Commit 8a24b171 authored by jayd1860's avatar jayd1860
Browse files

v1.33.2 

-- Add a uniform version file to be able to retrieve version with a single function
parent 05f91209

DataTree/DataTreeClass.m

+17 −3
Original line number Diff line number Diff line
@@ -23,12 +23,15 @@ classdef DataTreeClass < handle 
            global logger

            global cfg

                       

            obj.InitNamespace();

            

            obj.logger              = InitLogger(logger, 'DataTreeClass');

            cfg                     = InitConfig(cfg);



            obj.groups              = GroupClass().empty();

            obj.currElem            = TreeNodeClass().empty();

            obj.reg                 = RegistriesClass().empty();

            obj.dirnameGroups       = {};

            obj.logger              = InitLogger(logger, 'DataTree');

            cfg                     = InitConfig(cfg);

            

            

            %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -89,7 +92,7 @@ classdef DataTreeClass < handle 
            % Load user function registry

            obj.reg = RegistriesClass();

            if ~isempty(obj.reg.GetSavedRegistryPath())

                obj.logger.Write(sprintf('Loaded saved registry %s\n', obj.reg.GetSavedRegistryPath()));

                obj.logger.Write('Loaded saved registry %s\n', obj.reg.GetSavedRegistryPath());

            end

            

            % Initialize the current processing element within the group
@@ -100,6 +103,17 @@ classdef DataTreeClass < handle 
        end

        

        

        

        % --------------------------------------------------------------

        function InitNamespace(obj)

            nm = getNamespace();

            if isempty(nm)

                setNamespace('DataTreeClass');

            end

        end

        

        

        

        % --------------------------------------------------------------

        function delete(obj)

            if isa(obj.logger, 'Logger')

DataTree/GroupClass.m

+1 −1
Original line number Diff line number Diff line
@@ -23,7 +23,7 @@ classdef GroupClass < TreeNodeClass 
            obj.InitVersion();



            if nargin<3 || ~strcmp(varargin{3}, 'noprint')

                obj.logger.Write(sprintf('Current GroupClass version %s\n', obj.GetVersionStr()));

                obj.logger.Write('Current GroupClass version %s\n', obj.GetVersionStr());

            end

            

            obj.type    = 'group';

DataTree/Version.txt

0 → 100644
+1 −0
Original line number Diff line number Diff line 
1.4.0

DataTree/setpaths.m

0 → 100644
+270 −0
Original line number Diff line number Diff line 
function setpaths(options)



%

% USAGE:

%

%   setpaths

%   setpaths(1)

%   setpaths(0)

%

currdir = pwd;



try

    

    warning('off','MATLAB:rmpath:DirNotFound');

    

    appname = 'DataTreeClass';

    

    % Parse arguments

    addremove = 1;

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

        options = '';

    elseif isnumeric(options)

        if options == 0

            addremove = 0;

        else

            options = '';

        end

    end

    

    % Add libraries on which DataTreeClass depends

    addDependenciesSearchPaths()    

    

    % Create list of possible known similar apps that may conflic with current

    % app

    appNameExclList = {'AtlasViewerGUI','Homer3','Homer2_UI','brainScape','ResolveCommonFunctions'};

    appNameInclList = {};

    exclSearchList  = {'.git','Data','Docs','*_install','*.app'};

    

    appThis         = filesepStandard_startup(pwd);

    appThisPaths    = findDotMFolders(appThis, exclSearchList);

    if addremove == 0

        if ~isempty(which('deleteNamespace.m'))

            deleteNamespace(appname);

        end

        removeSearchPaths(appThis);

        return;

    end

    

    appExclList = {};

    appInclList = {};

    

    % Find all root folders of apps to exclude from search paths

    for ii = 1:length(appNameExclList)

        foo = which([appNameExclList{ii}, '.m'],'-all');

        for jj = 1:length(foo)

            p = filesepStandard_startup(fileparts(foo{jj}));

            if pathscompare_startup(appThis, p)

                continue

            end

            fprintf('Exclude paths for %s\n', p);

            appExclList = [appExclList; p]; %#ok<AGROW>

        end

    end

    

    % Find all root folders of apps to include in search paths

    for ii = 1:length(appNameInclList)

        foo = which([appNameInclList{ii}, '.m'],'-all');

        for jj = 1:length(foo)

            if jj > 1

                p = filesepStandard_startup(fileparts(foo{jj}));

                appExclList = [appExclList; p]; %#ok<AGROW>

                fprintf('Exclude paths for %s\n', p);

            else

                p = filesepStandard_startup(fileparts(foo{jj}));

                appInclList = [appInclList; p]; %#ok<AGROW>

                fprintf('Include paths for %s\n', p);

            end

        end

    end

    

    % Remove all search paths for all other apps except for current one, to

    % make that we use only search from the current app for download shared

    % libraries (i.e, submodules).

    for ii = 1:length(appExclList)

        removeSearchPaths(appExclList{ii})

    end

    for ii = 1:length(appInclList)

        removeSearchPaths(appInclList{ii})

    end

    

    addSearchPaths(appThisPaths);

    

    if ~isempty(which('setNamespace.m'))

        setNamespace(appname);

    end

    

    % Add back all search paths for all other apps except for current app

    for ii = 1:length(appInclList)

        % This app's path has already been added

        if pathscompare_startup(appInclList{ii}, appThis)

            continue;

        end

        foo = findDotMFolders(appInclList{ii}, exclSearchList);

        addSearchPaths(foo);

    end

        

    if  ~isempty(which('setpaths_proprietary.m'))

        setpaths_proprietary(options);

    end

    

    warning('on','MATLAB:rmpath:DirNotFound');

    

catch ME

    

    cd(currdir);

    close all force;

    fclose all;

    rethrow(ME)

    

end



appnames = [appname; dependencies()];

PrintSystemInfo([], appnames)



cd(currdir);





% ---------------------------------------------------

function d = dependencies()

d = {

    'Utils';

    'FuncRegistry';

    };





% ---------------------------------------------------

function setpermissions(appPath)

if isunix() || ismac()

    if ~isempty(strfind(appPath, '/bin')) %#ok<*STREMP>

        fprintf(sprintf('chmod 755 %s/*\n', appPath));

        files = dir([appPath, '/*']);

        if ~isempty(files)

            system(sprintf('chmod 755 %s/*', appPath));

        end

    end

end





% ----------------------------------------------------

function addSearchPaths(appPaths, options)

if ischar(appPaths)

    p = genpath(appPaths);

    if ispc

        delimiter = ';';

    else

        delimiter = ':';

    end        

    appPaths = str2cell(p, delimiter);

end

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

    options = '';

end



for kk = 1:length(appPaths)

    if strfind(appPaths{kk}, '.git')

        continue;

    end

    addpath(appPaths{kk}, '-end');

    setpermissions(appPaths{kk});

end

fprintf('ADDED search paths for app %s\n', appPaths{1});







% ----------------------------------------------------

function removeSearchPaths(app)

p = path;

if ispc()

    delimiter = ';';

elseif ismac() || isunix()

    delimiter = ':';

end

[~,appname] = fileparts(fileparts(app));

r = version('-release');

msg = sprintf('Removing search paths for %s ...', appname);

h = waitbar(0, msg);

p = str2cell_startup(p, delimiter);

for kk = 1:length(p)

    if mod(kk,100)==0

        waitbar(kk/length(p), h);

    end

    if ~isempty(strfind(lower(p{kk}), 'matlab')) && ~isempty(strfind(p{kk}, r))

        continue;

    end

    if ~isempty(strfind(filesepStandard_startup(p{kk}), app))

        rmpath(p{kk});

    end

end

close(h);

fprintf('REMOVED search paths for app %s\n', app);









% ----------------------------------------------------

function   addDependenciesSearchPaths()

d = dependencies();

for ii = 1:length(d)

    rootpath = '';

    if exist([pwd, '/', d{ii}],'dir')

        rootpath = [pwd, '/'];

    elseif exist([pwd, '/../', d{ii}],'dir')

        rootpath = [pwd, '/../'];

    end

    if ~exist([rootpath, d{ii}],'dir')

        fprintf('ERROR: Could not find required dependency %s\n', d{ii})

        continue;

    end

    addSearchPaths([rootpath, d{ii}]);

end







% -----------------------------------------------------------------------------

function [C,k] = str2cell(str, delimiters, options)



% Option tells weather to keep leading whitespaces. 

% (Trailing whitespaces are always removed)

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

    options = '';

end



if ~strcmpi(options, 'keepblanks')

    str = strtrim(str);

end

str = deblank(str);



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

    delimiters{1} = sprintf('\n');

elseif ~iscell(delimiters)

    foo{1} = delimiters;

    delimiters = foo;

end



% Get indices of all the delimiters

k=[];

for kk=1:length(delimiters)

    k = [k, find(str==delimiters{kk})];

end

j = find(~ismember(1:length(str),k));



% The following line seems to hurt performance a little bit. It was 

% meant to preallocate to speed things up but it does not seem to do that.

% C = repmat({blanks(max(diff([k,length(str)])))}, length(k)+1, 1);

C = {};

ii=1; kk=1; 

while ii<=length(j)

    C{kk} = str(j(ii));

    ii=ii+1;

    jj=2;

    while (ii<=length(j)) && ((j(ii)-j(ii-1))==1)

        C{kk}(jj) = str(j(ii));

        jj=jj+1;

        ii=ii+1;

    end

    C{kk}(jj:end)='';

    kk=kk+1;

end

C(kk:end) = [];

FuncRegistry/FindUserFuncDir.m

+6 −2
Original line number Diff line number Diff line
@@ -6,10 +6,14 @@ cfg = InitConfig(cfg); 
userfuncdir = {};

dirnameApp = getAppDir();



if ~ispathvalid([dirnameApp, 'FuncRegistry/UserFunctions/'])

rootdirRegsitry = [dirnameApp, 'FuncRegistry/UserFunctions/'];

if ~ispathvalid(rootdirRegsitry)

    rootdirRegsitry = filesepStandard([dirnameApp, '../FuncRegistry/UserFunctions/']);

    if ~ispathvalid(rootdirRegsitry)

    return;

end

userfuncdir{1} = [dirnameApp, 'FuncRegistry/UserFunctions/'];

end

userfuncdir{1} = rootdirRegsitry;

dirs = dir([userfuncdir{1}, '*']);

for ii = 1:length(dirs)

    if ~dirs(ii).isdir

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