Merge #200573: lispPackages_new: fix a bunch of packages

...into staging-next

pkgs/development/lisp-modules-new/lisp-packages.nix

@@ -133,10 +133,6 @@ let
     in stdenv.mkDerivation (rec {
       inherit pname version nativeLibs javaLibs lispLibs lisp systems asds;
 
-      src = if builtins.length patches > 0
-            then apply-patches args
-            else args.src;
-
       # When src is null, we are building a lispWithPackages and only
       # want to make use of the dependency environment variables
       # generated by build-asdf-system
@@ -201,7 +197,7 @@ let
         #
         # NOTE: It's important to read files from `src` instead of
         # from pwd to get go-to-definition working with SLIME
-        export CL_SOURCE_REGISTRY=$CL_SOURCE_REGISTRY:${src}//
+        export CL_SOURCE_REGISTRY=$CL_SOURCE_REGISTRY:$src//
 
         # Similiarily for native deps
         export LD_LIBRARY_PATH=${makeLibraryPath nativeLibs}:$LD_LIBRARY_PATH
@@ -209,7 +205,7 @@ let
 
         # Make asdf compile from `src` to pwd and load `lispLibs`
         # from storeDir. Otherwise it could try to recompile lisp deps.
-        export ASDF_OUTPUT_TRANSLATIONS="${src}:$(pwd):${storeDir}:${storeDir}"
+        export ASDF_OUTPUT_TRANSLATIONS="$src:$(pwd):${storeDir}:${storeDir}"
 
         # track lisp dependencies for graph generation
         # TODO: Do the propagation like for lisp, native and java like this:
@@ -248,24 +244,12 @@ let
       dontStrip = true;
       dontFixup = true;
 
-    } // args));
-
-  # Need to do that because we always want to compile straight from
-  # `src` for go-to-definition to work in SLIME.
-  apply-patches = { patches, src, ... }:
-    stdenv.mkDerivation {
-      inherit patches src;
-      pname = "source";
-      version = "patched";
-      dontConfigure = true;
-      dontBuild = true;
-      dontStrip = true;
-      dontFixup = true;
-      installPhase = ''
-        mkdir -pv $out
-        cp -r * $out
-      '';
-    };
+    } // (args // {
+      src = if builtins.length (args.patches or []) > 0
+            then pkgs.applyPatches { inherit (args) src patches; }
+            else args.src;
+      patches = [];
+    })));
 
   # Build the set of lisp packages using `lisp`
   # These packages are defined manually for one reason or another:

pkgs/development/lisp-modules-new/packages.nix

@@ -102,6 +102,7 @@ let
       url = "https://github.com/cffi/cffi/archive/3f842b92ef808900bf20dae92c2d74232c2f6d3a.tar.gz";
       sha256 = "1jilvmbbfrmb23j07lwmkbffc6r35wnvas5s4zjc84i856ccclm2";
     };
+    patches = [ ./patches/cffi-libffi-darwin-ffi-h.patch ];
   });
 
   cl-unicode = build-with-compile-into-pwd {
@@ -423,6 +424,13 @@ let
     patches = [ ./patches/qtools-use-nix-libs.patch ];
   };
 
+  magicl = build-with-compile-into-pwd {
+    inherit (ql.magicl) pname version src lispLibs;
+    nativeBuildInputs = [ pkgs.gfortran ];
+    nativeLibs = [ pkgs.openblas ];
+    patches = [ ./patches/magicl-dont-build-fortran-twice.patch ];
+  };
+
   };
 
 in packages

pkgs/development/lisp-modules-new/patches/cffi-libffi-darwin-ffi-h.patch

@@ -0,0 +1,14 @@
+--- a/libffi/libffi-types.lisp
++++ b/libffi/libffi-types.lisp
+@@ -43,9 +43,6 @@
+ 
+ (pkg-config-cflags "libffi" :optional t)
+ 
+-#+darwin
+-(include "ffi/ffi.h")
+-#-darwin
+ (include "ffi.h")
+ 
+ (cenum status
+
+Diff finished.  Sun Nov 13 00:23:10 2022

pkgs/development/lisp-modules-new/patches/magicl-dont-build-fortran-twice.patch

@@ -0,0 +1,21 @@
+--- a/magicl.asd
++++ b/magicl.asd
+@@ -143,6 +143,7 @@
+            (shared-object (make-pathname :type #+darwin "dylib" #-darwin "so"
+                                          :name "libexpokit"
+                                          :defaults fortran-file)))
++      (unless (probe-file (nn shared-object))
+       (uiop:run-program
+        (list "gfortran" "-fPIC" "-std=legacy"
+              "-c"
+@@ -155,7 +156,7 @@
+              (nn object-file)
+              #+darwin "-lblas"
+              #+darwin "-llapack"))
+-      (delete-file object-file))))
++      (delete-file object-file)))))
+ 
+ 
+ (asdf:defsystem #:magicl/ext-expokit
+
+Diff finished.  Mon Oct 10 22:03:54 2022

pkgs/development/lisp-modules-new/ql.nix

@@ -19,6 +19,9 @@ let
     cl-cffi-gtk-cairo = pkg: {
       nativeLibs = [ cairo ];
     };
+    cl-cairo2 = pkg: {
+      nativeLibs = [ cairo ];
+    };
     cl-cffi-gtk-gdk = pkg: {
       nativeLibs = [ gtk3 ];
     };
@@ -130,6 +133,24 @@ let
       nativeLibs = [ libfixposix ];
       systems = [ "iolib" "iolib/os" "iolib/pathnames" ];
     };
+    "cl-ana.hdf-cffi" = pkg: {
+      nativeBuildInputs = [ hdf5 ];
+      nativeLibs = [ hdf5 ];
+      NIX_LDFLAGS = [ "-lhdf5" ];
+    };
+    gsll = pkg: {
+      nativeBuildInputs = [ gsl ];
+      nativeLibs = [ gsl ];
+    };
+    cl-libyaml = pkg: {
+      nativeLibs = [ libyaml ];
+    };
+    cl-libxml2 = pkg: {
+      nativeLibs = [ libxml2 ];
+    };
+    cl-readline = pkg: {
+      nativeLibs = [ readline ];
+    };
   };
 
   qlpkgs =