Merge remote-tracking branch 'origin/staging-next' into staging

7 files changed, 70 insertions, 68 deletions

diff --git a/pkgs/applications/science/logic/alt-ergo/default.nix b/pkgs/applications/science/logic/alt-ergo/default.nix
index d7396d5d9a61b..7077d56f8069b 100644
--- a/pkgs/applications/science/logic/alt-ergo/default.nix
+++ b/pkgs/applications/science/logic/alt-ergo/default.nix
@@ -21,6 +21,9 @@ let alt-ergo-lib = ocamlPackages.buildDunePackage rec {
   nativeBuildInputs = [ which ];
   buildInputs = with ocamlPackages; [ dune-configurator ];
   propagatedBuildInputs = with ocamlPackages; [ num ocplib-simplex seq stdlib-shims zarith ];
+  preBuild = ''
+    substituteInPlace src/lib/util/version.ml --replace 'version="dev"' 'version="${version}"'
+  '';
 }; in
 
 let alt-ergo-parsers = ocamlPackages.buildDunePackage rec {
diff --git a/pkgs/applications/science/logic/isabelle/components/isabelle-linter.nix b/pkgs/applications/science/logic/isabelle/components/isabelle-linter.nix
index 7fca547f67c8e..565537cf439c0 100644
--- a/pkgs/applications/science/logic/isabelle/components/isabelle-linter.nix
+++ b/pkgs/applications/science/logic/isabelle/components/isabelle-linter.nix
@@ -2,16 +2,28 @@
 
 stdenv.mkDerivation rec {
   pname = "isabelle-linter";
-  version = "Isabelle2021-1-v1.0.0";
+  version = "unstable-2022-09-05";
 
   src = fetchFromGitHub {
     owner = "isabelle-prover";
     repo = "isabelle-linter";
-    rev = version;
-    sha256 = "0v6scc2rhj6bjv530gzz6i57czzcgpkw7a9iqnfdnm5gvs5qjk7a";
+    rev = "0424fc05426d5f7a23adf19ad08c690c17184e86";
+    sha256 = "02afbgmi195ibichjkpni2wjgjkszv7i6qkmmprwrmb4jd2wdvd5";
   };
 
-  installPhase = import ./mkBuild.nix { inherit isabelle; path = "${pname}-${version}"; };
+  nativeBuildInputs = [ isabelle ];
+
+  buildPhase = ''
+    export HOME=$TMP
+    isabelle components -u $(pwd)
+    isabelle scala_build
+  '';
+
+  installPhase = ''
+    dir=$out/Isabelle${isabelle.version}/contrib/${pname}-${version}
+    mkdir -p $dir
+    cp -r * $dir/
+  '';
 
   meta = with lib; {
     description = "Linter component for Isabelle.";
diff --git a/pkgs/applications/science/logic/isabelle/components/mkBuild.nix b/pkgs/applications/science/logic/isabelle/components/mkBuild.nix
deleted file mode 100644
index a05b5196b0076..0000000000000
--- a/pkgs/applications/science/logic/isabelle/components/mkBuild.nix
+++ /dev/null
@@ -1,36 +0,0 @@
-{ isabelle, path }:
-
-let
-  dir = "$out/isabelle/${isabelle.dirname}";
-  iDir = "${isabelle}/${isabelle.dirname}";
-in ''
-  shopt -s extglob
-  mkdir -p ${dir}/lib/classes
-
-  cDir=$out/${isabelle.dirname}/contrib/${path}
-  mkdir -p $cDir
-  cp -r !(isabelle) $cDir
-
-  cd ${dir}
-  ln -s ${iDir}/!(lib|bin) ./
-  ln -s ${iDir}/lib/!(classes) lib/
-  ln -s ${iDir}/lib/classes/* lib/classes/
-
-  mkdir bin/
-  cp ${iDir}/bin/* bin/
-
-  export HOME=$TMP
-  bin/isabelle components -u $cDir
-  bin/isabelle scala_build
-
-  cd lib/classes
-  for f in ${iDir}/lib/classes/*; do
-    rm $(basename $f)
-  done
-
-  lDir=$out/${isabelle.dirname}/lib/classes/
-  mkdir -p $lDir
-  cp -r * $lDir
-  cd $out
-  rm -rf isabelle
-''
diff --git a/pkgs/applications/science/logic/isabelle/default.nix b/pkgs/applications/science/logic/isabelle/default.nix
index 009af3463a25a..1bb7ede6da7b7 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/applications/science/logic/naproche/default.nix b/pkgs/applications/science/logic/naproche/default.nix
index 047ed73262eee..ecc347080081b 100644
--- a/pkgs/applications/science/logic/naproche/default.nix
+++ b/pkgs/applications/science/logic/naproche/default.nix
@@ -2,13 +2,13 @@
 
 with haskellPackages; mkDerivation {
   pname = "Naproche-SAD";
-  version = "2022-04-19";
+  version = "2022-10-24";
 
   src = fetchFromGitHub {
     owner = "naproche";
     repo = "naproche";
-    rev = "2514c04e715395b7a839e11b63046eafb9c6a1da";
-    sha256 = "1bdgyk4fk65xi7n778rbgddpg4zhggj8wjslxbizrzi81my9a3vm";
+    rev = "c8c4ca2d5fdb92bf17e0e54c99bd2a9691255d80";
+    sha256 = "0xvh6kkl5k5ygp2nrbq3k0snvzczbmcp1yrwdkah3fzhf9i3yykx";
   };
 
   isExecutable = true;
diff --git a/pkgs/applications/science/math/calc/default.nix b/pkgs/applications/science/math/calc/default.nix
index 41adb1cfbe6cb..d521da2f114cd 100644
--- a/pkgs/applications/science/math/calc/default.nix
+++ b/pkgs/applications/science/math/calc/default.nix
@@ -3,14 +3,14 @@
 
 stdenv.mkDerivation rec {
   pname = "calc";
-  version = "2.14.1.0";
+  version = "2.14.1.2";
 
   src = fetchurl {
     urls = [
-      "https://github.com/lcn2/calc/releases/download/${version}/${pname}-${version}.tar.bz2"
+      "https://github.com/lcn2/calc/releases/download/v${version}/${pname}-${version}.tar.bz2"
       "http://www.isthe.com/chongo/src/calc/${pname}-${version}.tar.bz2"
     ];
-    sha256 = "sha256-C1YWZS4x7htUWF3MhRLQIYChL4rdwJxASdPQjttUr0A=";
+    sha256 = "sha256-3o8jKmEYxNQtExOkjqTVU24mtSok+T/RnRw6goNzThM=";
   };
 
   postPatch = ''
diff --git a/pkgs/applications/science/molecular-dynamics/viennarna/default.nix b/pkgs/applications/science/molecular-dynamics/viennarna/default.nix
index 1629a6bba268c..3d20eeabe2685 100644
--- a/pkgs/applications/science/molecular-dynamics/viennarna/default.nix
+++ b/pkgs/applications/science/molecular-dynamics/viennarna/default.nix
@@ -9,11 +9,11 @@
 
 stdenv.mkDerivation rec {
   pname = "ViennaRNA";
-  version = "2.4.18";
+  version = "2.5.1";
 
   src = fetchurl {
-    url = "https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_4_x/${pname}-${version}.tar.gz";
-    sha256 = "17b0mcfkms0gn1a3faa4cakig65k9nk282x6mdh1mmjwbqzp5akw";
+    url = "https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_5_x/${pname}-${version}.tar.gz";
+    sha256 = "sha256-BUAEN88VWV4QsaJd9snEiFbzVhMPnR44D6iGa20n9Fc=";
   };
 
   buildInputs = [
@@ -34,7 +34,5 @@ stdenv.mkDerivation rec {
     license = licenses.unfree;
     maintainers = with maintainers; [ prusnak ];
     platforms = platforms.unix;
-    # Perl bindings fail on aarch64-darwin with "Undefined symbols for architecture arm64"
-    broken = stdenv.isDarwin && stdenv.isAarch64;
   };
 }