Merge branch 'develop' into missing_corners

.github/workflows/ci.yml

@@ -139,7 +139,7 @@ jobs:
         cd sc
         git fetch --tags
         # git checkout v2.8.5
-        git checkout -b test-branch 116a91b62d23ccb383880e662075471510ecd5c5
+        git checkout -b test-branch 64a7508885cc6a55895758023e00227a6786111f
 
     - name: Run bootstrap script
       run: ./bootstrap

.github/workflows/ci_cmake.yml

@@ -52,21 +52,9 @@ jobs:
     - name: CMake build
       run: cmake --build build --parallel
 
-    - name: CMake install (for examples)
-      run: cmake --install build
-
     - name: CMake self-tests
       run: ctest --test-dir build --preset default
 
-    - name: CMake configure examples
-      run: |
-        cmake -B example/build -S example -Dmpi=yes \
-          -DCMAKE_PREFIX_PATH:PATH=${{ runner.temp }} \
-          -DBUILD_SHARED_LIBS:BOOL=${{ matrix.shared }}
-
-    - name: CMake build examples
-      run: cmake --build example/build --parallel
-
     - name: Create package
       if: github.event.action == 'published'
       run: cpack --config build/CPackConfig.cmake
@@ -116,21 +104,9 @@ jobs:
     - name: CMake build
       run: cmake --build build --parallel
 
-    - name: CMake install (for examples)
-      run: cmake --install build
-
     - name: CMake self-tests
       run: ctest --test-dir build --preset default
 
-    - name: CMake configure examples
-      run: |
-        cmake -B example/build -S example -Dmpi=yes \
-          -DCMAKE_PREFIX_PATH:PATH=${{ runner.temp }} \
-          -DBUILD_SHARED_LIBS:BOOL=${{ matrix.shared }}
-
-    - name: CMake build examples
-      run: cmake --build example/build --parallel
-
     - name: Create package
       if: github.event.action == 'published'
       run: cpack --config build/CPackConfig.cmake
@@ -173,18 +149,9 @@ jobs:
     - name: CMake build
       run: cmake --build build --parallel
 
-    - name: CMake install (for examples)
-      run: cmake --install build
-
     - name: CMake self-tests
       run: ctest --test-dir build --preset default
 
-    - name: CMake configure examples without MPI
-      run: cmake -B example/build -S example -Dmpi:BOOL=no -DCMAKE_PREFIX_PATH:PATH=${{ runner.temp }} -DBUILD_SHARED_LIBS:BOOL=${{ matrix.shared }}
-
-    - name: CMake build examples
-      run: cmake --build example/build --parallel
-
     - name: Create package
       if: github.event.action == 'published'
       run: cpack --config build/CPackConfig.cmake

CMakeLists.txt

@@ -123,6 +123,9 @@ DESTINATION cmake)
 include(cmake/pkgconf.cmake)
 include(cmake/install.cmake)
 
+# --- build examples
+add_subdirectory(example)
+
 include(FeatureSummary)
 add_feature_info(MPI mpi "MPI features of ${PROJECT_NAME}")
 add_feature_info(OpenMP openmp "OpenMP features of ${PROJECT_NAME}")

doc/Doxyfile.in

@@ -856,7 +856,7 @@ WARN_LOGFILE           =
 # Note: If this tag is empty the current directory is searched.
 
 INPUT                  = @top_srcdir@/src \
-                         @top_srcdir@/doc/mainpage.dox
+                         @top_srcdir@/doc/doxygen
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -885,7 +885,8 @@ INPUT_ENCODING         = UTF-8
 # *.py, *.pyw, *.f90, *.f95, *.f03, *.f08, *.f18, *.f, *.for, *.vhd, *.vhdl,
 # *.ucf, *.qsf and *.ice.
 
-FILE_PATTERNS          = *.h
+FILE_PATTERNS          = *.h \
+                         *.dox
 
 # The RECURSIVE tag can be used to specify whether or not subdirectories should
 # be searched for input files as well.
@@ -934,7 +935,7 @@ EXCLUDE_SYMBOLS        = SC_EXTERN_C_BEGIN \
 # that contain example code fragments that are included (see the \include
 # command).
 
-EXAMPLE_PATH           = @top_srcdir@/example/steps
+EXAMPLE_PATH           = @top_srcdir@/example/
 
 # If the value of the EXAMPLE_PATH tag contains directories, you can use the
 # EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and
@@ -955,7 +956,7 @@ EXAMPLE_RECURSIVE      = NO
 # that contain images that are to be included in the documentation (see the
 # \image command).
 
-IMAGE_PATH             =
+IMAGE_PATH             = @top_srcdir@/doc/images
 
 # 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
@@ -2167,15 +2168,15 @@ ENABLE_PREPROCESSING   = YES
 # The default value is: NO.
 # This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
-MACRO_EXPANSION        = NO
+MACRO_EXPANSION        = YES
 
 # If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES then
 # the macro expansion is limited to the macros specified with the PREDEFINED and
 # EXPAND_AS_DEFINED tags.
 # The default value is: NO.
 # This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
-EXPAND_ONLY_PREDEF     = NO
+EXPAND_ONLY_PREDEF     = YES
 
 # If the SEARCH_INCLUDES tag is set to YES, the include files in the
 # INCLUDE_PATH will be searched if a #include is found.
@@ -2207,7 +2208,8 @@ INCLUDE_FILE_PATTERNS  =
 # recursively expanded use the := operator instead of the = operator.
 # This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
-PREDEFINED             = @PACKAGE_PREFIX@_DOXYGEN
+PREDEFINED             = @PACKAGE_PREFIX@_DOXYGEN __attribute__(x)= \
+                         P4EST_WITH_METIS
 
 # If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this
 # tag can be used to specify a list of macro names that should be expanded. The

doc/author_carlin.txt

@@ -0,0 +1 @@
+I place my contributions to p4est under the FreeBSD license. Louis Carlin ([email protected])

doc/author_heister.txt

@@ -0,0 +1 @@
+I place my contributions to p4est under the FreeBSD license. Timo Heister ([email protected])

doc/author_hirsch.txt

@@ -0,0 +1 @@
+I place my contributions to p4est under the FreeBSD license - Michael Hirsch.

doc/author_hongli.txt

@@ -0,0 +1 @@
+I place my contributions to p4est under the FreeBSD license. Hongli Lin ([email protected])

doc/author_markert.txt

@@ -0,0 +1 @@
+I place my contributions to p4est under the FreeBSD license. Johannes Markert ([email protected])

doc/doxygen/example_points.dox

@@ -0,0 +1,78 @@
+/*
+  This file is part of p4est.
+  p4est is a C library to manage a collection (a forest) of multiple
+  connected adaptive quadtrees or octrees in parallel.
+
+  Copyright (C) 2010 The University of Texas System
+  Written by Carsten Burstedde, Lucas C. Wilcox, and Tobin Isaac
+
+  p4est is free software; you can redistribute it and/or modify
+  it under the terms of the GNU General Public License as published by
+  the Free Software Foundation; either version 2 of the License, or
+  (at your option) any later version.
+
+  p4est is distributed in the hope that it will be useful,
+  but WITHOUT ANY WARRANTY; without even the implied warranty of
+  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+  GNU General Public License for more details.
+
+  You should have received a copy of the GNU General Public License
+  along with p4est; if not, write to the Free Software Foundation, Inc.,
+  51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+*/
+
+/** \page example_points Documentation for the point example program
+ *
+ * The points example refines a domain according to a given set of points.
+ */
+
+/** \example points/generate_points2.c
+ *
+ * Auxiliary program to generate a file of points in parallel.
+ * It uses the MPI I/O functionality of libsc to create one large file.
+ * The file is written to in parallel and using partitioned file access.
+ *
+ * The file contains first a binary integer \ref p4est_gloidx_t
+ * storing the global number of points and then the list of point
+ * coordinates as 3-tuples of binary type double.
+ *
+ * The usage of the program is
+ *
+ *     p4est_points_generate <configuration> <globalnumpoints> <prefix>
+ *
+ * where configuration is one of
+ *
+ *  - `unit`        The 2D unit square,
+ *  - `brick`       A 2x3 grid of squares,
+ *  - `three`       Three squares meeting at a non-planary angle,
+ *  - `moebius`     A five-square moebius strip embedded in 3D space,
+ *  - `star`        A star composed of six rhomboids,
+ *  - `periodic`    The all-periodic unit square
+ *
+ * and prefix is an output basename or filename to which we append `.pts`.
+ */
+
+/** \example points/generate_points3.c
+ *
+ * Auxiliary program to generate a file of points in parallel.
+ * It uses the MPI I/O functionality of libsc to create one large file.
+ * The file is written to in parallel and using partitioned file access.
+ *
+ * The file contains first a binary integer \ref p4est_gloidx_t
+ * storing the global number of points and then the list of point
+ * coordinates as 3-tuples of binary type double.
+ *
+ * The usage of the program is
+ *
+ *     p8est_points_generate <configuration> <globalnumpoints> <prefix>
+ *
+ * where configuration is one of
+ *
+ *  - `unit`        The unit cube,
+ *  - `brick`       An example brick connectivity using configuration
+ *                  (2,3,4) as the number of trees per direction.
+ *  - `periodic`    The unit cube with all-periodic boundary conditions.
+ *  - `rotwrap`     The unit cube with various self-periodic b.c.
+ *  - `twocubes`    Two connected cubes.
+ *  - `rotcubes`    A collection of six connected rotated cubes.
+ */