Merge master into staging-next

nixos/modules/installer/tools/tools.nix

@@ -42,7 +42,7 @@ let
   nixos-option =
     if lib.versionAtLeast (lib.getVersion config.nix.package) "2.4pre"
     then null
-    else pkgs.callPackage ./nixos-option { };
+    else pkgs.nixos-option;
 
   nixos-version = makeProg {
     name = "nixos-version";

pkgs/applications/blockchains/zcash/default.nix

@@ -6,16 +6,16 @@
 
 rustPlatform.buildRustPackage.override { stdenv = stdenv; } rec {
   pname = "zcash";
-  version = "4.4.0";
+  version = "4.4.1";
 
   src = fetchFromGitHub {
     owner = "zcash";
     repo  = "zcash";
     rev = "v${version}";
-    sha256 = "19vhblyqkaf1lapx8s4v88xjpslqmrd1jnar46rschzcz0mm9sq4";
+    sha256 = "0nhrjizx518khrl8aygag6a1ianzzqpchasggi963f807kv7ipb7";
   };
 
-  cargoSha256 = "1yiy1506ijndxb9bx79p7fkfvw1c5zdsljil4m55xz1mv8dzhbgm";
+  cargoSha256 = "101j8cn2lg3l1gn53yg3svzwx783z331g9kzn9ici4azindyx903";
 
   nativeBuildInputs = [ autoreconfHook cargo hexdump makeWrapper pkg-config ];
   buildInputs = [ boost174 libevent libsodium utf8cpp ]

pkgs/applications/networking/cluster/kube3d/default.nix

@@ -2,13 +2,13 @@
 
 buildGoModule rec {
   pname = "kube3d";
-  version = "4.4.6";
+  version = "4.4.7";
 
   src = fetchFromGitHub {
     owner = "rancher";
     repo = "k3d";
     rev = "v${version}";
-    sha256 = "sha256-gId7zDrtkTjFN59yaFyeYwrDZV24hkkV+4dPr8Jr22E=";
+    sha256 = "sha256-S1vHmXUCP1ayPo3vvHAbNCqNm1ueJ0jE4NUBvg5P3MU=";
   };
 
   vendorSha256 = null;

pkgs/applications/science/math/engauge-digitizer/default.nix

@@ -0,0 +1,60 @@
+{ lib, stdenv, fetchFromGitHub, fftw, libjpeg, log4cpp, openjpeg
+, libpng12, poppler, qtbase, qt5, qmake, wrapQtAppsHook
+}:
+
+stdenv.mkDerivation rec {
+  pname = "engauge-digitizer";
+  version = "12.1";
+
+  src = fetchFromGitHub {
+    owner = "markummitchell";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "12gflxqaa4w6vifwpaqwl0l3f9qq5pbrh45s1rpc584nmr0897a7";
+  };
+
+  nativeBuildInputs = [ qmake wrapQtAppsHook ];
+
+  buildInputs = [
+    qtbase
+    qt5.qttools
+    poppler
+    libpng12
+    openjpeg
+    openjpeg.dev
+    log4cpp
+    libjpeg
+    fftw
+  ];
+
+  qmakeFlags = [
+    "CONFIG+=jpeg2000"
+    "CONFIG+=pdf"
+    "CONFIG+=log4cpp_null"
+  ];
+
+  POPPLER_INCLUDE = "${poppler.dev}/include/poppler/qt5";
+
+  POPPLER_LIB = "${poppler}/lib";
+
+  OPENJPEG_INCLUDE = "${openjpeg.dev}/include/${openjpeg.pname}-${lib.versions.majorMinor openjpeg.version}";
+
+  OPENJPEG_LIB = "${openjpeg}/lib";
+
+  installPhase = ''
+    runHook preInstall
+
+    mkdir -p $out/bin
+    cp bin/engauge $out/bin/
+
+    runHook postInstall
+  '';
+
+  meta = with lib; {
+    description = "Engauge Digitizer is a tool for recovering graph data from an image file";
+    homepage = "https://markummitchell.github.io/engauge-digitizer";
+    license = with licenses; [ gpl2Only ];
+    platforms = platforms.linux;
+    maintainers = [ maintainers.sheepforce ];
+  };
+}

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

@@ -0,0 +1,34 @@
+{ lib, fetchFromGitLab, buildDunePackage, bigstring, alcotest, cstruct, hex }:
+
+buildDunePackage rec {
+  pname = "uecc";
+  version = "0.3";
+
+  src = fetchFromGitLab {
+    owner = "nomadic-labs";
+    repo = "ocaml-uecc";
+    rev = "v${version}";
+    sha256 = "0m3cw34254baajscrwlrj0jp5n0yad3dhgi4jh3pz89iqykj15fr";
+  };
+
+  useDune2 = true;
+
+  propagatedBuildInputs = [
+    bigstring
+  ];
+
+  checkInputs = [
+    alcotest
+    cstruct
+    hex
+  ];
+
+  doCheck = true;
+
+  meta = {
+    description = "Bindings for ECDH and ECDSA for 8-bit, 32-bit, and 64-bit processors";
+    homepage = https://gitlab.com/nomadic-labs/ocaml-uecc;
+    license = lib.licenses.isc;
+    maintainers = [ lib.maintainers.ulrikstrid ];
+  };
+}

pkgs/development/python-modules/apache-airflow/default.nix

@@ -1,165 +1,202 @@
 { lib
 , stdenv
+, python
 , buildPythonPackage
 , fetchFromGitHub
-, fetchpatch
+, writeText
 , alembic
+, argcomplete
+, attrs
+, blinker
 , cached-property
-, configparser
+, cattrs
+, clickclick
 , colorlog
 , croniter
+, cryptography
 , dill
 , flask
 , flask-appbuilder
-, flask-admin
 , flask-caching
 , flask_login
-, flask-swagger
 , flask_wtf
-, flask-bcrypt
-, funcsigs
-, future
 , GitPython
+, graphviz
 , gunicorn
+, httpx
 , iso8601
-, json-merge-patch
+, importlib-resources
+, importlib-metadata
+, inflection
+, itsdangerous
 , jinja2
-, ldap3
+, jsonschema
-, lxml
 , lazy-object-proxy
+, lockfile
 , markdown
+, markupsafe
+, marshmallow-oneofschema
+, numpy
+, openapi-spec-validator
 , pandas
 , pendulum
 , psutil
 , pygments
+, pyjwt
 , python-daemon
 , python-dateutil
-, requests
+, python-nvd3
+, python-slugify
+, python3-openid
+, pyyaml
+, rich
 , setproctitle
-, snakebite
 , sqlalchemy
+, sqlalchemy-jsonfield
+, swagger-ui-bundle
 , tabulate
 , tenacity
 , termcolor
-, text-unidecode
-, thrift
-, tzlocal
 , unicodecsv
-, zope_deprecation
+, werkzeug
-, nose
+, pytest
-, pythonOlder
+, freezegun
-, pythonAtLeast
+, mkYarnPackage
 }:
+let
 
-buildPythonPackage rec {
+  version = "2.1.1rc1";
-  pname = "apache-airflow";
-  version = "1.10.5";
-  # Upstream does not yet support python 3.8
-  # https://github.com/apache/airflow/issues/8674
-  disabled = pythonOlder "3.5" || pythonAtLeast "3.8";
 
-  src = fetchFromGitHub rec {
+  airflow-src = fetchFromGitHub rec {
     owner = "apache";
     repo = "airflow";
     rev = version;
-    sha256 = "14fmhfwx977c9jdb2kgm93i6acx43l45ggj30rb37r68pzpb6l6h";
+    sha256 = "1vzzmcfgqni9rkf7ggh8mswnm3ffwaishcz1ysrwx0a96ilhm9q2";
   };
 
-  patches = [
+  # airflow bundles a web interface, which is built using webpack by an undocumented shell script in airflow's source tree.
-       # Not yet accepted: https://github.com/apache/airflow/pull/6562
+  # This replicates this shell script, fixing bugs in yarn.lock and package.json
-     (fetchpatch {
+
-       name = "avoid-warning-from-abc.collections";
+  airflow-frontend = mkYarnPackage {
-       url = "https://patch-diff.githubusercontent.com/raw/apache/airflow/pull/6562.patch";
+    name = "airflow-frontend";
-       sha256 = "0swpay1qlb7f9kgc56631s1qd9k82w4nw2ggvkm7jvxwf056k61z";
+
-     })
+    src = "${airflow-src}/airflow/www";
-       # Not yet accepted: https://github.com/apache/airflow/pull/6561
+    packageJSON = ./package.json;
-     (fetchpatch {
+    yarnLock = ./yarn.lock;
-       name = "pendulum2-compatibility";
+    yarnNix = ./yarn.nix;
-       url = "https://patch-diff.githubusercontent.com/raw/apache/airflow/pull/6561.patch";
+
-       sha256 = "17hw8qyd4zxvib9zwpbn32p99vmrdz294r31gnsbkkcl2y6h9knk";
+    distPhase = "true";
-     })
+
-  ];
+    configurePhase = ''
+      cp -r $node_modules node_modules
+    '';
+
+    buildPhase = ''
+      yarn --offline build
+      find package.json yarn.lock static/css static/js -type f | sort | xargs md5sum > static/dist/sum.md5
+    '';
+
+    installPhase = ''
+      mkdir -p $out/static/
+      cp -r static/dist $out/static
+    '';
+  };
+
+in
+buildPythonPackage rec {
+  pname = "apache-airflow";
+  inherit version;
+  src = airflow-src;
 
   propagatedBuildInputs = [
     alembic
+    argcomplete
+    attrs
+    blinker
     cached-property
+    cattrs
+    clickclick
     colorlog
-    configparser
     croniter
+    cryptography
     dill
     flask
-    flask-admin
     flask-appbuilder
-    flask-bcrypt
     flask-caching
     flask_login
-    flask-swagger
     flask_wtf
-    funcsigs
-    future
     GitPython
+    graphviz
     gunicorn
+    httpx
     iso8601
-    json-merge-patch
+    importlib-resources
+    importlib-metadata
+    inflection
+    itsdangerous
     jinja2
-    ldap3
+    jsonschema
-    lxml
     lazy-object-proxy
+    lockfile
     markdown
+    markupsafe
+    marshmallow-oneofschema
+    numpy
+    openapi-spec-validator
     pandas
     pendulum
     psutil
     pygments
+    pyjwt
     python-daemon
     python-dateutil
-    requests
+    python-nvd3
+    python-slugify
+    python3-openid
+    pyyaml
+    rich
     setproctitle
     sqlalchemy
+    sqlalchemy-jsonfield
+    swagger-ui-bundle
     tabulate
     tenacity
     termcolor
-    text-unidecode
-    thrift
-    tzlocal
     unicodecsv
-    zope_deprecation
+    werkzeug
+  ];
+
+  buildInputs = [
+    airflow-frontend
   ];
 
   checkInputs = [
-    snakebite
+    freezegun
-    nose
+    pytest
   ];
 
+  INSTALL_PROVIDERS_FROM_SOURCES = "true";
+
   postPatch = ''
-    substituteInPlace setup.py \
+    substituteInPlace setup.cfg \
+      --replace "importlib_resources~=1.4" "importlib_resources" \
+      --replace "importlib_metadata~=1.7" "importlib_metadata" \
+      --replace "tenacity~=6.2.0" "tenacity" \
+      --replace "pyjwt<2" "pyjwt" \
       --replace "flask>=1.1.0, <2.0" "flask" \
-      --replace "jinja2>=2.10.1, <2.11.0" "jinja2" \
-      --replace "pandas>=0.17.1, <1.0.0" "pandas" \
-      --replace "flask-caching>=1.3.3, <1.4.0" "flask-caching" \
-      --replace "flask-appbuilder>=1.12.5, <2.0.0" "flask-appbuilder" \
-      --replace "flask-admin==1.5.3" "flask-admin" \
       --replace "flask-login>=0.3, <0.5" "flask-login" \
-      --replace "cached_property~=1.5" "cached_property" \
+      --replace "flask-wtf>=0.14.3, <0.15" "flask-wtf" \
-      --replace "dill>=0.2.2, <0.3" "dill" \
+      --replace "jinja2>=2.10.1, <2.12.0" "jinja2" \
-      --replace "configparser>=3.5.0, <3.6.0" "configparser" \
+      --replace "attrs>=20.0, <21.0" "attrs" \
-      --replace "colorlog==4.0.2" "colorlog" \
+      --replace "cattrs~=1.1, <1.7.0" "cattrs" \
-      --replace "funcsigs==1.0.0" "funcsigs" \
+      --replace "markupsafe>=1.1.1, <2.0" "markupsafe" \
-      --replace "flask-swagger==0.2.13" "flask-swagger" \
+      --replace "docutils<0.17" "docutils" \
-      --replace "python-daemon>=2.1.1, <2.2" "python-daemon" \
+      --replace "sqlalchemy>=1.3.18, <1.4" "sqlalchemy" \
-      --replace "alembic>=1.0, <2.0" "alembic" \
+      --replace "sqlalchemy_jsonfield~=1.0" "sqlalchemy-jsonfield" \
-      --replace "markdown>=2.5.2, <3.0" "markdown" \
+      --replace "werkzeug~=1.0, >=1.0.1" "werkzeug" \
-      --replace "future>=0.16.0, <0.17" "future" \
+      --replace "itsdangerous>=1.1.0, <2.0" "itsdangerous"
-      --replace "tenacity==4.12.0" "tenacity" \
-      --replace "text-unidecode==1.2" "text-unidecode" \
-      --replace "tzlocal>=1.4,<2.0.0" "tzlocal" \
-      --replace "sqlalchemy~=1.3" "sqlalchemy" \
-      --replace "gunicorn>=19.5.0, <20.0" "gunicorn"
 
-    # dumb-init is only needed for CI and Docker, not relevant for NixOS.
+    substituteInPlace tests/core/test_core.py \
-    substituteInPlace setup.py \
-      --replace "'dumb-init>=1.2.2'," ""
-
-    substituteInPlace tests/core.py \
       --replace "/bin/bash" "${stdenv.shell}"
   '';
 
@@ -174,11 +211,14 @@ buildPythonPackage rec {
    export PATH=$PATH:$out/bin
 
    airflow version
-   airflow initdb
+   airflow db init
-   airflow resetdb -y
+   airflow db reset -y
-   nosetests tests.core.CoreTest
+
-   ## all tests
+   pytest tests/core/test_core.py
-   # nosetests --cover-package=airflow
+  '';
+
+  postInstall = ''
+    cp -rv ${airflow-frontend}/static/dist $out/lib/${python.libPrefix}/site-packages/airflow/www/static
   '';
 
   meta = with lib; {

pkgs/development/python-modules/apache-airflow/package.json

@@ -0,0 +1,80 @@
+{
+  "name": "airflow-frontend",
+  "version": "2.1.1rc1",
+  "description": "Apache Airflow is a platform to programmatically author, schedule and monitor workflows.",
+  "scripts": {
+    "test": "echo \"Error: no test specified\" && exit 1",
+    "dev": "NODE_ENV=dev webpack --watch --colors --progress --debug --output-pathinfo --devtool eval-cheap-source-map --mode development",
+    "prod": "NODE_ENV=production node --max_old_space_size=4096 ./node_modules/webpack/bin/webpack.js -p --colors --progress",
+    "build": "NODE_ENV=production webpack --colors --progress",
+    "lint": "eslint --ignore-path=.eslintignore --ext .js,.html .",
+    "lint:fix": "eslint --fix --ignore-path=.eslintignore --ext .js,.html ."
+  },
+  "author": "Apache",
+  "license": "Apache-2.0",
+  "repository": {
+    "type": "git",
+    "url": "git+https://github.com/apache/airflow.git"
+  },
+  "homepage": "https://airflow.apache.org/",
+  "keywords": [
+    "big",
+    "data",
+    "workflow",
+    "airflow",
+    "d3",
+    "nerds",
+    "database",
+    "flask"
+  ],
+  "devDependencies": {
+    "babel": "^6.23.0",
+    "babel-core": "^6.26.3",
+    "babel-eslint": "^10.1.0",
+    "babel-loader": "^8.1.0",
+    "babel-plugin-css-modules-transform": "^1.6.1",
+    "babel-polyfill": "^6.26.0",
+    "clean-webpack-plugin": "^3.0.0",
+    "copy-webpack-plugin": "^6.0.3",
+    "css-loader": "^3.4.2",
+    "eslint": "^7.5.0",
+    "eslint-config-airbnb-base": "^14.2.0",
+    "eslint-plugin-html": "^6.0.2",
+    "eslint-plugin-import": "^2.22.0",
+    "eslint-plugin-node": "^11.1.0",
+    "eslint-plugin-promise": "^4.2.1",
+    "eslint-plugin-standard": "^4.0.1",
+    "file-loader": "^6.0.0",
+    "imports-loader": "^1.1.0",
+    "mini-css-extract-plugin": "1.6.0",
+    "moment-locales-webpack-plugin": "^1.2.0",
+    "optimize-css-assets-webpack-plugin": "6.0.0",
+    "style-loader": "^1.2.1",
+    "stylelint": "^13.6.1",
+    "stylelint-config-standard": "^20.0.0",
+    "url-loader": "4.1.0",
+    "webpack": "^4.16.3",
+    "webpack-cli": "^3.1.0",
+    "webpack-manifest-plugin": "^2.2.0"
+  },
+  "dependencies": {
+    "bootstrap-3-typeahead": "^4.0.2",
+    "codemirror": "^5.59.1",
+    "d3": "^3.4.4",
+    "d3-shape": "^2.1.0",
+    "d3-tip": "^0.9.1",
+    "dagre-d3": "^0.6.4",
+    "datatables.net": "^1.10.23",
+    "datatables.net-bs": "^1.10.23",
+    "eonasdan-bootstrap-datetimepicker": "^4.17.47",
+    "jquery": ">=3.4.0",
+    "jshint": "^2.12.0",
+    "moment-timezone": "^0.5.28",
+    "nvd3": "^1.8.6",
+    "redoc": "^2.0.0-rc.48",
+    "url-search-params-polyfill": "^8.1.0"
+  },
+  "resolutions": {
+    "lodash": "^4.17.21"
+  }
+}

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

@@ -1,6 +1,7 @@
 { lib
 , attrs
 , bson
+, pythonOlder
 , buildPythonPackage
 , fetchFromGitHub
 , hypothesis
@@ -18,6 +19,10 @@ buildPythonPackage rec {
   version = "1.7.0";
   format = "pyproject";
 
+  # https://cattrs.readthedocs.io/en/latest/history.html#id33:
+  # "Python 2, 3.5 and 3.6 support removal. If you need it, use a version below 1.1.0."
+  disabled = pythonOlder "3.7";
+
   src = fetchFromGitHub {
     owner = "Tinche";
     repo = pname;

pkgs/development/python-modules/flask-appbuilder/default.nix

@@ -5,7 +5,6 @@
 , colorama
 , click
 , email_validator
-, fetchpatch
 , flask
 , flask-babel
 , flask_login
@@ -26,23 +25,18 @@
 
 buildPythonPackage rec {
   pname = "flask-appbuilder";
-  version = "3.3.0";
+  version = "3.3.1";
 
   src = fetchPypi {
     pname = "Flask-AppBuilder";
     inherit version;
-    sha256 = "00dsfv1apl6483wy20aj91f9h5ak2casbx5vcajv2nd3i7c7v8gx";
+    sha256 = "13rlpdf3ipm39zpc62sywn8qjn6gwfbgr43x7lqpxr28br2jcg3j";
   };
 
-  patches = [
+  # See here: https://github.com/dpgaspar/Flask-AppBuilder/commit/7097a7b133f27c78d2b54d2a46e4a4c24478a066.patch
-    # https://github.com/dpgaspar/Flask-AppBuilder/pull/1610
+  #           https://github.com/dpgaspar/Flask-AppBuilder/pull/1610
-    (fetchpatch {
+  # The patch from the PR doesn't apply cleanly so I edited it manually.
-      name = "flask_jwt_extended-and-pyjwt-patch";
+  patches = [ ./upgrade-to-flask_jwt_extended-4.patch ];
-      url = "https://github.com/dpgaspar/Flask-AppBuilder/commit/7097a7b133f27c78d2b54d2a46e4a4c24478a066.patch";
-      sha256 = "sha256-ZpY8+2Hoz3z01GVtw2OIbQcsmAwa7iwilFWzgcGhY1w=";
-      includes = [ "flask_appbuilder/security/manager.py" "setup.py" ];
-    })
-  ];
 
   propagatedBuildInputs = [
     apispec
@@ -70,9 +64,15 @@ buildPythonPackage rec {
   postPatch = ''
     substituteInPlace setup.py \
       --replace "apispec[yaml]>=3.3, <4" "apispec[yaml] >=3.3, <5" \
+      --replace "click>=6.7, <8" "click" \
+      --replace "Flask>=0.12, <2" "Flask" \
       --replace "Flask-Login>=0.3, <0.5" "Flask-Login >=0.3, <0.6" \
       --replace "Flask-Babel>=1, <2" "Flask-Babel >=1, <3" \
-      --replace "marshmallow-sqlalchemy>=0.22.0, <0.24.0" "marshmallow-sqlalchemy >=0.22.0, <0.25.0"
+      --replace "Flask-WTF>=0.14.2, <0.15.0" "Flask-WTF" \
+      --replace "marshmallow-sqlalchemy>=0.22.0, <0.24.0" "marshmallow-sqlalchemy" \
+      --replace "Flask-JWT-Extended>=3.18, <4" "Flask-JWT-Extended>=4.1.0" \
+      --replace "PyJWT>=1.7.1, <2.0.0" "PyJWT>=2.0.1" \
+      --replace "SQLAlchemy<1.4.0" "SQLAlchemy"
   '';
 
   # Majority of tests require network access or mongo

pkgs/development/python-modules/flask-appbuilder/upgrade-to-flask_jwt_extended-4.patch

@@ -0,0 +1,45 @@
+diff --git a/flask_appbuilder/security/api.py b/flask_appbuilder/security/api.py
+index 2e2dfd612..df1bd5a25 100644
+--- a/flask_appbuilder/security/api.py
++++ b/flask_appbuilder/security/api.py
+@@ -3,7 +3,7 @@
+     create_access_token,
+     create_refresh_token,
+     get_jwt_identity,
+-    jwt_refresh_token_required,
++    jwt_required,
+ )
+ 
+ from ..api import BaseApi, safe
+@@ -118,7 +118,7 @@ def login(self):
+         return self.response(200, **resp)
+ 
+     @expose("/refresh", methods=["POST"])
+-    @jwt_refresh_token_required
++    @jwt_required(refresh=True)
+     @safe
+     def refresh(self):
+         """
+diff --git a/flask_appbuilder/security/manager.py b/flask_appbuilder/security/manager.py
+index fe7697007..3b22ab255 100644
+--- a/flask_appbuilder/security/manager.py
++++ b/flask_appbuilder/security/manager.py
+@@ -297,7 +297,7 @@ def create_jwt_manager(self, app) -> JWTManager:
+         """
+         jwt_manager = JWTManager()
+         jwt_manager.init_app(app)
+-        jwt_manager.user_loader_callback_loader(self.load_user_jwt)
++        jwt_manager.user_lookup_loader(self.load_user_jwt)
+         return jwt_manager
+ 
+     def create_builtin_roles(self):
+@@ -1944,7 +1944,8 @@ def del_permission_role(self, role, perm_view):
+     def load_user(self, pk):
+         return self.get_user_by_id(int(pk))
+ 
+-    def load_user_jwt(self, pk):
++    def load_user_jwt(self, _jwt_header, jwt_data):
++        pk = jwt_data["sub"]
+         user = self.load_user(pk)
+         # Set flask g.user to JWT user, we can't do it on before request
+         g.user = user

pkgs/development/python-modules/marshmallow-oneofschema/default.nix

@@ -0,0 +1,22 @@
+{ lib, buildPythonPackage, fetchPypi, marshmallow, setuptools }:
+
+buildPythonPackage rec {
+  pname = "marshmallow-oneofschema";
+  version = "2.1.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0s0yr7nv06sfgxglghl2vq74g3m49j60k1hi2qzfsv4bj8hvs35k";
+  };
+
+  propagatedBuildInputs = [ marshmallow setuptools ];
+
+  pythonImportsCheck = [ "marshmallow_oneofschema" ];
+
+  meta = with lib; {
+    homepage = "https://github.com/marshmallow-code/marshmallow-oneofschema";
+    description = "Marshmallow library extension that allows schema (de)multiplexing";
+    license = licenses.mit;
+    maintainers = [ maintainers.ivan-tkatchev ];
+  };
+}

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

@@ -8,14 +8,14 @@
 
 buildPythonPackage rec {
   pname = "pyfronius";
-  version = "0.5.2";
+  version = "0.5.3";
   disabled = pythonOlder "3.6";
 
   src = fetchFromGitHub {
     owner = "nielstron";
     repo = pname;
     rev = version;
-    sha256 = "013nlxbpicm4d07q8cjkbwh6xbji8am5la9vv5iqjyk0h4c2hgr7";
+    sha256 = "sha256-AtCpraIYNrEkTygtLMivrXfKCKVKIIUCDo3GYFpg8fk=";
   };
 
   propagatedBuildInputs = [

pkgs/development/python-modules/python-nvd3/default.nix

@@ -0,0 +1,27 @@
+{ lib, buildPythonPackage, fetchFromGitHub, python-slugify, jinja2, setuptools, coverage }:
+
+buildPythonPackage rec {
+  pname = "python-nvd3";
+  version = "0.15.0";
+
+  src = fetchFromGitHub {
+    owner = "areski";
+    repo = "python-nvd3";
+    rev = "dc8e772597ed72f413b229856fc9a3318e57fcfc";
+    sha256 = "1vjnicszcc9j0rgb58104fk9sry5xad1xli64jana9bkx42c6x1v";
+  };
+
+  propagatedBuildInputs = [ python-slugify jinja2 setuptools ];
+  checkInputs = [ coverage ];
+
+  checkPhase = ''
+    coverage run --source=nvd3 setup.py test
+  '';
+
+  meta = with lib; {
+    homepage = "https://github.com/areski/python-nvd3";
+    description = "Python Wrapper for NVD3 - It's time for beautiful charts";
+    license = licenses.mit;
+    maintainers = [ maintainers.ivan-tkatchev ];
+  };
+}

pkgs/development/python-modules/sqlalchemy-jsonfield/default.nix

@@ -0,0 +1,44 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, sqlalchemy
+, setuptools-scm
+, setuptools
+, tox
+, sphinx
+, pytest
+, pytest-cov
+, pytest-html
+, pytest-sugar
+, coverage
+, pymysql
+, psycopg2 }:
+
+buildPythonPackage rec {
+  pname = "sqlalchemy-jsonfield";
+  version = "1.0.0";
+
+  src = fetchFromGitHub {
+    owner = "penguinolog";
+    repo = "sqlalchemy_jsonfield";
+    rev = version;
+    sha256 = "015pl4z84spfw8389hk1szlm37jgw2basvbmzmkacdqi0685zx24";
+  };
+
+  SETUPTOOLS_SCM_PRETEND_VERSION = "v${version}";
+
+  nativeBuildInputs = [ setuptools-scm ];
+  propagatedBuildInputs = [ sqlalchemy setuptools ];
+  checkInputs = [ tox sphinx pytest pytest-cov pytest-html pytest-sugar coverage pymysql psycopg2 ];
+
+  checkPhase = ''
+    TOX_TESTENV_PASSENV="PYTHONPATH SETUPTOOLS_SCM_PRETEND_VERSION" tox -e functional
+  '';
+
+  meta = with lib; {
+    homepage = "https://github.com/penguinolog/sqlalchemy_jsonfield";
+    description = "SQLALchemy JSONField implementation for storing dicts at SQL independently from JSON type support";
+    license = licenses.asl20;
+    maintainers = [ maintainers.ivan-tkatchev ];
+  };
+}

pkgs/games/empty-epsilon/0001-bundle-system-glm-in-seriousproton.patch

@@ -0,0 +1,34 @@
+From 9718cdb4bdaf7203d07789b2dc5eec4060538889 Mon Sep 17 00:00:00 2001
+From: Maximilian Bosch <maximilian@mbosch.me>
+Date: Fri, 9 Jul 2021 11:37:22 +0200
+Subject: [PATCH] bundle system-glm in seriousproton
+
+---
+ CMakeLists.txt | 5 ++++-
+ 1 file changed, 4 insertions(+), 1 deletion(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index cbd68ca..730df82 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -81,6 +81,9 @@ if(NOT ${SFML_FOUND})
+     )
+ endif()
+ 
++
++find_package(glm)
++
+ add_subdirectory(src/Box2D)
+ add_subdirectory(src/lua)
+ add_subdirectory(src/GL)
+@@ -205,7 +208,7 @@ target_compile_options(seriousproton_deps
+ 
+ target_link_libraries(seriousproton_deps
+     INTERFACE 
+-        box2d lua glew ${SFML_LIBRARIES}
++        box2d lua glew ${SFML_LIBRARIES} glm
+         "$<$<BOOL:${WIN32}>:wsock32>"
+         # LTO flag must be on the linker's list as well.
+         "$<$<AND:$<BOOL:${CMAKE_COMPILER_IS_GNUCC}>,$<OR:$<CONFIG:RelWithDebInfo>,$<CONFIG:Release>>>:-flto>"
+-- 
+2.31.1

pkgs/games/empty-epsilon/default.nix

@@ -1,11 +1,11 @@
-{ lib, stdenv, fetchFromGitHub, cmake, sfml, libX11, glew, python3 }:
+{ lib, stdenv, fetchFromGitHub, cmake, sfml, libX11, glew, python3, fetchpatch, applyPatches, glm}:
 
 let
 
   major = "2021";
-  minor = "03";
+  minor = "06";
-  patch.seriousproton = "30";
+  patch.seriousproton = "23";
-  patch.emptyepsilon = "31";
+  patch.emptyepsilon = "23";
 
   version.seriousproton = "${major}.${minor}.${patch.seriousproton}";
   version.emptyepsilon = "${major}.${minor}.${patch.emptyepsilon}";
@@ -14,15 +14,32 @@ let
     pname = "serious-proton";
     version = version.seriousproton;
 
-    src = fetchFromGitHub {
+    src = applyPatches {
-      owner = "daid";
+      src = fetchFromGitHub {
-      repo = "SeriousProton";
+        owner = "daid";
-      rev = "EE-${version.seriousproton}";
+        repo = "SeriousProton";
-      sha256 = "sha256-wxb/CxJ/HKsVngeahjygZFPMMxitkHdVD0EQ3svxgIU=";
+        rev = "EE-${version.seriousproton}";
+        sha256 = "sha256-02cHHWKoe99257qLgxtMjeXnhi0UYajh4v87B57felM=";
+      };
+
+      patches = [
+        # Various CMake fixes for `json11`. Can be removed on the next release.
+        (fetchpatch {
+          url = "https://github.com/daid/SeriousProton/commit/adbba45fd9ae5e020e43e5d7f9326f1355391209.patch";
+          sha256 = "sha256-gMTpIGPGCREmZ/ZxvEc7RVsVUxWXbu2BPUCE3A62sCI=";
+        })
+
+        # Simplified variant of
+        # * https://github.com/daid/SeriousProton/commit/0d1ac45b738195db5e2785531db713328f547e60
+        # * https://github.com/daid/SeriousProton/commit/32509f2db91a58b9528aeb1bb505e9426b52b825
+        #
+        # To fix configure errors when building EmptyEpsilon, can be removed on the next release.
+        ./0001-bundle-system-glm-in-seriousproton.patch
+      ];
     };
 
     nativeBuildInputs = [ cmake ];
-    buildInputs = [ sfml libX11 ];
+    buildInputs = [ sfml libX11 glm ];
 
     meta = with lib; {
       description = "C++ game engine coded on top of SFML used for EmptyEpsilon";
@@ -44,11 +61,23 @@ stdenv.mkDerivation {
     owner = "daid";
     repo = "EmptyEpsilon";
     rev = "EE-${version.emptyepsilon}";
-    sha256 = "sha256-x0XJPMU0prubTb4ti/W/dH5P9abNwbjqkeUhKQpct9o=";
+    sha256 = "sha256-dc/Ic1/DULTQO6y9xSop2HxFvUh4kN57oSF/HBmbmF4=";
   };
 
+  patches = [
+    # Various CMake fixes that can be removed when upgrading to the next release.
+    (fetchpatch {
+      url = "https://github.com/daid/EmptyEpsilon/commit/ee0cd42bfe5fd20b8339e8e02eb7f69766168d57.patch";
+      sha256 = "sha256-8dXtl/izfzqbwHtjuugjH34vYP+d4AobqZhxL2GXTzw=";
+    })
+    (fetchpatch {
+      url = "https://github.com/daid/EmptyEpsilon/commit/69d93e6acdae3259755924f9d35e7e5ae949d377.patch";
+      sha256 = "sha256-30AGo4mi73GrW9GNS3vF3mTOS7J5/41LvjOzNjeFhOg=";
+    })
+  ];
+
   nativeBuildInputs = [ cmake ];
-  buildInputs = [ serious-proton sfml glew libX11 python3 ];
+  buildInputs = [ serious-proton sfml glew libX11 python3 glm ];
 
   cmakeFlags = [
     "-DSERIOUS_PROTON_DIR=${serious-proton.src}"

pkgs/os-specific/linux/kernel/linux-testing-bcachefs.nix

@@ -1,24 +1,33 @@
-{ lib, buildPackages, fetchFromGitHub, fetchpatch, perl, buildLinux, ... } @ args:
+{ lib
+, fetchpatch
+, kernel
+, date ? "2021-07-08"
+, commit ? "3693b2ca83ff9eda49660b31299d2bebe3a1075f"
+, diffHash ? "1sfq3vwc2kxa761s292f2cqrm0vvqvkdx6drpyn5yaxwnapwidcw"
+, kernelPatches # must always be defined in bcachefs' all-packages.nix entry because it's also a top-level attribute supplied by callPackage
+, argsOverride ? {}
+, ...
+} @ args:
 
-buildLinux (args // {
+kernel.override ( args // {
-  version = "5.9.0-2020.11.20";
-  modDirVersion = "5.9.0";
 
-  src = fetchFromGitHub {
+  argsOverride = {
-    owner = "koverstreet";
+    version = "${kernel.version}-bcachefs-unstable-${date}";
-    repo = "bcachefs";
+    extraMeta = {
-    # commit does not exist on any branch on the target repository
+      branch = "master";
-    rev = "6a505b63ed3003faf5000f19fd08bbd477d93fbc";
+      maintainers = with lib.maintainers; [ davidak chiiruno ];
-    sha256 = "1rf34gzv9npafp1c3i6lymk3b0gnqp4rb0wl33pw6yrpgnsry3cc";
+      platforms = [ "x86_64-linux" ];
-  };
+    };
+  } // argsOverride;
 
-  extraConfig = "BCACHEFS_FS m";
+  kernelPatches = [ {
+      name = "bcachefs-${commit}";
+      patch = fetchpatch {
+        name = "bcachefs-${commit}.diff";
+        url = "https://evilpiepirate.org/git/bcachefs.git/rawdiff/?id=${commit}&id2=v${lib.versions.majorMinor kernel.version}";
+        sha256 = diffHash;
+      };
+      extraConfig = "BCACHEFS_FS m";
+    } ] ++ kernelPatches;
 
-  extraMeta = {
+})
-    branch = "master";
-    hydraPlatforms = []; # Should the testing kernels ever be built on Hydra?
-    maintainers = with lib.maintainers; [ davidak chiiruno ];
-    platforms = [ "x86_64-linux" ];
-  };
-
-} // (args.argsOverride or {}))

pkgs/servers/imgproxy/default.nix

@@ -3,12 +3,12 @@
 
 buildGoModule rec {
   pname = "imgproxy";
-  version = "2.16.5";
+  version = "2.16.6";
 
   src = fetchFromGitHub {
     owner = pname;
     repo = pname;
-    sha256 = "sha256-CLmnc33mVvm7CR0Qv4zsLiQ/jyRIkr1N53mMfD3flNM=";
+    sha256 = "sha256-wrd8G2y8oepaHMJaU4Bcvkf91ABX4ZapQSlztq4Gg84=";
     rev = "v${version}";
   };
 

pkgs/servers/sql/mysql/8.0.x.nix

@@ -1,16 +1,16 @@
 { lib, stdenv, fetchurl, bison, cmake, pkg-config
 , boost, icu, libedit, libevent, lz4, ncurses, openssl, protobuf, re2, readline, zlib, zstd
-, numactl, perl, cctools, CoreServices, developer_cmds, libtirpc, rpcsvc-proto
+, numactl, perl, cctools, CoreServices, developer_cmds, libtirpc, rpcsvc-proto, curl
 }:
 
 let
 self = stdenv.mkDerivation rec {
   pname = "mysql";
-  version = "8.0.22";
+  version = "8.0.25";
 
   src = fetchurl {
     url = "https://dev.mysql.com/get/Downloads/MySQL-${self.mysqlVersion}/${pname}-${version}.tar.gz";
-    sha256 = "9fd85bb243940ef8234d21384ef421a0962fd4d13406fc1420efa902115ce17a";
+    sha256 = "c16aa9cf621bc028efba2bb11f3c36a323b125fa0d108ff92fab60e46309206e";
   };
 
   patches = [
@@ -27,7 +27,7 @@ self = stdenv.mkDerivation rec {
   '';
 
   buildInputs = [
-    boost icu libedit libevent lz4 ncurses openssl protobuf re2 readline zlib
+    boost curl icu libedit libevent lz4 ncurses openssl protobuf re2 readline zlib
     zstd
   ] ++ lib.optionals stdenv.isLinux [
     numactl libtirpc

pkgs/servers/web-apps/lemmy/default.nix

@@ -0,0 +1,40 @@
+{ lib
+, stdenv
+, rustPlatform
+, fetchFromGitHub
+, openssl
+, postgresql
+, libiconv
+, Security
+}:
+
+rustPlatform.buildRustPackage rec {
+  pname = "lemmy-server";
+  version = "0.11.2";
+
+  src = fetchFromGitHub {
+    owner = "LemmyNet";
+    repo = "lemmy";
+    rev = version;
+    sha256 = "sha256-wDRBeAYjPpAd3DL99fH4Yng994hGmAmxlBqzOeXTP88=";
+  };
+
+  cargoSha256 = "sha256-7wF5mUjSeJvCNLZcR6XB31RX2RLOOEyTGpOQxg+NcWk=";
+
+  buildInputs = [ postgresql ]
+    ++ lib.optionals stdenv.isDarwin [ libiconv Security ];
+
+  # Using OPENSSL_NO_VENDOR is not an option on darwin
+  # As of version 0.10.35 rust-openssl looks for openssl on darwin
+  # with a hardcoded path to /usr/lib/libssl.x.x.x.dylib
+  # https://github.com/sfackler/rust-openssl/blob/master/openssl-sys/build/find_normal.rs#L115
+  OPENSSL_LIB_DIR = "${openssl.out}/lib";
+  OPENSSL_INCLUDE_DIR = "${openssl.dev}/include";
+
+  meta = with lib; {
+    description = "Ultra relevant and instant full-text search API";
+    homepage = "https://join-lemmy.org/";
+    license = licenses.agpl3Only;
+    maintainers = with maintainers; [ happysalada ];
+  };
+}

pkgs/tools/backup/zrepl/default.nix

@@ -1,5 +1,9 @@
-{ lib, buildGoModule, fetchFromGitHub }:
+{ lib
-
+, buildGoModule
+, fetchFromGitHub
+, makeWrapper
+, openssh
+}:
 buildGoModule rec {
   pname = "zrepl";
   version = "0.4.0";
@@ -15,10 +19,17 @@ buildGoModule rec {
 
   subPackages = [ "." ];
 
+  nativeBuildInputs = [
+    makeWrapper
+  ];
+
   postInstall = ''
     mkdir -p $out/lib/systemd/system
     substitute dist/systemd/zrepl.service $out/lib/systemd/system/zrepl.service \
       --replace /usr/local/bin/zrepl $out/bin/zrepl
+
+    wrapProgram $out/bin/zrepl \
+      --prefix PATH : ${lib.makeBinPath [ openssh ]}
   '';
 
   meta = with lib; {

pkgs/tools/filesystems/bcachefs-tools/default.nix

@@ -1,18 +1,34 @@
-{ lib, stdenv, fetchFromGitHub, pkg-config, attr, libuuid, libscrypt, libsodium, keyutils
+{ lib
-, liburcu, zlib, libaio, udev, zstd, lz4, valgrind, python3Packages, nixosTests
+, stdenv
-, fuseSupport ? false, fuse3 ? null }:
+, fetchFromGitHub
-
+, pkg-config
-assert fuseSupport -> fuse3 != null;
+, docutils
+, libuuid
+, libscrypt
+, libsodium
+, keyutils
+, liburcu
+, zlib
+, libaio
+, zstd
+, lz4
+, python3Packages
+, udev
+, valgrind
+, nixosTests
+, fuse3
+, fuseSupport ? false
+}:
 
 stdenv.mkDerivation {
   pname = "bcachefs-tools";
-  version = "2020-11-17";
+  version = "unstable-2021-07-08";
 
   src = fetchFromGitHub {
     owner = "koverstreet";
     repo = "bcachefs-tools";
-    rev = "41bec63b265a38dd9fa168b6042ea5bf07135048";
+    rev = "050d5f7bcf08bd02f5077a1c5559f352fa449e1e";
-    sha256 = "1y3187kpw1bmnl97isv28k2sw8cmrnsn31a0dw745adwm0n7z6fj";
+    sha256 = "15bl9ni0ckmvs5d7hi6v26z690rrmkb7dx00skn6gwq87ffz3imw";
   };
 
   postPatch = ''
@@ -22,7 +38,7 @@ stdenv.mkDerivation {
                 "INITRAMFS_DIR=${placeholder "out"}/etc/initramfs-tools"
   '';
 
-  nativeBuildInputs = [ pkg-config ];
+  nativeBuildInputs = [ pkg-config docutils ];
 
   buildInputs = [
     libuuid libscrypt libsodium keyutils liburcu zlib libaio
@@ -48,6 +64,6 @@ stdenv.mkDerivation {
     homepage = "https://bcachefs.org/";
     license = licenses.gpl2;
     maintainers = with maintainers; [ davidak chiiruno ];
-    platforms = platforms.linux;
+    platforms = [ "x86_64-linux" ]; # does not build on aarch64, see https://github.com/koverstreet/bcachefs-tools/issues/39
   };
 }

pkgs/tools/misc/gitlint/default.nix

@@ -2,12 +2,41 @@
 , buildPythonApplication
 , fetchFromGitHub
 , gitMinimal
-, arrow
+, python3
-, click
-, sh
-, wheel
 }:
 
+let
+  py = python3.override {
+    packageOverrides = self: super: {
+
+      click = super.click.overridePythonAttrs (oldAttrs: rec {
+        version = "7.1.2";
+        src = oldAttrs.src.override {
+          inherit version;
+          sha256 = "06kbzd6sjfkqan3miwj9wqyddfxc2b6hi7p5s4dvqjb3gif2bdfj";
+        };
+      });
+
+      arrow = super.arrow.overridePythonAttrs (oldAttrs: rec {
+        version = "1.0.3";
+        src = oldAttrs.src.override {
+          inherit version;
+          sha256 = "0793badh4hgbk2c5g70hmbl7n3d4g5d87bcflld0w9rjwy59r71r";
+        };
+      });
+
+      sh = super.sh.overridePythonAttrs (oldAttrs: rec {
+        version = "1.14.1";
+        src = oldAttrs.src.override {
+          inherit version;
+          sha256 = "13hxgifab9ichla13qaa7sh8r0il7vs1r21js72s0n355zr9mair";
+        };
+      });
+    };
+  };
+in
+with py.pkgs;
+
 buildPythonApplication rec {
   pname = "gitlint";
   version = "0.15.1";
@@ -19,7 +48,9 @@ buildPythonApplication rec {
     sha256 = "sha256-CqmE4V+svSuQAsoX0I3NpUqPU5CQf3fyCHJPrjUjHF4=";
   };
 
-  nativeBuildInputs = [ wheel ];
+  nativeBuildInputs = [
+    wheel
+  ];
 
   propagatedBuildInputs = [
     arrow
@@ -35,10 +66,10 @@ buildPythonApplication rec {
     gitMinimal
   ];
 
-  meta = {
+  meta = with lib; {
     description = "Linting for your git commit messages";
-    homepage = "http://jorisroovers.github.io/gitlint";
+    homepage = "https://jorisroovers.com/gitlint/";
-    license = lib.licenses.mit;
+    license = licenses.mit;
-    maintainers = with lib.maintainers; [ ethancedwards8 ];
+    maintainers = with maintainers; [ ethancedwards8 fab ];
   };
 }

pkgs/tools/nix/nixos-option/default.nix

@@ -1,4 +1,5 @@
 {lib, stdenv, boost, cmake, pkg-config, nix, ... }:
+
 stdenv.mkDerivation rec {
   name = "nixos-option";
   src = ./.;

pkgs/top-level/all-packages.nix

@@ -4348,6 +4348,8 @@ in
     autoreconfHook = buildPackages.autoreconfHook269;
   };
 
+  engauge-digitizer = libsForQt5.callPackage ../applications/science/math/engauge-digitizer { };
+
   epubcheck = callPackage ../tools/text/epubcheck { };
 
   luckybackup = libsForQt5.callPackage ../tools/backup/luckybackup {
@@ -19509,6 +19511,10 @@ in
 
   leafnode = callPackage ../servers/news/leafnode { };
 
+  lemmy = callPackage ../servers/web-apps/lemmy {
+    inherit (darwin.apple_sdk.frameworks) Security;
+  };
+
   lighttpd = callPackage ../servers/http/lighttpd { };
 
   livepeer = callPackage ../servers/livepeer { };
@@ -19843,7 +19849,7 @@ in
     inherit (darwin) cctools developer_cmds;
     inherit (darwin.apple_sdk.frameworks) CoreServices;
     boost = boost173; # Configure checks for specific version.
-    protobuf = protobuf3_7;
+    protobuf = protobuf3_11;
     icu =  icu67;
   };
 
@@ -20842,11 +20848,9 @@ in
     ];
   };
 
-  linux_testing_bcachefs = callPackage ../os-specific/linux/kernel/linux-testing-bcachefs.nix {
+  linux_testing_bcachefs = callPackage ../os-specific/linux/kernel/linux-testing-bcachefs.nix rec {
-    kernelPatches =
+    kernel = linux_5_13;
-      [ kernelPatches.bridge_stp_helper
+    kernelPatches = kernel.kernelPatches;
-        kernelPatches.request_key_helper
-      ];
   };
 
   linux_hardkernel_4_14 = callPackage ../os-specific/linux/kernel/linux-hardkernel-4.14.nix {
@@ -31185,6 +31189,8 @@ in
 
   nix-linter = haskell.lib.justStaticExecutables (haskellPackages.nix-linter);
 
+  nixos-option = callPackage ../tools/nix/nixos-option { };
+
   nix-pin = callPackage ../tools/package-management/nix-pin { };
 
   nix-prefetch = callPackage ../tools/package-management/nix-prefetch { };

pkgs/top-level/ocaml-packages.nix

@@ -1215,6 +1215,8 @@ let
 
     uchar = callPackage ../development/ocaml-modules/uchar { };
 
+    uecc = callPackage ../development/ocaml-modules/uecc { };
+
     utop = callPackage ../development/tools/ocaml/utop { };
 
     uuidm = callPackage ../development/ocaml-modules/uuidm { };

pkgs/top-level/python-packages.nix

@@ -4321,6 +4321,8 @@ in {
 
   marshmallow-enum = callPackage ../development/python-modules/marshmallow-enum { };
 
+  marshmallow-oneofschema = callPackage ../development/python-modules/marshmallow-oneofschema { };
+
   marshmallow-polyfield = callPackage ../development/python-modules/marshmallow-polyfield { };
 
   marshmallow-sqlalchemy = callPackage ../development/python-modules/marshmallow-sqlalchemy { };
@@ -4888,6 +4890,8 @@ in {
 
   nvchecker = callPackage ../development/python-modules/nvchecker { };
 
+  python-nvd3 = callPackage ../development/python-modules/python-nvd3 { };
+
   nwdiag = callPackage ../development/python-modules/nwdiag { };
 
   oath = callPackage ../development/python-modules/oath { };
@@ -8240,6 +8244,8 @@ in {
 
   SQLAlchemy-ImageAttach = callPackage ../development/python-modules/sqlalchemy-imageattach { };
 
+  sqlalchemy-jsonfield = callPackage ../development/python-modules/sqlalchemy-jsonfield { };
+
   sqlalchemy_migrate = callPackage ../development/python-modules/sqlalchemy-migrate { };
 
   sqlalchemy-utils = callPackage ../development/python-modules/sqlalchemy-utils { };