Fix build, runtime, and documentation issues

- LinearProblem: fix isSymmetric/isHermitian returning None instead of bool;
  fix setSymmetry/setHermitian not updating internal flags; defer Trilinos
  "number of equations" parameter until numEquations is actually known
- Mesh_readGmsh: rewrite get_line() to fix buffer overflow and O(n) scan bug;
  use clean offset-tracking loop with 1 MB safety cap
- SConstruct: disable ParMETIS and PT-Scotch for Trilinos when mpi=none
  (both libraries require MPI and caused link failures in no-MPI builds)
- dependencies.py: replace hardcoded numpy include paths with portable
  `python -c 'import numpy; print(numpy.get_include())'` on all platforms
- debian_options.py + options.md: update parmetis paths for Ubuntu 24.04+
  (/usr/include + /usr/lib instead of /usr/include/parmetis)
- installation.md: add pandoc and libnetcdf-c++4-dev dependencies; add
  missing doc build commands to Docker/quick-start section
- BelosMultiVecTraits_Tpetra.hpp: disable Kokkos finalize hook that causes
  double-free crash on shutdown (upstream Trilinos issue #11976)
- Example scripts: add missing mkDir("output") calls before writing output

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Author: Lutz Gross

SConstruct

@@ -676,10 +676,13 @@ if env['build_trilinos'] != 'never':
 
         metis_enable = 'ON' if env['metis'] else 'OFF'
         metis_inc, metis_lib = get_inc_lib_paths(env['metis_prefix']) if env['metis'] else ('', '')
-        parmetis_enable = 'ON' if env['parmetis'] else 'OFF'
-        parmetis_inc, parmetis_lib = get_inc_lib_paths(env['parmetis_prefix']) if env['parmetis'] else ('', '')
-        scotch_enable = 'ON' if env['scotch'] else 'OFF'
-        scotch_inc, scotch_lib = get_inc_lib_paths(env['scotch_prefix']) if env['scotch'] else ('', '')
+        # ParMETIS and PT-Scotch require MPI
+        parmetis_for_trilinos = env['parmetis'] and env['mpi'] != 'none'
+        parmetis_enable = 'ON' if parmetis_for_trilinos else 'OFF'
+        parmetis_inc, parmetis_lib = get_inc_lib_paths(env['parmetis_prefix']) if parmetis_for_trilinos else ('', '')
+        scotch_for_trilinos = env['scotch'] and env['mpi'] != 'none'
+        scotch_enable = 'ON' if scotch_for_trilinos else 'OFF'
+        scotch_inc, scotch_lib = get_inc_lib_paths(env['scotch_prefix']) if scotch_for_trilinos else ('', '')
 
         # Allow override of compilers for Trilinos (useful for avoiding libc++ issues on macOS)
         trilinos_cc_compiler = env.get('trilinos_cc', '') or env['CC']

doc/examples/usersguide/MT.py

@@ -43,6 +43,7 @@
 # ... mesh resolution:
 h0, h1=L0/NE0, L1/NE1
 
+mkDir("output")
 # create Domain:
 domain = Rectangle(n0=NE0, n1=NE1, l0=L0, l1=L1)
 

doc/examples/usersguide/diffusion.py

@@ -30,6 +30,7 @@
 if not HAVE_FINLEY:
     print("Finley module not available")
 else:
+    mkDir("output")
     xc=[0.02,0.002]
     r=0.001
     qc=50.e6

doc/examples/usersguide/dirac.py

@@ -36,6 +36,7 @@
 if not HAVE_FINLEY:
     print("Finley module not available")
 else:
+    mkDir("output")
     mydomain=Rectangle(30,30, l0=3, l1=2, 
                 diracPoints=[(1.,1.), (2.,1.)],  diracTags=['in', 'out'])
     # fix the solution on the boundary

doc/examples/usersguide/heatedblock.py

@@ -30,7 +30,7 @@
     HAVE_FINLEY = False
 
 if HAVE_FINLEY:
-
+    mkDir("output")
     #... set some parameters ...
     lam=1.
     mu=0.1

doc/examples/usersguide/helmholtz.py

@@ -31,6 +31,7 @@
 if not HAVE_FINLEY:
     print("Finley module not available")
 else:
+    mkDir("output")
     #... set some parameters ...
     kappa=1.
     omega=0.1

doc/examples/usersguide/inclusion.py

@@ -32,6 +32,7 @@
 if not HAVE_FINLEY:
     print("Finley module not available")
 else:
+    mkDir("output")
     # ... generate domain ...
     print("read in mesh")
     domain = ReadGmsh("inclusion.msh", 2, optimize=True)

doc/examples/usersguide/poisson.py

@@ -30,6 +30,7 @@
 if not HAVE_FINLEY:
     print("Finley module not available")
 else:
+    mkDir("output")
     mydomain = Rectangle(l0=1.,l1=1.,n0=40, n1=20)
     # define characteristic function of Gamma^D
     x = mydomain.getX()

doc/examples/usersguide/poisson_vtk.py

@@ -30,6 +30,7 @@
 if not HAVE_FINLEY:
     print("Finley module not available")
 else:
+    mkDir("output")
     # generate domain:
     mydomain = Rectangle(l0=1.,l1=1.,n0=40, n1=20)
     # define characteristic function of Gamma^D

doc/examples/usersguide/simpletest.py

@@ -4,6 +4,7 @@
 from esys.finley import ReadGmsh
 from esys.escript.pdetools import Locator
 
+mkDir("output")
 print("read in mesh")   
 domain=ReadGmsh("simplemesh.msh", 3,  optimize=True )