Add workaround for symlink/directory conflict (bz 2097773).

Modify the jmol patch to timeout after 5 minutes.  This is a workaround
for recently observed jmol hangs, but is not a proper fix.

sagemath-jmol.patch

@@ -1,6 +1,6 @@
 diff -up src/sage/interfaces/jmoldata.py.orig src/sage/interfaces/jmoldata.py
---- src/sage/interfaces/jmoldata.py.orig	2021-05-09 16:00:11.000000000 -0600
+--- src/sage/interfaces/jmoldata.py.orig	2022-05-15 16:11:11.000000000 -0600
-+++ src/sage/interfaces/jmoldata.py	2021-05-28 11:36:18.844565672 -0600
++++ src/sage/interfaces/jmoldata.py	2022-07-06 11:03:43.155375965 -0600
 @@ -148,8 +148,6 @@ class JmolData(SageObject):
              sage: print(os.path.exists(testfile)) # optional -- java
              True
@@ -10,16 +10,24 @@ diff -up src/sage/interfaces/jmoldata.py.orig src/sage/interfaces/jmoldata.py
          target_native = targetfile
  
          if sys.platform == 'cygwin':
-@@ -173,10 +171,8 @@ class JmolData(SageObject):
+@@ -171,12 +169,14 @@ class JmolData(SageObject):
+         with open(scratchout, 'w') as jout:
+             # Now call the java application and write the file.
              env = dict(os.environ)
-             env['LC_ALL'] = 'C'
+-            env['LC_ALL'] = 'C'
-             env['LANG'] = 'C'
+-            env['LANG'] = 'C'
 -            subprocess.call(["java", "-Xmx512m", "-Djava.awt.headless=true",
 -                "-jar", jmolpath, "-iox", "-g", size_arg,
 -                "-J", launchscript, "-j", imagescript],
 -                stdout=jout, stderr=jout, env=env)
++            env['LC_ALL'] = 'C.UTF-8'
++            env['LANG'] = 'C.UTF-8'
++            try:
 +                subprocess.call(["jmol", "-n", "-g", size_arg,
-+                "-J", launchscript, "-j", imagescript], stdout=jout)
++                    "-J", launchscript, "-j", imagescript],
++                    timeout=300, stdout=jout, stderr=jout, env=env)
++            except:
++                pass
          if not os.path.isfile(targetfile):
              raise RuntimeError(f"Jmol failed to create file {targetfile}: {Path(scratchout).read_text()}")
          os.unlink(scratchout)

sagemath.spec

@@ -84,7 +84,7 @@
 Name:		sagemath
 Summary:	A free open-source mathematics software system
 Version:	9.6
-Release:	1%{?dist}
+Release:	2%{?dist}
 # The file ${SAGE_ROOT}/COPYING.txt is the upstream license breakdown file
 # Additionally, every $files section has a comment with the license name
 # before files with that license
@@ -1030,6 +1030,9 @@ sed -i 's/3\.11\.0/3.12.0/g' configure
 # Allow use of libfplll 5.4.2
 sed -i 's/5\.4\.1/5.4.2/g' configure
 
+# Allow use of eclib 20220621
+sed -i 's/20210625/20220621/g' configure
+
 # Do not build with -march=native
 sed -i 's/CFLAGS_MARCH="-march=native"/CFLAGS_MARCH=""/' configure
 
@@ -1037,7 +1040,6 @@ sed -i 's/CFLAGS_MARCH="-march=native"/CFLAGS_MARCH=""/' configure
 ########################################################################
 %build
 export LC_ALL=C.UTF-8
-export CC=%{__cc}
 export CPPFLAGS="-I%{_includedir}/4ti2 -I%{_includedir}/arb -I%{_includedir}/cddlib"
 export ECMBIN=%{_bindir}/gmp-ecm
 export SAGE_ROOT=%{buildroot}%{SAGE_ROOT}
@@ -1678,10 +1680,9 @@ mkdir -p %{SAGE_LOCAL}/var/lib/sage/installed/database_cremona_ellcurve-%{cremon
 rm -fr %{SAGE_LOCAL}/var/lib/sage/installed/database_cremona_ellcurve-%{cremona_ver}
 
 %if %{with docs}
-########################################################################
-# Fix directory/symlink conflicts introduced by fix for bz 1875606.
-# This can be removed when Fedora 36 reaches EOL.
 %pretrans -n sagemath-doc-en -p <lua>
+-- Fix directory/symlink conflicts introduced by fix for bz 1875606.
+-- This can be removed when Fedora 36 reaches EOL.
 paths = {
   "%{SAGE_DOC}/html/en/_static/config",
   "%{SAGE_DOC}/html/en/_static/extensions",
@@ -1765,6 +1766,20 @@ for _, path in ipairs(paths) do
     end
   end
 end
+
+-- Fix directory/symlink conflicts introduced by sagemath 3.5 -> 3.6 upgrade.
+-- This can be removed when Fedora 40 reaches EOL.
+paths2 = {
+  "%{SAGE_DOC}/html/en/reference/plot3d/_static",
+  "%{SAGE_DOC}/html/en/reference/repl/_static"
+}
+
+for _, path in ipairs(paths2) do
+  st = posix.stat(path)
+  if st and st.type == "link" then
+    os.remove(path)
+  end
+end
 %endif
 
 
@@ -2021,6 +2036,11 @@ end
 
 ########################################################################
 %changelog
+* Tue Jul  5 2022 Jerry James <loganjerry@gmail.com> - 9.6-2
+- Add workaround for symlink/directory conflict (bz 2097773)
+- Modify the jmol patch to timeout after 5 minutes.  This is a workaround for
+  recently observed jmol hangs, but is not a proper fix.
+
 * Wed Jun  1 2022 Jerry James <loganjerry@gmail.com> - 9.6-1
 - Version 9.6
 - Fix path to libSingular.so (bz 2073208)