Matlab AT release 2.3 (#394)

* release 2.3

* release 2.3

* updated project

* updated project

* Version number in Matlab sidebar

* Small fix in installation doc

* clean relase script

* Added instructions to get correct plots in help files

Author: lfarv

ToolboxPackagingConfiguration.prj

@@ -1,5 +1,5 @@
 <deployment-project plugin="plugin.toolbox" plugin-version="1.0">
-  <configuration build-checksum="24182281" file="/Users/famille/dev/libraries/at/ToolboxPackagingConfiguration.prj" location="/Users/famille/dev/libraries/at" name="ToolboxPackagingConfiguration" target="target.toolbox" target-name="Package Toolbox">
+  <configuration build-checksum="770107251" file="/Users/famille/dev/libraries/at/ToolboxPackagingConfiguration.prj" location="/Users/famille/dev/libraries/at" name="ToolboxPackagingConfiguration" target="target.toolbox" target-name="Package Toolbox">
     <param.appname>Accelerator Toolbox</param.appname>
     <param.authnamewatermark>atcollab</param.authnamewatermark>
     <param.email />
@@ -15,7 +15,7 @@ compute accelerator parameters and beam properties.
 AT is based on a 6-D modular tracking engine written in C/C++ for efficiency. Lattice manipulation and computation of accelerator physics parameters are performed in MATLAB.
 
 View on GitHub</param.description>
-    <param.screenshot>${PROJECT_ROOT}/developer/mdoc/AT.png</param.screenshot>
+    <param.screenshot>${PROJECT_ROOT}/developer/matlab/AT.png</param.screenshot>
     <param.version>2.3</param.version>
     <param.output>${PROJECT_ROOT}/Accelerator Toolbox.mltbx</param.output>
     <param.products.name />
@@ -88,7 +88,7 @@ docs/p</param.exclude.filters>
     <param.exported.on.package>false</param.exported.on.package>
     <param.required.addons>
       <requiredaddons>
-        <requiredAddOn earliest="earliest" fromRepository="true" id="e562b2d1-4a80-11e4-9553-005056977bd0" include="false" latest="latest">export_fig(2)</requiredAddOn>
+        <requiredAddOn earliest="earliest" fromRepository="true" id="e562b2d1-4a80-11e4-9553-005056977bd0" include="false" latest="latest">export_fig</requiredAddOn>
       </requiredaddons>
     </param.required.addons>
     <param.matlab.project.id>25a6ccb8-d1d3-4459-847b-7335e59e8646</param.matlab.project.id>
@@ -148,7 +148,7 @@ docs/p</param.exclude.filters>
     </build-deliverables>
     <workflow />
     <matlab>
-      <root>/Applications/MATLAB_R2021b.app</root>
+      <root>/Applications/MATLAB_R2022a.app</root>
       <toolboxes>
         <toolbox name="matlabcoder" />
       </toolboxes>
@@ -167,7 +167,7 @@ docs/p</param.exclude.filters>
       <vista>false</vista>
       <linux>false</linux>
       <solaris>false</solaris>
-      <osver>12.2</osver>
+      <osver>12.3.1</osver>
       <os32>false</os32>
       <os64>true</os64>
       <arch>maci64</arch>

atmat/Contents.m

@@ -1,5 +1,5 @@
 % Accelerator Toolbox
-% Version 2.2-dev.377 (atcollab) 25-Feb-2022
+% Version 2.3 (atcollab) 01-Apr-2022
 %
 %   atdiag           - Tests AT intallation
 %   atdisplay        - checks the verbosity level in the global variable GLOBVAL

atmat/at.m

@@ -1,5 +1,5 @@
 % Accelerator Toolbox
-% Version 2.2-dev.377 (atcollab) 25-Feb-2022
+% Version 2.3 (atcollab) 01-Apr-2022
 %
 % The Accelerator Toolbox was originally created by Andrei Terebilo.
 % Development is now continued by a multi-laboratory collaboration, <a href="matlab:web('https://github.com/atcollab')">atcollab</a>
@@ -140,4 +140,4 @@
 %
 %       <a href="matlab:help symplectify">symplectify</a>              - Makes a matrix more symplectic
 %
-%<a href="matlab:web('/Applications/MATLAB_R2021b.app/help/3ptoolbox/atacceleratortoolbox/doc/AT_page.html')">See documentation for AT</a>
+%<a href="matlab:web('/Applications/MATLAB_R2022a.app/help/3ptoolbox/atacceleratortoolbox/doc/AT_page.html')">See documentation for AT</a>

developer/matlab/README.md

@@ -45,10 +45,13 @@ gen_toc();
 ```
 - Generates _atroot_/developer/matlab/m/*.m files*
 - Publishes these files in _atroot_/../docs/matlab/*.html
+- Publishes _atroot_/developer/matlab/mlx/*.mlx in _atroot_/../docs/matlab/*.html
 - Generates the User's guide files for the help browser
 
-#### Custom files
-All _atroot_/developer/matlab/mlx/*.mlx must be manually exported as html into _atroot_/../docs/matlab
+**Warning:**
+
+.mlx files must be run with Matlab 2021a to get plots with the right size. Otherwise,
+at the end of the data of each plot, replace `style="height: auto;"` with `style="width: 560;"`
 
 #### Search database
 ```Matlab

developer/matlab/atrelease.m

@@ -5,18 +5,18 @@ function atrelease()
 %  Copyright 2016-2020 The MathWorks, Inc.
 
 %% Set toolbox name
+v = ver(atroot);
 shortname = 'atmat';
-tbxname = 'accelerator-toolbox';
+longname = v.Name;
 
-%% Get release script directory: AT root directory
-cfdir = fullfile(fileparts( mfilename( 'fullpath')),'..','..');
+%% Get AT root directory
+rootdir = fullfile(atroot,'..');
 
 %% Check MATLAB and related tools, e.g.:
 assert( ~verLessThan( 'MATLAB', '9.6' ), 'MATLAB R2019a or higher is required to use Toolbox Tools.' )
 
 %% Check installation
 fprintf( 1, 'Checking installation...' );
-v = ver( shortname );
 switch numel( v )
     case 0
         fprintf( 1, ' failed.\n' );
@@ -37,7 +37,7 @@ function atrelease()
     gen_help()
     gen_toc();
     % Remove all mex-files
-    atclearmex(fullfile(cfdir,'atmat'));
+    atclearmex(atroot);
     fprintf( 1, ' Done.\n' );
 catch e
     fprintf( 1, ' failed.\n' );
@@ -46,7 +46,7 @@ function atrelease()
 
 %Build doc search database
 try
-    builddocsearchdb(fullfile(cfdir,'docs','matlab'));
+    builddocsearchdb(fullfile(rootdir,'docs','matlab'));
 catch me
     warning( me.message )
 end
@@ -65,8 +65,8 @@ function atrelease()
 %%  Package and rename.
 fprintf( 1, 'Packaging...' );
 try
-    package_name = fullfile(cfdir,'matlab_releases',sprintf('%s.v%s.mltbx',tbxname,version));
-    prj = fullfile( cfdir, 'ToolboxPackagingConfiguration.prj');
+    package_name = fullfile(rootdir,'matlab_releases',sprintf('%s.v%s.mltbx',tbxname,version));
+    prj = fullfile( rootdir, 'ToolboxPackagingConfiguration.prj');
     matlab.addons.toolbox.packageToolbox( prj);
     fprintf( 1, ' Done.\n' );
 catch e

developer/matlab/gen_toc.m

@@ -1,20 +1,22 @@
 function gen_toc()
 %GEN_TOC	Build the HTML files used by the Matlab help browser
 
-[here,~, ~]=fileparts(mfilename('fullpath'));
+[devdir,~, ~]=fileparts(mfilename('fullpath'));
 docdir = fullfile(atroot,'..','docs','matlab');
 tocfile = fullfile(docdir,'helptoc.xml');
-[fid,fmess,fmid] = copyfile(fullfile(here,'helptoc.xml'),tocfile);
+[fid,fmess,fmid] = copyfile(fullfile(devdir,'helptoc.xml'),tocfile);
 if fid <= 0
     error(fmid,'%s: %s',tocfile,fmess);
 end
 fid=openmfile(tocfile,'at');
 
+% User guide
 ugname=fullfile('m','ugsummary.m');
 hid=openmfile(ugname,'wt');
 fprintf(fid,'        <tocitem target="ugsummary.html"\n');
 fprintf(fid,'            image="HelpIcon.USER_GUIDE">AT User Guide\n');
 fprintf(hid,'%%%% AT User Guide\n%%\n%%%%\n');
+%   Loop on UG chapters
 for m=atchapters()
     mname = fullfile('m', m.id+".m");
     fprintf(hid,'%% <matlab:web(fullfile(docroot,''3ptoolbox'',''atacceleratortoolbox'',''doc'',''%s.html'')) %s>\n%%\n',m.id,m.title);
@@ -28,27 +30,31 @@ function gen_toc()
 fprintf(fid,'        </tocitem>\n');
 fclose(hid);
 
-howtoname=fullfile('m','howtosummary.m');
-hid=openmfile(howtoname,'wt');
-fprintf(fid,'        <tocitem target="howtosummary.html"\n');
-fprintf(fid,'            image="HelpIcon.USER_GUIDE">How to…\n');
-fprintf(hid,'%%%% How to…\n%%\n%%%%\n');
-for m=howtochapters()
-    fprintf(hid,'%% <matlab:web(fullfile(docroot,''3ptoolbox'',''atacceleratortoolbox'',''doc'',''%s.html'')) %s>\n%%\n',m.id,m.title);
-    fprintf(fid,'            <tocitem target="%s.html">%s</tocitem>\n',m.id,m.title);
-end
-fprintf(fid,'        </tocitem>\n');
-fclose(hid);
+% How to...
+mlxloop('howtos','How to…',@howtochapters);
+
+% Release notes
+mlxloop('release_notes','Release notes');
 
+% Web site
 fprintf(fid,'        <tocitem target="https://atcollab.github.io/at/" \n');
 fprintf(fid,'                 image="$toolbox/matlab/icons/webicon.gif">\n');
 fprintf(fid,'        AT Web Site\n');
 fprintf(fid,'        </tocitem>\n');
+
 fprintf(fid,'    </tocitem>\n');
 fprintf(fid,'</toc>\n');
 fclose(fid);
+
 publish(ugname,'evalCode',false,'outputDir',docdir);
-publish(howtoname,'evalCode',false,'outputDir',docdir);
+
+% Publish custom files
+for dd=reshape(dir(fullfile(devdir,'mlx')),1,[])
+    [~,nn,xx]=fileparts(dd.name);
+    if strcmp(xx,'.mlx')
+        export(fullfile(dd.folder,dd.name),fullfile(docdir,strcat(nn,'.html')));
+    end
+end
 
     function mloop(fid,mlist)
         for item=mlist
@@ -68,6 +74,33 @@ function mloop(fid,mlist)
         end
     end
 
+    function mlxloop(secdir,secname,chapfun)
+        if nargin<3, chapfun=@lst; end
+        dirname=fullfile(devdir,secdir);
+        sumname=fullfile(devdir,'m',[secdir '.m']);
+        sumid=openmfile(sumname,'wt');
+        fprintf(fid,'        <tocitem target="%s" \n', [secdir '.html']);
+        fprintf(fid,'                 image="$toolbox/matlab/icons/webicon.gif">\n');
+        fprintf(fid,'        %s\n',secname);
+        fprintf(sumid,'%%%% %s\n%% \n%%%%\n', secname);
+        for mm=chapfun()
+            target=fullfile(secdir,mm.id+".html");
+            export(fullfile(secdir,mm.id+".mlx"),fullfile(docdir,target));
+            fprintf(sumid,'%% <matlab:web(fullfile(docroot,''3ptoolbox'',''atacceleratortoolbox'',''doc'',''%s'')) %s>\n%%\n',target,mm.title);
+            fprintf(fid,'            <tocitem target="%s">%s</tocitem>\n',target,mm.title);
+        end
+        fclose(sumid);
+        publish(sumname,'evalCode',false,'outputDir',docdir);
+        fprintf(fid,'        </tocitem>\n');
+        delete(sumname);
+        function res=lst()
+            vals=reshape(dir(fullfile(dirname,'*.mlx')),1,[]);
+            [~,nms,~]=arrayfun(@fileparts,{vals.name},'UniformOutput',false);
+            nms=string(sort(nms));
+            res=struct('id',nms,'title',nms);
+        end
+    end
+
     function fid=openmfile(fpath,mode)
         [fid,mess]=fopen(fpath,mode);
         if fid < 0

developer/matlab/mlx/CavityControl.mlx renamed to developer/matlab/howtos/CavityControl.mlx

@@ -3,8 +3,7 @@ function setversion(version)
 %
 %SERVERSION(VERSION)
 
-gitroot=fullfile(fileparts(mfilename('fullpath')),'..','..');
-versfile=fullfile(gitroot,'atmat','Contents.m');
+versfile=fullfile(atroot,'Contents.m');
 tmpfile=fullfile(tempdir,'Contents.m');
 fout=fopen(tmpfile,'wt');
 fin=fopen(versfile,'rt');