function is_ok=cosmo_publish_run_scripts(varargin)
% helper function to publish example scripts (for developers)
%
% cosmo_publish_build_html([force|fn])
%
% Inputs:
% fn filename of matlab file to publish (in the examples
% directory)
% '-force' force rebuild, even if an output file is newer than the
% corresponding output file
% '-dry' dry run: do not build any files, but show the output that
% would be shown.
% '-o', d write output in directory d. By default d is
% 'doc/source/_static/publish/' relative to the CoSMoMVPA
% root directory.
%
% Notes:
% - if no filename is given, then all files are rebuilt if necessary
% - this function is intended for developers (to build the website)
% - whether an output file is out of date is first determined using
% git: if git shows no changes to the last commit of the input file
% then it is assumed it is not out of date. If the input file has
% been changed since the last commit (or never been comitted), then
% the modification date is used to determine whether it is out of date.
% - requirements
% * a Unix-like system
% * a working installation of git
% * CoSMoMVPA code present in a git repository
%
% # For CoSMoMVPA's copyright information and license terms, #
% # see the COPYING file distributed with CoSMoMVPA. #
% ensure 'publish' function is available
cosmo_check_external('!publish',true);
[srcfn_cell,opt]=process_input(varargin{:});
trgdir=get_output_dir(opt);
trgext=['.' opt.format];
summaryfn=['index.' opt.format];
orig_path=path();
path_resetter=onCleanup(@()path(orig_path));
% go to mvpa dir
orig_pwd=pwd();
pwd_resetter=onCleanup(@()cd(orig_pwd));
mvpa_dir=fileparts(mfilename('fullpath'));
cd(mvpa_dir);
if ~isdir(trgdir) && ~opt.dryrun;
mkdir_recursively(trgdir);
end
nsrc=numel(srcfn_cell);
outputs=cell(nsrc,1);
total_time_took=0;
output_pos=0;
is_ok=true;
for k=1:nsrc
srcfn=srcfn_cell{k};
[srcpth,srcnm]=fileparts(srcfn);
if k==1
addpath(srcpth);
end
trgfn=fullfile(trgdir,[srcnm trgext]);
[needs_update,build_msg]=target_needs_update(srcfn,trgfn);
if opt.force
build_msg=sprintf('update forced: %s',srcfn);
end
fprintf(build_msg);
do_update=needs_update || opt.force;
if do_update
fprintf('\n building ... ');
clock_start=clock();
if opt.dryrun
fprintf('<dry run>');
is_built=true;
else
is_built=publish_helper(srcfn,trgfn);
end
clock_end=clock();
time_took=etime(clock_end,clock_start);
total_time_took=total_time_took+time_took;
if is_built
outcome_msg=' done';
else
outcome_msg=' !! failed';
is_ok=false;
end
status_msg=sprintf('%s (%.1f sec)', outcome_msg,time_took);
else
status_msg='';
end
fprintf('%s\n', status_msg);
output_pos=output_pos+1;
outputs{output_pos}=srcnm;
end
fprintf('Processed %d files (%.1f sec)\n',output_pos,total_time_took);
outputfn=fullfile(trgdir, summaryfn);
if ~opt.dryrun
write_index(outputfn,opt)
end
function write_index(index_outputfn,opt)
[outputdir,outputnm]=fileparts(index_outputfn);
inputdir=fullfile(get_root_dir(),'examples');
d=dir(fullfile(inputdir,'*.m'));
fid=fopen(index_outputfn,'w');
cleaner3=onCleanup(@()fclose(fid));
fprintf(fid,['<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN"'...
'>\n']);
fprintf(fid,['<HTML><HEAD><TITLE>Index of matlab outputs'...
'</TITLE></HEAD>\n<BODY>Matlab output<UL>\n']);
for k=1:numel(d)
[unused,nm]=fileparts(d(k).name);
outputfn=sprintf('%s.%s',nm,opt.format);
if exist(fullfile(outputdir,outputfn),'file')
fprintf(fid,'<LI><A HREF="%s">%s</A></LI>\n',outputfn,nm);
end
end
fprintf(fid,['</UL>Back to <A HREF="../../%s.html">index'...
'</A>.</BODY></HTML>\n'],outputnm);
fprintf('Index written to %s\n', index_outputfn);
function trgdir=get_output_dir(opt)
trgdir=opt.output_dir;
if isempty(trgdir)
trgdir=fullfile(get_root_dir(),'doc/source/_static/publish/');
end
function d=get_root_dir()
d=fileparts(fileparts(mfilename('fullpath')));
function is_built=publish_helper(srcfn,trgfn)
is_built=false;
try
publish_wrapper(srcfn,trgfn);
is_built=true;
catch
me=lasterror();
if exist(trgfn,'file')
delete(trgfn);
end
msg=sprintf('Unable to build %s: %s\n',srcfn,...
me.message);
s=me.stack;
for j=1:numel(s)
msg=sprintf('%s\n %s:%s', msg, s(j).file, s(j).line);
end
cosmo_warning('%s',msg);
end
function publish_wrapper(srcfn,trgfn)
[srcdir,srcnm]=fileparts(srcfn);
trgdir=fileparts(trgfn);
orig_pwd=pwd();
pwd_resetter=onCleanup(@()cd(orig_pwd));
orig_fig_handles=findobj('Type','figure');
fig_cleaner=onCleanup(@()close(setdiff(findobj('Type','figure'),...
orig_fig_handles)));
addpath(srcdir);
cd(trgdir);
if cosmo_wtf('is_matlab')
args={struct('outputDir',trgdir,'catchError',false)};
else
args={'format','html','imageFormat','jpg'};
end
publish(srcnm,args{:});
function [srcfn_cell,opt]=process_input(varargin)
% set defaults
srcpat='';
opt=struct();
opt.force=false;
opt.dryrun=false;
opt.format='html'; % currently not changeable
opt.output_dir='';
% process arguments
n=numel(varargin);
k=0;
while k<n
k=k+1;
arg=varargin{k};
if ischar(arg)
if strcmp(arg,'-force')
opt.force=true;
elseif strcmp(arg,'-dry')
opt.dryrun=true;
elseif strcmp(arg,'-o')
if k==n
error('Missing argument after %s',arg);
end
k=k+1;
opt.output_dir=varargin{k};
elseif ~isempty(srcpat)
error('multiple inputs found, this is not supported');
else
srcpat=arg;
end
else
error('Illegal argument at position %d - expected string', k);
end
end
srcfn_cell=get_srcfn_cell(srcpat);
function srcfn_cell=get_srcfn_cell(srcpat)
default_pattern={'run_*','demo_*'};
if isdir(srcpat)
p=srcpat;
nms=default_pattern;
e='.m';
else
[p,nm,e]=fileparts(srcpat);
if isempty(p)
p=fullfile(get_root_dir(),'examples');
end
if isempty(nm)
nms=default_pattern;
else
nms={nm};
end
if isempty(e)
e='.m';
end
end
ds=cellfun(@(nm)dir(fullfile(p,[nm e])),nms,'UniformOutput',false);
d=cat(1,ds{:});
n=numel(d);
if n==0
error('No input files found');
end
srcfn_cell=cellfun(@(fn)fullfile(p,fn),{d.name},'UniformOutput',false);
function [tf,msg]=target_needs_update(srcfn,trgfn)
% helper function to see if html is out of date
[unused,root,srcext]=fileparts(srcfn);
[unused,root_alt,trgext]=fileparts(trgfn);
assert(isequal(root,root_alt));
srcname=[root,srcext];
trgname=[root,trgext];
t_trg=time_last_changed(trgfn);
if isnan(t_trg)
% does not exist, so needs update
tf=true;
msg=sprintf('not found: %s', trgname);
return;
end
if is_in_staging(srcfn) || is_untracked(srcfn)
% changes since last commit, see when changes were made
t_src=time_last_changed(srcfn);
tf=isnan(t_src) || t_trg<t_src;
msg=sprintf('modified: %s', srcname);
else
% no changes since last commit, see when last commit was made
t_src=time_last_commit(srcfn);
tf=isnan(t_src) || t_trg<t_src;
msg=sprintf('recent commit: %s',srcname);
end
if ~tf
msg=sprintf('up to date: %s',trgname);
end
function t=time_last_changed(fn)
d=dir(fn);
if isempty(d)
t=NaN;
return
end
assert(numel(d)==1);
t=(d.datenum-datenum(1970,1,1))*86400;
function r=run_git(args)
prefix='export TERM=ansi; git ';
cmd=[prefix args];
[e,r]=unix(cmd);
if e
fprintf(2,'Unable to run git, or an error was produced\n');
error(r);
end
function tf=is_untracked(srcfn)
untracked=run_git('ls-files . --exclude-standard --others');
tf=cosmo_match({srcfn},untracked);
function t=time_last_commit(srcfn)
cmd=sprintf('log -n 1 --pretty=format:%%ct -- %s',srcfn);
r=run_git(cmd);
t=str2double(regexp(r,'(\d*)','match','once'));
if isempty(t)
t=NaN;
end
assert(numel(t)==1);
function tf=is_in_staging(fn)
in_staging_str=run_git('diff HEAD --name-only | xargs basename');
in_staging=cosmo_strsplit(in_staging_str,'\n');
basefn=cosmo_strsplit(fn,filesep,-1);
tf=cosmo_match({basefn},in_staging);
function mkdir_recursively(trgdir)
parent=fileparts(trgdir);
if ~isdir(parent)
mkdir_recursively(parent);
end
mkdir(trgdir);
