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RAVEN 2.10.3
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‎.github/pull_request_template.md

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@@ -1,14 +1,14 @@
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### Main improvements in this PR:
22
<!-- Pointwise mention what changes were made in what function. Examples:
3-
- Fixes:
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- fix:
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- `functionName` failed to do action X
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- Documentation:
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- Updated all documentation
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- Features:
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- Introduced option to do function Y (issue #12345) -->
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- documentation:
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- updated all documentation
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- features:
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- introduced option to do function Y (solves #12345) -->
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#### Instructions on merging this PR:
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<!-- Chose ONE of the following two options
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and replace [ ] with [X] to check the box.-->
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- [ ] This PR has `develop` as target branch, and will be resolved with a *squash-merge*.
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- [ ] This PR has `main` as target branch, and will be resolved with a *merge commit*.
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- [ ] This PR has `main` as target branch, and will be resolved as descriped [here](https://github.com/SysBioChalmers/RAVEN/wiki/Development-policy#make-a-new-release).

‎core/generateNewIds.m

Lines changed: 7 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -26,6 +26,9 @@
2626
else
2727
error('type should be either ''rxns'' or ''mets''.')
2828
end
29+
if nargin<4
30+
quantity=1;
31+
end
2932
if nargin<5
3033
numLength=4;
3134
end
@@ -44,7 +47,10 @@
4447
fprintf(['No ' type ' ids with prefix "' prefix ...
4548
'" currently exist in the model. The first new id will be "' ...
4649
[prefix,num2str(1,['%0' num2str(numLength) 'd'])] '"\n'],'%s')
47-
lastId=0;
50+
end
51+
52+
if isnan(lastId)
53+
lastId = 0;
4854
end
4955

5056
newIds=cell(quantity,1);

‎doc/core/generateNewIds.html

Lines changed: 29 additions & 23 deletions
Original file line numberDiff line numberDiff line change
@@ -85,33 +85,39 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
8585
0026 <span class="keyword">else</span>
8686
0027 error(<span class="string">'type should be either ''rxns'' or ''mets''.'</span>)
8787
0028 <span class="keyword">end</span>
88-
0029 <span class="keyword">if</span> nargin&lt;5
89-
0030 numLength=4;
88+
0029 <span class="keyword">if</span> nargin&lt;4
89+
0030 quantity=1;
9090
0031 <span class="keyword">end</span>
91-
0032
92-
0033 <span class="comment">% Subset only existingIds that have the prefix</span>
93-
0034 existingIds=existingIds(~cellfun(@isempty,regexp(existingIds,[<span class="string">'^'</span> prefix])));
91+
0032 <span class="keyword">if</span> nargin&lt;5
92+
0033 numLength=4;
93+
0034 <span class="keyword">end</span>
9494
0035
95-
0036 <span class="keyword">if</span> ~isempty(existingIds)
96-
0037 existingIds=regexprep(existingIds,[<span class="string">'^'</span> prefix],<span class="string">''</span>);
97-
0038 existingIds=sort(existingIds);
98-
0039 lastId=existingIds{end};
99-
0040 numLength=length(lastId);
100-
0041 lastId=str2double(lastId);
101-
0042 <span class="keyword">else</span>
102-
0043 lastId=0;
103-
0044 fprintf([<span class="string">'No '</span> type <span class="string">' ids with prefix &quot;'</span> prefix <span class="keyword">...</span>
104-
0045 <span class="string">'&quot; currently exist in the model. The first new id will be &quot;'</span> <span class="keyword">...</span>
105-
0046 [prefix,num2str(1,[<span class="string">'%0'</span> num2str(numLength) <span class="string">'d'</span>])] <span class="string">'&quot;\n'</span>],<span class="string">'%s'</span>)
106-
0047 lastId=0;
107-
0048 <span class="keyword">end</span>
108-
0049
109-
0050 newIds=cell(quantity,1);
95+
0036 <span class="comment">% Subset only existingIds that have the prefix</span>
96+
0037 existingIds=existingIds(~cellfun(@isempty,regexp(existingIds,[<span class="string">'^'</span> prefix])));
97+
0038
98+
0039 <span class="keyword">if</span> ~isempty(existingIds)
99+
0040 existingIds=regexprep(existingIds,[<span class="string">'^'</span> prefix],<span class="string">''</span>);
100+
0041 existingIds=sort(existingIds);
101+
0042 lastId=existingIds{end};
102+
0043 numLength=length(lastId);
103+
0044 lastId=str2double(lastId);
104+
0045 <span class="keyword">else</span>
105+
0046 lastId=0;
106+
0047 fprintf([<span class="string">'No '</span> type <span class="string">' ids with prefix &quot;'</span> prefix <span class="keyword">...</span>
107+
0048 <span class="string">'&quot; currently exist in the model. The first new id will be &quot;'</span> <span class="keyword">...</span>
108+
0049 [prefix,num2str(1,[<span class="string">'%0'</span> num2str(numLength) <span class="string">'d'</span>])] <span class="string">'&quot;\n'</span>],<span class="string">'%s'</span>)
109+
0050 <span class="keyword">end</span>
110110
0051
111-
0052 <span class="keyword">for</span> k=1:quantity
112-
0053 newIds{k}=[prefix,num2str(k+lastId,[<span class="string">'%0'</span> num2str(numLength) <span class="string">'d'</span>])];
111+
0052 <span class="keyword">if</span> isnan(lastId)
112+
0053 lastId = 0;
113113
0054 <span class="keyword">end</span>
114-
0055 <span class="keyword">end</span></pre></div>
114+
0055
115+
0056 newIds=cell(quantity,1);
116+
0057
117+
0058 <span class="keyword">for</span> k=1:quantity
118+
0059 newIds{k}=[prefix,num2str(k+lastId,[<span class="string">'%0'</span> num2str(numLength) <span class="string">'d'</span>])];
119+
0060 <span class="keyword">end</span>
120+
0061 <span class="keyword">end</span></pre></div>
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<hr><address>Generated by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" title="Matlab Documentation in HTML">m2html</a></strong> &copy; 2005</address>
116122
</body>
117123
</html>

‎doc/io/closeModel.html

Lines changed: 15 additions & 15 deletions
Original file line numberDiff line numberDiff line change
@@ -63,51 +63,51 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
6363
0011
6464
0012 closedModel=model;
6565
0013
66-
0014 closedModel.comps{numel(closedModel.comps)+1}=<span class="string">'b'</span>;
67-
0015 closedModel.compNames{numel(closedModel.compNames)+1}=<span class="string">'boundary'</span>;
66+
0014 closedModel.comps{numel(closedModel.comps)+1,1}=<span class="string">'b'</span>;
67+
0015 closedModel.compNames{numel(closedModel.compNames)+1,1}=<span class="string">'boundary'</span>;
6868
0016 <span class="keyword">if</span> isfield(closedModel,<span class="string">'compMiriams'</span>)
69-
0017 closedModel.compMiriams{numel(closedModel.compMiriams)+1}=[];
70-
0018 <span class="keyword">end</span>;
69+
0017 closedModel.compMiriams{numel(closedModel.compMiriams)+1,1}=[];
70+
0018 <span class="keyword">end</span>
7171
0019 closedModel.unconstrained=zeros(numel(closedModel.mets),1);
7272
0020
7373
0021 <span class="keyword">for</span> i=1:numel(closedModel.rxns)
7474
0022 <span class="keyword">if</span> sum(abs(closedModel.S(:,i)))==1
7575
0023 closedModel.mets{numel(closedModel.mets)+1}=strcat(closedModel.mets{find(closedModel.S(:,i))},<span class="string">'_b'</span>);
7676
0024 <span class="keyword">if</span> isfield(closedModel,<span class="string">'metNames'</span>)
7777
0025 closedModel.metNames{numel(closedModel.metNames)+1}=closedModel.metNames{find(closedModel.S(:,i))};
78-
0026 <span class="keyword">end</span>;
78+
0026 <span class="keyword">end</span>
7979
0027 closedModel.metComps(numel(closedModel.metComps)+1)=numel(closedModel.comps);
8080
0028 <span class="keyword">if</span> isfield(closedModel,<span class="string">'inchis'</span>)
8181
0029 closedModel.inchis{numel(closedModel.inchis)+1}=closedModel.inchis{find(closedModel.S(:,i))};
82-
0030 <span class="keyword">end</span>;
82+
0030 <span class="keyword">end</span>
8383
0031 <span class="keyword">if</span> isfield(closedModel,<span class="string">'metSmiles'</span>)
8484
0032 closedModel.metSmiles{numel(closedModel.metSmiles)+1}=closedModel.metSmiles{find(closedModel.S(:,i))};
85-
0033 <span class="keyword">end</span>;
85+
0033 <span class="keyword">end</span>
8686
0034 <span class="keyword">if</span> isfield(closedModel,<span class="string">'metFormulas'</span>)
8787
0035 closedModel.metFormulas{numel(closedModel.metFormulas)+1}=closedModel.metFormulas{find(closedModel.S(:,i))};
88-
0036 <span class="keyword">end</span>;
88+
0036 <span class="keyword">end</span>
8989
0037 <span class="keyword">if</span> isfield(closedModel,<span class="string">'metMiriams'</span>)
9090
0038 closedModel.metMiriams{numel(closedModel.metMiriams)+1}=closedModel.metMiriams{find(closedModel.S(:,i))};
91-
0039 <span class="keyword">end</span>;
91+
0039 <span class="keyword">end</span>
9292
0040 <span class="keyword">if</span> isfield(closedModel,<span class="string">'metFrom'</span>)
9393
0041 closedModel.metFrom{numel(closedModel.metFrom)+1}=<span class="string">''</span>;
94-
0042 <span class="keyword">end</span>;
94+
0042 <span class="keyword">end</span>
9595
0043 <span class="keyword">if</span> isfield(closedModel,<span class="string">'metCharges'</span>)
9696
0044 closedModel.metCharges(numel(closedModel.metCharges)+1)=closedModel.metCharges(find(closedModel.S(:,i)));
97-
0045 <span class="keyword">end</span>;
97+
0045 <span class="keyword">end</span>
9898
0046 <span class="keyword">if</span> isfield(closedModel,<span class="string">'metDeltaG'</span>)
9999
0047 closedModel.metDeltaG(numel(closedModel.metDeltaG)+1)=closedModel.metDeltaG(find(closedModel.S(:,i)));
100-
0048 <span class="keyword">end</span>;
100+
0048 <span class="keyword">end</span>
101101
0049 closedModel.unconstrained(numel(closedModel.unconstrained)+1)=1;
102102
0050 closedModel.b(numel(closedModel.b)+1)=0;
103103
0051 closedModel.S=[closedModel.S;sparse(1,size(closedModel.S,2))];
104104
0052 <span class="keyword">if</span> sum(closedModel.S(:,i))==1
105105
0053 closedModel.S(numel(closedModel.mets),i)=-1;
106106
0054 <span class="keyword">else</span>
107107
0055 closedModel.S(numel(closedModel.mets),i)=1;
108-
0056 <span class="keyword">end</span>;
109-
0057 <span class="keyword">end</span>;
110-
0058 <span class="keyword">end</span>;
108+
0056 <span class="keyword">end</span>
109+
0057 <span class="keyword">end</span>
110+
0058 <span class="keyword">end</span>
111111
0059
112112
0060 <span class="keyword">end</span></pre></div>
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<hr><address>Generated by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" title="Matlab Documentation in HTML">m2html</a></strong> &copy; 2005</address>

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