fix: Merge branch 'master' into featSFHFixedAges

.github/workflows/cicd.yml

@@ -1051,6 +1051,7 @@ jobs:
                 test-branchSubsampling.pl,
                 test-CGM-mass-cooled.pl,
                 test-concentration-Ludlow2016.pl,
+                test-concentration-Johnson2021.pl,
                 test-tidallyTruncatedNFWFit.pl,
                 test-constraint-deterministic-spins.pl,
                 test-constraint-mass-function.pl,

.github/workflows/prChecks.yml

@@ -242,9 +242,9 @@ jobs:
       - name: Comment on the PR if any warnings were found
         if: steps.check_files.outputs.files_exists == 'true'
         continue-on-error: true
-        uses: thollander/actions-comment-pull-request@v2
+        uses: thollander/actions-comment-pull-request@v3
         with:
-          filePath: warnings.md
+          file-path: warnings.md
   # Spell check LaTeX files
   Spell-Check-LaTeX:
     runs-on: ubuntu-latest
@@ -286,6 +286,6 @@ jobs:
           files: warnings.md
       - name: Comment on the PR if any warnings were found
         if: steps.check_files.outputs.files_exists == 'true'
-        uses: thollander/actions-comment-pull-request@v2
+        uses: thollander/actions-comment-pull-request@v3
         with:
-          filePath: warnings.md
+          file-path: warnings.md

doc/Advanced.tex

@@ -59,7 +59,13 @@ \section{Parameter Files}\label{sec:ParameterFiles}
 
 Parameters can also be defined with an ``{\normalfont \ttfamily id}'' attribute. Such parameters are targets for pointers elsewhere in the file, and as such are inactive (i.e. they will be ignored by \glc\ except as targets for pointers). A pointer to a target is created by specifying an element with the same parameter name and an ``{\normalfont \ttfamily idRef}'' element with a value equal to that of the {\normalfont \ttfamily id} element of the target. The pointer then acts as a regular parameter, adopting the value and subparameters of the target. Targets can be targeted by multiple pointers. This allows for a single object to be shared between multiple other objects.
 
-A parameter value can be given by a math expression\footnote{This functionality requires that {\normalfont \ttfamily libmatheval} is installed.}. In the above example {\normalfont \ttfamily parameter5Name} has a value of ``{\normalfont \ttfamily =10.0*[parameter4Name::subParameter1Name]}''. The initial ``{\normalfont \ttfamily =}'' indicates that this is a math expression which should be evaluated. In this case, the expression is ten times value value of ``{\normalfont \ttfamily [parameter4Name::subParameter1Name]}'', which refers to the value of the sub-parameter {\normalfont \ttfamily subParameter1Name} of parameter {\normalfont \ttfamily parameter4Name}. In this way the values of parameters can be derived from those of other parameters.
+It is possible to make a parameter conditional upon the value of another parameter. This can be useful, for example, if you want to include a specific \refClass{nodeOperatorClass} only if merger trees are being read from file, and not if trees are being constructed internally. This is achieved using the {\normalfont \ttfamily active} attribute of a parameter. For example:
+\begin{verbatim}
+    <nodeOperator value="assemblyHistoryHeuristics" active="[mergerTreeConstructor] == read">
+\end{verbatim}
+which will result in the {\normalfont \ttfamily assemblyHistoryHeuristics} {\normalfont \ttfamily nodeOperator} being active only if the {\normalfont \ttfamily mergerTreeConstructor} is set to {\normalfont \ttfamily new}. The content of the {\normalfont \ttfamily active} element must be a parameter name enclosed in {\normalfont \ttfamily []}, followed by an operator ({\normalfont \ttfamily ==} or {\normalfont \ttfamily !=}), followed by the text to match. The parameter name can include a full path as described below. Note that, while numerical parameters can be used in {\normalfont \ttfamily active} elements, the comparison is always textual, not numerical.
+
+A parameter value can be given by a math expression\footnote{This functionality requires that {\normalfont \ttfamily libmatheval} is installed.}. In the above example {\normalfont \ttfamily parameter5Name} has a value of ``{\normalfont \ttfamily =10.0*[parameter4Name:subParameter1Name]}''. The initial ``{\normalfont \ttfamily =}'' indicates that this is a math expression which should be evaluated. In this case, the expression is ten times value value of ``{\normalfont \ttfamily [parameter4Name:subParameter1Name]}'', which refers to the value of the sub-parameter {\normalfont \ttfamily subParameter1Name} of parameter {\normalfont \ttfamily parameter4Name}. In this way the values of parameters can be derived from those of other parameters.
 
 Lastly, a text parameter can also be evaluated by starting it with an initial ``{\normalfont \ttfamily =}''. For text parameters, other parameters can be referenced and their values are simply inserted. So, for example:
 \begin{verbatim}

parameters/reference/evolutionGalaxyFormation.xml

@@ -28,6 +28,7 @@
     <efficiencyStrippingOutflow  value="0.1"  />
     <trackStrippedGas            value="true" />
   </componentHotHalo>
+  <componentPosition          value="null"    />
   <componentSatellite         value="orbiting"/>
   <componentSpheroid          value="standard" >
     <ratioAngularMomentumScaleRadius value="0.5"   />

parameters/reference/evolutionGalaxyFormationNBody.xml

@@ -28,7 +28,8 @@
     <efficiencyStrippingOutflow  value="0.1"  />
     <trackStrippedGas            value="true" />
   </componentHotHalo>
-  <componentPosition          value="cartesian"/>
+  <componentPosition          value="null"      active="[mergerTreeConstructor] == build"/>
+  <componentPosition          value="cartesian" active="[mergerTreeConstructor] == read" />
   <componentSatellite         value="preset"   />
   <componentSpheroid          value="standard" >
     <ratioAngularMomentumScaleRadius value="0.5"   />
@@ -206,12 +207,12 @@
       <fractionMassFormation value="0.5"/>
     </nodeOperator>
     <!-- Position interpolation -->
-    <nodeOperator value="positionInterpolated">
+    <nodeOperator value="positionInterpolated" active="[componentPosition] == cartesian">
       <wrapPeriodic value="false"/>	<!-- Do not wrap interpolated positions back into the box - this is not needed as we replicate the box. -->
       <lengthBox    value="=[geometryLightcone::lengthReplication]*(([cosmologyParameters::HubbleConstant]/100.0)^[geometryLightcone::lengthHubbleExponent])*([geometryLightcone::lengthUnitsInSI]/3.08567758e+22)"/>
     </nodeOperator>
     <!-- Heuristic analysis -->
-    <nodeOperator value="assemblyHistoryHeuristics">
+    <nodeOperator value="assemblyHistoryHeuristics" active="[mergerTreeConstructor] == read">
       <exponentGrowth value="100.0"/>
       <sigmaThreshold value="5.0"/>
       <nbodyHaloMassError value="trenti2010">

perl/Fortran/Utils.pm

@@ -346,8 +346,8 @@ sub Get_Fortran_Line {
 	if ( $tmpLine !~ m/!/ ) {
 	    ## This regex tests for the possible existance of any comment. If no "!" is present there can be no comment, and most lines don't contain comments, so we can quickly ignored them.
 	    $commentPosition = -1;
-	} elsif ( $tmpLine =~ m/^([^'"\{]+)![^\$]/ ) {
-	    ## This regex checks for a "!" prior to any of "'{, and not followed by a "$" (which indicates an OpenMP directive). If found, this must be the start of a comment.
+	} elsif ( $tmpLine =~ m/^([^'"\{]+?)![^\$]/ ) {
+	    ## This regex checks for the first "!" prior to any of "'{, and not followed by a "$" (which indicates an OpenMP directive). If found, this must be the start of a comment.
 	    $commentPosition = length($1);
 	} else {
 	    # General case. Comments begin with a "!" symbol, but not if it is found inside a string literal, or inside braces, "{}".

perl/Galacticus/Build/Components/TreeNodes.pm

@@ -123,7 +123,7 @@ sub Build_Tree_Node_Class {
 	 {
 	     type        => "procedure"                                                                                                       ,
 	     name        => "isPrimaryProgenitor"                                                                                             ,
-	     function    => "Tree_Node_Is_Primary_Progenitor"                                                                                 ,
+	     function    => "treeNodeIsPrimaryProgenitor"                                                                                 ,
 	     description => "Return true if this node is the primary progenitor of its descendant, false otherwise."                          ,
 	     returnType  => "\\logicalzero"                                                                                                   ,
 	     arguments   => ""

source/dark_matter_profiles.structure.scale.concentration.F90

@@ -343,12 +343,12 @@ Root function used to find the mass of a halo corresponding to the definition us
     call state_(stateCount)%darkMatterProfile%scaleSet(radiusCore)
     call Calculations_Reset(state_(stateCount)%nodeWork)
     ! Find the non-alt density.
-    densityOuter=+state_(stateCount)%self%cosmologyFunctions_   %matterDensityEpochal(                                                          state_(stateCount)%basic%time()) &
-         &       *state_(stateCount)%self%virialDensityContrast_%densityContrast     (state_(stateCount)%basic%mass(),state_(stateCount)%basic%time())
+    densityOuter=+state_(stateCount)%self%cosmologyFunctions_           %matterDensityEpochal  (                                state_(stateCount)%basic%time()) &
+         &       *state_(stateCount)%self%virialDensityContrast_        %densityContrast       (state_(stateCount)%basic%mass(),state_(stateCount)%basic%time())
     ! Solve for radius which encloses required non-alt density.
-    radiusOuter=state_(stateCount)%self%darkMatterProfileDMODefinition%radiusEnclosingDensity(state_(stateCount)%nodeWork,densityOuter)
+    radiusOuter =+state_(stateCount)%self%darkMatterProfileDMODefinition%radiusEnclosingDensity(state_(stateCount)%nodeWork    ,densityOuter)
     ! Get the mass within this radius.
-    massOuter  =state_(stateCount)%self%darkMatterProfileDMODefinition%enclosedMass          (state_(stateCount)%nodeWork, radiusOuter)
+    massOuter   =+state_(stateCount)%self%darkMatterProfileDMODefinition%enclosedMass          (state_(stateCount)%nodeWork    , radiusOuter)
     ! Return root function.
     concentrationMassRoot=massOuter-state_(stateCount)%mass
     return