From 7eb97482cd6b4eb7ad8242d2ba306477ddd7899a Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Wed, 6 May 2026 11:06:44 +0200
Subject: [PATCH 01/22] replace boost/cstdint.hpp with csdtint

---
 rtlib/adp.hh               | 3 +--
 rtlib/bigint.hh            | 2 +-
 rtlib/bitops.hh            | 2 +-
 rtlib/hashtng.hh           | 2 +-
 rtlib/list.hh              | 3 +--
 rtlib/multipool.hh         | 3 +--
 rtlib/pool.hh              | 3 +--
 rtlib/rope.hh              | 2 +-
 rtlib/shape.hh             | 2 +-
 rtlib/string.hh            | 3 +--
 src/runtime.hh             | 3 +--
 src/yieldsize.hh           | 3 +--
 testdata/sandbox/accu.cc   | 2 +-
 testdata/sandbox/limits.cc | 2 +-
 14 files changed, 14 insertions(+), 21 deletions(-)

diff --git a/rtlib/adp.hh b/rtlib/adp.hh
index 558617175..035d1a12b 100644
--- a/rtlib/adp.hh
+++ b/rtlib/adp.hh
@@ -26,8 +26,7 @@
 #define RTLIB_ADP_HH_
 
 #include <algorithm>
-// needed for uint64_t (Integer ...)
-#include <boost/cstdint.hpp>
+#include <cstdint>
 
 #include "empty.hh"
 #include "algebra.hh"
diff --git a/rtlib/bigint.hh b/rtlib/bigint.hh
index 2e9357bad..8c0ac5605 100644
--- a/rtlib/bigint.hh
+++ b/rtlib/bigint.hh
@@ -33,7 +33,7 @@ typedef mpz_class BigInt;
 
 #else
 
-#include <boost/cstdint.hpp>
+#include <cstdint>
 
 typedef uint64_t BigInt;
 
diff --git a/rtlib/bitops.hh b/rtlib/bitops.hh
index 4f7740760..1ff749c9c 100644
--- a/rtlib/bitops.hh
+++ b/rtlib/bitops.hh
@@ -26,7 +26,7 @@
 
 #include <cassert>
 
-#include <boost/cstdint.hpp>
+#include <cstdint>
 
 template <typename T>
 int
diff --git a/rtlib/hashtng.hh b/rtlib/hashtng.hh
index 76dcc0334..152cdb8be 100644
--- a/rtlib/hashtng.hh
+++ b/rtlib/hashtng.hh
@@ -31,7 +31,7 @@
 #include <vector>
 #include <algorithm>
 #include <utility>
-#include <boost/cstdint.hpp>
+#include <cstdint>
 
 
 #include "bitops.hh"
diff --git a/rtlib/list.hh b/rtlib/list.hh
index 3a3407931..eb5074d27 100644
--- a/rtlib/list.hh
+++ b/rtlib/list.hh
@@ -40,8 +40,7 @@
 #include <utility>
 // #include <set>
 
-// tr1 has it
-#include <boost/cstdint.hpp>
+#include <cstdint>
 
 
 #include "empty.hh"
diff --git a/rtlib/multipool.hh b/rtlib/multipool.hh
index ec4a70687..da1aaf740 100644
--- a/rtlib/multipool.hh
+++ b/rtlib/multipool.hh
@@ -30,8 +30,7 @@
 
 #include <vector>
 
-// tr1 has it
-#include <boost/cstdint.hpp>
+#include <cstdint>
 
 #include "map_pool.hh"
 
diff --git a/rtlib/pool.hh b/rtlib/pool.hh
index 0698e6c0b..849d38b26 100644
--- a/rtlib/pool.hh
+++ b/rtlib/pool.hh
@@ -28,8 +28,7 @@
 #include <cassert>
 #include <cstdlib>
 
-// tr1 has it
-#include <boost/cstdint.hpp>
+#include <cstdint>
 
 #include "map_pool.hh"
 
diff --git a/rtlib/rope.hh b/rtlib/rope.hh
index 4722d69c6..4cef95cbd 100644
--- a/rtlib/rope.hh
+++ b/rtlib/rope.hh
@@ -33,7 +33,7 @@
 #include <sstream>
 
 #include <string>
-#include <boost/cstdint.hpp>
+#include <cstdint>
 #include <boost/algorithm/string/replace.hpp>
 
 #include "../rtlib/cstr.h"
diff --git a/rtlib/shape.hh b/rtlib/shape.hh
index ab89e32a2..ae606c1a3 100644
--- a/rtlib/shape.hh
+++ b/rtlib/shape.hh
@@ -35,7 +35,7 @@
 #include <algorithm>
 #include <utility>
 
-#include <boost/cstdint.hpp>
+#include <cstdint>
 
 #include "shape_alph.hh"
 #include "bitops.hh"
diff --git a/rtlib/string.hh b/rtlib/string.hh
index 70769add1..bdc74fca5 100644
--- a/rtlib/string.hh
+++ b/rtlib/string.hh
@@ -34,8 +34,7 @@
 #include <vector>
 #include <cstdint>
 
-// tr1 has it
-#include <boost/cstdint.hpp>
+#include <cstdint>
 
 // FIXME profile this
 #include "pool.hh"
diff --git a/src/runtime.hh b/src/runtime.hh
index 3f2b23626..13768a773 100644
--- a/src/runtime.hh
+++ b/src/runtime.hh
@@ -32,8 +32,7 @@
 #include "yieldsize.hh"
 #include "table.hh"
 
-// tr1 has it
-#include <boost/cstdint.hpp>
+#include <cstdint>
 
 
 #ifndef UINT32_MAX
diff --git a/src/yieldsize.hh b/src/yieldsize.hh
index 0d7d9d00c..c3be353b5 100644
--- a/src/yieldsize.hh
+++ b/src/yieldsize.hh
@@ -30,8 +30,7 @@
 #include <vector>
 #include <list>
 
-// tr1 has it
-#include <boost/cstdint.hpp>
+#include <cstdint>
 
 class Filter;
 
diff --git a/testdata/sandbox/accu.cc b/testdata/sandbox/accu.cc
index 8e641b7ff..783016cd5 100644
--- a/testdata/sandbox/accu.cc
+++ b/testdata/sandbox/accu.cc
@@ -1,5 +1,5 @@
 
-#include <boost/cstdint.hpp>
+#include <cstdint>
 
 #include <boost/accumulators/accumulators.hpp>
 #include <boost/accumulators/statistics/stats.hpp>
diff --git a/testdata/sandbox/limits.cc b/testdata/sandbox/limits.cc
index 4c8409ce5..b3f7834ec 100644
--- a/testdata/sandbox/limits.cc
+++ b/testdata/sandbox/limits.cc
@@ -1,6 +1,6 @@
 
 #include <cassert>
-#include <boost/cstdint.hpp>
+#include <cstdint>
 #define UINT32_MAX 4294967295U
 
 int main(int argc, char **argv)

From 21bc10e009047c17d46b62db16f063e32c9d4891 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Wed, 6 May 2026 11:09:48 +0200
Subject: [PATCH 02/22] codestyle

---
 rtlib/string.hh | 2 --
 src/runtime.hh  | 4 +---
 2 files changed, 1 insertion(+), 5 deletions(-)

diff --git a/rtlib/string.hh b/rtlib/string.hh
index bdc74fca5..ef9ec4c81 100644
--- a/rtlib/string.hh
+++ b/rtlib/string.hh
@@ -34,8 +34,6 @@
 #include <vector>
 #include <cstdint>
 
-#include <cstdint>
-
 // FIXME profile this
 #include "pool.hh"
 
diff --git a/src/runtime.hh b/src/runtime.hh
index 13768a773..1921b74f3 100644
--- a/src/runtime.hh
+++ b/src/runtime.hh
@@ -28,13 +28,11 @@
 #include <iostream>
 #include <vector>
 #include <cassert>
+#include <cstdint>
 
 #include "yieldsize.hh"
 #include "table.hh"
 
-#include <cstdint>
-
-
 #ifndef UINT32_MAX
 #define UINT32_MAX 4294967295U
 #endif

From e58abcb03bd19636068de21ea9d665679dec9c73 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Wed, 6 May 2026 15:08:10 +0200
Subject: [PATCH 03/22] update github runner

---
 .github/workflows/c-cpp.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml
index d325bb4bc..0236df99b 100644
--- a/.github/workflows/c-cpp.yml
+++ b/.github/workflows/c-cpp.yml
@@ -22,7 +22,7 @@ jobs:
         # https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners
         # as of 21st Sep 2021, ubuntu-16.04 is no longer supported by github actions: https://github.blog/changelog/2021-04-29-github-actions-ubuntu-16-04-lts-virtual-environment-will-be-removed-on-september-20-2021/
         # 18.04 burnout: https://github.com/actions/runner-images/issues/6002
-        os: [ubuntu-20.04, ubuntu-22.04, ubuntu-24.04]
+        os: [ubuntu-22.04, ubuntu-24.04]
     runs-on: ${{ matrix.os }}
     steps:
     - name: Update apt
@@ -71,7 +71,7 @@ jobs:
     strategy:
       matrix:
         # https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners
-        os: [macos-13]
+        os: [macos-14]
     runs-on: ${{ matrix.os }}
     steps:
     - name: Install dependencies

From 082f51ef69f90ac34d6551807e7da52f69782442 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Wed, 6 May 2026 15:35:33 +0200
Subject: [PATCH 04/22] dynamically identify boost install dir

---
 .github/workflows/c-cpp.yml | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml
index 0236df99b..ac50c4c82 100644
--- a/.github/workflows/c-cpp.yml
+++ b/.github/workflows/c-cpp.yml
@@ -94,7 +94,14 @@ jobs:
     - name: configure
       run: ./configure --prefix $GITHUB_WORKSPACE
     - name: patch configuration for OSX
-      run: gsed -E "s|^YACC = .+$|YACC = /usr/local/opt/bison@3.8/bin/bison|" -i config.mf && gsed -E "s|^SED = .+$|SED = /usr/local/opt/gnu-sed/libexec/gnubin/sed|" -i config.mf && gsed -E "s/ -D_XOPEN_SOURCE=500 / /" -i config.mf && gsed -E "s/ -std=c\+\+17 / -std=c\+\+11 /" -i config.mf
+      run: |
+        BOOST_PREFIX=$(brew --prefix boost)
+        gsed -E "s|^BOOST_CPPFLAGS = .+$|BOOST_CPPFLAGS = -I${BOOST_PREFIX}/include|" -i config.mf
+        gsed -E "s|^BOOST_LDFLAGS = .+$|BOOST_LDFLAGS = -L${BOOST_PREFIX}/lib|" -i config.mf
+        gsed -E "s|^YACC = .+$|YACC = /usr/local/opt/bison@3.8/bin/bison|" -i config.mf
+        gsed -E "s|^SED = .+$|SED = /usr/local/opt/gnu-sed/libexec/gnubin/sed|" -i config.mf
+        gsed -E "s/ -D_XOPEN_SOURCE=500 / /" -i config.mf
+        gsed -E "s/ -std=c\+\+17 / -std=c\+\+11 /" -i config.mf
     - name: make
       run: make -j 3
     - name: make install

From 60ddfe577c407f22880fd2f2c639f9e96849f5c9 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Wed, 6 May 2026 15:40:09 +0200
Subject: [PATCH 05/22] switch order

---
 .github/workflows/c-cpp.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml
index ac50c4c82..d1b3f0eed 100644
--- a/.github/workflows/c-cpp.yml
+++ b/.github/workflows/c-cpp.yml
@@ -91,8 +91,6 @@ jobs:
       run: git clone --branch master https://github.com/jlab/gapc-test-suite.git $GITHUB_WORKSPACE/../gapc-test-suite
 
     - uses: actions/checkout@v3
-    - name: configure
-      run: ./configure --prefix $GITHUB_WORKSPACE
     - name: patch configuration for OSX
       run: |
         BOOST_PREFIX=$(brew --prefix boost)
@@ -102,6 +100,8 @@ jobs:
         gsed -E "s|^SED = .+$|SED = /usr/local/opt/gnu-sed/libexec/gnubin/sed|" -i config.mf
         gsed -E "s/ -D_XOPEN_SOURCE=500 / /" -i config.mf
         gsed -E "s/ -std=c\+\+17 / -std=c\+\+11 /" -i config.mf
+    - name: configure
+      run: ./configure --prefix $GITHUB_WORKSPACE
     - name: make
       run: make -j 3
     - name: make install

From 4cc5b918407d53c94783580e4ea3b049515b66f5 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Wed, 6 May 2026 15:49:43 +0200
Subject: [PATCH 06/22] define boost location

---
 .github/workflows/c-cpp.yml | 13 +++----------
 1 file changed, 3 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml
index d1b3f0eed..78941c642 100644
--- a/.github/workflows/c-cpp.yml
+++ b/.github/workflows/c-cpp.yml
@@ -35,7 +35,7 @@ jobs:
 
     - uses: actions/checkout@v3
     - name: configure
-      run: ./configure --prefix $GITHUB_WORKSPACE
+      run: ./configure --prefix $GITHUB_WORKSPACE --with-boost $(brew --prefix boost)
     - name: make
       run: make -j 2
     - name: make install
@@ -91,17 +91,10 @@ jobs:
       run: git clone --branch master https://github.com/jlab/gapc-test-suite.git $GITHUB_WORKSPACE/../gapc-test-suite
 
     - uses: actions/checkout@v3
-    - name: patch configuration for OSX
-      run: |
-        BOOST_PREFIX=$(brew --prefix boost)
-        gsed -E "s|^BOOST_CPPFLAGS = .+$|BOOST_CPPFLAGS = -I${BOOST_PREFIX}/include|" -i config.mf
-        gsed -E "s|^BOOST_LDFLAGS = .+$|BOOST_LDFLAGS = -L${BOOST_PREFIX}/lib|" -i config.mf
-        gsed -E "s|^YACC = .+$|YACC = /usr/local/opt/bison@3.8/bin/bison|" -i config.mf
-        gsed -E "s|^SED = .+$|SED = /usr/local/opt/gnu-sed/libexec/gnubin/sed|" -i config.mf
-        gsed -E "s/ -D_XOPEN_SOURCE=500 / /" -i config.mf
-        gsed -E "s/ -std=c\+\+17 / -std=c\+\+11 /" -i config.mf
     - name: configure
       run: ./configure --prefix $GITHUB_WORKSPACE
+    - name: patch configuration for OSX
+      run: gsed -E "s|^YACC = .+$|YACC = /usr/local/opt/bison@3.8/bin/bison|" -i config.mf && gsed -E "s|^SED = .+$|SED = /usr/local/opt/gnu-sed/libexec/gnubin/sed|" -i config.mf && gsed -E "s/ -D_XOPEN_SOURCE=500 / /" -i config.mf && gsed -E "s/ -std=c\+\+17 / -std=c\+\+11 /" -i config.mf
     - name: make
       run: make -j 3
     - name: make install

From 5911221494e03883807414a6075ebe869902f5f9 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Wed, 6 May 2026 16:13:53 +0200
Subject: [PATCH 07/22] move to osx job

---
 .github/workflows/c-cpp.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml
index 78941c642..fa1f5c1ee 100644
--- a/.github/workflows/c-cpp.yml
+++ b/.github/workflows/c-cpp.yml
@@ -35,7 +35,7 @@ jobs:
 
     - uses: actions/checkout@v3
     - name: configure
-      run: ./configure --prefix $GITHUB_WORKSPACE --with-boost $(brew --prefix boost)
+      run: ./configure --prefix $GITHUB_WORKSPACE
     - name: make
       run: make -j 2
     - name: make install
@@ -92,7 +92,7 @@ jobs:
 
     - uses: actions/checkout@v3
     - name: configure
-      run: ./configure --prefix $GITHUB_WORKSPACE
+      run: ./configure --prefix $GITHUB_WORKSPACE --with-boost $(brew --prefix boost)
     - name: patch configuration for OSX
       run: gsed -E "s|^YACC = .+$|YACC = /usr/local/opt/bison@3.8/bin/bison|" -i config.mf && gsed -E "s|^SED = .+$|SED = /usr/local/opt/gnu-sed/libexec/gnubin/sed|" -i config.mf && gsed -E "s/ -D_XOPEN_SOURCE=500 / /" -i config.mf && gsed -E "s/ -std=c\+\+17 / -std=c\+\+11 /" -i config.mf
     - name: make

From 23d3691460e276a43047de4d74ad92b835a575a1 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Wed, 6 May 2026 16:18:40 +0200
Subject: [PATCH 08/22] explicit path

---
 .github/workflows/c-cpp.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml
index fa1f5c1ee..bf8b73fb3 100644
--- a/.github/workflows/c-cpp.yml
+++ b/.github/workflows/c-cpp.yml
@@ -92,7 +92,7 @@ jobs:
 
     - uses: actions/checkout@v3
     - name: configure
-      run: ./configure --prefix $GITHUB_WORKSPACE --with-boost $(brew --prefix boost)
+      run: ./configure --prefix $GITHUB_WORKSPACE --with-boost /opt/homebrew/Cellar/boost/1.90.0_1
     - name: patch configuration for OSX
       run: gsed -E "s|^YACC = .+$|YACC = /usr/local/opt/bison@3.8/bin/bison|" -i config.mf && gsed -E "s|^SED = .+$|SED = /usr/local/opt/gnu-sed/libexec/gnubin/sed|" -i config.mf && gsed -E "s/ -D_XOPEN_SOURCE=500 / /" -i config.mf && gsed -E "s/ -std=c\+\+17 / -std=c\+\+11 /" -i config.mf
     - name: make

From 3ffdef604c6ad25ce85df6b5c87bd20e75943771 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Wed, 6 May 2026 16:22:12 +0200
Subject: [PATCH 09/22] syntax

---
 .github/workflows/c-cpp.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml
index bf8b73fb3..fb396e41b 100644
--- a/.github/workflows/c-cpp.yml
+++ b/.github/workflows/c-cpp.yml
@@ -92,7 +92,7 @@ jobs:
 
     - uses: actions/checkout@v3
     - name: configure
-      run: ./configure --prefix $GITHUB_WORKSPACE --with-boost /opt/homebrew/Cellar/boost/1.90.0_1
+      run: ./configure --prefix $GITHUB_WORKSPACE --with-boost=/opt/homebrew/Cellar/boost/1.90.0_1/
     - name: patch configuration for OSX
       run: gsed -E "s|^YACC = .+$|YACC = /usr/local/opt/bison@3.8/bin/bison|" -i config.mf && gsed -E "s|^SED = .+$|SED = /usr/local/opt/gnu-sed/libexec/gnubin/sed|" -i config.mf && gsed -E "s/ -D_XOPEN_SOURCE=500 / /" -i config.mf && gsed -E "s/ -std=c\+\+17 / -std=c\+\+11 /" -i config.mf
     - name: make

From 94d8e919d8e167a8f881d24735aa483b5f24e4c9 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Wed, 6 May 2026 18:17:49 +0200
Subject: [PATCH 10/22] point to bison

---
 .github/workflows/c-cpp.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml
index fb396e41b..2c3cd715e 100644
--- a/.github/workflows/c-cpp.yml
+++ b/.github/workflows/c-cpp.yml
@@ -75,12 +75,12 @@ jobs:
     runs-on: ${{ matrix.os }}
     steps:
     - name: Install dependencies
-      run: brew install bison@3.8 cmake boost gsl gnu-sed libomp gmp cabal-install ghc
-    - name: pioritize bison3.8
+      run: brew install bison cmake boost gsl gnu-sed libomp gmp cabal-install ghc
+    - name: pioritize homebrew bison
       # macos-13 has also installed a quite old bison2.3 version and it is found first according
       # to default PATH settings. Thus, configure.ac will test the wrong version and NOT set
       # BISONNEW as a compiler flag (see configure.ac)
-      run: echo "PATH=/usr/local/opt/bison@3.8/bin:$PATH" >> $GITHUB_ENV
+      run: echo "PATH=/opt/homebrew/opt/bison/bin:$PATH" >> $GITHUB_ENV
     - name: update cabal
       run: cabal update
     - name: add random Haskell lib
@@ -94,7 +94,7 @@ jobs:
     - name: configure
       run: ./configure --prefix $GITHUB_WORKSPACE --with-boost=/opt/homebrew/Cellar/boost/1.90.0_1/
     - name: patch configuration for OSX
-      run: gsed -E "s|^YACC = .+$|YACC = /usr/local/opt/bison@3.8/bin/bison|" -i config.mf && gsed -E "s|^SED = .+$|SED = /usr/local/opt/gnu-sed/libexec/gnubin/sed|" -i config.mf && gsed -E "s/ -D_XOPEN_SOURCE=500 / /" -i config.mf && gsed -E "s/ -std=c\+\+17 / -std=c\+\+11 /" -i config.mf
+      run: gsed -E "s|^YACC = .+$|YACC = /opt/homebrew/opt/bison/bin/bison|" -i config.mf && gsed -E "s|^SED = .+$|SED = /usr/local/opt/gnu-sed/libexec/gnubin/sed|" -i config.mf && gsed -E "s/ -D_XOPEN_SOURCE=500 / /" -i config.mf && gsed -E "s/ -std=c\+\+17 / -std=c\+\+11 /" -i config.mf
     - name: make
       run: make -j 3
     - name: make install

From 3fe9d05312ebcb99a7acaa6bdaf6fd24002e64b3 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Wed, 6 May 2026 18:34:52 +0200
Subject: [PATCH 11/22] fix sed path

---
 .github/workflows/c-cpp.yml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml
index 2c3cd715e..848b60d27 100644
--- a/.github/workflows/c-cpp.yml
+++ b/.github/workflows/c-cpp.yml
@@ -94,7 +94,11 @@ jobs:
     - name: configure
       run: ./configure --prefix $GITHUB_WORKSPACE --with-boost=/opt/homebrew/Cellar/boost/1.90.0_1/
     - name: patch configuration for OSX
-      run: gsed -E "s|^YACC = .+$|YACC = /opt/homebrew/opt/bison/bin/bison|" -i config.mf && gsed -E "s|^SED = .+$|SED = /usr/local/opt/gnu-sed/libexec/gnubin/sed|" -i config.mf && gsed -E "s/ -D_XOPEN_SOURCE=500 / /" -i config.mf && gsed -E "s/ -std=c\+\+17 / -std=c\+\+11 /" -i config.mf
+      run: |
+        gsed -E "s|^YACC = .+$|YACC = /opt/homebrew/opt/bison/bin/bison|" -i config.mf
+        gsed -E "s|^SED = .+$|SED = /opt/homebrew/opt/gnu-sed/libexec/gnubin/sed|" -i config.mf
+        gsed -E "s/ -D_XOPEN_SOURCE=500 / /" -i config.mf
+        gsed -E "s/ -std=c\+\+17 / -std=c\+\+11 /" -i config.mf
     - name: make
       run: make -j 3
     - name: make install

From 723e643b08d46537e700b47f00b8f3ca1251247c Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Wed, 6 May 2026 19:32:53 +0200
Subject: [PATCH 12/22] add artifact export

---
 .github/workflows/c-cpp.yml | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml
index 848b60d27..b3ee580d7 100644
--- a/.github/workflows/c-cpp.yml
+++ b/.github/workflows/c-cpp.yml
@@ -106,6 +106,13 @@ jobs:
 
     - name: test-mod
       run: make test-mod TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth TRUTH_SUFFIX=_osx
+    - name: Export test results
+      if: failure()
+      uses: actions/upload-artifact@v7
+      with:
+        name: test-mod_results
+        path: ./testdata/modtest/temp
+
     - name: test-mod_outside
       run: make -j 2 test-mod_outside TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth TRUTH_SUFFIX=_osx
     - name: test-regress

From 83e5bb777350efb8db78038aedc822848d5055e1 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Wed, 6 May 2026 21:20:35 +0200
Subject: [PATCH 13/22] use new branch for OSX truth

---
 .github/workflows/c-cpp.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml
index b3ee580d7..89ca48ffa 100644
--- a/.github/workflows/c-cpp.yml
+++ b/.github/workflows/c-cpp.yml
@@ -88,7 +88,7 @@ jobs:
     #- name: add base Haskell lib containers (prelude, Data.Map, Data.Map.Strict)
     #  run: cabal install --lib base
     - name: Checkout truth
-      run: git clone --branch master https://github.com/jlab/gapc-test-suite.git $GITHUB_WORKSPACE/../gapc-test-suite
+      run: git clone --branch migrate_osx14 https://github.com/jlab/gapc-test-suite.git $GITHUB_WORKSPACE/../gapc-test-suite
 
     - uses: actions/checkout@v3
     - name: configure

From 5ec632836ef67dabbd3e467d64476964081aae8a Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Wed, 6 May 2026 21:38:22 +0200
Subject: [PATCH 14/22] also export outside mod tests

---
 .github/workflows/c-cpp.yml | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml
index 89ca48ffa..6ac7df13b 100644
--- a/.github/workflows/c-cpp.yml
+++ b/.github/workflows/c-cpp.yml
@@ -106,7 +106,7 @@ jobs:
 
     - name: test-mod
       run: make test-mod TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth TRUTH_SUFFIX=_osx
-    - name: Export test results
+    - name: Export test-mod results
       if: failure()
       uses: actions/upload-artifact@v7
       with:
@@ -115,6 +115,13 @@ jobs:
 
     - name: test-mod_outside
       run: make -j 2 test-mod_outside TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth TRUTH_SUFFIX=_osx
+    - name: Export test-mod_outside results
+      if: failure()
+      uses: actions/upload-artifact@v7
+      with:
+        name: test-mod_outside_results
+        path: ./testdata/modtest/temp
+
     - name: test-regress
       run: make test-regress TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth
     - name: test-ambiguity

From 436d33b155f80b9a868fbb09640c0be937130dbe Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Wed, 6 May 2026 22:12:39 +0200
Subject: [PATCH 15/22] trigger build

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index ec8788ef6..5392d6383 100644
--- a/README.md
+++ b/README.md
@@ -9,7 +9,7 @@
  | |_) |  __/ | | | | | | | (_| | | | | \__ \ | |__| |/ ____ \| |     
  |____/ \___|_|_|_| |_| |_|\__,_|_| |_| |___/  \_____/_/    \_\_|     
 ```                                                                      
-                                                                    
+                                                                  
 ## Dependencies
 
 Bellman's GAP was tested on the following dependencies.

From aa58d1eba6f29ca4a7e1cf9948c498b14aef3598 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Thu, 7 May 2026 09:32:57 +0200
Subject: [PATCH 16/22] aim to make it a random access iterator

---
 rtlib/vector_sparse.hh | 20 +++++++++++++++++---
 1 file changed, 17 insertions(+), 3 deletions(-)

diff --git a/rtlib/vector_sparse.hh b/rtlib/vector_sparse.hh
index b968358c4..b02adf87d 100644
--- a/rtlib/vector_sparse.hh
+++ b/rtlib/vector_sparse.hh
@@ -116,7 +116,7 @@ class Stapel {
 
   T &pop() {
     assert(top_);
-    return array[top_--];
+    return array[--top_];
   }
 
   T &top() {
@@ -285,7 +285,7 @@ template <typename T, typename U = size_t> class Vector_Sparse {
    public:
     typedef T value_type;
     typedef std::random_access_iterator_tag iterator_category;
-    typedef U difference_type;
+    typedef std::ptrdiff_t difference_type;
     typedef T* pointer;
     typedef T& reference;
 
@@ -343,7 +343,21 @@ template <typename T, typename U = size_t> class Vector_Sparse {
 
     Iterator operator+=(const difference_type &other) {
       i += other;
-      return Iterator(v, i);
+      return *this;
+    }
+
+    Iterator& operator-=(difference_type other) {
+      i -= other;
+      return *this;
+    }
+    reference operator[](difference_type n) {
+      return v(*(i + n));
+    }
+    pointer operator->() {
+      return &v(*i);
+    }
+    const reference operator*() const {
+      return v(*i);
     }
 
     bool operator>(const Iterator &other) const {

From edc4d60aef216c9972c9058a7b7a0c6dcec3da03 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Thu, 7 May 2026 11:19:43 +0200
Subject: [PATCH 17/22] more generic pointer to boost + explicit addition of
 libgmp

---
 .github/workflows/c-cpp.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml
index 6ac7df13b..0834b567b 100644
--- a/.github/workflows/c-cpp.yml
+++ b/.github/workflows/c-cpp.yml
@@ -92,13 +92,14 @@ jobs:
 
     - uses: actions/checkout@v3
     - name: configure
-      run: ./configure --prefix $GITHUB_WORKSPACE --with-boost=/opt/homebrew/Cellar/boost/1.90.0_1/
+      run: ./configure --prefix $GITHUB_WORKSPACE --with-boost=/opt/homebrew/opt/boost/
     - name: patch configuration for OSX
       run: |
         gsed -E "s|^YACC = .+$|YACC = /opt/homebrew/opt/bison/bin/bison|" -i config.mf
         gsed -E "s|^SED = .+$|SED = /opt/homebrew/opt/gnu-sed/libexec/gnubin/sed|" -i config.mf
         gsed -E "s/ -D_XOPEN_SOURCE=500 / /" -i config.mf
-        gsed -E "s/ -std=c\+\+17 / -std=c\+\+11 /" -i config.mf
+        gsed -E "s/ -std=c\+\+17 / -std=c\+\+11 -I\/opt\/homebrew\/opt\/gmp\/include /" -i config.mf
+        gsed -E "s/\$\(LDFLAGS_EXTRA\) \\/\$\(LDFLAGS_EXTRA\) -L/opt/homebrew/opt/gmp/lib \\/" -i config.mf
     - name: make
       run: make -j 3
     - name: make install

From 886748a0f2f98b1f09a19249d03df92fe0242786 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Thu, 7 May 2026 11:36:51 +0200
Subject: [PATCH 18/22] fix gsed expression

---
 .github/workflows/c-cpp.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml
index 0834b567b..3af448723 100644
--- a/.github/workflows/c-cpp.yml
+++ b/.github/workflows/c-cpp.yml
@@ -99,7 +99,7 @@ jobs:
         gsed -E "s|^SED = .+$|SED = /opt/homebrew/opt/gnu-sed/libexec/gnubin/sed|" -i config.mf
         gsed -E "s/ -D_XOPEN_SOURCE=500 / /" -i config.mf
         gsed -E "s/ -std=c\+\+17 / -std=c\+\+11 -I\/opt\/homebrew\/opt\/gmp\/include /" -i config.mf
-        gsed -E "s/\$\(LDFLAGS_EXTRA\) \\/\$\(LDFLAGS_EXTRA\) -L/opt/homebrew/opt/gmp/lib \\/" -i config.mf
+        gsed -E 's|\$\(LDFLAGS_EXTRA\) \\|\$\(LDFLAGS_EXTRA\) -L/opt/homebrew/opt/gmp/lib \\|' -i config.mf
     - name: make
       run: make -j 3
     - name: make install

From 4f98d1045c3690a5724ad8a915cb7119d04c3e0c Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Thu, 7 May 2026 13:39:06 +0200
Subject: [PATCH 19/22] turn off regress tests for a sec

---
 .github/workflows/c-cpp.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml
index 3af448723..88487d174 100644
--- a/.github/workflows/c-cpp.yml
+++ b/.github/workflows/c-cpp.yml
@@ -123,8 +123,8 @@ jobs:
         name: test-mod_outside_results
         path: ./testdata/modtest/temp
 
-    - name: test-regress
-      run: make test-regress TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth
+    #- name: test-regress
+    #  run: make test-regress TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth
     - name: test-ambiguity
       run: make test-ambiguity TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth
     - name: test-unit

From 0414aec05bcacb43de88e5c18142f290f320b720 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Thu, 7 May 2026 13:52:28 +0200
Subject: [PATCH 20/22] also point to libgsl header and lib

---
 .github/workflows/c-cpp.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml
index 88487d174..bb734c74b 100644
--- a/.github/workflows/c-cpp.yml
+++ b/.github/workflows/c-cpp.yml
@@ -98,8 +98,8 @@ jobs:
         gsed -E "s|^YACC = .+$|YACC = /opt/homebrew/opt/bison/bin/bison|" -i config.mf
         gsed -E "s|^SED = .+$|SED = /opt/homebrew/opt/gnu-sed/libexec/gnubin/sed|" -i config.mf
         gsed -E "s/ -D_XOPEN_SOURCE=500 / /" -i config.mf
-        gsed -E "s/ -std=c\+\+17 / -std=c\+\+11 -I\/opt\/homebrew\/opt\/gmp\/include /" -i config.mf
-        gsed -E 's|\$\(LDFLAGS_EXTRA\) \\|\$\(LDFLAGS_EXTRA\) -L/opt/homebrew/opt/gmp/lib \\|' -i config.mf
+        gsed -E "s/ -std=c\+\+17 / -std=c\+\+11 -I\/opt\/homebrew\/opt\/gmp\/include -I\/opt\/homebrew\/opt\/gsl\/include /" -i config.mf
+        gsed -E 's|\$\(LDFLAGS_EXTRA\) \\|\$\(LDFLAGS_EXTRA\) -L/opt/homebrew/opt/gmp/lib -L/opt/homebrew/opt/gsl/lib \\|' -i config.mf
     - name: make
       run: make -j 3
     - name: make install

From e062625b2c51ca0130af7737b843c0595f28fd28 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Thu, 7 May 2026 14:14:37 +0200
Subject: [PATCH 21/22] reactivate regress tests (even though checkpointing
 might fail) and upgrade to actions/checkout@v6

---
 .github/workflows/c-cpp.yml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml
index bb734c74b..787aed046 100644
--- a/.github/workflows/c-cpp.yml
+++ b/.github/workflows/c-cpp.yml
@@ -33,7 +33,7 @@ jobs:
     - name: Checkout truth
       run: git clone --branch master https://github.com/jlab/gapc-test-suite.git $GITHUB_WORKSPACE/../gapc-test-suite
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v6
     - name: configure
       run: ./configure --prefix $GITHUB_WORKSPACE
     - name: make
@@ -90,7 +90,7 @@ jobs:
     - name: Checkout truth
       run: git clone --branch migrate_osx14 https://github.com/jlab/gapc-test-suite.git $GITHUB_WORKSPACE/../gapc-test-suite
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v6
     - name: configure
       run: ./configure --prefix $GITHUB_WORKSPACE --with-boost=/opt/homebrew/opt/boost/
     - name: patch configuration for OSX
@@ -123,8 +123,8 @@ jobs:
         name: test-mod_outside_results
         path: ./testdata/modtest/temp
 
-    #- name: test-regress
-    #  run: make test-regress TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth
+    - name: test-regress
+      run: make test-regress TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth
     - name: test-ambiguity
       run: make test-ambiguity TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth
     - name: test-unit
@@ -144,7 +144,7 @@ jobs:
       run: sudo apt-get update
     - name: Install dependencies
       run: sudo apt-get install flex bison make libboost-all-dev libgsl-dev python3 python3-pip python3-biopython
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v6
     - name: configure
       run: ./configure
     - name: make
@@ -171,7 +171,7 @@ jobs:
   cpplint:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v6
     - uses: actions/setup-python@v4
     - run: pip install cpplint
     - run: cpplint --recursive --counting 'detailed' --filter="-runtime/references,-build/include_subdir" --extensions=cc,hh src/ rtlib/

From 632d8337ad7c2bcd84f1edcf06c5bf60dea00667 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Thu, 7 May 2026 16:17:47 +0200
Subject: [PATCH 22/22] revert

---
 .github/workflows/c-cpp.yml | 2 +-
 README.md                   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml
index 787aed046..85b767a02 100644
--- a/.github/workflows/c-cpp.yml
+++ b/.github/workflows/c-cpp.yml
@@ -88,7 +88,7 @@ jobs:
     #- name: add base Haskell lib containers (prelude, Data.Map, Data.Map.Strict)
     #  run: cabal install --lib base
     - name: Checkout truth
-      run: git clone --branch migrate_osx14 https://github.com/jlab/gapc-test-suite.git $GITHUB_WORKSPACE/../gapc-test-suite
+      run: git clone --branch master https://github.com/jlab/gapc-test-suite.git $GITHUB_WORKSPACE/../gapc-test-suite
 
     - uses: actions/checkout@v6
     - name: configure
diff --git a/README.md b/README.md
index 5392d6383..ec8788ef6 100644
--- a/README.md
+++ b/README.md
@@ -9,7 +9,7 @@
  | |_) |  __/ | | | | | | | (_| | | | | \__ \ | |__| |/ ____ \| |     
  |____/ \___|_|_|_| |_| |_|\__,_|_| |_| |___/  \_____/_/    \_\_|     
 ```                                                                      
-                                                                  
+                                                                    
 ## Dependencies
 
 Bellman's GAP was tested on the following dependencies.