NixOS · Sep 29, 2020 · Sep 29, 2020 · Sep 29, 2020 · Sep 29, 2020 · Sep 29, 2020
diff --git a/pkgs/applications/editors/vim/macvim.nix b/pkgs/applications/editors/vim/macvim.nix
@@ -27,13 +27,13 @@ in
 stdenv.mkDerivation {
   pname = "macvim";
 
-  version = "8.2.539";
+  version = "8.2.1719";
 
   src = fetchFromGitHub {
     owner = "macvim-dev";
     repo = "macvim";
-    rev = "snapshot-163";
-    sha256 = "0ibc6h7zmk81dygkxd8a2rcq72zbqmr9kh64xhsm9h0p70505cdk";
+    rev = "snapshot-166";
+    sha256 = "1p51q59l1dl5lnf1ms960lm8zfg39p8xq0pdjw6wdyypjj3r8v3v";
   };
 
   enableParallelBuilding = true;
@@ -68,8 +68,6 @@ stdenv.mkDerivation {
       "--disable-sparkle"
   ];
 
-  makeFlags = ''PREFIX=$(out) CPPFLAGS="-Wno-error"'';
-
   # Remove references to Sparkle.framework from the project.
   # It's unused (we disabled it with --disable-sparkle) and this avoids
   # copying the unnecessary several-megabyte framework into the result.
@@ -85,7 +83,10 @@ stdenv.mkDerivation {
 
     DEV_DIR=$(/usr/bin/xcode-select -print-path)/Platforms/MacOSX.platform/Developer
     configureFlagsArray+=(
-      "--with-developer-dir=$DEV_DIR"
+      --with-developer-dir="$DEV_DIR"
+      LDFLAGS="-L${ncurses}/lib"
+      CPPFLAGS="-isystem ${ncurses.dev}/include"
+      CFLAGS="-Wno-error=implicit-function-declaration"
     )
   ''
   # For some reason having LD defined causes PSMTabBarControl to fail at link-time as it

diff --git a/pkgs/applications/editors/vim/macvim.patch b/pkgs/applications/editors/vim/macvim.patch
@@ -1,5 +1,5 @@
 diff --git a/src/MacVim/vimrc b/src/MacVim/vimrc
-index 23a06bf..dfb10fe 100644
+index af43549..dfb10fe 100644
 --- a/src/MacVim/vimrc
 +++ b/src/MacVim/vimrc
 @@ -14,35 +14,5 @@ set backspace+=indent,eol,start
@@ -29,22 +29,22 @@ index 23a06bf..dfb10fe 100644
 -" or an installation from python.org:
 -if exists("&pythonthreedll") && exists("&pythonthreehome") &&
 -      \ !filereadable(&pythonthreedll)
--  if filereadable("/opt/local/Library/Frameworks/Python.framework/Versions/3.7/Python")
--    " MacPorts python 3.7
--    set pythonthreedll=/opt/local/Library/Frameworks/Python.framework/Versions/3.7/Python
--  elseif filereadable("/Library/Frameworks/Python.framework/Versions/3.7/Python")
+-  if filereadable("/opt/local/Library/Frameworks/Python.framework/Versions/3.8/Python")
+-    " MacPorts python 3.8
+-    set pythonthreedll=/opt/local/Library/Frameworks/Python.framework/Versions/3.8/Python
+-  elseif filereadable("/Library/Frameworks/Python.framework/Versions/3.8/Python")
 -    " https://www.python.org/downloads/mac-osx/
--    set pythonthreedll=/Library/Frameworks/Python.framework/Versions/3.7/Python
+-    set pythonthreedll=/Library/Frameworks/Python.framework/Versions/3.8/Python
 -  endif
 -endif
 -
 +" Default cscopeprg to the Nix-installed path
 +set cscopeprg=@CSCOPE@
 diff --git a/src/Makefile b/src/Makefile
-index 24c6934..d0f094e 100644
+index fd2d5e1..37a6d6a 100644
 --- a/src/Makefile
 +++ b/src/Makefile
-@@ -1407,7 +1407,7 @@ MACVIMGUI_SRC	= gui.c gui_beval.c MacVim/gui_macvim.m MacVim/MMBackend.m \
+@@ -1397,7 +1397,7 @@ MACVIMGUI_SRC	= gui.c gui_beval.c MacVim/gui_macvim.m MacVim/MMBackend.m \
  		  MacVim/MacVim.m
  MACVIMGUI_OBJ	= objects/gui.o objects/gui_beval.o \
  		  objects/gui_macvim.o objects/MMBackend.o objects/MacVim.o
@@ -54,10 +54,10 @@ index 24c6934..d0f094e 100644
  MACVIMGUI_LIBS_DIR =
  MACVIMGUI_LIBS1	= -framework Cocoa -framework Carbon
 diff --git a/src/auto/configure b/src/auto/configure
-index 730d6d5..0259112 100755
+index 06257a5..68437df 100755
 --- a/src/auto/configure
 +++ b/src/auto/configure
-@@ -5859,10 +5859,7 @@ $as_echo "not found" >&6; }
+@@ -5872,10 +5872,7 @@ $as_echo "not found" >&6; }
 
      for path in "${vi_cv_path_mzscheme_pfx}/lib" "${SCHEME_LIB}"; do
        if test "X$path" != "X"; then
@@ -69,7 +69,7 @@ index 730d6d5..0259112 100755
  	  MZSCHEME_LIBS="${path}/libmzscheme3m.a"
  	  MZSCHEME_CFLAGS="-DMZ_PRECISE_GC"
  	elif test -f "${path}/libracket3m.a"; then
-@@ -6247,23 +6244,6 @@ $as_echo ">>> too old; need Perl version 5.003_01 or later <<<" >&6; }
+@@ -6260,23 +6257,6 @@ $as_echo ">>> too old; need Perl version 5.003_01 or later <<<" >&6; }
    fi
 
    if test "x$MACOS_X" = "xyes"; then
@@ -93,7 +93,7 @@ index 730d6d5..0259112 100755
                  PERL_LIBS=`echo "$PERL_LIBS" | sed -e 's/-arch\ ppc//' -e 's/-arch\ i386//' -e 's/-arch\ x86_64//'`
      PERL_CFLAGS=`echo "$PERL_CFLAGS" | sed -e 's/-arch\ ppc//' -e 's/-arch\ i386//' -e 's/-arch\ x86_64//'`
    fi
-@@ -6486,13 +6466,7 @@ __:
+@@ -6499,13 +6479,7 @@ __:
  eof
  	    	    eval "`cd ${PYTHON_CONFDIR} && make -f "${tmp_mkf}" __ | sed '/ directory /d'`"
  	    rm -f -- "${tmp_mkf}"
@@ -108,15 +108,15 @@ index 730d6d5..0259112 100755
  	      vi_cv_path_python_plibs="-L${PYTHON_CONFDIR} -lpython${vi_cv_var_python_version}"
  	      	      	      	      if test -n "${python_LINKFORSHARED}" && test -n "${python_PYTHONFRAMEWORKPREFIX}"; then
  	        python_link_symbol=`echo ${python_LINKFORSHARED} | sed 's/\([^ \t][^ \t]*[ \t][ \t]*[^ \t][^ \t]*\)[ \t].*/\1/'`
-@@ -6507,7 +6481,6 @@ eof
+@@ -6520,7 +6494,6 @@ eof
  	      fi
  	      vi_cv_path_python_plibs="${vi_cv_path_python_plibs} ${python_BASEMODLIBS} ${python_LIBS} ${python_SYSLIBS} ${python_LINKFORSHARED}"
  	      	      vi_cv_path_python_plibs=`echo $vi_cv_path_python_plibs | sed s/-ltermcap//`
 -	    fi
 
  fi
 
-@@ -6586,13 +6559,6 @@ rm -f core conftest.err conftest.$ac_objext \
+@@ -6599,13 +6572,6 @@ rm -f core conftest.err conftest.$ac_objext \
  $as_echo "no" >&6; }
  	fi
 
@@ -130,32 +130,33 @@ index 730d6d5..0259112 100755
  			{ $as_echo "$as_me:${as_lineno-$LINENO}: checking if compile and link flags for Python are sane" >&5
  $as_echo_n "checking if compile and link flags for Python are sane... " >&6; }
  	cflags_save=$CFLAGS
-@@ -7486,11 +7452,7 @@ $as_echo "$tclver - OK" >&6; };
+@@ -7499,11 +7465,7 @@ $as_echo "$tclver - OK" >&6; };
 
        { $as_echo "$as_me:${as_lineno-$LINENO}: checking for location of Tcl include" >&5
  $as_echo_n "checking for location of Tcl include... " >&6; }
 -      if test "x$MACOS_X" != "xyes"; then
  	tclinc="$tclloc/include $tclloc/include/tcl $tclloc/include/tcl$tclver /usr/local/include /usr/local/include/tcl$tclver /usr/include /usr/include/tcl$tclver"
 -      else
--		tclinc="/System/Library/Frameworks/Tcl.framework/Headers"
+-				tclinc="$tclloc/include $tclloc/include/tcl $tclloc/include/tcl$tclver /System/Library/Frameworks/Tcl.framework/Headers `xcrun --show-sdk-path`/System/Library/Frameworks/Tcl.framework/Versions/Current/Headers"
 -      fi
        TCL_INC=
        for try in $tclinc; do
  	if test -f "$try/tcl.h"; then
-@@ -7508,12 +7470,8 @@ $as_echo "<not found>" >&6; }
+@@ -7521,13 +7483,8 @@ $as_echo "<not found>" >&6; }
        if test -z "$SKIP_TCL"; then
  	{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for location of tclConfig.sh script" >&5
  $as_echo_n "checking for location of tclConfig.sh script... " >&6; }
 -	if test "x$MACOS_X" != "xyes"; then
  	  tclcnf=`echo $tclinc | sed s/include/lib/g`
  	  tclcnf="$tclcnf `echo $tclinc | sed s/include/lib64/g`"
 -	else
--	  	  tclcnf="/System/Library/Frameworks/Tcl.framework"
+-	  	  	  	  tclcnf=`echo $tclinc | sed s/include/lib/g`
+-	  tclcnf="$tclcnf /System/Library/Frameworks/Tcl.framework `xcrun --show-sdk-path`/System/Library/Frameworks/Tcl.framework"
 -	fi
  	for try in $tclcnf; do
  	  if test -f "$try/tclConfig.sh"; then
  	    { $as_echo "$as_me:${as_lineno-$LINENO}: result: $try/tclConfig.sh" >&5
-@@ -7703,10 +7661,6 @@ $as_echo "$rubyhdrdir" >&6; }
+@@ -7717,10 +7674,6 @@ $as_echo "$rubyhdrdir" >&6; }
  	if test -f "$rubylibdir/$librubya"; then
  	  librubyarg="$librubyarg"
  	  RUBY_LIBS="$RUBY_LIBS -L$rubylibdir"
@@ -167,10 +168,10 @@ index 730d6d5..0259112 100755
 
  	if test "X$librubyarg" != "X"; then
 diff --git a/src/vim.h b/src/vim.h
-index 87d1c92..8a7d5a5 100644
+index bbc01ee..5a93591 100644
 --- a/src/vim.h
 +++ b/src/vim.h
-@@ -250,17 +250,6 @@
+@@ -244,17 +244,6 @@
  # define SUN_SYSTEM
  #endif
 

diff --git a/pkgs/development/libraries/gegl/4.0.nix b/pkgs/development/libraries/gegl/4.0.nix
@@ -45,6 +45,15 @@ stdenv.mkDerivation rec {
     sha256 = "097427icgpgvcx40019b3dm8m84cchz79pixzpz648drs8p1wdqg";
   };
 
+  patches = [
+    # fix build with darwin: https://github.com/NixOS/nixpkgs/issues/99108
+    # https://gitlab.gnome.org/GNOME/gegl/-/merge_requests/83
+    (fetchpatch {
+      url = "https://gitlab.gnome.org/GNOME/gegl/-/merge_requests/83.patch";
+      sha256 = "CSBYbJ2xnEN23xrla1qqr244jxOR5vNK8ljBSXdg4yE=";
+    })
+  ];
+
   nativeBuildInputs = [
     pkgconfig
     gettext

diff --git a/pkgs/development/python-modules/namedlist/default.nix b/pkgs/development/python-modules/namedlist/default.nix
@@ -6,11 +6,11 @@
 
 buildPythonPackage rec {
   pname = "namedlist";
-  version = "1.7";
+  version = "1.8";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "11n9c4a5ak9971awkf1g92m6mcmiprhrw98ik2cmjsqxmz73j2qr";
+    sha256 = "34f89fc992592c80b39a709e136edcf41ea17f24ba31eaf84a314a02c8b9bcef";
   };
 
   # Test file has a `unittest.main()` at the bottom that fails the tests;
@@ -26,7 +26,7 @@ buildPythonPackage rec {
 
   meta = {
     description = "Similar to namedtuple, but instances are mutable";
-    homepage = "https://bitbucket.org/ericvsmith/namedlist";
+    homepage = "https://gitlab.com/ericvsmith/namedlist";
     license = lib.licenses.asl20;
     maintainers = with lib.maintainers; [ ivan ];
   };

diff --git a/pkgs/development/python-modules/ruffus/default.nix b/pkgs/development/python-modules/ruffus/default.nix
@@ -9,39 +9,34 @@
 
 buildPythonPackage rec {
   pname = "ruffus";
-  version = "2.8.1";
+  version = "2.8.4";
 
   src = fetchFromGitHub {
     owner = "cgat-developers";
     repo = pname;
     rev = "v${version}";
-    sha256 = "1gyabqafq4s2sy0prh3k1m8859shzjmfxr7fimx10liflvki96a9";
+    sha256 = "0fnzpchwwqsy5h18fs0n90s51w25n0dx0l74j0ka6lvhjl5sxn4c";
   };
 
   propagatedBuildInputs = [ gevent ];
 
-  postPatch = ''
-    sed -i -e 's|/bin/bash|${stdenv.shell}|'          ruffus/test/Makefile
-    sed -i -e 's|\tpytest|\t${pytest}/bin/pytest|'    ruffus/test/Makefile
-    sed -i -e 's|\tpython|\t${python.interpreter}|'   ruffus/test/Makefile
-    sed -i -e 's|/usr/bin/env bash|${stdenv.shell}|'  ruffus/test/run_all_unit_tests.cmd
-    sed -i -e 's|python3|${python.interpreter}|'      ruffus/test/run_all_unit_tests3.cmd
-    sed -i -e 's|python %s|${python.interpreter} %s|' ruffus/test/test_drmaa_wrapper_run_job_locally.py
-  '';
-
-  makefile = "ruffus/test/Makefile";
-
   checkInputs = [
-    gevent
     hostname
     pytest
   ];
 
+  # tests very flaky & hang often on darwin
+  doCheck = !stdenv.isDarwin;
+  # test files do indeed need to be executed separately
   checkPhase = ''
-    export HOME=$TMPDIR
-    cd ruffus/test
-    make all PYTEST_OPTIONS="-q --disable-warnings"
+    pushd ruffus/test
+    rm test_with_logger.py  # spawns 500 processes
+    for f in test_*.py ; do
+      HOME=$TMPDIR pytest -v --disable-warnings $f
+    done
+    popd
   '';
+  pythonImportsCheck = [ "ruffus" ];
 
   meta = with stdenv.lib; {
     description = "Light-weight Python Computational Pipeline Management";

diff --git a/pkgs/servers/http/openresty/default.nix b/pkgs/servers/http/openresty/default.nix
@@ -8,12 +8,12 @@
 
 callPackage ../nginx/generic.nix args rec {
   pname = "openresty";
-  nginxVersion = "1.15.8";
-  version = "${nginxVersion}.3";
+  nginxVersion = "1.17.8";
+  version = "${nginxVersion}.2";
 
   src = fetchurl {
     url = "https://openresty.org/download/openresty-${version}.tar.gz";
-    sha256 = "1a1la7vszv1parsnhphydblz64ffhycazncn3ividnvqg2mg735n";
+    sha256 = "1813w33hjm1hcqvl3b3f67qgi5zfjiqg6s01hiy12a5j3jqilcig";
   };
 
   fixPatch = patch: let name = patch.name or (builtins.baseNameOf patch); in