From 6dbb32b56bcd88c3090239f9e7b546e3b30d4edb Mon Sep 17 00:00:00 2001
From: Christopher Dilks <c-dilks@users.noreply.github.com>
Date: Thu, 30 May 2024 09:10:56 -0400
Subject: [PATCH] doc: add algorithm full name to API documentation (#223)

---
 doc/gen/Doxyfile                                              | 2 +-
 src/iguana/algorithms/clas12/EventBuilderFilter/Algorithm.h   | 2 +-
 src/iguana/algorithms/clas12/FTEnergyCorrection/Algorithm.h   | 2 +-
 src/iguana/algorithms/clas12/LorentzTransformer/Algorithm.h   | 2 +-
 src/iguana/algorithms/clas12/MomentumCorrection/Algorithm.h   | 2 +-
 src/iguana/algorithms/clas12/PhotonGBTFilter/Algorithm.h      | 4 ++--
 src/iguana/algorithms/clas12/SectorFinder/Algorithm.h         | 2 +-
 src/iguana/algorithms/clas12/ZVertexFilter/Algorithm.h        | 2 +-
 src/iguana/algorithms/example/ExampleAlgorithm/Algorithm.h    | 2 +-
 src/iguana/algorithms/physics/InclusiveKinematics/Algorithm.h | 2 +-
 10 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/doc/gen/Doxyfile b/doc/gen/Doxyfile
index 5ebcbf19..f4fd72ab 100644
--- a/doc/gen/Doxyfile
+++ b/doc/gen/Doxyfile
@@ -286,7 +286,7 @@ TAB_SIZE               = 4
 ALIASES =
 # algorithm properties
 ALIASES += brief_algo="@brief **%Algorithm:** "
-ALIASES += begin_doc_algo{1}="\xrefitem algo \"Algorithm Type:\" \"List of all Algorithms\" \1 \par %Algorithm Properties:^^<table>"
+ALIASES += begin_doc_algo{2|}="\par %Algorithm Name:^^&emsp;&emsp;&emsp;`%\1`\xrefitem algo \"Algorithm Type:\" \"List of all Algorithms\" \2 \par %Algorithm Inputs and Outputs:^^<table>"
 ALIASES += input_banks{1}="<tr><td>**Input Banks**</td><td>`\1`</td></tr>"
 ALIASES += output_banks{1}="<tr><td>**Output Banks**</td><td>`\1`</td></tr>"
 ALIASES += end_doc="</table>"
diff --git a/src/iguana/algorithms/clas12/EventBuilderFilter/Algorithm.h b/src/iguana/algorithms/clas12/EventBuilderFilter/Algorithm.h
index ec08a213..dc65804c 100644
--- a/src/iguana/algorithms/clas12/EventBuilderFilter/Algorithm.h
+++ b/src/iguana/algorithms/clas12/EventBuilderFilter/Algorithm.h
@@ -6,7 +6,7 @@ namespace iguana::clas12 {
 
   /// @brief_algo Filter the `REC::Particle` (or similar) bank by PID from the Event Builder
   ///
-  /// @begin_doc_algo{Filter}
+  /// @begin_doc_algo{clas12::EventBuilderFilter | Filter}
   /// @input_banks{REC::Particle}
   /// @output_banks{REC::Particle}
   /// @end_doc
diff --git a/src/iguana/algorithms/clas12/FTEnergyCorrection/Algorithm.h b/src/iguana/algorithms/clas12/FTEnergyCorrection/Algorithm.h
index 93ec995d..0e487bc1 100644
--- a/src/iguana/algorithms/clas12/FTEnergyCorrection/Algorithm.h
+++ b/src/iguana/algorithms/clas12/FTEnergyCorrection/Algorithm.h
@@ -7,7 +7,7 @@ namespace iguana::clas12 {
 
   /// @brief_algo Forward Tagger energy correction
   ///
-  /// @begin_doc_algo{Transformer}
+  /// @begin_doc_algo{clas12::FTEnergyCorrection | Transformer}
   /// @input_banks{RECFT::Particle}
   /// @output_banks{RECFT::Particle}
   /// @end_doc
diff --git a/src/iguana/algorithms/clas12/LorentzTransformer/Algorithm.h b/src/iguana/algorithms/clas12/LorentzTransformer/Algorithm.h
index f4a5a3a5..aa7a56ef 100644
--- a/src/iguana/algorithms/clas12/LorentzTransformer/Algorithm.h
+++ b/src/iguana/algorithms/clas12/LorentzTransformer/Algorithm.h
@@ -7,7 +7,7 @@ namespace iguana::clas12 {
 
   /// @brief_algo Lorentz transform momenta in `REC::Particle` (or similar banks)
   ///
-  /// @begin_doc_algo{Transformer}
+  /// @begin_doc_algo{clas12::LorentzTransformer | Transformer}
   /// @input_banks{REC::Particle}
   /// @output_banks{REC::Particle}
   /// @end_doc
diff --git a/src/iguana/algorithms/clas12/MomentumCorrection/Algorithm.h b/src/iguana/algorithms/clas12/MomentumCorrection/Algorithm.h
index 9a1d8cfb..0652605b 100644
--- a/src/iguana/algorithms/clas12/MomentumCorrection/Algorithm.h
+++ b/src/iguana/algorithms/clas12/MomentumCorrection/Algorithm.h
@@ -9,7 +9,7 @@ namespace iguana::clas12 {
   ///
   /// Adapted from <https://clasweb.jlab.org/wiki/index.php/CLAS12_Momentum_Corrections#tab=Correction_Code>
   ///
-  /// @begin_doc_algo{Transformer}
+  /// @begin_doc_algo{clas12::MomentumCorrection | Transformer}
   /// @input_banks{RUN::config, REC::Particle, REC::Particle::Sector}
   /// @output_banks{REC::Particle}
   /// @end_doc
diff --git a/src/iguana/algorithms/clas12/PhotonGBTFilter/Algorithm.h b/src/iguana/algorithms/clas12/PhotonGBTFilter/Algorithm.h
index b75be5ca..8f9002b2 100644
--- a/src/iguana/algorithms/clas12/PhotonGBTFilter/Algorithm.h
+++ b/src/iguana/algorithms/clas12/PhotonGBTFilter/Algorithm.h
@@ -18,7 +18,7 @@ namespace iguana::clas12 {
   ///
   /// For each photon (labeled the photon of interest or POI), we obtain its intrinsic features (energy, angle, pcal edep, etc.) and features corresponding to its nearest neighbors (angle of proximity, energy difference, etc.). This requires the reading of both the REC::Particle and REC::Calorimeter banks. An input std::vector<float> is produced and passed to the pretrained GBT models, which yield a classification score between 0 and 1. An option variable `threshold` then determines the minimum photon `p-value` to survive the cut.
   ///
-  /// @begin_doc_algo{Filter}
+  /// @begin_doc_algo{clas12::PhotonGBTFilter | Filter}
   /// @input_banks{REC::Particle, REC::Calorimeter, RUN::config}
   /// @output_banks{REC::Particle}
   /// @end_doc
@@ -146,4 +146,4 @@ namespace iguana::clas12 {
        };
   };
     
-}
\ No newline at end of file
+}
diff --git a/src/iguana/algorithms/clas12/SectorFinder/Algorithm.h b/src/iguana/algorithms/clas12/SectorFinder/Algorithm.h
index 4153a912..1f5bba6e 100644
--- a/src/iguana/algorithms/clas12/SectorFinder/Algorithm.h
+++ b/src/iguana/algorithms/clas12/SectorFinder/Algorithm.h
@@ -6,7 +6,7 @@ namespace iguana::clas12 {
 
   /// @brief_algo Find the sector for all rows in `REC::Particle`
   ///
-  /// @begin_doc_algo{Creator}
+  /// @begin_doc_algo{clas12::SectorFinder | Creator}
   /// @input_banks{REC::Particle}
   /// @output_banks{%REC::Particle::Sector}
   /// @end_doc
diff --git a/src/iguana/algorithms/clas12/ZVertexFilter/Algorithm.h b/src/iguana/algorithms/clas12/ZVertexFilter/Algorithm.h
index 1420b5dc..2a285852 100644
--- a/src/iguana/algorithms/clas12/ZVertexFilter/Algorithm.h
+++ b/src/iguana/algorithms/clas12/ZVertexFilter/Algorithm.h
@@ -6,7 +6,7 @@ namespace iguana::clas12 {
 
   /// @brief_algo Filter the `REC::Particle` (or similar) bank by cutting on Z Vertex
   ///
-  /// @begin_doc_algo{Filter}
+  /// @begin_doc_algo{clas12::ZVertexFilter | Filter}
   /// @input_banks{REC::Particle}
   /// @output_banks{REC::Particle}
   /// @end_doc
diff --git a/src/iguana/algorithms/example/ExampleAlgorithm/Algorithm.h b/src/iguana/algorithms/example/ExampleAlgorithm/Algorithm.h
index 719542da..90750d40 100644
--- a/src/iguana/algorithms/example/ExampleAlgorithm/Algorithm.h
+++ b/src/iguana/algorithms/example/ExampleAlgorithm/Algorithm.h
@@ -30,7 +30,7 @@ namespace iguana::example {
   ///
   /// Provide a more detailed description of your algorithm here.
   ///
-  /// @begin_doc_algo{Filter}
+  /// @begin_doc_algo{example::ExampleAlgorithm | Filter}
   /// @input_banks{REC::Particle}
   /// @output_banks{REC::Particle}
   /// @end_doc
diff --git a/src/iguana/algorithms/physics/InclusiveKinematics/Algorithm.h b/src/iguana/algorithms/physics/InclusiveKinematics/Algorithm.h
index fe4600c1..5d9c0e2d 100644
--- a/src/iguana/algorithms/physics/InclusiveKinematics/Algorithm.h
+++ b/src/iguana/algorithms/physics/InclusiveKinematics/Algorithm.h
@@ -23,7 +23,7 @@ namespace iguana::physics {
 
   /// @brief_algo Calculate inclusive kinematics quantities defined in `iguana::physics::InclusiveKinematicsVars`
   ///
-  /// @begin_doc_algo{Creator}
+  /// @begin_doc_algo{physics::InclusiveKinematics | Creator}
   /// @input_banks{REC::Particle}
   /// @output_banks{%physics::InclusiveKinematics}
   /// @end_doc