Merge improved bot and formatting

This PR runs the formatting scripts on all files, fixes a few config issues for formatting and
deletes old bot comments before adding new ones.

Related PR: #674

.github/bot-pr-base.sh

@@ -41,6 +41,14 @@ HEAD_URL="https://${GITHUB_ACTOR}:${GITHUB_TOKEN}@github.com/$HEAD_REPO"
 
 JOB_URL="https://github.com/$GITHUB_REPOSITORY/actions/runs/$GITHUB_RUN_ID"
 
+bot_delete_comments_matching() {
+  local search_matching="$1"
+  COMMENTS=$(api_get "$ISSUE_URL/comments" | jq -r '.[] | select((.user.login == "ginkgo-bot") and (.body | startswith('"\"$search_matching\""'))) | .url')
+  for URL in $COMMENTS; do
+    api_delete "$URL" > /dev/null
+  done
+}
+
 bot_comment() {
   api_post "$ISSUE_URL/comments" "{\"body\":\"$1\"}" > /dev/null
 }

.github/check-format.sh

@@ -9,11 +9,11 @@ LIST_FILES=$(git diff --name-only | sed '$!s/$/\\n/' | tr -d '\n')
 git diff > /tmp/format.patch
 mv /tmp/format.patch .
 
+bot_delete_comments_matching "Error: The following files need to be formatted"
+
 if [[ "$LIST_FILES" != "" ]]; then
   MESSAGE="The following files need to be formatted:\n"'```'"\n$LIST_FILES\n"'```'
   MESSAGE="$MESSAGE\nYou can find a formatting patch under **Artifacts** [here]"
   MESSAGE="$MESSAGE($JOB_URL) or run "'`format!` if you have write access to Ginkgo'
   bot_error "$MESSAGE"
-else
-  bot_comment "No formatting necessary"
 fi

.github/format.sh

@@ -12,6 +12,4 @@ if [[ "$LIST_FILES" != "" ]]; then
 
 Co-authored-by: $USER_COMBINED"
   git push fork $LOCAL_BRANCH:$HEAD_BRANCH 2>&1 || bot_error "Cannot push formatted branch, are edits for maintainers allowed?"
-else
-  bot_comment "No formatting necessary"
 fi

.github/rebase.sh

@@ -14,6 +14,8 @@ git config user.name "$USER_NAME"
 LOCAL_BRANCH=rebase-tmp-$HEAD_BRANCH
 git checkout -b $LOCAL_BRANCH fork/$HEAD_BRANCH
 
+bot_delete_comments_matching "Error: Rebase failed"
+
 # do the rebase
 git rebase base/$BASE_BRANCH 2>&1 || bot_error "Rebase failed, see the related [Action]($JOB_URL) for details"
 

.github/workflows/bot-pr-comment.yml

@@ -14,7 +14,7 @@ jobs:
         fetch-depth: 0
     - name: Add appropriate labels
       env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        GITHUB_TOKEN: ${{ secrets.BOT_TOKEN }}
       run: cp .github/label.sh /tmp && /tmp/label.sh
   check_format:
     name: check-format
@@ -28,7 +28,7 @@ jobs:
         fetch-depth: 0
     - name: Check for formatting changes
       env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        GITHUB_TOKEN: ${{ secrets.BOT_TOKEN }}
       run: cp .github/check-format.sh /tmp && /tmp/check-format.sh
     - name: Upload code formatting patch
       if: failure()
@@ -48,7 +48,7 @@ jobs:
         fetch-depth: 0
     - name: Commit formatting changes
       env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        GITHUB_TOKEN: ${{ secrets.BOT_TOKEN }}
       run: cp .github/format.sh /tmp && /tmp/format.sh
   rebase:
     name: rebase
@@ -62,5 +62,5 @@ jobs:
         fetch-depth: 0
     - name: Automatic Rebase
       env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        GITHUB_TOKEN: ${{ secrets.BOT_TOKEN }}
       run: cp .github/rebase.sh /tmp && /tmp/rebase.sh

.github/workflows/bot-pr-created.yml

@@ -15,5 +15,5 @@ jobs:
           fetch-depth: 0
       - name: Add appropriate labels
         env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_TOKEN: ${{ secrets.BOT_TOKEN }}
         run: .github/label.sh

.github/workflows/bot-pr-updated.yml

@@ -15,7 +15,7 @@ jobs:
           fetch-depth: 0
       - name: Check for formatting changes
         env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_TOKEN: ${{ secrets.BOT_TOKEN }}
         run: cp .github/check-format.sh /tmp && /tmp/check-format.sh
       - name: Upload code formatting patch
         if: failure()

benchmark/solver/solver.cpp

@@ -48,7 +48,6 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #include "benchmark/utils/loggers.hpp"
 #include "benchmark/utils/overhead_linop.hpp"
 #include "benchmark/utils/preconditioners.hpp"
-#include "ginkgo/core/preconditioner/isai.hpp"
 
 
 // some Ginkgo shortcuts

benchmark/utils/preconditioners.hpp

@@ -30,7 +30,6 @@ THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 ******************************<GINKGO LICENSE>*******************************/
 
-
 #ifndef GKO_BENCHMARK_UTILS_PRECONDITIONERS_HPP_
 #define GKO_BENCHMARK_UTILS_PRECONDITIONERS_HPP_
 

core/base/allocator.hpp

@@ -172,4 +172,4 @@ using unordered_map =
 
 }  // namespace gko
 
-#endif  // GKO_CORE_BASE_ALLOCATOR_HPP_
+#endif  // GKO_CORE_BASE_ALLOCATOR_HPP_

core/base/utils.hpp

@@ -30,8 +30,11 @@ THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 ******************************<GINKGO LICENSE>*******************************/
 
-#ifndef GKO_INTERNAL_CORE_BASE_UTILS_HPP_
-#define GKO_INTERNAL_CORE_BASE_UTILS_HPP_
+#ifndef GKO_CORE_BASE_UTILS_HPP_
+#define GKO_CORE_BASE_UTILS_HPP_
+
+
+#include <ginkgo/core/base/utils.hpp>
 
 
 #include <memory>
@@ -40,7 +43,6 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 #include <ginkgo/core/base/polymorphic_object.hpp>
 #include <ginkgo/core/base/types.hpp>
-#include <ginkgo/core/base/utils.hpp>
 #include <ginkgo/core/matrix/csr.hpp>
 
 
@@ -64,8 +66,7 @@ namespace detail {
 
 
 template <typename Dest>
-struct conversion_sort_helper {
-};
+struct conversion_sort_helper {};
 
 template <typename ValueType, typename IndexType>
 struct conversion_sort_helper<matrix::Csr<ValueType, IndexType>> {
@@ -222,4 +223,4 @@ std::shared_ptr<const Dest> convert_to_with_sorting(
 }  // namespace gko
 
 
-#endif  // GKO_INTERNAL_CORE_BASE_UTILS_HPP_
+#endif  // GKO_CORE_BASE_UTILS_HPP_

core/device_hooks/dpcpp_hooks.cpp

@@ -30,7 +30,6 @@ THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 ******************************<GINKGO LICENSE>*******************************/
 
-
 #include <memory>
 #include <string>
 

core/preconditioner/isai_kernels.hpp

@@ -34,10 +34,12 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #define GKO_CORE_PRECONDITIONER_ISAI_KERNELS_HPP_
 
 
-#include <ginkgo/core/matrix/csr.hpp>
 #include <ginkgo/core/preconditioner/isai.hpp>
 
 
+#include <ginkgo/core/matrix/csr.hpp>
+
+
 namespace gko {
 namespace kernels {
 

core/test/utils/unsort_matrix.hpp

@@ -33,6 +33,7 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #ifndef GKO_CORE_TEST_UTILS_UNSORT_MATRIX_HPP_
 #define GKO_CORE_TEST_UTILS_UNSORT_MATRIX_HPP_
 
+
 #include <algorithm>
 #include <random>
 

cuda/base/types.hpp

@@ -34,6 +34,9 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #define GKO_CUDA_BASE_TYPES_HPP_
 
 
+#include <ginkgo/core/base/types.hpp>
+
+
 #include <type_traits>
 
 
@@ -43,9 +46,6 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #include <thrust/complex.h>
 
 
-#include <ginkgo/core/base/types.hpp>
-
-
 namespace gko {
 
 

cuda/factorization/factorization_kernels.cu

@@ -35,6 +35,7 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 #include <ginkgo/core/base/array.hpp>
 
+
 #include "core/components/prefix_sum.hpp"
 #include "core/matrix/csr_builder.hpp"
 #include "cuda/base/config.hpp"

cuda/factorization/par_ilut_approx_filter_kernel.cu

@@ -44,7 +44,6 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 
 #include "core/components/prefix_sum.hpp"
-#include "core/factorization/par_ilut_kernels.hpp"
 #include "core/matrix/coo_builder.hpp"
 #include "core/matrix/csr_builder.hpp"
 #include "core/matrix/csr_kernels.hpp"

cuda/factorization/par_ilut_filter_kernel.cu

@@ -159,4 +159,4 @@ GKO_INSTANTIATE_FOR_EACH_VALUE_AND_INDEX_TYPE(
 }  // namespace par_ilut_factorization
 }  // namespace cuda
 }  // namespace kernels
-}  // namespace gko
+}  // namespace gko

cuda/solver/idr_kernels.cu

@@ -33,8 +33,8 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #include "core/solver/idr_kernels.hpp"
 
 
-#include <time.h>
 #include <random>
+#include <time.h>
 
 
 #include <ginkgo/core/base/exception_helpers.hpp>

cuda/test/reorder/rcm_kernels.cpp

@@ -30,7 +30,6 @@ THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 ******************************<GINKGO LICENSE>*******************************/
 
-
 #include <ginkgo/core/reorder/rcm.hpp>
 
 

dev_tools/scripts/config

@@ -6,10 +6,26 @@
     - FixInclude: "hip/hip_runtime.h"
 - "(cuda|hip|omp|dpcpp)/test/factorization/par_ilu_kernels"
     - FixInclude: "core/factorization/par_ilu_kernels.hpp"
+- "(cuda|hip|omp|dpcpp)/test/factorization/par_ilut_kernels"
+    - FixInclude: "core/factorization/par_ilut_kernels.hpp"
+- "(cuda|hip|omp|dpcpp)/test/factorization/par_ict_kernels"
+    - FixInclude: "core/factorization/par_ict_kernels.hpp"
+- "cuda/factorization/par_ilut_select_common"
+    - FixInclude: "cuda/factorization/par_ilut_select_common.cuh"
+- "hip/factorization/par_ilut_select_common"
+    - FixInclude: "hip/factorization/par_ilut_select_common.hip.hpp"
+- "(cuda|hip|dpcpp)/factorization/par_ilut_"
+    - FixInclude: "core/factorization/par_ilut_kernels.hpp"
+- "(cuda|hip|dpcpp)/factorization/par_ict_"
+    - FixInclude: "core/factorization/par_ict_kernels.hpp"
 - "(cuda|hip|dpcpp)/preconditioner/jacobi_"
     - FixInclude: "core/preconditioner/jacobi_kernels.hpp"
 - "core/test/base/(extended_float|iterator_factory)"
     - RemoveTest: "true"
+- "core/test/base/allocator"
+    - FixInclude: "core/base/allocator.hpp"
+- "reference/test/base/utils"
+    - FixInclude: "core/base/utils.hpp"
 - "_builder\.cpp"
     - RemoveTest: "true"
 - "_builder\.hpp"

dev_tools/scripts/regroup

@@ -2,7 +2,7 @@ IncludeBlocks: Regroup
 IncludeCategories:
   - Regex: '^<(rapidjson|gflags|gtest|papi).*'
     Priority: 3
-  - Regex: '^<(omp|cu|hip|thrust|CL).*'
+  - Regex: '^<(omp|cu|hip|thrust|CL/|cooperative).*'
     Priority: 2
   - Regex: '^<ginkgo.*'
     Priority: 5

examples/ginkgo-overhead/ginkgo-overhead.cpp

@@ -38,7 +38,8 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #include <iostream>
 
 
-[[noreturn]] void print_usage_and_exit(const char *name) {
+[[noreturn]] void print_usage_and_exit(const char *name)
+{
     std::cerr << "Usage: " << name << " [NUM_ITERS]" << std::endl;
     std::exit(-1);
 }

hip/base/types.hip.hpp

@@ -34,10 +34,10 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #define GKO_HIP_BASE_TYPES_HIP_HPP_
 
 
-#include <type_traits>
+#include <ginkgo/core/base/types.hpp>
 
 
-#include <ginkgo/core/base/types.hpp>
+#include <type_traits>
 
 
 #include <hip/hip_complex.h>

hip/factorization/par_ilut_approx_filter_kernel.hip.cpp

@@ -33,10 +33,10 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #include "core/factorization/par_ilut_kernels.hpp"
 
 
-#include <hip/hip_runtime.h>
+#include <algorithm>
 
 
-#include <algorithm>
+#include <hip/hip_runtime.h>
 
 
 #include <ginkgo/core/base/array.hpp>
@@ -47,7 +47,6 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 
 #include "core/components/prefix_sum.hpp"
-#include "core/factorization/par_ilut_kernels.hpp"
 #include "core/matrix/coo_builder.hpp"
 #include "core/matrix/csr_builder.hpp"
 #include "core/matrix/csr_kernels.hpp"

hip/factorization/par_ilut_filter_kernel.hip.cpp

@@ -163,4 +163,4 @@ GKO_INSTANTIATE_FOR_EACH_VALUE_AND_INDEX_TYPE(
 }  // namespace par_ilut_factorization
 }  // namespace hip
 }  // namespace kernels
-}  // namespace gko
+}  // namespace gko

hip/factorization/par_ilut_select_kernel.hip.cpp

@@ -33,10 +33,10 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #include "core/factorization/par_ilut_kernels.hpp"
 
 
-#include <hip/hip_runtime.h>
+#include <algorithm>
 
 
-#include <algorithm>
+#include <hip/hip_runtime.h>
 
 
 #include <ginkgo/core/base/array.hpp>

hip/solver/idr_kernels.hip.cpp

@@ -33,8 +33,8 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #include "core/solver/idr_kernels.hpp"
 
 
-#include <time.h>
 #include <random>
+#include <time.h>
 
 
 #include <hip/hip_runtime.h>

include/ginkgo/core/base/abstract_factory.hpp

@@ -30,8 +30,8 @@ THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 ******************************<GINKGO LICENSE>*******************************/
 
-#ifndef GKO_CORE_BASE_ABSTRACT_FACTORY_HPP_
-#define GKO_CORE_BASE_ABSTRACT_FACTORY_HPP_
+#ifndef GKO_PUBLIC_CORE_BASE_ABSTRACT_FACTORY_HPP_
+#define GKO_PUBLIC_CORE_BASE_ABSTRACT_FACTORY_HPP_
 
 
 #include <ginkgo/core/base/polymorphic_object.hpp>
@@ -289,4 +289,4 @@ struct enable_parameters_type {
 }  // namespace gko
 
 
-#endif  // GKO_CORE_BASE_ABSTRACT_FACTORY_HPP_
+#endif  // GKO_PUBLIC_CORE_BASE_ABSTRACT_FACTORY_HPP_

include/ginkgo/core/base/array.hpp

@@ -30,8 +30,8 @@ THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 ******************************<GINKGO LICENSE>*******************************/
 
-#ifndef GKO_CORE_BASE_ARRAY_HPP_
-#define GKO_CORE_BASE_ARRAY_HPP_
+#ifndef GKO_PUBLIC_CORE_BASE_ARRAY_HPP_
+#define GKO_PUBLIC_CORE_BASE_ARRAY_HPP_
 
 
 #include <algorithm>
@@ -619,4 +619,4 @@ class copy_back_deleter<Array<T>> {
 }  // namespace gko
 
 
-#endif  // GKO_CORE_BASE_ARRAY_HPP_
+#endif  // GKO_PUBLIC_CORE_BASE_ARRAY_HPP_