{"action":"created","comment":{"url":"https://api.github.com/repos/ginkgo-project/ginkgo/pulls/comments/242635026","pull_request_review_id":186194094,"id":242635026,"node_id":"MDI0OlB1bGxSZXF1ZXN0UmV2aWV3Q29tbWVudDI0MjYzNTAyNg==","diff_hunk":"@@ -31,16 +31,16 @@ ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT\n SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.\n ******************************<GINKGO LICENSE>*******************************/\n \n-#include \"core/preconditioner/jacobi.hpp\"\n+#include <ginkgo/core/preconditioner/jacobi.hpp>\n \n \n-#include \"core/base/exception_helpers.hpp\"\n-#include \"core/base/executor.hpp\"\n+#include <ginkgo/core/base/exception_helpers.hpp>\n+#include <ginkgo/core/base/executor.hpp>\n+#include <ginkgo/core/base/math.hpp>\n+#include <ginkgo/core/base/utils.hpp>\n+#include <ginkgo/core/matrix/csr.hpp>\n+#include <ginkgo/core/matrix/dense.hpp>\n #include \"core/base/extended_float.hpp\"","path":"core/preconditioner/jacobi.cpp","position":16,"original_position":16,"commit_id":"d86f569c95cdb859c61647aa2b89effbedca7e82","original_commit_id":"09c789aaeecf7e02112a327adf7d24fa097a937c","user":{"login":"gflegar","id":1261711,"node_id":"MDQ6VXNlcjEyNjE3MTE=","avatar_url":"https://avatars1.githubusercontent.com/u/1261711?v=4","gravatar_id":"","url":"https://api.github.com/users/gflegar","html_url":"https://github.com/gflegar","followers_url":"https://api.github.com/users/gflegar/followers","following_url":"https://api.github.com/users/gflegar/following{/other_user}","gists_url":"https://api.github.com/users/gflegar/gists{/gist_id}","starred_url":"https://api.github.com/users/gflegar/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gflegar/subscriptions","organizations_url":"https://api.github.com/users/gflegar/orgs","repos_url":"https://api.github.com/users/gflegar/repos","events_url":"https://api.github.com/users/gflegar/events{/privacy}","received_events_url":"https://api.github.com/users/gflegar/received_events","type":"User","site_admin":false},"body":"It's because perl reads line-by-line by default, so even though you regex matches multiple lines, it never gets multiple lines, see also: https://stackoverflow.com/a/9671078/9385966\r\n\r\nThis should do the trick:\r\n\r\n```sh\r\nperl -0777 -i -pe 's/(#include <.*)\\n(#include \")/\\1\\n\\n\\n\\2/g'\r\n```","created_at":"2018-12-18T17:37:19Z","updated_at":"2018-12-18T17:37:20Z","html_url":"https://github.com/ginkgo-project/ginkgo/pull/183#discussion_r242635026","pull_request_url":"https://api.github.com/repos/ginkgo-project/ginkgo/pulls/183","author_association":"MEMBER","_links":{"self":{"href":"https://api.github.com/repos/ginkgo-project/ginkgo/pulls/comments/242635026"},"html":{"href":"https://github.com/ginkgo-project/ginkgo/pull/183#discussion_r242635026"},"pull_request":{"href":"https://api.github.com/repos/ginkgo-project/ginkgo/pulls/183"}},"in_reply_to_id":242522702},"pull_request":{"url":"https://api.github.com/repos/ginkgo-project/ginkgo/pulls/183","id":238495960,"node_id":"MDExOlB1bGxSZXF1ZXN0MjM4NDk1OTYw","html_url":"https://github.com/ginkgo-project/ginkgo/pull/183","diff_url":"https://github.com/ginkgo-project/ginkgo/pull/183.diff","patch_url":"https://github.com/ginkgo-project/ginkgo/pull/183.patch","issue_url":"https://api.github.com/repos/ginkgo-project/ginkgo/issues/183","number":183,"state":"open","locked":false,"title":"Install include files to correct locations","user":{"login":"thoasm","id":17714526,"node_id":"MDQ6VXNlcjE3NzE0NTI2","avatar_url":"https://avatars0.githubusercontent.com/u/17714526?v=4","gravatar_id":"","url":"https://api.github.com/users/thoasm","html_url":"https://github.com/thoasm","followers_url":"https://api.github.com/users/thoasm/followers","following_url":"https://api.github.com/users/thoasm/following{/other_user}","gists_url":"https://api.github.com/users/thoasm/gists{/gist_id}","starred_url":"https://api.github.com/users/thoasm/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/thoasm/subscriptions","organizations_url":"https://api.github.com/users/thoasm/orgs","repos_url":"https://api.github.com/users/thoasm/repos","events_url":"https://api.github.com/users/thoasm/events{/privacy}","received_events_url":"https://api.github.com/users/thoasm/received_events","type":"User","site_admin":false},"body":"PR for the issue #176: Preventing name clashes with other libraries by installing __public__ header to `${CMAKE_INSTALL_PREFIX}/include/ginkgo/`. \r\nFor that, a separation is introduced between __public__ header, which are intended for other users, and __private__ header, which are for internal purposes and not designed to be visible to users.\r\n\r\nPublic headers are now stored in `<ginkgo_project_directory>/include/ginkgo/` (and installed to the previously mentioned `${CMAKE_INSTALL_PREFIX}/include/ginkgo/` by `make install`), while the private header / files remain at `<ginkgo_project_directory>/{core,cuda,reference,omp}`.\r\n\r\nA file is currently chosen to be a public header when all the following criteria are met:\r\n1. It is/was inside `core/`\r\n2. The file ends with `.hpp`\r\n3. It is __NOT__ inside `core/synthesizer`\r\n4. It is __NOT__ inside `core/test`\r\n5. It does __NOT__ end with `_kernels.hpp`\r\n6. It is __NEITHER__ of the following header:\r\n    - `core/base/extended_float.hpp`\r\n    - `core/preconditioner/jacobi_utils.hpp`\r\n\r\n## How to install\r\nIt is recommended to set `CMAKE_INSTALL_PREFIX` while performing cmake in order to install it at a location of your choice. If it is not set, I would assume the global one is used on most systems: `/usr/local/`, which requires root access.\r\nTo prevent that, `CMAKE_INSTALL_PREFIX` can be set with `-DCMAKE_INSTALL_PREFIX=<Path_to_install_ginkgo>` while performing `cmake`. Here is an example:\r\n```bash\r\ncmake -G \"Unix Makefiles\" -DCMAKE_BUILD_TYPE=Release \\\r\n-DDEVEL_TOOLS=ON -DBUILD_TESTS=ON -DBUILD_REFERENCE=ON -DBUILD_OMP=ON -DBUILD_CUDA=OFF \\\r\n-DCMAKE_INSTALL_PREFIX=\"<Path_to_install_ginkgo>\" ..\r\n```\r\nAfter that, `make install` can be run directly or after `make` (if it was not build before, `-j 10` or more should be specified, otherwise it takes a long time).\r\n\r\n## Using installed Ginkgo\r\nThe easiest way is to use `find_package` from CMake in the new project. The core components are: \r\n```cmake\r\nfind_package(Ginkgo REQUIRED)\r\n# ...\r\nadd_executable(<binary_name> <List_of_Source_files>)\r\ntarget_link_libraries(<binary_name> PRIVATE Ginkgo::ginkgo)\r\n```\r\nIf a custom installation path was set, it needs to be forwarded to cmake. That can be done with `CMAKE_PREFIX_PATH` (Can contain multiple paths, separated with `:` on Unix and `;` on Windows) while running `cmake`, for example:\r\n```bash\r\ncmake -DCMAKE_PREFIX_PATH=<Previously_Set_Install_Directory> ..\r\n```\r\nAlternatively, it can also be specified in the CMakeFile. `find_package` can take the installation path directly with `find_package(Ginkgo REQUIRED PATHS <Previously_Set_Install_Directory>)`.\r\nIf it is set inside the CMakeFile, there is no need to set the `CMAKE_PREFIX_PATH` variable.\r\n\r\nHere an example of the `CMakeFileLists.txt` using the second approach with the example code `3pt_stencil` from the ginkgo examples:\r\n```cmake\r\n# Example CMake file for 3pt_stencil\r\ncmake_minimum_required(VERSION 3.0)\r\n\r\nfind_package(Ginkgo REQUIRED\r\n            PATHS <Previously_Set_Install_Directory> # Needs to be set to the actual location\r\n            )\r\n\r\nadd_executable(3pt_stencil 3pt_stencil.cpp)\r\ntarget_link_libraries(3pt_stencil PRIVATE Ginkgo::ginkgo)\r\n# We have no include files here. If needed, they can be appended after `PRIVATE`\r\ntarget_include_directories(3pt_stencil PRIVATE )\r\n```\r\n\r\nIt is also possible to use the installed Ginkgo without CMake:\r\n- Forward the include folder `CMAKE_INSTALL_PREFIX/include` to the compiler (in `gcc` with `-I<Include_Folder>` without the `<>`);\r\n- Forward the library folder `CMAKE_INSTALL_PREFIX/lib/ginkgo` (in `gcc` with -L<Library_Folder>) with the link flags `\"-lginkgo -lginkgo_omp -lginkgo_cuda -lginkgo_reference\"` when it was compiled in release mode.\r\n\r\nWhen running the binary, the library folder has to be specified when running the executable (e.g. with `LD_LIBRARY_PATH=<Library_Folder>:${LD_LIBRARY_PATH} /path/to/binary`). I guess there is an easier alternative that I am not aware of.\r\n\r\n\r\n### TODO\r\n- [x] Move the proper files to the new location `include/ginkgo/` in the project folder\r\n- [x] Change all includes to use `#include <ginkgo/core/[...]>` for the public header\r\n- [x] Remove all dependencies to private header from the public header\r\n    - [x] `core/log/stream.hpp`\r\n    - [x] `core/base/version.hpp`\r\n    - [x] `core/base/lin_op.hpp`\r\n- [x] Add `name_demangling.hpp` to the __public__ headers, so the `benchmark/preconditioner/preconditioner.cpp` can access it for example (maybe others need it too, not 100% clear at the time of writing).\r\n- [x] Make sure that __only__ the public header are installed\r\n- [x] Ensure that it builds properly\r\n- [x] Ensure it works when installed (with the CMake `find_module`)\r\n- [x] Write an install-test (after installing the project, compile a program that includes the `<ginkgo/ginkgo.h>` header and try if each public header is 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