Combine startup files to one file in root directory. This fixes a bug…

startup.m

@@ -1,27 +1,162 @@
 function startup()
-    run_startup();
-    dirs = {'autodiff', 'model-io', 'multiscale', 'modules', 'solvers', ...
-        'visualization','co2lab'};
-    base_path = fileparts(mfilename('fullpath')); %#ok
-    clear fn
-    for i = 1:numel(dirs)
-        mrstPath('addroot', fullfile(base_path, dirs{i}));
-    end
-    run_local();
-end
-
-function d = rootdir()
+%Amend MATLAB PATH to handle MRST implementation.
+
+%{
+Copyright 2009-2024 SINTEF Digital, Mathematics & Cybernetics.
+
+This file is part of The MATLAB Reservoir Simulation Toolbox (MRST).
+
+MRST is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+MRST is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with MRST.  If not, see <http://www.gnu.org/licenses/>.
+%}
+
+   build_mrst_path_tree();
+
+   % Register known third-party modules
+   mod_3rdparty = { 'matlab_bgl' };
+   activate_3rdparty_modules(mod_3rdparty);
+
+   % If there exists a startup_user.m file in the root dir of MRST, we
+   % execute this file.
+   run_local();
+
+   % Run platform (Octave/Matlab) specific startup routines
+   run_platform_specific();
+
+   % Automatically load selected modules for backwards compatibility.
+   autoload = {};
+   load_compat_modules(autoload);
+
+   % Display welcome message
+   mrstStartupMessage();
+
+   % Attempt to load settings - and perform first-time setup if required.
+   settings = mrstSettings(); %#ok
+end
+
+%--------------------------------------------------------------------------
+
+function d = rootdir
    d = fileparts(mfilename('fullpath'));
 end
 
-function run_startup()
-   run(fullfile(rootdir(), 'core', 'startup.m'));
+%--------------------------------------------------------------------------
+
+function build_mrst_path_tree
+   d = rootdir();
+
+   m = fullfile(d, 'modules');
+   p = split_path(genpath(d));
+
+   % Remove octave_only folders from path
+   oct_only = ~cellfun(@isempty, regexp(p, 'octave_only'));
+
+   i =     strncmp(m, p, length(m));
+   i = i | ~cellfun(@isempty, regexp(p, '\.(git|hg|svn)'));
+   i = i | ~cellfun(@isempty, regexp(p, '3rdparty'));
+   i = i | ~cellfun(@isempty, regexp(p, 'output'));
+   i = i | cellfun(@isempty, p);
+   i = i | oct_only;
+
+   addpath(p{~i});
+
+   if mrstPlatform('octave')
+       % If we are on Octave, we add in the octave_only paths at the end to
+       % ensure that they can overwrite any of the core files where needed.
+       % We first turn off the shadowing warning since we may have
+       % compatibility fixes included in this folder.
+       os = 'Octave:shadowed-function';
+       warnstate = warning('query', os);
+       warning('off', os);
+       addpath(p{oct_only});
+       warning(warnstate);
+   end
+
+   % Add modules as root directories
+   dirs = {'autodiff', 'model-io', 'multiscale', 'modules', 'solvers', ...
+      'visualization','co2lab'};
+   base_path = fileparts(mfilename('fullpath')); %#ok
+   clear fn
+   for i = 1:numel(dirs)
+      mrstPath('addroot', fullfile(base_path, dirs{i}));
+   end
+
+end
+
+%--------------------------------------------------------------------------
+
+function p = split_path(p)
+   try
+      p = regexp(p, pathsep, 'split');
+   catch  %#ok
+      % Octave compatibility.  It is an error to get here in an M run.
+      p = strsplit(p, pathsep);
+   end
 end
 
+%--------------------------------------------------------------------------
+
+function activate_3rdparty_modules(mod_3rdparty)
+   d          = rootdir();
+   thirdparty = @(m) fullfile(d, 'core', 'utils', '3rdparty', m);
+
+   for mod = reshape(mod_3rdparty, 1, [])
+      mrstPath('add', mod{1}, thirdparty(mod{1}));
+   end
+end
+
+%--------------------------------------------------------------------------
+
+function load_compat_modules(mlist)
+   if isempty(mlist), return, end
+
+   p = mrstPath('search', mlist{:});
+
+   if isempty(p)
+      mlist = {};
+   elseif iscellstr(p)
+      mlist = mlist(~ cellfun(@isempty, p));
+   end
+
+   if ~isempty(mlist)
+      pl = 's'; if numel(mlist) == 1, pl = ''; end
+
+      fprintf(['Note: Automatically loading selected ', ...
+               'module%s for backwards compatibility:\n'], pl);
+
+      fprintf('  * %s\n', mlist{:});
+
+      mrstModule('add', mlist{:})
+   end
+end
+
+%--------------------------------------------------------------------------
+
 function run_local()
    do_run_local(fullfile(rootdir(), 'startup_user.m'));
 end
 
+%--------------------------------------------------------------------------
+
+function run_platform_specific()
+   if mrstPlatform('octave')
+      do_run_local(fullfile(rootdir(), 'utils', ...
+                            'octave_only', 'startup_octave.m'));
+   end
+end
+
+%--------------------------------------------------------------------------
+
 function do_run_local(local)
    if exist(local, 'file') == 2
       run(local);