Reorder includes. (#5749)

* Reorder includes.

* R.

R-package/src/xgboost_R.cc

@@ -1,14 +1,17 @@
 // Copyright (c) 2014 by Contributors
-#include <dmlc/logging.h>
+#include <cstring>
-#include <dmlc/omp.h>
+#include <cstdio>
-#include <xgboost/c_api.h>
 #include <vector>
 #include <string>
 #include <utility>
-#include <cstring>
-#include <cstdio>
 #include <sstream>
-#include "./xgboost_R.h"
+
+#include <dmlc/logging.h>
+#include <dmlc/omp.h>
+#include <xgboost/c_api.h>
+
+#include "xgboost_R.h"
+
 
 /*!
  * \brief macro to annotate begin of api

include/xgboost/base.h

@@ -6,14 +6,15 @@
 #ifndef XGBOOST_BASE_H_
 #define XGBOOST_BASE_H_
 
-#include <dmlc/base.h>
-#include <dmlc/omp.h>
 #include <cmath>
 #include <iostream>
 #include <vector>
 #include <string>
 #include <utility>
 
+#include <dmlc/base.h>
+#include <dmlc/omp.h>
+
 /*!
  * \brief string flag for R library, to leave hooks when needed.
  */

include/xgboost/data.h

@@ -7,6 +7,13 @@
 #ifndef XGBOOST_DATA_H_
 #define XGBOOST_DATA_H_
 
+#include <memory>
+#include <numeric>
+#include <algorithm>
+#include <string>
+#include <utility>
+#include <vector>
+
 #include <dmlc/base.h>
 #include <dmlc/data.h>
 #include <dmlc/serializer.h>
@@ -15,13 +22,6 @@
 #include <xgboost/span.h>
 #include <xgboost/host_device_vector.h>
 
-#include <memory>
-#include <numeric>
-#include <algorithm>
-#include <string>
-#include <utility>
-#include <vector>
-
 namespace xgboost {
 // forward declare dmatrix.
 class DMatrix;

include/xgboost/feature_map.h

@@ -7,13 +7,13 @@
 #ifndef XGBOOST_FEATURE_MAP_H_
 #define XGBOOST_FEATURE_MAP_H_
 
-#include <xgboost/logging.h>
-
 #include <vector>
 #include <string>
 #include <cstring>
 #include <iostream>
 
+#include <xgboost/logging.h>
+
 namespace xgboost {
 /*!
  * \brief Feature map data structure to help text model dump.

include/xgboost/gbm.h

@@ -8,13 +8,6 @@
 #ifndef XGBOOST_GBM_H_
 #define XGBOOST_GBM_H_
 
-#include <dmlc/registry.h>
-#include <dmlc/any.h>
-#include <xgboost/base.h>
-#include <xgboost/data.h>
-#include <xgboost/host_device_vector.h>
-#include <xgboost/model.h>
-
 #include <vector>
 #include <utility>
 #include <string>
@@ -22,6 +15,13 @@
 #include <unordered_map>
 #include <memory>
 
+#include <dmlc/registry.h>
+#include <dmlc/any.h>
+#include <xgboost/base.h>
+#include <xgboost/data.h>
+#include <xgboost/host_device_vector.h>
+#include <xgboost/model.h>
+
 namespace xgboost {
 
 class Json;

include/xgboost/generic_parameters.h

@@ -5,11 +5,11 @@
 #ifndef XGBOOST_GENERIC_PARAMETERS_H_
 #define XGBOOST_GENERIC_PARAMETERS_H_
 
+#include <string>
+
 #include <xgboost/logging.h>
 #include <xgboost/parameter.h>
 
-#include <string>
-
 namespace xgboost {
 struct GenericParameter : public XGBoostParameter<GenericParameter> {
   // Constant representing the device ID of CPU.

include/xgboost/json.h

@@ -4,15 +4,15 @@
 #ifndef XGBOOST_JSON_H_
 #define XGBOOST_JSON_H_
 
-#include <xgboost/logging.h>
-#include <xgboost/parameter.h>
-#include <string>
-
 #include <map>
 #include <memory>
 #include <vector>
 #include <functional>
 #include <utility>
+#include <string>
+
+#include <xgboost/logging.h>
+#include <xgboost/parameter.h>
 
 namespace xgboost {
 

include/xgboost/json_io.h

@@ -3,7 +3,6 @@
  */
 #ifndef XGBOOST_JSON_IO_H_
 #define XGBOOST_JSON_IO_H_
-#include <xgboost/json.h>
 
 #include <memory>
 #include <string>
@@ -14,6 +13,8 @@
 #include <sstream>
 #include <locale>
 
+#include <xgboost/json.h>
+
 namespace xgboost {
 
 template <typename Allocator>

include/xgboost/learner.h

@@ -8,6 +8,12 @@
 #ifndef XGBOOST_LEARNER_H_
 #define XGBOOST_LEARNER_H_
 
+#include <utility>
+#include <map>
+#include <memory>
+#include <string>
+#include <vector>
+
 #include <dmlc/any.h>
 #include <rabit/rabit.h>
 #include <xgboost/base.h>
@@ -17,12 +23,6 @@
 #include <xgboost/host_device_vector.h>
 #include <xgboost/model.h>
 
-#include <utility>
-#include <map>
-#include <memory>
-#include <string>
-#include <vector>
-
 namespace xgboost {
 
 class Metric;

include/xgboost/linear_updater.h

@@ -3,6 +3,11 @@
  */
 #pragma once
 
+#include <functional>
+#include <string>
+#include <utility>
+#include <vector>
+
 #include <dmlc/registry.h>
 #include <xgboost/base.h>
 #include <xgboost/data.h>
@@ -10,12 +15,6 @@
 #include <xgboost/host_device_vector.h>
 #include <xgboost/model.h>
 
-#include <functional>
-#include <string>
-#include <utility>
-#include <vector>
-
-
 namespace xgboost {
 
 class Json;

include/xgboost/logging.h

@@ -8,18 +8,18 @@
 #ifndef XGBOOST_LOGGING_H_
 #define XGBOOST_LOGGING_H_
 
-#include <dmlc/logging.h>
-#include <dmlc/thread_local.h>
-
-#include <xgboost/base.h>
-#include <xgboost/parameter.h>
-
 #include <sstream>
 #include <map>
 #include <string>
 #include <utility>
 #include <vector>
 
+#include <dmlc/logging.h>
+#include <dmlc/thread_local.h>
+
+#include <xgboost/base.h>
+#include <xgboost/parameter.h>
+
 namespace xgboost {
 
 class BaseLogger {

include/xgboost/metric.h

@@ -7,6 +7,11 @@
 #ifndef XGBOOST_METRIC_H_
 #define XGBOOST_METRIC_H_
 
+#include <vector>
+#include <string>
+#include <functional>
+#include <utility>
+
 #include <dmlc/registry.h>
 #include <xgboost/model.h>
 #include <xgboost/generic_parameters.h>
@@ -14,11 +19,6 @@
 #include <xgboost/base.h>
 #include <xgboost/host_device_vector.h>
 
-#include <vector>
-#include <string>
-#include <functional>
-#include <utility>
-
 namespace xgboost {
 /*!
  * \brief interface of evaluation metric used to evaluate model performance.

include/xgboost/objective.h

@@ -7,6 +7,11 @@
 #ifndef XGBOOST_OBJECTIVE_H_
 #define XGBOOST_OBJECTIVE_H_
 
+#include <vector>
+#include <utility>
+#include <string>
+#include <functional>
+
 #include <dmlc/registry.h>
 #include <xgboost/base.h>
 #include <xgboost/data.h>
@@ -14,11 +19,6 @@
 #include <xgboost/generic_parameters.h>
 #include <xgboost/host_device_vector.h>
 
-#include <vector>
-#include <utility>
-#include <string>
-#include <functional>
-
 namespace xgboost {
 
 /*! \brief interface of objective function */

include/xgboost/parameter.h

@@ -8,11 +8,12 @@
 #ifndef XGBOOST_PARAMETER_H_
 #define XGBOOST_PARAMETER_H_
 
-#include <dmlc/parameter.h>
-#include <xgboost/base.h>
 #include <string>
 #include <type_traits>
 
+#include <dmlc/parameter.h>
+#include <xgboost/base.h>
+
 /*!
  * \brief Specialization of FieldEntry for enum class (backed by int)
  *

include/xgboost/predictor.h

@@ -5,10 +5,6 @@
  *  performs predictions for a gradient booster.
  */
 #pragma once
-#include <xgboost/base.h>
-#include <xgboost/data.h>
-#include <xgboost/generic_parameters.h>
-#include <xgboost/host_device_vector.h>
 
 #include <functional>
 #include <memory>
@@ -18,6 +14,11 @@
 #include <vector>
 #include <mutex>
 
+#include <xgboost/base.h>
+#include <xgboost/data.h>
+#include <xgboost/generic_parameters.h>
+#include <xgboost/host_device_vector.h>
+
 // Forward declarations
 namespace xgboost {
 class TreeUpdater;

include/xgboost/span.h

@@ -29,15 +29,15 @@
 #ifndef XGBOOST_SPAN_H_
 #define XGBOOST_SPAN_H_
 
-#include <xgboost/base.h>
-#include <xgboost/logging.h>
-
 #include <cinttypes>          // size_t
 #include <limits>             // numeric_limits
 #include <iterator>
 #include <type_traits>
 #include <cstdio>
 
+#include <xgboost/base.h>
+#include <xgboost/logging.h>
+
 /*!
  * The version number 1910 is picked up from GSL.
  *

include/xgboost/tree_model.h

@@ -7,6 +7,14 @@
 #ifndef XGBOOST_TREE_MODEL_H_
 #define XGBOOST_TREE_MODEL_H_
 
+#include <limits>
+#include <vector>
+#include <string>
+#include <cstring>
+#include <algorithm>
+#include <tuple>
+#include <stack>
+
 #include <dmlc/io.h>
 #include <dmlc/parameter.h>
 
@@ -16,14 +24,6 @@
 #include <xgboost/feature_map.h>
 #include <xgboost/model.h>
 
-#include <limits>
-#include <vector>
-#include <string>
-#include <cstring>
-#include <algorithm>
-#include <tuple>
-#include <stack>
-
 namespace xgboost {
 
 struct PathElement;  // forward declaration

include/xgboost/tree_updater.h

@@ -8,6 +8,11 @@
 #ifndef XGBOOST_TREE_UPDATER_H_
 #define XGBOOST_TREE_UPDATER_H_
 
+#include <functional>
+#include <vector>
+#include <utility>
+#include <string>
+
 #include <dmlc/registry.h>
 #include <xgboost/base.h>
 #include <xgboost/data.h>
@@ -16,11 +21,6 @@
 #include <xgboost/host_device_vector.h>
 #include <xgboost/model.h>
 
-#include <functional>
-#include <vector>
-#include <utility>
-#include <string>
-
 namespace xgboost {
 
 class Json;

src/c_api/c_api.cc

@@ -1,7 +1,4 @@
 // Copyright (c) 2014-2020 by Contributors
-#include <rabit/rabit.h>
-#include <rabit/c_api.h>
-
 #include <cstdio>
 #include <cstring>
 #include <fstream>
@@ -10,6 +7,9 @@
 #include <string>
 #include <memory>
 
+#include <rabit/rabit.h>
+#include <rabit/c_api.h>
+
 #include "xgboost/base.h"
 #include "xgboost/data.h"
 #include "xgboost/host_device_vector.h"

src/cli_main.cc

@@ -7,6 +7,14 @@
 #define _CRT_SECURE_NO_WARNINGS
 #define _CRT_SECURE_NO_DEPRECATE
 #define NOMINMAX
+
+#include <iomanip>
+#include <ctime>
+#include <string>
+#include <cstdio>
+#include <cstring>
+#include <vector>
+
 #include <dmlc/timer.h>
 
 #include <xgboost/learner.h>
@@ -15,12 +23,6 @@
 #include <xgboost/logging.h>
 #include <xgboost/parameter.h>
 
-#include <iomanip>
-#include <ctime>
-#include <string>
-#include <cstdio>
-#include <cstring>
-#include <vector>
 #include "common/common.h"
 #include "common/config.h"
 #include "common/io.h"

src/common/base64.h

@@ -8,10 +8,11 @@
 #ifndef XGBOOST_COMMON_BASE64_H_
 #define XGBOOST_COMMON_BASE64_H_
 
-#include <xgboost/logging.h>
 #include <cctype>
 #include <cstdio>
 #include <string>
+
+#include "xgboost/logging.h"
 #include "./io.h"
 
 namespace xgboost {

src/common/common.h

@@ -6,9 +6,6 @@
 #ifndef XGBOOST_COMMON_COMMON_H_
 #define XGBOOST_COMMON_COMMON_H_
 
-#include <xgboost/base.h>
-#include <xgboost/logging.h>
-
 #include <exception>
 #include <limits>
 #include <type_traits>
@@ -16,6 +13,9 @@
 #include <string>
 #include <sstream>
 
+#include <xgboost/base.h>
+#include <xgboost/logging.h>
+
 #if defined(__CUDACC__)
 #include <thrust/system/cuda/error.h>
 #include <thrust/system_error.h>

src/common/compressed_iterator.h

@@ -3,11 +3,11 @@
  * \file compressed_iterator.h
  */
 #pragma once
-#include <xgboost/base.h>
 #include <cmath>
 #include <cstddef>
 #include <algorithm>
 
+#include "xgboost/base.h"
 #include "common.h"
 
 #ifdef __CUDACC__

src/common/hist_util.cc

@@ -2,19 +2,21 @@
  * Copyright 2017-2020 by Contributors
  * \file hist_util.cc
  */
+#include <numeric>
+#include <vector>
+
 #include <dmlc/timer.h>
 #include <dmlc/omp.h>
 
 #include <rabit/rabit.h>
-#include <numeric>
-#include <vector>
 
 #include "xgboost/base.h"
-#include "../common/common.h"
 #include "hist_util.h"
 #include "random.h"
 #include "column_matrix.h"
 #include "quantile.h"
+
+#include "../common/common.h"
 #include "./../tree/updater_quantile_hist.h"
 
 #if defined(XGBOOST_MM_PREFETCH_PRESENT)

src/common/hist_util.cu

@@ -1,6 +1,10 @@
 /*!
  * Copyright 2018 XGBoost contributors
  */
+#include <memory>
+#include <mutex>
+#include <utility>
+#include <vector>
 
 #include <xgboost/logging.h>
 
@@ -13,11 +17,6 @@
 #include <thrust/binary_search.h>
 #include <thrust/execution_policy.h>
 
-#include <memory>
-#include <mutex>
-#include <utility>
-#include <vector>
-
 #include "device_helpers.cuh"
 #include "hist_util.h"
 #include "hist_util.cuh"

src/common/hist_util.h

@@ -7,8 +7,6 @@
 #ifndef XGBOOST_COMMON_HIST_UTIL_H_
 #define XGBOOST_COMMON_HIST_UTIL_H_
 
-#include <xgboost/data.h>
-#include <xgboost/generic_parameters.h>
 #include <limits>
 #include <vector>
 #include <algorithm>
@@ -16,6 +14,9 @@
 #include <utility>
 #include <map>
 
+#include "xgboost/data.h"
+#include "xgboost/generic_parameters.h"
+
 #include "row_set.h"
 #include "threading_utils.h"
 #include "../tree/param.h"

src/common/host_device_vector.cc

@@ -4,12 +4,12 @@
 #ifndef XGBOOST_USE_CUDA
 
 // dummy implementation of HostDeviceVector in case CUDA is not used
-
-#include <xgboost/base.h>
-#include <xgboost/data.h>
 #include <cstdint>
 #include <memory>
 #include <utility>
+
+#include "xgboost/base.h"
+#include "xgboost/data.h"
 #include "xgboost/host_device_vector.h"
 
 namespace xgboost {

src/common/host_device_vector.cu

@@ -1,14 +1,12 @@
 /*!
  * Copyright 2017 XGBoost contributors
  */
+#include <algorithm>
+#include <cstdint>
 
 #include <thrust/fill.h>
 #include <thrust/device_ptr.h>
 
-#include <algorithm>
-#include <cstdint>
-#include <mutex>
-
 #include "xgboost/data.h"
 #include "xgboost/host_device_vector.h"
 #include "device_helpers.cuh"

src/common/io.h

@@ -7,11 +7,11 @@
 
 #ifndef XGBOOST_COMMON_IO_H_
 #define XGBOOST_COMMON_IO_H_
+#include <string>
+#include <cstring>
 
 #include <dmlc/io.h>
 #include <rabit/rabit.h>
-#include <string>
-#include <cstring>
 
 #include "common.h"
 

src/common/math.h

@@ -7,14 +7,14 @@
 #ifndef XGBOOST_COMMON_MATH_H_
 #define XGBOOST_COMMON_MATH_H_
 
-#include <xgboost/base.h>
-
 #include <algorithm>
 #include <cmath>
 #include <limits>
 #include <utility>
 #include <vector>
 
+#include <xgboost/base.h>
+
 namespace xgboost {
 namespace common {
 /*!

src/common/probability_distribution.cc

@@ -4,9 +4,9 @@
  * \brief Implementation of a few useful probability distributions
  * \author Avinash Barnwal and Hyunsu Cho
  */
-
-#include <xgboost/logging.h>
 #include <cmath>
+
+#include "xgboost/logging.h"
 #include "probability_distribution.h"
 
 namespace xgboost {

src/common/quantile.h

@@ -7,14 +7,15 @@
 #ifndef XGBOOST_COMMON_QUANTILE_H_
 #define XGBOOST_COMMON_QUANTILE_H_
 
-#include <dmlc/base.h>
-#include <xgboost/logging.h>
 #include <cmath>
 #include <vector>
 #include <cstring>
 #include <algorithm>
 #include <iostream>
 
+#include <dmlc/base.h>
+#include <xgboost/logging.h>
+
 namespace xgboost {
 namespace common {
 /*!

src/common/random.h

@@ -7,8 +7,6 @@
 #ifndef XGBOOST_COMMON_RANDOM_H_
 #define XGBOOST_COMMON_RANDOM_H_
 
-#include <rabit/rabit.h>
-#include <xgboost/logging.h>
 #include <algorithm>
 #include <vector>
 #include <limits>
@@ -17,6 +15,8 @@
 #include <numeric>
 #include <random>
 
+#include "rabit/rabit.h"
+#include "xgboost/logging.h"
 #include "xgboost/host_device_vector.h"
 
 namespace xgboost {

src/common/row_set.h

@@ -7,11 +7,12 @@
 #ifndef XGBOOST_COMMON_ROW_SET_H_
 #define XGBOOST_COMMON_ROW_SET_H_
 
-#include <xgboost/data.h>
 #include <algorithm>
 #include <vector>
 #include <utility>
 
+#include "xgboost/data.h"
+
 namespace xgboost {
 namespace common {
 

src/common/survival_util.cc

@@ -6,9 +6,10 @@
  * \author Avinash Barnwal, Hyunsu Cho and Toby Hocking
  */
 
-#include <dmlc/registry.h>
 #include <algorithm>
 #include <cmath>
+
+#include <dmlc/registry.h>
 #include "survival_util.h"
 
 /*

src/common/survival_util.h

@@ -8,8 +8,9 @@
 #ifndef XGBOOST_COMMON_SURVIVAL_UTIL_H_
 #define XGBOOST_COMMON_SURVIVAL_UTIL_H_
 
-#include <xgboost/parameter.h>
 #include <memory>
+
+#include "xgboost/parameter.h"
 #include "probability_distribution.h"
 
 DECLARE_FIELD_ENUM_CLASS(xgboost::common::ProbabilityDistributionType);

src/common/timer.cc

@@ -1,14 +1,15 @@
 /*!
  * Copyright by Contributors 2019
  */
-#include <rabit/rabit.h>
 #include <algorithm>
 #include <type_traits>
 #include <utility>
 #include <vector>
 #include <sstream>
-#include "timer.h"
+
+#include <rabit/rabit.h>
 #include "xgboost/json.h"
+#include "timer.h"
 
 #if defined(XGBOOST_USE_NVTX)
 #include <nvToolsExt.h>

src/common/timer.h

@@ -2,7 +2,6 @@
  * Copyright by Contributors 2017-2019
  */
 #pragma once
-#include <xgboost/logging.h>
 #include <chrono>
 #include <iostream>
 #include <map>
@@ -10,6 +9,8 @@
 #include <utility>
 #include <vector>
 
+#include <xgboost/logging.h>
+
 namespace xgboost {
 namespace common {
 

src/common/transform.h

@@ -3,15 +3,14 @@
  */
 #ifndef XGBOOST_COMMON_TRANSFORM_H_
 #define XGBOOST_COMMON_TRANSFORM_H_
-
-#include <dmlc/omp.h>
-#include <dmlc/common.h>
-
-#include <xgboost/data.h>
 #include <utility>
 #include <vector>
 #include <type_traits>  // enable_if
 
+#include <dmlc/omp.h>
+#include <dmlc/common.h>
+
+#include "xgboost/data.h"
 #include "xgboost/host_device_vector.h"
 #include "xgboost/span.h"
 

src/common/version.cc

@@ -1,12 +1,12 @@
 /*!
  * Copyright 2019 XGBoost contributors
  */
-#include <dmlc/io.h>
-
 #include <string>
 #include <tuple>
 #include <vector>
 
+#include <dmlc/io.h>
+
 #include "xgboost/logging.h"
 #include "xgboost/json.h"
 #include "xgboost/version_config.h"

src/common/version.h

@@ -4,10 +4,10 @@
 #ifndef XGBOOST_COMMON_VERSION_H_
 #define XGBOOST_COMMON_VERSION_H_
 
-#include <dmlc/io.h>
 #include <string>
 #include <tuple>
 
+#include <dmlc/io.h>
 #include "xgboost/base.h"
 
 namespace xgboost {

src/data/adapter.h

@@ -4,8 +4,6 @@
  */
 #ifndef XGBOOST_DATA_ADAPTER_H_
 #define XGBOOST_DATA_ADAPTER_H_
-#include <dmlc/data.h>
-
 #include <cstddef>
 #include <functional>
 #include <limits>
@@ -14,6 +12,8 @@
 #include <utility>
 #include <vector>
 
+#include <dmlc/data.h>
+
 #include "xgboost/logging.h"
 #include "xgboost/base.h"
 #include "xgboost/data.h"

src/data/data.cc

@@ -2,8 +2,11 @@
  * Copyright 2015-2020 by Contributors
  * \file data.cc
  */
-#include <dmlc/registry.h>
 #include <cstring>
+#include <vector>
+#include <string>
+
+#include <dmlc/registry.h>
 
 #include "dmlc/io.h"
 #include "xgboost/data.h"

src/data/device_dmatrix.cu

@@ -3,14 +3,16 @@
  * \file device_dmatrix.cu
  * \brief Device-memory version of DMatrix.
  */
+#include <memory>
+#include <utility>
 
 #include <thrust/execution_policy.h>
 #include <thrust/iterator/discard_iterator.h>
 #include <thrust/iterator/transform_output_iterator.h>
+
 #include <xgboost/base.h>
 #include <xgboost/data.h>
-#include <memory>
+
-#include <utility>
 #include "../common/hist_util.h"
 #include "adapter.h"
 #include "device_adapter.cuh"

src/data/device_dmatrix.h

@@ -6,11 +6,11 @@
 #ifndef XGBOOST_DATA_DEVICE_DMATRIX_H_
 #define XGBOOST_DATA_DEVICE_DMATRIX_H_
 
+#include <memory>
+
 #include <xgboost/base.h>
 #include <xgboost/data.h>
 
-#include <memory>
-
 #include "adapter.h"
 #include "simple_batch_iterator.h"
 #include "simple_dmatrix.h"

src/data/ellpack_page_source.h

@@ -5,10 +5,11 @@
 #ifndef XGBOOST_DATA_ELLPACK_PAGE_SOURCE_H_
 #define XGBOOST_DATA_ELLPACK_PAGE_SOURCE_H_
 
-#include <xgboost/data.h>
 #include <memory>
 #include <string>
 
+#include <xgboost/data.h>
+
 #include "../common/timer.h"
 #include "../common/hist_util.h"
 #include "sparse_page_source.h"

src/data/simple_dmatrix.h

@@ -7,12 +7,11 @@
 #ifndef XGBOOST_DATA_SIMPLE_DMATRIX_H_
 #define XGBOOST_DATA_SIMPLE_DMATRIX_H_
 
-#include <xgboost/base.h>
-#include <xgboost/data.h>
-
 #include <memory>
 #include <string>
 
+#include <xgboost/base.h>
+#include <xgboost/data.h>
 
 namespace xgboost {
 namespace data {

src/data/sparse_page_dmatrix.h

@@ -7,13 +7,14 @@
 #ifndef XGBOOST_DATA_SPARSE_PAGE_DMATRIX_H_
 #define XGBOOST_DATA_SPARSE_PAGE_DMATRIX_H_
 
-#include <xgboost/data.h>
 #include <algorithm>
 #include <memory>
 #include <string>
 #include <utility>
 #include <vector>
 
+#include "xgboost/data.h"
+
 #include "ellpack_page_source.h"
 #include "sparse_page_source.h"
 

src/data/sparse_page_source.h

@@ -7,9 +7,6 @@
 #ifndef XGBOOST_DATA_SPARSE_PAGE_SOURCE_H_
 #define XGBOOST_DATA_SPARSE_PAGE_SOURCE_H_
 
-#include <dmlc/threadediter.h>
-#include <dmlc/timer.h>
-
 #include <algorithm>
 #include <limits>
 #include <locale>
@@ -19,6 +16,9 @@
 #include <vector>
 #include <fstream>
 
+#include <dmlc/threadediter.h>
+#include <dmlc/timer.h>
+
 #include "xgboost/base.h"
 #include "xgboost/data.h"
 

src/data/sparse_page_writer.h

@@ -6,8 +6,6 @@
 #ifndef XGBOOST_DATA_SPARSE_PAGE_WRITER_H_
 #define XGBOOST_DATA_SPARSE_PAGE_WRITER_H_
 
-#include <xgboost/data.h>
-#include <dmlc/io.h>
 #include <vector>
 #include <algorithm>
 #include <cstring>
@@ -16,9 +14,12 @@
 #include <memory>
 #include <functional>
 
+#include <xgboost/data.h>
+#include <dmlc/io.h>
+
 #if DMLC_ENABLE_STD_THREAD
 #include <dmlc/concurrency.h>
-#include <thread>
+#include <thread>  // NOLINT
 #endif  // DMLC_ENABLE_STD_THREAD
 
 namespace xgboost {

src/gbm/gblinear.cc

@@ -5,14 +5,14 @@
  *        the update rule is parallel coordinate descent (shotgun)
  * \author Tianqi Chen
  */
-#include <dmlc/omp.h>
-#include <dmlc/parameter.h>
-
 #include <vector>
 #include <string>
 #include <sstream>
 #include <algorithm>
 
+#include <dmlc/omp.h>
+#include <dmlc/parameter.h>
+
 #include "xgboost/gbm.h"
 #include "xgboost/json.h"
 #include "xgboost/predictor.h"

src/gbm/gblinear_model.h

@@ -2,14 +2,14 @@
  * Copyright 2018-2019 by Contributors
  */
 #pragma once
-#include <dmlc/io.h>
-#include <dmlc/parameter.h>
-#include <xgboost/learner.h>
-
 #include <vector>
 #include <string>
 #include <cstring>
 
+#include <dmlc/io.h>
+#include <dmlc/parameter.h>
+
+#include <xgboost/learner.h>
 #include "xgboost/base.h"
 #include "xgboost/feature_map.h"
 #include "xgboost/model.h"

src/gbm/gbm.cc

@@ -3,11 +3,12 @@
  * \file gbm.cc
  * \brief Registry of gradient boosters.
  */
-#include <dmlc/registry.h>
 #include <string>
 #include <vector>
 #include <memory>
 
+#include <dmlc/registry.h>
+
 #include "xgboost/gbm.h"
 #include "xgboost/learner.h"
 #include "xgboost/generic_parameters.h"

src/gbm/gbtree.cc

@@ -4,9 +4,6 @@
  * \brief gradient boosted tree implementation.
  * \author Tianqi Chen
  */
-#include <dmlc/omp.h>
-#include <dmlc/parameter.h>
-
 #include <vector>
 #include <memory>
 #include <utility>
@@ -14,6 +11,9 @@
 #include <limits>
 #include <algorithm>
 
+#include <dmlc/omp.h>
+#include <dmlc/parameter.h>
+
 #include "xgboost/data.h"
 #include "xgboost/gbm.h"
 #include "xgboost/logging.h"

src/gbm/gbtree.h

@@ -7,8 +7,6 @@
 #ifndef XGBOOST_GBM_GBTREE_H_
 #define XGBOOST_GBM_GBTREE_H_
 
-#include <dmlc/omp.h>
-
 #include <vector>
 #include <map>
 #include <memory>
@@ -16,6 +14,7 @@
 #include <string>
 #include <unordered_map>
 
+#include <dmlc/omp.h>
 #include "xgboost/base.h"
 #include "xgboost/data.h"
 #include "xgboost/logging.h"

src/gbm/gbtree_model.h

@@ -4,6 +4,10 @@
  */
 #ifndef XGBOOST_GBM_GBTREE_MODEL_H_
 #define XGBOOST_GBM_GBTREE_MODEL_H_
+#include <memory>
+#include <utility>
+#include <string>
+#include <vector>
 
 #include <dmlc/parameter.h>
 #include <dmlc/io.h>
@@ -12,11 +16,6 @@
 #include <xgboost/parameter.h>
 #include <xgboost/learner.h>
 
-#include <memory>
-#include <utility>
-#include <string>
-#include <vector>
-
 namespace xgboost {
 
 class Json;

src/learner.cc

@@ -4,10 +4,6 @@
  * \brief Implementation of learning algorithm.
  * \author Tianqi Chen
  */
-#include <dmlc/io.h>
-#include <dmlc/parameter.h>
-#include <dmlc/thread_local.h>
-
 #include <atomic>
 #include <mutex>
 #include <algorithm>
@@ -20,7 +16,11 @@
 #include <utility>
 #include <vector>
 
-#include "dmlc/any.h"
+#include <dmlc/io.h>
+#include <dmlc/parameter.h>
+#include <dmlc/thread_local.h>
+#include <dmlc/any.h>
+
 #include "xgboost/base.h"
 #include "xgboost/data.h"
 #include "xgboost/model.h"

src/logging.cc

@@ -4,11 +4,11 @@
  * \brief Implementation of loggers.
  * \author Tianqi Chen
  */
-#include <rabit/rabit.h>
-
 #include <iostream>
 #include <map>
 
+#include <rabit/rabit.h>
+
 #include "xgboost/parameter.h"
 #include "xgboost/logging.h"
 

src/metric/elementwise_metric.cu

@@ -6,10 +6,11 @@
  *
  *  The expressions like wsum == 0 ? esum : esum / wsum is used to handle empty dataset.
  */
+#include <cmath>
+
 #include <rabit/rabit.h>
 #include <xgboost/metric.h>
 #include <dmlc/registry.h>
-#include <cmath>
 
 #include "metric_common.h"
 #include "../common/math.h"

src/metric/multiclass_metric.cu

@@ -4,10 +4,11 @@
  * \brief evaluation metrics for multiclass classification.
  * \author Kailong Chen, Tianqi Chen
  */
-#include <rabit/rabit.h>
-#include <xgboost/metric.h>
 #include <cmath>
 
+#include <rabit/rabit.h>
+#include "xgboost/metric.h"
+
 #include "metric_common.h"
 #include "../common/math.h"
 #include "../common/common.h"

src/metric/rank_metric.cc

@@ -19,15 +19,15 @@
 //   this cannot be used when the translation unit is compiled using the 'nvcc' compiler (as the
 //   corresponding headers that brings in those function declaration can't be included with CUDA).
 //   This precludes the CPU and GPU logic to coexist inside a .cu file
-
-#include <rabit/rabit.h>
-#include <xgboost/metric.h>
-#include <dmlc/registry.h>
 #include <cmath>
-
 #include <vector>
 
+#include <rabit/rabit.h>
+#include <dmlc/registry.h>
+
+#include "xgboost/metric.h"
 #include "xgboost/host_device_vector.h"
+
 #include "../common/math.h"
 #include "metric_common.h"
 

src/metric/rank_metric.cu

@@ -4,6 +4,9 @@
  * \brief prediction rank based metrics.
  * \author Kailong Chen, Tianqi Chen
  */
+#include <cmath>
+#include <vector>
+
 #include <rabit/rabit.h>
 #include <dmlc/registry.h>
 
@@ -11,9 +14,6 @@
 #include <xgboost/host_device_vector.h>
 #include <thrust/iterator/discard_iterator.h>
 
-#include <cmath>
-#include <vector>
-
 #include "metric_common.h"
 
 #include "../common/math.h"

src/metric/survival_metric.cc

@@ -4,16 +4,16 @@
  * \brief Metrics for survival analysis
  * \author Avinash Barnwal, Hyunsu Cho and Toby Hocking
  */
-
-#include <rabit/rabit.h>
-#include <xgboost/metric.h>
-#include <xgboost/host_device_vector.h>
-#include <dmlc/registry.h>
 #include <cmath>
 #include <memory>
 #include <vector>
 #include <limits>
 
+#include <dmlc/registry.h>
+#include <rabit/rabit.h>
+
+#include "xgboost/metric.h"
+#include "xgboost/host_device_vector.h"
 #include "xgboost/json.h"
 
 #include "../common/math.h"

src/objective/aft_obj.cc

@@ -3,10 +3,6 @@
  * \file rank.cc
  * \brief Definition of aft loss.
  */
-
-#include <dmlc/omp.h>
-#include <xgboost/logging.h>
-#include <xgboost/objective.h>
 #include <vector>
 #include <limits>
 #include <algorithm>
@@ -14,6 +10,10 @@
 #include <utility>
 #include <cmath>
 
+#include <dmlc/omp.h>
+#include <xgboost/logging.h>
+#include <xgboost/objective.h>
+
 #include "xgboost/json.h"
 
 #include "../common/math.h"

src/objective/multiclass_obj.cu

@@ -4,13 +4,13 @@
  * \brief Definition of multi-class classification objectives.
  * \author Tianqi Chen
  */
-#include <dmlc/omp.h>
-
 #include <vector>
 #include <algorithm>
 #include <limits>
 #include <utility>
 
+#include <dmlc/omp.h>
+
 #include "xgboost/parameter.h"
 #include "xgboost/data.h"
 #include "xgboost/logging.h"

src/objective/objective.cc

@@ -3,11 +3,11 @@
  * \file objective.cc
  * \brief Registry of all objective functions.
  */
-#include <xgboost/objective.h>
-#include <dmlc/registry.h>
-
 #include <sstream>
 
+#include <dmlc/registry.h>
+
+#include "xgboost/objective.h"
 #include "xgboost/host_device_vector.h"
 
 namespace dmlc {

src/objective/rank_obj.cu

@@ -1,14 +1,15 @@
 /*!
  * Copyright 2015-2019 XGBoost contributors
  */
-#include <dmlc/omp.h>
-#include <dmlc/timer.h>
-#include <xgboost/logging.h>
-#include <xgboost/objective.h>
 #include <vector>
 #include <algorithm>
 #include <utility>
 
+#include <dmlc/omp.h>
+#include <dmlc/timer.h>
+
+#include "xgboost/logging.h"
+#include "xgboost/objective.h"
 #include "xgboost/json.h"
 #include "xgboost/parameter.h"
 

src/objective/regression_loss.h

@@ -3,10 +3,10 @@
  */
 #ifndef XGBOOST_OBJECTIVE_REGRESSION_LOSS_H_
 #define XGBOOST_OBJECTIVE_REGRESSION_LOSS_H_
+#include <algorithm>
 
 #include <dmlc/omp.h>
 #include <xgboost/logging.h>
-#include <algorithm>
 #include "../common/math.h"
 
 namespace xgboost {

src/objective/regression_obj.cu

@@ -4,13 +4,13 @@
  * \brief Definition of single-value regression and classification objectives.
  * \author Tianqi Chen, Kailong Chen
  */
+#include <cmath>
+#include <memory>
+#include <vector>
 
 #include <dmlc/omp.h>
 #include <xgboost/logging.h>
 #include <xgboost/objective.h>
-#include <cmath>
-#include <memory>
-#include <vector>
 
 #include "xgboost/host_device_vector.h"
 #include "xgboost/json.h"

src/predictor/cpu_predictor.cc

@@ -1,13 +1,13 @@
 /*!
  * Copyright by Contributors 2017-2020
  */
-#include <dmlc/omp.h>
-#include <dmlc/any.h>
-
 #include <cstddef>
 #include <limits>
 #include <mutex>
 
+#include <dmlc/omp.h>
+#include <dmlc/any.h>
+
 #include "xgboost/base.h"
 #include "xgboost/data.h"
 #include "xgboost/predictor.h"

src/predictor/gpu_predictor.cu

@@ -1,11 +1,12 @@
 /*!
  * Copyright 2017-2020 by Contributors
  */
+#include <memory>
+
 #include <thrust/copy.h>
 #include <thrust/device_ptr.h>
 #include <thrust/device_vector.h>
 #include <thrust/fill.h>
-#include <memory>
 
 #include "xgboost/data.h"
 #include "xgboost/predictor.h"

src/predictor/predictor.cc

@@ -1,9 +1,9 @@
 /*!
  * Copyright 2017-2020 by Contributors
  */
-#include <dmlc/registry.h>
 #include <mutex>
 
+#include <dmlc/registry.h>
 #include "xgboost/predictor.h"
 #include "xgboost/data.h"
 #include "xgboost/generic_parameters.h"

src/tree/constraints.cu

@@ -1,15 +1,15 @@
 /*!
  * Copyright 2019 XGBoost contributors
  */
+#include <algorithm>
+#include <string>
+#include <set>
+
 #include <thrust/copy.h>
 #include <thrust/device_vector.h>
 #include <thrust/execution_policy.h>
 #include <thrust/iterator/counting_iterator.h>
 
-#include <algorithm>
-#include <string>
-#include <set>
-
 #include "xgboost/logging.h"
 #include "xgboost/span.h"
 #include "constraints.cuh"

src/tree/gpu_hist/gradient_based_sampler.cu

@@ -1,15 +1,16 @@
 /*!
  * Copyright 2019 by XGBoost Contributors
  */
+#include <algorithm>
+#include <limits>
+
 #include <thrust/functional.h>
 #include <thrust/random.h>
 #include <thrust/transform.h>
+
 #include <xgboost/host_device_vector.h>
 #include <xgboost/logging.h>
 
-#include <algorithm>
-#include <limits>
-
 #include "../../common/compressed_iterator.h"
 #include "../../common/random.h"
 #include "gradient_based_sampler.cuh"

src/tree/gpu_hist/histogram.cu

@@ -1,12 +1,13 @@
 /*!
  * Copyright 2020 by XGBoost Contributors
  */
-#include <thrust/reduce.h>
-#include <thrust/iterator/transform_iterator.h>
 #include <algorithm>
 #include <ctgmath>
 #include <limits>
 
+#include <thrust/reduce.h>
+#include <thrust/iterator/transform_iterator.h>
+
 #include "xgboost/base.h"
 #include "row_partitioner.cuh"
 

src/tree/gpu_hist/row_partitioner.cu

@@ -1,10 +1,12 @@
 /*!
  * Copyright 2017-2019 XGBoost contributors
  */
+#include <vector>
+
 #include <thrust/iterator/discard_iterator.h>
 #include <thrust/iterator/transform_output_iterator.h>
 #include <thrust/sequence.h>
-#include <vector>
+
 #include "../../common/device_helpers.cuh"
 #include "row_partitioner.cuh"
 

src/tree/split_evaluator.cc

@@ -3,9 +3,6 @@
  * \file split_evaluator.cc
  * \brief Contains implementations of different split evaluators.
  */
-#include <dmlc/json.h>
-#include <dmlc/registry.h>
-
 #include <algorithm>
 #include <unordered_set>
 #include <vector>
@@ -15,6 +12,9 @@
 #include <sstream>
 #include <utility>
 
+#include <dmlc/json.h>
+#include <dmlc/registry.h>
+
 #include "xgboost/logging.h"
 #include "xgboost/parameter.h"
 

src/tree/split_evaluator.h

@@ -7,15 +7,15 @@
 
 #ifndef XGBOOST_TREE_SPLIT_EVALUATOR_H_
 #define XGBOOST_TREE_SPLIT_EVALUATOR_H_
-
-#include <dmlc/registry.h>
-#include <xgboost/base.h>
 #include <functional>
 #include <memory>
 #include <string>
 #include <utility>
 #include <vector>
 
+#include <dmlc/registry.h>
+#include <xgboost/base.h>
+
 #include "param.h"
 
 #define ROOT_PARENT_ID (-1 & ((1U << 31) - 1))

src/tree/tree_model.cc

@@ -3,6 +3,12 @@
  * \file tree_model.cc
  * \brief model structure for tree
  */
+#include <sstream>
+#include <limits>
+#include <cmath>
+#include <iomanip>
+#include <stack>
+
 #include <dmlc/registry.h>
 #include <dmlc/json.h>
 
@@ -10,12 +16,6 @@
 #include <xgboost/logging.h>
 #include <xgboost/json.h>
 
-#include <sstream>
-#include <limits>
-#include <cmath>
-#include <iomanip>
-#include <stack>
-
 #include "param.h"
 #include "../common/common.h"
 

src/tree/updater_basemaker-inl.h

@@ -7,15 +7,13 @@
 #ifndef XGBOOST_TREE_UPDATER_BASEMAKER_INL_H_
 #define XGBOOST_TREE_UPDATER_BASEMAKER_INL_H_
 
-#include <rabit/rabit.h>
-
-
 #include <vector>
 #include <algorithm>
 #include <string>
 #include <limits>
 #include <utility>
 
+#include <rabit/rabit.h>
 #include "xgboost/base.h"
 #include "xgboost/json.h"
 #include "xgboost/tree_updater.h"

src/tree/updater_colmaker.cc

@@ -4,12 +4,13 @@
  * \brief use columnwise update to construct a tree
  * \author Tianqi Chen
  */
-#include <rabit/rabit.h>
 #include <memory>
 #include <vector>
 #include <cmath>
 #include <algorithm>
 
+#include <rabit/rabit.h>
+
 #include "xgboost/parameter.h"
 #include "xgboost/tree_updater.h"
 #include "xgboost/logging.h"

src/tree/updater_gpu_hist.cu

@@ -1,9 +1,6 @@
 /*!
  * Copyright 2017-2020 XGBoost contributors
  */
-#include <thrust/copy.h>
-#include <thrust/reduce.h>
-#include <xgboost/tree_updater.h>
 #include <algorithm>
 #include <cmath>
 #include <memory>
@@ -12,6 +9,10 @@
 #include <utility>
 #include <vector>
 
+#include <thrust/copy.h>
+#include <thrust/reduce.h>
+
+#include "xgboost/tree_updater.h"
 #include "xgboost/host_device_vector.h"
 #include "xgboost/parameter.h"
 #include "xgboost/span.h"

src/tree/updater_histmaker.cc

@@ -4,10 +4,10 @@
  * \brief use histogram counting to construct a tree
  * \author Tianqi Chen
  */
-#include <rabit/rabit.h>
 #include <vector>
 #include <algorithm>
 
+#include <rabit/rabit.h>
 #include "xgboost/tree_updater.h"
 #include "xgboost/base.h"
 #include "xgboost/logging.h"

src/tree/updater_prune.cc

@@ -4,17 +4,18 @@
  * \brief prune a tree given the statistics
  * \author Tianqi Chen
  */
-#include <rabit/rabit.h>
-#include <xgboost/tree_updater.h>
-
 #include <string>
 #include <memory>
 
+#include <rabit/rabit.h>
+
+#include "xgboost/tree_updater.h"
 #include "xgboost/base.h"
 #include "xgboost/json.h"
 #include "./param.h"
 #include "../common/io.h"
 #include "../common/timer.h"
+
 namespace xgboost {
 namespace tree {
 

src/tree/updater_quantile_hist.cc

@@ -4,9 +4,6 @@
  * \brief use quantized feature values to construct a tree
  * \author Philip Cho, Tianqi Checn, Egor Smirnov
  */
-#include <dmlc/timer.h>
-#include <rabit/rabit.h>
-
 #include <cmath>
 #include <memory>
 #include <vector>
@@ -17,6 +14,8 @@
 #include <string>
 #include <utility>
 
+#include <dmlc/timer.h>
+#include <rabit/rabit.h>
 #include "xgboost/logging.h"
 #include "xgboost/tree_updater.h"
 

src/tree/updater_quantile_hist.h

@@ -7,10 +7,6 @@
 #ifndef XGBOOST_TREE_UPDATER_QUANTILE_HIST_H_
 #define XGBOOST_TREE_UPDATER_QUANTILE_HIST_H_
 
-#include <dmlc/timer.h>
-#include <rabit/rabit.h>
-#include <xgboost/tree_updater.h>
-
 #include <memory>
 #include <vector>
 #include <string>
@@ -19,8 +15,13 @@
 #include <unordered_map>
 #include <utility>
 
+#include <dmlc/timer.h>
+#include <rabit/rabit.h>
+
+#include "xgboost/tree_updater.h"
 #include "xgboost/data.h"
 #include "xgboost/json.h"
+
 #include "constraints.h"
 #include "./param.h"
 #include "./split_evaluator.h"

src/tree/updater_refresh.cc

@@ -4,12 +4,12 @@
  * \brief refresh the statistics and leaf value on the tree on the dataset
  * \author Tianqi Chen
  */
-#include <rabit/rabit.h>
-#include <xgboost/tree_updater.h>
-
 #include <vector>
 #include <limits>
 
+#include <rabit/rabit.h>
+
+#include "xgboost/tree_updater.h"
 #include "xgboost/json.h"
 #include "./param.h"
 #include "../common/io.h"

src/tree/updater_skmaker.cc

@@ -5,12 +5,13 @@
           a refresh is needed to make the statistics exactly correct
  * \author Tianqi Chen
  */
-#include <rabit/rabit.h>
-#include <xgboost/base.h>
-#include <xgboost/tree_updater.h>
 #include <vector>
 #include <algorithm>
 
+#include <rabit/rabit.h>
+#include "xgboost/base.h"
+#include "xgboost/tree_updater.h"
+
 #include "../common/quantile.h"
 #include "../common/group_data.h"
 #include "./updater_basemaker-inl.h"

src/tree/updater_sync.cc

@@ -3,11 +3,11 @@
  * \file updater_sync.cc
  * \brief synchronize the tree in all distributed nodes
  */
-#include <xgboost/tree_updater.h>
 #include <vector>
 #include <string>
 #include <limits>
 
+#include "xgboost/tree_updater.h"
 #include "xgboost/json.h"
 #include "../common/io.h"