start of geometry glueing tool

.gitattributes

@@ -0,0 +1,3 @@
+data/paramak_reactor.step filter=lfs diff=lfs merge=lfs -text
+data/paramak_reactor-salome_glued.brep filter=lfs diff=lfs merge=lfs -text
+data/paramak_reactor.brep filter=lfs diff=lfs merge=lfs -text

.github/workflows/main.yml

@@ -9,15 +9,16 @@ jobs:
     - name: Install system packages
       run: |
         apt-get -y update
-        apt-get -y install git g++ cmake libocct-foundation-dev libocct-data-exchange-dev
+        apt-get -y install git git-lfs g++ cmake libocct-foundation-dev libocct-data-exchange-dev
     - uses: actions/checkout@v2
       with:
+        lfs: true
         submodules: recursive
     - name: Build
       run: |
         git submodule update
-        cmake build . -B build
+        cmake build . -B build -DWERROR=ON
         cmake --build build
     - name: Test
       run: |
-        env -C build ctest
+        env -C build ctest -V

CMakeLists.txt

@@ -1,14 +1,35 @@
-cmake_minimum_required(VERSION 3.10)
+cmake_minimum_required(VERSION 3.13)
 
 project(overlap_checker LANGUAGES CXX)
 
-set(CMAKE_CXX_STANDARD 11)
+set(CMAKE_CXX_STANDARD 17)
 
 include(CheckSymbolExists)
 include(CTest)
 
+# Code Coverage Configuration
+add_library(coverage_config INTERFACE)
+
+option(CODE_COVERAGE "Enable coverage reporting" OFF)
+if(CODE_COVERAGE AND CMAKE_CXX_COMPILER_ID MATCHES "Clang")
+  # Add required flags (GCC & LLVM/Clang)
+  target_compile_options(coverage_config INTERFACE
+    -g -O0        # debug, no optimization
+    -fprofile-instr-generate -fcoverage-mapping
+    )
+  target_link_options(coverage_config INTERFACE
+    -fprofile-instr-generate -fcoverage-mapping)
+elseif(CODE_COVERAGE)
+  message(SEND_ERROR "Clang is required for coverage at the moment")
+endif()
+
+option(WERROR "Enable -Werror compile flag" OFF)
+if(WERROR)
+  add_compile_options(-Werror)
+endif()
+
 check_symbol_exists(argp_parse "argp.h" HAVE_ARGP)
-if(NOT (HAVE_ARGP))
+if(NOT HAVE_ARGP)
   message(SEND_ERROR "GNU argp is required for command line parsing")
 endif()
 

README.md

@@ -24,6 +24,15 @@ Under ArchLinux the above dependencies would be installed via:
 pacman -S cmake catch2 opencascade
 ```
 
+## Git Large File Storage (LFS)
+
+Testing this code involves a number of geometry files that aren't
+suitable for tracking directly in Git. We're using Git LFS instead to
+track these so this must be installed first, if you want to run
+regression tests.  See https://git-lfs.github.com/ for details.
+
+## Compiling
+
 Next we set up a build directory, compile the code, and run the unit
 tests via:
 
@@ -123,6 +132,9 @@ grep overlap overlaps.csv | overlap_collecter test_geometry.brep common.brep
 
 # perform imprinting
 imprint_solids test_geometry.brep imprinted.brep < overlaps.csv
+
+# merging of imprinted solids
+merge_solids imprinted.brep merged.brep
 ```
 
 # Tool descriptions
@@ -148,6 +160,9 @@ from the input file and outputs them to standard out, under the
 expectation that this is directed to a file so it can be used by other
 tools.
 
+Note that the `brep_flatten` tool might be useful if you already have
+a BREP file that you got from somewhere else.
+
 ## `overlap_checker`
 
 This tool performs pairwise comparisons between all nearby solids
@@ -180,4 +195,83 @@ uses the same tolerance options as `overlap_checker`, and hence
 vertices/edges of "touching" shapes might move due nearby shapes being
 within this tolerance.
 
+## `merge_solids`
+
+This tool glues shared parts of solids together. It works from
+verticies upto compound solid, merging any shared edges/faces as
+appropriate. This is an intermediate step in our neutronics workflow
+and aims to produce output compatible with [occ_faceter][].
+
 [pyvenv]: https://docs.python.org/3/tutorial/venv.html
+[occ_faceter]: https://github.com/makeclean/occ_faceter/
+
+
+# File formats
+
+The geometry data is stored in [BREP][brep_format] format with some constraints
+designed to simplify subsequent processing tasks. Our workflow is
+centered around [solids][occt_topological_types] and their materials.
+Each solid has a defined material, and it's important to be able to
+maintain this link during the processing steps. During import, e.g.
+`step_to_brep`, the hierchial structure is flattened to a list of
+solids, represented in OCCT and the BREP file as a COMPOUND. A CSV
+file describing material information is also written that uses the
+same ordering.
+
+Subsequent tools that modify the shapes, e.g. `imprint_solids`,
+maintain the top-level order. For example if there is an intersection
+between shapes 3 and 4, the overlapping volume will be added to the
+larger shape (e.g. shape 4). Hence, after imprinting shape 3 will be
+slightly smaller while shape 4 will now be a COMPSOLID containing two
+SOLIDS, one solid being this small intersecting volume and a copy of
+shape 4 that has been modified to remove this intersection.
+
+As a visual representation, our BREP format has a COMPOUND as the
+top-level shape with either SOLIDS or COMPSOLIDs inside. For example,
+after the above imprinting we might have:
+
+```
+ * COMPOUND
+   * SOLID
+   * SOLID
+   * SOLID
+   * SOLID
+   * COMPSOLID
+     * SOLID
+     * SOLID
+   * SOLID
+```
+
+note that numbering is zero based.
+
+[brep_format]: https://dev.opencascade.org/doc/occt-6.7.0/overview/html/occt_brep_format.html
+[occt_topological_types]: https://dev.opencascade.org/doc/overview/html/occt_user_guides__modeling_data.html#occt_modat_5_2_1
+
+
+# Coverage
+
+Currently a few commands I found useful to run:
+
+```shell
+# configure with coverage enabled
+env CXX=clang++ cmake build . -B build \
+  -DCMAKE_EXPORT_COMPILE_COMMANDS=ON -DCMAKE_BUILD_TYPE=Debug -DCODE_COVERAGE=ON
+
+cd build
+
+# run program
+./merge_solids ../data/paramak_reactor.brep out.brep
+
+# convert data into a format usable by llvm-cov
+llvm-profdata merge -o testcov.profdata default.profraw
+
+# generate html coverage report
+llvm-cov show -output-dir=report -format=html ./merge_solids -instr-profile=testcov.profdata
+```
+
+can use `LLVM_PROFILE_FILE=paramak_reactor-merge.profraw` to output
+raw profile to another file. see [cov1][1] and [cov2][2] for more
+details
+
+[cov1]: https://alastairs-place.net/blog/2016/05/20/code-coverage-from-the-command-line-with-clang/
+[cov2]: https://clang.llvm.org/docs/SourceBasedCodeCoverage.html

src/CMakeLists.txt

@@ -3,27 +3,39 @@
 link_libraries(
   TKernel
   TKBO TKBRep TKPrim
-  TKG3d TKLCAF TKMath
+  TKG2d TKG3d TKLCAF TKMath
   TKTopAlgo TKXCAF TKSTEP
-  TKXSBase TKXDESTEP TKShHealing)
+  TKXSBase TKXDESTEP TKShHealing
+  TKGeomAlgo)
 
-add_library(shared OBJECT utils.cpp geometry.cpp thread_pool.cpp)
+# supported by GCC and Clang
+add_compile_options(-Wall -Wextra -Wconversion)
 
+link_libraries(coverage_config)
 link_libraries(pthread)
 
+add_library(shared OBJECT utils.cpp geometry.cpp thread_pool.cpp)
+
 add_executable(step_to_brep step_to_brep.cpp $<TARGET_OBJECTS:shared>)
 
+add_executable(brep_flatten brep_flatten.cpp $<TARGET_OBJECTS:shared>)
+
 add_executable(overlap_checker overlap_checker.cpp $<TARGET_OBJECTS:shared>)
 
 add_executable(overlap_collecter overlap_collecter.cpp $<TARGET_OBJECTS:shared>)
 
 add_executable(imprint_solids imprint_solids.cpp $<TARGET_OBJECTS:shared>)
 
+add_executable(merge_solids merge_solids.cpp salome/geom_gluer.cpp $<TARGET_OBJECTS:shared>)
 
 if(BUILD_TESTING)
   add_executable(test_runner geometry.cpp utils.cpp thread_pool.cpp)
   target_compile_definitions(test_runner PUBLIC -DINCLUDE_TESTS)
   target_link_libraries(test_runner Catch2WithMain)
 
   add_test(NAME unit-tests COMMAND test_runner)
+
+  add_test(NAME shape-merge
+    COMMAND bash ${PROJECT_SOURCE_DIR}/tests/test_merge_solids.sh
+    WORKING_DIRECTORY ${PROJECT_BINARY_DIR})
 endif()