From d3a0efbf162f3dceaaf684109e1178c150b32de3 Mon Sep 17 00:00:00 2001
From: Jiaming Yuan <jm.yuan@outlook.com>
Date: Wed, 3 Jun 2020 13:30:47 +0800
Subject: [PATCH] Reorder includes. (#5749)

* Reorder includes.

* R.
---
 R-package/src/xgboost_R.cc                  | 15 +++++++++------
 include/xgboost/base.h                      |  5 +++--
 include/xgboost/data.h                      | 14 +++++++-------
 include/xgboost/feature_map.h               |  4 ++--
 include/xgboost/gbm.h                       | 14 +++++++-------
 include/xgboost/generic_parameters.h        |  4 ++--
 include/xgboost/json.h                      |  8 ++++----
 include/xgboost/json_io.h                   |  3 ++-
 include/xgboost/learner.h                   | 12 ++++++------
 include/xgboost/linear_updater.h            | 11 +++++------
 include/xgboost/logging.h                   | 12 ++++++------
 include/xgboost/metric.h                    | 10 +++++-----
 include/xgboost/objective.h                 | 10 +++++-----
 include/xgboost/parameter.h                 |  5 +++--
 include/xgboost/predictor.h                 |  9 +++++----
 include/xgboost/span.h                      |  6 +++---
 include/xgboost/tree_model.h                | 16 ++++++++--------
 include/xgboost/tree_updater.h              | 10 +++++-----
 src/c_api/c_api.cc                          |  6 +++---
 src/cli_main.cc                             | 14 ++++++++------
 src/common/base64.h                         |  3 ++-
 src/common/common.h                         |  6 +++---
 src/common/compressed_iterator.h            |  2 +-
 src/common/hist_util.cc                     |  8 +++++---
 src/common/hist_util.cu                     |  9 ++++-----
 src/common/hist_util.h                      |  5 +++--
 src/common/host_device_vector.cc            |  6 +++---
 src/common/host_device_vector.cu            |  6 ++----
 src/common/io.h                             |  4 ++--
 src/common/math.h                           |  4 ++--
 src/common/probability_distribution.cc      |  4 ++--
 src/common/quantile.h                       |  5 +++--
 src/common/random.h                         |  4 ++--
 src/common/row_set.h                        |  3 ++-
 src/common/survival_util.cc                 |  3 ++-
 src/common/survival_util.h                  |  3 ++-
 src/common/timer.cc                         |  5 +++--
 src/common/timer.h                          |  3 ++-
 src/common/transform.h                      |  9 ++++-----
 src/common/version.cc                       |  4 ++--
 src/common/version.h                        |  2 +-
 src/data/adapter.h                          |  4 ++--
 src/data/data.cc                            |  5 ++++-
 src/data/device_dmatrix.cu                  |  6 ++++--
 src/data/device_dmatrix.h                   |  4 ++--
 src/data/ellpack_page_source.h              |  3 ++-
 src/data/simple_dmatrix.h                   |  5 ++---
 src/data/sparse_page_dmatrix.h              |  3 ++-
 src/data/sparse_page_source.h               |  6 +++---
 src/data/sparse_page_writer.h               |  7 ++++---
 src/gbm/gblinear.cc                         |  6 +++---
 src/gbm/gblinear_model.h                    |  8 ++++----
 src/gbm/gbm.cc                              |  3 ++-
 src/gbm/gbtree.cc                           |  6 +++---
 src/gbm/gbtree.h                            |  3 +--
 src/gbm/gbtree_model.h                      |  9 ++++-----
 src/learner.cc                              | 10 +++++-----
 src/logging.cc                              |  4 ++--
 src/metric/elementwise_metric.cu            |  3 ++-
 src/metric/multiclass_metric.cu             |  5 +++--
 src/metric/rank_metric.cc                   | 10 +++++-----
 src/metric/rank_metric.cu                   |  6 +++---
 src/metric/survival_metric.cc               | 10 +++++-----
 src/objective/aft_obj.cc                    |  8 ++++----
 src/objective/multiclass_obj.cu             |  4 ++--
 src/objective/objective.cc                  |  6 +++---
 src/objective/rank_obj.cu                   |  9 +++++----
 src/objective/regression_loss.h             |  2 +-
 src/objective/regression_obj.cu             |  6 +++---
 src/predictor/cpu_predictor.cc              |  6 +++---
 src/predictor/gpu_predictor.cu              |  3 ++-
 src/predictor/predictor.cc                  |  2 +-
 src/tree/constraints.cu                     |  8 ++++----
 src/tree/gpu_hist/gradient_based_sampler.cu |  7 ++++---
 src/tree/gpu_hist/histogram.cu              |  5 +++--
 src/tree/gpu_hist/row_partitioner.cu        |  4 +++-
 src/tree/split_evaluator.cc                 |  6 +++---
 src/tree/split_evaluator.h                  |  6 +++---
 src/tree/tree_model.cc                      | 12 ++++++------
 src/tree/updater_basemaker-inl.h            |  4 +---
 src/tree/updater_colmaker.cc                |  3 ++-
 src/tree/updater_gpu_hist.cu                |  7 ++++---
 src/tree/updater_histmaker.cc               |  2 +-
 src/tree/updater_prune.cc                   |  7 ++++---
 src/tree/updater_quantile_hist.cc           |  5 ++---
 src/tree/updater_quantile_hist.h            |  9 +++++----
 src/tree/updater_refresh.cc                 |  6 +++---
 src/tree/updater_skmaker.cc                 |  7 ++++---
 src/tree/updater_sync.cc                    |  2 +-
 89 files changed, 294 insertions(+), 264 deletions(-)

diff --git a/R-package/src/xgboost_R.cc b/R-package/src/xgboost_R.cc
index cb86ef469..0d5311705 100644
--- a/R-package/src/xgboost_R.cc
+++ b/R-package/src/xgboost_R.cc
@@ -1,14 +1,17 @@
 // Copyright (c) 2014 by Contributors
-#include <dmlc/logging.h>
-#include <dmlc/omp.h>
-#include <xgboost/c_api.h>
+#include <cstring>
+#include <cstdio>
 #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
diff --git a/include/xgboost/base.h b/include/xgboost/base.h
index 480242611..81b618a92 100644
--- a/include/xgboost/base.h
+++ b/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.
  */
diff --git a/include/xgboost/data.h b/include/xgboost/data.h
index d7ab895a8..908b8a15b 100644
--- a/include/xgboost/data.h
+++ b/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;
diff --git a/include/xgboost/feature_map.h b/include/xgboost/feature_map.h
index a48e28ba1..47c20f8e2 100644
--- a/include/xgboost/feature_map.h
+++ b/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.
diff --git a/include/xgboost/gbm.h b/include/xgboost/gbm.h
index d359f5c29..95c54b959 100644
--- a/include/xgboost/gbm.h
+++ b/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;
diff --git a/include/xgboost/generic_parameters.h b/include/xgboost/generic_parameters.h
index 752342b9a..19e77b304 100644
--- a/include/xgboost/generic_parameters.h
+++ b/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.
diff --git a/include/xgboost/json.h b/include/xgboost/json.h
index c190505bf..59861aa44 100644
--- a/include/xgboost/json.h
+++ b/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 {
 
diff --git a/include/xgboost/json_io.h b/include/xgboost/json_io.h
index a58afe172..261d71097 100644
--- a/include/xgboost/json_io.h
+++ b/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>
diff --git a/include/xgboost/learner.h b/include/xgboost/learner.h
index a608bc1b8..cbe064aca 100644
--- a/include/xgboost/learner.h
+++ b/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;
diff --git a/include/xgboost/linear_updater.h b/include/xgboost/linear_updater.h
index 39a0c324a..d46abdcb2 100644
--- a/include/xgboost/linear_updater.h
+++ b/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;
diff --git a/include/xgboost/logging.h b/include/xgboost/logging.h
index 07a2e67cf..ff8570db4 100644
--- a/include/xgboost/logging.h
+++ b/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 {
diff --git a/include/xgboost/metric.h b/include/xgboost/metric.h
index 8e9d2afe6..b7cc77a8c 100644
--- a/include/xgboost/metric.h
+++ b/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.
diff --git a/include/xgboost/objective.h b/include/xgboost/objective.h
index 1c0942ed0..957ff9da4 100644
--- a/include/xgboost/objective.h
+++ b/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 */
diff --git a/include/xgboost/parameter.h b/include/xgboost/parameter.h
index 3186651ed..465c101e4 100644
--- a/include/xgboost/parameter.h
+++ b/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)
  *
diff --git a/include/xgboost/predictor.h b/include/xgboost/predictor.h
index 0e3f7568c..b1790e777 100644
--- a/include/xgboost/predictor.h
+++ b/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;
diff --git a/include/xgboost/span.h b/include/xgboost/span.h
index 29b0b9a79..04b737666 100644
--- a/include/xgboost/span.h
+++ b/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.
  *
diff --git a/include/xgboost/tree_model.h b/include/xgboost/tree_model.h
index e7f6dc8ec..aa728a918 100644
--- a/include/xgboost/tree_model.h
+++ b/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
diff --git a/include/xgboost/tree_updater.h b/include/xgboost/tree_updater.h
index a091c81b0..805d6161c 100644
--- a/include/xgboost/tree_updater.h
+++ b/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;
diff --git a/src/c_api/c_api.cc b/src/c_api/c_api.cc
index 0ba795a39..f79eceda9 100644
--- a/src/c_api/c_api.cc
+++ b/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"
diff --git a/src/cli_main.cc b/src/cli_main.cc
index 5c602f374..dc4592099 100644
--- a/src/cli_main.cc
+++ b/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"
diff --git a/src/common/base64.h b/src/common/base64.h
index 4c876b5f8..ed8f7d759 100644
--- a/src/common/base64.h
+++ b/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 {
diff --git a/src/common/common.h b/src/common/common.h
index f9300f3d5..f4c82e13e 100644
--- a/src/common/common.h
+++ b/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>
diff --git a/src/common/compressed_iterator.h b/src/common/compressed_iterator.h
index 9f60722fb..a042d1ad4 100644
--- a/src/common/compressed_iterator.h
+++ b/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__
diff --git a/src/common/hist_util.cc b/src/common/hist_util.cc
index e3ca953d2..a5b4db155 100644
--- a/src/common/hist_util.cc
+++ b/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)
diff --git a/src/common/hist_util.cu b/src/common/hist_util.cu
index 716d49f9a..cde46a2b4 100644
--- a/src/common/hist_util.cu
+++ b/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"
diff --git a/src/common/hist_util.h b/src/common/hist_util.h
index d60960301..aef3f7921 100644
--- a/src/common/hist_util.h
+++ b/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"
diff --git a/src/common/host_device_vector.cc b/src/common/host_device_vector.cc
index 1dd9997fa..e5dc746c0 100644
--- a/src/common/host_device_vector.cc
+++ b/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 {
diff --git a/src/common/host_device_vector.cu b/src/common/host_device_vector.cu
index 3ffcf757e..87e58cc5b 100644
--- a/src/common/host_device_vector.cu
+++ b/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"
diff --git a/src/common/io.h b/src/common/io.h
index 528296dc7..6b9cac43f 100644
--- a/src/common/io.h
+++ b/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"
 
diff --git a/src/common/math.h b/src/common/math.h
index 41905310e..4e5add27e 100644
--- a/src/common/math.h
+++ b/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 {
 /*!
diff --git a/src/common/probability_distribution.cc b/src/common/probability_distribution.cc
index 51bcc495b..593e87fd9 100644
--- a/src/common/probability_distribution.cc
+++ b/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 {
diff --git a/src/common/quantile.h b/src/common/quantile.h
index 067b041bc..569f06aaf 100644
--- a/src/common/quantile.h
+++ b/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 {
 /*!
diff --git a/src/common/random.h b/src/common/random.h
index 45af80ce0..4ee61387d 100644
--- a/src/common/random.h
+++ b/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 {
diff --git a/src/common/row_set.h b/src/common/row_set.h
index 25f7c739d..2ac1cf467 100644
--- a/src/common/row_set.h
+++ b/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 {
 
diff --git a/src/common/survival_util.cc b/src/common/survival_util.cc
index 5630da355..4d78a49ca 100644
--- a/src/common/survival_util.cc
+++ b/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"
 
 /*
diff --git a/src/common/survival_util.h b/src/common/survival_util.h
index 50c6aab51..fac8b4728 100644
--- a/src/common/survival_util.h
+++ b/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);
diff --git a/src/common/timer.cc b/src/common/timer.cc
index 49d08a35c..1cbf869bc 100644
--- a/src/common/timer.cc
+++ b/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>
diff --git a/src/common/timer.h b/src/common/timer.h
index b2dc2a428..3fd54e186 100644
--- a/src/common/timer.h
+++ b/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 {
 
diff --git a/src/common/transform.h b/src/common/transform.h
index fa2d0d379..3d5970dec 100644
--- a/src/common/transform.h
+++ b/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"
 
diff --git a/src/common/version.cc b/src/common/version.cc
index 3fb2e5c24..c0cdffb99 100644
--- a/src/common/version.cc
+++ b/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"
diff --git a/src/common/version.h b/src/common/version.h
index 96885f6a8..3c3b97f16 100644
--- a/src/common/version.h
+++ b/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 {
diff --git a/src/data/adapter.h b/src/data/adapter.h
index e252e1da7..cd26d0bf4 100644
--- a/src/data/adapter.h
+++ b/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"
diff --git a/src/data/data.cc b/src/data/data.cc
index 2a620b7d4..ff907d031 100644
--- a/src/data/data.cc
+++ b/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"
diff --git a/src/data/device_dmatrix.cu b/src/data/device_dmatrix.cu
index d11d01b16..88d6a33a0 100644
--- a/src/data/device_dmatrix.cu
+++ b/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"
diff --git a/src/data/device_dmatrix.h b/src/data/device_dmatrix.h
index 781461baa..ad7e8aa3b 100644
--- a/src/data/device_dmatrix.h
+++ b/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"
diff --git a/src/data/ellpack_page_source.h b/src/data/ellpack_page_source.h
index a1ce587c2..c5f787f7f 100644
--- a/src/data/ellpack_page_source.h
+++ b/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"
diff --git a/src/data/simple_dmatrix.h b/src/data/simple_dmatrix.h
index 9d2130b41..7958785c6 100644
--- a/src/data/simple_dmatrix.h
+++ b/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 {
diff --git a/src/data/sparse_page_dmatrix.h b/src/data/sparse_page_dmatrix.h
index 393172658..79c95c581 100644
--- a/src/data/sparse_page_dmatrix.h
+++ b/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"
 
diff --git a/src/data/sparse_page_source.h b/src/data/sparse_page_source.h
index 108af403b..214795fad 100644
--- a/src/data/sparse_page_source.h
+++ b/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"
 
diff --git a/src/data/sparse_page_writer.h b/src/data/sparse_page_writer.h
index f63fcf0f8..f303f8427 100644
--- a/src/data/sparse_page_writer.h
+++ b/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 {
diff --git a/src/gbm/gblinear.cc b/src/gbm/gblinear.cc
index e554f8a55..4742f4971 100644
--- a/src/gbm/gblinear.cc
+++ b/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"
diff --git a/src/gbm/gblinear_model.h b/src/gbm/gblinear_model.h
index f2d0d9a86..4aff2f717 100644
--- a/src/gbm/gblinear_model.h
+++ b/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"
diff --git a/src/gbm/gbm.cc b/src/gbm/gbm.cc
index 87a6ded29..a8218e6a4 100644
--- a/src/gbm/gbm.cc
+++ b/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"
diff --git a/src/gbm/gbtree.cc b/src/gbm/gbtree.cc
index 61a3021cb..bf5156306 100644
--- a/src/gbm/gbtree.cc
+++ b/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"
diff --git a/src/gbm/gbtree.h b/src/gbm/gbtree.h
index 534c3ad54..ad9c63d14 100644
--- a/src/gbm/gbtree.h
+++ b/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"
diff --git a/src/gbm/gbtree_model.h b/src/gbm/gbtree_model.h
index 7ac7d8f47..374f31ef9 100644
--- a/src/gbm/gbtree_model.h
+++ b/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;
diff --git a/src/learner.cc b/src/learner.cc
index 34649480c..e6c3fee80 100644
--- a/src/learner.cc
+++ b/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"
diff --git a/src/logging.cc b/src/logging.cc
index f03e1be02..c8aa1d320 100644
--- a/src/logging.cc
+++ b/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"
 
diff --git a/src/metric/elementwise_metric.cu b/src/metric/elementwise_metric.cu
index 85dead9c3..82e8be3a9 100644
--- a/src/metric/elementwise_metric.cu
+++ b/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"
diff --git a/src/metric/multiclass_metric.cu b/src/metric/multiclass_metric.cu
index 377a05010..b019f2e47 100644
--- a/src/metric/multiclass_metric.cu
+++ b/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"
diff --git a/src/metric/rank_metric.cc b/src/metric/rank_metric.cc
index b55c764d2..61df43355 100644
--- a/src/metric/rank_metric.cc
+++ b/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"
 
diff --git a/src/metric/rank_metric.cu b/src/metric/rank_metric.cu
index 290b1fb02..9bcbc6882 100644
--- a/src/metric/rank_metric.cu
+++ b/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"
diff --git a/src/metric/survival_metric.cc b/src/metric/survival_metric.cc
index cc0614fe7..1ea0d6f02 100644
--- a/src/metric/survival_metric.cc
+++ b/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"
diff --git a/src/objective/aft_obj.cc b/src/objective/aft_obj.cc
index bf66d9991..40882d257 100644
--- a/src/objective/aft_obj.cc
+++ b/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"
diff --git a/src/objective/multiclass_obj.cu b/src/objective/multiclass_obj.cu
index 29af5e0d2..c968e2685 100644
--- a/src/objective/multiclass_obj.cu
+++ b/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"
diff --git a/src/objective/objective.cc b/src/objective/objective.cc
index 8f65cec0d..8641f042f 100644
--- a/src/objective/objective.cc
+++ b/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 {
diff --git a/src/objective/rank_obj.cu b/src/objective/rank_obj.cu
index e7a220dbc..44fd51193 100644
--- a/src/objective/rank_obj.cu
+++ b/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"
 
diff --git a/src/objective/regression_loss.h b/src/objective/regression_loss.h
index 60ede53dd..2f1cf829a 100644
--- a/src/objective/regression_loss.h
+++ b/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 {
diff --git a/src/objective/regression_obj.cu b/src/objective/regression_obj.cu
index 810ee9a6b..4bc3973d9 100644
--- a/src/objective/regression_obj.cu
+++ b/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"
diff --git a/src/predictor/cpu_predictor.cc b/src/predictor/cpu_predictor.cc
index ebc15128b..f1c533241 100644
--- a/src/predictor/cpu_predictor.cc
+++ b/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"
diff --git a/src/predictor/gpu_predictor.cu b/src/predictor/gpu_predictor.cu
index 15d974b42..084a01fd4 100644
--- a/src/predictor/gpu_predictor.cu
+++ b/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"
diff --git a/src/predictor/predictor.cc b/src/predictor/predictor.cc
index eb68d382b..49e1e816d 100644
--- a/src/predictor/predictor.cc
+++ b/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"
diff --git a/src/tree/constraints.cu b/src/tree/constraints.cu
index b6db0eda0..8c23064b1 100644
--- a/src/tree/constraints.cu
+++ b/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"
diff --git a/src/tree/gpu_hist/gradient_based_sampler.cu b/src/tree/gpu_hist/gradient_based_sampler.cu
index eb441f39e..558e8a236 100644
--- a/src/tree/gpu_hist/gradient_based_sampler.cu
+++ b/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"
diff --git a/src/tree/gpu_hist/histogram.cu b/src/tree/gpu_hist/histogram.cu
index edc3046d1..bf9094556 100644
--- a/src/tree/gpu_hist/histogram.cu
+++ b/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"
 
diff --git a/src/tree/gpu_hist/row_partitioner.cu b/src/tree/gpu_hist/row_partitioner.cu
index 2b7fbe4af..742d8e2f7 100644
--- a/src/tree/gpu_hist/row_partitioner.cu
+++ b/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"
 
diff --git a/src/tree/split_evaluator.cc b/src/tree/split_evaluator.cc
index be166156b..bbacca279 100644
--- a/src/tree/split_evaluator.cc
+++ b/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"
 
diff --git a/src/tree/split_evaluator.h b/src/tree/split_evaluator.h
index 2b3876491..77b31d916 100644
--- a/src/tree/split_evaluator.h
+++ b/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))
diff --git a/src/tree/tree_model.cc b/src/tree/tree_model.cc
index 8f45621ca..8818a07d9 100644
--- a/src/tree/tree_model.cc
+++ b/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"
 
diff --git a/src/tree/updater_basemaker-inl.h b/src/tree/updater_basemaker-inl.h
index 66ab91982..42f4901dd 100644
--- a/src/tree/updater_basemaker-inl.h
+++ b/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"
diff --git a/src/tree/updater_colmaker.cc b/src/tree/updater_colmaker.cc
index 951cfdb5e..563160059 100644
--- a/src/tree/updater_colmaker.cc
+++ b/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"
diff --git a/src/tree/updater_gpu_hist.cu b/src/tree/updater_gpu_hist.cu
index 25d2645e1..8a52de9e8 100644
--- a/src/tree/updater_gpu_hist.cu
+++ b/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"
diff --git a/src/tree/updater_histmaker.cc b/src/tree/updater_histmaker.cc
index c4fdbe3c0..cc17b5143 100644
--- a/src/tree/updater_histmaker.cc
+++ b/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"
diff --git a/src/tree/updater_prune.cc b/src/tree/updater_prune.cc
index 76a8916a0..5aa904ed8 100644
--- a/src/tree/updater_prune.cc
+++ b/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 {
 
diff --git a/src/tree/updater_quantile_hist.cc b/src/tree/updater_quantile_hist.cc
index 30eb01a72..51b47a386 100644
--- a/src/tree/updater_quantile_hist.cc
+++ b/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"
 
diff --git a/src/tree/updater_quantile_hist.h b/src/tree/updater_quantile_hist.h
index d74c16f72..388584df3 100644
--- a/src/tree/updater_quantile_hist.h
+++ b/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"
diff --git a/src/tree/updater_refresh.cc b/src/tree/updater_refresh.cc
index d63d88c80..5748d9b3a 100644
--- a/src/tree/updater_refresh.cc
+++ b/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"
diff --git a/src/tree/updater_skmaker.cc b/src/tree/updater_skmaker.cc
index 69cb4e58b..b4468b517 100644
--- a/src/tree/updater_skmaker.cc
+++ b/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"
diff --git a/src/tree/updater_sync.cc b/src/tree/updater_sync.cc
index 578bfb83c..6ec814d4f 100644
--- a/src/tree/updater_sync.cc
+++ b/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"