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Homological Discrete Vector Fields

Open umenohana13 opened this issue 5 months ago • 99 comments

Summary of Changes

The pull request contains the first version of:

  • user manual (still incomplete - persistant homology and Alexander duality are not documented)
  • reference manual (slightly incomplete as well - the IO classes stores in tools_io are "lightly" documented as they will be revised to integrate IOs inside CGAL)
  • code (same: the tools_io file will be revised)

Release Management

  • Affected package(s): HDVF / Surface_mesh_topology
  • Issue(s) solved (if any):
  • Feature/Small Feature (if any): https://cgalwiki.geometryfactory.com/CGAL/Members/wiki/Features/Homological_Discrete_Vector_Fields
  • License and copyright ownership: Not yet validated by my lab but most probably LGPL / LIS laboratory

umenohana13 avatar Jul 29 '25 11:07 umenohana13

/build:v0

afabri avatar Jul 29 '25 12:07 afabri

There was an error while building the doc:

/home/runner/work/cgal/cgal/build_doc/doc_tags/HDVF.tag:6815: warning: Duplicate anchor Implementation found
/home/runner/work/cgal/cgal/Documentation/doc/Documentation/packages.txt:1498: warning: image file name pkg-small.png is ambiguous.
Possible candidates:
   /home/runner/work/cgal/cgal/Documentation/doc/Documentation/fig/pkg-small.png
   /home/runner/work/cgal/cgal/HDVF/doc/HDVF/fig/pkg-small.png

/home/runner/work/cgal/cgal/Documentation/doc/Documentation/packages.txt:1509: warning: unable to resolve reference to 'PkgDEPENDENCY' for \ref command
/home/runner/work/cgal/cgal/HDVF/doc/HDVF/Concepts/SparseMatrix.h:127: warning: Found ';' while parsing initializer list! (doxygen could be confused by a macro call without semicolon)
/home/runner/work/cgal/cgal/HDVF/include/CGAL/OSM/Bitboard.h:2: warning: the name 'Bitboard.hpp' supplied as the argument in the \file statement is not an input file
/home/runner/work/cgal/cgal/HDVF/doc/HDVF/Concepts/HDVF.h:213: warning: argument 'gamma' of command @param is not found in the argument list of HDVF::find_pairs_A(int q, bool &found, size_t tau) const
/home/runner/work/cgal/cgal/HDVF/doc/HDVF/Concepts/HDVF.h:213: warning: The following parameter of HDVF::find_pairs_A(int q, bool &found, size_t tau) const is not documented:
  parameter 'tau'
/home/runner/work/cgal/cgal/HDVF/include/CGAL/HDVF/Geometric_chain_complex_tools.h:111: warning: argument 'hdvf' of command @param is not found in the argument list of CGAL::HDVF::hdvf_persistence_geometric_chain_complex_output_vtk(Hdvf_persistence< CoefType, ComplexType, DegType, FiltrationType > &per_hdvf, ComplexType &complex, string filename="per", bool co_faces=false)
/home/runner/work/cgal/cgal/HDVF/include/CGAL/HDVF/Geometric_chain_complex_tools.h:111: warning: The following parameter of CGAL::HDVF::hdvf_persistence_geometric_chain_complex_output_vtk(Hdvf_persistence< CoefType, ComplexType, DegType, FiltrationType > &per_hdvf, ComplexType &complex, string filename="per", bool co_faces=false) is not documented:
  parameter 'per_hdvf'
/home/runner/work/cgal/cgal/HDVF/include/CGAL/HDVF/Cubical_chain_complex.hpp:44: warning: found paragraph command (id: 'Description') outside of subsubsection context!
/home/runner/work/cgal/cgal/HDVF/include/CGAL/HDVF/Cubical_chain_complex.hpp:252: warning: argument 'q' of command @param is not found in the argument list of CGAL::HDVF::Cubical_chain_complex< CoefficientType >::bottom_faces(size_t id_cell, int dim) const
/home/runner/work/cgal/cgal/HDVF/include/CGAL/HDVF/Cubical_chain_complex.hpp:252: warning: The following parameter of CGAL::HDVF::Cubical_chain_complex::bottom_faces(size_t id_cell, int dim) const is not documented:
  parameter 'dim'
/home/runner/work/cgal/cgal/HDVF/include/CGAL/HDVF/Hdvf_duality.h:117: warning: argument 'gamma' of command @param is not found in the argument list of CGAL::HDVF::Hdvf_duality< CoefficientType, ComplexType >::find_pair_A(int q, bool &found, size_t tau) const
/home/runner/work/cgal/cgal/HDVF/include/CGAL/HDVF/Hdvf_duality.h:117: warning: The following parameter of CGAL::HDVF::Hdvf_duality::find_pair_A(int q, bool &found, size_t tau) const is not documented:
  parameter 'tau'
/home/runner/work/cgal/cgal/HDVF/include/CGAL/HDVF/Hdvf_duality.h:141: warning: argument 'gamma' of command @param is not found in the argument list of CGAL::HDVF::Hdvf_duality< CoefficientType, ComplexType >::find_pairs_A(int q, bool &found, size_t tau) const
/home/runner/work/cgal/cgal/HDVF/include/CGAL/HDVF/Hdvf_duality.h:141: warning: The following parameter of CGAL::HDVF::Hdvf_duality::find_pairs_A(int q, bool &found, size_t tau) const is not documented:
  parameter 'tau'
/home/runner/work/cgal/cgal/HDVF/include/CGAL/HDVF/Hdvf_persistence.h:252: warning: argument 'co_faces' of command @param is not found in the argument list of CGAL::HDVF::Hdvf_persistence< CoefficientType, ComplexType, DegType, FiltrationType >::Hdvf_persistence(const ComplexType &K, const Filtration &f, int hdvf_opt=OPT_BND, bool with_export=false)
/home/runner/work/cgal/cgal/HDVF/include/CGAL/OSM/Sparse_matrix.h:812: warning: argument 'matrix' of command @param is not found in the argument list of CGAL::OSM::cget_column(const Sparse_matrix< _CT, COLUMN > &_matrix, size_t _index)
/home/runner/work/cgal/cgal/HDVF/include/CGAL/OSM/Sparse_matrix.h:812: warning: argument 'index' of command @param is not found in the argument list of CGAL::OSM::cget_column(const Sparse_matrix< _CT, COLUMN > &_matrix, size_t _index)
/home/runner/work/cgal/cgal/HDVF/include/CGAL/OSM/Sparse_matrix.h:812: warning: The following parameters of CGAL::OSM::cget_column(const Sparse_matrix< _CT, COLUMN > &_matrix, size_t _index) are not documented:
  parameter '_matrix'
  parameter '_index'
/home/runner/work/cgal/cgal/HDVF/include/CGAL/OSM/Sparse_matrix.h:825: warning: argument 'matrix' of command @param is not found in the argument list of CGAL::OSM::cget_row(const Sparse_matrix< _CT, ROW > &_matrix, const size_t _index)
/home/runner/work/cgal/cgal/HDVF/include/CGAL/OSM/Sparse_matrix.h:825: warning: argument 'index' of command @param is not found in the argument list of CGAL::OSM::cget_row(const Sparse_matrix< _CT, ROW > &_matrix, const size_t _index)
/home/runner/work/cgal/cgal/HDVF/include/CGAL/OSM/Sparse_matrix.h:825: warning: The following parameters of CGAL::OSM::cget_row(const Sparse_matrix< _CT, ROW > &_matrix, const size_t _index) are not documented:
  parameter '_matrix'
  parameter '_index'
/home/runner/work/cgal/cgal/HDVF/include/CGAL/OSM/Sparse_chain.h:304: warning: argument 'column' of command @param is not found in the argument list of CGAL::OSM::operator%(const Sparse_chain< _CT, COLUMN > &_column, const Sparse_chain< _CT, ROW > &_row)
/home/runner/work/cgal/cgal/HDVF/include/CGAL/OSM/Sparse_chain.h:304: warning: argument 'row' of command @param is not found in the argument list of CGAL::OSM::operator%(const Sparse_chain< _CT, COLUMN > &_column, const Sparse_chain< _CT, ROW > &_row)
/home/runner/work/cgal/cgal/HDVF/include/CGAL/OSM/Sparse_chain.h:304: warning: The following parameters of CGAL::OSM::operator%%(const Sparse_chain< _CT, COLUMN > &_column, const Sparse_chain< _CT, ROW > &_row) are not documented:
  parameter '_column'
  parameter '_row'
/home/runner/work/cgal/cgal/HDVF/include/CGAL/OSM/Sparse_chain.h:287: warning: argument 'column' of command @param is not found in the argument list of CGAL::OSM::operator*(const Sparse_chain< _CT, COLUMN > &_column, const Sparse_chain< _CT, ROW > &_row)
/home/runner/work/cgal/cgal/HDVF/include/CGAL/OSM/Sparse_chain.h:287: warning: argument 'row' of command @param is not found in the argument list of CGAL::OSM::operator*(const Sparse_chain< _CT, COLUMN > &_column, const Sparse_chain< _CT, ROW > &_row)
/home/runner/work/cgal/cgal/HDVF/include/CGAL/OSM/Sparse_chain.h:287: warning: The following parameters of CGAL::OSM::operator*(const Sparse_chain< _CT, COLUMN > &_column, const Sparse_chain< _CT, ROW > &_row) are not documented:
  parameter '_column'
  parameter '_row'
/home/runner/work/cgal/cgal/HDVF/include/CGAL/OSM/Sparse_chain.h:490: warning: The following parameter of CGAL::OSM::operator/(const Sparse_chain< _CT, _CTF > &_chain, const std::vector< size_t > &_indexes) is not documented:
  parameter '_chain'
/home/runner/work/cgal/cgal/HDVF/include/CGAL/OSM/Sparse_chain.h:505: warning: The following parameter of CGAL::OSM::operator/(const Sparse_chain< _CT, _CTF > &_chain, size_t _index) is not documented:
  parameter '_chain'
/home/runner/work/cgal/cgal/HDVF/include/CGAL/OSM/Bitboard.h:379: warning: argument '_bitboards' of command @param is not found in the argument list of CGAL::OSM::Bitboard::Bitboard(const std::vector< std::uint64_t > &_bitboard)
/home/runner/work/cgal/cgal/HDVF/include/CGAL/OSM/Bitboard.h:379: warning: The following parameter of CGAL::OSM::Bitboard::Bitboard(const std::vector< std::uint64_t > &_bitboard) is not documented:
  parameter '_bitboard'
/home/runner/work/cgal/cgal/HDVF/include/CGAL/OSM/Bitboard.h:393: warning: The following parameter of CGAL::OSM::Bitboard::Bitboard(const std::size_t _size, bool empty=true) is not documented:
  parameter 'empty'
/home/runner/work/cgal/cgal/HDVF/include/CGAL/OSM/Bitboard.h:407: warning: argument '_bitboards' of command @param is not found in the argument list of CGAL::OSM::Bitboard::Bitboard(const Bitboard &_bitboard)
/home/runner/work/cgal/cgal/HDVF/include/CGAL/OSM/Bitboard.h:407: warning: The following parameter of CGAL::OSM::Bitboard::Bitboard(const Bitboard &_bitboard) is not documented:
  parameter '_bitboard'
/home/runner/work/cgal/cgal/HDVF/include/CGAL/OSM/Sparse_chain.h:732: warning: argument '_indexes' of command @param is not found in the argument list of CGAL::OSM::Sparse_chain< CoefficientType, ChainTypeFlag >::operator/(const Sparse_chain< _CT, _CTF > &chain, const std::vector< size_t > &indices)
/home/runner/work/cgal/cgal/HDVF/include/CGAL/OSM/Sparse_chain.h:757: warning: argument '_index' of command @param is not found in the argument list of CGAL::OSM::Sparse_chain< CoefficientType, ChainTypeFlag >::operator/(const Sparse_chain< _CT, _CTF > &chain, size_t index)
/home/runner/work/cgal/cgal/HDVF/include/CGAL/HDVF/Sub_sparse_matrix.h:84: warning: argument 'rowCount' of command @param is not found in the argument list of CGAL::OSM::Sub_sparse_matrix< CoefficientType, ChainTypeFlag >::Sub_sparse_matrix(const Sub_sparse_matrix &otherToCopy)
/home/runner/work/cgal/cgal/HDVF/include/CGAL/HDVF/Sub_sparse_matrix.h:84: warning: argument 'columnCount' of command @param is not found in the argument list of CGAL::OSM::Sub_sparse_matrix< CoefficientType, ChainTypeFlag >::Sub_sparse_matrix(const Sub_sparse_matrix &otherToCopy)
/home/runner/work/cgal/cgal/HDVF/include/CGAL/HDVF/Sub_sparse_matrix.h:84: warning: argument 'subChain' of command @param is not found in the argument list of CGAL::OSM::Sub_sparse_matrix< CoefficientType, ChainTypeFlag >::Sub_sparse_matrix(const Sub_sparse_matrix &otherToCopy)
/home/runner/work/cgal/cgal/HDVF/include/CGAL/HDVF/Sub_sparse_matrix.h:84: warning: The following parameter of CGAL::OSM::Sub_sparse_matrix::Sub_sparse_matrix(const Sub_sparse_matrix &otherToCopy) is not documented:
  parameter 'otherToCopy'
/home/runner/work/cgal/cgal/HDVF/doc/HDVF/HDVF.txt:93: warning: unable to resolve reference to 'fig__HDVFchain_complexes:' for \ref command
/home/runner/work/cgal/cgal/HDVF/doc/HDVF/HDVF.txt:113: warning: unable to resolve reference to 'fig__HDVFcubical_complex:' for \ref command
/home/runner/work/cgal/cgal/HDVF/doc/HDVF/HDVF.txt:123: warning: unable to resolve reference to 'fig__HDVFchain_complexes:' for \ref command
/home/runner/work/cgal/cgal/HDVF/doc/HDVF/HDVF.txt:217: warning: expected whitespace after \ref command
/home/runner/work/cgal/cgal/HDVF/doc/HDVF/HDVF.txt:680: warning: expected whitespace after \ref command
/home/runner/work/cgal/cgal/HDVF/doc/HDVF/HDVF.txt:694: warning: expected whitespace after \ref command
/home/runner/work/cgal/cgal/HDVF/doc/HDVF/HDVF.txt:714: warning: unable to resolve reference to 'example_hdvf_simplicial.cpp' for \ref command
/home/runner/work/cgal/cgal/HDVF/doc/HDVF/HDVF.txt:715: warning: unable to resolve reference to 'example_hdvf_cubical.cpp' for \ref command
/home/runner/work/cgal/cgal/HDVF/doc/HDVF/HDVF.txt:730: warning: unable to resolve reference to 'example_matrix_chain.cpp' for \ref command
/home/runner/work/cgal/cgal/HDVF/doc/HDVF/HDVF.txt:757: warning: unable to resolve reference to '\include' for \ref command
/home/runner/work/cgal/cgal/HDVF/doc/HDVF/HDVF.txt:757: warning: expected whitespace after \include command
/home/runner/work/cgal/cgal/HDVF/doc/HDVF/HDVF.txt:759: warning: image file bench.png is not found in IMAGE_PATH: assuming external image.
/home/runner/work/cgal/cgal/HDVF/doc/HDVF/HDVF.txt:759: warning: image file bench.png is not found in IMAGE_PATH: assuming external image.

https://github.com/CGAL/cgal/actions/runs/16595899805

github-actions[bot] avatar Jul 29 '25 12:07 github-actions[bot]

/force-build:v0

afabri avatar Aug 01 '25 08:08 afabri

There was an error while building the doc:

/home/runner/work/cgal/cgal/build_doc/doc_tags/HDVF.tag:6856: warning: Duplicate anchor Implementation found
/home/runner/work/cgal/cgal/Documentation/doc/Documentation/packages.txt:1498: warning: image file name pkg-small.png is ambiguous.
Possible candidates:
   /home/runner/work/cgal/cgal/Documentation/doc/Documentation/fig/pkg-small.png
   /home/runner/work/cgal/cgal/HDVF/doc/HDVF/fig/pkg-small.png

/home/runner/work/cgal/cgal/Documentation/doc/Documentation/packages.txt:1509: warning: unable to resolve reference to 'PkgDEPENDENCY' for \ref command

https://github.com/CGAL/cgal/actions/runs/16670414309

github-actions[bot] avatar Aug 01 '25 08:08 github-actions[bot]

/force-build:v0

afabri avatar Aug 01 '25 09:08 afabri

The documentation is built. It will be available, after a few minutes, here: https://cgal.github.io/9004/v0/Manual/index.html

github-actions[bot] avatar Aug 01 '25 10:08 github-actions[bot]

/force-build:v0

afabri avatar Aug 01 '25 10:08 afabri

The documentation is built. It will be available, after a few minutes, here: https://cgal.github.io/9004/v0/Manual/index.html

github-actions[bot] avatar Aug 01 '25 11:08 github-actions[bot]

/force-build:v0

afabri avatar Aug 01 '25 12:08 afabri

The documentation is built. It will be available, after a few minutes, here: https://cgal.github.io/9004/v0/Manual/index.html

github-actions[bot] avatar Aug 01 '25 12:08 github-actions[bot]

/force-build:v0

afabri avatar Aug 04 '25 09:08 afabri

The documentation is built. It will be available, after a few minutes, here: https://cgal.github.io/9004/v0/Manual/index.html

github-actions[bot] avatar Aug 04 '25 09:08 github-actions[bot]

@umenohana13 I started fixing errors showing up in the CI, but there are too many to make. It is now headers compiled in isolation which do not #include all they use. And missing std:: before cout etc.

afabri avatar Aug 04 '25 16:08 afabri

/force-build:v0

afabri avatar Aug 06 '25 08:08 afabri

The documentation is built. It will be available, after a few minutes, here: https://cgal.github.io/9004/v0/Manual/index.html

github-actions[bot] avatar Aug 06 '25 08:08 github-actions[bot]

/build:v1

afabri avatar Aug 07 '25 12:08 afabri

The documentation is built. It will be available, after a few minutes, here: https://cgal.github.io/9004/v1/Manual/index.html

github-actions[bot] avatar Aug 07 '25 12:08 github-actions[bot]

/force-build:v1

afabri avatar Aug 07 '25 21:08 afabri

The documentation is built. It will be available, after a few minutes, here: https://cgal.github.io/9004/v1/Manual/index.html

github-actions[bot] avatar Aug 07 '25 21:08 github-actions[bot]

/force-build:v1

afabri avatar Aug 11 '25 06:08 afabri

The documentation is built. It will be available, after a few minutes, here: https://cgal.github.io/9004/v1/Manual/index.html

github-actions[bot] avatar Aug 11 '25 06:08 github-actions[bot]

/force-build:v1

afabri avatar Aug 18 '25 07:08 afabri

The documentation is built. It will be available, after a few minutes, here: https://cgal.github.io/9004/v1/Manual/index.html

github-actions[bot] avatar Aug 18 '25 07:08 github-actions[bot]

/force-build:v1

afabri avatar Aug 21 '25 05:08 afabri

The documentation is built. It will be available, after a few minutes, here: https://cgal.github.io/9004/v1/Manual/index.html

github-actions[bot] avatar Aug 21 '25 05:08 github-actions[bot]

/force-build:v1

afabri avatar Aug 25 '25 05:08 afabri

There was an error while building the doc:

https://github.com/CGAL/cgal/actions/runs/17200484887

github-actions[bot] avatar Aug 25 '25 06:08 github-actions[bot]

@afabri Looks like the documentation didn't succeed as https://cgal.geometryfactory.com could not be reached, looks like the machine / connection is down.

albert-github avatar Aug 25 '25 12:08 albert-github

/force-build:v1

afabri avatar Aug 28 '25 18:08 afabri

The documentation is built. It will be available, after a few minutes, here: https://cgal.github.io/9004/v1/Manual/index.html

github-actions[bot] avatar Aug 28 '25 18:08 github-actions[bot]