Fix Doxygen

.github/workflows/codechecks.yml

@@ -12,4 +12,4 @@ jobs:
  - name: Run clang-format
  run: |
  cd src
- find **/*.hpp **/*.cpp | xargs clang-format --dry-run --style=Google --Werror
+ find **/*.h **/*.cpp | xargs clang-format --dry-run --style=Google --Werror

docs/Doxyfile

@@ -109,7 +109,7 @@ INPUT = "src" \
  "docs/pages"
 INPUT_ENCODING = UTF-8
 FILE_PATTERNS = *.cpp \
- *.hpp \
+ *.h \
  *.inc \
  *.markdown \
  *.md \
@@ -122,7 +122,7 @@ EXCLUDE_SYMBOLS =
 EXAMPLE_PATH = 
 EXAMPLE_PATTERNS = *
 EXAMPLE_RECURSIVE = NO
-IMAGE_PATH = images
+IMAGE_PATH = "docs"
 INPUT_FILTER =
 FILTER_PATTERNS =
 FILTER_SOURCE_FILES = NO
@@ -159,7 +159,6 @@ HTML_EXTRA_FILES =
 HTML_COLORSTYLE_HUE = 220
 HTML_COLORSTYLE_SAT = 100
 HTML_COLORSTYLE_GAMMA = 80
-HTML_TIMESTAMP = YES
 HTML_DYNAMIC_SECTIONS = NO
 HTML_INDEX_NUM_ENTRIES = 100
 GENERATE_DOCSET = NO

docs/pages/developer_guide.md

@@ -44,15 +44,15 @@ comment to format all your files:
 
 ```bash
 cd src
-find **/*.hpp **/*.cpp | xargs clang-format -i --style=Google
+find **/*.h **/*.cpp | xargs clang-format -i --style=Google
 ```
 
 You can also just check **if** a file would be formatted without actually formatting
 it with:
 
 ```bash
 cd src
-find **/*.hpp **/*.cpp | xargs clang-format --dry-run --style=Google --Werror
+find **/*.h **/*.cpp | xargs clang-format --dry-run --style=Google --Werror
 ```
 
 The latter check is also performed in the GitHub CI/CD (a.k.a. Actions) and

src/algebra/Integrator.h

@@ -28,8 +28,8 @@
 // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 /**
- * @file integrator.hpp
- * @brief ALGEBRA::Integrator source file
+ * @file Integrator.h
+ * @brief algebra::Integrator source file
  */
 #ifndef SVZERODSOLVER_ALGEBRA_INTEGRATOR_HPP_
 #define SVZERODSOLVER_ALGEBRA_INTEGRATOR_HPP_
@@ -60,8 +60,7 @@ namespace algebra {
  * total number of global unknowns. The DAE system is solved implicitly using
  * the generalized-\f$\alpha\f$ method \cite JANSEN2000305.
  *
- * @tparam T Scalar type (e.g. `float`, `double`)
- * `ALGEBRA::SparseSystem`)
+ * `algebra::SparseSystem`)
  */
 class Integrator {
  private:

src/algebra/SparseSystem.h

@@ -28,8 +28,8 @@
 // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 /**
- * @file sparsesystem.hpp
- * @brief ALGEBRA::SparseSystem source file
+ * @file SparseSystem.h
+ * @brief algebra::SparseSystem source file
  */
 #ifndef SVZERODSOLVER_ALGREBRA_SPARSESYSTEM_HPP_
 #define SVZERODSOLVER_ALGREBRA_SPARSESYSTEM_HPP_
@@ -51,7 +51,6 @@ namespace algebra {
  * This class contains all attributes and methods to create, modify, and
  * solve sparse systems.
  *
- * @tparam T Scalar type (e.g. `float`, `double`)
  */
 class SparseSystem {
  public:
@@ -120,7 +119,7 @@ class SparseSystem {
 
  /**
  * @brief Delete dynamically allocated memory (class member
- * Eigen::SparseLU<Eigen::SparseMatrix<T>> *solver)
+ * Eigen::SparseLU<Eigen::SparseMatrix> *solver)
  */
  void clean();
 };

src/algebra/State.h

@@ -28,8 +28,8 @@
 // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 /**
- * @file state.hpp
- * @brief ALGEBRA::State source file
+ * @file State.h
+ * @brief algebra::State source file
  */
 #ifndef SVZERODSOLVER_ALGEBRA_STATE_HPP_
 #define SVZERODSOLVER_ALGEBRA_STATE_HPP_
@@ -43,7 +43,6 @@ namespace algebra {
  * Stores the current state of a system, i.e. the current value and
  * derivate of all variables.
  *
- * @tparam T Scalar type (e.g. `float`, `double`)
  */
 class State {
  public:

src/interface/interface.cpp

@@ -27,10 +27,7 @@
 // LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
 // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-/**
- * @file interface.cpp
- * @brief svZeroDSolver callable interface.
- */
+
 #include "interface.h"
 
 #include <cmath>

src/interface/interface.h

@@ -27,6 +27,10 @@
 // LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
 // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+/**
+ * @file interface.h
+ * @brief svZeroDSolver callable interface.
+ */
 
 #include <map>
 #include <nlohmann/json.hpp>
@@ -61,7 +65,6 @@ class SolverInterface {
  // This is set by the external solver via the interface.
  double external_step_size_ = 0.1;
 
- // 0D solver parameters.
  // These are read in from the input JSON solver configuration file.
  double time_step_size_ = 0.0;
  int num_time_steps_ = 0;

src/model/Block.h

@@ -28,8 +28,8 @@
 // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 /**
- * @file block.hpp
- * @brief MODEL::Block source file
+ * @file Block.h
+ * @brief model::Block source file
  */
 #ifndef SVZERODSOLVER_MODEL_BLOCK_HPP_
 #define SVZERODSOLVER_MODEL_BLOCK_HPP_

src/model/BloodVessel.h

@@ -28,8 +28,8 @@
 // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 /**
- * @file bloodvessel.hpp
- * @brief MODEL::BloodVessel source file
+ * @file BloodVessel.h
+ * @brief model::BloodVessel source file
  */
 #ifndef SVZERODSOLVER_MODEL_BLOODVESSEL_HPP_
 #define SVZERODSOLVER_MODEL_BLOODVESSEL_HPP_
@@ -130,7 +130,6 @@ namespace zd_model {
  * * `2` Inductance
  * * `3` Stenosis coefficient
  *
- * @tparam T Scalar type (e.g. `float`, `double`)
  */
 class BloodVessel : public Block {
  public:

src/model/BloodVesselJunction.h

@@ -28,8 +28,8 @@
 // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 /**
- * @file bloodvesseljunction.hpp
- * @brief MODEL::BloodVesselJunction source file
+ * @file BloodVesselJunction.h
+ * @brief model::BloodVesselJunction source file
  */
 #ifndef SVZERODSOLVER_MODEL_BLOODVESSELJUNCTION_HPP_
 #define SVZERODSOLVER_MODEL_BLOODVESSELJUNCTION_HPP_
@@ -140,7 +140,6 @@ namespace zd_model {
  * * `i+num_outlets` Inductance for inner blood vessel `i`
  * * `i+2*num_outlets` Stenosis coefficient for inner blood vessel `i`
  *
- * @tparam T Scalar type (e.g. `float`, `double`)
  */
 class BloodVesselJunction : public Block {
  public:

src/model/ClosedLoopCoronaryBC.h

@@ -28,8 +28,8 @@
 // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 /**
- * @file closedloopcoronarybc.hpp
- * @brief MODEL::ClosedLoopCoronaryBC source file
+ * @file ClosedLoopCoronaryBC.h
+ * @brief model::ClosedLoopCoronaryBC source file
  */
 #ifndef SVZERODSOLVER_MODEL_CLOSEDLOOPCORONARYBC_HPP_
 #define SVZERODSOLVER_MODEL_CLOSEDLOOPCORONARYBC_HPP_
@@ -117,8 +117,6 @@ enum class Side { LEFT, RIGHT, NONE };
  * * `3` Ca
  * * `4` Cim
  *
- * @tparam T Scalar type (e.g. `float`, `double`)
- * @tparam side Side of the block (e.g. `Side::LEFT`, `Side::RIGHT`)
  */
 class ClosedLoopCoronaryBC : public Block {
  public:

src/model/ClosedLoopHeartPulmonary.h

@@ -28,8 +28,8 @@
 // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 /**
- * @file closedloopheartpulmonary.hpp
- * @brief MODEL::ClosedLoopHeartPulmonary source file
+ * @file ClosedLoopHeartPulmonary.h
+ * @brief model::ClosedLoopHeartPulmonary source file
  */
 #ifndef SVZERODSOLVER_MODEL_CLOSEDLOOPHEARTPULMONARY_HPP_
 #define SVZERODSOLVER_MODEL_CLOSEDLOOPHEARTPULMONARY_HPP_
@@ -87,7 +87,6 @@ namespace zd_model {
  * * `25` Right atrium resting volume
  * * `26` Left atrium resting volume
  *
- * @tparam T Scalar type (e.g. `float`, `double`)
  */
 class ClosedLoopHeartPulmonary : public Block {
  public:

src/model/ClosedLoopRCRBC.h

@@ -28,8 +28,8 @@
 // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 /**
- * @file closedloopRCRbc.hpp
- * @brief MODEL::ClosedLoopRCRBC source file
+ * @file ClosedLoopRCRbc.h
+ * @brief model::ClosedLoopRCRBC source file
  */
 #ifndef SVZERODSOLVER_MODEL_CLOSEDLOOPRCRBC_HPP_
 #define SVZERODSOLVER_MODEL_CLOSEDLOOPRCRBC_HPP_
@@ -109,7 +109,6 @@ namespace zd_model {
  * * `1` Capacitance
  * * `2` Distal resistance
  *
- * @tparam T Scalar type (e.g. `float`, `double`)
  */
 class ClosedLoopRCRBC : public Block {
  public:

src/model/DOFHandler.h

@@ -28,8 +28,8 @@
 // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 /**
- * @file dofhandler.hpp
- * @brief MODEL::DOFHandler source file
+ * @file DofHandler.h
+ * @brief model::DOFHandler source file
  */
 #ifndef SVZERODSOLVER_MODEL_DOFHANDLER_HPP_
 #define SVZERODSOLVER_MODEL_DOFHANDLER_HPP_

src/model/FlowReferenceBC.h

@@ -28,8 +28,8 @@
 // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 /**
- * @file flowreferencebc.hpp
- * @brief MODEL::FlowReferenceBC source file
+ * @file FlowReferenceBC.h
+ * @brief model::FlowReferenceBC source file
  */
 #ifndef SVZERODSOLVER_MODEL_FLOWREFERENCEBC_HPP_
 #define SVZERODSOLVER_MODEL_FLOWREFERENCEBC_HPP_
@@ -79,7 +79,6 @@ namespace zd_model {
  *
  * * `0` Flow
  *
- * @tparam T Scalar type (e.g. `float`, `double`)
  */
 class FlowReferenceBC : public Block {
  public:

src/model/Junction.h

@@ -28,8 +28,8 @@
 // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 /**
- * @file junction.hpp
- * @brief MODEL::Junction source file
+ * @file Junction.h
+ * @brief model::Junction source file
  */
 #ifndef SVZERODSOLVER_MODEL_JUNCTION_HPP_
 #define SVZERODSOLVER_MODEL_JUNCTION_HPP_
@@ -85,7 +85,6 @@ namespace zd_model {
  * \underbrace{1}_{P_i} & \dots & \underbrace{1}_{P_j} & \dots\end{array}\right]
  * \quad \mathrm{with} \quad i \neq j \f]
  *
- * @tparam T Scalar type (e.g. `float`, `double`)
  */
 class Junction : public Block {
  public:

src/model/Model.h

@@ -28,8 +28,8 @@
 // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 /**
- * @file model.h
- * @brief MODEL::Model source file
+ * @file Model.h
+ * @brief model::Model source file
  */
 
 #ifndef SVZERODSOLVER_MODEL_MODEL_HPP_
@@ -67,7 +67,6 @@ namespace zd_model {
  * This class represents a full 0D model. It contains attributes and
  * methods to store and modify 0D elements.
  *
- * @tparam T Scalar type (e.g. `float`, `double`)
  */
 class Model {
  public:
@@ -104,15 +103,15 @@ class Model {
  * @brief Get a block by its name
  *
  * @param name Name of the Block
- * @return Block<T>* The block
+ * @return Block* The block
  */
  Block *get_block(std::string_view name);
 
  /**
  * @brief Get a block by its global ID
  *
  * @param block_id Global ID of the Block
- * @return Block<T>* The block
+ * @return Block* The block
  */
  Block *get_block(int block_id);
 
@@ -173,7 +172,7 @@ class Model {
  * @brief Get a parameter by its global ID
  *
  * @param param_id Global ID of the parameter
- * @return Parameter<T>* The parameter
+ * @return Parameter* The parameter
  */
  Parameter *get_parameter(int param_id);
 

src/model/Node.h

@@ -28,8 +28,8 @@
 // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 /**
- * @file node.hpp
- * @brief MODEL::Node source file
+ * @file Node.h
+ * @brief model::Node source file
  */
 #ifndef SVZERODSOLVER_MODEL_NODE_HPP_
 #define SVZERODSOLVER_MODEL_NODE_HPP_
@@ -51,7 +51,6 @@ class Model;
  * Nodes connect two blocks with each other. Each node corresponds to a
  * flow and pressure value of the system.
  *
- * @tparam T Scalar type (e.g. `float`, `double`)
  */
 class Node {
  public:

src/model/OpenLoopCoronaryBC.h

@@ -28,8 +28,8 @@
 // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 /**
- * @file openloopcoronarybc.hpp
- * @brief MODEL::OpenLoopCoronaryBC source file
+ * @file OpenLoopCoronaryBC.h
+ * @brief model::OpenLoopCoronaryBC source file
  */
 #ifndef SVZERODSOLVER_MODEL_OPENLOOPCORONARYBC_HPP_
 #define SVZERODSOLVER_MODEL_OPENLOOPCORONARYBC_HPP_
@@ -105,7 +105,6 @@ namespace zd_model {
  * * `5` Pim
  * * `6` Pv
  *
- * @tparam T Scalar type (e.g. `float`, `double`)
  */
 class OpenLoopCoronaryBC : public Block {
  public: