Merge master and resolve conflicts in azure-pipeline

GUDHI · Aug 27, 2024 · db48fe3 · db48fe3
2 parents 68ff7d8 + 9aa70a7
commit db48fe3
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diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -1,88 +1,100 @@
 jobs:
-
-  - job: 'OSx'
+  - job: "OSx"
     displayName: "Build and test OSx"
     timeoutInMinutes: 0
     cancelTimeoutInMinutes: 60
     pool:
       vmImage: macOS-latest
     variables:
-      pythonVersion: '3.9'
+      pythonVersion: "3.9"
       cmakeBuildType: Release
 
     steps:
-    # Use a specific Python version
-    - task: UsePythonVersion@0
-      displayName: Use Python $(pythonVersion)
-      inputs:
-        versionSpec: $(pythonVersion)
-        addToPath: true
-        architecture: 'x64'
+      # Use a specific Python version
+      - task: UsePythonVersion@0
+        displayName: Use Python $(pythonVersion)
+        inputs:
+          versionSpec: $(pythonVersion)
+          addToPath: true
+          architecture: "x64"
 
-    - bash: |
+      - bash: |
         git submodule update --init
         python -m pip install --user -r ext/gudhi-deploy/build-requirements.txt
         python -m pip install --user -r ext/gudhi-deploy/test-requirements.txt
         python -m pip uninstall -y pykeops
         brew update || true
         brew install ninja graphviz doxygen boost eigen gmp mpfr tbb cgal || true
-      displayName: 'Install build dependencies'
-    - bash: |
+        displayName: 'Install build dependencies'
+      - bash: |
         mkdir build
         cd build
         which python
         cmake -DCMAKE_BUILD_TYPE:STRING=$(cmakeBuildType) -GNinja -DWITH_GUDHI_EXAMPLE=ON -DWITH_GUDHI_TEST=ON -DWITH_GUDHI_UTILITIES=ON -DWITH_GUDHI_PYTHON=ON -DWITH_GUDHI_REMOTE_TEST=ON -DPython_EXECUTABLE=$(which python) ..
         ninja
         ninja doxygen
         ctest --output-on-failure
-      displayName: 'Build, test and documentation generation'
+        displayName: 'Build, test and documentation generation'
 
-  - job: 'Windows'
+  - job: "Windows"
     displayName: "Build and test Windows"
     timeoutInMinutes: 0
     cancelTimeoutInMinutes: 60
     pool:
       vmImage: windows-latest
     variables:
-      pythonVersion: '3.9'
+      pythonVersion: "3.9"
       cmakeVcpkgFlags: -DVCPKG_TARGET_TRIPLET=x64-windows -DCMAKE_TOOLCHAIN_FILE=c:\vcpkg\scripts\buildsystems\vcpkg.cmake
       cmakeFlags: -DWITH_GUDHI_EXAMPLE=ON -DWITH_GUDHI_TEST=ON -DWITH_GUDHI_UTILITIES=ON -DWITH_GUDHI_PYTHON=OFF
 
     steps:
-    # Use a specific Python version
-    - task: UsePythonVersion@0
-      displayName: Use Python $(pythonVersion)
-      inputs:
-        versionSpec: $(pythonVersion)
-        addToPath: true
-        architecture: 'x64'
+      # Use a specific Python version
+      - task: UsePythonVersion@0
+        displayName: Use Python $(pythonVersion)
+        inputs:
+          versionSpec: $(pythonVersion)
+          addToPath: true
+          architecture: "x64"
 
     - script: |
         git submodule update --init
         python -m pip install --user -r ext/gudhi-deploy/build-requirements.txt
+        IF %ERRORLEVEL% NEQ 0 EXIT 1
         python -m pip install --user -r ext/gudhi-deploy/test-requirements.txt
+        IF %ERRORLEVEL% NEQ 0 EXIT 1
         # Only vcpkg release libs for CI
         echo.set(VCPKG_BUILD_TYPE release)>> C:\vcpkg\triplets\x64-windows.cmake
         vcpkg install boost-filesystem:x64-windows boost-test:x64-windows boost-program-options:x64-windows tbb:x64-windows eigen3:x64-windows cgal:x64-windows
+        IF %ERRORLEVEL% NEQ 0 EXIT 1
         choco install -y ninja --force --force-dependencies
+        IF %ERRORLEVEL% NEQ 0 EXIT 1
       displayName: 'Install build dependencies'
     - script: |
         $ErrorActionPreference = 'Stop'
         call "C:\Program Files\Microsoft Visual Studio\2022\Enterprise\VC\Auxiliary\Build\vcvars64.bat"
         mkdir build
         cd build
         cmake -DCMAKE_BUILD_TYPE=Release -G "Ninja" -DFORCE_EIGEN_DEFAULT_DENSE_INDEX_TYPE_TO_INT=ON $(cmakeVcpkgFlags) $(cmakeFlags) ..
+        IF %ERRORLEVEL% NEQ 0 EXIT 1
         ninja
+        IF %ERRORLEVEL% NEQ 0 EXIT 1
         ctest --output-on-failure -C Release -E diff_files
+        IF %ERRORLEVEL% NEQ 0 EXIT 1
         for /f %%i in ('where python') do set PYTHON_EXE=%%i
         echo %PYTHON_EXE%
         cmake  -DWITH_GUDHI_PYTHON=ON -DWITH_GUDHI_REMOTE_TEST=ON -DPython_EXECUTABLE=%PYTHON_EXE% .
+        IF %ERRORLEVEL% NEQ 0 EXIT 1
         cd src\python
         copy "C:\vcpkg\installed\x64-windows\bin\mpfr*.dll" ".\gudhi\"
+        IF %ERRORLEVEL% NEQ 0 EXIT 1
         copy "C:\vcpkg\installed\x64-windows\bin\gmp*.dll" ".\gudhi\"
+        IF %ERRORLEVEL% NEQ 0 EXIT 1
         copy "C:\vcpkg\installed\x64-windows\bin\tbb*.dll" ".\gudhi\"
+        IF %ERRORLEVEL% NEQ 0 EXIT 1
         python setup.py build_ext --inplace
+        IF %ERRORLEVEL% NEQ 0 EXIT 1
         SET PYTHONPATH=%CD%;%PYTHONPATH%
         echo %PYTHONPATH%
         ctest --output-on-failure -C Release
+        IF %ERRORLEVEL% NEQ 0 EXIT 1
       displayName: 'Build and test'
diff --git a/src/Persistence_matrix/doc/Intro_persistence_matrix.h b/src/Persistence_matrix/doc/Intro_persistence_matrix.h
@@ -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.
  * 
  * @}

diff --git a/src/Persistence_matrix/example/CMakeLists.txt b/src/Persistence_matrix/example/CMakeLists.txt
@@ -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>)
diff --git a/...ple/representative_cycles_from_matrix.cpp → ...ple_representative_cycles_from_matrix.cpp b/...ple/representative_cycles_from_matrix.cpp → ...ple_representative_cycles_from_matrix.cpp
@@ -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;

diff --git a/...matrix/example/simplex_tree_to_matrix.cpp → ...xample/example_simplex_tree_to_matrix.cpp b/...matrix/example/simplex_tree_to_matrix.cpp → ...xample/example_simplex_tree_to_matrix.cpp
@@ -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>
 

diff --git a/...Persistence_matrix/include/gudhi/matrix.h → ...Persistence_matrix/include/gudhi/Matrix.h b/...Persistence_matrix/include/gudhi/matrix.h → ...Persistence_matrix/include/gudhi/Matrix.h
@@ -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.
  */
@@ -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>
@@ -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>

diff --git a/...de/gudhi/Persistence_matrix/base_matrix.h → ...de/gudhi/Persistence_matrix/Base_matrix.h b/...de/gudhi/Persistence_matrix/base_matrix.h → ...de/gudhi/Persistence_matrix/Base_matrix.h
@@ -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.
  */
@@ -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,

diff --git a/...rix/base_matrix_with_column_compression.h → ...rix/Base_matrix_with_column_compression.h b/...rix/base_matrix_with_column_compression.h → ...rix/Base_matrix_with_column_compression.h
@@ -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.
  */
@@ -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

diff --git a/...udhi/Persistence_matrix/boundary_matrix.h → ...udhi/Persistence_matrix/Boundary_matrix.h b/...udhi/Persistence_matrix/boundary_matrix.h → ...udhi/Persistence_matrix/Boundary_matrix.h
@@ -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.
  */
@@ -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

diff --git a/...e/gudhi/Persistence_matrix/chain_matrix.h → ...e/gudhi/Persistence_matrix/Chain_matrix.h b/...e/gudhi/Persistence_matrix/chain_matrix.h → ...e/gudhi/Persistence_matrix/Chain_matrix.h
@@ -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.
  */
@@ -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.

diff --git a/...sistence_matrix/overlay_ididx_to_matidx.h → .../Persistence_matrix/Id_to_index_overlay.h b/...sistence_matrix/overlay_ididx_to_matidx.h → .../Persistence_matrix/Id_to_index_overlay.h
@@ -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.
  */
@@ -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

diff --git a/...istence_matrix/overlay_posidx_to_matidx.h → ...stence_matrix/Position_to_index_overlay.h b/...istence_matrix/overlay_posidx_to_matidx.h → ...stence_matrix/Position_to_index_overlay.h
@@ -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.
  */
@@ -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

diff --git a/...lude/gudhi/Persistence_matrix/ru_matrix.h → ...lude/gudhi/Persistence_matrix/RU_matrix.h b/...lude/gudhi/Persistence_matrix/ru_matrix.h → ...lude/gudhi/Persistence_matrix/RU_matrix.h
@@ -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.
  */
@@ -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