From f6b110fb50d805b5cc0178fd4ff85a90b955ee2d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20van=20Br=C3=BCgge?= <supermanitu@gmail.com>
Date: Mon, 19 Sep 2022 21:40:46 +0100
Subject: [PATCH] isabelle: 2021-1 -> 2022

---
 .../science/logic/isabelle/default.nix        | 59 +++++++++++++------
 pkgs/top-level/all-packages.nix               |  6 +-
 2 files changed, 45 insertions(+), 20 deletions(-)

diff --git a/pkgs/applications/science/logic/isabelle/default.nix b/pkgs/applications/science/logic/isabelle/default.nix
index 009af3463a25..1bb7ede6da7b 100644
--- a/pkgs/applications/science/logic/isabelle/default.nix
+++ b/pkgs/applications/science/logic/isabelle/default.nix
@@ -1,5 +1,24 @@
-{ lib, stdenv, fetchurl, coreutils, nettools, java, scala, polyml, z3, veriT, vampire, eprover-ho, naproche, rlwrap, perl, makeDesktopItem, isabelle-components, isabelle, symlinkJoin, fetchhg }:
-# nettools needed for hostname
+{ lib
+, stdenv
+, fetchurl
+, coreutils
+, nettools
+, java
+, scala_3
+, polyml
+, z3
+, veriT
+, vampire
+, eprover-ho
+, naproche
+, rlwrap
+, perl
+, makeDesktopItem
+, isabelle-components
+, isabelle
+, symlinkJoin
+, fetchhg
+}:
 
 let
   sha1 = stdenv.mkDerivation {
@@ -29,7 +48,7 @@ let
   };
 in stdenv.mkDerivation rec {
   pname = "isabelle";
-  version = "2021-1";
+  version = "2022";
 
   dirname = "Isabelle${version}";
 
@@ -39,26 +58,27 @@ in stdenv.mkDerivation rec {
       fetchurl
         {
           url = "https://isabelle.in.tum.de/website-${dirname}/dist/${dirname}_macos.tar.gz";
-          sha256 = "0n1ls9vwf0ps1x8zpb7c1xz1wkasgvc34h5bz280hy2z6iqwmwbc";
+          sha256 = "0b84rx9b7b5y8m1sg7xdp17j6yngd2dkx6v5bkd8h7ly102lai18";
         }
     else
       fetchurl {
         url = "https://isabelle.in.tum.de/website-${dirname}/dist/${dirname}_linux.tar.gz";
-        sha256 = "0jfaqckhg388jh9b4msrpkv6wrd6xzlw18m0bngbby8k8ywalp9i";
+        sha256 = "1ih4gykkp1an43qdgc5xzyvf30fhs0dah3y0a5ksbmvmjsfnxyp7";
       };
 
+  nativeBuildInputs = [ java ];
+
   buildInputs = [ polyml z3 veriT vampire eprover-ho nettools ]
     ++ lib.optionals (!stdenv.isDarwin) [ java ];
 
-  sourceRoot = "${dirname}${lib.optionalString stdenv.isDarwin ".app"}";
+  sourceRoot = dirname;
 
-  postUnpack = if stdenv.isDarwin then ''
-    mv $sourceRoot ${dirname}
-    sourceRoot=${dirname}
-  '' else null;
+  postUnpack = lib.optionalString stdenv.isDarwin ''
+    mv $sourceRoot.app $sourceRoot
+  '';
 
   postPatch = ''
-    patchShebangs .
+    patchShebangs lib/Tools/ bin/
 
     cat >contrib/z3*/etc/settings <<EOF
       Z3_HOME=${z3}
@@ -111,7 +131,8 @@ in stdenv.mkDerivation rec {
 
     substituteInPlace src/Tools/Setup/src/Environment.java \
       --replace 'cmd.add("/usr/bin/env");' "" \
-      --replace 'cmd.add("bash");' "cmd.add(\"$SHELL\");"
+      --replace 'cmd.add("bash");' "cmd.add(\"$SHELL\");" \
+      --replace 'private static read_file(path: Path): String =' 'private static String read_file(Path path) throws IOException'
 
     substituteInPlace src/Pure/General/sha1.ML \
       --replace '"$ML_HOME/" ^ (if ML_System.platform_is_windows then "sha1.dll" else "libsha1.so")' '"${sha1}/lib/libsha1.so"'
@@ -120,15 +141,18 @@ in stdenv.mkDerivation rec {
   '' + lib.optionalString (stdenv.hostPlatform.system == "x86_64-darwin") ''
     substituteInPlace lib/scripts/isabelle-platform \
       --replace 'ISABELLE_APPLE_PLATFORM64=arm64-darwin' ""
-  '' + (if ! stdenv.isLinux then "" else ''
+  '' + lib.optionalString stdenv.isLinux ''
     arch=${if stdenv.hostPlatform.system == "x86_64-linux" then "x86_64-linux" else "x86-linux"}
     for f in contrib/*/$arch/{bash_process,epclextract,nunchaku,SPASS,zipperposition}; do
       patchelf --set-interpreter $(cat ${stdenv.cc}/nix-support/dynamic-linker) "$f"
     done
+    for f in contrib/*/platform_$arch/{bash_process,epclextract,nunchaku,SPASS,zipperposition}; do
+      patchelf --set-interpreter $(cat ${stdenv.cc}/nix-support/dynamic-linker) "$f"
+    done
     for d in contrib/kodkodi-*/jni/$arch; do
       patchelf --set-rpath "${lib.concatStringsSep ":" [ "${java}/lib/openjdk/lib/server" "${stdenv.cc.cc.lib}/lib" ]}" $d/*.so
     done
-  '');
+  '';
 
   buildPhase = ''
     export HOME=$TMP # The build fails if home is not set
@@ -145,11 +169,12 @@ in stdenv.mkDerivation rec {
     do
       ARGS["''${#ARGS[@]}"]="src/Tools/Setup/$SRC"
     done
-    ${java}/bin/javac -d "$TARGET_DIR" -classpath ${scala}/lib/scala-compiler.jar "''${ARGS[@]}"
-    ${java}/bin/jar -c -f "$TARGET_DIR/isabelle_setup.jar" -e "isabelle.setup.Setup" -C "$TARGET_DIR" isabelle
+    echo "Building isabelle setup"
+    javac -d "$TARGET_DIR" -classpath "${scala_3.bare}/lib/scala3-interfaces-${scala_3.version}.jar:${scala_3.bare}/lib/scala3-compiler_3-${scala_3.version}.jar" "''${ARGS[@]}"
+    jar -c -f "$TARGET_DIR/isabelle_setup.jar" -e "isabelle.setup.Setup" -C "$TARGET_DIR" isabelle
     rm -rf "$TARGET_DIR/isabelle"
 
-    # Prebuild HOL Session
+    echo "Building HOL heap"
     bin/isabelle build -v -o system_heaps -b HOL
   '';
 
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 8dba9defae36..c78b671e55f7 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -35596,14 +35596,14 @@ with pkgs;
   isabelle = callPackage ../applications/science/logic/isabelle {
     polyml = polyml.overrideAttrs (_: {
       pname = "polyml-for-isabelle";
-      version = "2021-1";
+      version = "2022";
       configureFlags = [ "--enable-intinf-as-int" "--with-gmp" "--disable-shared" ];
       buildFlags = [ "compiler" ];
       src = fetchFromGitHub {
         owner = "polyml";
         repo = "polyml";
-        rev = "39d96a2def903ed019c6855e3b688df5070d633a";
-        sha256 = "sha256-S7d2Vr/nB+rCX9d4qQj4f7edVZKocKIjc5rrx9A/B4Q=";
+        rev = "bafe319bc3a65bf63bd98a4721a6f4dd9e0eabd6";
+        sha256 = "1ygs09zzq8icq1gc8qf4sb24lxx7sbcyd5hw3vw67a3ryaki0qw2";
       };
     });