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[Persistence_matrix] rename files to correspond to gudhi convention #1106

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Aug 9, 2024
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[Persistence_matrix] rename files to correspond to gudhi convention #1106

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241e15c
rename files to correspond to gudhi convention
hschreiber Jul 8, 2024
0652a8a
merge with upstream branch
hschreiber Aug 1, 2024
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4 changes: 2 additions & 2 deletions src/Persistence_matrix/doc/Intro_persistence_matrix.h
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Expand Up @@ -43,10 +43,10 @@ namespace persistence_matrix {
* \subsection matrixexamples Examples
*
* Here is a list of examples using the module:
* \li \gudhi_example_link{Persistence_matrix,representative_cycles_from_matrix.cpp} - A simple example on how to
* \li \gudhi_example_link{Persistence_matrix,example_representative_cycles_from_matrix.cpp} - A simple example on how to
* use the matrix to compute representative cycles.
*
* \li \gudhi_example_link{Persistence_matrix,simplex_tree_to_matrix.cpp} - A simplex example on how to build
* \li \gudhi_example_link{Persistence_matrix,example_simplex_tree_to_matrix.cpp} - A simplex example on how to build
* a the different matrices from a simplex tree.
*
* @}
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12 changes: 6 additions & 6 deletions src/Persistence_matrix/example/CMakeLists.txt
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@@ -1,8 +1,8 @@
add_executable_with_targets(Matrix_examples_representative_cycles representative_cycles_from_matrix.cpp TBB::tbb)
add_test(NAME Matrix_examples_representative_cycles COMMAND $<TARGET_FILE:Matrix_examples_representative_cycles>)
add_executable_with_targets(Persistence_matrix_example_representative_cycles_from_matrix example_representative_cycles_from_matrix.cpp TBB::tbb)
add_test(NAME Persistence_matrix_example_representative_cycles_from_matrix COMMAND $<TARGET_FILE:Persistence_matrix_example_representative_cycles_from_matrix>)

add_executable_with_targets(Matrix_examples_simplex_tree_matrix simplex_tree_to_matrix.cpp TBB::tbb)
add_test(NAME Matrix_examples_simplex_tree_matrix COMMAND $<TARGET_FILE:Matrix_examples_simplex_tree_matrix>)
add_executable_with_targets(Persistence_matrix_example_simplex_tree_to_matrix example_simplex_tree_to_matrix.cpp TBB::tbb)
add_test(NAME Persistence_matrix_example_simplex_tree_to_matrix COMMAND $<TARGET_FILE:Persistence_matrix_example_simplex_tree_to_matrix>)

add_executable_with_targets(Matrix_examples_field_operations example_field_operations.cpp TBB::tbb)
add_test(NAME Matrix_examples_field_operations COMMAND $<TARGET_FILE:Matrix_examples_field_operations>)
add_executable_with_targets(Persistence_matrix_example_field_operations example_field_operations.cpp TBB::tbb)
add_test(NAME Persistence_matrix_example_field_operations COMMAND $<TARGET_FILE:Persistence_matrix_example_field_operations>)
2 changes: 1 addition & 1 deletion ...ple/representative_cycles_from_matrix.cpp → ...ple_representative_cycles_from_matrix.cpp
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Expand Up @@ -10,7 +10,7 @@

#include <iostream>

#include <gudhi/matrix.h>
#include <gudhi/Matrix.h>
#include <gudhi/persistence_matrix_options.h>

using Gudhi::persistence_matrix::Default_options;
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2 changes: 1 addition & 1 deletion ...matrix/example/simplex_tree_to_matrix.cpp → ...xample/example_simplex_tree_to_matrix.cpp
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Expand Up @@ -10,7 +10,7 @@

#include <vector>

#include <gudhi/matrix.h>
#include <gudhi/Matrix.h>
#include <gudhi/persistence_matrix_options.h>
#include <gudhi/Simplex_tree.h>

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16 changes: 8 additions & 8 deletions ...Persistence_matrix/include/gudhi/matrix.h → ...Persistence_matrix/include/gudhi/Matrix.h
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Expand Up @@ -8,7 +8,7 @@
* - YYYY/MM Author: Description of the modification
*/

/** @file matrix.h
/** @file Matrix.h
* @author Hannah Schreiber
* @brief Contains @ref Gudhi::persistence_matrix::Matrix class.
*/
Expand All @@ -31,8 +31,8 @@

#include <gudhi/Fields/Z2_field_operators.h>

#include <gudhi/Persistence_matrix/overlay_ididx_to_matidx.h>
#include <gudhi/Persistence_matrix/overlay_posidx_to_matidx.h>
#include <gudhi/Persistence_matrix/Id_to_index_overlay.h>
#include <gudhi/Persistence_matrix/Position_to_index_overlay.h>

#include <gudhi/Persistence_matrix/matrix_dimension_holders.h>
#include <gudhi/Persistence_matrix/matrix_row_access.h>
Expand All @@ -45,11 +45,11 @@
#include <gudhi/Persistence_matrix/chain_vine_swap.h>
#include <gudhi/Persistence_matrix/chain_rep_cycles.h>

#include <gudhi/Persistence_matrix/base_matrix.h>
#include <gudhi/Persistence_matrix/base_matrix_with_column_compression.h>
#include <gudhi/Persistence_matrix/boundary_matrix.h>
#include <gudhi/Persistence_matrix/ru_matrix.h>
#include <gudhi/Persistence_matrix/chain_matrix.h>
#include <gudhi/Persistence_matrix/Base_matrix.h>
#include <gudhi/Persistence_matrix/Base_matrix_with_column_compression.h>
#include <gudhi/Persistence_matrix/Boundary_matrix.h>
#include <gudhi/Persistence_matrix/RU_matrix.h>
#include <gudhi/Persistence_matrix/Chain_matrix.h>

#include <gudhi/Persistence_matrix/allocators/cell_constructors.h>
#include <gudhi/Persistence_matrix/columns/cell_types.h>
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4 changes: 2 additions & 2 deletions ...de/gudhi/Persistence_matrix/base_matrix.h → ...de/gudhi/Persistence_matrix/Base_matrix.h
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Expand Up @@ -9,7 +9,7 @@
*/

/**
* @file base_matrix.h
* @file Base_matrix.h
* @author Hannah Schreiber
* @brief Contains the @ref Gudhi::persistence_matrix::Base_matrix class.
*/
Expand All @@ -25,7 +25,7 @@ namespace Gudhi {
namespace persistence_matrix {

/**
* @class Base_matrix base_matrix.h gudhi/Persistence_matrix/base_matrix.h
* @class Base_matrix Base_matrix.h gudhi/Persistence_matrix/Base_matrix.h
* @ingroup persistence_matrix
*
* @brief A @ref basematrix "basic matrix" structure allowing to easily manipulate and access entire columns and rows,
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6 changes: 3 additions & 3 deletions ...rix/base_matrix_with_column_compression.h → ...rix/Base_matrix_with_column_compression.h
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Expand Up @@ -9,7 +9,7 @@
*/

/**
* @file base_matrix_with_column_compression.h
* @file Base_matrix_with_column_compression.h
* @author Hannah Schreiber
* @brief Contains the @ref Gudhi::persistence_matrix::Base_matrix_with_column_compression class.
*/
Expand All @@ -30,8 +30,8 @@ namespace Gudhi {
namespace persistence_matrix {

/**
* @class Base_matrix_with_column_compression base_matrix_with_column_compression.h \
* gudhi/Persistence_matrix/base_matrix_with_column_compression.h
* @class Base_matrix_with_column_compression Base_matrix_with_column_compression.h \
* gudhi/Persistence_matrix/Base_matrix_with_column_compression.h
* @ingroup persistence_matrix
*
* @brief A @ref basematrix "base matrix" (also see @ref Base_matrix), but with column compression. That is, all
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6 changes: 3 additions & 3 deletions ...udhi/Persistence_matrix/boundary_matrix.h → ...udhi/Persistence_matrix/Boundary_matrix.h
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Expand Up @@ -9,7 +9,7 @@
*/

/**
* @file boundary_matrix.h
* @file Boundary_matrix.h
* @author Hannah Schreiber
* @brief Contains the @ref Gudhi::persistence_matrix::Boundary_matrix class.
*/
Expand All @@ -25,9 +25,9 @@
namespace Gudhi {
namespace persistence_matrix {

// TODO: factorize/inherit/compose with base matrix?
// TODO: factorize/inherit/compose with Base_matrix?
/**
* @class Boundary_matrix boundary_matrix.h gudhi/Persistence_matrix/boundary_matrix.h
* @class Boundary_matrix Boundary_matrix.h gudhi/Persistence_matrix/Boundary_matrix.h
* @ingroup persistence_matrix
*
* @brief %Matrix structure to store the ordered @ref boundarymatrix "boundary matrix" \f$ R \f$ of a filtered complex
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6 changes: 3 additions & 3 deletions ...e/gudhi/Persistence_matrix/chain_matrix.h → ...e/gudhi/Persistence_matrix/Chain_matrix.h
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Expand Up @@ -9,7 +9,7 @@
*/

/**
* @file chain_matrix.h
* @file Chain_matrix.h
* @author Hannah Schreiber
* @brief Contains the @ref Gudhi::persistence_matrix::Chain_matrix class.
*/
Expand All @@ -25,13 +25,13 @@
#include <utility> //std::swap, std::move & std::exchange
#include <algorithm> //std::sort

#include <gudhi/Persistence_matrix/overlay_ididx_to_matidx.h> //friend
#include <gudhi/Persistence_matrix/Id_to_index_overlay.h> //friend

namespace Gudhi {
namespace persistence_matrix {

/**
* @class Chain_matrix chain_matrix.h gudhi/Persistence_matrix/chain_matrix.h
* @class Chain_matrix Chain_matrix.h gudhi/Persistence_matrix/Chain_matrix.h
* @ingroup persistence_matrix
*
* @brief %Matrix structure storing a compatible base of a filtered chain complex. See @cite zigzag.
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4 changes: 2 additions & 2 deletions ...sistence_matrix/overlay_ididx_to_matidx.h → .../Persistence_matrix/Id_to_index_overlay.h
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Expand Up @@ -9,7 +9,7 @@
*/

/**
* @file overlay_ididx_to_matidx.h
* @file Id_to_index_overlay.h
* @author Hannah Schreiber
* @brief Contains the @ref Gudhi::persistence_matrix::Id_to_index_overlay class.
*/
Expand All @@ -28,7 +28,7 @@ namespace Gudhi {
namespace persistence_matrix {

/**
* @class Id_to_index_overlay overlay_ididx_to_matidx.h gudhi/Persistence_matrix/overlay_ididx_to_matidx.h
* @class Id_to_index_overlay Id_to_index_overlay.h gudhi/Persistence_matrix/Id_to_index_overlay.h
* @ingroup persistence_matrix
*
* @brief Overlay for @ref mp_matrices "non-basic matrices" replacing all input and output @ref MatIdx indices of
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4 changes: 2 additions & 2 deletions ...istence_matrix/overlay_posidx_to_matidx.h → ...stence_matrix/Position_to_index_overlay.h
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Expand Up @@ -9,7 +9,7 @@
*/

/**
* @file overlay_posidx_to_matidx.h
* @file Position_to_index_overlay.h
* @author Hannah Schreiber
* @brief Contains the @ref Gudhi::persistence_matrix::Position_to_index_overlay class.
*/
Expand All @@ -25,7 +25,7 @@ namespace Gudhi {
namespace persistence_matrix {

/**
* @class Position_to_index_overlay overlay_posidx_to_matidx.h gudhi/Persistence_matrix/overlay_posidx_to_matidx.h
* @class Position_to_index_overlay Position_to_index_overlay.h gudhi/Persistence_matrix/Position_to_index_overlay.h
* @ingroup persistence_matrix
*
* @brief Overlay for @ref chainmatrix "chain matrices" replacing all input and output @ref MatIdx indices of the
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4 changes: 2 additions & 2 deletions ...lude/gudhi/Persistence_matrix/ru_matrix.h → ...lude/gudhi/Persistence_matrix/RU_matrix.h
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Expand Up @@ -9,7 +9,7 @@
*/

/**
* @file ru_matrix.h
* @file RU_matrix.h
* @author Hannah Schreiber
* @brief Contains the @ref Gudhi::persistence_matrix::RU_matrix class.
*/
Expand All @@ -25,7 +25,7 @@ namespace Gudhi {
namespace persistence_matrix {

/**
* @class RU_matrix ru_matrix.h gudhi/Persistence_matrix/ru_matrix.h
* @class RU_matrix RU_matrix.h gudhi/Persistence_matrix/RU_matrix.h
* @ingroup persistence_matrix
*
* @brief %Matrix structure to store the ordered @ref boundarymatrix "boundary matrix" \f$ R \cdot U \f$ of a filtered
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