setpaths.m

function setpaths(options_str)

%
% USAGE:
%
%   setpaths
%   setpaths(1)
%   setpaths(0)
%   setpaths(options)
%
% DESCRIPTION:
%
%   Sets all the paths needed by a tool
%
% INPUTS:
%
%   options:   Char string containing one or more options. To select mutiple options, combine
%              together the 4 mutually exclusive options below in any order, separating
%              individual options with ',',':' or '|'. The list of mutually exclusive
%              options are:
%
%           {'add','remove'}               (default: add)         Add or remove paths of current
%                                                                 workspace to search path
%           {'conflcheck','noconflcheck'}  (default: conflcheck)
%           {'mvpathconfl','rmpathconfl'}  (default: mvpathconfl) 'conflcheck' option must be selected
%                                                                  for this this option not to be ignored
%           {'quiet','verbose'}            (default: quiet)
%           {'nodiffnames','diffnames'}    (default: nodiffnames) Diffs files that share a name with a file already on the path
%
%
% EXAMPLES:
%
%   Example 1: Add paths for current workspace quietly and do not do any
%              checking for conflicting workspaces.
%
%   setpaths;
%      setpaths(1);
%
%   Example 2: Quietly add paths for current workspace to have precedence over any
%              conflicting workspace. The paths for any conflicting workspace will
%              be made lower precedence than current workspace.
%
%      setpaths('add:conflcheck');
%
%
%   Example 3: Quietly remove paths for current workspace quietly.
%
%   setpaths(0);
%      setpaths('remove');
%      setpaths('remove:quiet');
%
%
%   Example 4: Add paths for the current workspace verbosely and remove all
%              paths of conflicting workspaces.
%
%      setpaths('rmpathconfl:verbose');
%      setpaths('add:rmpathconfl:verbose');
%      setpaths('add:conflcheck:rmpathconfl:verbose');
%      setpaths('rmpathconfl|verbose|add|conflcheck');
%

% Start world by trying to add standard 'Utils' path if it exists 
% If it exists, assume that's where intialation functions are. 
if exist([pwd, '/Utils'], 'dir')==7
    addpath([pwd, '/Utils']);
    addpath([pwd, '/Utils/namespace']);
end
setNamespace('Homer3');

% Parse arguments
if ~exist('options_str','var')
    options_str = 'rmpathconfl';
end
options = parseOptions(options_str);

if ~options.add
    options.conflcheck = false;
end

[paths, wspaths, paths_excl_str] = getpaths(options);
% if ~isempty(wspaths)
%     if pathscompare(wspaths{1}, pwd)
%         fprintf('Current workspace %s already at the top of the search path.\n', wspaths{1});
%         addwspaths(wspaths, paths_excl_str, options);
%         return;
%     end
% end

% Add or remove paths for this application
rootpath = pwd;
rootpath(rootpath=='\')='/';
paths_str = '';

dnum = 0;
diffqueue = {};  % Files to be diff'd

for ii=1:length(paths)
    
    paths{ii} = [rootpath, paths{ii}];
    
    if options.diffnames
        % See if any of the imported functions already exist
        
        files = dir(fullfile(paths{ii},'*.m'));
        
        for f = 1:length(files)
            % When exists returns 2 but excluding the working dir
            if ( (exist(files(f).name(1:end-2),'file') == 2) & (~isequal(files(f).folder,pwd())))
                if options.verbose
                    fprintf('This file shadows one already on the path: %s\n',[files(f).folder '\' files(f).name(1:end-2)]);
                    fprintf('Here is the original: %s\n', which(files(f).name(1:end-2)));
                end
                if (strcmp( fileread([files(f).folder '\' files(f).name]), fileread(which(files(f).name(1:end-2))) ))
                    if options.verbose
                        fprintf('The files are the same.\n');
                    end
                else
                    if options.verbose
                        fprintf('The files have some differences.\n')
                    end
                    dnum = dnum + 1;
                    diffqueue{end+1} = {[files(f).folder '\' files(f).name], which(files(f).name(1:end-2))};
                end
            end
        end
    end
    
    if options.verbose
        if options.add
            fprintf('Adding path %s\n', paths{ii});
        else
            fprintf('Removing path %s\n', paths{ii});
        end
    end
    
    if ~exist(paths{ii}, 'dir')
        fprintf('Path %s does not exist\n', paths{ii});
        menu('WARNING: The current folder does NOT look like the application root folder. Please change current folder to the root application folder and rerun setpaths.', 'OK');
        return;
    end
    
    paths_str = [paths_str, delimiter, paths{ii}];
    
end

% If there are different files with same name
if dnum > 0  % True only if options.diffpaths is
    fprintf('There are %i files that shadow different files already on the path.\n', dnum);
    diffchoice = input(sprintf('Would you like to diff them now? y/n '),'s');
    if (size(diffchoice,2) > 0) & ((diffchoice == 'y') | (diffchoice == 'yes'))
        for i = 1:size(diffqueue,2)
            % Use visual diff tool
            visdiff(diffqueue{i}{1}, diffqueue{i}{2});
        end
    end
end

% Add current workspace at the top of the stack of conflicting workspaces
wspaths = [pwd; wspaths];
paths_excl_str = [paths_str, paths_excl_str];

% Either add all conflicting workspaces to the search path or remove the
% current one, depending on user selection
if options.add
    fprintf('ADDED search paths for workspace %s\n', pwd);
    addwspaths(wspaths, paths_excl_str, options);
    setpermissions(paths);
else
    fprintf('REMOVED search paths for workspace %s\n', pwd);
    rmpath(paths_excl_str{1});
    deleteNamespace('Homer3');
end


% ---------------------------------------------------
function idx = findExePaths(paths)

idx = [];
kk = 1;
for ii=1:length(paths)
    if ~isempty(strfind(paths{ii}, '/bin'))
        idx(kk) = ii;
        kk=kk+1;
    end
end



% ---------------------------------------------------
function addwspaths(wspaths, paths_excl_str, options)

if isempty(wspaths)
    return;
end

% Add the primary workspace to the search path
addpath(paths_excl_str{1}, '-end');

if options.rmpathconfl
    msg = 'Removed the following similar workspaces from the search path to avoid conflicts:';
else
    msg = 'Order of precedence of similar workspaces:';
end

% Add all the other similar workspaces that have been found and removed
if length(wspaths)>1
    fprintf('\n');
    fprintf('%s\n', msg);
    for ii = 2:length(wspaths)
        fprintf('  %s\n', wspaths{ii});
        if options.rmpathconfl
            continue;
        end
        addpath(paths_excl_str{ii}, '-end');
    end
end

if exist([pwd, '/Utils/setpaths_proprietary.m'],'file')
    setpaths_proprietary(options);
end



% ---------------------------------------------------
function setpermissions(paths)

if isunix()
    idx = findExePaths(paths);
    for ii=1:length(idx)
        fprintf(sprintf('chmod 755 %s/*\n', paths{idx(ii)}));
        files = dir([paths{idx(ii)}, '/*']);
        if ~isempty(files)
            system(sprintf('chmod 755 %s/*', paths{idx(ii)}));
        end
    end
end