "sha256-ThJwBKpxoTwHP84OlVKH62gQ3kfv83J8HNs5Mizi8Ck=";
+    hash = "sha256-9Zs5Z+3JiBiJkV9Ixl5pPmLv0dUT59CT0UkQDsmneWc=";
   };
 
   propagatedBuildInputs = with python3.pkgs; [

pkgs/top-level/all-packages.nix

@@ -2858,6 +2858,8 @@ with pkgs;
 
   boxes = callPackage ../tools/text/boxes { };
 
+  boxxy = callPackage ../tools/misc/boxxy { };
+
   boundary = callPackage ../tools/networking/boundary { };
 
   chamber = callPackage ../tools/admin/chamber {  };
@@ -9781,7 +9783,13 @@ with pkgs;
     pythonPackages = python3Packages;
   };
 
-  mirakurun = callPackage ../applications/video/mirakurun { };
+  mirakurun = callPackage ../applications/video/mirakurun {
+    yarn = yarn.override { nodejs = nodejs-16_x; };
+    inherit (callPackage ../development/tools/yarn2nix-moretea/yarn2nix {
+      nodejs = nodejs-16_x;
+      yarn = yarn.override { nodejs = nodejs-16_x; };
+    }) mkYarnPackage;
+  };
 
   miredo = callPackage ../tools/networking/miredo { };
 
@@ -10793,8 +10801,6 @@ with pkgs;
 
   pdf-quench = callPackage ../applications/misc/pdf-quench { };
 
-  jbig2enc = callPackage ../tools/graphics/jbig2enc { };
-
   pdfarranger = callPackage ../applications/misc/pdfarranger { };
 
   briss = callPackage ../tools/graphics/briss { };
@@ -20501,6 +20507,8 @@ with pkgs;
 
   jbig2dec = callPackage ../development/libraries/jbig2dec { };
 
+  jbig2enc = callPackage ../development/libraries/jbig2enc { };
+
   jcal = callPackage ../development/libraries/jcal { };
 
   jbigkit = callPackage ../development/libraries/jbigkit { };

pkgs/top-level/python-aliases.nix

@@ -156,6 +156,7 @@ mapAliases ({
   pycallgraph = throw "pycallgraph has been removed, it was using setuptools 2to3 translation feature, which has been removed in setuptools 58"; # added 2022-01-18
   pychef = throw "pychef has been removed because it's been archived upstream and abandoned since 2017."; # added 2022-11-14
   pycryptodome-test-vectors = throw "pycryptodome-test-vectors has been removed because it is an internal package to pycryptodome"; # added 2022-05-28
+  pyflunearyou = pyoutbreaksnearme; # added 2023-02-11
   pyialarmxr = pyialarmxr-homeassistant; # added 2022-06-07
   pyialarmxr-homeassistant = throw "The package was removed together with the component support in home-assistant 2022.7.0"; # added 2022-07-07
   PyICU = pyicu; # Added 2022-12-22

pkgs/top-level/python-packages.nix

@@ -853,6 +853,8 @@ self: super: with self; {
 
   awslambdaric = callPackage ../development/python-modules/awslambdaric { };
 
+  awswrangler = callPackage ../development/python-modules/awswrangler { };
+
   axis = callPackage ../development/python-modules/axis { };
 
   azure-appconfiguration = callPackage ../development/python-modules/azure-appconfiguration { };
@@ -7267,6 +7269,8 @@ self: super: with self; {
 
   pyorthanc = callPackage ../development/python-modules/pyorthanc { };
 
+  pyoutbreaksnearme = callPackage ../development/python-modules/pyoutbreaksnearme { };
+
   pyoverkiz = callPackage ../development/python-modules/pyoverkiz { };
 
   pyownet = callPackage ../development/python-modules/pyownet { };
@@ -8059,8 +8063,6 @@ self: super: with self; {
 
   pyflume = callPackage ../development/python-modules/pyflume { };
 
-  pyflunearyou = callPackage ../development/python-modules/pyflunearyou { };
-
   pyfma = callPackage ../development/python-modules/pyfma { };
 
   pyfribidi = callPackage ../development/python-modules/pyfribidi { };