Commit 277d8341 authored by Jay Dubb's avatar Jay Dubb
Browse files

-- In setpaths exclude more folders to avoid problems and headaches with... 

-- In setpaths exclude more folders to avoid problems and headaches with unexpected matlab behavior because of inclusion of weird .m files from a build of AV. So for instance exclude *.app and *_install folders which contain a large amount of files which should never be included in matlab search paths.
-- Add ability to findDotMFolders to exclude folders based on wildcard patterns rather than only explicit names. This allows exclusion of many folders that fit a pattern without having to explicitly list ALL of them
-- Fix several bugs in the build for MAC
-- Finally fixed the requirement that you have to run MAC installation specifically from ~/Downloads/homer3_install. Added code to makesetup.pl to create a more intelligent setup.command which does not depend on execution from a specific folder.
parent d8641441

Install/Buildexe.m

+10 −4
Original line number Diff line number Diff line 
function Buildexe(appName, exclList, flags)

function Buildexe(appName, exclList, inclList, flags)



%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% BuildExe allows building of the current directories project in
@@ -14,15 +14,19 @@ rootdir = filesepStandard(pwd); 
if ~exist('appName','var')

    [~, appName] = fileparts(rootdir);

end

rootdir = filesepStandard(fileparts(which(appName)));



if ~exist('exclList','var')

    exclList = {};

end

if ~exist('inclList','var')

    inclList = {};

end

if ~exist('flags','var')

    flags = {};

end



rootdir = filesepStandard(fileparts(which(appName)));





% Matlab compiler generates a readme file that overwrites the app readme

% that already xists. Before we start build , move readme to temp file and 

% at end of build delete the newly generated readme and move the temp one
@@ -62,6 +66,8 @@ appDotMFilesStr = sprintf('-v %s', appDotMFileMain'); 


% Get all .m files which will go into making the app executable

appDotMFiles = findDotMFiles(rootdir, exclList);

appDotMFiles = [appDotMFiles; inclList];





% Create compile switches string

compileSwitches = '';

Install/Buildme.m

+10 −1
Original line number Diff line number Diff line
@@ -11,13 +11,22 @@ exclLst = { 
    'Docs';

    'UnitTests'; ...

    'Install';

    'submodules';

    'Data';

    'setpaths.m';

    'getpaths.m';

    };



Buildexe(appname, exclLst)

rootdir = filesepStandard(fileparts(which(platform.exename{1})));

for ii = 1:length(platform.exename)

    rootdir = filesepStandard(fileparts(which(platform.exename{ii})));

    if ~isempty(rootdir)

        break;

    end    

end

if isempty(rootdir)

    return;

end

for ii = 1:length(platform.exename)

    if exist([rootdir,  platform.exename{ii}],'file')

        movefile([rootdir,  platform.exename{ii}], dirnameInstall);

Install/Buildme_Setup.m

+17 −1
Original line number Diff line number Diff line
@@ -6,5 +6,21 @@ end 
if exist(dirnameInstall,'dir')

    cd(dirnameInstall);

end

Buildexe('setup');



p = filesepStandard(fileparts(which(getNamespace())));

inclList = {

    [p, 'Utils/Shared/Logger.m'];

    [p, 'Utils/Shared/str2cell.m'];

    [p, 'Utils/Shared/printStack.m'];

    [p, 'Utils/Shared/pathscompare.m'];

    [p, 'Utils/Shared/parseOptions.m'];

    [p, 'Utils/Shared/optionExists.m'];

    [p, 'Utils/Shared/fullpath.m'];

    [p, 'Utils/Shared/filesepStandard.m'];

    };



Buildexe('setup', {}, inclList);

if ispathvalid([dirnameInstall, 'Buildme.log'])

    movefile([dirnameInstall, 'Buildme.log'], [dirnameInstall, 'Buildme_Setup.log'])

end

cd(currdir);

Install/cleanup.m

+5 −5
Original line number Diff line number Diff line
@@ -3,14 +3,14 @@ global platform 


installfilename = sprintf('%s_install', lower(getAppname()));



if ~exist('dirnameInstall','var') | isempty(dirnameInstall)

if ~exist('dirnameInstall','var') || isempty(dirnameInstall)

    if exist('./Install','dir')

        dirnameInstall = filesepStandard([pwd, '/Install']);

    else

        dirnameInstall = filesepStandard(pwd);

    end

end

if ~exist('dirnameApp','var') | isempty(dirnameApp)

if ~exist('dirnameApp','var') || isempty(dirnameApp)

    dirnameApp = getAppDir();

end

if ~exist('options','var')
@@ -21,7 +21,7 @@ end 
if exist([dirnameInstall, installfilename],'dir')

    rmdir_safe([dirnameInstall, installfilename]);

end

for ii=1:length(platform.exename(1))

for ii = 1:length(platform.exename)

    if exist([dirnameInstall, platform.exename{ii}],'file')==2

        delete([dirnameInstall, platform.exename{ii}]);

    elseif exist([dirnameInstall, platform.exename{ii}],'dir')==7
@@ -49,8 +49,8 @@ if optionExists(options,'start') 
    if exist([dirnameInstall, 'Buildme.log'],'file')

        delete([dirnameInstall, 'Buildme.log']);

    end

    if exist([dirnameApp, 'Buildme.log'],'file')

        delete([dirnameApp, 'Buildme.log']);

    if exist([dirnameApp, 'Buildme_Setup.log'],'file')

        delete([dirnameApp, 'Buildme_Setup.log']);

    end

end

if exist([dirnameInstall, 'mccExcludedFiles.log'],'file')

Install/createInstallFile.m

+19 −12
Original line number Diff line number Diff line 
function createInstallFile(options)

global installfilename

global platform



platform = [];



% Start with a clean slate

cleanup('','','start');



installfilename = sprintf('%s_install', lower(getAppname()));

[~, exename] = getAppname();
@@ -11,7 +17,7 @@ if ~exist('options','var') || isempty(options) 
end



% Find installation path and add it to matlab search paths

dirnameApp = getAppDir;

dirnameApp = getAppDir();

if isempty(dirnameApp)

    MessageBox('Cannot create installation package. Could not find root application folder.');

    deleteNamespace(exename)
@@ -26,9 +32,6 @@ end 
addpath(dirnameInstall, '-end')

cd(dirnameInstall);



% Start with a clean slate

cleanup(dirnameInstall, dirnameApp, 'start');



% Set the executable names based on the platform type

platform = setplatformparams();
@@ -47,10 +50,14 @@ mkdir([dirnameInstall, installfilename, '/SubjDataSample']); 
if ~strcmp(options, 'nobuild')

    Buildme_Setup();

    Buildme();

    if ~ispc()

        c = str2cell(version(),'.');

        mcrver = sprintf('v%s%s', c{1}, c{2});

        if islinux()

        perl('./makesetup.pl','./run_setup.sh','./setup.sh');

            perl('./makesetup.pl','./run_setup.sh','./setup.sh', mcrver);

        elseif ismac()

        perl('./makesetup.pl','./run_setup.sh','./setup.command');

            perl('./makesetup.pl','./run_setup.sh','./setup.command', mcrver);

        end

    end

end

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