Merge staging-next into staging

27 files changed, 360 insertions, 155 deletions

diff --git a/pkgs/development/compilers/acme/default.nix b/pkgs/development/compilers/acme/default.nix
index 89c5620f5fc..f2f2c9cf8aa 100644
--- a/pkgs/development/compilers/acme/default.nix
+++ b/pkgs/development/compilers/acme/default.nix
@@ -2,12 +2,12 @@
 
 stdenv.mkDerivation rec {
   pname = "acme";
-  version = "120";
+  version = "unstable-2020-12-27";
 
   src = fetchsvn {
     url = "svn://svn.code.sf.net/p/acme-crossass/code-0/trunk";
-    rev = version;
-    sha256 = "0w17b8f8bis22m6l5bg8qg8nniy20f8yg2xmzjipblmc39vpv6s2";
+    rev = "314";
+    sha256 = "08zg26rh19nlif7id91nv0syx5n243ssxhfw0nk2r2bhjm5jrjz1";
   };
 
   sourceRoot = "code-0-r${src.rev}/src";
diff --git a/pkgs/development/compilers/llvm/11/llvm.nix b/pkgs/development/compilers/llvm/11/llvm.nix
index 2c29a30d76f..442e1ee3a6d 100644
--- a/pkgs/development/compilers/llvm/11/llvm.nix
+++ b/pkgs/development/compilers/llvm/11/llvm.nix
@@ -152,7 +152,7 @@ in stdenv.mkDerivation (rec {
     ln -s $lib/lib/libLLVM.dylib $lib/lib/libLLVM-${release_version}.dylib
   '';
 
-  doCheck = stdenv.isLinux && (!stdenv.isx86_32);
+  doCheck = stdenv.isLinux && (!stdenv.isx86_32) && (!stdenv.hostPlatform.isMusl);
 
   checkTarget = "check-all";
 
diff --git a/pkgs/development/interpreters/bats/default.nix b/pkgs/development/interpreters/bats/default.nix
index bbc38e51542..aa3abc65534 100644
--- a/pkgs/development/interpreters/bats/default.nix
+++ b/pkgs/development/interpreters/bats/default.nix
@@ -1,29 +1,37 @@
-{ stdenv, fetchzip, coreutils, gnugrep }:
+{ stdenv, lib, fetchzip, bash, makeWrapper, coreutils, gnugrep, doCheck ? true }:
 
 stdenv.mkDerivation rec {
   pname = "bats";
-  version = "1.2.0";
+  version = "1.2.1";
 
   src = fetchzip {
     url = "https://github.com/bats-core/bats-core/archive/v${version}.tar.gz";
-    sha256 = "0f59zh4d4pa1a7ybs5zl6h0csbqqv11lbnq0jl1dgwm1s6p49bsq";
+    hash = "sha256-grB/rJaDU0fuw4Hm3/9nI2px8KZnSWqRjTJPd7Mmb7s=";
   };
 
+  nativeBuildInputs = [ makeWrapper ];
+
   patchPhase = ''
-    patchShebangs ./install.sh
+    patchShebangs .
+  '';
 
-    substituteInPlace ./libexec/bats-core/bats \
-        --replace 'type -p greadlink readlink' 'type -p ${coreutils}/bin/readlink'
-    substituteInPlace ./libexec/bats-core/bats-format-tap-stream \
-        --replace grep ${gnugrep}/bin/grep
+  installPhase = ''
+    ./install.sh $out
+    wrapProgram $out/bin/bats --suffix PATH : "${lib.makeBinPath [ bash coreutils gnugrep ]}"
   '';
 
-  installPhase = "./install.sh $out";
+  inherit doCheck;
+  checkPhase = ''
+    # test generates file with absolute shebang dynamically
+    substituteInPlace test/install.bats --replace \
+      "/usr/bin/env bash" "${bash}/bin/bash"
+    bin/bats test
+  '';
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     homepage = "https://github.com/bats-core/bats-core";
     description = "Bash Automated Testing System";
-    maintainers = [ maintainers.lnl7 ];
+    maintainers = with maintainers; [ abathur ];
     license = licenses.mit;
     platforms = platforms.unix;
   };
diff --git a/pkgs/development/interpreters/guile/default.nix b/pkgs/development/interpreters/guile/default.nix
index 52a3488d051..238e1c7b7ad 100644
--- a/pkgs/development/interpreters/guile/default.nix
+++ b/pkgs/development/interpreters/guile/default.nix
@@ -58,7 +58,8 @@
   # "libgcc_s.so.1 must be installed for pthread_cancel to work".
 
   # don't have "libgcc_s.so.1" on darwin
-  LDFLAGS = stdenv.lib.optionalString (!stdenv.isDarwin) "-lgcc_s";
+  LDFLAGS = stdenv.lib.optionalString
+    (!stdenv.isDarwin && !stdenv.hostPlatform.isStatic) "-lgcc_s";
 
   configureFlags = [ "--with-libreadline-prefix=${readline.dev}" ]
     ++ stdenv.lib.optionals stdenv.isSunOS [
diff --git a/pkgs/development/interpreters/wasmer/default.nix b/pkgs/development/interpreters/wasmer/default.nix
index 7b390c54716..60ce4d89f19 100644
--- a/pkgs/development/interpreters/wasmer/default.nix
+++ b/pkgs/development/interpreters/wasmer/default.nix
@@ -22,6 +22,12 @@ rustPlatform.buildRustPackage rec {
 
   nativeBuildInputs = [ cmake pkg-config ];
 
+  # Since wasmer 0.17 no backends are enabled by default. Backends are now detected
+  # using the [makefile](https://github.com/wasmerio/wasmer/blob/master/Makefile).
+  # Enabling cranelift as this used to be the old default. At least one backend is
+  # needed for the run subcommand to work.
+  cargoBuildFlags = [ "--features 'backend-cranelift'" ];
+
   LIBCLANG_PATH = "${llvmPackages.libclang}/lib";
 
   meta = with lib; {
diff --git a/pkgs/development/libraries/bashup-events/3.2.nix b/pkgs/development/libraries/bashup-events/3.2.nix
new file mode 100644
index 00000000000..f7e88c38251
--- /dev/null
+++ b/pkgs/development/libraries/bashup-events/3.2.nix
@@ -0,0 +1,26 @@
+{ callPackage, fetchFromGitHub }:
+
+callPackage ./generic.nix {
+  variant = "3.2";
+  version = "2019-07-27";
+  branch = "master";
+  src = fetchFromGitHub {
+    owner = "bashup";
+    repo = "events";
+    rev = "83744c21bf720afb8325343674c62ab46a8f3d94";
+    hash = "sha256-0VDjd+1T1JBmSDGovWOOecUZmNztlwG32UcstfdigbI=";
+  };
+  fake = {
+    # Note: __ev.encode is actually defined, but it happens in a
+    # quoted arg to eval, which resholve currently doesn't (and may
+    # never) parse into. See abathur/resholve/issues/2.
+    function = [ "__ev.encode" ];
+  };
+  keep = {
+    # allow vars in eval
+    eval = [ "e" "f" "q" "r" ];
+    # allow vars executed as commands
+    "$f" = true;
+    "$n" = true;
+  };
+}
diff --git a/pkgs/development/libraries/bashup-events/4.4.nix b/pkgs/development/libraries/bashup-events/4.4.nix
new file mode 100644
index 00000000000..f880009ea71
--- /dev/null
+++ b/pkgs/development/libraries/bashup-events/4.4.nix
@@ -0,0 +1,20 @@
+{ callPackage, fetchFromGitHub }:
+
+callPackage ./generic.nix {
+  variant = "4.4";
+  version = "2020-04-04";
+  branch = "bash44";
+  src = fetchFromGitHub {
+    owner = "bashup";
+    repo = "events";
+    rev = "e97654f5602fc4e31083b27afa18dcc89b3e8296";
+    hash = "sha256-51OSIod3mEg3MKs4rrMgRcOimDGC+3UIr4Bl/cTRyGM=";
+  };
+  keep = {
+    # allow vars in eval
+    eval = [ "e" "bashup_ev" "n" ];
+    # allow vars executed as commands
+    "$f" = true;
+    "$n" = true;
+  };
+}
diff --git a/pkgs/development/libraries/bashup-events/default.nix b/pkgs/development/libraries/bashup-events/default.nix
new file mode 100644
index 00000000000..bcefdd0fcac
--- /dev/null
+++ b/pkgs/development/libraries/bashup-events/default.nix
@@ -0,0 +1,6 @@
+{ callPackage }:
+
+{
+  bashup-events32 = callPackage ./3.2.nix { };
+  bashup-events44 = callPackage ./4.4.nix { };
+}
diff --git a/pkgs/development/libraries/bashup-events/generic.nix b/pkgs/development/libraries/bashup-events/generic.nix
new file mode 100644
index 00000000000..78ef4c2f336
--- /dev/null
+++ b/pkgs/development/libraries/bashup-events/generic.nix
@@ -0,0 +1,83 @@
+{
+  # general
+  lib
+, callPackage
+, runCommand
+, resholvePackage
+, bash
+, shellcheck
+, doCheck ? true
+, doInstallCheck ? true
+  # variant-specific
+, variant
+, version
+, branch
+, src
+, fake ? false
+, keep
+}:
+let
+  # extracting this so that it's trivial to test in other shells
+  installCheck = shell:
+    ''
+      echo "testing bashup.events in ${shell}"
+      ${shell} <<'EOF'
+      source $out/bin/bashup.events
+      neat(){
+        echo $0: Hi from event \'test event\'. I can have both $1 and $2 arguments.
+        exit 0
+      }
+      event on "test event" @2 neat curried
+      echo event registered
+      event emit "test event" runtime
+      exit 1 # fail if emitting event didn't exit clean
+      EOF
+    '';
+
+in
+resholvePackage rec {
+  # bashup.events doesn't version yet but it has two variants with
+  # differing features/performance characteristics:
+  # - branch master: a variant for bash 3.2+
+  # - branch bash44: a variant for bash 4.4+
+  pname = "bashup-events${variant}-unstable";
+  # should be YYYY-MM-DD
+  inherit version;
+  inherit src;
+
+  installPhase = ''
+    install -Dt $out/bin bashup.events
+  '';
+
+  inherit doCheck;
+  checkInputs = [ shellcheck bash ];
+
+  # check based on https://github.com/bashup/events/blob/master/.dkrc
+  checkPhase = ''
+    SHELLCHECK_OPTS='-e SC2016,SC2145' ${shellcheck}/bin/shellcheck ./bashup.events
+    ${bash}/bin/bash -n ./bashup.events
+    ${bash}/bin/bash ./bashup.events
+  '';
+
+  solutions = {
+    events = {
+      inputs = [ ];
+      interpreter = "none";
+      scripts = [ "bin/bashup.events" ];
+      inherit keep;
+    } // lib.optionalAttrs (lib.isAttrs fake) { inherit fake; };
+  };
+
+  inherit doInstallCheck;
+  installCheckInputs = [ bash ];
+  installCheckPhase = installCheck "${bash}/bin/bash";
+
+  meta = with lib; {
+    inherit branch;
+    description = "An event listener/callback API for creating extensible bash programs";
+    homepage = "https://github.com/bashup/events";
+    license = licenses.cc0;
+    maintainers = with maintainers; [ abathur ];
+    platforms = platforms.all;
+  };
+}
diff --git a/pkgs/development/libraries/fcft/default.nix b/pkgs/development/libraries/fcft/default.nix
index 1ce09b63cbe..fd6f26c9789 100644
--- a/pkgs/development/libraries/fcft/default.nix
+++ b/pkgs/development/libraries/fcft/default.nix
@@ -1,21 +1,28 @@
 { stdenv, lib, fetchgit, pkg-config, meson, ninja, scdoc
-,freetype, fontconfig, harfbuzz, pixman, tllist, check }:
+, freetype, fontconfig, pixman, tllist, check
+, withHarfBuzz ? true
+, harfbuzz
+}:
 
 stdenv.mkDerivation rec {
   pname = "fcft";
-  version = "2.3.1";
+  version = "2.3.2";
 
   src = fetchgit {
     url = "https://codeberg.org/dnkl/fcft.git";
     rev = version;
-    sha256 = "sha256-FD3KfaQbSEA1XdmS6YxH+c5fSsra9Ro/KKslb7Brv7U=";
+    sha256 = "0k2i57rakm4g86f7hbhkby8af0vv7v63a70lk3m58mkycpy5q2rm";
   };
 
   nativeBuildInputs = [ pkg-config meson ninja scdoc ];
-  buildInputs = [ freetype fontconfig pixman tllist harfbuzz ];
+  buildInputs = [ freetype fontconfig pixman tllist ]
+    ++ lib.optional withHarfBuzz harfbuzz;
   checkInputs = [ check ];
 
-  mesonFlags = [ "--buildtype=release" ];
+  mesonFlags = [
+    "--buildtype=release"
+    "-Dtext-shaping=${if withHarfBuzz then "enabled" else "disabled"}"
+  ];
 
   doCheck = true;
 
diff --git a/pkgs/development/libraries/libinfinity/default.nix b/pkgs/development/libraries/libinfinity/default.nix
index e018c1a9f5e..15d9b05ebd4 100644
--- a/pkgs/development/libraries/libinfinity/default.nix
+++ b/pkgs/development/libraries/libinfinity/default.nix
@@ -13,10 +13,10 @@ let
 
   self = stdenv.mkDerivation rec {
     pname = "libinfinity";
-    version = "0.7.1";
+    version = "0.7.2";
     src = fetchurl {
-      url = "http://releases.0x539.de/libinfinity/${pname}-${version}.tar.gz";
-      sha256 = "1jw2fhrcbpyz99bij07iyhy9ffyqdn87vl8cb1qz897y3f2f0vk2";
+      url = "https://github.com/gobby/${pname}/releases/download/${version}/${pname}-${version}.tar.gz";
+      sha256 = "17i3g61hxz9pzl3ryd1yr15142r25m06jfzjrpdy7ic1b8vjjw3f";
     };
 
     outputs = [ "bin" "out" "dev" "man" "devdoc" ];
@@ -43,7 +43,7 @@ let
     };
 
     meta = {
-      homepage = "http://gobby.0x539.de/";
+      homepage = "https://gobby.github.io/";
       description = "An implementation of the Infinote protocol written in GObject-based C";
       license = stdenv.lib.licenses.lgpl2Plus;
       maintainers = [ stdenv.lib.maintainers.phreedom ];
diff --git a/pkgs/development/libraries/poly2tri-c/default.nix b/pkgs/development/libraries/poly2tri-c/default.nix
index a3e42b3ae4b..5799410fe1d 100644
--- a/pkgs/development/libraries/poly2tri-c/default.nix
+++ b/pkgs/development/libraries/poly2tri-c/default.nix
@@ -12,7 +12,7 @@ stdenv.mkDerivation rec {
   outputs = [ "bin" "out" "dev" ];
 
   src = fetchFromGitHub {
-    owner = "Paul-Browne";
+    owner = "Mattey40";
     repo = "poly2tri-c";
     rev = "p2tc-${version}";
     sha256 = "158vm3wqfxs22b74kqc4prlvjny38qqm3kz5wrgasmx0qciwh0g8";
diff --git a/pkgs/development/misc/resholve/README.md b/pkgs/development/misc/resholve/README.md
index ddba7fc1493..6b99aebb597 100644
--- a/pkgs/development/misc/resholve/README.md
+++ b/pkgs/development/misc/resholve/README.md
@@ -6,9 +6,28 @@ until then I'll outline how to use the `resholvePackage` function.
 
 > Fair warning: resholve does *not* aspire to resolving all valid Shell
 > scripts. It depends on the OSH/Oil parser, which aims to support most (but
-> not all) Bash, and aims to be a ~90% sort of solution.
+> not all) Bash. resholve aims to be a ~90% sort of solution.
 
-Let's start with a simple example from one of my own projects:
+## API Concepts
+
+The main difference between `resholvePackage` and other builder functions
+is the `solutions` attrset, which describes which scripts to resolve and how.
+Each "solution" (k=v pair) in this attrset describes one resholve invocation.
+
+> NOTE: For most shell packages, one invocation will probably be enough:
+> - Packages with a single script will only need one solution.
+> - Packages with multiple scripts can still use one solution if the scripts
+>   don't require conflicting directives.
+> - Packages with scripts that require conflicting directives can use multiple
+>   solutions to resolve the scripts separately, but produce a single package.
+
+## Basic Example
+
+Here's a simple example from one of my own projects, with annotations:
+<!--
+TODO: ideally this will use a nixpkgs example; but we don't have any IN yet
+and the first package PR (bashup-events) is too complex for this context.
+-->
 
 ```nix
 { stdenv, lib, resholvePackage, fetchFromGitHub, bashup-events44, bashInteractive_5, doCheck ? true, shellcheck }:
@@ -22,10 +41,20 @@ resholvePackage rec {
   };
 
   solutions = {
+    # Give each solution a short name. This is what you'd use to
+    # override its settings, and it shows in (some) error messages.
     profile = {
-      # the only *required* arguments
+      # the only *required* arguments are the 3 below
+
+      # Specify 1 or more $out-relative script paths. Unlike many
+      # builders, resholvePackage modifies the output files during
+      # fixup (to correctly resolve in-package sourcing).
       scripts = [ "bin/shellswain.bash" ];
+
+      # "none" for no shebang, "${bash}/bin/bash" for bash, etc.
       interpreter = "none";
+
+      # packages resholve should resolve executables from
       inputs = [ bashup-events44 ];
     };
   };
@@ -39,100 +68,91 @@ resholvePackage rec {
 }
 ```
 
-I'll focus on the `solutions` attribute, since this is the only part
-that differs from other derivations.
-
-Each "solution" (k=v pair)
-describes one resholve invocation. For most shell packages, one
-invocation will probably be enough. resholve will make you be very
-explicit about your script's dependencies, and it may also need your
-help sorting out some references or problems that it can't safely
-handle on its own.
-
-If you have more than one script, and your scripts need conflicting
-directives, you can specify more than one solution to resolve the
-scripts separately, but still produce a single package.
-
-Let's take a closer look:
-
-```nix
-  solutions = {
-    # each solution has a short name; this is what you'd use to
-    # override the settings of this solution, and it may also show up
-    # in (some) error messages.
-    profile = {
-      # specify one or more $out-relative script paths (unlike many
-      # builders, resholve will modify the output files during fixup
-      # to correctly resolve scripts that source within the package)
-      scripts = [ "bin/shellswain.bash" ];
-      # "none" for no shebang, "${bash}/bin/bash" for bash, etc.
-      interpreter = "none";
-      # packages resholve should resolve executables from
-      inputs = [ bashup-events44 ];
-    };
-  };
-```
-
-resholve has a (growing) number of options for handling more complex
-scripts. I won't cover these in excruciating detail here. You can find
-more information about these in `man resholve` via `nixpkgs.resholve`.
-
-Instead, we'll look at the general form of the solutions attrset:
-
-```nix
-solutions = {
-  shortname = {
-    # required
-    # $out-relative paths to try resolving
-    scripts = [ "bin/shunit2" ];
-    # packages to resolve executables from
-    inputs = [ coreutils gnused gnugrep findutils ];
-    # path for shebang, or 'none' to omit shebang
-    interpreter = "${bash}/bin/bash";
-
-    # optional
-    fake = { fake directives };
-    fix = { fix directives };
-    keep = { keep directives };
-    # file to inject before first code-line of script
-    prologue = file;
-    # file to inject after last code-line of script
-    epilogue = file;
-    # extra command-line flags passed to resholve; generally this API
-    # should align with what resholve supports, but flags may help if
-    # you need to override the version of resholve.
-    flags = [ ];
-  };
-};
-```
-
-The main way you'll adjust how resholve handles your scripts are the
-fake, fix, and keep directives. The manpage covers their purpose and
-how to format them on the command-line, so I'll focus on how you'll
-need to translate them into Nix types.
+## Options
+
+`resholvePackage` maps Nix types/idioms into the flags and environment variables
+that the `resholve` CLI expects. Here's an overview:
+
+| Option        | Type    | Containing                                            |
+| ------------- | ------- | ----------------------------------------------------- |
+| scripts       | list    | $out-relative string paths to resolve                 |
+| inputs        | list    | packages to resolve executables from                  |
+| interpreter   | string  | 'none' or abspath for shebang                         |
+| prologue      | file    | text to insert before the first code-line             |
+| epilogue      | file    | text to isnert after the last code-line               |
+| flags         | list    | strings to pass as flags                              |
+| fake          | attrset | [directives](#controlling-resolution-with-directives) |
+| fix           | attrset | [directives](#controlling-resolution-with-directives) |
+| keep          | attrset | [directives](#controlling-resolution-with-directives) |
+
+## Controlling resolution with directives
+
+In order to resolve a script, resholve will make you disambiguate how it should
+handle any potential problems it encounters with directives. There are currently
+3 types:
+1. `fake` directives tell resholve to pretend it knows about an identifier
+   such as a function, builtin, external command, etc. if there's a good reason
+   it doesn't already know about it. Common examples:
+   - builtins for a non-bash shell
+   - loadable builtins
+   - platform-specific external commands in cross-platform conditionals
+2. `fix` directives give resholve permission to fix something that it can't
+   safely fix automatically. Common examples:
+   - resolving commands in aliases (this is appropriate for standalone scripts
+     that use aliases non-interactively--but it would prevent profile/rc
+     scripts from using the latest current-system symlinks.)
+   - resolve commands in a variable definition
+   - resolve an absolute command path from inputs as if it were a bare reference
+3. `keep` directives tell resholve not to raise an error (i.e., ignore)
+   something it would usually object to. Common examples:
+   - variables used as/within the first word of a command
+   - pre-existing absolute or user-relative (~) command paths
+   - dynamic (variable) arguments to commands known to accept/run other commands
+
+> NOTE: resholve has a (growing) number of directives detailed in `man resholve`
+> via `nixpkgs.resholve`.
+
+Each of these 3 types is represented by its own attrset, where you can think
+of the key as a scope. The value should be:
+- `true` for any directives that the resholve CLI accepts as a single word
+- a list of strings for all other options
+<!--
+TODO: these should be fully-documented here, but I'm already maintaining
+more copies of their specification/behavior than I like, and continuing to
+add more at this early date will only ensure that I spend more time updating
+docs and less time filling in feature gaps.
+
+Full documentation may be greatly accellerated if someone can help me sort out
+single-sourcing. See: https://github.com/abathur/resholve/issues/19
+-->
+
+This will hopefully make more sense when you see it. Here are CLI examples
+from the manpage, and the Nix equivalents:
 
 ```nix
 # --fake 'f:setUp;tearDown builtin:setopt source:/etc/bashrc'
 fake = {
-    function = [ "setUp" "tearDown" ];
-    builtin = [ "setopt" ];
-    source = [ "/etc/bashrc" ];
+  # fake accepts the initial of valid identifier types as a CLI convienience.
+  # Use full names in the Nix API.
+  function = [ "setUp" "tearDown" ];
+  builtin = [ "setopt" ];
+  source = [ "/etc/bashrc" ];
 };
 
 # --fix 'aliases xargs:ls $GIT:gix'
 fix = {
-    # all single-word directives use `true` as value
-    aliases = true;
-    xargs = [ "ls" ];
-    "$GIT" = [ "gix" ];
+  # all single-word directives use `true` as value
+  aliases = true;
+  xargs = [ "ls" ];
+  "$GIT" = [ "gix" ];
 };
 
 # --keep 'which:git;ls .:$HOME $LS:exa /etc/bashrc ~/.bashrc'
 keep = {
-    which = [ "git" "ls" ];
-    "." = [ "$HOME" ];
-    "$LS" = [ "exa" ];
-    "/etc/bashrc" = true;
-    "~/.bashrc" = true;
+  which = [ "git" "ls" ];
+  "." = [ "$HOME" ];
+  "$LS" = [ "exa" ];
+  "/etc/bashrc" = true;
+  "~/.bashrc" = true;
 };
 ```
diff --git a/pkgs/development/python-modules/alerta-server/default.nix b/pkgs/development/python-modules/alerta-server/default.nix
index ce1e702a7ba..968fdf2402c 100644
--- a/pkgs/development/python-modules/alerta-server/default.nix
+++ b/pkgs/development/python-modules/alerta-server/default.nix
@@ -4,11 +4,11 @@
 
 buildPythonPackage rec {
   pname = "alerta-server";
-  version = "8.1.0";
+  version = "8.2.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "32a97eee95aea5527f6efa844c18b727fe4a6d61356ea3c0769a29a163ddcb7e";
+    sha256 = "ee06d0f828b679402847989de9013a1271db282af377f5dce776347623dde345";
   };
 
   propagatedBuildInputs = [
diff --git a/pkgs/development/python-modules/aresponses/default.nix b/pkgs/development/python-modules/aresponses/default.nix
index 2407adefd5c..53353a13788 100644
--- a/pkgs/development/python-modules/aresponses/default.nix
+++ b/pkgs/development/python-modules/aresponses/default.nix
@@ -5,12 +5,13 @@
 , isPy3k
 , pytest
 , pytest-asyncio
+, pytest-cov
 , pytestCheckHook
 }:
 
 buildPythonPackage rec {
   pname = "aresponses";
-  version = "2.1.0";
+  version = "2.1.2";
 
   disabled = !isPy3k;
 
@@ -18,7 +19,7 @@ buildPythonPackage rec {
     owner = "CircleUp";
     repo = pname;
     rev = version;
-    sha256 = "0dc1y4s6kpmr0ar63kkyghvisgbmb8qq5wglmjclrpzd5180mjcl";
+    sha256 = "007wrk4wdy97a81imgzxd6sm5dly9v7abmxh9fyfi0vp1p7s75bw";
   };
 
   propagatedBuildInputs = [
@@ -32,8 +33,9 @@ buildPythonPackage rec {
 
   checkInputs = [
     aiohttp
-    pytestCheckHook
     pytest-asyncio
+    pytest-cov
+    pytestCheckHook
   ];
 
   # Disable tests which requires network access
@@ -42,6 +44,8 @@ buildPythonPackage rec {
     "test_passthrough"
   ];
 
+  __darwinAllowLocalNetworking = true;
+
   pythonImportsCheck = [ "aresponses" ];
 
   meta = with lib; {
diff --git a/pkgs/development/python-modules/cx_oracle/default.nix b/pkgs/development/python-modules/cx_oracle/default.nix
index ceacad12059..89946964544 100644
--- a/pkgs/development/python-modules/cx_oracle/default.nix
+++ b/pkgs/development/python-modules/cx_oracle/default.nix
@@ -2,13 +2,13 @@
 
 buildPythonPackage rec {
   pname = "cx_Oracle";
-  version = "8.0.1";
+  version = "8.1.0";
 
   buildInputs = [ odpic ];
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "f10ada7f821a325c6befdd6fef1cac44ebc830736d0b75dda7b8ac9f851087b2";
+    sha256 = "e1698c5522ee1355e552b30bfa0a58e6e772475b882c5d69d158bd7e6aed45de";
   };
 
   preConfigure = ''
diff --git a/pkgs/development/python-modules/mongoengine/default.nix b/pkgs/development/python-modules/mongoengine/default.nix
index 3ac24f7430d..c8969d9e2d4 100644
--- a/pkgs/development/python-modules/mongoengine/default.nix
+++ b/pkgs/development/python-modules/mongoengine/default.nix
@@ -12,14 +12,14 @@
 
 buildPythonPackage rec {
   pname = "mongoengine";
-  version = "0.21.0";
+  version = "0.22.0";
   disabled = isPy27;
 
   src = fetchFromGitHub {
     owner = "MongoEngine";
     repo = pname;
     rev = "v${version}";
-    sha256 = "02amfdirdw3nc0kgiyax7yndk5b65g83kbjvwwxbgnlcrb9vjzcd";
+    sha256 = "14n9rl8w3i1fq96f3jzsg7gy331d7fmrapva6m38ih53rnf38bdf";
   };
 
   propagatedBuildInputs = [
diff --git a/pkgs/development/python-modules/nibabel/default.nix b/pkgs/development/python-modules/nibabel/default.nix
index e67bdcc3194..91195abce1c 100644
--- a/pkgs/development/python-modules/nibabel/default.nix
+++ b/pkgs/development/python-modules/nibabel/default.nix
@@ -34,6 +34,5 @@ buildPythonPackage rec {
     description = "Access a multitude of neuroimaging data formats";
     license = licenses.mit;
     maintainers = with maintainers; [ ashgillman ];
-    platforms = platforms.x86_64;  # https://github.com/nipy/nibabel/issues/861
   };
 }
diff --git a/pkgs/development/python-modules/py3status/default.nix b/pkgs/development/python-modules/py3status/default.nix
index a2aeaceef6d..71314a08eeb 100644
--- a/pkgs/development/python-modules/py3status/default.nix
+++ b/pkgs/development/python-modules/py3status/default.nix
@@ -33,9 +33,8 @@ buildPythonPackage rec {
 
   doCheck = false;
   propagatedBuildInputs = [
-    pytz requests tzlocal i3ipc pydbus pygobject3 pyserial setuptools dbus-python
+    pytz requests tzlocal i3ipc pydbus pygobject3 pyserial setuptools dbus-python file
   ];
-  buildInputs = [ file ];
   prePatch = ''
     sed -i -e "s|'file|'${file}/bin/file|" py3status/parse_config.py
     sed -i -e "s|\[\"acpi\"|\[\"${acpi}/bin/acpi\"|" py3status/modules/battery_level.py
diff --git a/pkgs/development/python-modules/sqlite-utils/default.nix b/pkgs/development/python-modules/sqlite-utils/default.nix
index 99a6369de55..2bb700f6755 100644
--- a/pkgs/development/python-modules/sqlite-utils/default.nix
+++ b/pkgs/development/python-modules/sqlite-utils/default.nix
@@ -15,12 +15,12 @@
 
 buildPythonPackage rec {
   pname = "sqlite-utils";
-  version = "3.2";
+  version = "3.3";
   disabled = pythonOlder "3.6";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "83d60e0f0de5e4a367e2ad414dc008c0602e2af35325b09e41c7b2c69808dcc1";
+    sha256 = "1linla3za1gb3w0n0k6h3q8in62qhipizff259p14gzmyr95rjjv";
   };
 
   propagatedBuildInputs = [
@@ -37,11 +37,6 @@ buildPythonPackage rec {
     hypothesis
   ];
 
-  # disabled until upstream updates tests
-  disabledTests = lib.optionals (lib.versionAtLeast sqlite.version "3.34.0") [
-    "test_optimize"
-  ];
-
   meta = with lib; {
     description = "Python CLI utility and library for manipulating SQLite databases";
     homepage = "https://github.com/simonw/sqlite-utils";
diff --git a/pkgs/development/python-modules/waqiasync/default.nix b/pkgs/development/python-modules/waqiasync/default.nix
new file mode 100644
index 00000000000..3b8dfce6114
--- /dev/null
+++ b/pkgs/development/python-modules/waqiasync/default.nix
@@ -0,0 +1,32 @@
+{ lib
+, aiohttp
+, async-timeout
+, buildPythonPackage
+, fetchPypi
+}:
+
+buildPythonPackage rec {
+  pname = "waqiasync";
+  version = "1.0.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1yxls7ywfg954c3vxgnp98qa1b8dsq9b2fld11fb9sx1k4mjc29d";
+  };
+
+  propagatedBuildInputs = [
+    aiohttp
+    async-timeout
+  ];
+
+  # Project has no tests
+  doCheck = false;
+  pythonImportsCheck = [ "waqiasync" ];
+
+  meta = with lib; {
+    description = "Python library for http://aqicn.org";
+    homepage = "https://github.com/andrey-git/waqi-async";
+    license = with licenses; [ mit ];
+    maintainers = with maintainers; [ fab ];
+  };
+}
diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 362e7b81da4..746e6eefe53 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -280,6 +280,7 @@ let
     mwaved = [ pkgs.fftw.dev ];
     ncdf4 = [ pkgs.netcdf ];
     nloptr = [ pkgs.nlopt pkgs.pkgconfig ];
+    n1qn1 = [ pkgs.gfortran ];
     odbc = [ pkgs.unixODBC ];
     pander = [ pkgs.pandoc pkgs.which ];
     pbdMPI = [ pkgs.openmpi ];
@@ -415,6 +416,11 @@ let
     systemfonts = [ pkgs.pkgconfig ];
     tesseract = [ pkgs.pkgconfig ];
     Cairo = [ pkgs.pkgconfig ];
+    CLVTools = [ pkgs.gsl ];
+    JMcmprsk = [ pkgs.gsl ];
+    mashr = [ pkgs.gsl ];
+    hadron = [ pkgs.gsl ];
+    AMOUNTAIN = [ pkgs.gsl ];
     Rsymphony = [ pkgs.pkgconfig pkgs.doxygen pkgs.graphviz pkgs.subversion ];
     tcltk2 = [ pkgs.tcl pkgs.tk ];
     tikzDevice = [ pkgs.which pkgs.texlive.combined.scheme-medium ];
@@ -802,7 +808,7 @@ let
     openssl = old.openssl.overrideDerivation (attrs: {
       preConfigure = ''
         patchShebangs configure
-        '';
+      '';
       PKGCONFIG_CFLAGS = "-I${pkgs.openssl.dev}/include";
       PKGCONFIG_LIBS = "-Wl,-rpath,${pkgs.openssl.out}/lib -L${pkgs.openssl.out}/lib -lssl -lcrypto";
     });
@@ -857,6 +863,12 @@ let
         '';
     });
 
+    libgeos = old.libgeos.overrideDerivation (attrs: {
+      preConfigure = ''
+        patchShebangs configure
+        '';
+    });
+
     protolite = old.protolite.overrideDerivation (attrs: {
       preConfigure = ''
         patchShebangs configure
diff --git a/pkgs/development/r-modules/patches/qtbase.patch b/pkgs/development/r-modules/patches/qtbase.patch
deleted file mode 100644
index 14427b72630..00000000000
--- a/pkgs/development/r-modules/patches/qtbase.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff -ru -x '*~' qtbase_orig/src/Makefile qtbase/src/Makefile
---- qtbase_orig/src/Makefile	2012-03-03 03:57:47.000000000 +0900
-+++ qtbase/src/Makefile	2014-11-01 23:06:51.383876323 +0900
-@@ -10,6 +10,9 @@
- 	      -DR_INCLUDES=${R_INCLUDE_DIR} \
- 	      -DCMAKE_INSTALL_PREFIX=../src; \
- 	make install
-+# I could not control RPATH via CMake. HELP WANTED!
-+	patchelf --set-rpath ${CMAKE_LIBRARY_PATH} qtbase.so
-+	find ../inst/local/ -executable -type f -print0 | xargs -0 patchelf --set-rpath ${CMAKE_LIBRARY_PATH} 
- 
- clean:
- 	rm -rf ../kdebindings-build
diff --git a/pkgs/development/tools/continuous-integration/fly/default.nix b/pkgs/development/tools/continuous-integration/fly/default.nix
index f993faf544d..855fd879a8e 100644
--- a/pkgs/development/tools/continuous-integration/fly/default.nix
+++ b/pkgs/development/tools/continuous-integration/fly/default.nix
@@ -2,16 +2,16 @@
 
 buildGoModule rec {
   pname = "fly";
-  version = "6.7.2";
+  version = "6.7.3";
 
   src = fetchFromGitHub {
     owner = "concourse";
     repo = "concourse";
     rev = "v${version}";
-    sha256 = "0c5alf2a0088i25mglla9dl4m3wr5y8pnl5cczgn06sz8qp9a0s0";
+    sha256 = "sha256-XaoM/1YuHBl8ndPz3EByW1X0CzTuvJ5ju11mStbJnEU=";
   };
 
-  vendorSha256 = "1fxbxkg7disndlmb065abnfn7sn79qclkcbizmrq49f064w1ijr4";
+  vendorSha256 = "sha256-xeptlcJLj+R1BdC8Rdi3hsJVxdrmvfeTMsrhMNGrXi8=";
 
   doCheck = false;
 
diff --git a/pkgs/development/tools/git-quick-stats/default.nix b/pkgs/development/tools/git-quick-stats/default.nix
index 500c9a55c1d..2b775de4e43 100644
--- a/pkgs/development/tools/git-quick-stats/default.nix
+++ b/pkgs/development/tools/git-quick-stats/default.nix
@@ -11,13 +11,13 @@
 
 stdenv.mkDerivation rec {
   pname = "git-quick-stats";
-  version = "2.1.4";
+  version = "2.1.5";
 
   src = fetchFromGitHub {
     repo = "git-quick-stats";
     owner = "arzzen";
     rev = version;
-    sha256 = "0fg0fijghcz7hvbc9y8dfksz0qmsz700kc2mfb03y90kja99v68y";
+    sha256 = "sha256-d5B+SSUXtOD4x+dChQsUCkiHuHcW3lOrL4QhQekY7cA=";
   };
 
   nativeBuildInputs = [ makeWrapper ];
diff --git a/pkgs/development/tools/swiftformat/default.nix b/pkgs/development/tools/swiftformat/default.nix
index cb3ed5217f0..823496693f2 100644
--- a/pkgs/development/tools/swiftformat/default.nix
+++ b/pkgs/development/tools/swiftformat/default.nix
@@ -7,13 +7,13 @@
 
 stdenv.mkDerivation rec {
   pname = "swiftformat";
-  version = "0.44.9";
+  version = "0.47.10";
 
   src = fetchFromGitHub {
     owner = "nicklockwood";
     repo = "SwiftFormat";
     rev = version;
-    sha256 = "0zajvbaf3r02k53lv5zdxf13apc6chnjmj69zkyac48lpnpbcxq6";
+    sha256 = "1gqxpymbhpmap0i2blg9akarlql4mkzv45l4i212gsxcs991b939";
   };
 
   preConfigure = "LD=$CC";
diff --git a/pkgs/development/web/flyctl/default.nix b/pkgs/development/web/flyctl/default.nix
index 63d60547bec..96893870fa9 100644
--- a/pkgs/development/web/flyctl/default.nix
+++ b/pkgs/development/web/flyctl/default.nix
@@ -2,13 +2,13 @@
 
 buildGoModule rec {
   pname = "flyctl";
-  version = "0.0.154";
+  version = "0.0.161";
 
   src = fetchFromGitHub {
     owner = "superfly";
     repo = "flyctl";
     rev = "v${version}";
-    sha256 = "0hf33jm0ph4a79jg9irz0ynvdyah942cm5hb6j04hmg24x1037jm";
+    sha256 = "sha256-mM+jo1zKfA8u0IxtruQp4va0f7PldJQJV1/ypF1K0fI=";
   };
 
   preBuild = ''
@@ -17,7 +17,7 @@ buildGoModule rec {
 
   subPackages = [ "." ];
 
-  vendorSha256 = "0fmbwk0j2aayvi3cx8cfp4b3h89v88qm4kslbmhlj8mny9rd7lys";
+  vendorSha256 = "sha256-8rzXltsAXF9qIX1BrBwwi+145nQcXjrEBdIXgSgVYRw=";
 
   doCheck = false;