Feature improve doxygen

.github/workflows/cpp-linter.yaml

@@ -45,7 +45,7 @@ jobs:
           ignore: '.github|_deps|CMakeFiles|spdlog*'
           format-review: true
           tidy-review: true
-          files-changed-only: false
+          files-changed-only: true
           thread-comments: true
           tidy-checks: 'boost-*,bugprone-*,performance-*,readability-*,portability-*,modernize-*,clang-analyzer-*,cppcoreguidelines-*,-modernize-use-trailing-return-type,-modernize-use-emplace,-readability-redundant-access-specifiers'
 

README.md

@@ -1,5 +1,8 @@
+
 <a name="nutens"></a>
-# <img src="doc/nuTens-logo.png" alt="nuTens" class="right" align="top" width="400"/>
+# nuTens  
+<img src="nuTens-logo.png" alt="nuTens"  align="right" width="400"/>
+
 
 nuTens is a software library which uses [tensors](https://en.wikipedia.org/wiki/Tensor_(machine_learning)) to efficiently calculate neutrino oscillation probabilities. 
 

doc/doxygen.config

@@ -966,7 +966,7 @@ EXAMPLE_RECURSIVE      = NO
 # that contain images that are to be included in the documentation (see the
 # \image command).
 
-IMAGE_PATH             =
+IMAGE_PATH             = ./doc
 
 # The INPUT_FILTER tag can be used to specify a program that doxygen should
 # invoke to filter for each input file. Doxygen will invoke the filter program
@@ -1223,7 +1223,7 @@ HTML_EXTRA_STYLESHEET  = doc/tweaks.css
 # files will be copied as-is; there are no commands or markers available.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_EXTRA_FILES       =
+HTML_EXTRA_FILES       = nuTens-logo.png
 
 # The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen
 # will adjust the colors in the style sheet and background images according to

nuTens/instrumentation.hpp

@@ -6,16 +6,19 @@
 #include <string>
 #include <thread>
 #include <utility>
-/*! \file instrumentation.hpp
-    \brief Define utilities for instrumentation of the code
 
-    This is the home of anything that gets placed inside other classes or functions in order to instrument the code.
-   e.g. for profiling or debugging. Everything should ideally be macro-fied so it can be included only for certain
-   builds, or specified by build time options.
-*/
+/*!
+ * @file instrumentation.hpp
+ * @brief Define utilities for instrumentation of the code
+ *
+ * This is the home of anything that gets placed inside other classes or functions in order to instrument the code.
+ * e.g. for profiling or debugging. Everything should ideally be macro-fied so it can be included only for certain
+ * builds, or specified by build time options.
+ */
 
 struct ProfileResult
 {
+    /// @struct ProfileResult
     /// @brief Hold the results of a profiled function to be written out.
 
     std::string name;
@@ -26,21 +29,64 @@
 
 class ProfileWriter
 {
-    /*! @class ProfileWriter
+    /*!
+     * @class ProfileWriter
      * @brief Singleton class to collect timing information for functions and write out to a file that can be inspected
      * later with visual profiling tool
      *
      * Writes out profiling information in a json format readable by chrome tracing
      * (https://www.chromium.org/developers/how-tos/trace-event-profiling-tool/) Use the macros provided to instrument
-     * the code like: \code{.cpp}
+     * the source code like:
+     *
+     * @code{.cpp}
+     * \\ header.hpp
+     *
+     * class ClassName
+     * {
+     *   returnType func(args);
+     * }
+     *
+     *
+     * \\ implementation.cpp
+     *
+     * ClassName::func(args)
+     * {
+     *   NT_PROFILE();
+     *
+     *   \\ implementation code
+     *
+     * }
+     * @endcode
+     *
+     * In order to instantiate the ProfileWriter in an application you will then need to use NT_PROFILE_BEGINSESSION()
+     * and NT_PROFILE_ENDSESSION() like:
+     *
+     * @code{.cpp}
+     *
+     * \\ application.cpp
+     *
+     * void main()
+     * {
+     *   NT_PROFILE_BEGINSESSION(sessionName);
      *
-     * \code{.cpp}
+     *   \\ ... code ...
+     *   ClassName instance;
      *
-     * Then open up your favourite chromium based browser and go to chrome://tracing. You can then just drag and drop
-     * the profiling json file and should see a lovely display of the collected profile information.
+     *   instance.func(args);
+     *
+     *   \\ ... code ...
+     *
+     *   NT_PROFILE_ENDSSION();
+     * }
+     *
+     * @endcode
+     *
+     * This will save a json file called <sessionName>-profile.json.
+     * Then you can open up your favourite chromium based browser and go to chrome://tracing. You can then just drag and
+     * drop the profiling json file and should see a lovely display of the collected profile information.
      */
 
-    /// \todo currently only suppor the format used by chrome tracing. Would be nice to support other formats too.
+    /// @todo currently only suppor the format used by chrome tracing. Would be nice to support other formats too.
     /// Should just be a case of adding additional option for writeProfile and header and footer
 
   public:
@@ -119,19 +165,22 @@
     uint _profileCount{0};
 };
 
 class InstrumentationTimer
-/*!
- * @class InstrumentationTimer
- * @brief Class to perform the actual timing
- *
- *
- *
- */
 {
+    /*!
+     * @class InstrumentationTimer
+     * @brief Class to perform timing
+     *
+     * Gets created at the start of the scope to time then will be deleted when the scope ends.
+     * When deleted, will write out timing information to the output stream defined by ProfileWriter.
+     *
+     *
+     */
+
   public:
     /// @brief Construct an InstrumentationTimer object and start the clock
-    /// @param[in] name The name of the profile. Typically use __FUNCSIG__ so it's clear which part of the code is being
-    /// profiled.
+    /// @param[in] name The name of the profile. Typically use __PRETTY_FUNCTION__ so it's clear which part of the code
+    /// is being profiled.
     InstrumentationTimer(std::string name) : _name(std::move(name)), _stopped(false)
     {
         _startTimepoint = std::chrono::high_resolution_clock::now();
@@ -182,6 +231,7 @@
 #endif
 
 /// @brief Profile the current scope
+/// Shold always be used at the very start of the scope.
 #ifdef USE_PROFILING
 // NOLINTNEXTLINE
 #define NT_PROFILE() InstrumentationTimer timer##__LINE__(std::string(__PRETTY_FUNCTION__))
@@ -190,6 +240,7 @@
 #endif
 
 /// @brief End the profiling session
+/// Should be used at the very end of an application, after all functions containing a NT_PROFILE() have been called
 #ifdef USE_PROFILING
 // NOLINTNEXTLINE
 #define NT_PROFILE_ENDSESSION() ProfileWriter::get().endSession()

nuTens/propagator/base-matter-solver.hpp

@@ -3,6 +3,8 @@
 #include <nuTens/instrumentation.hpp>
 #include <nuTens/tensors/tensor.hpp>
 
+/// @file base-matter-solver.hpp
+
 class BaseMatterSolver
 {
     /// @class BaseMatterSolver

nuTens/propagator/const-density-solver.hpp

@@ -3,6 +3,8 @@
 #include <nuTens/propagator/base-matter-solver.hpp>
 #include <nuTens/propagator/constants.hpp>
 
+/// @file const-density-solver.hpp
+
 class ConstDensityMatterSolver : public BaseMatterSolver
 {
     /*!
@@ -78,7 +80,7 @@
     /// shape should look like {Nbatches, 1, 1}.
     /// @param[out] eigenvectors The returned eigenvectors
     /// @param[out] eigenvalues The corresponding eigenvalues
     void calculateEigenvalues(const Tensor &energies, Tensor &eigenvectors, Tensor &eigenvalues);
 
   private:
     Tensor PMNS;

nuTens/propagator/constants.hpp

@@ -1,8 +1,8 @@
 #pragma once
 
-/// @file constant.hpp
+/// @file constants.hpp
+/// @brief Defines constants to be used across the project
 
-//! Define constants to be used across the project
 namespace Constants
 {
 

nuTens/propagator/propagator.hpp

@@ -5,6 +5,8 @@
 #include <nuTens/tensors/tensor.hpp>
 #include <vector>
 
+/// @file propagator.hpp
+
 class Propagator
 {
     /*!

nuTens/tensors/dtypes.hpp

@@ -1,8 +1,14 @@
 #pragma once
 
+/*!
+ * @file dtypes.hpp
+ * @brief Defines various datatypes used in the project
+ */
+
 namespace NTdtypes
 {
 
+/// Types of scalar values
 enum scalarType
 {
     kInt,
@@ -12,6 +18,7 @@ enum scalarType
     kComplexDouble,
 };
 
+/// Devices that a Tensor can live on
 enum deviceType
 {
     kCPU,

nuTens/tensors/tensor.hpp

@@ -13,6 +13,11 @@
 #include <torch/torch.h>
 #endif
 
+/*!
+ * @file tensor.hpp
+ * @brief Defines the interface of a Tensor object
+ */
+
 class Tensor
 {
     /*!