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%FIND_PACKAGE_REFS update references in <path> and its subfolders to
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%package structure in <base_path>.
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%
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% base_path... repository with new package structure
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% path... repository which needs to be updated
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%
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% *optional* given as name/value pair
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% extension... file extension; default '.m'
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% recursive... recursive behavior; default false
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% show_files... show file names, otherwise progressbar; default false
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% filename... change output file name and path; default
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% ./references.txt
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%
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% Example:
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% find_package_refs('./cSAXS_matlab_base', './cSAXS_matlab_ptycho')
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% find_package_refs('./cSAXS_matlab_base', './cSAXS_matlab_ptycho', 'recursive', false);
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%
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%
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%*-----------------------------------------------------------------------*
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%| |
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%| Except where otherwise noted, this work is licensed under a |
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%| Creative Commons Attribution-NonCommercial-ShareAlike 4.0 |
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%| International (CC BY-NC-SA 4.0) license. |
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%| |
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%| Copyright (c) 2017 by Paul Scherrer Institute (http://www.psi.ch) |
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%| |
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%| Author: CXS group, PSI |
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%*-----------------------------------------------------------------------*
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% You may use this code with the following provisions:
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%
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% If the code is fully or partially redistributed, or rewritten in another
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% computing language this notice should be included in the redistribution.
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%
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% If this code, or subfunctions or parts of it, is used for research in a
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% publication or if it is fully or partially rewritten for another
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% computing language the authors and institution should be acknowledged
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% in written form in the publication: “Data processing was carried out
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% using the “cSAXS matlab package” developed by the CXS group,
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% Paul Scherrer Institut, Switzerland.”
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% Variations on the latter text can be incorporated upon discussion with
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% the CXS group if needed to more specifically reflect the use of the package
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% for the published work.
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%
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% A publication that focuses on describing features, or parameters, that
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% are already existing in the code should be first discussed with the
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% authors.
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%
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% This code and subroutines are part of a continuous development, they
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% are provided “as they are” without guarantees or liability on part
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% of PSI or the authors. It is the user responsibility to ensure its
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% proper use and the correctness of the results.
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function find_package_refs(base_path, path, varargin )
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% check path
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if ~exist(path)
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error('Could not find %s', path)
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end
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if ~exist(base_path)
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error('Could not find %s', base_path)
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end
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% set default values
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extension = '.m';
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recursive = false;
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show_files = true;
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filename_with_path = '../references.txt';
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% parse the variable input arguments vararg = cell(0,0);
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if ~isempty(varargin)
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for ind = 1:2:length(varargin)
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name = varargin{ind};
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value = varargin{ind+1};
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switch lower(name)
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case 'extension'
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extension = value;
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case 'recursive'
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recursive = value;
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case 'show_files'
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show_files = value;
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case 'filename'
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filename_with_path = value;
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end
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end
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end
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% avoid overwriting files
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if exist(filename_with_path,'file')
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disp(['File ' filename_with_path ' exists,' ])
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userans = input(['Do you want to overwrite (y/N)? '],'s');
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if strcmpi(userans,'y')
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disp(['Saving to ' filename_with_path]);
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else
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disp(['Did not save ' filename_with_path])
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return
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end
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else
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display(['Saving to ' filename_with_path]);
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end
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fileID = fopen(filename_with_path,'w');
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file_list = [];
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% get the target file list
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if recursive
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[~, target_fl] = system(['find ' path ' -name "*' extension '"']);
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target_fl = strsplit(target_fl, '\n');
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else
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[target_fl_temp] = dir([path '/*' extension]);
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for ii=1:length(target_fl_temp)
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target_fl{ii} = [path '/' target_fl_temp(ii).name];
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end
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end
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% get the package file list
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[~, base_fl] = system(['find ' base_path ' -name "*' extension '"']);
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base_fl = strsplit(base_fl, '\n');
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for ii=1:length(base_fl)
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pckg_name = {};
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substr = strsplit(base_fl{ii}, '/');
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fn = substr{end};
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if isempty(fn)
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continue
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else
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% get the updated package name
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for jj=1:length(substr)
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try
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if strcmp(substr{jj}(1), '+')
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pckg_name{end+1} = substr{jj}(2:end);
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end
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catch
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continue
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end
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end
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end
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pckg_name_full = strjoin(pckg_name, '.');
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if show_files
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fprintf('-- Updating references to file %s.\n', fn);
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end
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% call external function and update reference
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for kk=1:length(target_fl)
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if ~isempty(target_fl{kk})
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temp_fn = strsplit(target_fl{kk}, '/');
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temp_fn = temp_fn{end};
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if ~isfield(file_list, temp_fn(1:end-length(extension)))
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file_list.(temp_fn(1:end-length(extension))).pckgs = [];
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file_list.(temp_fn(1:end-length(extension))).files = [];
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file_list.(temp_fn(1:end-length(extension))).subfunctions = [];
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end
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[~, cnt] = system(['grep -n ' fn(1:end-length(extension)) ' ' target_fl{kk} '| wc -l']);
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count = str2double(cnt);
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if strcmp(fn, temp_fn) && count<=1
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fprintf('Skipping %s\n', fn)
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continue
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elseif count >=1
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[~, cnt] = system(['grep -n ''^function'' ' target_fl{kk} '| wc -l']);
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count = str2double(cnt) -1;
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file_list.(temp_fn(1:end-length(extension))).pckgs{end+1} = pckg_name_full;
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file_list.(temp_fn(1:end-length(extension))).files{end+1} = [pckg_name_full '.' fn(1:end-length(extension))];
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file_list.(temp_fn(1:end-length(extension))).subfunctions = (count>0)*count;
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end
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end
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end
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if ~show_files
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utils.progressbar(ii, length(base_fl))
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end
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end
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fn = fieldnames(file_list);
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for ii=1:length(fn)
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if ~isempty(unique(file_list.(fn{ii}).pckgs(:)))
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fprintf(fileID, [fn{ii} '\n']);
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fprintf(fileID, [strjoin(unique(file_list.(fn{ii}).pckgs(:)), '\t') '\n']);
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fprintf(fileID, [strjoin(unique(file_list.(fn{ii}).files(:)), '\t') '\n']);
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fprintf(fileID, ['Subfunctions: ' num2str(file_list.(fn{ii}).subfunctions)]);
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fprintf(fileID, ['\n\n']);
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end
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end
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fclose(fileID);
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end
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