Merge pull request #406 from bgoli/fbc-v3-final

Finalizing the FBC version 3 specification

sbml-level-3/version-1/fbc/spec/apdx-validation.tex

@@ -185,13 +185,13 @@ \subsubsection*{Rules for extended \class{Model} object}
 a \ListOfGeneProducts object. (Reference: SBML Level~3 Specification for
 Flux Balance Constraints, Version~3, \sec{model-class}.)}
 
-\validRule{fbc-20213}{\changed{Apart from the general notes and annotations
+\validRule{fbc-20213}{\newtxt{Apart from the general notes and annotations
 subobjects permitted on all SBML objects, a
 \ListOfUserDefinedConstraints container object may only contain
 \UserDefinedConstraint objects. (Reference: SBML Level~3 Specification
 for Flux Balance Constraints, Version~3, \sec{model-class}.)}}
 
-\validRule{fbc-20214}{\changed{A \ListOfUserDefinedConstraints object may have
+\validRule{fbc-20214}{\newtxt{A \ListOfUserDefinedConstraints object may have
 the optional SBML Level~3 Core attributes \token{metaid} and
 \token{sboTerm}. No other attributes from the SBML Level~3 Core
 namespaces are permitted on a \ListOfUserDefinedConstraints object.
@@ -599,7 +599,7 @@ \subsubsection*{Rules for \class{GeneProduct} object}
 \Model object. (Reference: SBML Level~3 Specification for Flux Balance
 Constraints, Version~3, \sec{geneproduct-class}.)}
 
-\begin{blockChanged}
+%\begin{blockChanged}
 \subsubsection*{Rules for \class{UserDefinedConstraintComponent} object}
 
 \validRule{fbc-21301}{An \UserDefinedConstraintComponent object may have
@@ -765,4 +765,4 @@ \subsubsection*{Rules for \class{KeyValuePair} object}
 SBML Level~3 Specification for Flux Balance Constraints, Version~3,
 \sec{listofkeyvaluepairs-class}.)}
 
-\end{blockChanged}
+%\end{blockChanged}

sbml-level-3/version-1/fbc/spec/best-practices.tex

@@ -56,7 +56,7 @@ \subsubsection*{Reaction definition and flux bounds}
 \newpage
 \subsection{An example of a strict FBC Version 2 model (XML)}
 \label{best-practices-V2}
-This section highlights the best practices for a complete \FBC Version 2 model. To improve readability, detailed annotations as described in Section~\ref{best-practices-cobraV2} and unit definitions have been omitted.
+This section highlights the best practices for a complete \FBC Version 2 model encoded in \FBC Version 3. To improve readability, detailed annotations as described in Section~\ref{best-practices-cobraV2} and unit definitions have been omitted.
 
 \exampleFile{examples/v2harmony-ex_bp-complete.txt}
 

sbml-level-3/version-1/fbc/spec/examples/ex-v3-userdefinedconstraints.txt

@@ -1,28 +1,26 @@
-<listOfParameters>
- <parameter id="uc1" value="5" constant="True"/>
- <parameter id="uc2lb" value="2" constant="True"/>
- <parameter id="uc2ub" value="INF" constant="True"/>
- <parameter id="ucco1a" value="1" constant="True"/>
- <parameter id="ucco1b" value="-1" constant="True"/>
- <parameter id="ucco2a" value="2" constant="True"/>
- <parameter id="ucco2b" value="-1" constant="True"/>
- <parameter id="p1var" value="NaN" constant="False"/>
+<listOfParameters>10r
+ <parameter id="inf" value="INF" constant="True"/>
+ <parameter id="five" value="5" constant="True"/>
+ <parameter id="two" value="2" constant="True"/>
+ <parameter id="one" value="1" constant="True"/>
+ <parameter id="negone" value="-1" constant="True"/>
+ <parameter id="p1var" constant="False"/>
 </listOfParameters>
 
 <fbc:listOfUserConstraints>
- <fbc:userContraint fbc:id="uc1" fbc:lowerBound="uc1" fbc:upperBound="uc1">
+ <fbc:userContraint fbc:id="uc1" fbc:lowerBound="five" fbc:upperBound="five">
   <fbc:listOfUserConstraintComponents>
-   <fbc:userConstraintComponent fbc:coefficient="ucco1a" fbc:variable="RGLX"
+   <fbc:userConstraintComponent fbc:coefficient="one" fbc:variable="RGLX"
     variableType="linear"/>
-   <fbc:userConstraintComponent fbc:coefficient="ucco1b" fbc:variable="RBTK"
+   <fbc:userConstraintComponent fbc:coefficient="negone" fbc:variable="RBTK"
     variableType="linear"/>
   </fbc:listOfUserConstraintComponents>
  </fbc:userContraint>
- <fbc:userContraint fbc:id="uc2" fbc:lowerBound="uc2lb" fbc:upperBound="uc2ub">
+ <fbc:userContraint fbc:id="uc2" fbc:lowerBound="two" fbc:upperBound="inf">
   <fbc:listOfUserConstraintComponents>
-   <fbc:userConstraintComponent fbc:coefficient="ucco2a" fbc:variable="p1var"
+   <fbc:userConstraintComponent fbc:coefficient="two" fbc:variable="p1var"
     variableType="linear"/>
-   <fbc:userConstraintComponent fbc:coefficient="ucco2b" fbc:variable="RGDP"
+   <fbc:userConstraintComponent fbc:coefficient="negone" fbc:variable="RGDP"
     variableType="linear"/>
   </fbc:listOfUserConstraintComponents>
  </fbc:userContraint>

sbml-level-3/version-1/fbc/spec/intro.tex

@@ -54,7 +54,7 @@ \subsection{Proposal corresponding to this package specification}
   \vspace*{1ex}
 %\end{center}
 
-\changed{Issues with this and other SBML packages can be filed at \small\url{https://github.com/sbmlteam/sbml-specifications/issues}.  Issues pertaining to this package in particular are labeled with the 'L3 Package: fbc' tag.}
+\newtxt{Issues with this and other SBML packages can be filed at \small\url{https://github.com/sbmlteam/sbml-specifications/issues}.  Issues pertaining to this package in particular are labeled with the 'L3 Package: fbc' tag.}
 The version of the proposal used as the starting point for this specification is the version of March 2012. Previous versions of the current proposal are:
 
 \begin{description}

sbml-level-3/version-1/fbc/spec/main.tex

@@ -71,7 +71,10 @@
 \newcommand{\sboref}{\url{http://biomodels.net/SBO/}\xspace}
 
 \newcommand{\bgoli}[1]{\textcolor{Mahogany}{\protect\marginpar{bgoli} #1}\xspace}
-\newcommand{\newtxt}[1]{\textcolor{Mahogany}{#1}\xspace}
+
+% red changed text removed from final version
+%\newcommand{\newtxt}[1]{\textcolor{Mahogany}{#1}\xspace}
+\newcommand{\newtxt}[1]{#1}
 \definecolor{ashgrey}{rgb}{0.7, 0.75, 0.71}
 %\newenvironment{deprecated}{\color{ashgrey}}{\ignorespacesafterend}
 \newenvironment{deprecated}{}{\ignorespacesafterend}