coot/source/v1

--- script/build-it-3-3.orig    2025-10-30 02:02:30.578448242 +0900
+++ script/build-it-3-3 2025-10-30 13:07:43.084423130 +0900
@@ -641,11 +641,11 @@
     lib_as=`cd $fat_dir && ls -1 lib/lib*.a`
 
     if [ "$clear_type" = "clear-dynamic" ] ; then
-       keep_lib_archs="$lib_as"
+       keep_lib_archs="$lib_sos"
     fi
 
     if [ "$clear_type" = "clear-static" ] ; then
-       keep_lib_archs="$lib_sos"
+       keep_lib_archs="$lib_as"
     fi
 
     file_list="etc info man share libexec  \
@@ -1053,7 +1053,7 @@
          if test -e /etc/os-release ; then
              # 20240914 strip quote marks also now
              dist_name=$(grep ^ID= /etc/os-release | sed -e 's/ID=//' -e 's/"//g')
-             dist_ver=$(grep ^VERSION_ID /etc/os-release | sed -e 's/VERSION_ID=//')
+             dist_ver=$(grep ^VERSION_ID /etc/os-release | sed -e 's/VERSION_ID=//' -e 's/"//g')
          else
              for i in fedora-release redhat-release redhat-release-workstation centos-release sl-release openSUSE-release ; do
                  rpm -q --qf '%{name}' ${i}
@@ -3168,7 +3168,7 @@
    (
    # see https://github.com/ninja-build/ninja/releases
    unset LD_LIBRARY_PATH
-   ninja_version=1.10.2
+   ninja_version=1.13.0
    ${WGET} https://github.com/ninja-build/ninja/archive/refs/tags/v$ninja_version.tar.gz
    tar xf ${AUTOBUILD_SOURCES}/v$ninja_version.tar.gz
    cd ninja-$ninja_version
@@ -3647,7 +3647,7 @@
       #    |              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
       # compilation terminated.
       # numpy_version=2.2.2 # hellish build complexity
-      numpy_version=1.26.4
+      numpy_version=2.3.4
       echo BUILDING numpy $numpy_version
       echo BUILDING numpy $numpy_version >&2
       (
@@ -4092,7 +4092,7 @@
           if test "$dist_name" = ubuntu ; then
               echo don.t mess with LDFLAGS here on ubuntu
           else
-              if test "$dist_name" = almalinux ; then
+              if test "$dist_name" = almalinux || test "$dist_name" = rocky ; then
                   echo don.t mess with LDFLAGS on almalinux
               else
                  if test "$dist_name" = arch ; then
@@ -5038,7 +5038,7 @@
 # 20220707-PE does this improve thie linking (get pass the problem with g_module_open_full)?
 # We get checking dynamic linker characteristics... awk: symbol lookup error: /home/pemsley/autobuild/Linux-emsley-vm-fedora-2.lmb.internal-gtk4/lib/libreadline.so.8: undefined symbol: UP
 # on fedora if LD_LIBRARY_PATH is set
-if [ "$dist_name" = fedora ] ;  then
+if [ "$dist_name" = fedora -o "$dist_name" = rocky ] ;  then
     :
 else
     if [ "$dist_name" = arch ] ;  then

--- coot/layla/state.cpp.orig   2025-10-30 04:12:50.496436337 +0900
+++ coot/layla/state.cpp        2025-10-30 04:22:44.485422416 +0900
@@ -66,7 +66,7 @@
     std::string package_dir = coot::package_data_dir();
     typedef std::tuple<std::string, std::unique_ptr<InchiKeyDatabase>*> HelperTuple1;
     HelperTuple1* helper_tuple = new std::tuple(coot::util::append_dir_dir(package_dir, "data"), &this->inchi_key_database);
-    g_idle_add_once(+[](gpointer user_data){
+    g_idle_add_full(G_PRIORITY_DEFAULT_IDLE,+[](gpointer user_data) -> gboolean {
         HelperTuple1* helper_tuple = (HelperTuple1*) user_data;
         std::string inchi_key_database_path = coot::util::append_dir_file(std::get<0>(*helper_tuple), "Components-inchikey.ich");
         g_info("Loading InChIKey database from: %s", inchi_key_database_path.c_str());
@@ -104,7 +104,7 @@
             g_object_unref(G_FILE(source_object));
         }, ht2);
         delete helper_tuple;
-    }, helper_tuple);
+    }, helper_tuple, nullptr);
 
 
     g_signal_connect(canvas_widget, "smiles-changed", G_CALLBACK(+[](CootLigandEditorCanvas* self, gpointer user_data){

--- build-it-3-3.orig   2025-08-19 07:16:40.705240603 +0900
+++ build-it-3-3        2025-08-19 13:27:54.684257616 +0900
@@ -641,11 +641,11 @@
     lib_as=`cd $fat_dir && ls -1 lib/lib*.a`
 
     if [ "$clear_type" = "clear-dynamic" ] ; then
-       keep_lib_archs="$lib_as"
+       keep_lib_archs="$lib_sos"
     fi
 
     if [ "$clear_type" = "clear-static" ] ; then
-       keep_lib_archs="$lib_sos"
+       keep_lib_archs="$lib_as"
     fi
 
     file_list="etc info man share libexec  \
@@ -3057,7 +3057,7 @@
    (
    which pip3
    $python_version -m pip install --upgrade pip
-   $python_version -m pip install setuptools
+   $python_version -m pip install 'setuptools<70'
    # pip3 install pycairo
    # pip3 install pygobject
    ) >  $HOSTLOGDIR/13-pip-upgrade.txt 2>&1
@@ -3107,7 +3107,7 @@
 #
 
 # we need python3 to have setuptools for meson - sigh
-python3 -m pip install setuptools
+python3 -m pip install 'setuptools<70'
 
 build_meson=true
 if command -v meson --version ; then
@@ -3169,6 +3169,7 @@
    # see https://github.com/ninja-build/ninja/releases
    unset LD_LIBRARY_PATH
    ninja_version=1.10.2
+   ninja_version=1.12.0
    ${WGET} https://github.com/ninja-build/ninja/archive/refs/tags/v$ninja_version.tar.gz
    tar xf ${AUTOBUILD_SOURCES}/v$ninja_version.tar.gz
    cd ninja-$ninja_version
@@ -4493,7 +4494,7 @@
     echo PKG_CONFIG_PATH $PKG_CONFIG_PATH
     which pip3
     pip3 install wheel
-    pip3 install pygobject
+    pip3 install pygobject==3.48.2
     ) > $HOSTLOGDIR/34-pip-wheel-pygobject.txt 2>&1
     echo BUILDING: "done" install pygobject with pip3 >&2
 fi