[REVIEW] deleting prims and updating paths (#3067)

* deleting prims and updating paths * changelog * style check * pinning RAFT to latest commit * style checks * likely fixing conda builds * correcting option in cpu ci build * removing testing label
rapidsai · Oct 31, 2020 · 7e6d413 · 7e6d413
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -16,6 +16,7 @@
 - PR #2996: Removing the max_depth restriction for switching to the batched backend
 - PR #3004: Remove Single Process Multi GPU (SPMG) code
 - PR #3044: Move leftover `linalg` and `stats` to RAFT namespaces
+- PR #3067: Deleting prims moved to RAFT and updating header paths
 - PR #3074: Reducing dask coordinate descent test runtime
 
 ## Bug Fixes

diff --git a/cpp/bench/common/ml_benchmark.hpp b/cpp/bench/common/ml_benchmark.hpp
@@ -17,8 +17,8 @@
 #pragma once
 
 #include <benchmark/benchmark.h>
-#include <common/cudart_utils.h>
 #include <cuda_runtime.h>
+#include <raft/cudart_utils.h>
 #include <cuml/common/cuml_allocator.hpp>
 #include <cuml/common/logger.hpp>
 #include <cuml/common/utils.hpp>

diff --git a/cpp/bench/prims/add.cu b/cpp/bench/prims/add.cu
@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-#include <linalg/add.cuh>
+#include <raft/linalg/add.cuh>
 #include "../common/ml_benchmark.hpp"
 
 namespace MLCommon {

diff --git a/cpp/bench/prims/distance_common.cuh b/cpp/bench/prims/distance_common.cuh
@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-#include <common/cudart_utils.h>
+#include <raft/cudart_utils.h>
 #include <distance/distance.cuh>
 #include "../common/ml_benchmark.hpp"
 

diff --git a/cpp/bench/prims/fused_l2_nn.cu b/cpp/bench/prims/fused_l2_nn.cu
@@ -14,11 +14,11 @@
  * limitations under the License.
  */
 
-#include <common/cudart_utils.h>
+#include <raft/cudart_utils.h>
 #include <distance/fused_l2_nn.cuh>
 #include <limits>
-#include <linalg/norm.cuh>
-#include <random/rng.cuh>
+#include <raft/linalg/norm.cuh>
+#include <raft/random/rng.cuh>
 #include "../common/ml_benchmark.hpp"
 
 namespace MLCommon {

diff --git a/cpp/bench/prims/gram_matrix.cu b/cpp/bench/prims/gram_matrix.cu
@@ -18,7 +18,7 @@
 #include <matrix/grammatrix.cuh>
 #include <matrix/kernelfactory.cuh>
 #include <memory>
-#include <random/rng.cuh>
+#include <raft/random/rng.cuh>
 #include <sstream>
 #include <string>
 #include <vector>

diff --git a/cpp/bench/prims/map_then_reduce.cu b/cpp/bench/prims/map_then_reduce.cu
@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-#include <linalg/map_then_reduce.cuh>
+#include <raft/linalg/map_then_reduce.cuh>
 #include "../common/ml_benchmark.hpp"
 
 namespace MLCommon {

diff --git a/cpp/bench/prims/matrix_vector_op.cu b/cpp/bench/prims/matrix_vector_op.cu
@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-#include <linalg/matrix_vector_op.cuh>
+#include <raft/linalg/matrix_vector_op.cuh>
 #include "../common/ml_benchmark.hpp"
 
 namespace MLCommon {

diff --git a/cpp/bench/prims/permute.cu b/cpp/bench/prims/permute.cu
@@ -14,9 +14,9 @@
  * limitations under the License.
  */
 
-#include <common/cudart_utils.h>
+#include <raft/cudart_utils.h>
+#include <raft/random/rng.cuh>
 #include <random/permute.cuh>
-#include <random/rng.cuh>
 #include "../common/ml_benchmark.hpp"
 
 namespace MLCommon {

diff --git a/cpp/bench/prims/reduce.cu b/cpp/bench/prims/reduce.cu
@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-#include <linalg/reduce.cuh>
+#include <raft/linalg/reduce.cuh>
 #include "../common/ml_benchmark.hpp"
 
 namespace MLCommon {

diff --git a/cpp/bench/prims/rng.cu b/cpp/bench/prims/rng.cu
@@ -14,8 +14,8 @@
  * limitations under the License.
  */
 
-#include <common/cudart_utils.h>
-#include <random/rng.cuh>
+#include <raft/cudart_utils.h>
+#include <raft/random/rng.cuh>
 #include "../common/ml_benchmark.hpp"
 
 namespace MLCommon {

diff --git a/cpp/bench/sg/arima_loglikelihood.cu b/cpp/bench/sg/arima_loglikelihood.cu
@@ -22,9 +22,9 @@
 
 #include <cuml/tsa/arima_common.h>
 #include <cuml/tsa/batched_arima.hpp>
-#include <random/rng.cuh>
+#include <raft/random/rng.cuh>
 
-#include <common/cudart_utils.h>
+#include <raft/cudart_utils.h>
 #include "benchmark.cuh"
 
 namespace ML {

diff --git a/cpp/bench/sg/benchmark.cuh b/cpp/bench/sg/benchmark.cuh
@@ -17,8 +17,8 @@
 #pragma once
 
 #include <benchmark/benchmark.h>
-#include <common/cudart_utils.h>
 #include <cuda_runtime.h>
+#include <raft/cudart_utils.h>
 #include <cuml/common/logger.hpp>
 #include <cuml/cuml.hpp>
 #include "../common/ml_benchmark.hpp"

diff --git a/cpp/bench/sg/dataset.cuh b/cpp/bench/sg/dataset.cuh
@@ -16,15 +16,15 @@
 
 #pragma once
 
-#include <common/cudart_utils.h>
-#include <linalg/transpose.h>
+#include <raft/cudart_utils.h>
+#include <raft/linalg/transpose.h>
 #include <common/cumlHandle.hpp>
-#include <cuda_utils.cuh>
 #include <cuml/cuml.hpp>
 #include <cuml/datasets/make_blobs.hpp>
 #include <fstream>
 #include <iostream>
-#include <linalg/unary_op.cuh>
+#include <raft/cuda_utils.cuh>
+#include <raft/linalg/unary_op.cuh>
 #include <random/make_regression.cuh>
 #include <sstream>
 #include <string>

diff --git a/cpp/bench/sg/dataset_ts.cuh b/cpp/bench/sg/dataset_ts.cuh
@@ -17,11 +17,11 @@
 #pragma once
 
 #include <common/cumlHandle.hpp>
-#include <cuda_utils.cuh>
 #include <cuml/cuml.hpp>
+#include <raft/cuda_utils.cuh>
 
-#include <common/cudart_utils.h>
-#include <random/rng.cuh>
+#include <raft/cudart_utils.h>
+#include <raft/random/rng.cuh>
 
 namespace ML {
 namespace Bench {

diff --git a/cpp/bench/sg/umap.cu b/cpp/bench/sg/umap.cu
@@ -14,9 +14,9 @@
  * limitations under the License.
  */
 
-#include <cuda_utils.cuh>
 #include <cuml/cuml.hpp>
 #include <cuml/manifold/umap.hpp>
+#include <raft/cuda_utils.cuh>
 #include <utility>
 #include "benchmark.cuh"
 

diff --git a/cpp/cmake/Dependencies.cmake b/cpp/cmake/Dependencies.cmake
@@ -39,7 +39,7 @@ else(DEFINED ENV{RAFT_PATH})
 
   ExternalProject_Add(raft
     GIT_REPOSITORY    https://github.com/rapidsai/raft.git
-    GIT_TAG           3f8a4bf6f81289f1fdaae9a5bd4a10de8674aa5c
+    GIT_TAG           9b3afe67895fbea397fb2c72375157aadfc132d8
     PREFIX            ${RAFT_DIR}
     CONFIGURE_COMMAND ""
     BUILD_COMMAND     ""

diff --git a/cpp/include/cuml/tsa/arima_common.h b/cpp/include/cuml/tsa/arima_common.h
@@ -20,7 +20,7 @@
 
 #include <algorithm>
 
-#include <common/cudart_utils.h>
+#include <raft/cudart_utils.h>
 #include <thrust/execution_policy.h>
 #include <thrust/for_each.h>
 #include <thrust/iterator/counting_iterator.h>

diff --git a/cpp/src/arima/batched_arima.cu b/cpp/src/arima/batched_arima.cu
@@ -28,14 +28,14 @@
 #include <cuml/tsa/batched_arima.hpp>
 #include <cuml/tsa/batched_kalman.hpp>
 
-#include <common/cudart_utils.h>
+#include <raft/cudart_utils.h>
 #include <common/cumlHandle.hpp>
 #include <common/device_buffer.hpp>
 #include <common/nvtx.hpp>
-#include <cuda_utils.cuh>
 #include <linalg/batched/matrix.cuh>
-#include <linalg/matrix_vector_op.cuh>
 #include <metrics/batched/information_criterion.cuh>
+#include <raft/cuda_utils.cuh>
+#include <raft/linalg/matrix_vector_op.cuh>
 #include <timeSeries/arima_helpers.cuh>
 
 namespace ML {

diff --git a/cpp/src/arima/batched_kalman.cu b/cpp/src/arima/batched_kalman.cu
@@ -24,14 +24,14 @@
 #include <cuml/cuml.hpp>
 #include <cuml/tsa/batched_kalman.hpp>
 
-#include <common/cudart_utils.h>
+#include <raft/cudart_utils.h>
 #include <raft/linalg/cublas_wrappers.h>
 #include <common/cumlHandle.hpp>
 #include <common/device_buffer.hpp>
 #include <common/nvtx.hpp>
-#include <cuda_utils.cuh>
 #include <linalg/batched/matrix.cuh>
-#include <linalg/binary_op.cuh>
+#include <raft/cuda_utils.cuh>
+#include <raft/linalg/binary_op.cuh>
 #include <sparse/batched/csr.cuh>
 #include <timeSeries/arima_helpers.cuh>
 

diff --git a/cpp/src/common/allocatorAdapter.hpp b/cpp/src/common/allocatorAdapter.hpp
@@ -22,7 +22,7 @@
 
 #include <cuml/cuml.hpp>
 
-#include <common/cudart_utils.h>
+#include <raft/cudart_utils.h>
 #include <cuml/common/cuml_allocator.hpp>
 
 namespace ML {

diff --git a/cpp/src/common/cumlHandle.cpp b/cpp/src/common/cumlHandle.cpp
@@ -15,7 +15,7 @@
  */
 
 #include "cumlHandle.hpp"
-#include <common/cudart_utils.h>
+#include <raft/cudart_utils.h>
 #include <raft/linalg/cublas_wrappers.h>
 #include <raft/linalg/cusolver_wrappers.h>
 #include <raft/sparse/cusparse_wrappers.h>

diff --git a/cpp/src/common/cuml_api.cpp b/cpp/src/common/cuml_api.cpp
@@ -14,8 +14,8 @@
  * limitations under the License.
  */
 
-#include <common/cudart_utils.h>
 #include <cuml/cuml_api.h>
+#include <raft/cudart_utils.h>
 #include <cuml/common/utils.hpp>
 #include <functional>
 #include <raft/mr/device/allocator.hpp>

diff --git a/cpp/src/common/tensor.hpp b/cpp/src/common/tensor.hpp
@@ -16,7 +16,7 @@
 
 #pragma once
 
-#include <common/cudart_utils.h>
+#include <raft/cudart_utils.h>
 #include <cuml/common/cuml_allocator.hpp>
 #include <vector>
 

diff --git a/cpp/src/dbscan/adjgraph/algo.cuh b/cpp/src/dbscan/adjgraph/algo.cuh
@@ -20,7 +20,7 @@
 #include <thrust/scan.h>
 #include <common/allocatorAdapter.hpp>
 #include <common/cumlHandle.hpp>
-#include <cuda_utils.cuh>
+#include <raft/cuda_utils.cuh>
 #include "../common.cuh"
 #include "pack.h"
 

diff --git a/cpp/src/dbscan/adjgraph/naive.cuh b/cpp/src/dbscan/adjgraph/naive.cuh
@@ -16,10 +16,10 @@
 
 #pragma once
 
-#include <common/cudart_utils.h>
+#include <raft/cudart_utils.h>
 #include <common/cumlHandle.hpp>
 #include <common/host_buffer.hpp>
-#include <cuda_utils.cuh>
+#include <raft/cuda_utils.cuh>
 #include "../common.cuh"
 #include "pack.h"
 

diff --git a/cpp/src/dbscan/dbscan.cu b/cpp/src/dbscan/dbscan.cu
@@ -13,8 +13,8 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-#include <common/cudart_utils.h>
 #include <cuml/cuml_api.h>
+#include <raft/cudart_utils.h>
 #include <common/cumlHandle.hpp>
 #include <cuml/cluster/dbscan.hpp>
 #include "dbscan.cuh"

diff --git a/cpp/src/dbscan/runner.cuh b/cpp/src/dbscan/runner.cuh
@@ -16,12 +16,12 @@
 
 #pragma once
 
-#include <common/cudart_utils.h>
+#include <raft/cudart_utils.h>
 #include <common/cumlHandle.hpp>
 #include <common/device_buffer.hpp>
 #include <common/nvtx.hpp>
-#include <cuda_utils.cuh>
 #include <label/classlabels.cuh>
+#include <raft/cuda_utils.cuh>
 #include <sparse/csr.cuh>
 #include "adjgraph/runner.cuh"
 #include "vertexdeg/runner.cuh"

diff --git a/cpp/src/dbscan/vertexdeg/naive.cuh b/cpp/src/dbscan/vertexdeg/naive.cuh
@@ -17,7 +17,7 @@
 #pragma once
 
 #include <common/cumlHandle.hpp>
-#include <cuda_utils.cuh>
+#include <raft/cuda_utils.cuh>
 #include "pack.h"
 
 namespace Dbscan {

diff --git a/cpp/src/decisiontree/batched-levelalgo/builder_base.cuh b/cpp/src/decisiontree/batched-levelalgo/builder_base.cuh
@@ -21,8 +21,8 @@
 #include <common/device_buffer.hpp>
 #include <common/grid_sync.cuh>
 #include <common/host_buffer.hpp>
-#include <cuda_utils.cuh>
 #include <cuml/tree/decisiontree.hpp>
+#include <raft/cuda_utils.cuh>
 #include "input.cuh"
 #include "kernels.cuh"
 #include "node.cuh"

diff --git a/cpp/src/decisiontree/batched-levelalgo/kernels.cuh b/cpp/src/decisiontree/batched-levelalgo/kernels.cuh
@@ -17,7 +17,7 @@
 #pragma once
 
 #include <common/grid_sync.cuh>
-#include <cuda_utils.cuh>
+#include <raft/cuda_utils.cuh>
 #include "input.cuh"
 #include "metrics.cuh"
 #include "node.cuh"

diff --git a/cpp/src/decisiontree/batched-levelalgo/metrics.cuh b/cpp/src/decisiontree/batched-levelalgo/metrics.cuh
@@ -17,7 +17,7 @@
 #pragma once
 
 #include <common/grid_sync.cuh>
-#include <cuda_utils.cuh>
+#include <raft/cuda_utils.cuh>
 #include "input.cuh"
 #include "node.cuh"
 #include "split.cuh"

diff --git a/cpp/src/decisiontree/batched-levelalgo/split.cuh b/cpp/src/decisiontree/batched-levelalgo/split.cuh
@@ -16,8 +16,8 @@
 
 #pragma once
 
-#include <cuda_utils.cuh>
-#include <linalg/unary_op.cuh>
+#include <raft/cuda_utils.cuh>
+#include <raft/linalg/unary_op.cuh>
 
 namespace ML {
 namespace DecisionTree {

diff --git a/cpp/src/decisiontree/decisiontree_impl.cuh b/cpp/src/decisiontree/decisiontree_impl.cuh
@@ -14,8 +14,8 @@
  * limitations under the License.
  */
 
-#include <common/cudart_utils.h>
 #include <decisiontree/quantile/quantile.h>
+#include <raft/cudart_utils.h>
 #include <common/iota.cuh>
 #include <cuml/common/logger.hpp>
 #include <iomanip>

diff --git a/cpp/src/decisiontree/levelalgo/common_helper.cuh b/cpp/src/decisiontree/levelalgo/common_helper.cuh
@@ -16,10 +16,10 @@
 
 #pragma once
 
-#include <common/cudart_utils.h>
 #include <cuml/tree/flatnode.h>
+#include <raft/cudart_utils.h>
 #include <cuml/common/logger.hpp>
-#include <random/rng.cuh>
+#include <raft/random/rng.cuh>
 #include <stats/minmax.cuh>
 #include "common_kernel.cuh"
 

diff --git a/cpp/src/decisiontree/levelalgo/common_kernel.cuh b/cpp/src/decisiontree/levelalgo/common_kernel.cuh
@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 #pragma once
-#include <cuda_utils.cuh>
+#include <raft/cuda_utils.cuh>
 #define LEAF 0xFFFFFFFF
 #define PUSHRIGHT 0x00000001
 #include <stats/minmax.cuh>