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fix: readYAMLmodel if entries are broken over multiple lines #588

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Merged
edkerk merged 3 commits into from
Oct 24, 2025
Merged

fix: readYAMLmodel if entries are broken over multiple lines #588

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a1e9d84
fix: readYAMLmodel if broken over multiple lines
edkerk Sep 9, 2025
22d11c5
fix: readYAMLmodel if empty string is ''
edkerk Sep 9, 2025
2938df6
chore: updateDocumentation
edkerk Sep 9, 2025
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6 changes: 3 additions & 3 deletions doc/io/readYAMLmodel.html
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Original file line number Diff line number Diff line change
Expand Up @@ -102,7 +102,7 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
0045 <span class="comment">% leading spaces to avoid metaData to be concatenated.</span>
0046 newLine=regexp(line_raw,<span class="string">'^ {6,}([\w\(\)].*)'</span>,<span class="string">'tokenExtents'</span>);
0047 brokenLine=find(~cellfun(<span class="string">'isempty'</span>,newLine));
0048 <span class="keyword">for</span> i=1:numel(brokenLine)
0048 <span class="keyword">for</span> i=flip(1:numel(brokenLine))
0049 extraLine = char(line_raw(brokenLine(i)));
0050 extraLine = extraLine(newLine{brokenLine(i)}{1}(1):end);
0051 line_raw{brokenLine(i)-1} = strjoin({line_raw{brokenLine(i)-1},extraLine},<span class="string">' '</span>);
Expand All @@ -115,7 +115,7 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
0058 line_value = regexprep(line_raw, <span class="string">'.*:$'</span>,<span class="string">''</span>);
0059 line_value = regexprep(line_value, <span class="string">'[^&quot;:]+: &quot;?(.+)&quot;?$'</span>,<span class="string">'$1'</span>);
0060 line_value = regexprep(line_value, <span class="string">'(&quot;)|(^ {4,}- )'</span>,<span class="string">''</span>);
0061
0061 line_value(strcmp(line_value,<span class="string">''''''</span>)) = {<span class="string">''</span>};
0062 line_value(strcmp(line_value,line_raw)) = {<span class="string">''</span>};
0063
0064 modelFields = {<span class="string">'id'</span>,char();<span class="keyword">...</span>
Expand Down Expand Up @@ -197,7 +197,7 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
0140 geneMiriams=cell(100000,3); genMirNo=1;
0141 subSystems=cell(100000,2); subSysNo=1;
0142 eccodes=cell(100000,2); ecCodeNo=1;
0143 equations=cell(100000,3); equatiNo=1;
0143 equations=cell(100000,3); equatiNo=1;
0144
0145 <span class="keyword">for</span> i=1:numel(line_key)
0146 tline_raw = line_raw{i};
Expand Down
6 changes: 3 additions & 3 deletions io/readYAMLmodel.m
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Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,7 @@
% leading spaces to avoid metaData to be concatenated.
newLine=regexp(line_raw,'^ {6,}([\w\(\)].*)','tokenExtents');
brokenLine=find(~cellfun('isempty',newLine));
for i=1:numel(brokenLine)
for i=flip(1:numel(brokenLine))
extraLine = char(line_raw(brokenLine(i)));
extraLine = extraLine(newLine{brokenLine(i)}{1}(1):end);
line_raw{brokenLine(i)-1} = strjoin({line_raw{brokenLine(i)-1},extraLine},' ');
Expand All @@ -58,7 +58,7 @@
line_value = regexprep(line_raw, '.*:$','');
line_value = regexprep(line_value, '[^":]+: "?(.+)"?$','$1');
line_value = regexprep(line_value, '(")|(^ {4,}- )','');

line_value(strcmp(line_value,'''''')) = {''};
line_value(strcmp(line_value,line_raw)) = {''};

modelFields = {'id',char();...
Expand Down Expand Up @@ -140,7 +140,7 @@
geneMiriams=cell(100000,3); genMirNo=1;
subSystems=cell(100000,2); subSysNo=1;
eccodes=cell(100000,2); ecCodeNo=1;
equations=cell(100000,3); equatiNo=1;
equations=cell(100000,3); equatiNo=1;

for i=1:numel(line_key)
tline_raw = line_raw{i};
Expand Down
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