fixing startup, updating fmm

startup.m

@@ -1,86 +1,113 @@
-iremopts = 0;
-if ~exist('opts','var')
+function startup(opts)
+%STARTUP chunkIE startup routine 
+%
+% adds necessary folders to path. checks if FLAM and fmm2d directories are
+% in the right locations. installs fmm2d if needed and possible
+%
+% Optional input:
+%
+% opts = options structure (defaults)
+%   opts.testfmm - boolean (false), test fmm intallation
+%   opts.fmmremex - boolean (false), force recompile of mex routine
+%   opts.fmmrecompile - boolean (false), force recompile of fmm2d library
+%
+
+if nargin < 1
     opts = [];
-    iremopts = 1;
 end
 
-ifflam = true;
-if(isfield(opts,'ifflam'))
-   ifflam = opts.ifflam;
+fmmremex = false;
+if isfield(opts,'fmmremex')
+    fmmremex = opts.fmmremex;
+end
+
+fmmrecompile = false;
+if isfield(opts,'fmmrecompile')
+    fmmrecompile = opts.fmmrecompile;
 end
 
-iftest= false;
+fmmremex = or(fmmremex,fmmrecompile);
 
-if isfield(opts, 'iftest')
-  iftest = opts.iftest;
+testfmm = false;
+if isfield(opts, 'testfmm')
+  testfmm = opts.testfmm;
 end
 
+% add paths 
 addpath('./chunkie')
-if(ifflam)
-  if(exist('chunkie/FLAM/startup.m'))
+if(exist('./chunkie/FLAM/startup.m','file'))
     run 'chunkie/FLAM/startup.m';
-  end
-end
-
-iffmm0 = true;
-
-
-if(isfield(opts,'iffmm'))
-  iffmm0 = opts.iffmm;
+else
+    msg = "CHUNKIE STARTUP: warning FLAM not found in usual location\n " + ...
+        "Check that the submodule was included. ";
+    warning('CHUNKIESTARTUP:flamnotfoundwarn',msg);
 end
 
-iffmm = true;
+% install fmm2d if needed, add to path if found
+if(exist('chunkie/fmm2d/matlab','dir'))
+    cd './chunkie/fmm2d';
+    addpath './matlab';
+    icheck = exist(['fmm2d.' mexext], 'file');
+    if icheck ~=3 || fmmremex || fmmrecompile
+        if ismac || isunix
+            [status,cmdout] = system('which gfortran');
+            if(~status)
+                fprintf('------- chunkIE startup: building fmm2d ----- \n');
+                fprintf('fortran compiler found at: %s\n',cmdout);
+                iffmm = true;
+                path1 = getenv('PATH');
+                cmdout2 = extractBefore(cmdout, 'gfortran');
+                path1 = [path1 cmdout2];
+                setenv('PATH', path1);
+                if ismac
+                    fprintf('Here\n');
+                    !cp -f make.inc.macos.gnu make.inc;
+                end
+                if fmmrecompile
+                    !make clean
+                end
+                !make matlab;  
+                testfmm = true; % test if new install
 
-if(iffmm0)
-    if ismac || isunix
-        [status,cmdout] = system('which gfortran');
-        if(~status)
-            fprintf('fortran compiler found at: %s\n',cmdout);
-            iffmm = true;
-            path1 = getenv('PATH');
-            cmdout2 = extractBefore(cmdout, 'gfortran');
-            path1 = [path1 cmdout2];
-            setenv('PATH', path1);
-        if ismac
-            !cp -f chunkie/fmm2d/make.inc.macos.gnu.x86-64 chunkie/fmm2d/make.inc;
-        end
+            else    
+                msg = "CHUNKIE STARTUP: unable to find a suitable compiler for FMM2D. " + ...
+                    "See manual install instructions on github";
+                warning('CHUNKIESTARTUP:compilerwarn',msg)
+            end
+
         else
-            fprintf('Fortran compiler not found\n');
-            iffmm = false;
+            msg = "CHUNKIE STARTUP: automatic install not supported on your operating system. " + ...
+                "See manual install instructions on github";
+            warning('CHUNKIESTARTUP:OSnosupport',msg)
+        end        
+    end
+    cd matlab;
+    if testfmm
+        runtests;
+    end
+    cd ../../../;
+else
+    if fmmremex || fmmrecompile
+        msg = "CHUNKIE STARTUP: fmm2d reinstall requested but source files not found in usual location.\n" + ...
+        "Check that the submodule was included. ";
+        warning('CHUNKIESTARTUP:fmm2dsourcenotfoundwarn',msg);
+    end
+    icheck = exist(['fmm2d.' mexext], 'file');
+    if icheck == 3
+        msg = "CHUNKIE STARTUP: fmm2d mex file found on PATH but not in usual location " + ...
+        "There may be unexpected behavior if this is a different fmm2d version or if other fmm2d MATLAB files are not known to MATLAB.";
+        warning('CHUNKIESTARTUP:fmm2ddifflocwarn',msg);
+
+        if testfmm
+            msg = "CHUNKIE STARTUP: testing fmm2d not supported if not installed in usual location";
+            warning('CHUNKIESTARTUP:fmm2dnotestwarn',msg);
         end
-
     else
-       fprintf('Fortran installations not supported through startup.m\n');
-       fprintf('Follow manual installation instructions on github\n');
-       iffmm = false;
-    end
-end
+        msg = ['CHUNKIE STARTUP: warning fmm2d folder not found in usual location ' ...
+            'and no fmm2d mex file is known to MATLAB.\n If mex file exists ' ...
+            'in another location, add that location to path.\n '...
+            'Else, check that the submodule was included. '];
 
-
-
-
-if(iffmm)
-  if(exist('chunkie/fmm2d/matlab','dir'))
-      cd './chunkie/fmm2d';
-      addpath './matlab';
-      icheck = exist(['fmm2d.' mexext], 'file');
-      if icheck ~=3
-        !make matlab;  
-      end
-
-      cd matlab;
-      if iftest
-        runtests;
-      end
-      cd ../../../;
-  else
-      fprintf('Fmm installation not in standard location\n');
-      fprintf('Manual installation required');
-  end
-end
-
-clear ifflam iftest iffmm0 cmdout cmdout2 icheck iffmm path1 status
-if iremopts
-    clear opts
+        warning('CHUNKIESTARTUP:fmm2dmexnotfoundwarn',msg);
+    end
 end
-clear iremopts