Merge remote-tracking branch 'origin/master' into haskell-updates

doc/languages-frameworks/coq.section.md

@@ -29,14 +29,19 @@ The recommended way of defining a derivation for a Coq library, is to use the `c
 * `releaseRev` (optional, defaults to `(v: v)`), provides a default mapping from release names to revision hashes/branch names/tags,
 * `displayVersion` (optional), provides a way to alter the computation of `name` from `pname`, by explaining how to display version numbers,
 * `namePrefix` (optional, defaults to `[ "coq" ]`), provides a way to alter the computation of `name` from `pname`, by explaining which dependencies must occur in `name`,
-* `extraNativeBuildInputs` (optional), by default `nativeBuildInputs` just contains `coq`, this allows to add more native build inputs, `nativeBuildInputs` are executables and `buildInputs` are libraries and dependencies,
+* `nativeBuildInputs` (optional), is a list of executables that are required to build the current derivation, in addition to the default ones (namely `which`, `dune` and `ocaml` depending on whether `useDune2`, `useDune2ifVersion` and `mlPlugin` are set).
-* `extraBuildInputs` (optional), this allows to add more build inputs,
+* `extraNativeBuildInputs` (optional, deprecated), an additional list of derivation to add to `nativeBuildInputs`,
-* `mlPlugin` (optional, defaults to `false`). Some extensions (plugins) might require OCaml and sometimes other OCaml packages. Standard dependencies can be added by setting the current option to `true`. For a finer grain control, the `coq.ocamlPackages` attribute can be used in `extraBuildInputs` to depend on the same package set Coq was built against.
+* `overrideNativeBuildInputs` (optional) replaces the default list of derivation to which `nativeBuildInputs` and `extraNativeBuildInputs` adds extra elements,
-* `useDune2ifVersion` (optional, default to `(x: false)` uses Dune2 to build the package if the provided predicate evaluates to true on the version, e.g. `useDune2if = versions.isGe "1.1"`  will use dune if the version of the package is greater or equal to `"1.1"`,
+* `buildInputs` (optional), is a list of libraries and dependencies that are required to build and run the current derivation, in addition to the default one `[ coq ]`,
+* `extraBuildInputs` (optional, deprecated), an additional list of derivation to add to `buildInputs`,
+* `overrideBuildInputs` (optional) replaces the default list of derivation to which `buildInputs` and `extraBuildInputs` adds extras elements,
+* `propagatedBuildInputs` (optional) is passed as is to `mkDerivation`, we recommend to use this for Coq libraries and Coq plugin dependencies, as this makes sure the paths of the compiled libraries and plugins will always be added to the build environements of subsequent derivation, which is necessary for Coq packages to work correctly,
+* `mlPlugin` (optional, defaults to `false`). Some extensions (plugins) might require OCaml and sometimes other OCaml packages. Standard dependencies can be added by setting the current option to `true`. For a finer grain control, the `coq.ocamlPackages` attribute can be used in `nativeBuildInputs`, `buildInputs`, and `propagatedBuildInputs` to depend on the same package set Coq was built against.
+* `useDune2ifVersion` (optional, default to `(x: false)` uses Dune2 to build the package if the provided predicate evaluates to true on the version, e.g. `useDune2ifVersion = versions.isGe "1.1"`  will use dune if the version of the package is greater or equal to `"1.1"`,
 * `useDune2` (optional, defaults to `false`) uses Dune2 to build the package if set to true, the presence of this attribute overrides the behavior of the previous one.
 * `opam-name` (optional, defaults to concatenating with a dash separator the components of `namePrefix` and `pname`), name of the Dune package to build.
 * `enableParallelBuilding` (optional, defaults to `true`), since it is activated by default, we provide a way to disable it.
-* `extraInstallFlags` (optional), allows to extend `installFlags` which initializes the variable `COQMF_COQLIB` so as to install in the proper subdirectory. Indeed Coq libraries should be installed in `$(out)/lib/coq/${coq.coq-version}/user-contrib/`. Such directories are automatically added to the `$COQPATH` environment variable by the hook defined in the Coq derivation.
+* `extraInstallFlags` (optional), allows to extend `installFlags` which initializes the variables `DESTDIR` and `COQMF_COQLIB` so as to install in the proper subdirectory. Indeed Coq libraries should be installed in `$(out)/lib/coq/${coq.coq-version}/user-contrib/`. Such directories are automatically added to the `$COQPATH` environment variable by the hook defined in the Coq derivation.
 * `setCOQBIN` (optional, defaults to `true`), by default, the environment variable `$COQBIN` is set to the current Coq's binary, but one can disable this behavior by setting it to `false`,
 * `useMelquiondRemake` (optional, default to `null`) is an attribute set, which, if given, overloads the `preConfigurePhases`, `configureFlags`, `buildPhase`, and `installPhase` attributes of the derivation for a specific use in libraries using `remake` as set up by Guillaume Melquiond for `flocq`, `gappalib`, `interval`, and `coquelicot` (see the corresponding derivation for concrete examples of use of this option). For backward compatibility, the attribute `useMelquiondRemake.logpath` must be set to the logical root of the library (otherwise, one can pass `useMelquiondRemake = {}` to activate this without backward compatibility).
 * `dropAttrs`, `keepAttrs`, `dropDerivationAttrs` are all optional and allow to tune which attribute is added or removed from the final call to `mkDerivation`.

lib/strings.nix

@@ -339,9 +339,10 @@ rec {
 
   /* Translate a Nix value into a shell variable declaration, with proper escaping.
 
-     Supported value types are strings (mapped to regular variables), lists of strings
+     The value can be a string (mapped to a regular variable), a list of strings
-     (mapped to Bash-style arrays) and attribute sets of strings (mapped to Bash-style
+     (mapped to a Bash-style array) or an attribute set of strings (mapped to a
-     associative arrays). Note that "strings" include string-coercible values like paths.
+     Bash-style associative array). Note that "string" includes string-coercible
+     values like paths or derivations.
 
      Strings are translated into POSIX sh-compatible code; lists and attribute sets
      assume a shell that understands Bash syntax (e.g. Bash or ZSH).
@@ -356,7 +357,7 @@ rec {
   */
   toShellVar = name: value:
     lib.throwIfNot (isValidPosixName name) "toShellVar: ${name} is not a valid shell variable name" (
-    if isAttrs value then
+    if isAttrs value && ! isCoercibleToString value then
       "declare -A ${name}=(${
         concatStringsSep " " (lib.mapAttrsToList (n: v:
           "[${escapeShellArg n}]=${escapeShellArg v}"

lib/tests/misc.nix

@@ -269,6 +269,15 @@ runTests {
           strings
           possibly newlines
         '';
+        drv = {
+          outPath = "/drv";
+          foo = "ignored attribute";
+        };
+        path = /path;
+        stringable = {
+          __toString = _: "hello toString";
+          bar = "ignored attribute";
+        };
       }}
     '';
     expected = ''
@@ -277,6 +286,9 @@ runTests {
       declare -A assoc=(['with some']='strings
       possibly newlines
       ')
+      drv='/drv'
+      path='/path'
+      stringable='hello toString'
     '';
   };
 

maintainers/maintainer-list.nix

@@ -9572,8 +9572,8 @@
     githubId = 14816024;
     name = "oxalica";
     keys = [{
-      longkeyid = "rsa4096/0xCED392DE0C483D00";
+      longkeyid = "ed25519/0x7571654CF88E31C2";
-      fingerprint = "5CB0 E9E5 D5D5 71F5 7F54  0FEA CED3 92DE 0C48 3D00";
+      fingerprint = "F90F FD6D 585C 2BA1 F13D  E8A9 7571 654C F88E 31C2";
     }];
   };
   oxij = {

nixos/doc/manual/from_md/release-notes/rl-2205.section.xml

@@ -2297,6 +2297,14 @@
           package has been updated to 6.0.0 and now requires .NET 6.0.
         </para>
       </listitem>
+      <listitem>
+        <para>
+          The <literal>phpPackages.box</literal> package has been
+          updated from 2.7.5 to 3.16.0. See the
+          <link xlink:href="https://github.com/box-project/box/blob/master/UPGRADE.md#from-27-to-30">upgrade
+          guide</link> for more details.
+        </para>
+      </listitem>
       <listitem>
         <para>
           The <literal>zrepl</literal> package has been updated from

nixos/doc/manual/release-notes/rl-2205.section.md

@@ -827,6 +827,8 @@ In addition to numerous new and upgraded packages, this release has the followin
 
 - The `vscode-extensions.ionide.ionide-fsharp` package has been updated to 6.0.0 and now requires .NET 6.0.
 
+- The `phpPackages.box` package has been updated from 2.7.5 to 3.16.0. See the [upgrade guide](https://github.com/box-project/box/blob/master/UPGRADE.md#from-27-to-30) for more details.
+
 - The `zrepl` package has been updated from 0.4.0 to 0.5:
 
   - The RPC protocol version was bumped; all zrepl daemons in a setup must be updated and restarted before replication can resume.

nixos/modules/services/backup/automysqlbackup.nix

@@ -112,7 +112,7 @@ in
 
     services.mysql.ensureUsers = optional (config.services.mysql.enable && cfg.config.mysql_dump_host == "localhost") {
       name = user;
-      ensurePermissions = { "*.*" = "SELECT, SHOW VIEW, TRIGGER, LOCK TABLES"; };
+      ensurePermissions = { "*.*" = "SELECT, SHOW VIEW, TRIGGER, LOCK TABLES, EVENT"; };
     };
 
   };

pkgs/applications/editors/emacs/elisp-packages/melpa-packages.nix

@@ -217,6 +217,12 @@ let
         flycheck-rtags = fix-rtags super.flycheck-rtags;
 
         pdf-tools = super.pdf-tools.overrideAttrs (old: {
+          # Temporary work around for:
+          #   - https://github.com/vedang/pdf-tools/issues/102
+          #   - https://github.com/vedang/pdf-tools/issues/103
+          #   - https://github.com/vedang/pdf-tools/issues/109
+          CXXFLAGS = "-std=c++17";
+
           nativeBuildInputs = [
             pkgs.autoconf
             pkgs.automake

pkgs/applications/editors/vim/plugins/generated.nix

@@ -1384,6 +1384,18 @@ final: prev:
     meta.homepage = "https://github.com/neoclide/coc.nvim/";
   };
 
+  coconut-vim = buildVimPluginFrom2Nix {
+    pname = "coconut.vim";
+    version = "2017-10-10";
+    src = fetchFromGitHub {
+      owner = "manicmaniac";
+      repo = "coconut.vim";
+      rev = "cea47739aab9f163d240d1609e7eea326fd55072";
+      sha256 = "03rq3lpplgywvm620jzx085l74180163q8gls4gjrad2fgm9n96n";
+    };
+    meta.homepage = "https://github.com/manicmaniac/coconut.vim/";
+  };
+
   codi-vim = buildVimPluginFrom2Nix {
     pname = "codi.vim";
     version = "2022-04-30";
@@ -2566,6 +2578,18 @@ final: prev:
     meta.homepage = "https://github.com/gfanto/fzf-lsp.nvim/";
   };
 
+  fzf-lua = buildVimPluginFrom2Nix {
+    pname = "fzf-lua";
+    version = "2022-05-07";
+    src = fetchFromGitHub {
+      owner = "ibhagwan";
+      repo = "fzf-lua";
+      rev = "b614a9d315512ec4ce9c1df41474e5ab8e12f7df";
+      sha256 = "0gb7q4fbv3754ck44h6dd93dcy8j4czhhna1d2kgq21614xs303k";
+    };
+    meta.homepage = "https://github.com/ibhagwan/fzf-lua/";
+  };
+
   fzf-vim = buildVimPluginFrom2Nix {
     pname = "fzf.vim";
     version = "2022-04-07";

pkgs/applications/editors/vim/plugins/overrides.nix

@@ -293,6 +293,10 @@ self: super: {
     '';
   });
 
+  fzf-lua = super.fzf-lua.overrideAttrs (old: {
+    propagatedBuildInputs = [ fzf ];
+  });
+
   fzf-vim = super.fzf-vim.overrideAttrs (old: {
     dependencies = with self; [ fzfWrapper ];
   });

pkgs/applications/editors/vim/plugins/vim-plugin-names

@@ -116,6 +116,7 @@ https://github.com/iamcco/coc-spell-checker/,,
 https://github.com/coc-extensions/coc-svelte/,,
 https://github.com/iamcco/coc-tailwindcss/,,
 https://github.com/neoclide/coc.nvim/,release,
+https://github.com/manicmaniac/coconut.vim/,HEAD,
 https://github.com/metakirby5/codi.vim/,,
 https://github.com/tjdevries/colorbuddy.nvim/,,
 https://github.com/lilydjwg/colorizer/,,
@@ -214,6 +215,7 @@ https://github.com/BeneCollyridam/futhark-vim/,,
 https://github.com/rktjmp/fwatch.nvim/,,
 https://github.com/stsewd/fzf-checkout.vim/,,
 https://github.com/gfanto/fzf-lsp.nvim/,,
+https://github.com/ibhagwan/fzf-lua/,HEAD,
 https://github.com/junegunn/fzf.vim/,,
 https://github.com/NTBBloodbath/galaxyline.nvim/,,
 https://github.com/jsfaint/gen_tags.vim/,,

pkgs/applications/misc/1password/default.nix

@@ -12,12 +12,12 @@ let
     if extension == "zip" then fetchzip args else fetchurl args;
 
   pname = "1password-cli";
-  version = "2.1.0";
+  version = "2.2.0";
   sources = rec {
-    aarch64-linux = fetch "linux_arm64" "sha256-DTYWqhawyAQBIxMUksZheyN8WSVPyhCghZC8orxKsBk=" "zip";
+    aarch64-linux = fetch "linux_arm64" "sha256-fKW2qSQkkC4GcnHcLLszX1pcqK67SaofVX017/cIkD0=" "zip";
-    i686-linux = fetch "linux_386" "sha256-JBjiKxbJnFILSOVnOUIcY3GpbOT2UOJlasTSPRyYz4I=" "zip";
+    i686-linux = fetch "linux_386" "sha256-TmQ3nWG12DTpAJaxbK+hnJak0RrFhhw6rJWfV7q8wb4=" "zip";
-    x86_64-linux = fetch "linux_amd64" "sha256-PfVOvUF8Rls29VzfIj1U6/VFv1H6lj2K3Dz6DWmh2fs=" "zip";
+    x86_64-linux = fetch "linux_amd64" "sha256-66kFScxPmy4WgK9p1W6qBoAeYJwungHgGkTurjEJy+4=" "zip";
-    aarch64-darwin = fetch "apple_universal" "sha256-Cn3/+Dvk5hW9rvxu4I9ghHSS1yWSAeQq3gx+6dvFiIk=" "pkg";
+    aarch64-darwin = fetch "apple_universal" "sha256-DD1j093SjnaPtkQ4XuU1zkRi6XPXtwnBxiqC6wZbV+w=" "pkg";
     x86_64-darwin = aarch64-darwin;
   };
   platforms = builtins.attrNames sources;

pkgs/applications/misc/dbeaver/default.nix

@@ -73,6 +73,7 @@
       productTargetPath = "product/community/target/products/org.jkiss.dbeaver.core.product";
 
       platformMap = {
+        aarch64-darwin = "aarch64";
         aarch64-linux = "aarch64";
         x86_64-darwin = "x86_64";
         x86_64-linux  = "x86_64";
@@ -127,7 +128,7 @@
       Teradata, Firebird, Derby, etc.
     '';
     license = licenses.asl20;
-    platforms = [ "x86_64-linux" "x86_64-darwin" "aarch64-linux" ];
+    platforms = [ "x86_64-linux" "x86_64-darwin" "aarch64-linux" "aarch64-darwin" ];
     maintainers = with maintainers; [ jojosch mkg20001 ];
   };
 }

pkgs/applications/misc/joshuto/default.nix

@@ -1,4 +1,4 @@
-{ lib, rustPlatform, fetchFromGitHub, stdenv, SystemConfiguration }:
+{ lib, rustPlatform, fetchFromGitHub, stdenv, SystemConfiguration, Foundation }:
 
 rustPlatform.buildRustPackage rec {
   pname = "joshuto";
@@ -13,7 +13,7 @@ rustPlatform.buildRustPackage rec {
 
   cargoSha256 = "sha256-vhTfAoAwDJ9BjhgUEkV2H+KAetJR1YqwaZ7suF6yMXA=";
 
-  buildInputs = lib.optional stdenv.isDarwin SystemConfiguration;
+  buildInputs = lib.optionals stdenv.isDarwin [ SystemConfiguration Foundation ];
 
   meta = with lib; {
     description = "Ranger-like terminal file manager written in Rust";

pkgs/applications/misc/twitch-chat-downloader/default.nix

@@ -9,16 +9,22 @@
 
 buildPythonApplication rec {
   pname = "twitch-chat-downloader";
-  version = "3.2.1";
+  version = "3.2.2";
 
   src = fetchPypi {
     inherit version;
     pname = "tcd";
-    sha256 = "f9b5ea2ad3badb7deffdd9604368ccb54170cd7929efbaa2d7b534e089ae6338";
+    sha256 = "ee6a8e22c54ccfd29988554b13fe56b2a1bf524e110fa421d77e27baa8dcaa19";
   };
 
   postPatch = ''
-    substituteInPlace setup.py --replace "'pipenv>=2020.5.28'," ""
+    substituteInPlace setup.py \
+      --replace "'pipenv==2022.4.30'," "" \
+      --replace "setuptools==62.1." "setuptools" \
+      --replace "requests==2.27.1" "requests" \
+      --replace "twitch-python==0.0.20" "twitch-python" \
+      --replace "pytz==2022.1" "pytz" \
+      --replace "python-dateutil==2.8.2" "python-dateutil"
   '';
 
   propagatedBuildInputs = [ requests twitch-python pytz python-dateutil ];

pkgs/applications/networking/browsers/brave/default.nix

@@ -90,11 +90,11 @@ in
 
 stdenv.mkDerivation rec {
   pname = "brave";
-  version = "1.38.111";
+  version = "1.38.115";
 
   src = fetchurl {
     url = "https://github.com/brave/brave-browser/releases/download/v${version}/brave-browser_${version}_amd64.deb";
-    sha256 = "sha256-sUTQktCQOVyXbw58u9ilFZaKg6D24Okpa+rUIO56ors=";
+    sha256 = "sha256-YQpFsB3VVzsOa7PoZ+TLv10Dzm9z819cmyw7atnG/Cs=";
   };
 
   dontConfigure = true;

pkgs/applications/networking/browsers/chromium/upstream-info.json

@@ -45,9 +45,9 @@
     }
   },
   "ungoogled-chromium": {
-    "version": "101.0.4951.54",
+    "version": "101.0.4951.64",
-    "sha256": "1d808a7mvg0nd0mm20c1ny5kdvb2xvrs8vz4nnk456ix8pywcv62",
+    "sha256": "1xyqm32y9v1hn8ji6qfw6maynqgg3266j58dq4x4aqsm2gj9cn4w",
-    "sha256bin64": "1m6s6xf2wvz535w6jskk3pnibvsjpzmbxvd9rlxmqr08y219gp5y",
+    "sha256bin64": "14ijrj7h2y72ppyysz6jv40c01lbnan7z69cl24asch2zjlgwv8v",
     "deps": {
       "gn": {
         "version": "2022-03-14",
@@ -56,8 +56,8 @@
         "sha256": "0nql15ckjqkm001xajq3qyn4h4q80i7x6dm9zinxxr1a8q5lppx3"
       },
       "ungoogled-patches": {
-        "rev": "101.0.4951.54-1",
+        "rev": "101.0.4951.64-1",
-        "sha256": "0zhzy7llqddvym992pwhkgqh2f6ywjqqg0bhahl6c0np95gzhpbs"
+        "sha256": "0k7w6xvjf1yzyak9ywvcdw762d8zbx6d8haz35q87jz0mxfn2mr3"
       }
     }
   }

pkgs/applications/networking/instant-messengers/element/element-desktop-package.json

@@ -2,7 +2,7 @@
   "name": "element-desktop",
   "productName": "Element",
   "main": "lib/electron-main.js",
-  "version": "1.10.11",
+  "version": "1.10.12",
   "description": "A feature-rich client for Matrix.org",
   "author": "Element",
   "repository": {
@@ -81,11 +81,11 @@
     "rimraf": "^3.0.2",
     "tar": "^6.1.2",
     "ts-node": "^10.4.0",
-    "typescript": "^4.5.3"
+    "typescript": "4.5.5"
   },
   "hakDependencies": {
-    "matrix-seshat": "^2.3.0",
+    "matrix-seshat": "^2.3.3",
-    "keytar": "^5.6.0"
+    "keytar": "^7.9.0"
   },
   "build": {
     "appId": "im.riot.app",

pkgs/applications/networking/instant-messengers/element/pin.json

@@ -1,6 +1,6 @@
 {
-  "version": "1.10.11",
+  "version": "1.10.12",
-  "desktopSrcHash": "n74KFmHI6ZQWBEJCR55VZHS//myh2RePcJRVOmZ6XHo=",
+  "desktopSrcHash": "K1p/+dZRtKb+AiU2EcikAsmiTIKPw0zaVzAfUDzsYZY=",
-  "desktopYarnHash": "0jm0i1yyfkg1ll11pb3qif1vdxx6rp0yl9kd8jg9nhsg2jzw66pr",
+  "desktopYarnHash": "09ri87ynfgxrv22sykggiy6nlcf20qwj7zj9qq0rz3c2acr6g9mn",
-  "webHash": "02m64bhg1ls4a5igmizkkxnqfmbfhs0xy24ycr75vxmn0zmwa3yd"
+  "webHash": "1m7pvliymyggg6qx8gj6l3j2f4rml0km1vmk1zdspxa4l6p0qxd8"
 }

pkgs/applications/networking/misc/zammad/default.nix

@@ -21,7 +21,7 @@
 
 let
   pname = "zammad";
-  version = "5.1.0";
+  version = "5.1.1";
 
   src = applyPatches {
 

pkgs/applications/networking/misc/zammad/gemset.nix

@@ -664,10 +664,10 @@
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "04vxmjr200akcil9fqxc9ghbb9q0lyrh2q03xxncycd5vln910fi";
+      sha256 = "1pfk942d6qwhw151hxaz7n4knk6whyxqvvywdx2cdw9yhykyaqzq";
       type = "gem";
     };
-    version = "6.2.0";
+    version = "6.2.1";
   };
   factory_bot_rails = {
     dependencies = ["factory_bot" "railties"];
@@ -1452,10 +1452,10 @@
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "1p6b3q411h2mw4dsvhjrp1hh66hha5cm69fqg85vn2lizz71n6xz";
+      sha256 = "1g43ii497cwdqhfnaxfl500bq5yfc5hfv5df1lvf6wcjnd708ihd";
       type = "gem";
     };
-    version = "1.13.3";
+    version = "1.13.4";
   };
   nori = {
     groups = ["default"];
@@ -1700,10 +1700,10 @@
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "19mf9f5zx23cjjn0p77wz1igzpfr22mxhljgavffl8fwqq74v4ih";
+      sha256 = "01ldw5ba6xfn2k97n75n52qs4f0fy8xmn58c4247xf476nfvg035";
       type = "gem";
     };
-    version = "3.2.5";
+    version = "3.2.6";
   };
   power_assert = {
     groups = ["default" "development" "test"];
@@ -1786,10 +1786,10 @@
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "1xvkz9xrd1cqnlm0qac1iwwxzndx3cc17zrjncpa4lzjfwbxhsnm";
+      sha256 = "0df9bknc2dllk8v9fhgidzbvbryaxa8fgifrk40cdz9csjsphbky";
       type = "gem";
     };
-    version = "4.3.11";
+    version = "4.3.12";
   };
   pundit = {
     dependencies = ["activesupport"];
@@ -1833,6 +1833,17 @@
     };
     version = "2.2.3";
   };
+  rack-attack = {
+    dependencies = ["rack"];
+    groups = ["default"];
+    platforms = [];
+    source = {
+      remotes = ["https://rubygems.org"];
+      sha256 = "1rc6simyql7ax5zzp667x6krl0xxxh3asc1av6gcn8j6cyl86wsx";
+      type = "gem";
+    };
+    version = "6.6.0";
+  };
   rack-livereload = {
     dependencies = ["rack"];
     groups = ["development" "test"];
@@ -2273,10 +2284,10 @@
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "134zg0dzd7216lyczkhv01v27ikkmipjihcy2bzi0qv72p1i923i";
+      sha256 = "1wybcipkfawg4pragmayiig03xc084x3hbwywsh1dr9x9pa8f9hj";
       type = "gem";
     };
-    version = "1.1.5";
+    version = "1.1.6";
   };
   slack-notifier = {
     groups = ["default"];

pkgs/applications/networking/misc/zammad/package.json

@@ -14,5 +14,5 @@
     "stylelint-prettier": "^2.0.0"
   },
   "name": "Zammad",
-  "version": "5.1.0"
+  "version": "5.1.1"
 }

pkgs/applications/networking/misc/zammad/source.json

@@ -1,7 +1,8 @@
 {
   "owner": "zammad",
   "repo": "zammad",
-  "rev": "eefae45c2ad6e6a96b8df631d2f50f290ecbd27d",
+  "rev": "d71bd90ef964426230664cdfbaa2572325bfed4f",
-  "sha256": "EjowvM//+UsAfEH9/0jgLkiD7EWH34M1NQ9U2DotBqc=",
+  "sha256": "yzDTkjnRBl71REtSKRblkanJWhj7gp/+exhWjxGCFWw=",
   "fetchSubmodules": true
 }
+

pkgs/applications/office/libreoffice/default.nix

@@ -1,29 +1,125 @@
-{ stdenv, fetchurl, lib, pam, python3, libxslt, perl, ArchiveZip, box2d, gettext
+{ stdenv
-, IOCompress, zlib, libjpeg, expat, freetype, libwpd
+, fetchurl
-, libxml2, db, curl, fontconfig, libsndfile, neon
+, lib
-, bison, flex, zip, unzip, gtk3, libmspack, getopt, file, cairo, which
+, pam
-, icu, boost, jdk, ant, cups, xorg, fontforge, jre_minimal
+, python3
-, openssl, gperf, cppunit, poppler, util-linux
+, libxslt
-, librsvg, libGLU, libGL, bsh, CoinMP, libwps, libabw, libmysqlclient
+, perl
-, autoconf, automake, openldap, bash, hunspell, librdf_redland, nss, nspr
+, ArchiveZip
-, libwpg, dbus-glib, clucene_core, libcdr, lcms
+, box2d
-, unixODBC, mdds, sane-backends, mythes, libexttextcat, libvisio
+, gettext
-, fontsConf, pkg-config, bluez5, libtool, carlito
+, IOCompress
-, libatomic_ops, graphite2, harfbuzz, libodfgen, libzmf
+, zlib
-, librevenge, libe-book, libmwaw, glm, gst_all_1
+, libjpeg
-, gdb, commonsLogging, librdf_rasqal, wrapGAppsHook
+, expat
-, gnome, glib, ncurses, libepoxy, gpgme, abseil-cpp
+, freetype
+, libwpd
+, libxml2
+, db
+, curl
+, fontconfig
+, libsndfile
+, neon
+, bison
+, flex
+, zip
+, unzip
+, gtk3
+, libmspack
+, getopt
+, file
+, cairo
+, which
+, icu
+, boost
+, jdk
+, ant
+, cups
+, xorg
+, fontforge
+, jre_minimal
+, openssl
+, gperf
+, cppunit
+, poppler
+, util-linux
+, librsvg
+, libGLU
+, libGL
+, bsh
+, CoinMP
+, libwps
+, libabw
+, libmysqlclient
+, autoconf
+, automake
+, openldap
+, bash
+, hunspell
+, librdf_redland
+, nss
+, nspr
+, libwpg
+, dbus-glib
+, clucene_core
+, libcdr
+, lcms
+, unixODBC
+, mdds
+, sane-backends
+, mythes
+, libexttextcat
+, libvisio
+, fontsConf
+, pkg-config
+, bluez5
+, libtool
+, carlito
+, libatomic_ops
+, graphite2
+, harfbuzz
+, libodfgen
+, libzmf
+, librevenge
+, libe-book
+, libmwaw
+, glm
+, gst_all_1
+, gdb
+, commonsLogging
+, librdf_rasqal
+, wrapGAppsHook
+, gnome
+, glib
+, ncurses
+, libepoxy
+, gpgme
+, abseil-cpp
 , langs ? [ "ca" "cs" "da" "de" "en-GB" "en-US" "eo" "es" "fr" "hu" "it" "ja" "nl" "pl" "pt" "pt-BR" "ro" "ru" "sl" "uk" "zh-CN" ]
 , withHelp ? true
-, kdeIntegration ? false, mkDerivation ? null, qtbase ? null, qtx11extras ? null
+, kdeIntegration ? false
-, ki18n ? null, kconfig ? null, kcoreaddons ? null, kio ? null, kwindowsystem ? null
+, mkDerivation ? null
+, qtbase ? null
+, qtx11extras ? null
+, ki18n ? null
+, kconfig ? null
+, kcoreaddons ? null
+, kio ? null
+, kwindowsystem ? null
 , wrapQtAppsHook ? null
 , variant ? "fresh"
+, symlinkJoin
 } @ args:
 
 assert builtins.elem variant [ "fresh" "still" ];
 
 let
+  inherit (lib)
+    flatten flip
+    concatMapStrings concatMapStringsSep concatStringsSep
+    getDev getLib
+    optional optionals optionalString;
+
   jre' = jre_minimal.override {
     modules = [ "java.base" "java.desktop" "java.logging" ];
   };
@@ -34,27 +130,43 @@ let
 
   inherit (primary-src) major minor subdir version;
 
-  langsSpaces = lib.concatStringsSep " " langs;
+  langsSpaces = concatStringsSep " " langs;
 
   mkDrv = if kdeIntegration then mkDerivation else stdenv.mkDerivation;
 
   srcs = {
     third_party =
-      map (x : ((fetchurl {inherit (x) url sha256 name;}) // {inherit (x) md5name md5;}))
+      map (x: ((fetchurl { inherit (x) url sha256 name; }) // { inherit (x) md5name md5; }))
-      (importVariant "download.nix" ++ [
+        (importVariant "download.nix" ++ [
-        (rec {
+          (rec {
-          name = "unowinreg.dll";
+            name = "unowinreg.dll";
-          url = "https://dev-www.libreoffice.org/extern/${md5name}";
+            url = "https://dev-www.libreoffice.org/extern/${md5name}";
-          sha256 = "1infwvv1p6i21scywrldsxs22f62x85mns4iq8h6vr6vlx3fdzga";
+            sha256 = "1infwvv1p6i21scywrldsxs22f62x85mns4iq8h6vr6vlx3fdzga";
-          md5 = "185d60944ea767075d27247c3162b3bc";
+            md5 = "185d60944ea767075d27247c3162b3bc";
-          md5name = "${md5}-${name}";
+            md5name = "${md5}-${name}";
-        })
+          })
-      ]);
+        ]);
 
     translations = primary-src.translations;
     help = primary-src.help;
   };
-in (mkDrv rec {
+
+  # See `postPatch` for details
+  kdeDeps = symlinkJoin {
+    name = "libreoffice-kde-dependencies-${version}";
+    paths = flatten (map (e: [ (getDev e) (getLib e) ]) [
+      qtbase
+      qtx11extras
+      kconfig
+      kcoreaddons
+      ki18n
+      kio
+      kwindowsystem
+    ]);
+  };
+
+in
+(mkDrv rec {
   pname = "libreoffice";
   inherit version;
 
@@ -71,10 +183,10 @@ in (mkDrv rec {
 
   postUnpack = ''
     mkdir -v $sourceRoot/${tarballPath}
-  '' + (lib.flip lib.concatMapStrings srcs.third_party (f: ''
+  '' + (flip concatMapStrings srcs.third_party (f: ''
-      ln -sfv ${f} $sourceRoot/${tarballPath}/${f.md5name}
+    ln -sfv ${f} $sourceRoot/${tarballPath}/${f.md5name}
-      ln -sfv ${f} $sourceRoot/${tarballPath}/${f.name}
+    ln -sfv ${f} $sourceRoot/${tarballPath}/${f.name}
-    ''))
+  ''))
   + ''
     ln -sv ${srcs.help} $sourceRoot/${tarballPath}/${srcs.help.name}
     ln -svf ${srcs.translations} $sourceRoot/${tarballPath}/${srcs.translations.name}
@@ -97,16 +209,20 @@ in (mkDrv rec {
 
   ### QT/KDE
   #
-  # We have to resort to the ugly patching of configure.ac as it assumes that
+  # configure.ac assumes that the first directory that contains headers and
-  # the first directory that contains headers and libraries during the check
+  # libraries during its checks contains *all* the relevant headers/libs which
-  # contains all the relevant headers/libs which doesn't work with both as they
+  # obviously doesn't work for us, so we have 2 options:
-  # are in multiple directories due to each having their own derivation.
+  #
-  postPatch = let
+  # 1. patch configure.ac in order to specify the direct paths to various Qt/KDE
-    inc = e: path:
+  # dependencies which is ugly and brittle, or
-      "${lib.getDev e}/include/KF5/${path}";
+  #
-    libs = list:
+  # 2. use symlinkJoin to pull in the relevant dependencies and just patch in
-      lib.concatMapStringsSep " " (e: "-L${lib.getLib e}/lib") list;
+  # that path which is *also* ugly, but far less likely to break
-  in ''
+  #
+  # The 2nd option is not very Nix'y, but I'll take robust over nice any day.
+  # Additionally, it's much easier to fix if LO breaks on the next upgrade (just
+  # add the missing dependencies to it).
+  postPatch = ''
     substituteInPlace shell/source/unix/exec/shellexec.cxx \
       --replace /usr/bin/xdg-open ${if kdeIntegration then "kde-open5" else "xdg-open"}
 
@@ -119,21 +235,12 @@ in (mkDrv rec {
     substituteInPlace configure.ac --replace \
       'GPGMEPP_CFLAGS=-I/usr/include/gpgme++' \
       'GPGMEPP_CFLAGS=-I${gpgme.dev}/include/gpgme++'
-  '' + lib.optionalString kdeIntegration ''
+  '' + optionalString kdeIntegration ''
-      substituteInPlace configure.ac \
+    substituteInPlace configure.ac \
-        --replace kcoreaddons_version.h KCoreAddons/kcoreaddons_version.h \
+      --replace '$QT5INC ' '$QT5INC ${kdeDeps}/include ' \
-        --replace '$QT5INC'             ${qtbase.dev}/include \
+      --replace '$QT5LIB ' '$QT5LIB ${kdeDeps}/lib ' \
-        --replace '$QT5LIB'             ${qtbase.out}/lib \
+      --replace '$KF5INC ' '$KF5INC ${kdeDeps}/include ${kdeDeps}/include/KF5 '\
-        --replace '-I$qt5_incdir '      '-I${qtx11extras.dev}/include '\
+      --replace '$KF5LIB ' '$KF5LIB ${kdeDeps}/lib '
-        --replace '-L$qt5_libdir '      '${libs [ qtbase qtx11extras ]} ' \
-        --replace '$KF5INC'             ${kcoreaddons.dev}/include \
-        --replace '$KF5LIB'             ${kcoreaddons.out}/lib \
-        --replace '$kf5_incdir/KCore'   ${inc kcoreaddons "KCore"} \
-        --replace '$kf5_incdir/KI18n'   ${inc ki18n "KI18n"} \
-        --replace '$kf5_incdir/KConfig' ${inc kconfig "KConfig"} \
-        --replace '$kf5_incdir/KWindow' ${inc kwindowsystem "KWindow"} \
-        --replace '$kf5_incdir/KIO'     ${inc kio "KIO"} \
-        --replace '-L$kf5_libdir '      '${libs [ kconfig kcoreaddons ki18n kio kwindowsystem ]} '
   '';
 
   dontUseCmakeConfigure = true;
@@ -239,18 +346,16 @@ in (mkDrv rec {
     ''
     # This to avoid using /lib:/usr/lib at linking
     + ''
-    sed -i '/gb_LinkTarget_LDFLAGS/{ n; /rpath-link/d;}' solenv/gbuild/platform/unxgcc.mk
+      sed -i '/gb_LinkTarget_LDFLAGS/{ n; /rpath-link/d;}' solenv/gbuild/platform/unxgcc.mk
 
-    find -name "*.cmd" -exec sed -i s,/lib:/usr/lib,, {} \;
+      find -name "*.cmd" -exec sed -i s,/lib:/usr/lib,, {} \;
     '';
 
   makeFlags = [ "SHELL=${bash}/bin/bash" ];
 
   enableParallelBuilding = true;
 
-  buildPhase = ''
+  buildTargets = [ "build-nocheck" ];
-    make build-nocheck
-  '';
 
   doCheck = true;
 
@@ -278,19 +383,18 @@ in (mkDrv rec {
 
     mkdir -p $dev
     cp -r include $dev
-  '' + lib.optionalString kdeIntegration ''
+  '' + optionalString kdeIntegration ''
-      for prog in $out/bin/*
+    for prog in $out/bin/*; do
-      do
+      wrapQtApp $prog
-        wrapQtApp $prog
+    done
-      done
   '';
 
   dontWrapQtApps = true;
 
   configureFlags = [
     (if withHelp then "" else "--without-help")
-    "--with-boost=${boost.dev}"
+    "--with-boost=${getDev boost}"
-    "--with-boost-libdir=${boost.out}/lib"
+    "--with-boost-libdir=${getLib boost}/lib"
     "--with-beanshell-jar=${bsh}"
     "--with-vendor=NixOS"
     "--disable-report-builder"
@@ -299,7 +403,7 @@ in (mkDrv rec {
     "--enable-dbus"
     "--enable-release-build"
     "--enable-epm"
-    "--with-ant-home=${ant}/lib/ant"
+    "--with-ant-home=${getLib ant}/lib/ant"
     "--with-system-cairo"
     "--with-system-libs"
     "--with-system-headers"
@@ -347,44 +451,128 @@ in (mkDrv rec {
     # https://github.com/NixOS/nixpkgs/commit/5c5362427a3fa9aefccfca9e531492a8735d4e6f
     "--without-system-orcus"
     "--without-system-xmlsec"
-  ] ++ lib.optionals kdeIntegration [
+  ] ++ optionals kdeIntegration [
     "--enable-kf5"
     "--enable-qt5"
     "--enable-gtk3-kde5"
   ];
 
-  checkPhase = ''
+  checkTarget = concatStringsSep " " [
-    make unitcheck
+    "unitcheck"
-    make slowcheck
+    "slowcheck"
-  '';
+  ];
 
   nativeBuildInputs = [
-    gdb fontforge autoconf automake bison pkg-config libtool jdk
+    autoconf
-  ] ++ lib.optional (!kdeIntegration) wrapGAppsHook
+    automake
-    ++ lib.optional kdeIntegration wrapQtAppsHook;
+    bison
-
+    fontforge
-  buildInputs = with xorg;
+    gdb
-    [ ant ArchiveZip boost box2d cairo clucene_core
+    jdk
-      IOCompress cppunit cups curl db dbus-glib expat file flex fontconfig
+    libtool
-      freetype getopt gperf gtk3
+    pkg-config
-      hunspell icu jre' lcms libcdr libexttextcat unixODBC libjpeg
+  ]
-      libmspack librdf_redland librsvg libsndfile libvisio libwpd libwpg libX11
+  ++ [ (if kdeIntegration then wrapQtAppsHook else wrapGAppsHook) ];
-      libXaw libXext libXi libXinerama libxml2 libxslt libXtst
+
-      libXdmcp libpthreadstubs libGLU libGL mythes
+  buildInputs = with xorg; [
-      glib libmysqlclient
+    ArchiveZip
-      neon nspr nss openldap openssl pam perl pkg-config poppler
+    CoinMP
-      python3 sane-backends unzip which zip zlib
+    IOCompress
-      mdds bluez5 libwps libabw libzmf
+    abseil-cpp
-      libxshmfence libatomic_ops graphite2 harfbuzz gpgme util-linux
+    ant
-      librevenge libe-book libmwaw glm ncurses libepoxy
+    bluez5
-      libodfgen CoinMP librdf_rasqal gnome.adwaita-icon-theme gettext abseil-cpp
+    boost
-    ]
+    box2d
-    ++ (with gst_all_1; [
+    cairo
-      gstreamer
+    clucene_core
-      gst-plugins-base gst-plugins-good gst-plugins-bad gst-plugins-ugly
+    cppunit
-      gst-libav
+    cups
-    ])
+    curl
-    ++ lib.optional kdeIntegration [ qtbase qtx11extras kcoreaddons kio ];
+    db
+    dbus-glib
+    expat
+    file
+    flex
+    fontconfig
+    freetype
+    getopt
+    gettext
+    glib
+    glm
+    gnome.adwaita-icon-theme
+    gperf
+    gpgme
+    graphite2
+    gtk3
+    harfbuzz
+    hunspell
+    icu
+    jre'
+    lcms
+    libGL
+    libGLU
+    libX11
+    libXaw
+    libXdmcp
+    libXext
+    libXi
+    libXinerama
+    libXtst
+    libabw
+    libatomic_ops
+    libcdr
+    libe-book
+    libepoxy
+    libexttextcat
+    libjpeg
+    libmspack
+    libmwaw
+    libmysqlclient
+    libodfgen
+    libpthreadstubs
+    librdf_rasqal
+    librdf_redland
+    librevenge
+    librsvg
+    libsndfile
+    libvisio
+    libwpd
+    libwpg
+    libwps
+    libxml2
+    libxshmfence
+    libxslt
+    libzmf
+    mdds
+    mythes
+    ncurses
+    neon
+    nspr
+    nss
+    openldap
+    openssl
+    pam
+    perl
+    pkg-config
+    poppler
+    python3
+    sane-backends
+    unixODBC
+    unzip
+    util-linux
+    which
+    zip
+    zlib
+  ]
+  ++ (with gst_all_1; [
+    gst-libav
+    gst-plugins-bad
+    gst-plugins-base
+    gst-plugins-good
+    gst-plugins-ugly
+    gstreamer
+  ])
+  ++ optionals kdeIntegration [ qtbase qtx11extras kcoreaddons kio ];
 
   passthru = {
     inherit srcs;

pkgs/applications/science/electronics/vhd2vl/default.nix

@@ -1,6 +1,5 @@
 { lib, stdenv
 , fetchFromGitHub
-, fetchpatch
 , bison
 , flex
 , verilog
@@ -19,12 +18,8 @@ stdenv.mkDerivation rec {
   };
 
   patches = lib.optionals (!stdenv.isAarch64) [
-    # fix build with verilog 11.0 - https://github.com/ldoolitt/vhd2vl/pull/15
+    # fix build with verilog 11.0
-    # for some strange reason, this is not needed for aarch64
+    ./test.patch
-    (fetchpatch {
-      url = "https://github.com/ldoolitt/vhd2vl/commit/ce9b8343ffd004dfe8779a309f4b5a594dbec45e.patch";
-      sha256 = "1qaqhm2mk66spb2dir9n91b385rarglc067js1g6pcg8mg5v3hhf";
-    })
   ];
 
   nativeBuildInputs = [
@@ -37,6 +32,13 @@ stdenv.mkDerivation rec {
     verilog
   ];
 
+  # the "translate" target both (a) builds the software and (b) runs
+  # the tests (without validating the results)
+  buildTargets = [ "translate" ];
+
+  # the "diff" target examines the test results
+  checkTarget = "diff";
+
   installPhase = ''
     runHook preInstall
     install -D -m755 src/vhd2vl $out/bin/vdh2vl

pkgs/applications/science/electronics/vhd2vl/test.patch

@@ -0,0 +1,35 @@
+--- a/translated_examples/fifo.v  1970-01-01 00:00:01.000000000 +0000
++++ a/temp/verilog/fifo.v 2022-05-11 03:44:43.173604945 +0000
+@@ -107,7 +107,7 @@
+   //--- Read address counter --------------
+   //---------------------------------------
+   assign add_RD_CE = (iempty == 1'b1) ? 1'b0 : (RD == 1'b0) ? 1'b0 : 1'b1;
+-  assign n_add_RD = (add_RD) + 4'h1;
++  assign n_add_RD = add_RD + 4'h1;
+   always @(posedge clk_RD, posedge rst) begin
+     if((rst == 1'b1)) begin
+       add_RD <= {5{1'b0}};
+diff -u '--exclude=Makefile' '--exclude-from=examples/exclude' translated_examples/test.v temp/verilog/test.v
+--- a/translated_examples/test.v  1970-01-01 00:00:01.000000000 +0000
++++ a/temp/verilog/test.v 2022-05-11 03:44:43.189604945 +0000
+@@ -125,7 +125,7 @@
+     endcase
+   end
+
+-  assign code1[1:0] = a[6:5] ^ ({a[4],b[6]});
++  assign code1[1:0] = a[6:5] ^ {a[4],b[6]};
+   // Asynch process
+   always @(we, addr, config1, bip) begin
+     if(we == 1'b1) begin
+diff -u '--exclude=Makefile' '--exclude-from=examples/exclude' translated_examples/withselect.v temp/verilog/withselect.v
+--- a/translated_examples/withselect.v    1970-01-01 00:00:01.000000000 +0000
++++ a/temp/verilog/withselect.v   2022-05-11 03:44:43.193604945 +0000
+@@ -33,7 +33,7 @@
+     endcase
+   end
+
+-  assign code1[1:0] = a[6:5] ^ ({a[4],b[6]});
++  assign code1[1:0] = a[6:5] ^ {a[4],b[6]};
+   assign foo = {(((1 + 1))-((0))+1){1'b0}};
+   assign egg = {78{1'b0}};
+   assign baz = {(((bus_width * 4))-((bus_width * 3 - 1))+1){1'b1}};

pkgs/applications/science/logic/coq/default.nix

@@ -70,9 +70,10 @@ let
       { case = range "8.7" "8.10";  out = ocamlPackages_4_09; }
       { case = range "8.5" "8.6";   out = ocamlPackages_4_05; }
     ] ocamlPackages_4_12;
-  ocamlNativeBuildInputs = [ ocamlPackages.ocaml ocamlPackages.findlib ]
+  ocamlNativeBuildInputs = [ ocamlPackages.ocaml ]
     ++ optional (coqAtLeast "8.14") ocamlPackages.dune_2;
-  ocamlBuildInputs = []
+  ocamlPropagatedNativeBuildInputs = [ ocamlPackages.findlib ];
+  ocamlPropagatedBuildInputs = [ ]
     ++ optional (!coqAtLeast "8.10") ocamlPackages.camlp5
     ++ optional (!coqAtLeast "8.13") ocamlPackages.num
     ++ optional (coqAtLeast "8.13") ocamlPackages.zarith;
@@ -82,7 +83,8 @@ self = stdenv.mkDerivation {
 
   passthru = {
     inherit coq-version;
-    inherit ocamlPackages ocamlBuildInputs ocamlNativeBuildInputs;
+    inherit ocamlPackages ocamlNativeNuildInputs;
+    inherit ocamlPropagatedBuildInputs ocamlPropagatedNativeBuildInputs;
     # For compatibility
     inherit (ocamlPackages) ocaml camlp5 findlib num ;
     emacsBufferSetup = pkgs: ''
@@ -136,13 +138,16 @@ self = stdenv.mkDerivation {
     ++ optional buildIde copyDesktopItems
     ++ optional (buildIde && coqAtLeast "8.10") wrapGAppsHook
     ++ optional (!coqAtLeast "8.6") gnumake42;
-  buildInputs = [ ncurses ] ++ ocamlBuildInputs
+  buildInputs = [ ncurses ]
     ++ optionals buildIde
       (if coqAtLeast "8.10"
        then [ ocamlPackages.lablgtk3-sourceview3 glib gnome.adwaita-icon-theme ]
        else [ ocamlPackages.lablgtk ])
   ;
 
+  propagatedNativeBuildInputs = ocamlPropagatedNativeBuildInputs;
+  propagatedBuildInputs = ocamlPropagatedBuildInputs;
+
   postPatch = ''
     UNAME=$(type -tp uname)
     RM=$(type -tp rm)

pkgs/applications/science/logic/monosat/default.nix

@@ -65,7 +65,7 @@ let
     };
   };
 
-  python = { buildPythonPackage, cython }: buildPythonPackage {
+  python = { buildPythonPackage, cython, pytestCheckHook }: buildPythonPackage {
     inherit pname version src patches;
 
     propagatedBuildInputs = [ core cython ];
@@ -85,5 +85,12 @@ let
       substituteInPlace setup.py \
         --replace 'library_dir = "../../../../"' 'library_dir = "${core}/lib/"'
     '';
+
+    checkInputs = [ pytestCheckHook ];
+
+    disabledTests = [
+      "test_assertAtMostOne"
+      "test_assertEqual"
+    ];
   };
 in core

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

@@ -1,5 +1,4 @@
-{ lib, stdenv, fetchurl, fetchFromGitHub
+{ lib, stdenv, fetchFromGitHub
-, assembleReductionMatrix ? false
 , useCoefficients ? false
 , indicateProgress ? false
 , useGoogleHashmap ? false, sparsehash ? null
@@ -14,7 +13,7 @@ assert useGoogleHashmap -> sparsehash != null;
 
 let
   inherit (lib) optional;
-  version = "1.0";
+  version = "1.2.1";
 in
 stdenv.mkDerivation {
   pname = "ripser";
@@ -23,25 +22,17 @@ stdenv.mkDerivation {
   src = fetchFromGitHub {
     owner = "Ripser";
     repo = "ripser";
-    rev = "f69c6af6ca6883dd518c48faf41cf8901c379598";
+    rev = "v${version}";
-    sha256 = "1mw2898s7l29hgajsaf75bs9bjn2sn4g2mvmh41a602jpwp9r0rz";
+    sha256 = "sha256-BxmkPQ/nl5cF+xwQMTjXnLgkLgdmT/39y7Kzl2wDfpE=";
   };
 
-  #Patch from dev branch to make compilation work.
-  #Will be removed when it gets merged into master.
-  patches = [(fetchurl {
-    url = "https://github.com/Ripser/ripser/commit/dc78d8ce73ee35f3828f0aad67a4e53620277ebf.patch";
-    sha256 = "1y93aqpqz8fm1cxxrf90dhh67im3ndkr8dnxgbw5y96296n4r924";
-  })];
-
   buildInputs = optional useGoogleHashmap sparsehash;
 
   buildFlags = [
     "-std=c++11"
-    "-Ofast"
+    "-O3"
     "-D NDEBUG"
   ]
-  ++ optional assembleReductionMatrix "-D ASSEMBLE_REDUCTION_MATRIX"
   ++ optional useCoefficients "-D USE_COEFFICIENTS"
   ++ optional indicateProgress "-D INDICATE_PROGRESS"
   ++ optional useGoogleHashmap "-D USE_GOOGLE_HASHMAP"

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

@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchurl, wxGTK, subversion, apr, aprutil, python2 }:
+{ lib, stdenv, fetchurl, wxGTK, subversion, apr, aprutil, python3, fetchpatch }:
 
 stdenv.mkDerivation rec {
   pname = "rapidsvn";
@@ -9,13 +9,28 @@ stdenv.mkDerivation rec {
     sha256 = "1bmcqjc12k5w0z40k7fkk8iysqv4fw33i80gvcmbakby3d4d4i4p";
   };
 
-  buildInputs = [ wxGTK subversion apr aprutil python2 ];
+  buildInputs = [ wxGTK subversion apr aprutil python3 ];
+
+  NIX_CFLAGS_COMPILE = [ "-std=c++14" ];
 
   configureFlags = [ "--with-svn-include=${subversion.dev}/include"
     "--with-svn-lib=${subversion.out}/lib" ];
 
   patches = [
     ./fix-build.patch
+    # Python 3 compatibility patches
+    (fetchpatch {
+      url = "https://github.com/RapidSVN/RapidSVN/pull/44/commits/2e26fd5d6a413d6c3a055c17ac4840b95d1537e9.patch";
+      hash = "sha256-8acABzscgZh1bfAt35KHfU+nfaiO7P1b+lh34Bj0REI=";
+    })
+    (fetchpatch {
+      url = "https://github.com/RapidSVN/RapidSVN/pull/44/commits/92927af764f92b3731333ed3dba637f98611167a.patch";
+      hash = "sha256-4PdShGcfFwxjdI3ygbnKFAa8l9dGERq/xSl54WisgKM=";
+    })
+    (fetchpatch {
+      url = "https://github.com/RapidSVN/RapidSVN/pull/44/commits/3e375f11d94cb8faddb8b7417354a9fb51f304ec.patch";
+      hash = "sha256-BUpCMEH7jctOLtJktDUE52bxexfLemLItZ0IgdAnq9g=";
+    })
   ];
 
   meta = {
@@ -23,5 +38,7 @@ stdenv.mkDerivation rec {
     homepage = "http://rapidsvn.tigris.org/";
     license = lib.licenses.gpl3Plus;
     maintainers = [ lib.maintainers.viric ];
+    platforms = lib.platforms.unix;
+    broken = stdenv.isDarwin;
   };
 }

pkgs/applications/virtualization/podman/default.nix

@@ -17,13 +17,13 @@
 
 buildGoModule rec {
   pname = "podman";
-  version = "4.0.3";
+  version = "4.1.0";
 
   src = fetchFromGitHub {
     owner = "containers";
     repo = "podman";
     rev = "v${version}";
-    sha256 = "sha256-o/CIs+3LnbaUUpOQI1hijrxH7f1qBnrQw56TJ18jKQw=";
+    sha256 = "sha256-3MR4ZhkhMLAK3KHu7JEV9z1/wlyCkxfx1i267TGxwt8=";
   };
 
   vendorSha256 = null;
@@ -97,5 +97,8 @@ buildGoModule rec {
     changelog = "https://github.com/containers/podman/blob/v${version}/RELEASE_NOTES.md";
     license = licenses.asl20;
     maintainers = with maintainers; [ marsam ] ++ teams.podman.members;
+    # requires >= 10.13 SDK https://github.com/NixOS/nixpkgs/issues/101229
+    # Undefined symbols for architecture x86_64: "_utimensat"
+    broken = stdenv.isDarwin && stdenv.isx86_64;
   };
 }

pkgs/applications/virtualization/runc/default.nix

@@ -16,13 +16,13 @@
 
 buildGoModule rec {
   pname = "runc";
-  version = "1.1.1";
+  version = "1.1.2";
 
   src = fetchFromGitHub {
     owner = "opencontainers";
     repo = "runc";
     rev = "v${version}";
-    sha256 = "sha256-6g2km+Y45INo2MTWMFFQFhfF8DAR5Su+YrJS8k3LYBY=";
+    sha256 = "sha256-tMneqB81w8lQp5RWWCjALyKbOY3xog+oqb6cYKasG/8=";
   };
 
   vendorSha256 = null;

pkgs/build-support/coq/default.nix

@@ -1,4 +1,4 @@
-{ lib, stdenv, coqPackages, coq, fetchzip }@args:
+{ lib, stdenv, coqPackages, coq, which, fetchzip }@args:
 let lib = import ./extra-lib.nix {inherit (args) lib;}; in
 with builtins; with lib;
 let
@@ -15,8 +15,12 @@ in
   releaseRev ? (v: v),
   displayVersion ? {},
   release ? {},
+  buildInputs ? [],
+  nativeBuildInputs ? [],
   extraBuildInputs ? [],
   extraNativeBuildInputs ? [],
+  overrideBuildInputs ? [],
+  overrideNativeBuildInputs ? [],
   namePrefix ? [ "coq" ],
   enableParallelBuilding ? true,
   extraInstallFlags ? [],
@@ -35,7 +39,11 @@ let
   args-to-remove = foldl (flip remove) ([
     "version" "fetcher" "repo" "owner" "domain" "releaseRev"
     "displayVersion" "defaultVersion" "useMelquiondRemake"
-    "release" "extraBuildInputs" "extraNativeBuildInputs" "extraPropagatedBuildInputs" "namePrefix"
+    "release"
+    "buildInputs" "nativeBuildInputs"
+    "extraBuildInputs" "extraNativeBuildInputs"
+    "overrideBuildInputs" "overrideNativeBuildInputs"
+    "namePrefix"
     "meta" "useDune2ifVersion" "useDune2" "opam-name"
     "extraInstallFlags" "setCOQBIN" "mlPlugin"
     "dropAttrs" "dropDerivationAttrs" "keepAttrs" ] ++ dropAttrs) keepAttrs;
@@ -57,9 +65,16 @@ let
     ] "") + optionalString (v == null) "-broken";
   append-version = p: n: p + display-pkg n "" coqPackages.${n}.version + "-";
   prefix-name = foldl append-version "" namePrefix;
-  var-coqlib-install =
-    (optionalString (versions.isGe "8.7" coq.coq-version || coq.coq-version == "dev") "COQMF_") + "COQLIB";
   useDune2 = args.useDune2 or (useDune2ifVersion fetched.version);
+  coqlib-flags = switch coq.coq-version [
+    { case = v: versions.isLe "8.6" v && v != "dev" ;
+      out = [ "COQLIB=$(out)/lib/coq/${coq.coq-version}/" ]; }
+  ] [ "COQLIBINSTALL=$(out)/lib/coq/${coq.coq-version}/user-contrib"
+      "COQPLUGININSTALL=$(OCAMLFIND_DESTDIR)" ];
+  docdir-flags = switch coq.coq-version [
+    { case = v: versions.isLe "8.6" v && v != "dev";
+      out = [ "DOCDIR=$(out)/share/coq/${coq.coq-version}/" ]; }
+  ] [ "COQDOCINSTALL=$(out)/share/coq/${coq.coq-version}/user-contrib" ];
 in
 
 stdenv.mkDerivation (removeAttrs ({
@@ -68,12 +83,12 @@ stdenv.mkDerivation (removeAttrs ({
 
   inherit (fetched) version src;
 
-  nativeBuildInputs = [ coq ]
+  nativeBuildInputs = args.overrideNativeBuildInputs
-    ++ optionals useDune2 [coq.ocaml coq.ocamlPackages.dune_2]
+    or ([ which ] ++ optional useDune2 coq.ocamlPackages.dune_2
-    ++ optionals mlPlugin coq.ocamlNativeBuildInputs
+        ++ optional (useDune2 || mlPlugin) coq.ocaml
-    ++ extraNativeBuildInputs;
+        ++ (args.nativeBuildInputs or []) ++ extraNativeBuildInputs);
-  buildInputs = optionals mlPlugin coq.ocamlBuildInputs
+  buildInputs = args.overrideBuildInputs
-    ++ extraBuildInputs;
+    or ([ coq ] ++ (args.buildInputs or []) ++ extraBuildInputs);
   inherit enableParallelBuilding;
 
   meta = ({ platforms = coq.meta.platforms; } //
@@ -88,9 +103,7 @@ stdenv.mkDerivation (removeAttrs ({
 // (optionalAttrs setCOQBIN { COQBIN = "${coq}/bin/"; })
 // (optionalAttrs (!args?installPhase && !args?useMelquiondRemake) {
   installFlags =
-    [ "${var-coqlib-install}=$(out)/lib/coq/${coq.coq-version}/" ] ++
+    [ "DESTDIR=$(out)" ] ++ coqlib-flags ++ docdir-flags ++
-    optional (match ".*doc$" (args.installTargets or "") != null)
-      "DOCDIR=$(out)/share/coq/${coq.coq-version}/" ++
     extraInstallFlags;
 })
 // (optionalAttrs useDune2 {

pkgs/data/documentation/nginx-doc/default.nix

@@ -0,0 +1,40 @@
+{ lib, stdenv, libxml2, libxslt, fetchhg }:
+
+# Upstream maintains documentation (sources of https://nginx.org) in separate
+# mercurial repository, which do not correspond to particular git commit, but at
+# least has "introduced in version X.Y" comments.
+#
+# In other words, documentation does not necessary matches capabilities of
+# $out/bin/nginx, but we have no better options.
+stdenv.mkDerivation {
+  pname = "nginx-doc-unstable";
+  version = "2022-05-05";
+  src = fetchhg {
+    url = "https://hg.nginx.org/nginx.org";
+    rev = "a3aee2697d4e";
+    sha256 = "029n4mnmjw94h01qalmjgf1c2h3h7wm798xv5knk3padxiy4m28b";
+  };
+  patches = [ ./exclude-google-analytics.patch ];
+  nativeBuildInputs = [ libxslt libxml2 ];
+
+  # Generated documentation is not local-friendly, since it assumes that link to directory
+  # is the same as link to index.html in that directory, which is not how browsers behave
+  # with local filesystem.
+  #
+  # TODO: patch all relative links that do not end with .html.
+
+  # /en subdirectory must exist, relative links expect it.
+  installPhase = ''
+    mkdir -p $out/share/doc/nginx
+    mv libxslt/en $out/share/doc/nginx
+  '';
+
+  meta = with lib; {
+    description = "A reverse proxy and lightweight webserver (documentation)";
+    homepage    = "https://nginx.org/";
+    license     = licenses.bsd2;
+    platforms   = platforms.all;
+    priority    = 6;
+    maintainers = with maintainers; [ kaction ];
+  };
+}

pkgs/data/documentation/nginx-doc/exclude-google-analytics.patch

@@ -0,0 +1,29 @@
+Kill google analytics from local documentation.
+
+diff -r bb0a2fbdc886 xslt/ga.xslt
+--- a/xslt/ga.xslt	Mon Apr 06 11:17:11 2020 +0100
++++ b/xslt/ga.xslt	Thu Apr 09 10:29:02 2020 -0400
+@@ -6,23 +6,6 @@
+ <xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform" version="1.0">
+ 
+ <xsl:template name="ga">
+-
+-    <script>
+-        (function(w, d, s, l, i) {
+-            w[l] = w[l] || [];
+-            w[l].push({
+-                'gtm.start': new Date().getTime(),
+-                event: 'gtm.js'
+-            });
+-            var f = d.getElementsByTagName(s)[0],
+-                j = d.createElement(s),
+-                dl = l != 'dataLayer' ? '&amp;l=' + l : '';
+-            j.async = true;
+-            j.src = '//www.googletagmanager.com/gtm.js?id=' + i + dl;
+-            f.parentNode.insertBefore(j, f);
+-        })(window, document, 'script', 'dataLayer', 'GTM-TPSP33');
+-    </script>
+-
+ </xsl:template>
+ 
+ </xsl:stylesheet>

pkgs/desktops/pantheon/apps/elementary-calculator/default.nix

@@ -2,49 +2,41 @@
 , stdenv
 , fetchFromGitHub
 , nix-update-script
-, pkg-config
 , meson
 , ninja
-, vala
+, pkg-config
-, desktop-file-utils
-, libxml2
-, gtk3
 , python3
-, granite
+, vala
+, wrapGAppsHook4
+, granite7
+, gtk4
 , libgee
-, libhandy
-, appstream
-, wrapGAppsHook
 }:
 
 stdenv.mkDerivation rec {
   pname = "elementary-calculator";
-  version = "1.7.2";
+  version = "2.0.0";
 
   src = fetchFromGitHub {
     owner = "elementary";
     repo = "calculator";
     rev = version;
-    sha256 = "sha256-U0wXrw9ZJwkqZAtTTHmTzqYhwF9V2JZEZZdDak3kPIc=";
+    sha256 = "sha256-NE7x5vSfwakwJJe2VGRFiYc7GCB1M6xU5945EC6Em34=";
   };
 
   nativeBuildInputs = [
-    appstream
-    desktop-file-utils
-    libxml2
     meson
     ninja
     pkg-config
     python3
     vala
-    wrapGAppsHook
+    wrapGAppsHook4
   ];
 
   buildInputs = [
-    granite
+    granite7
-    gtk3
+    gtk4
     libgee
-    libhandy
   ];
 
   postPatch = ''

pkgs/desktops/pantheon/desktop/elementary-greeter/default.nix

@@ -30,13 +30,13 @@
 
 stdenv.mkDerivation rec {
   pname = "elementary-greeter";
-  version = "6.0.2";
+  version = "6.1.0";
 
   src = fetchFromGitHub {
     owner = "elementary";
     repo = "greeter";
     rev = version;
-    sha256 = "sha256-0chBM8JuCYgZXHneiSxSICZwBVm2Vgx+bas9wUjbnyg=";
+    sha256 = "sha256-CY+dPSyQ/ovSdI80uEipDdnWy1KjbZnwpn9sd8HrbPQ=";
   };
 
   patches = [

pkgs/development/compilers/alan/2.nix

@@ -14,6 +14,10 @@ stdenv.mkDerivation rec {
 
   makefile = "Makefile.unix";
 
+  # Add a workarounf for -fno-common tollchains like upstream gcc-10.
+  # alan-3 is already fixed, but the backport is nontrivial.
+  NIX_CFLAGS_COMPILE = "-fcommon";
+
   installPhase = ''
     mkdir -p $out/bin $out/share/alan2
     cp compiler/alan $out/bin/alan2

pkgs/development/compilers/go/1.18.nix

@@ -54,11 +54,11 @@ in
 
 stdenv.mkDerivation rec {
   pname = "go";
-  version = "1.18.1";
+  version = "1.18.2";
 
   src = fetchurl {
     url = "https://go.dev/dl/go${version}.src.tar.gz";
-    sha256 = "sha256-79Q+DxQC4IO3OgPURLe2V2u0xTmsRiCLY6kWtprKQIg=";
+    sha256 = "sha256-LETQPqLDQJITerkZumAvLCYaA40I60aFKKPzoo5WZ+I=";
   };
 
   # perl is used for testing go vet

pkgs/development/coq-modules/CoLoR/default.nix

@@ -20,7 +20,7 @@ with lib; mkCoqDerivation {
   release."1.4.0".rev    = "168c6b86c7d3f87ee51791f795a8828b1521589a";
   release."1.4.0".sha256 = "1d2whsgs3kcg5wgampd6yaqagcpmzhgb6a0hp6qn4lbimck5dfmm";
 
-  extraBuildInputs = [ bignums ];
+  propagatedBuildInputs = [ bignums ];
   enableParallelBuilding = false;
 
   meta = {

pkgs/development/coq-modules/HoTT/default.nix

@@ -8,7 +8,7 @@ with lib; mkCoqDerivation {
   release."20170921".rev    = "e3557740a699167e6adb1a65855509d55a392fa1";
   release."20170921".sha256 = "0zwfp8g62b50vmmbb2kmskj3v6w7qx1pbf43yw0hr7asdz2zbx5v";
 
-  extraBuildInputs = [ autoconf automake ];
+  nativeBuildInputs = [ autoconf automake ];
 
   preConfigure = ''
     patchShebangs ./autogen.sh

pkgs/development/coq-modules/QuickChick/default.nix

@@ -36,8 +36,7 @@ let recent = lib.versions.isGe "8.7" coq.coq-version; in
     "substituteInPlace Makefile --replace quickChickTool.byte quickChickTool.native";
 
   mlPlugin = true;
-  extraNativeBuildInputs = lib.optional recent coq.ocamlPackages.ocamlbuild;
+  nativeBuildInputs = lib.optional recent coq.ocamlPackages.ocamlbuild;
-  extraBuildInputs = lib.optional recent coq.ocamlPackages.num;
   propagatedBuildInputs = [ ssreflect ]
     ++ lib.optionals recent [ coq-ext-lib simple-io ];
   extraInstallFlags = [ "-f Makefile.coq" ];

pkgs/development/coq-modules/VST/default.nix

@@ -31,7 +31,7 @@ mkCoqDerivation {
   release."2.9".sha256 = "sha256:1adwzbl1pprrrwrm7cm493098fizxanxpv7nyfbvwdhgbhcnv6qf";
   release."2.8".sha256 = "sha256-cyK88uzorRfjapNQ6XgQEmlbWnDsiyLve5po1VG52q0=";
   releaseRev = v: "v${v}";
-  extraBuildInputs = [ ITree ];
+  buildInputs = [ ITree ];
   propagatedBuildInputs = [ compcert ];
 
   preConfigure = ''

pkgs/development/coq-modules/bignums/default.nix

@@ -5,7 +5,7 @@ with lib; mkCoqDerivation {
   owner = "coq";
   displayVersion = { bignums = ""; };
   inherit version;
-  defaultVersion = if versions.isGe "8.5" coq.coq-version
+  defaultVersion = if versions.isGe "8.6" coq.coq-version
     then "${coq.coq-version}.0" else null;
 
   release."8.15.0".sha256 = "093klwlhclgyrba1iv18dyz1qp5f0lwiaa7y0qwvgmai8rll5fns";

pkgs/development/coq-modules/compcert/default.nix

@@ -1,5 +1,5 @@
 { lib, fetchzip, mkCoqDerivation, coq, flocq, compcert
-, ocamlPackages, fetchpatch, makeWrapper, coq2html
+, fetchpatch, makeWrapper, coq2html
 , stdenv, tools ? stdenv.cc
 , version ? null
 }:
@@ -15,9 +15,9 @@ let compcert = mkCoqDerivation rec {
   releaseRev = v: "v${v}";
 
   defaultVersion =  with versions; switch coq.version [
-      { case = range "8.8" "8.11"; out = "3.8"; }
+      { case = range "8.13" "8.15"; out = "3.10"; }
       { case = isEq "8.12"       ; out = "3.9"; }
-      { case = range "8.12" "8.15"; out = "3.10"; }
+      { case = range "8.8" "8.11"; out = "3.8"; }
     ] null;
 
   release = {
@@ -26,8 +26,9 @@ let compcert = mkCoqDerivation rec {
     "3.10".sha256 = "sha256:19rmx8r8v46101ij5myfrz60arqjy7q3ra3fb8mxqqi3c8c4l4j6";
   };
 
+  mlPlugin = true;
   nativeBuildInputs = [ makeWrapper ];
-  buildInputs = with ocamlPackages; [ ocaml findlib menhir menhirLib ] ++ [ coq coq2html ];
+  buildInputs = with coq.ocamlPackages; [ menhir menhirLib ] ++ [ coq2html ];
   propagatedBuildInputs = [ flocq ];
 
   enableParallelBuilding = true;
@@ -48,9 +49,13 @@ let compcert = mkCoqDerivation rec {
   '';
 
   installTargets = "documentation install";
+  installFlags = []; # trust ./configure
+  preInstall = ''
+    mkdir -p $out/share/man
+    mkdir -p $man/share
+  '';
   postInstall = ''
     # move man into place
-    mkdir -p $man/share
     mv $out/share/man/ $man/share/
 
     # move docs into place

pkgs/development/coq-modules/coq-bits/default.nix

@@ -1,34 +1,18 @@
-{ lib, mkCoqDerivation, coq, mathcomp, version ? null }:
+{ lib, mkCoqDerivation, coq, mathcomp-algebra, version ? null }:
 
 with lib; mkCoqDerivation {
   pname = "coq-bits";
   repo = "bits";
   inherit version;
-  defaultVersion =
+  defaultVersion = with versions; switch coq.coq-version [
-    if versions.isGe "8.10" coq.version
+    { case = isGe "8.10"; out = "1.1.0"; }
-    then "1.1.0"
+    { case = isGe "8.7";  out = "1.0.0"; }
-    else if versions.isGe "8.7" coq.version
+  ] null;
-    then "1.0.0"
-    else null;
 
-  release = {
+  release."1.1.0".sha256 = "sha256-TCw1kSXeW0ysIdLeNr+EGmpGumEE9i8tinEMp57UXaE=";
-    "1.0.0" = {
+  release."1.0.0".sha256 = "0nv5mdgrd075dpd8bc7h0xc5i95v0pkm0bfyq5rj6ii1s54dwcjl";
-      rev = "1.0.0";
-      sha256 = "0nv5mdgrd075dpd8bc7h0xc5i95v0pkm0bfyq5rj6ii1s54dwcjl";
-    };
-    "1.1.0" = {
-      rev = "1.1.0";
-      sha256 = "sha256-TCw1kSXeW0ysIdLeNr+EGmpGumEE9i8tinEMp57UXaE=";
-    };
-  };
-
-  extraBuildInputs = [ mathcomp.ssreflect mathcomp.fingroup ];
-  propagatedBuildInputs = [ mathcomp.algebra ];
 
-  installPhase = ''
+  propagatedBuildInputs = [ mathcomp-algebra ];
-    make -f Makefile CoqMakefile
-    make -f CoqMakefile COQLIB=$out/lib/coq/${coq.coq-version}/ install
-  '';
 
   meta = {
     description = "A formalization of bitset operations in Coq";

pkgs/development/coq-modules/coq-elpi/default.nix

@@ -7,7 +7,7 @@ with builtins; with lib; let
     { case = "8.13"; out = { version = "1.13.7"; };}
     { case = "8.14"; out = { version = "1.13.7"; };}
     { case = "8.15"; out = { version = "1.14.1"; };}
-  ] {});
+  ] { version = "1.14.1"; } );
 in mkCoqDerivation {
   pname = "elpi";
   repo  = "coq-elpi";
@@ -48,8 +48,8 @@ in mkCoqDerivation {
   release."1.6.0".sha256      = "0kf99i43mlf750fr7fric764mm495a53mg5kahnbp6zcjcxxrm0b";
   releaseRev = v: "v${v}";
 
-  extraNativeBuildInputs = [ which elpi ];
   mlPlugin = true;
+  propagatedBuildInputs = [ elpi ];
 
   meta = {
     description = "Coq plugin embedding ELPI.";

pkgs/development/coq-modules/coqeal/default.nix

@@ -1,6 +1,6 @@
 { coq, mkCoqDerivation, mathcomp, bignums, paramcoq, multinomials,
   mathcomp-real-closed,
-  lib, which, version ? null }:
+  lib, version ? null }:
 
 with lib;
 
@@ -22,7 +22,6 @@ with lib;
   release."1.0.4".sha256 = "1g5m26lr2lwxh6ld2gykailhay4d0ayql4bfh0aiwqpmmczmxipk";
   release."1.0.3".sha256 = "0hc63ny7phzbihy8l7wxjvn3haxx8jfnhi91iw8hkq8n29i23v24";
 
-  extraBuildInputs = [ which ];
   propagatedBuildInputs = [ mathcomp.algebra bignums paramcoq multinomials ];
 
   meta = {

pkgs/development/coq-modules/coqhammer/default.nix

@@ -28,8 +28,10 @@ with lib; mkCoqDerivation {
   release."1.3-coq8.12".sha256   = "1q1y3cwhd98pkm98g71fsdjz85bfwgcz2xn7s7wwmiraifv5l6z8";
   release."1.3-coq8.11".sha256   = "08zf8qfna7b9p2myfaz4g7bas3a1q1156x78n5isqivlnqfrjc1b";
   release."1.3-coq8.10".sha256   = "1fj8497ir4m79hyrmmmmrag01001wrby0h24wv6525vz0w5py3cd";
-  release."1.1.1-coq8.9".sha256  = "1knjmz4hr8vlp103j8n4fyb2lfxysnm512gh3m2kp85n6as6fvb9";
+  release."1.1.1-coq8.9" = { sha256 = "1knjmz4hr8vlp103j8n4fyb2lfxysnm512gh3m2kp85n6as6fvb9";
-  release."1.1-coq8.8".sha256    = "0ms086wp4jmrzyglb8wymchzyflflk01nsfsk4r6qv8rrx81nx9h";
+                             rev    = "f8b4d81a213aa1f25afbe53c7c9ca1b15e3d42bc"; };
+  release."1.1-coq8.8" =   { sha256 = "0ms086wp4jmrzyglb8wymchzyflflk01nsfsk4r6qv8rrx81nx9h";
+                             rev    = "c3cb54b4d5f33fab372d33c7189861368a08fa22"; };
 
   release."1.3.1-coq8.13".version  = "1.3.1";
   release."1.3.1-coq8.12".version  = "1.3.1";

pkgs/development/coq-modules/coqprime/default.nix

@@ -20,7 +20,6 @@ with lib; mkCoqDerivation {
   release."8.7.2".sha256 = "15zlcrx06qqxjy3nhh22wzy0rb4npc8l4nx2bbsfsvrisbq1qb7k";
   releaseRev = v: "v${v}";
 
-  extraBuildInputs = [ which ];
   propagatedBuildInputs = [ bignums ];
 
   meta = with lib; {

pkgs/development/coq-modules/coqtail-math/default.nix

@@ -14,9 +14,7 @@ mkCoqDerivation {
   release."8.14".sha256 = "sha256:1k8f8idjnx0mf4z479vcx55iz42rjxrbplbznv80m2famxakq03c";
   release."20201124".rev    = "5c22c3d7dcd8cf4c47cf84a281780f5915488e9e";
   release."20201124".sha256 = "sha256-wd+Lh7dpAD4zfpyKuztDmSFEZo5ZiFrR8ti2jUCVvoQ=";
-
+  mlPlugin = true;
-  extraNativeBuildInputs = with coq.ocamlPackages; [ ocaml findlib ];
-
   meta = {
     license = licenses.lgpl3Only;
     maintainers = [ maintainers.siraben ];

pkgs/development/coq-modules/coquelicot/default.nix

@@ -1,4 +1,4 @@
-{ lib, mkCoqDerivation, which, autoconf,
+{ lib, mkCoqDerivation, autoconf,
   coq, ssreflect, version ? null }:
 
 with lib; mkCoqDerivation {
@@ -16,7 +16,7 @@ with lib; mkCoqDerivation {
   release."3.0.2".sha256 = "1rqfbbskgz7b1bcpva8wh3v3456sq2364y804f94sc8y5sij23nl";
   releaseRev = v: "coquelicot-${v}";
 
-  extraNativeBuildInputs = [ which autoconf ];
+  nativeBuildInputs = [ autoconf ];
   propagatedBuildInputs = [ ssreflect ];
   useMelquiondRemake.logpath = "Coquelicot";
 

pkgs/development/coq-modules/dpdgraph/default.nix

@@ -39,9 +39,9 @@ mkCoqDerivation {
   release."0.6".sha256   = "0qvar8gfbrcs9fmvkph5asqz4l5fi63caykx3bsn8zf0xllkwv0n";
   releaseRev = v: "v${v}";
 
-  extraNativeBuildInputs = [ autoreconfHook ];
+  nativeBuildInputs = [ autoreconfHook ];
   mlPlugin = true;
-  extraBuildInputs = [ coq.ocamlPackages.ocamlgraph ];
+  buildInputs = [ coq.ocamlPackages.ocamlgraph ];
 
   # dpd_compute.ml uses deprecated Pervasives.compare
   # Versions prior to 0.6.5 do not have the WARN_ERR build flag

pkgs/development/coq-modules/fiat/HEAD.nix

@@ -8,10 +8,10 @@ with lib; mkCoqDerivation rec {
   inherit version;
   defaultVersion = if coq.coq-version == "8.5" then "2016-10-24" else null;
   release."2016-10-24".rev    = "7feb6c64be9ebcc05924ec58fe1463e73ec8206a";
-  release."2016-10-24".sha256 = "0griqc675yylf9rvadlfsabz41qy5f5idya30p5rv6ysiakxya64";
+  release."2016-10-24".sha256 = "16y57vibq3f5i5avgj80f4i3aw46wdwzx36k5d3pf3qk17qrlrdi";
 
   mlPlugin = true;
-  extraBuildInputs = [ python27 ];
+  buildInputs = [ python27 ];
 
   prePatch = "patchShebangs etc/coq-scripts";
 

pkgs/development/coq-modules/flocq/default.nix

@@ -1,4 +1,4 @@
-{ lib, which, autoconf, automake,
+{ lib, bash, autoconf, automake,
   mkCoqDerivation, coq, version ? null }:
 
 with lib; mkCoqDerivation {
@@ -16,7 +16,7 @@ with lib; mkCoqDerivation {
   release."2.6.1".sha256 = "0q5a038ww5dn72yvwn5298d3ridkcngb1dik8hdyr3xh7gr5qibj";
   releaseRev = v: "flocq-${v}";
 
-  nativeBuildInputs = [ which autoconf ];
+  nativeBuildInputs = [ bash autoconf ];
   mlPlugin = true;
   useMelquiondRemake.logpath = "Flocq";
 

pkgs/development/coq-modules/gappalib/default.nix

@@ -13,7 +13,7 @@ with lib; mkCoqDerivation {
   release."1.4.4".sha256 = "114q2hgw64j6kqa9mg3qcp1nlf0ia46z2xadq81fnkxqm856ml7l";
   releaseRev = v: "gappalib-coq-${v}";
 
-  extraNativeBuildInputs = [ which autoconf ];
+  nativeBuildInputs = [ autoconf ];
   mlPlugin = true;
   propagatedBuildInputs = [ flocq ];
   useMelquiondRemake.logpath = "Gappa";

pkgs/development/coq-modules/heq/default.nix

@@ -1,22 +1,26 @@
 {lib, fetchzip, mkCoqDerivation, coq, version ? null }:
 
+let fetcher = {rev, repo, owner, sha256, domain, ...}:
+  fetchzip {
+    url = "https://${domain}/${owner}/${repo}/download/${repo}-${rev}.zip";
+    inherit sha256;
+   }; in
 with lib; mkCoqDerivation {
   pname = "heq";
   repo = "Heq";
-  owner = "gil";
+  owner = "gil.hur";
-  domain = "mpi-sws.org";
+  domain = "sf.snu.ac.kr";
   inherit version fetcher;
   defaultVersion = if versions.isLt "8.8" coq.coq-version then "0.92" else null;
   release."0.92".sha256 = "0cf8y6728n81wwlbpq3vi7l2dbzi7759klypld4gpsjjp1y1fj74";
 
   mlPlugin = true;
-  propagatedBuildInputs = [ coq ];
-
-  extraInstallFlags = [ "COQLIB=$out/lib/coq/${coq.coq-version}" ];
   preBuild = "cd src";
 
+  extraInstallFlags = [ "COQLIB=$(out)/lib/coq/${coq.coq-version}/" ];
+
   meta = {
-    homepage = "https://www.mpi-sws.org/~gil/Heq/";
+    homepage = "https://ropas.snu.ac.kr/~gil.hur/Heq/";
     description = "Heq : a Coq library for Heterogeneous Equality";
     maintainers = with maintainers; [ jwiegley ];
   };

pkgs/development/coq-modules/hierarchy-builder/default.nix

@@ -1,4 +1,4 @@
-{ lib, mkCoqDerivation, which, coq, coq-elpi, version ? null }:
+{ lib, mkCoqDerivation, coq, coq-elpi, version ? null }:
 
 with lib; let hb = mkCoqDerivation {
   pname = "hierarchy-builder";
@@ -17,13 +17,10 @@ with lib; let hb = mkCoqDerivation {
   release."0.10.0".sha256 = "1a3vry9nzavrlrdlq3cys3f8kpq3bz447q8c4c7lh2qal61wb32h";
   releaseRev = v: "v${v}";
 
-  extraNativeBuildInputs = [ which ];
-
   propagatedBuildInputs = [ coq-elpi ];
 
   mlPlugin = true;
 
-  installFlags = [ "DESTDIR=$(out)" "COQMF_COQLIB=lib/coq/${coq.coq-version}" ];
   extraInstallFlags = [ "VFILES=structures.v" ];
 
   meta = {

pkgs/development/coq-modules/interval/default.nix

@@ -1,4 +1,5 @@
-{ lib, mkCoqDerivation, which, autoconf, coq, coquelicot, flocq, mathcomp-ssreflect, mathcomp-fingroup, bignums ? null, gnuplot_qt, version ? null }:
+{ lib, mkCoqDerivation, autoconf, coq, coquelicot, flocq,
+  mathcomp-ssreflect, mathcomp-fingroup, bignums ? null, gnuplot_qt, version ? null }:
 
 mkCoqDerivation rec {
   pname = "interval";
@@ -20,8 +21,9 @@ mkCoqDerivation rec {
   release."3.3.0".sha256 = "0lz2hgggzn4cvklvm8rpaxvwaryf37i8mzqajqgdxdbd8f12acsz";
   releaseRev = v: "interval-${v}";
 
-  extraNativeBuildInputs = [ which autoconf ];
+  nativeBuildInputs = [ autoconf ];
-  propagatedBuildInputs = [ bignums coquelicot flocq mathcomp-ssreflect mathcomp-fingroup ]
+  propagatedBuildInputs = lib.optional (lib.versions.isGe "8.6" coq.coq-version) bignums
+    ++ [ coquelicot flocq mathcomp-ssreflect mathcomp-fingroup ]
     ++ lib.optionals (lib.versions.isGe "4.2.0" defaultVersion) [ gnuplot_qt ];
   useMelquiondRemake.logpath = "Interval";
   mlPlugin = true;

pkgs/development/coq-modules/itauto/default.nix

@@ -17,7 +17,7 @@ mkCoqDerivation rec {
   ] null;
 
   mlPlugin = true;
-  extraNativeBuildInputs = (with coq.ocamlPackages; [ ocamlbuild ]);
+  nativeBuildInputs = (with coq.ocamlPackages; [ ocamlbuild ]);
   enableParallelBuilding = false;
 
   meta = {

pkgs/development/coq-modules/ltac2/default.nix

@@ -17,7 +17,6 @@ with lib; mkCoqDerivation {
   release."0.1-8.7".rev     = "v0.1-8.7";
   release."0.1-8.7".sha256  = "0l6wiwi4cvd0i324fb29i9mdh0ijlxzggw4mrjjy695l2qdnlgg0";
 
-  nativeBuildInputs = [ which ];
   mlPlugin = true;
 
   meta = {

pkgs/development/coq-modules/math-classes/default.nix

@@ -9,7 +9,7 @@ with lib; mkCoqDerivation {
   release."8.13.0".sha256 = "1ln7ziivfbxzbdvlhbvyg3v30jgblncmwcsam6gg3d1zz6r7cbby";
   release."8.15.0".sha256 = "10w1hm537k6jx8a8vghq1yx12rsa0sjk2ipv3scgir71ln30hllw";
 
-  extraBuildInputs = [ bignums ];
+  propagatedBuildInputs = [ bignums ];
 
   meta = {
     homepage = "https://math-classes.github.io";

pkgs/development/coq-modules/mathcomp/default.nix

@@ -10,9 +10,9 @@
 # See the documentation at doc/languages-frameworks/coq.section.md.        #
 ############################################################################
 
-{ lib, ncurses, which, graphviz, lua, fetchzip,
+{ lib, ncurses, graphviz, lua, fetchzip,
   mkCoqDerivation, recurseIntoAttrs, withDoc ? false, single ? false,
-  coqPackages, coq, ocamlPackages, version ? null }@args:
+  coqPackages, coq, version ? null }@args:
 with builtins // lib;
 let
   repo  = "math-comp";
@@ -60,8 +60,9 @@ let
         inherit version pname defaultVersion release releaseRev repo owner;
 
         mlPlugin = versions.isLe "8.6" coq.coq-version;
-        extraNativeBuildInputs = [ which ] ++ optionals withDoc [ graphviz lua ];
+        nativeBuildInputs = optionals withDoc [ graphviz lua ];
-        extraBuildInputs = [ ncurses ] ++ mathcomp-deps;
+        buildInputs = [ ncurses ];
+        propagatedBuildInputs = mathcomp-deps;
 
         buildFlags = optional withDoc "doc";
 

pkgs/development/coq-modules/metacoq/default.nix

@@ -1,4 +1,4 @@
-{ lib, which, fetchzip,
+{ lib, fetchzip,
   mkCoqDerivation, recurseIntoAttrs,  single ? false,
   coqPackages, coq, equations, version ? null }@args:
 with builtins // lib;
@@ -36,10 +36,8 @@ let
       derivation = mkCoqDerivation ({
         inherit version pname defaultVersion release releaseRev repo owner;
 
-        extraNativeBuildInputs = [ which ];
         mlPlugin = true;
-        extraBuildInputs = [ coq.ocamlPackages.zarith ];
+        propagatedBuildInputs = [ equations coq.ocamlPackages.zarith ] ++ metacoq-deps;
-        propagatedBuildInputs = [ equations ] ++ metacoq-deps;
 
         patchPhase =  ''
           patchShebangs ./configure.sh

pkgs/development/coq-modules/metalib/default.nix

@@ -13,7 +13,6 @@ with lib; mkCoqDerivation {
   release."8.10".sha256 = "0wbypc05d2lqfm9qaw98ynr5yc1p0ipsvyc3bh1rk9nz7zwirmjs";
 
   sourceRoot = "source/Metalib";
-  installFlags = "COQMF_COQLIB=$(out)/lib/coq/${coq.coq-version}";
 
   meta = {
     license = licenses.mit;

pkgs/development/coq-modules/semantics/default.nix

@@ -24,8 +24,8 @@ mkCoqDerivation rec {
   ] null;
 
   mlPlugin = true;
-  extraNativeBuildInputs = (with coq.ocamlPackages; [ ocamlbuild ]);
+  nativeBuildInputs = (with coq.ocamlPackages; [ ocamlbuild ]);
-  extraBuildInputs = (with coq.ocamlPackages; [ num ]);
+  propagatedBuildInputs = (with coq.ocamlPackages; [ num ]);
 
   postPatch = ''
     for p in Make Makefile.coq.local

pkgs/development/coq-modules/simple-io/default.nix

@@ -11,11 +11,9 @@ with lib; mkCoqDerivation {
   ] null;
   release."1.7.0".sha256 = "sha256:1a1q9x2abx71hqvjdai3n12jxzd49mhf3nqqh3ya2ssl2lj609ci";
   release."1.3.0".sha256 = "1yp7ca36jyl9kz35ghxig45x6cd0bny2bpmy058359p94wc617ax";
-  extraNativeBuildInputs = (with coq.ocamlPackages; [ cppo zarith ]);
-  propagatedBuildInputs = [ coq-ext-lib ]
-  ++ (with coq.ocamlPackages; [ ocaml ocamlbuild ]);
-
   mlPlugin = true;
+  nativeBuildInputs = [ coq.ocamlPackages.cppo ];
+  propagatedBuildInputs = [ coq-ext-lib coq.ocamlPackages.ocamlbuild ];
 
   doCheck = true;
   checkTarget = "test";

pkgs/development/coq-modules/smtcoq/default.nix

@@ -13,9 +13,11 @@ mkCoqDerivation {
     { case = isEq "8.13"; out = "itp22"; }
   ] null;
 
-  propagatedBuildInputs = [ trakt cvc4 ] ++ lib.optionals (!stdenv.isDarwin) [ veriT ];
+  propagatedBuildInputs = [ trakt cvc4 ]
-  extraNativeBuildInputs = with coq.ocamlPackages; [ ocaml ocamlbuild ];
+    ++ lib.optionals (!stdenv.isDarwin) [ veriT ]
-  extraBuildInputs = with coq.ocamlPackages; [ findlib num zarith ];
+    ++ (with coq.ocamlPackages; [ num zarith ]);
+  mlPlugin = true;
+  nativeBuildInputs = with coq.ocamlPackages; [ ocamlbuild ];
 
   meta = {
     description = "Communication between Coq and SAT/SMT solvers ";

pkgs/development/haskell-modules/configuration-hackage2nix/main.yaml

@@ -289,6 +289,7 @@ package-maintainers:
     - candid
     - leb128-cereal
     - tasty-expected-failure
+    - lhs2tex
   pacien:
     - ldgallery-compiler
   peti:

pkgs/development/haskell-modules/hackage-packages.nix

@@ -169845,6 +169845,7 @@ self: {
        ];
        description = "Preprocessor for typesetting Haskell sources with LaTeX";
        license = "GPL";
+       maintainers = with lib.maintainers; [ nomeata ];
      }) {};
 
   "lhslatex" = callPackage

pkgs/development/libraries/flatbuffers/1.12.nix

@@ -1,26 +0,0 @@
-{ callPackage, fetchpatch, lib, stdenv }:
-
-callPackage ./generic.nix {
-  version = "1.12.0";
-  sha256 = "0f7xd66vc1lzjbn7jzd5kyqrgxpsfxi4zc7iymhb5xrwyxipjl1g";
-
-  patches = [
-    (fetchpatch {
-      # Fixed a compilation error with GCC 10.0 to 11.0. June 1, 2020.
-      # Should be included in the next release after 1.12.0
-      url = "https://github.com/google/flatbuffers/commit/988164f6e1675bbea9c852e2d6001baf4d1fcf59.patch";
-      sha256 = "0d8c2bywqmkhdi0a41cry85wy4j58pl0vd6h5xpfqm3fr8w0mi9s";
-      excludes = [ "src/idl_gen_cpp.cpp" ];
-    })
-    (fetchpatch {
-      # Fixed a compilation error with GCC 10.0 to 11.0. July 6, 2020.
-      # Should be included in the next release after 1.12.0
-      url = "https://github.com/google/flatbuffers/pull/6020/commits/44c7a4cf439b0a298720b5a448bcc243a882b0c9.patch";
-      sha256 = "126xwkvnlc4ignjhxv9jygfd9j6kr1jx39hyk0ddpcmvzfqsccf4";
-    })
-  ];
-
-  preConfigure = lib.optionalString stdenv.buildPlatform.isDarwin ''
-    rm BUILD
-  '';
-}

pkgs/development/libraries/flatbuffers/2.0.nix

@@ -1,16 +0,0 @@
-{ callPackage, fetchpatch }:
-
-callPackage ./generic.nix {
-  version = "2.0.0";
-  sha256 = "1zbf6bdpps8369r1ql00irxrp58jnalycc8jcapb8iqg654vlfz8";
-
-  patches = [
-    # Pull patch pending upstream inclustion for gcc-12 support:
-    #  https://github.com/google/flatbuffers/pull/6946
-    (fetchpatch {
-      name = "gcc-12.patch";
-      url = "https://github.com/google/flatbuffers/commit/17d9f0c4cf47a9575b4f43a2ac33eb35ba7f9e3e.patch";
-      sha256 = "0sksk47hi7camja9ppnjr88jfdgj0nxqxy8976qs1nx73zkgbpf9";
-    })
-  ];
-}

pkgs/development/libraries/flatbuffers/default.nix

@@ -1,25 +1,30 @@
 { lib
 , stdenv
 , fetchFromGitHub
+, fetchpatch
 , cmake
-, version
-, sha256
-, patches ? [ ]
-, preConfigure ? null
 }:
 
 stdenv.mkDerivation rec {
   pname = "flatbuffers";
-  inherit version;
+  version = "2.0.0";
 
   src = fetchFromGitHub {
     owner = "google";
     repo = "flatbuffers";
     rev = "v${version}";
-    inherit sha256;
+    sha256 = "1zbf6bdpps8369r1ql00irxrp58jnalycc8jcapb8iqg654vlfz8";
   };
 
-  inherit patches preConfigure;
+  patches = [
+    # Pull patch pending upstream inclustion for gcc-12 support:
+    # https://github.com/google/flatbuffers/pull/6946
+    (fetchpatch {
+      name = "gcc-12.patch";
+      url = "https://github.com/google/flatbuffers/commit/17d9f0c4cf47a9575b4f43a2ac33eb35ba7f9e3e.patch";
+      sha256 = "0sksk47hi7camja9ppnjr88jfdgj0nxqxy8976qs1nx73zkgbpf9";
+    })
+  ];
 
   nativeBuildInputs = [ cmake ];
 

pkgs/development/libraries/xgboost/default.nix

@@ -25,7 +25,13 @@ stdenv.mkDerivation rec {
     sha256 = "sha256-h7zcHCOxe1h7HRB6idtjf4HUBEoHC4V2pqbN9hpe00g=";
   };
 
-  nativeBuildInputs = [ cmake ] ++ lib.optional stdenv.isDarwin llvmPackages.openmp;
+  nativeBuildInputs = [
+    cmake
+  ] ++ lib.optionals stdenv.isDarwin [
+    llvmPackages.openmp
+  ] ++ lib.optionals cudaSupport [
+    cudaPackages.autoAddOpenGLRunpathHook
+  ];
 
   buildInputs = [ gtest ] ++ lib.optional cudaSupport cudaPackages.cudatoolkit
                 ++ lib.optional ncclSupport cudaPackages.nccl;
@@ -37,6 +43,12 @@ stdenv.mkDerivation rec {
 
   inherit doCheck;
 
+  # By default, cmake build will run ctests with all checks enabled
+  # If we're building with cuda, we run ctest manually so that we can skip the GPU tests
+  checkPhase = lib.optionalString cudaSupport ''
+    ctest --force-new-ctest-process ${lib.optionalString cudaSupport "-E TestXGBoostLib"}
+  '';
+
   installPhase = let
     libname = "libxgboost${stdenv.hostPlatform.extensions.sharedLibrary}";
   in ''

pkgs/development/ocaml-modules/elpi/default.nix

@@ -1,12 +1,13 @@
-{ stdenv, lib, fetchzip, buildDunePackage, camlp5
+{ stdenv, lib, fetchzip, bash
+, buildDunePackage, camlp5
 , re, perl, ncurses
 , ppxlib, ppx_deriving
 , ppxlib_0_15, ppx_deriving_0_15
+, coqPackages
 , version ? "1.14.1"
 }:
 with lib;
-let fetched = import ../../../build-support/coq/meta-fetch/default.nix
+let fetched = coqPackages.metaFetch ({
-  {inherit lib stdenv fetchzip; } ({
     release."1.14.1".sha256 = "sha256-BZPVL8ymjrE9kVGyf6bpc+GA2spS5JBpkUtZi04nPis=";
     release."1.13.7".sha256 = "10fnwz30bsvj7ii1vg4l1li5pd7n0qqmwj18snkdr5j9gk0apc1r";
     release."1.13.5".sha256 = "02a6r23mximrdvs6kgv6rp0r2dgk7zynbs99nn7lphw2c4189kka";
@@ -32,6 +33,11 @@ buildDunePackage rec {
      else [ ppxlib_0_15 ppx_deriving_0_15 ]
   );
 
+  patchPhase = ''
+    sed -e "s/SHELL:=/SHELL?=/" -i Makefile || true
+  '';
+  buildPhase = "SHELL=${bash} make build";
+
   meta = {
     description = "Embeddable λProlog Interpreter";
     license = licenses.lgpl21Plus;

pkgs/development/php-packages/box/default.nix

@@ -1,14 +1,14 @@
 { mkDerivation, fetchurl, makeWrapper, lib, php }:
 let
   pname = "box";
-  version = "2.7.5";
+  version = "3.16.0";
 in
 mkDerivation {
   inherit pname version;
 
   src = fetchurl {
-    url = "https://github.com/box-project/box2/releases/download/${version}/box-${version}.phar";
+    url = "https://github.com/box-project/box/releases/download/${version}/box.phar";
-    sha256 = "1zmxdadrv0i2l8cz7xb38gnfmfyljpsaz2nnkjzqzksdmncbgd18";
+    sha256 = "sha256-9QjijzCdfpWjGb3NXxPc+7GOuRy3psrJtpvHeZ14vfk=";
   };
 
   dontUnpack = true;
@@ -27,7 +27,7 @@ mkDerivation {
   meta = with lib; {
     description = "An application for building and managing Phars";
     license = licenses.mit;
-    homepage = "https://box-project.github.io/box2/";
+    homepage = "https://github.com/box-project/box";
     maintainers = with maintainers; [ jtojnar ] ++ teams.php.members;
   };
 }

pkgs/development/php-packages/php-parallel-lint/default.nix

@@ -1,16 +1,16 @@
 { mkDerivation, fetchFromGitHub, makeWrapper, lib, php }:
 let
   pname = "php-parallel-lint";
-  version = "1.0.0";
+  version = "1.3.2";
 in
 mkDerivation {
   inherit pname version;
 
   src = fetchFromGitHub {
-    owner = "JakubOnderka";
+    owner = "php-parallel-lint";
     repo = "PHP-Parallel-Lint";
     rev = "v${version}";
-    sha256 = "16nv8yyk2z3l213dg067l6di4pigg5rd8yswr5xgd18jwbys2vnw";
+    sha256 = "sha256-pTHH19HwqyOj5pSmH7l0JlntNVtMdu4K9Cl+qyrrg9U=";
   };
 
   nativeBuildInputs = [
@@ -38,7 +38,7 @@ mkDerivation {
   meta = with lib; {
     description = "Tool to check syntax of PHP files faster than serial check with fancier output";
     license = licenses.bsd2;
-    homepage = "https://github.com/JakubOnderka/PHP-Parallel-Lint";
+    homepage = "https://github.com/php-parallel-lint/PHP-Parallel-Lint";
     maintainers = with maintainers; [ jtojnar ] ++ teams.php.members;
   };
 }

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

@@ -13,6 +13,7 @@
 , pymatgen
 , pytest
 , pythonOlder
+, pythonAtLeast
 , requests
 , scipy
 , toolz
@@ -24,7 +25,7 @@ buildPythonPackage rec {
   pname = "atomman";
   format = "setuptools";
 
-  disabled = pythonOlder "3.6";
+  disabled = pythonOlder "3.6" || pythonAtLeast "3.10";
 
   src = fetchFromGitHub {
     owner = "usnistgov";
@@ -57,8 +58,11 @@ buildPythonPackage rec {
   checkPhase = ''
     # pytestCheckHook doesn't work
     pytest tests -k "not test_rootdir and not test_version \
-      and not test_atomic_mass and not imageflags" \
+      and not test_atomic_mass and not imageflags \
-      --ignore tests/plot/test_interpolate.py
+      and not test_build_unit and not test_set_and_get_in_units \
+      and not test_set_literal and not test_scalar_model " \
+      --ignore tests/plot/test_interpolate.py \
+      --ignore tests/tools/test_vect_angle.py
   '';
 
   pythonImportsCheck = [

pkgs/development/python-modules/boolean-py/default.nix

@@ -1,21 +1,36 @@
-{ lib, buildPythonPackage, fetchFromGitHub
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, pytestCheckHook
+, pythonOlder
 }:
 
 buildPythonPackage rec {
-  pname = "boolean.py";
+  pname = "boolean-py";
-  version = "3.8";
+  version = "4.0";
+  format = "setuptools";
+
+  disabled = pythonOlder "3.7";
 
   src = fetchFromGitHub {
     owner = "bastikr";
     repo = "boolean.py";
     rev = "v${version}";
-    sha256 = "02jznrfrihhk69ai1vnh26s3rshl4kfc2id7li6xccavc2ws5y3b";
+    hash = "sha256-i6aNzGDhZip9YHXLiuh9crGm2qT2toBU2xze4PDLleg=";
   };
 
+  checkInputs = [
+    pytestCheckHook
+  ];
+
+  pythonImportsCheck = [
+    "boolean"
+  ];
+
   meta = with lib; {
-    homepage = "https://github.com/bastikr/boolean.py";
     description = "Implements boolean algebra in one module";
+    homepage = "https://github.com/bastikr/boolean.py";
     license = licenses.bsd2;
+    maintainers = with maintainers; [ ];
   };
-
 }

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

@@ -8,7 +8,6 @@ buildPythonPackage rec {
   version = "7.8.1";
   disabled = !isPy3k; # python2.7 abandoned upstream
 
-  # no tests in Pypi tarball
   src = fetchFromGitHub {
     owner = "chainer";
     repo = "chainer";
@@ -16,11 +15,6 @@ buildPythonPackage rec {
     sha256 = "1n07zjzc4g92m1sbgxvnansl0z00y4jnhma2mw06vnahs7s9nrf6";
   };
 
-  checkInputs = [
-    pytestCheckHook
-    mock
-  ];
-
   propagatedBuildInputs = [
     filelock
     protobuf
@@ -28,11 +22,19 @@ buildPythonPackage rec {
     typing-extensions
   ] ++ lib.optionals cudaSupport [ cupy ];
 
+  checkInputs = [
+    pytestCheckHook
+    mock
+  ];
+
   pytestFlagsArray = [ "tests/chainer_tests/utils_tests" ];
 
-  # cf. https://github.com/chainer/chainer/issues/8621
   preCheck = ''
+    # cf. https://github.com/chainer/chainer/issues/8621
     export CHAINER_WARN_VERSION_MISMATCH=0
+
+    # ignore pytest warnings not listed
+    rm setup.cfg
   '';
 
   disabledTests = [

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

@@ -1,5 +1,8 @@
 { lib
+, stdenv
 , buildPythonPackage
+, pythonOlder
+, pythonAtLeast
 , fetchFromGitHub
 , pillow
 , libX11
@@ -11,26 +14,38 @@
 
 buildPythonPackage rec {
   pname = "clickgen";
-  version = "1.1.9";
+  version = "1.2.0";
+  format = "setuptools";
+
+  disabled = pythonOlder "3.8" || pythonAtLeast "3.10";
 
   src = fetchFromGitHub {
     owner = "ful1e5";
     repo = "clickgen";
     rev = "v${version}";
-    sha256 = "108f3sbramd3hhs4d84s3i3lbwllfrkvjakjq4gdmbw6xpilvm0l";
+    sha256 = "sha256-01c8SVy+J004dq5KCUe62w7i/xUTxTfl/IpvUtGQgw0=";
   };
 
   buildInputs = [ libXcursor libX11 libpng ];
 
   propagatedBuildInputs = [ pillow ];
 
-  pythonImportsCheck = [ "clickgen" ];
+  checkInputs = [ pytestCheckHook ];
+
+  postBuild = ''
+    # Needs to build xcursorgen.so
+    cd src/xcursorgen
+    make
+    cd ../..
+  '';
 
   postInstall = ''
-    install -m644 clickgen/xcursorgen.so $out/${python.sitePackages}/clickgen/xcursorgen.so
+    install -m644 src/xcursorgen/xcursorgen.so $out/${python.sitePackages}/clickgen/xcursorgen.so
+    # Copying scripts directory needed by clickgen script at $out/bin/
+    cp -R src/clickgen/scripts $out/${python.sitePackages}/clickgen/scripts
   '';
 
-  checkInputs = [ pytestCheckHook ];
+  pythonImportsCheck = [ "clickgen" ];
 
   meta = with lib; {
     homepage = "https://github.com/ful1e5/clickgen";
@@ -41,5 +56,8 @@ buildPythonPackage rec {
     '';
     license = licenses.mit;
     maintainers = with maintainers; [ AdsonCicilioti ];
+    # fails with:
+    # ld: unknown option: -zdefs
+    broken = stdenv.isDarwin;
   };
 }

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

@@ -15,7 +15,7 @@
 
 buildPythonPackage rec {
   pname = "dash";
-  version = "2.3.1";
+  version = "2.4.1";
   format = "setuptools";
 
   disabled = pythonOlder "3.6";
@@ -23,8 +23,8 @@ buildPythonPackage rec {
   src = fetchFromGitHub {
     owner = "plotly";
     repo = pname;
-    rev = "v${version}";
+    rev = "refs/tags/v${version}";
-    sha256 = "sha256-gsP/WbALUkO3AB0uuX/ByhzaeIDSUUE1Cb8Cnh4GEh0=";
+    sha256 = "sha256-7B1LEcEgUGJ/gDCDD4oURqli8I5YTJo9jl7l4E1aLVQ=";
   };
 
   propagatedBuildInputs = [

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

@@ -61,5 +61,8 @@ buildPythonPackage rec {
     homepage = "https://github.com/h2oai/datatable";
     license = licenses.mpl20;
     maintainers = with maintainers; [ abbradar ];
+    # uses custom build system and adds -Wunused-variable -Werror
+    # warning: ‘dt::expr::doc_first’ defined but not used [-Wunused-variable]
+    broken = true;
   };
 }

pkgs/development/python-modules/dparse2/default.nix

@@ -0,0 +1,50 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, pythonOlder
+, toml
+, pyyaml
+, packaging
+, pytestCheckHook
+}:
+
+buildPythonPackage rec {
+  pname = "dparse2";
+  version = "0.6.1";
+  format = "setuptools";
+
+  disabled = pythonOlder "3.7";
+
+  src = fetchFromGitHub {
+    owner = "nexB";
+    repo = pname;
+    rev = version;
+    hash = "sha256-1tbNW7Gy7gvMnETdAM2ahHiwbhG9qvdYZggia1+7eGo=";
+  };
+
+  propagatedBuildInputs = [
+    toml
+    pyyaml
+    packaging
+  ];
+
+  checkInputs = [
+    pytestCheckHook
+  ];
+
+  disabledTestPaths = [
+    # Requries pipenv
+    "tests/test_parse.py"
+  ];
+
+  pythonImportsCheck = [
+    "dparse2"
+  ];
+
+  meta = with lib; {
+    description = "Module to parse Python dependency files";
+    homepage = "https://github.com/nexB/dparse2";
+    license = licenses.mit;
+    maintainers = with maintainers; [ fab ];
+  };
+}

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

@@ -12,7 +12,7 @@
 
 buildPythonPackage rec {
   pname = "eiswarnung";
-  version = "1.0.0";
+  version = "1.1.0";
   format = "pyproject";
 
   disabled = pythonOlder "3.9";
@@ -20,8 +20,8 @@ buildPythonPackage rec {
   src = fetchFromGitHub {
     owner = "klaasnicolaas";
     repo = "python-eiswarnung";
-    rev = "v${version}";
+    rev = "refs/tags/v${version}";
-    hash = "sha256-Cw/xRypErasdrOZJ/0dWLl4eYH01vBI9mYm98teIdRc=";
+    hash = "sha256-fyxqVSZcbo/rrItad5ZTwmp4N8s0HGBdxvx3LBax/hc=";
   };
 
   nativeBuildInputs = [

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

@@ -9,14 +9,14 @@
 
 buildPythonPackage rec {
   pname = "ftputil";
-  version = "5.0.3";
+  version = "5.0.4";
   format = "setuptools";
 
   disabled = pythonOlder "3.6";
 
   src = fetchPypi {
     inherit pname version;
-    hash = "sha256-m4buZ8GYDOHYmxN1K8SLlJP+4GNJy0doKFlOduCPhIg=";
+    hash = "sha256-aInbhkndINm21ApsXw+EzPNAp9rB4L/A8AJAkPwq+zM=";
   };
 
   checkInputs = [

pkgs/development/python-modules/google-cloud-pubsub/default.nix

@@ -15,14 +15,14 @@
 
 buildPythonPackage rec {
   pname = "google-cloud-pubsub";
-  version = "2.12.0";
+  version = "2.12.1";
   format = "setuptools";
 
   disabled = pythonOlder "3.6";
 
   src = fetchPypi {
     inherit pname version;
-    hash = "sha256-5RoIpyVm/y2+6pN4mJPWHbVUwxH6yWI/vIuCVNJU2aw=";
+    hash = "sha256-mTphUjL61NwaE7vKDgeCv+0WeA15FNQzvnY/6fHZ/QU=";
   };
 
   propagatedBuildInputs = [

pkgs/development/python-modules/license-expression/default.nix

@@ -9,7 +9,7 @@
 
 buildPythonPackage rec {
   pname = "license-expression";
-  version = "21.6.14";
+  version = "30.0.0";
 
   disabled = pythonOlder "3.6";
 
@@ -17,7 +17,7 @@ buildPythonPackage rec {
     owner = "nexB";
     repo = "license-expression";
     rev = "v${version}";
-    sha256 = "sha256-hwfYKKalo8WYFwPCsRRXNz+/F8/42PXA8jxbIQjJH/g=";
+    hash = "sha256-tGXNZm9xH8sXa7dtBFsTzGgT+hfbmkwps7breR7KUWU=";
   };
 
   dontConfigure = true;
@@ -34,10 +34,12 @@ buildPythonPackage rec {
     pytestCheckHook
   ];
 
-  pythonImportsCheck = [ "license_expression" ];
+  pythonImportsCheck = [
+    "license_expression"
+  ];
 
   meta = with lib; {
-    description = "Utility library to parse, normalize and compare License expressions for Python";
+    description = "Utility library to parse, normalize and compare License expressions";
     homepage = "https://github.com/nexB/license-expression";
     license = licenses.asl20;
     maintainers = with maintainers; [ fab ];

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

@@ -32,5 +32,8 @@ buildPythonPackage rec {
     description = "Mapbox SDK for Python";
     longDescription = "Low-level client API for Mapbox web services.";
     maintainers = with maintainers; [ ersin ];
+    # ImportError: cannot import name 'Mapping' from 'collections'
+    # and archived upstreamed
+    broken = true;
   };
 }

pkgs/development/python-modules/name-that-hash/default.nix

@@ -0,0 +1,44 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, poetry-core
+, click
+, rich
+}:
+
+buildPythonPackage rec {
+  pname = "name-that-hash";
+  version = "1.10";
+  format = "pyproject";
+
+  src = fetchFromGitHub {
+    owner = "HashPals";
+    repo = pname;
+    rev = version;
+    hash = "sha256-3sddUPoC3NfKQzmNgqPf/uHaYN9VZBqsmV712uz1Phg=";
+  };
+
+  # TODO remove on next update which bumps rich
+  postPatch = ''
+    substituteInPlace pyproject.toml --replace 'rich = ">=9.9,<11.0"' 'rich = ">=9.9"'
+  '';
+
+  nativeBuildInputs = [
+    poetry-core
+  ];
+
+  propagatedBuildInputs = [
+    click
+    rich
+  ];
+
+  pythonImportsCheck = [ "name_that_hash" ];
+
+  meta = with lib; {
+    longDescription = "Don't know what type of hash it is? Name That Hash will name that hash type! Identify MD5, SHA256 and 300+ other hashes.";
+    description = "Module and CLI for the identification of hashes";
+    homepage = "https://github.com/HashPals/Name-That-Hash";
+    license = with licenses; [ gpl3Plus ];
+    maintainers = with maintainers; [ eyjhb ];
+  };
+}

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

@@ -1,10 +1,14 @@
 { lib, buildPythonPackage, fetchFromGitHub, callPackage, setuptools, cffi
 , paramiko, requests, future, textfsm, jinja2, netaddr, pyyaml, pyeapi, netmiko
-, junos-eznc, ciscoconfparse, scp, lxml, ncclient, pytestCheckHook, ddt, mock }:
+, junos-eznc, ciscoconfparse, scp, lxml, ncclient, pytestCheckHook, ddt, mock
+, pythonOlder, pythonAtLeast }:
 
 buildPythonPackage rec {
   pname = "napalm";
   version = "3.3.1";
+  format = "setuptools";
+
+  disabled = pythonOlder "3.6" || pythonAtLeast "3.9";
 
   src = fetchFromGitHub {
     owner = "napalm-automation";

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

@@ -41,8 +41,8 @@ buildPythonPackage rec {
 
   meta = with lib; {
     description = "A unittest-based testing framework for python that makes writing and running tests easier";
-    homepage = "http://readthedocs.org/docs/nose/";
+    homepage = "https://nose.readthedocs.io/";
     license = licenses.lgpl3;
+    maintainers = with maintainers; [ ];
   };
-
 }

pkgs/development/python-modules/pip-tools/default.nix

@@ -8,6 +8,7 @@
 , click
 , setuptools-scm
 , pep517
+, stdenv
 }:
 
 buildPythonPackage rec {
@@ -26,6 +27,11 @@ buildPythonPackage rec {
     pytest-xdist
   ];
 
+  preCheck = lib.optionalString (stdenv.isDarwin && stdenv.isAarch64) ''
+    # https://github.com/python/cpython/issues/74570#issuecomment-1093748531
+    export no_proxy='*';
+  '';
+
   nativeBuildInputs = [
     setuptools-scm
   ];

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

@@ -20,7 +20,7 @@
 
 buildPythonPackage rec {
   pname = "plugwise";
-  version = "0.18.1";
+  version = "0.18.2";
   format = "setuptools";
 
   disabled = pythonOlder "3.7";
@@ -29,7 +29,7 @@ buildPythonPackage rec {
     owner = pname;
     repo = "python-plugwise";
     rev = "refs/tags/v${version}";
-    sha256 = "sha256-jdRwaw5hPP8VCmCp3l5idjzrHJ2vLhYpC6yPCmOF56Y=";
+    sha256 = "sha256-l97GF5dZlwps2mhw84A+8IBmTmvnaJ/5MeWYdeAu4Zw=";
   };
 
   propagatedBuildInputs = [

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

@@ -6,14 +6,14 @@
 
 buildPythonPackage rec {
   pname = "puremagic";
-  version = "1.12";
+  version = "1.13";
   format = "setuptools";
 
   disabled = pythonOlder "3.7";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "sha256-jAuuwImSExc2KjD6yi6WeMkdXpfOAE3Gp8HGaeBUeDg=";
+    sha256 = "sha256-yaHw/pOqWLUtYoM3l/JB0JToLXdi04n0BSccRdbCVDw=";
   };
 
   # test data not included on pypi

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

@@ -0,0 +1,60 @@
+{ lib
+, buildPythonPackage
+, cryptography
+, fetchFromGitHub
+, pytest-asyncio
+, pytestCheckHook
+, pythonOlder
+, typing-extensions
+, zeroconf
+}:
+
+buildPythonPackage rec {
+  pname = "python-rabbitair";
+  version = "0.0.8";
+  format = "pyproject";
+
+  disabled = pythonOlder "3.6";
+
+  src = fetchFromGitHub {
+    owner = "rabbit-air";
+    repo = pname;
+    rev = "v${version}";
+    hash = "sha256-CGr7NvnGRNTiKq5BpB/zmfgyd/2ggTbO0nj+Q+MavTs=";
+  };
+
+  propagatedBuildInputs = [
+    cryptography
+    zeroconf
+  ] ++ lib.optionals (pythonOlder "3.8") [
+    typing-extensions
+  ];
+
+  checkInputs = [
+    pytest-asyncio
+    pytestCheckHook
+  ];
+
+  pythonImportsCheck = [
+    "rabbitair"
+  ];
+
+  disabledTests = [
+    # Tests require network access
+    "test_info"
+    "test_no_response"
+    "test_protocol_error"
+    "test_sequential_requests"
+    "test_set_state"
+    "test_state_a2"
+    "test_state_a3"
+    "test_zeroconf"
+  ];
+
+  meta = with lib; {
+    description = "Module for the control of Rabbit Air air purifiers";
+    homepage = "https://github.com/rabbit-air/python-rabbitair";
+    license = with licenses; [ asl20 ];
+    maintainers = with maintainers; [ fab ];
+  };
+}

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

@@ -8,6 +8,7 @@
 , pyserial-asyncio
 , setuptools
 , pytestCheckHook
+, pythonAtLeast
 }:
 
 buildPythonPackage rec {
@@ -34,6 +35,11 @@ buildPythonPackage rec {
     pytestCheckHook
   ];
 
+  disabledTestPaths = lib.optionals (pythonAtLeast "3.10") [
+    # https://github.com/aequitas/python-rflink/issues/65
+    "tests/test_proxy.py"
+  ];
+
   postPatch = ''
     substituteInPlace setup.py \
       --replace "version=version_from_git()" "version='${version}'"

pkgs/development/python-modules/scikit-bio/default.nix

@@ -5,6 +5,7 @@
 , lockfile
 , cachecontrol
 , decorator
+, h5py
 , ipython
 , matplotlib
 , natsort
@@ -19,18 +20,18 @@
 }:
 
 buildPythonPackage rec {
-  version = "0.5.6";
+  version = "0.5.7";
   pname = "scikit-bio";
   disabled = !isPy3k;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "48b73ec53ce0ff2c2e3e05f3cfcf93527c1525a8d3e9dd4ae317b4219c37f0ea";
+    sha256 = "sha256-Y0PKDGIeL8xdHAQsi+MgBmTFMllWqDvqdRzxvMddHak=";
   };
 
-  buildInputs = [ cython ];
+  nativeBuildInputs = [ cython ];
   checkInputs = [ coverage ];
-  propagatedBuildInputs = [ lockfile cachecontrol decorator ipython matplotlib natsort numpy pandas scipy hdmedians scikit-learn ];
+  propagatedBuildInputs = [ lockfile cachecontrol decorator ipython matplotlib natsort numpy pandas scipy h5py hdmedians scikit-learn ];
 
   # cython package not included for tests
   doCheck = false;

pkgs/development/python-modules/sentry-sdk/default.nix

@@ -42,7 +42,7 @@
 
 buildPythonPackage rec {
   pname = "sentry-sdk";
-  version = "1.5.11";
+  version = "1.5.12";
   format = "setuptools";
 
   disabled = pythonOlder "3.7";
@@ -51,7 +51,7 @@ buildPythonPackage rec {
     owner = "getsentry";
     repo = "sentry-python";
     rev = version;
-    hash = "sha256-2WN18hzOn/gomNvQNbm9R8CcxN6G1XxoodBHqsG6es0=";
+    hash = "sha256-8M0FWfvaGp74Fb+qJlhyiJPUVHN2ZdEleZf27d+bftE=";
   };
 
   propagatedBuildInputs = [

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

@@ -12,12 +12,12 @@
 
 buildPythonPackage rec {
   pname = "Shapely";
-  version = "1.8.1.post1";
+  version = "1.8.2";
   disabled = pythonOlder "3.6";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "sha256-k/8G/wX74r6EO5PHsa2CkuVuZlugG0cI91rop1eXLp8=";
+    sha256 = "sha256-Vyr51QBv1eMhPjfuVIkSsDQfsmck1tyKTjlQwQGX67Y=";
   };
 
   nativeBuildInputs = [