Merge branch 'master' into staging

4 files changed, 74 insertions, 42 deletions

diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 8d6118bf097..7297a4ae9f6 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -697,6 +697,8 @@ in
 
   cozy = callPackage ../applications/audio/cozy-audiobooks { };
 
+  crumbs = callPackage ../applications/misc/crumbs { };
+
   deskew = callPackage ../applications/graphics/deskew { };
 
   detect-secrets = python3Packages.callPackage ../development/tools/detect-secrets { };
@@ -915,6 +917,8 @@ in
 
   bar = callPackage ../tools/system/bar {};
 
+  base16-shell-preview = callPackage ../misc/base16-shell-preview { };
+
   base16-builder = callPackage ../misc/base16-builder { };
 
   basex = callPackage ../tools/text/xml/basex { };
@@ -2557,6 +2561,8 @@ in
     inherit (pythonPackages) sphinx;
   };
 
+  wallutils = callPackage ../tools/graphics/wallutils { };
+
   wl-clipboard = callPackage ../tools/misc/wl-clipboard { };
 
   zabbix-cli = callPackage ../tools/misc/zabbix-cli { };
@@ -2571,7 +2577,7 @@ in
 
   cholmod-extra = callPackage ../development/libraries/science/math/cholmod-extra { };
 
-  emscriptenVersion = "1.37.36";
+  emscriptenVersion = "1.38.28";
 
   emscripten = callPackage ../development/compilers/emscripten { };
 
@@ -7754,6 +7760,7 @@ in
   cargo-asm = callPackage ../development/tools/rust/cargo-asm {
     inherit (darwin.apple_sdk.frameworks) Security;
   };
+  cargo-bloat = callPackage ../development/tools/rust/cargo-bloat { };
   cargo-expand = callPackage ../development/tools/rust/cargo-expand { };
   cargo-fuzz = callPackage ../development/tools/rust/cargo-fuzz { };
   cargo-xbuild = callPackage ../development/tools/rust/cargo-xbuild { };
@@ -9008,6 +9015,8 @@ in
 
   grail = callPackage ../development/libraries/grail { };
 
+  graphene-hardened-malloc = callPackage ../development/libraries/graphene-hardened-malloc { };
+
   gtk-doc = callPackage ../development/tools/documentation/gtk-doc { };
 
   gtkdialog = callPackage ../development/tools/misc/gtkdialog { };
@@ -9561,6 +9570,8 @@ in
 
   aalib = callPackage ../development/libraries/aalib { };
 
+  abseil-cpp = callPackage ../development/libraries/abseil-cpp { };
+
   accountsservice = callPackage ../development/libraries/accountsservice { };
 
   acl = callPackage ../development/libraries/acl { };
@@ -21879,6 +21890,8 @@ in
 
   ezminc = callPackage ../applications/science/biology/EZminc { };
 
+  exonerate = callPackage ../applications/science/biology/exonerate { };
+
   hisat2 = callPackage ../applications/science/biology/hisat2 { };
 
   htslib = callPackage ../development/libraries/science/biology/htslib { };
@@ -21945,6 +21958,8 @@ in
 
   plink-ng = callPackage ../applications/science/biology/plink-ng { };
 
+  prodigal = callPackage ../applications/science/biology/prodigal { };
+
   raxml = callPackage ../applications/science/biology/raxml { };
 
   raxml-mpi = appendToName "mpi" (raxml.override {
@@ -22063,7 +22078,9 @@ in
 
   nauty = callPackage ../applications/science/math/nauty {};
 
-  or-tools = callPackage ../development/libraries/science/math/or-tools {};
+  or-tools = callPackage ../development/libraries/science/math/or-tools {
+    pythonProtobuf = pythonPackages.protobuf;
+  };
 
   rubiks = callPackage ../development/libraries/science/math/rubiks { };
 
@@ -22155,6 +22172,8 @@ in
 
   dafny = dotnetPackages.Dafny;
 
+  groove = callPackage ../applications/science/programming/groove { };
+
   plm = callPackage ../applications/science/programming/plm { };
 
   scyther = callPackage ../applications/science/programming/scyther { };
diff --git a/pkgs/top-level/perl-packages.nix b/pkgs/top-level/perl-packages.nix
index 5c9e8f288a6..098b2652bf6 100644
--- a/pkgs/top-level/perl-packages.nix
+++ b/pkgs/top-level/perl-packages.nix
@@ -8187,7 +8187,7 @@ let
     };
     outputs = [ "out" ];
     buildInputs = [ pkgs.apacheHttpd pkgs.apr pkgs.aprutil ApacheTest ExtUtilsXSBuilder ];
-    propagatedBuildInputs = [ mod_perl2 ];
+    propagatedBuildInputs = [ (pkgs.apacheHttpdPackages.mod_perl.override { inherit perl; }) ];
     makeMakerFlags = "--with-apache2-src=${pkgs.apacheHttpd.dev} --with-apache2-apxs=${pkgs.apacheHttpd.dev}/bin/apxs --with-apache2-httpd=${pkgs.apacheHttpd.out}/bin/httpd --with-apr-config=${pkgs.apr.dev}/bin/apr-1-config --with-apu-config=${pkgs.aprutil.dev}/bin/apu-1-config";
     preConfigure = ''
       # override broken prereq check
@@ -8198,11 +8198,30 @@ let
       '';
     installPhase = ''
       mkdir $out
+
+      # install the library
       make install DESTDIR=$out
       cp -r $out/${pkgs.apacheHttpd.dev}/. $out/.
       cp -r $out/$out/. $out/.
+
+      # install the perl module
+      pushd glue/perl
+      perl Makefile.PL
+      make install DESTDIR=$out
+      cp -r $out/${perl}/lib/perl5 $out/lib/
+      popd
+
+      # install the apache module
+      # https://computergod.typepad.com/home/2007/06/webgui_and_suse.html
+      # NOTE: if using the apache module you must use "apreq" as the module name, not "apreq2"
+      # services.httpd.extraModules = [ { name = "apreq"; path = "''${pkgs.perlPackages.libapreq2}/modules/mod_apreq2.so"; } ];
+      pushd module
+      make install DESTDIR=$out
+      cp -r $out/${pkgs.apacheHttpd.out}/modules $out/
+      popd
+
       rm -r $out/nix
-      '';
+    '';
     doCheck = false; # test would need to start apache httpd
     meta = {
       license = stdenv.lib.licenses.asl20;
@@ -8461,6 +8480,20 @@ let
     };
   };
 
+  LinuxFD = buildPerlModule rec {
+    name = "Linux-FD-0.011";
+    src = fetchurl {
+      url = "mirror://cpan/authors/id/L/LE/LEONT/${name}.tar.gz";
+      sha256 = "6bb579d47644cb0ed35626ff77e909ae69063073c6ac09aa0614fef00fa37356";
+    };
+    buildInputs = [ ModuleBuild TestException ];
+    propagatedBuildInputs = [ SubExporter ];
+    meta = {
+      description = "Linux specific special filehandles";
+      license = with stdenv.lib.licenses; [ artistic1 gpl1Plus ];
+    };
+  };
+
   LinuxInotify2 = buildPerlPackage rec {
     name = "Linux-Inotify2-2.1";
     src = fetchurl {
diff --git a/pkgs/top-level/php-packages.nix b/pkgs/top-level/php-packages.nix
index c2a268b8bfe..9afb7df820f 100644
--- a/pkgs/top-level/php-packages.nix
+++ b/pkgs/top-level/php-packages.nix
@@ -114,33 +114,14 @@ let
     buildInputs = [ (if isPhp73 then pkgs.pcre2 else pkgs.pcre) ];
   };
 
-  memcached = if isPhp73 then memcached73 else memcached7;
-
-  memcached7 = assert !isPhp73; buildPecl rec {
-    name = "memcached-php7";
+  memcached = buildPecl rec {
+    version = "3.1.3";
+    name = "memcached-${version}";
 
     src = fetchgit {
       url = "https://github.com/php-memcached-dev/php-memcached";
-      rev = "e573a6e8fc815f12153d2afd561fc84f74811e2f";
-      sha256 = "0asfi6rsspbwbxhwmkxxnapd8w01xvfmwr1n9qsr2pryfk0w6y07";
-    };
-
-    configureFlags = [
-      "--with-zlib-dir=${pkgs.zlib.dev}"
-      "--with-libmemcached-dir=${pkgs.libmemcached}"
-    ];
-
-    nativeBuildInputs = [ pkgs.pkgconfig ];
-    buildInputs = with pkgs; [ cyrus_sasl zlib ];
-  };
-
-  memcached73 = assert isPhp73; buildPecl rec {
-    name = "memcached-php73";
-
-    src = fetchgit {
-      url = "https://github.com/php-memcached-dev/php-memcached";
-      rev = "6d8f5d524f35e72422b9e81319b96f23af02adcc";
-      sha256 = "1s1d5r3n2h9zys8sqvv52fld6jy21ki7cl0gbbvd9dixqc0lf1jh";
+      rev = "v${version}";
+      sha256 = "1w9g8k7bmq3nbzskskpsr5632gh9q75nqy7nkjdzgs17klq9khjk";
     };
 
     configureFlags = [
@@ -177,21 +158,11 @@ let
     buildInputs = [ pkgs.unixODBC ];
   };
 
-  xdebug =  if isPhp73 then xdebug73 else xdebug7;
-
-  xdebug7 = assert !isPhp73; buildPecl {
-    name = "xdebug-2.6.1";
-
-    sha256 = "0xxxy6n4lv7ghi9liqx133yskg07lw316vhcds43n1sjq3b93rns";
-
-    doCheck = true;
-    checkTarget = "test";
-  };
-
-  xdebug73 = assert isPhp73; buildPecl {
-    name = "xdebug-2.7.0beta1";
+  xdebug = buildPecl rec {
+    version = "2.7.1";
+    name = "xdebug-${version}";
 
-    sha256 = "1ghh14z55l4jklinkgjkfhkw53lp2r7lgmyh7q8kdnf7jnpwx84h";
+    sha256 = "1hr4gy87a3gp682ggwp831xk1fxasil9wan8cxv23q3m752x3sdp";
 
     doCheck = true;
     checkTarget = "test";
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 1572eb7f654..592ff04178a 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -555,6 +555,11 @@ in {
 
   ordered-set = callPackage ../development/python-modules/ordered-set { };
 
+  ortools = (toPythonModule (pkgs.or-tools.override {
+    inherit (self) python;
+    pythonProtobuf = self.protobuf;
+  })).python;
+
   osmnx = callPackage ../development/python-modules/osmnx { };
 
   outcome = callPackage ../development/python-modules/outcome {};
@@ -585,10 +590,14 @@ in {
 
   poetry = callPackage ../development/python-modules/poetry { };
 
+  pplpy = callPackage ../development/python-modules/pplpy { };
+
   pprintpp = callPackage ../development/python-modules/pprintpp { };
 
   progress = callPackage ../development/python-modules/progress { };
 
+  proglog = callPackage ../development/python-modules/proglog { };
+
   pure-python-adb-homeassistant = callPackage ../development/python-modules/pure-python-adb-homeassistant { };
 
   pymysql = callPackage ../development/python-modules/pymysql { };