[gentoo-commits] repo/gentoo:master commit in: sci-mathematics/isabelle/, sci-mathematics/isabelle/files/, profiles/

[Michał Górny]

commit:     7d2aafd09b8f128da73333201c48b793607077be
Author:     Michał Górny <mgorny <AT> gentoo <DOT> org>
AuthorDate: Sat Sep 14 15:44:37 2019 +0000
Commit:     Michał Górny <mgorny <AT> gentoo <DOT> org>
CommitDate: Sat Sep 14 15:44:37 2019 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=7d2aafd0

sci-mathematics/isabelle: Remove last-rited pkg

Signed-off-by: Michał Górny <mgorny <AT> gentoo.org>

 profiles/package.mask                              |   1 -
 sci-mathematics/isabelle/Manifest                  |  10 -
 .../files/isabelle-2012-graphbrowser.patch         |  11 -
 .../isabelle-2012-reverse-line-editor-order.patch  |  12 -
 .../isabelle/files/isabelle-2016-classpath.patch   |  32 --
 .../files/isabelle-2016-jfreechart-classpath.patch |  16 -
 ...abelle-2016.1-bash_process-1.2.1-settings.patch |   7 -
 ...-2016.1-disable-jedit-build-after-install.patch | 128 --------
 .../isabelle-2016.1-jortho-1.0-2-classpath.patch   |   8 -
 .../isabelle/files/isabelle-2016.1-libsha1.patch   |  11 -
 ...sabelle-2016.1-smt_read_only_certificates.patch |  33 ---
 .../files/isabelle-2016.1-smt_timeout.patch        |  22 --
 sci-mathematics/isabelle/isabelle-2016.1.ebuild    | 328 ---------------------
 sci-mathematics/isabelle/metadata.xml              |  29 --
 14 files changed, 648 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index feef25289e3..1eaa755ace9 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -1116,7 +1116,6 @@ dev-java/itext
 app-text/jpdftweak
 dev-util/deskzilla
 media-sound/tuxguitar
-sci-mathematics/isabelle
 
 # Michał Górny <mgorny@g.o> (2019-08-14)
 # No longer builds.  Homepage is gone, and its keep-alive fork is also

diff --git a/sci-mathematics/isabelle/Manifest b/sci-mathematics/isabelle/Manifest
deleted file mode 100644
index b5aab891dc5..00000000000
--- a/sci-mathematics/isabelle/Manifest
+++ /dev/null
@@ -1,10 +0,0 @@
-DIST Isabelle2016-1.tar.gz 39567637 BLAKE2B a664c89f2705e6b2709a8b3054d57ca443435967dd85f07e1651aa0bbfc41ee31dee88146243c8e0bddc2a1de86107158a89d13b2ff427f8dcf0308fe3dd2654 SHA512 c7da7900033a8c816f002b8899e398da7819dc457b3b1176dc9a19adffeb42d5524f2d14581a391487da1f36ffeabd0867bacab6462f3decfc0f7a9caf81a2d2
-DIST bash_process-isabelle-component-1.2.1.tar.gz 33182 BLAKE2B d139f5476b02b22a896fa742303a4e5c4de583972eb38a67e1a451fabe28d52c2c1310be865faf244104cad46758e1bf97f6222170999ff2e2da7c07e1398fe3 SHA512 d9817191af5660e38f1647401803115a93f0052291bfbbcb1cd9b41a4bab89b3ebdde22b40744a04ad3268aed8ca037ae59981c513f71b3ff6d89855d29e14c3
-DIST csdp-isabelle-component-6.x.tar.gz 493 BLAKE2B 364c8f390adfb4031958597e4435783e58ebbb3be49ee80d5ee6631770d9322190bd364530622ae66d490d91e499bb3bb626b01762fccf3f67c65b20b3f7756b SHA512 9be28ecbf61d0f6ad23e28d44bd7ceb8f06ab22f3a05a7c823a9c5bf52ddcf5e5c300c41e14451d6b8e6a4c32b1bbd17769c731cd890fab335a866cd5e735290
-DIST isabelle_fonts-isabelle-component-20160830.tar.gz 249427 BLAKE2B 8398e578e6b8f54ac163b33e29c8283fef29c5db2cd8562dca1d636e1947bebb54e79e55035398fca215f2fbdf868dfe318d91a7f76074ad97f2d4792b8b4432 SHA512 a185f79990478861832e9400ea37ffd02f582d3f916d26d901b8b0ec923027c412538bafe4a763a132adb9277a4b00a7a510762928ec49433ef550ae3fe59dbc
-DIST jedit_build-isabelle-component-20161024.tar.gz 10819946 BLAKE2B 2764d854eecd6783a0893934742f21db9ac47b1304f969803e01ffc402d57d2f3d38c9f07cb6ea6d77f12a48337892baecc7175b1d759989d7c46d0104b34a9f SHA512 0563b696307dd33b244e4ecc62664056a2b003c3291a5e3d7dd4f1c936dac2c3257ff90273cb2c8dc3bf9dea40fae745fabb57fc5f4ed420d0c8fd7d2b917433
-DIST jfreechart-isabelle-component-1.0.14-1.tar.gz 3444825 BLAKE2B 4a24f362d647c9bbe538d18a49f7579cf9c1914854b19c7f4cca29d876870eb5f994df4b53ae2bf6f8bf8aa697306bfebdb272493fb974c6df8050778d173376 SHA512 ee1d84a45e43029d5e3acee823176196da19789322e8d3c2c81d5504930ad81d50e16e5da87655e4151034901daefb4ce6b82334839e39134b3a7ce32203aa67
-DIST jortho-isabelle-component-1.0-2.tar.gz 1723761 BLAKE2B 4f5503c640d25d79a8520a2f137900a8397db141f5f6279e4622bf44c377a3bcd7224d9e59de2f57993867362350bc279aebc54dc548562bab6b78b210110fb7 SHA512 8bef5e025d13b76c86a727bf93887b846cc906b2ce00299c38f69ccf33fb9dc7411e55b6fd1c56ed993c180d83a7e9ed90122f7feb6ae4fb70df93802ac21211
-DIST polyml-isabelle-component-5.6-1.tar.gz 822 BLAKE2B eea808d3cd2ce2c6b5b531fce046eba59e39f671e48e76e3d9093a4d9fadef9fbf3afc20b98eeaf5e672e8e34ed11aaf62441266469f53d3d228252fe9f64f89 SHA512 403239aa48aab8c39e12cd5f82cb5e3ba7c31f9325d88f5137d3ec509bb25ab4eb8b1103a66b8ea5ad45c7c968ef092749c486217528a5db4223819106c00a59
-DIST ssh-java-isabelle-component-20161009.tar.gz 412919 BLAKE2B d05152d92669043ba23d7e0767470a529ac7688866ed8be64432d724329a0c24590586faf5e09c365c44740550441798681b9e8b80a323285516ec61a884beb8 SHA512 685a9b8791046c1bc21aa77614fb1b304e7438715377e179954ebfd1603434ff66fe23e90de928a5af6f51a48ae6ea6f05f9ff8941d98f7c3a43fdda02d3b519
-DIST xz-java-isabelle-component-1.5.tar.gz 315 BLAKE2B b7a385671469fb8643d74d90b4faae2f66621f7bafb0262b7fc7777c883cae4a5939cb5261230c21a6125ce12cafe5285a873fc0a37f78ef0e4059d310c2bd0e SHA512 6dfec49e12c4cafbb6b6386dd54477e86b6bb419a77c52d9606a0305aeea9cd11f087ed6bba77352c7bf9ec656052ef617e845f472e57b5cdfbccf22b2eeb4fa

diff --git a/sci-mathematics/isabelle/files/isabelle-2012-graphbrowser.patch b/sci-mathematics/isabelle/files/isabelle-2012-graphbrowser.patch
deleted file mode 100644
index 3e63f1c6223..00000000000
--- a/sci-mathematics/isabelle/files/isabelle-2012-graphbrowser.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- Isabelle2012-orig/lib/browser/build	2012-05-20 19:34:33.000000000 +1000
-+++ Isabelle2012/lib/browser/build	2012-05-26 22:18:41.952750622 +1000
-@@ -6,6 +6,8 @@
- #
- # Requires proper Isabelle settings environment.
- 
-+ISABELLE_HOME="$(cd "$(dirname "${0}")/../.."; pwd -P)"
-+source "$ISABELLE_HOME/lib/scripts/getsettings" || exit 2
- 
- ## diagnostics
- 

diff --git a/sci-mathematics/isabelle/files/isabelle-2012-reverse-line-editor-order.patch b/sci-mathematics/isabelle/files/isabelle-2012-reverse-line-editor-order.patch
deleted file mode 100644
index 233ea5b50fa..00000000000
--- a/sci-mathematics/isabelle/files/isabelle-2012-reverse-line-editor-order.patch
+++ /dev/null
@@ -1,12 +0,0 @@
---- Isabelle2012-orig/etc/settings	2012-05-23 03:07:38.000000000 +1000
-+++ Isabelle2012/etc/settings	2012-05-27 12:43:36.209715015 +1000
-@@ -62,8 +62,8 @@
- ###
- 
- ISABELLE_LINE_EDITOR=""
--[ -z "$ISABELLE_LINE_EDITOR" ] && ISABELLE_LINE_EDITOR="$(type -p rlwrap)"
- [ -z "$ISABELLE_LINE_EDITOR" ] && ISABELLE_LINE_EDITOR="$(type -p ledit)"
-+[ -z "$ISABELLE_LINE_EDITOR" ] && ISABELLE_LINE_EDITOR="$(type -p rlwrap)"
- 
- 
- ###

diff --git a/sci-mathematics/isabelle/files/isabelle-2016-classpath.patch b/sci-mathematics/isabelle/files/isabelle-2016-classpath.patch
deleted file mode 100644
index 032b18b71f3..00000000000
--- a/sci-mathematics/isabelle/files/isabelle-2016-classpath.patch
+++ /dev/null
@@ -1,32 +0,0 @@
-Index: Isabelle2016/lib/Tools/java
-===================================================================
---- Isabelle2016.orig/lib/Tools/java
-+++ Isabelle2016/lib/Tools/java
-@@ -10,5 +10,5 @@ declare -a JAVA_ARGS; eval "JAVA_ARGS=($
- unset CLASSPATH
- 
- isabelle_java java "${JAVA_ARGS[@]}" \
--  -classpath "$(platform_path "$ISABELLE_CLASSPATH")" "$@"
-+  -classpath "$(platform_path "$ISABELLE_CLASSPATH:$(java-config -p scala-2.11)")" "$@"
- 
-Index: Isabelle2016/lib/Tools/scala
-===================================================================
---- Isabelle2016.orig/lib/Tools/scala
-+++ Isabelle2016/lib/Tools/scala
-@@ -14,4 +14,4 @@ do
- done
- 
- isabelle_scala scala "${SCALA_ARGS[@]}" \
--  -classpath "$(platform_path "$ISABELLE_CLASSPATH")" "$@"
-+  -classpath "$(platform_path "$ISABELLE_CLASSPATH:$(java-config -p scala-2.11)")" "$@"
-Index: Isabelle2016/lib/Tools/scalac
-===================================================================
---- Isabelle2016.orig/lib/Tools/scalac
-+++ Isabelle2016/lib/Tools/scalac
-@@ -7,5 +7,5 @@
- isabelle_admin_build jars || exit $?
- 
- isabelle_scala scalac -Dfile.encoding=UTF-8 \
--  -classpath "$(platform_path "$ISABELLE_CLASSPATH")" "$@"
-+  -classpath "$(platform_path "$ISABELLE_CLASSPATH:$(java-config -p scala-2.11)")" "$@"
- 

diff --git a/sci-mathematics/isabelle/files/isabelle-2016-jfreechart-classpath.patch b/sci-mathematics/isabelle/files/isabelle-2016-jfreechart-classpath.patch
deleted file mode 100644
index 9a88ebef26c..00000000000
--- a/sci-mathematics/isabelle/files/isabelle-2016-jfreechart-classpath.patch
+++ /dev/null
@@ -1,16 +0,0 @@
---- Isabelle2016-orig/contrib/jfreechart-1.0.14-1/etc/settings	2013-09-12 07:46:57.000000000 +1000
-+++ Isabelle2016/contrib/jfreechart-1.0.14-1/etc/settings	2016-07-07 17:22:55.716464804 +1000
-@@ -1,9 +1,8 @@
- # -*- shell-script -*- :mode=shellscript:
- 
- JFREECHART_HOME="$COMPONENT"
--JFREECHART_JAR_NAMES="iText-2.1.5.jar jcommon-1.0.18.jar jfreechart-1.0.14.jar"
--
--classpath "$JFREECHART_HOME/lib/iText-2.1.5.jar"
--classpath "$JFREECHART_HOME/lib/jcommon-1.0.18.jar"
--classpath "$JFREECHART_HOME/lib/jfreechart-1.0.14.jar"
-+JFREECHART_JAR_NAMES="$(java-config --classpath itext | sed -e 's@:@ @g' -e 's@/[^ ]*/@@g') $(java-config --classpath jcommon-1.0 | sed -e 's@:@ @g' -e 's@/[^ ]*/@@g') $(java-config --classpath jfreechart-1.0 | sed -e 's@:@ @g' -e 's@/[^ ]*/@@g')"
- 
-+classpath "$(java-config --classpath itext)"
-+classpath "$(java-config --classpath jcommon-1.0)"
-+classpath "$(java-config --classpath jfreechart-1.0)"

diff --git a/sci-mathematics/isabelle/files/isabelle-2016.1-bash_process-1.2.1-settings.patch b/sci-mathematics/isabelle/files/isabelle-2016.1-bash_process-1.2.1-settings.patch
deleted file mode 100644
index 38d047199ce..00000000000
--- a/sci-mathematics/isabelle/files/isabelle-2016.1-bash_process-1.2.1-settings.patch
+++ /dev/null
@@ -1,7 +0,0 @@
---- Isabelle2016-1-orig/contrib/bash_process-1.2.1/etc/settings	2016-02-14 09:48:03.000000000 +1100
-+++ Isabelle2016-1/contrib/bash_process-1.2.1/etc/settings	2017-01-02 13:44:49.355549312 +1100
-@@ -1,3 +1,3 @@
- # -*- shell-script -*- :mode=shellscript:
- 
--ISABELLE_BASH_PROCESS="$COMPONENT/${ISABELLE_PLATFORM64:-$ISABELLE_PLATFORM32}/bash_process"
-+ISABELLE_BASH_PROCESS="$COMPONENT/bash_process"

diff --git a/sci-mathematics/isabelle/files/isabelle-2016.1-disable-jedit-build-after-install.patch b/sci-mathematics/isabelle/files/isabelle-2016.1-disable-jedit-build-after-install.patch
deleted file mode 100644
index 6bac5ccbe74..00000000000
--- a/sci-mathematics/isabelle/files/isabelle-2016.1-disable-jedit-build-after-install.patch
+++ /dev/null
@@ -1,128 +0,0 @@
---- Isabelle2016-1-orig/src/Tools/jEdit/lib/Tools/jedit	2016-12-13 01:03:49.000000000 +1100
-+++ Isabelle2016-1/src/Tools/jEdit/lib/Tools/jedit	2017-01-01 17:24:50.107722845 +1100
-@@ -239,125 +239,6 @@
-   "$ISABELLE_JEDIT_BUILD_HOME/contrib/jsr305-2.0.0.jar"
- )
- 
--
--# target
--
--TARGET="dist/jars/Isabelle-jEdit.jar"
--
--declare -a UPDATED=()
--
--if [ "$BUILD_JARS" = jars_fresh ]; then
--  OUTDATED=true
--else
--  OUTDATED=false
--  if [ ! -e "$TARGET" ]; then
--    OUTDATED=true
--  else
--    if [ -n "$ISABELLE_JEDIT_BUILD_HOME" ]; then
--      declare -a DEPS=(
--        "$JEDIT_JAR" "${JEDIT_JARS[@]}" "$PURE_JAR"
--        "${SOURCES[@]}" "${RESOURCES[@]}"
--      )
--    elif [ -e "$ISABELLE_HOME/Admin/build" ]; then
--      declare -a DEPS=("$PURE_JAR" "${SOURCES[@]}" "${RESOURCES[@]}")
--    else
--      declare -a DEPS=()
--    fi
--    for DEP in "${DEPS[@]}"
--    do
--      [ ! -e "$DEP" ] && fail "Missing file: $DEP"
--      [ "$DEP" -nt "$TARGET" ] && {
--        OUTDATED=true
--        UPDATED["${#UPDATED[@]}"]="$DEP"
--      }
--    done
--  fi
--fi
--
--
--# build
--
--if [ "$OUTDATED" = true ]
--then
--  echo "### Building Isabelle/jEdit ..."
--
--  [ "${#UPDATED[@]}" -gt 0 ] && {
--    echo "Changed files:"
--    for FILE in "${UPDATED[@]}"
--    do
--      echo "  $FILE"
--    done
--  }
--
--  [ -z "$ISABELLE_JEDIT_BUILD_HOME" ] && \
--    fail "Unknown ISABELLE_JEDIT_BUILD_HOME -- missing auxiliary component"
--
--  rm -rf dist || failed
--  mkdir -p dist dist/classes || failed
--
--  cp -p -R -f "$ISABELLE_JEDIT_BUILD_HOME/contrib/$ISABELLE_JEDIT_BUILD_VERSION/." dist/.
--  cp -p -R -f "${RESOURCES[@]}" dist/classes/.
--  cp src/jEdit.props dist/properties/.
--  cp -p -R -f src/modes/. dist/modes/.
--
--  perl -i -e 'while (<>) {
--    if (m/FILE="ml.xml"/ or m/FILE_NAME_GLOB="...sml,ml."/) { }
--    elsif (m/NAME="javacc"/) {
--      print qq!<MODE NAME="isabelle" FILE="isabelle.xml" FILE_NAME_GLOB="{*.thy,ROOT0.ML,ROOT.ML}"/>\n\n!;
--      print qq!<MODE NAME="isabelle-ml" FILE="isabelle-ml.xml" FILE_NAME_GLOB="*.ML"/>\n\n!;
--      print qq!<MODE NAME="isabelle-news" FILE="isabelle-news.xml"/>\n\n!;
--      print qq!<MODE NAME="isabelle-options" FILE="isabelle-options.xml"/>\n\n!;
--      print qq!<MODE NAME="isabelle-root" FILE="isabelle-root.xml" FILE_NAME_GLOB="ROOT"/>\n\n!;
--      print;
--    }
--    elsif (m/NAME="sqr"/) {
--      print qq!<MODE NAME="sml" FILE="sml.xml" FILE_NAME_GLOB="*.{sml,sig}"/>\n\n!;
--      print;
--    }
--    else { print; }
--  }' dist/modes/catalog
--
--  cd dist
--  isabelle_jdk jar xf jedit.jar
--  cp "$ISABELLE_HOME/lib/logo/isabelle_transparent-32.gif" \
--    "org/gjt/sp/jedit/icons/themes/classic/32x32/apps/isabelle.gif" || failed
--  cp "$ISABELLE_HOME/lib/logo/isabelle_transparent-32.gif" \
--    "org/gjt/sp/jedit/icons/themes/tango/32x32/apps/isabelle.gif" || failed
--  isabelle_jdk jar cfe jedit.jar org.gjt.sp.jedit.jEdit org || failed
--  rm -rf META-INF org
--  cd ..
--
--  cp -p -R -f "${JEDIT_JARS[@]}" dist/jars/. || failed
--  (
--    #FIXME workarounds for scalac 2.11.0
--    export CYGWIN="nodosfilewarning"
--    function stty() { :; }
--    export -f stty
--
--    for JAR in "$JEDIT_JAR" "${JEDIT_JARS[@]}" "$PURE_JAR"
--    do
--      classpath "$JAR"
--    done
--    export CLASSPATH="$(platform_path "$ISABELLE_CLASSPATH")"
--    exec "$SCALA_HOME/bin/scalac" $ISABELLE_SCALA_BUILD_OPTIONS -d dist/classes "${SOURCES[@]}"
--  ) || fail "Failed to compile sources"
--
--  cd dist/classes
--  isabelle_jdk jar cf "../jars/Isabelle-jEdit.jar" * || failed
--  cd ../..
--  rm -rf dist/classes
--
--  cp "$ISABELLE_JEDIT_BUILD_HOME/doc/jedit5.3.0manual-a4.pdf" dist/doc/jedit-manual.pdf
--  cp dist/doc/CHANGES.txt dist/doc/jedit-changes
--  cat > dist/doc/Contents <<EOF
--Original jEdit Documentation
--  jedit-manual    jEdit 5.3 User's Guide
--  jedit-changes   jEdit 5.3 Version History
--
--EOF
--
--fi
--
- popd >/dev/null
- 
- 

diff --git a/sci-mathematics/isabelle/files/isabelle-2016.1-jortho-1.0-2-classpath.patch b/sci-mathematics/isabelle/files/isabelle-2016.1-jortho-1.0-2-classpath.patch
deleted file mode 100644
index a34cae3fcf4..00000000000
--- a/sci-mathematics/isabelle/files/isabelle-2016.1-jortho-1.0-2-classpath.patch
+++ /dev/null
@@ -1,8 +0,0 @@
---- Isabelle2016-1-orig/contrib/jortho-1.0-2/etc/settings	2014-04-16 06:03:34.000000000 +1000
-+++ Isabelle2016-1/contrib/jortho-1.0-2/etc/settings	2017-01-02 00:13:01.619790577 +1100
-@@ -3,4 +3,4 @@
- JORTHO_HOME="$COMPONENT"
- JORTHO_DICTIONARIES="$JORTHO_HOME/dictionaries/en.gz:$JORTHO_HOME/dictionaries/en_US.gz:$JORTHO_HOME/dictionaries/en_GB-ise.gz:$JORTHO_HOME/dictionaries/en_GB-ize.gz:$JORTHO_HOME/dictionaries/en_CA.gz"
- 
--classpath "$JORTHO_HOME/jortho.jar"
-+classpath "$(java-config -p jortho)"

diff --git a/sci-mathematics/isabelle/files/isabelle-2016.1-libsha1.patch b/sci-mathematics/isabelle/files/isabelle-2016.1-libsha1.patch
deleted file mode 100644
index f19436acd1c..00000000000
--- a/sci-mathematics/isabelle/files/isabelle-2016.1-libsha1.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- Isabelle2016-1-orig/src/Pure/General/sha1.ML	2016-12-13 01:03:45.000000000 +1100
-+++ Isabelle2016-1/src/Pure/General/sha1.ML	2016-12-28 20:50:36.814706587 +1100
-@@ -146,7 +146,7 @@
- (* C library and memory *)
- 
- val library_path =
--  Path.explode ("$ML_HOME/" ^ (if ML_System.platform_is_windows then "sha1.dll" else "libsha1.so"));
-+  Path.explode ("$SHA1_HOME/" ^ (if ML_System.platform_is_windows then "sha1.dll" else "libsha1.so"));
- 
- fun with_memory n =
-   Thread_Attributes.uninterruptible (fn restore_attributes => fn f =>

diff --git a/sci-mathematics/isabelle/files/isabelle-2016.1-smt_read_only_certificates.patch b/sci-mathematics/isabelle/files/isabelle-2016.1-smt_read_only_certificates.patch
deleted file mode 100644
index d766a957021..00000000000
--- a/sci-mathematics/isabelle/files/isabelle-2016.1-smt_read_only_certificates.patch
+++ /dev/null
@@ -1,33 +0,0 @@
---- Isabelle2016-1-orig/src/HOL/SMT_Examples/Boogie.thy	2016-12-13 01:03:38.000000000 +1100
-+++ Isabelle2016-1/src/HOL/SMT_Examples/Boogie.thy	2016-12-30 23:46:11.947737290 +1100
-@@ -52,7 +52,7 @@
- section \<open>Verification condition proofs\<close>
- 
- declare [[smt_oracle = false]]
--declare [[smt_read_only_certificates = true]]
-+declare [[smt_read_only_certificates = false]]
- 
- 
- declare [[smt_certificates = "Boogie_Max.certs"]]
---- Isabelle2016-1-orig/src/HOL/SMT_Examples/SMT_Examples.thy	2016-12-13 01:03:38.000000000 +1100
-+++ Isabelle2016-1/src/HOL/SMT_Examples/SMT_Examples.thy	2016-12-30 23:46:11.953737338 +1100
-@@ -9,7 +9,7 @@
- begin
- 
- declare [[smt_certificates = "SMT_Examples.certs"]]
--declare [[smt_read_only_certificates = true]]
-+declare [[smt_read_only_certificates = false]]
- 
- 
- section \<open>Propositional and first-order logic\<close>
---- Isabelle2016-1-orig/src/HOL/SMT_Examples/SMT_Word_Examples.thy	2016-12-13 01:03:38.000000000 +1100
-+++ Isabelle2016-1/src/HOL/SMT_Examples/SMT_Word_Examples.thy	2016-12-30 23:46:11.967737450 +1100
-@@ -11,7 +11,7 @@
- declare [[smt_oracle = true]]
- declare [[z3_extensions = true]]
- declare [[smt_certificates = "SMT_Word_Examples.certs"]]
--declare [[smt_read_only_certificates = true]]
-+declare [[smt_read_only_certificates = false]]
- 
- text \<open>
- Currently, there is no proof reconstruction for words.

diff --git a/sci-mathematics/isabelle/files/isabelle-2016.1-smt_timeout.patch b/sci-mathematics/isabelle/files/isabelle-2016.1-smt_timeout.patch
deleted file mode 100644
index 249c94bd258..00000000000
--- a/sci-mathematics/isabelle/files/isabelle-2016.1-smt_timeout.patch
+++ /dev/null
@@ -1,22 +0,0 @@
---- Isabelle2016-1-orig/src/HOL/SMT.thy	2016-12-13 01:03:38.000000000 +1100
-+++ Isabelle2016-1/src/HOL/SMT.thy	2016-12-30 14:11:09.379863215 +1100
-@@ -201,7 +201,7 @@
- (given in seconds) to restrict their runtime.
- \<close>
- 
--declare [[smt_timeout = 20]]
-+declare [[smt_timeout = 300]]
- 
- text \<open>
- SMT solvers apply randomized heuristics. In case a problem is not
---- Isabelle2016-1-orig/src/HOL/Tools/SMT/smt_config.ML	2016-12-13 01:03:42.000000000 +1100
-+++ Isabelle2016-1/src/HOL/Tools/SMT/smt_config.ML	2016-12-30 14:11:27.186904132 +1100
-@@ -170,7 +170,7 @@
- (* options *)
- 
- val oracle = Attrib.setup_config_bool @{binding smt_oracle} (K true)
--val timeout = Attrib.setup_config_real @{binding smt_timeout} (K 30.0)
-+val timeout = Attrib.setup_config_real @{binding smt_timeout} (K 300.0)
- val reconstruction_step_timeout = Attrib.setup_config_real @{binding smt_reconstruction_step_timeout} (K 10.0)
- val random_seed = Attrib.setup_config_int @{binding smt_random_seed} (K 1)
- val read_only_certificates = Attrib.setup_config_bool @{binding smt_read_only_certificates} (K false)

diff --git a/sci-mathematics/isabelle/isabelle-2016.1.ebuild b/sci-mathematics/isabelle/isabelle-2016.1.ebuild
deleted file mode 100644
index 3e67fa95fbf..00000000000
--- a/sci-mathematics/isabelle/isabelle-2016.1.ebuild
+++ /dev/null
@@ -1,328 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI="6"
-
-inherit eutils check-reqs java-pkg-2 versionator
-
-MY_PN="Isabelle"
-MY_PV=$(replace_all_version_separators '-')
-MY_P="${MY_PN}${MY_PV}"
-
-BP_PV="1.2.1"
-BP_PN="bash_process"
-BP_P="${BP_PN}-${BP_PV}"
-BP_IC_PN="${BP_PN}-isabelle-component"
-BP_IC_P="${BP_IC_PN}-${BP_PV}"
-
-# csdp is used in the compile of HOL_ex in
-# Library/Sum_of_Squares/sos_wrapper.ML where it execs $ISABELLE_CSDP
-CSDP_PV="6.x"
-CSDP_PN="csdp"
-CSDP_P="${CSDP_PN}-${CSDP_PV}"
-CSDP_IC_PN="${CSDP_PN}-isabelle-component"
-CSDP_IC_P="${CSDP_IC_PN}-${CSDP_PV}"
-
-ISABELLE_FONTS_PV="20160830"
-ISABELLE_FONTS_PN="isabelle_fonts"
-ISABELLE_FONTS_P="${ISABELLE_FONTS_PN}-${ISABELLE_FONTS_PV}"
-ISABELLE_FONTS_IC_PN="${ISABELLE_FONTS_PN}-isabelle-component"
-ISABELLE_FONTS_IC_P="${ISABELLE_FONTS_IC_PN}-${ISABELLE_FONTS_PV}"
-
-JEDIT_PV="20161024"
-JEDIT_PN="jedit_build"
-JEDIT_P="${JEDIT_PN}-${JEDIT_PV}"
-JEDIT_IC_PN="${JEDIT_PN}-isabelle-component"
-JEDIT_IC_P="${JEDIT_IC_PN}-${JEDIT_PV}"
-
-JORTHO_PV="1.0-2"
-JORTHO_PN="jortho"
-JORTHO_P="${JORTHO_PN}-${JORTHO_PV}"
-JORTHO_IC_PN="${JORTHO_PN}-isabelle-component"
-JORTHO_IC_P="${JORTHO_IC_PN}-${JORTHO_PV}"
-
-JFREECHART_PV="1.0.14-1"
-JFREECHART_PN="jfreechart"
-JFREECHART_P="${JFREECHART_PN}-${JFREECHART_PV}"
-JFREECHART_IC_PN="${JFREECHART_PN}-isabelle-component"
-JFREECHART_IC_P="${JFREECHART_IC_PN}-${JFREECHART_PV}"
-
-POLYML_PV="5.6-1"
-POLYML_PN="polyml"
-POLYML_P="${POLYML_PN}-${POLYML_PV}"
-POLYML_IC_PN="${POLYML_PN}-isabelle-component"
-POLYML_IC_P="${POLYML_IC_PN}-${POLYML_PV}"
-
-SSH_JAVA_PV="20161009"
-SSH_JAVA_PN="ssh-java"
-SSH_JAVA_P="${SSH_JAVA_PN}-${SSH_JAVA_PV}"
-SSH_JAVA_IC_PN="${SSH_JAVA_PN}-isabelle-component"
-SSH_JAVA_IC_P="${SSH_JAVA_IC_PN}-${SSH_JAVA_PV}"
-
-XZ_JAVA_PV="1.5"
-XZ_JAVA_PN="xz-java"
-XZ_JAVA_P="${XZ_JAVA_PN}-${XZ_JAVA_PV}"
-XZ_JAVA_IC_PN="${XZ_JAVA_PN}-isabelle-component"
-XZ_JAVA_IC_P="${XZ_JAVA_IC_PN}-${XZ_JAVA_PV}"
-
-SS="2.12"
-
-DESCRIPTION="Isabelle is a generic proof assistant"
-HOMEPAGE="http://www.cl.cam.ac.uk/research/hvg/Isabelle/index.html"
-SRC_URI="http://isabelle.in.tum.de/website-${MY_P}/dist/${MY_P}.tar.gz
-		http://isabelle.in.tum.de/dist/contrib/${BP_P}.tar.gz -> ${BP_IC_P}.tar.gz
-		https://dev.gentoo.org/~gienah/snapshots/${CSDP_IC_P}.tar.gz
-		http://isabelle.in.tum.de/dist/contrib/${ISABELLE_FONTS_P}.tar.gz -> ${ISABELLE_FONTS_IC_P}.tar.gz
-		http://isabelle.in.tum.de/components/${JORTHO_P}.tar.gz -> ${JORTHO_IC_P}.tar.gz
-		http://isabelle.in.tum.de/components/${JEDIT_P}.tar.gz -> ${JEDIT_IC_P}.tar.gz
-		http://isabelle.in.tum.de/dist/contrib/${JFREECHART_P}.tar.gz -> ${JFREECHART_IC_P}.tar.gz
-		https://dev.gentoo.org/~gienah/snapshots/${POLYML_IC_P}.tar.gz
-		http://isabelle.in.tum.de/dist/contrib/${SSH_JAVA_P}.tar.gz -> ${SSH_JAVA_IC_P}.tar.gz
-		https://dev.gentoo.org/~gienah/snapshots/${XZ_JAVA_IC_P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0/${PV}"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc graphbrowsing ledit readline"
-
-#upstream says
-#bash 2.x/3.x, Poly/ML 5.x, Perl 5.x,
-#for document preparation: complete LaTeX
-DEPEND=">=app-shells/bash-3.0:*
-	>=dev-java/jcommon-1.0.18:1.0
-	dev-java/jortho:0
-	>=dev-java/jfreechart-1.0.14:1.0
-	>=dev-java/itext-2.1.5:0
-	dev-java/xz-java:0
-	>=dev-lang/ghc-7.6.3
-	>=dev-lang/polyml-5.6:=[-portable]
-	>=dev-lang/perl-5.8.8-r2
-	>=dev-lang/swi-prolog-6.6.6
-	sci-libs/coinor-csdp
-	=sci-mathematics/z3-4.4*[isabelle]
-	>=virtual/jdk-1.8
-	doc? (
-		virtual/latex-base
-		dev-tex/rail
-	)
-	dev-lang/scala:${SS}
-	ledit? (
-		app-misc/ledit
-	)
-	readline? (
-		app-misc/rlwrap
-	)"
-
-RDEPEND="
-	dev-perl/libwww-perl
-	sci-mathematics/sha1-polyml
-	>=virtual/jre-1.8"
-
-S="${WORKDIR}"/Isabelle${MY_PV}
-TARGETDIR="/usr/share/Isabelle"
-
-# Notes on QA warnings: * Class files not found via DEPEND in package.env
-# Stuff with $ in the name appear to be spurious:
-# isabelle/Markup_Tree$$anonfun$results$1$1.class
-# scala/tools/nsc/backend/jvm/GenJVM$BytecodeGenerator$$anonfun$computeLocalVarsIndex$1.class
-# It wants javafx, I am unsure how to fix this. I test isabelle with the Sun JDK:
-# javafx/application/Platform.class               javafx
-# Presumably the user can provide the jEdit plugins if they are necessary:
-# marker/MarkerSetsPlugin.class                   http://plugins.jedit.org/plugins/?MarkerSets
-# projectviewer/gui/OptionPaneBase.class          http://plugins.jedit.org/plugins/?ProjectViewer
-
-JAVA_GENTOO_CLASSPATH="itext,jcommon-1.0,jortho,jfreechart-1.0,scala-${SS},xz-java"
-
-CHECKREQS_MEMORY="8192M"
-CHECKREQS_DISK_BUILD="17G"
-CHECKREQS_DISK_USR="8G"
-
-src_unpack() {
-	unpack "${MY_P}.tar.gz"
-	cd "${S}/contrib" || die
-	unpack ${BP_IC_P}.tar.gz
-	unpack ${CSDP_IC_P}.tar.gz
-	unpack ${ISABELLE_FONTS_IC_P}.tar.gz
-	unpack ${JEDIT_IC_P}.tar.gz
-	unpack ${JORTHO_IC_P}.tar.gz
-	unpack ${JFREECHART_IC_P}.tar.gz
-	unpack ${POLYML_IC_P}.tar.gz
-	unpack ${SSH_JAVA_IC_P}.tar.gz
-	unpack ${XZ_JAVA_IC_P}.tar.gz
-}
-
-pkg_setup() {
-	java-pkg-2_pkg_setup
-	check-reqs_pkg_setup
-}
-
-src_prepare() {
-	java-pkg-2_src_prepare
-	java-pkg_getjars ${JAVA_GENTOO_CLASSPATH}
-	rm -rf "${S}/contrib/${BP_P}/{x86-cygwin,x86-darwin,x86_64-darwin,x86-linux,x86_64-linux}" \
-		|| die "Could not remove bash_process binaries"
-	rm -f "${S}/contrib/${JORTHI_P}/${JORTHO_PN}.jar" \
-		|| die "Could not remove  contrib/${JORTHI_P}/${JORTHO_PN}.jar"
-	eapply "${FILESDIR}/${PN}-2016-classpath.patch"
-	eapply "${FILESDIR}/${PN}-2016-jfreechart-classpath.patch"
-	eapply "${FILESDIR}/${PN}-2016.1-bash_process-1.2.1-settings.patch"
-	eapply "${FILESDIR}/${PN}-2012-graphbrowser.patch"
-	eapply "${FILESDIR}/${PN}-2016.1-libsha1.patch"
-	eapply "${FILESDIR}/${PN}-2016.1-smt_timeout.patch"
-	eapply "${FILESDIR}/${PN}-2016.1-smt_read_only_certificates.patch"
-	eapply "${FILESDIR}/${PN}-2016.1-disable-jedit-build-after-install.patch"
-	eapply "${FILESDIR}/${PN}-2016.1-jortho-1.0-2-classpath.patch"
-	local polymlver=$(poly -v | cut -d' ' -f2)
-	local polymlarch=$(poly -v | cut -d' ' -f9 | cut -d'-' -f1)
-	cat <<- EOF >> "${S}/etc/settings"
-		# Poly/ML Gentoo (${polymlarch,,})
-		ML_PLATFORM=${polymlarch,,}-linux
-		ML_HOME="${ROOT}usr/bin"
-		ML_SYSTEM=polyml-${polymlver}
-		ML_OPTIONS="-H 1000"
-		ML_SOURCES="${ROOT}usr/src/debug/dev-lang/polyml-${polymlver}"
-
-		ISABELLE_GHC="${ROOT}usr/bin/ghc"
-		ISABELLE_OCAML="${ROOT}usr/bin/ocaml"
-		ISABELLE_SWIPL="${ROOT}usr/bin/swipl"
-		ISABELLE_JDK_HOME="\$(java-config --jdk-home)"
-		ISABELLE_BUILD_JAVA_OPTIONS="-Djava.awt.headless=true"
-		SCALA_HOME="${ROOT}usr/share/scala-${SS}"
-		SHA1_HOME="${ROOT}usr/$(get_libdir)/sha1-polyml"
-	EOF
-	local Z3_P="$(best_version sci-mathematics/z3 | sed 's:sci-mathematics/::')"
-	cat <<- EOF >> "${S}/etc/components"
-		#bundled components
-		contrib/${BP_P}
-		contrib/${CSDP_P}
-		contrib/${ISABELLE_FONTS_P}
-		contrib/${JEDIT_P}
-		contrib/${JORTHO_P}
-		contrib/${JFREECHART_P}
-		contrib/${POLYML_P}
-		contrib/${SSH_JAVA_P}
-		contrib/${XZ_JAVA_P}
-		contrib/${Z3_P}
-	EOF
-	local Z3_RC="${ROOT}usr/share/Isabelle/contrib/${Z3_P}"
-	[ -d "${Z3_RC}" ] \
-		|| die "z3 isabelle component directory ${Z3_RC} does not exist"
-	ln -s "${Z3_RC}" \
-	   "${S}/contrib/${Z3_P}" \
-		|| die "Failed to create z3 isabelle component symbolic link"
-	if use ledit && ! use readline; then
-		eapply "${FILESDIR}/${PN}-2012-reverse-line-editor-order.patch"
-	fi
-	rm -f "${S}/contrib/${JFREECHART_P}/lib"/*.jar \
-		|| die "Could not rm bundled jar files supplied by Gentoo"
-}
-
-src_compile() {
-	unset DISPLAY
-	einfo "Building Isabelle. This may take some time."
-	pushd contrib/${BP_P} || die "Could not cd to contrib/${BP_P}"
-	$(tc-getCC) ${CFLAGS} ${LDFLAGS} -o ${BP_PN} ${BP_PN}.c \
-		|| die "Could not build ${BP_PN}"
-	popd || die
-	if use graphbrowsing
-	then
-		rm -f "${S}/lib/browser/GraphBrowser.jar" \
-			|| die "failed cleaning graph browser directory"
-		pushd "${S}/lib/browser" \
-			|| die "Could not change directory to lib/browser"
-		./build || die "failed building the graph browser"
-		popd
-	fi
-	./bin/isabelle jedit -b -f || die "pide build failed"
-	pushd "${S}"/src/Pure || die "Could not change directory to src/Pure"
-	../../bin/isabelle env ./build-jars -f || die "build-jars failed"
-	popd || die
-	./bin/isabelle build -a -b -s -v || die "isabelle build failed"
-}
-
-src_install() {
-	local Z3_P="$(best_version sci-mathematics/z3 | sed 's:sci-mathematics/::')"
-	rm "${S}/contrib/${Z3_P}" \
-		|| die "Failed to remove z3 isabelle component symbolic link"
-
-	insinto ${TARGETDIR}
-	doins -r src
-	doins -r lib
-	doins -r contrib
-	doins ROOTS
-
-	docompress -x /usr/share/doc/${PF}
-	dodoc -r doc
-	if use doc; then
-		dosym /usr/share/doc/${PF}/doc "${TARGETDIR}/doc"
-		# The build of sci-mathematics/haskabelle with use doc requires
-		# sci-mathematics/isabelle[doc?]. The haskabelle doc build requires
-		# the src/Doc directory stuff in the isabelle package.
-		doins -r src/Doc
-		for i in $(find ./src/Doc -type f -executable -print)
-		do
-			exeinto $(dirname "${TARGETDIR}/${i}")
-			doexe ${i}
-		done
-	fi
-
-	for i in $(find \
-		./{bin,lib,"contrib/${BP_P}/${BP_PN}",src/HOL,src/Pure,src/Tools} \
-		-type f -executable -print)
-	do
-		exeinto $(dirname "${TARGETDIR}/${i}")
-		doexe ${i}
-	done
-
-	insinto /etc/isabelle
-	doins -r etc/*
-	dosym /etc/isabelle "${TARGETDIR}/etc"
-
-	local LIBDIR="/usr/"$(get_libdir)"/Isabelle"${MY_PV}
-	dosym "${LIBDIR}/heaps" "${TARGETDIR}/heaps"
-	insinto ${LIBDIR}
-	doins -r heaps
-
-	./bin/isabelle install -d ${TARGETDIR} "${ED}usr/bin" \
-		|| die "isabelle install failed"
-	newicon lib/icons/"${PN}.xpm" "${PN}.xpm"
-	newicon lib/icons/"${PN}-mini.xpm" "${PN}-mini.xpm"
-
-	java-pkg_regjar \
-		$(find . -type f -name \*.jar -print | sed -e "s@^\.@${ED}${TARGETDIR}@g")
-
-	local DOCS=( "ANNOUNCE" "CONTRIBUTORS" "COPYRIGHT" "NEWS" "README" )
-	einstalldocs
-}
-
-pkg_postinst() {
-	# If any of the directories in /etc/isabelle/components do not exist, then
-	# even isabelle getenv ISABELLE_HOME fails.  Hence it is necessary to
-	# to delete any non-existing directories.  If an old Isabelle version was
-	# installed with component ebuilds like sci-mathematics/e, then the
-	# Isabelle version is upgraded, then the contrib directories will not
-	# exist initially, it is necessary to delete them from /etc/isabelle/components.
-	# Then these components are rebuilt (creating these directories) using the
-	# EAPI=5 subslot depends.
-	for i in $(egrep '^[^#].*$' "${ROOT}etc/isabelle/components")
-	do
-		if [ ! -d ${TARGETDIR}/${i} ]; then
-			sed -e "\@${i}@d" -i "${ROOT}etc/isabelle/components"
-		fi
-	done
-	if use ledit && use readline; then
-		elog "Both readline and ledit use flags specified.  The default setting"
-		elog "if both are installed is to use readline (rlwrap), this can be"
-		elog "modfied by editing the ISABELLE_LINE_EDITOR setting in"
-		elog "${ROOT}/etc/isabelle/settings"
-	fi
-	elog "Please ensure you have a pdf viewer installed, for example:"
-	elog "As root: emerge app-text/zathura-pdf-poppler"
-	elog "Please configure your preferred pdf viewer, something like:"
-	elog "As normal user: xdg-mime default zathura.desktop application/pdf"
-	elog "Or alternatively by editing the PDF_VIEWER variable in the system"
-	elog "settings file ${ROOT}etc/isabelle/settings and/or the user"
-	elog "settings file \$HOME/.isabelle/${MY_P}/etc/settings"
-	elog "For nitpick it is necessary to install:"
-	elog "emerge sci-mathematics/kodkodi"
-}

diff --git a/sci-mathematics/isabelle/metadata.xml b/sci-mathematics/isabelle/metadata.xml
deleted file mode 100644
index d59b385fb4a..00000000000
--- a/sci-mathematics/isabelle/metadata.xml
+++ /dev/null
@@ -1,29 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-<maintainer type="person">
-  <email>gienah@g.o</email>
-</maintainer>
-<maintainer type="project">
-  <email>sci-mathematics@g.o</email>
-  <name>Gentoo Mathematics Project</name>
-</maintainer>
-<longdescription lang="en">
-Isabelle is a generic proof assistant. It allows mathematical
-formulas to be expressed in a formal language and provides tools
-for proving those formulas in a logical calculus. The main
-application is the formalization of mathematical proofs and in
-particular formal verification, which includes proving the
-correctness of computer hardware or software and proving
-properties of computer languages and protocols.
-</longdescription>
-<use>
-  <flag name="graphbrowsing">Generate theory browsing information,
-  including HTML documents that show a theory's definition, the
-  theorems proved in its ML file and the relationship with its
-  ancestors and descendants.</flag>
-  <flag name="ledit">Use ledit for the isabelle tty line editor</flag> 
-  <flag name="readline">Use readline (rlwrap) for the isabelle tty line
-  editor</flag> 
-</use>
-</pkgmetadata>