Merge Use Reuse tool for license handling

This merge enables using the reuse tool [[1]](https://reuse.software/dev/) for adding our license to our files. This replaces the current `add_license.sh` script. The tool is automatically invoked as part of our pre-commit hooks.

.github/bot-pr-format-base.sh

@@ -15,7 +15,7 @@ git config user.name "ginkgo-bot"
 # save scripts from develop
 cp .clang-format .pre-commit-config.yaml /tmp
 pushd dev_tools/scripts || exit 1
-cp add_license.sh format_header.sh update_ginkgo_header.sh /tmp
+cp format_header.sh update_ginkgo_header.sh /tmp
 popd || exit 1
 
 # checkout current PR head
@@ -24,7 +24,6 @@ git checkout -b $LOCAL_BRANCH fork/$HEAD_BRANCH
 
 # restore files from develop
 cp /tmp/.clang-format .
-cp /tmp/.pre-commit-config .
-cp /tmp/add_license.sh dev_tools/scripts/
+cp /tmp/.pre-commit-config.yaml .
 cp /tmp/format_header.sh dev_tools/scripts/
 cp /tmp/update_ginkgo_header.sh dev_tools/scripts/

.github/check-format.sh

@@ -9,6 +9,8 @@ pipx run pre-commit run --show-diff-on-failure --color=always --from-ref "origin
 
 echo -n "Collecting information on changed files"
 
+git checkout -- dev_tools/scripts/*.sh
+
 # check for changed files, replace newlines by \n
 LIST_FILES=$(git diff --name-only | sed '$!s/$/\\n/' | tr -d '\n')
 echo -n .

.github/format-rebase.sh

@@ -10,8 +10,8 @@ DIFF_COMMAND="git diff --name-only --no-renames --diff-filter=AM HEAD~ | grep -E
 # do the formatting rebase
 git rebase --rebase-merges --empty=drop --no-keep-empty \
     --exec "cp /tmp/.clang-format /tmp/.pre-commit-config.yaml . && \
-            cp /tmp/add_license.sh /tmp/format_header.sh /tmp/update_ginkgo_header.sh dev_tools/scripts/ && \
-            dev_tools/scripts/add_license.sh && dev_tools/scripts/update_ginkgo_header.sh && \
+            cp /tmp/format_header.sh /tmp/update_ginkgo_header.sh dev_tools/scripts/ && \
+            dev_tools/scripts/update_ginkgo_header.sh && \
             for f in \$($DIFF_COMMAND | grep -E '$FORMAT_HEADER_REGEX'); do dev_tools/scripts/format_header.sh \$f; done && \
             pipx run pre-commit run && \
             git checkout dev_tools/scripts && (git diff >> /tmp/difflog; true) && (git diff --quiet || git commit -a --amend --no-edit --allow-empty)" \

.github/format.sh

@@ -11,7 +11,6 @@ echo "PR has ${NUM} changed files"
 TO_FORMAT="$(echo "$PR_FILES" | grep -E $EXTENSION_REGEX || true)"
 
 # format files
-dev_tools/scripts/add_license.sh
 dev_tools/scripts/update_ginkgo_header.sh
 for f in $(echo "$TO_FORMAT" | grep -E $FORMAT_HEADER_REGEX); do dev_tools/scripts/format_header.sh "$f"; done
 pipx run pre-commit run --files $TO_FORMAT || true

.pre-commit-config.yaml

@@ -4,4 +4,23 @@ repos:
   hooks:
   - id: clang-format
     types_or: [c, c++, cuda, inc]
-    exclude: third_party/SuiteSparse/AMD/.*
+    exclude: |
+      (?x)^(
+        third_party/SuiteSparse/AMD/.*|
+        third_party/identify_stream_usage/.*
+      )
+- repo: local
+  hooks:
+  # The official reuse hook only supports calling lint, so we need our own hook
+  - id: reuse-annotate
+    name: reuse-annotate
+    entry: reuse annotate --license BSD-3-Clause --copyright 'The Ginkgo authors' --year 2017-2023 --style c
+    language: python
+    additional_dependencies: [reuse]
+    types_or: [c, c++, cuda, inc]
+    exclude: |
+      (?x)^(
+        third_party/SuiteSparse/AMD/.*|
+        third_party/identify_stream_usage/.*|
+        examples/external-lib-interfacing/external-lib-interfacing.cpp
+      )$

CMakeLists.txt

@@ -377,11 +377,6 @@ if(GINKGO_DEVEL_TOOLS)
                       COMMAND bash -c "${PRE_COMMIT} run"
                       WORKING_DIRECTORY ${Ginkgo_SOURCE_DIR}
                       VERBATIM)
-
-    add_custom_target(add_license
-                      COMMAND ${Ginkgo_SOURCE_DIR}/dev_tools/scripts/add_license.sh
-                      WORKING_DIRECTORY ${Ginkgo_SOURCE_DIR})
-    add_dependencies(format add_license)
 endif()
 
 # MacOS needs to install bash, gnu-sed, findutils and coreutils

common/cuda_hip/base/batch_multi_vector_kernel_launcher.hpp.inc

@@ -2,7 +2,6 @@
 //
 // SPDX-License-Identifier: BSD-3-Clause
 
-
 template <typename ValueType>
 void scale(std::shared_ptr<const DefaultExecutor> exec,
            const batch::MultiVector<ValueType>* const alpha,

common/cuda_hip/base/batch_multi_vector_kernels.hpp.inc

@@ -2,7 +2,6 @@
 //
 // SPDX-License-Identifier: BSD-3-Clause
 
-
 template <typename ValueType, typename Mapping>
 __device__ __forceinline__ void scale(
     const gko::batch::multi_vector::batch_item<const ValueType>& alpha,

common/cuda_hip/components/syncfree.hpp.inc

@@ -2,7 +2,6 @@
 //
 // SPDX-License-Identifier: BSD-3-Clause
 
-
 struct syncfree_storage {
     using status_word = int;
 

common/cuda_hip/matrix/batch_dense_kernel_launcher.hpp.inc

@@ -2,7 +2,6 @@
 //
 // SPDX-License-Identifier: BSD-3-Clause
 
-
 template <typename ValueType>
 void simple_apply(std::shared_ptr<const DefaultExecutor> exec,
                   const batch::matrix::Dense<ValueType>* mat,

common/cuda_hip/matrix/batch_dense_kernels.hpp.inc

@@ -2,7 +2,6 @@
 //
 // SPDX-License-Identifier: BSD-3-Clause
 
-
 template <typename ValueType>
 __device__ __forceinline__ void simple_apply(
     const gko::batch::matrix::dense::batch_item<const ValueType>& mat,

common/cuda_hip/matrix/batch_ell_kernels.hpp.inc

@@ -2,7 +2,6 @@
 //
 // SPDX-License-Identifier: BSD-3-Clause
 
-
 template <typename ValueType, typename IndexType>
 __device__ __forceinline__ void simple_apply(
     const gko::batch::matrix::ell::batch_item<const ValueType, IndexType>& mat,

common/cuda_hip/solver/batch_bicgstab_kernels.hpp.inc

@@ -2,7 +2,6 @@
 //
 // SPDX-License-Identifier: BSD-3-Clause
 
-
 template <typename Group, typename BatchMatrixType_entry, typename ValueType>
 __device__ __forceinline__ void initialize(
     Group subgroup, const int num_rows, const BatchMatrixType_entry& mat_entry,

common/cuda_hip/stop/batch_criteria.hpp.inc

@@ -2,7 +2,6 @@
 //
 // SPDX-License-Identifier: BSD-3-Clause
 
-
 /**
  * @see reference/stop/batch_criteria.hpp
  */

dpcpp/solver/common_gmres_kernels.dp.inc

@@ -2,7 +2,6 @@
 //
 // SPDX-License-Identifier: BSD-3-Clause
 
-
 // Must be called with at least `max(stride_b * num_rows, krylov_dim *
 // num_cols)` threads in total.
 template <size_type block_size, typename ValueType>

examples/adaptiveprecision-blockjacobi/adaptiveprecision-blockjacobi.cpp

@@ -2,7 +2,6 @@
 //
 // SPDX-License-Identifier: BSD-3-Clause
 
-
 #include <ginkgo/ginkgo.hpp>
 
 

examples/ilu-preconditioned-solver/ilu-preconditioned-solver.cpp

@@ -2,7 +2,6 @@
 //
 // SPDX-License-Identifier: BSD-3-Clause
 
-
 #include <ginkgo/ginkgo.hpp>
 
 

examples/ir-ilu-preconditioned-solver/ir-ilu-preconditioned-solver.cpp

@@ -2,7 +2,6 @@
 //
 // SPDX-License-Identifier: BSD-3-Clause
 
-
 #include <ginkgo/ginkgo.hpp>
 
 

examples/iterative-refinement/iterative-refinement.cpp

@@ -2,7 +2,6 @@
 //
 // SPDX-License-Identifier: BSD-3-Clause
 
-
 #include <ginkgo/ginkgo.hpp>
 
 

examples/mixed-multigrid-preconditioned-solver/mixed-multigrid-preconditioned-solver.cpp

@@ -2,7 +2,6 @@
 //
 // SPDX-License-Identifier: BSD-3-Clause
 
-
 #include <ginkgo/ginkgo.hpp>
 
 

examples/mixed-multigrid-solver/mixed-multigrid-solver.cpp

@@ -2,7 +2,6 @@
 //
 // SPDX-License-Identifier: BSD-3-Clause
 
-
 #include <ginkgo/ginkgo.hpp>
 
 

examples/mixed-precision-ir/mixed-precision-ir.cpp

@@ -2,7 +2,6 @@
 //
 // SPDX-License-Identifier: BSD-3-Clause
 
-
 #include <ginkgo/ginkgo.hpp>
 
 

examples/multigrid-preconditioned-solver-customized/multigrid-preconditioned-solver-customized.cpp

@@ -2,7 +2,6 @@
 //
 // SPDX-License-Identifier: BSD-3-Clause
 
-
 #include <ginkgo/ginkgo.hpp>
 
 

examples/multigrid-preconditioned-solver/multigrid-preconditioned-solver.cpp

@@ -2,7 +2,6 @@
 //
 // SPDX-License-Identifier: BSD-3-Clause
 
-
 #include <ginkgo/ginkgo.hpp>
 
 

examples/par-ilu-convergence/par-ilu-convergence.cpp

@@ -2,7 +2,6 @@
 //
 // SPDX-License-Identifier: BSD-3-Clause
 
-
 #include <ginkgo/ginkgo.hpp>
 
 

examples/preconditioned-solver/preconditioned-solver.cpp

@@ -2,7 +2,6 @@
 //
 // SPDX-License-Identifier: BSD-3-Clause
 
-
 #include <ginkgo/ginkgo.hpp>
 
 

examples/preconditioner-export/preconditioner-export.cpp

@@ -2,7 +2,6 @@
 //
 // SPDX-License-Identifier: BSD-3-Clause
 
-
 #include <ginkgo/ginkgo.hpp>
 
 

include/ginkgo/core/log/papi.hpp

@@ -12,11 +12,11 @@
 #if GKO_HAVE_PAPI_SDE
 
 
+#include <sde_lib.h>
 #include <cstddef>
 #include <iostream>
 #include <map>
 #include <mutex>
-#include <sde_lib.h>
 
 
 #include <ginkgo/core/base/polymorphic_object.hpp>

third_party/SuiteSparse/wrapper32.cpp

@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2017-2023 The Ginkgo authors
+//
+// SPDX-License-Identifier: BSD-3-Clause
+
 #include <cassert>
 #include <cmath>
 #include <cstddef>

third_party/SuiteSparse/wrapper64.cpp

@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2017-2023 The Ginkgo authors
+//
+// SPDX-License-Identifier: BSD-3-Clause
+
 #include <cassert>
 #include <cmath>
 #include <cstddef>