Unverified Commit 8029897b authored by jayd1860's avatar jayd1860 Committed by GitHub
Browse files

-- Change setpaths to not download submodules by default. Use 'init' or... 

-- Change setpaths to not download submodules by default. Use 'init' or 'update' options to download automatically. If using github desktop then github desktop download submodules automatically. (#95)

-- Change downloadSharedLibs to change .gitmodules origin url to point to where ever parent came from
-- Add .gitattributes to exclude files from branch merges such as submodule references and .gitmodules
-- Sync getVernum with Homre3. (getVernum will eventually be moved to Utils/Shared library)
-- Improve creation of installation file and installation process using myCopyFile.m
parent e1d9273e

.gitattributes

0 → 100644
+3 −0
Original line number Diff line number Diff line 
Group/DataTree merge=ours 

Utils/Shared merge=ours

.gitmodules merge=ours

Install/getRelativePath.m

0 → 100644
+16 −0
Original line number Diff line number Diff line 
function path3 = getRelativePath(path1, path2)

path3 = '';

path1 = filesepStandard_startup(path1);

path2 = filesepStandard_startup(path2);



k = strfind(path1, path2);

if isempty(k) %#ok<*STREMP>

    return

end

if ispathvalid(path1, 'dir')

    j = 1;

else

    j = 0;

end

path3 = path1(length(path2)+1:end-j);

Install/myCopyFile.m

0 → 100644
+143 −0
Original line number Diff line number Diff line 
function myCopyFile(src, dst)

global logger %#ok<NUSED>

global h

global iStep

global nSteps



if nargin==0

    src = '';

    dst = '';

end

if nargin==1

    dst = '';

end

if ~ispathvalid(src)

    if ~ispathvalid([src, '.gz'])

        if ~ispathvalid([src, 'tar.gz'])

            if ~ispathvalid([src, '.zip'])

                if ~ispathvalid([src, '.tar'])

                    return

                end

            end

        end

    end

end



printFuncName = getStandardOutputFuncName();



[~,f,e] = fileparts(src);

if (isempty(f) || strcmp(f, '.')) && strcmp(e, '.')

    return;

end



src = filesepStandard(src, 'full');

dst = filesepStandard(dst, 'full:nameonly');





files = dir(src);



for ii = 1:length(files)

    if strcmp(files(ii).name, '.') || strcmp(files(ii).name, '..')

        continue;

    end

    

    % Set full path names of source and destination

    srcNew = unpack([filesepStandard(files(ii).folder), files(ii).name]);

    [~, f, e] = fileparts(srcNew);

    if ~strcmp(files(ii).name, [f,e])

        eval( sprintf('%s(''Skipping %%s\\n'', [filesepStandard(files(ii).folder), files(ii).name]);', printFuncName) );        

        files(ii).name = [f,e];

    end

    

    % Rules for copying

    if ispathvalid(srcNew,'dir')

        dstNew = [dst, '/', files(ii).name];

        if ~ispathvalid(dstNew)

            try

            mkdir(dstNew)

            catch

                d=1;

            end

        end

        myCopyFile(srcNew, dstNew);

    elseif ispathvalid(srcNew,'file')

        if ispathvalid(dst, 'dir')

            dstNew = [dst, '/', files(ii).name];

        elseif ispathvalid(src, 'dir')

            dstNew = [dst, '/', files(ii).name];

            mkdir(dst)

        else

            dstNew = dst;

            dstRoot = fileparts(dst);

            if ~ispathvalid(dstRoot)

                mkdir(dstRoot)

            end

        end

        try

            if ispathvalid(dstNew)

                return

            end

            eval( sprintf('%s(''Copying  %%s   to   %%s\\n'', srcNew, dstNew);', printFuncName) );

            copyfile(srcNew, dstNew);

            if ~isempty(iStep)

                if ishandles(h)

                    waitbar(iStep/nSteps, h);

                end

                iStep = iStep+1;

            end            

        catch ME

            printStack(ME);

        end

    else

        eval( sprintf('%s(''WARNING: Path %%s does not exist\\n'', srcNew);', printFuncName) );

    end

end

pause(.7)







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

function [src, ext] = unpack(src)

[pname1, fname1, ext1] = fileparts(src);

[~, ~, ext2] = fileparts(fname1);

ext = [ext2, ext1];

temp = [pname1, '/temp/'];

if ispathvalid(temp)

    rmdir(temp,'s');

end

switch(ext)

    case '.tar'

        mkdir(temp);

        untar(src, temp);

    case '.tar.gz'

        mkdir(temp);

        untar(src, temp);

    case '.gz'

        mkdir(temp);

        gunzip(src, temp);

    case '.zip'

        mkdir(temp);

        unzip(src, temp);

    otherwise

        return

end



f = dir([temp, '/*']);

for ii = 1:length(f)

    if strcmp(f(ii).name,'.')

        continue;

    end

    if strcmp(f(ii).name,'..')

        continue;

    end

    if ~ispathvalid([pname1, '/', f(ii).name])

        copyfile([temp, '/', f(ii).name], pname1)

        break;

    end

end

if ispathvalid(temp)

    rmdir(temp,'s');

end    

src = [pname1, '/', f(ii).name];

Utils/getVernum.m

+1 −1
Original line number Diff line number Diff line
@@ -20,7 +20,7 @@ function [vrnnum] = getVernum_AtlasViewerGUI() 


vrnnum{1} = '2';   % Major version #

vrnnum{2} = '16';  % Major sub-version #

vrnnum{3} = '0';   % Minor version #

vrnnum{3} = '1';   % Minor version #

vrnnum{4} = '0';   % Minor sub-version # or patch #: 'p1', 'p2', etc

Utils/submodules/downloadSharedLibs.m

+8 −6
Original line number Diff line number Diff line
@@ -8,6 +8,10 @@ if ~exist('options','var') || (isnumeric(options) && options==0) 
end



s = parseGitSubmodulesFile();

if ~optionExists_startup(options,'init') && ~optionExists_startup(options,'update') 

    addSearchPaths(s);

    return;

end



% Check for missing libs

kk = checkMissingLibraries(s);
@@ -77,10 +81,10 @@ msg{ii} = sprintf('Git was not able to install the following libraries required 
for jj = 1:size(s,1)

    msg{ii} = sprintf('    %s\n', s{jj,1}); ii = ii+1;

end

msg{ii} = sprintf('\n'); ii = ii+1; %#ok<SPRINTFN>

msg{ii} = sprintf('\n'); ii = ii+1;

msg{ii} = sprintf('Git might not be installed on your computer. \n'); ii = ii+1;

msg{ii} = sprintf('These libraries can still be installed without git. The assumed submodule branch that matches \n'); ii = ii+1;

msg{ii} = sprintf('the branch of the parent repo, ''%s'', is ''%s''\n\n', appname, branch); ii = ii+1;

msg{ii} = sprintf('the branch of the parent repo, ''%s'', is ''%s''\n\n', appname, branch); ii = ii+1; %#ok<NASGU>

msg = [msg{:}];



fprintf(msg)
@@ -95,7 +99,7 @@ msg{ii} = sprintf('WARNING: The following libraries required by this application 
for jj = 1:size(s,1)

    msg{ii} = sprintf('    %s\n', s{jj,1}); ii = ii+1;

end

msg{ii} = sprintf('\n'); ii = ii+1;

msg{ii} = sprintf('\n'); ii = ii+1; %#ok<*SPRINTFN>

msg{ii} = sprintf('Either a) install git and rerun setpaths or b) download the submodules manually and provide their locations. '); ii = ii+1;

msg{ii} = sprintf('Select option:');

msg = [msg{:}];
@@ -107,7 +111,6 @@ q = menu(msg, {'Quit setpaths, install git and rerun setpaths','Download submodu 


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

function addSearchPaths(s)

kk = [];

exclSearchList  = {'.git'};

for ii = 1:size(s,1)

    foo = findDotMFolders(s{ii,3}, exclSearchList);
@@ -123,7 +126,7 @@ end 
% ---------------------------------------------------

function setpermissions(appPath)

if isunix() || ismac()

    if ~isempty(strfind(appPath, '/bin'))

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

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

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

        if ~isempty(files)
@@ -158,7 +161,6 @@ fprintf('\nBranch guess: ''%s''\n', branchGuess); 
% Check to see if submodule urls exist. If not edfault to 'master' branches. 

for ii = 1:size(submodules,1)

    url             = submodules{ii,1};

    submodulepath   = submodules{ii,3};

    

    urlfull = sprintf('%s/archive/refs/heads/%s.zip', url, branchGuess);

    [~, urlExists] = urlread(urlfull); %#ok<*URLRD>

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