jlab · sjanssen2 · May 7, 2026 · May 6, 2026 · May 6, 2026 · May 6, 2026
diff --git 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
@@ -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
@@ -71,16 +71,16 @@ 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: ${{ matrix.os }}
     steps:
     - name: Install dependencies
-      run: brew install bison@3.8 cmake boost gsl gnu-sed libomp gmp cabal-install ghc
-    - name: pioritize bison3.8
+      run: brew install bison cmake boost gsl gnu-sed libomp gmp cabal-install ghc
+    - name: pioritize homebrew bison
       # macos-13 has also installed a quite old bison2.3 version and it is found first according
       # to default PATH settings. Thus, configure.ac will test the wrong version and NOT set
       # BISONNEW as a compiler flag (see configure.ac)
-      run: echo "PATH=/usr/local/opt/bison@3.8/bin:$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
@@ -90,20 +90,39 @@ 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
+      run: ./configure --prefix $GITHUB_WORKSPACE --with-boost=/opt/homebrew/opt/boost/
     - name: patch configuration for OSX
-      run: gsed -E "s|^YACC = .+$|YACC = /usr/local/opt/bison@3.8/bin/bison|" -i config.mf && gsed -E "s|^SED = .+$|SED = /usr/local/opt/gnu-sed/libexec/gnubin/sed|" -i config.mf && gsed -E "s/ -D_XOPEN_SOURCE=500 / /" -i config.mf && gsed -E "s/ -std=c\+\+17 / -std=c\+\+11 /" -i config.mf
+      run: |
+        gsed -E "s|^YACC = .+$|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\/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
       run: sudo make install
 
     - name: test-mod
       run: make test-mod TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth TRUTH_SUFFIX=_osx
+    - name: Export test-mod results
+      if: failure()
+      uses: actions/upload-artifact@v7
+      with:
+        name: test-mod_results
+        path: ./testdata/modtest/temp
+
     - name: test-mod_outside
       run: make -j 2 test-mod_outside TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth TRUTH_SUFFIX=_osx
+    - name: 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
@@ -125,7 +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
@@ -152,7 +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/

diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -34,9 +34,6 @@
 #include <vector>
 #include <cstdint>
 
-// tr1 has it
-#include <boost/cstdint.hpp>
-
 // FIXME profile this
 #include "pool.hh"
 

diff --git 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 {

diff --git a/src/runtime.hh b/src/runtime.hh
@@ -28,14 +28,11 @@
 #include <iostream>
 #include <vector>
 #include <cassert>
+#include <cstdint>
 
 #include "yieldsize.hh"
 #include "table.hh"
 
-// tr1 has it
-#include <boost/cstdint.hpp>
-
-
 #ifndef UINT32_MAX
 #define UINT32_MAX 4294967295U
 #endif

diff --git 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
@@ -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
@@ -1,6 +1,6 @@
 
 #include <cassert>
-#include <boost/cstdint.hpp>
+#include <cstdint>
 #define UINT32_MAX 4294967295U
 
 int main(int argc, char **argv)
-Original file line number
+Diff line change
@@ Expand Up / @@ -33,7 +33,7 @@ typedef mpz_class BigInt; @@
     #else
-    #include <boost/cstdint.hpp>
+    #include <cstdint>
     typedef uint64_t BigInt;
@@ Expand Down @@