Merge branch 'branch-0.14' into opg_degree

.gitignore

@@ -58,7 +58,14 @@ cpp/thirdparty/googletest/
 *.ipr
 *.iws
 
+## Datasets
 datasets/*
+!datasets/cyber.csv
+!datasets/karate-data.csv
+!datasets/karate_undirected.csv
+!datasets/netscience.csv
+
+
 .pydevproject
 
 # Jupyter Notebooks

CHANGELOG.md

@@ -19,14 +19,21 @@
 - PR #807 Updating the Python docs
 - PR #820 OPG infra and all-gather smoke test
 - PR #829 Updated README and CONTRIBUTIOIN docs
+- PR #836 Remove SNMG code
+- PR #831 Updated Notebook - Added K-Truss, ECG, and Betweenness Centrality
+- PR #832 Removed RMM ALLOC from db subtree
 - PR #833 Update graph functions to use new Graph class
+- PR #834 Updated local gpuci build
+- PR #845 Add .clang-format & format all files
 
 ## Bug Fixes
 - PR #763 Update RAPIDS conda dependencies to v0.14
 - PR #795 Fix some documentation
 - PR #800 Fix bfs error in optimization path
 - PR #825 Fix outdated CONTRIBUTING.md
-- PR #827 Fix indexing CI errors due to cudf updates 
+- PR #827 Fix indexing CI errors due to cudf updates
+- PR #844 Fixing tests, converting __getitem__ calls to .iloc
+
 
 # cuGraph 0.13.0 (Date TBD)
 

ci/checks/style.sh

@@ -13,7 +13,11 @@ source activate gdf
 
 # Run flake8 and get results/return code
 FLAKE=`flake8 python`
-RETVAL=$?
+FLAKE_RETVAL=$?
+
+# Run clang-format and check for a consistent code format
+CLANG_FORMAT=`python cpp/scripts/run-clang-format.py 2>&1`
+CLANG_FORMAT_RETVAL=$?
 
 # Output results if failure otherwise show pass
 if [ "$FLAKE" != "" ]; then
@@ -24,4 +28,17 @@ else
   echo -e "\n\n>>>> PASSED: flake8 style check\n\n"
 fi
 
+if [ "$CLANG_FORMAT_RETVAL" != "0" ]; then
+  echo -e "\n\n>>>> FAILED: clang format check; begin output\n\n"
+  echo -e "$CLANG_FORMAT"
+  echo -e "\n\n>>>> FAILED: clang format check; end output\n\n"
+else
+  echo -e "\n\n>>>> PASSED: clang format check\n\n"
+fi
+
+RETVALS=($FLAKE_RETVAL $CLANG_FORMAT_RETVAL)
+IFS=$'\n'
+RETVAL=`echo "${RETVALS[*]}" | sort -nr | head -n1`
+
 exit $RETVAL
+

ci/local/README.md

@@ -23,7 +23,7 @@ where:
 ```
 
 Example Usage:
-`bash build.sh -r ~/rapids/cugraph -i gpuci/rapidsai-base:cuda9.2-ubuntu16.04-gcc5-py3.6`
+`bash build.sh -r ~/rapids/cugraph -i gpuci/rapidsai-base:cuda10.1-ubuntu16.04-gcc5-py3.6`
 
 For a full list of available gpuCI docker images, visit our [DockerHub](https://hub.docker.com/r/gpuci/rapidsai-base/tags) page.
 
@@ -42,7 +42,7 @@ There are some caveats to be aware of when using this script, especially if you
 
 ### Docker Image Build Repository
 
-The docker image will generate build artifacts in a folder on your machine located in the `root` directory of the repository you passed to the script. For the above example, the directory is named `~/rapids/cugraph/build_rapidsai-base_cuda9.2-ubuntu16.04-gcc5-py3.6/`. Feel free to remove this directory after the script is finished.
+The docker image will generate build artifacts in a folder on your machine located in the `root` directory of the repository you passed to the script. For the above example, the directory is named `~/rapids/cugraph/build_rapidsai-base_cuda10.1-ubuntu16.04-gcc5-py3.6/`. Feel free to remove this directory after the script is finished.
 
 *Note*: The script *will not* override your local build repository. Your local environment stays in tact.
 

ci/local/build.sh

@@ -76,7 +76,7 @@ mkdir -p "${REPO_PATH}/${PYTHON_BUILD_DIR}"
 
 BUILD_SCRIPT="#!/bin/bash
 set -e
-WORKSPACE=${REPO_PATH_IN_CONTAINER}
+export WORKSPACE=${REPO_PATH_IN_CONTAINER}
 PREBUILD_SCRIPT=${REPO_PATH_IN_CONTAINER}/ci/gpu/prebuild.sh
 BUILD_SCRIPT=${REPO_PATH_IN_CONTAINER}/ci/gpu/build.sh
 cd \${WORKSPACE}
@@ -123,12 +123,20 @@ fi
 
 # Run the generated build script in a container
 docker pull "${DOCKER_IMAGE}"
-docker run --runtime=nvidia --rm -it -e NVIDIA_VISIBLE_DEVICES="${NVIDIA_VISIBLE_DEVICES}" \
+
+DOCKER_MAJOR=$(docker -v|sed 's/[^[0-9]*\([0-9]*\).*/\1/')
+GPU_OPTS="--gpus device=${NVIDIA_VISIBLE_DEVICES}"
+if [ "$DOCKER_MAJOR" -lt 19 ]
+then
+    GPU_OPTS="--runtime=nvidia -e NVIDIA_VISIBLE_DEVICES='${NVIDIA_VISIBLE_DEVICES}'"
+fi
+
+docker run --rm -it ${GPU_OPTS} \
        -u "$(id -u)":"$(id -g)" \
        -v "${REPO_PATH}":"${REPO_PATH_IN_CONTAINER}" \
        -v "${CPP_CONTAINER_BUILD_DIR}":"${CPP_BUILD_DIR_IN_CONTAINER}" \
        -v "${PYTHON_CONTAINER_BUILD_DIR}":"${PYTHON_BUILD_DIR_IN_CONTAINER}" \
        -v "$PASSWD_FILE":/etc/passwd:ro \
        -v "$GROUP_FILE":/etc/group:ro \
        --cap-add=SYS_PTRACE \
-       "${DOCKER_IMAGE}" bash -c "${COMMAND}"
+       "${DOCKER_IMAGE}" bash -c "${COMMAND}"

cpp/.clang-format

@@ -0,0 +1,156 @@
+---
+# Refer to the following link for the explanation of each params:
+#   http://releases.llvm.org/8.0.0/tools/clang/docs/ClangFormatStyleOptions.html
+Language: Cpp
+# BasedOnStyle: Google
+AccessModifierOffset: -1
+AlignAfterOpenBracket: Align
+AlignConsecutiveAssignments: true
+AlignConsecutiveDeclarations: false
+AlignEscapedNewlines: Left
+AlignOperands: true
+AlignTrailingComments: true
+AllowAllParametersOfDeclarationOnNextLine: true
+AllowShortBlocksOnASingleLine: true 
+AllowShortCaseLabelsOnASingleLine: true
+AllowShortFunctionsOnASingleLine: All
+AllowShortIfStatementsOnASingleLine: true
+AllowShortLoopsOnASingleLine: true
+# This is deprecated
+AlwaysBreakAfterDefinitionReturnType: None
+AlwaysBreakAfterReturnType: None
+AlwaysBreakBeforeMultilineStrings: true
+AlwaysBreakTemplateDeclarations: Yes
+BinPackArguments:  false       
+BinPackParameters: false
+BraceWrapping:
+  AfterClass:            false
+  AfterControlStatement: false
+  AfterEnum:             false
+  AfterFunction:         false
+  AfterNamespace:        false
+  AfterObjCDeclaration:  false
+  AfterStruct:           false
+  AfterUnion:            false
+  AfterExternBlock:      false
+  BeforeCatch:           false
+  BeforeElse:            false
+  IndentBraces:          false
+  # disabling the below splits, else, they'll just add to the vertical length of source files!
+  SplitEmptyFunction: false
+  SplitEmptyRecord: false
+  SplitEmptyNamespace: false
+BreakBeforeBinaryOperators: None
+BreakBeforeBraces: WebKit
+BreakBeforeInheritanceComma: false
+BreakInheritanceList: BeforeColon
+BreakBeforeTernaryOperators: true
+BreakConstructorInitializersBeforeComma: false
+BreakConstructorInitializers: BeforeColon
+BreakAfterJavaFieldAnnotations: false
+BreakStringLiterals: true
+ColumnLimit: 100
+CommentPragmas: '^ IWYU pragma:'
+CompactNamespaces: false
+ConstructorInitializerAllOnOneLineOrOnePerLine: true
+# Kept the below 2 to be the same as `IndentWidth` to keep everything uniform
+ConstructorInitializerIndentWidth: 2
+ContinuationIndentWidth: 2
+Cpp11BracedListStyle: true
+DerivePointerAlignment: true
+DisableFormat: false
+ExperimentalAutoDetectBinPacking: false
+FixNamespaceComments: true
+ForEachMacros:
+  - foreach
+  - Q_FOREACH
+  - BOOST_FOREACH
+IncludeBlocks: Preserve
+IncludeCategories:
+  - Regex:           '^<ext/.*\.h>'
+    Priority:        2
+  - Regex:           '^<.*\.h>'
+    Priority:        1
+  - Regex:           '^<.*'
+    Priority:        2
+  - Regex:           '.*'
+    Priority:        3
+IncludeIsMainRegex: '([-_](test|unittest))?$'
+IndentCaseLabels: true
+IndentPPDirectives: None
+IndentWidth:     2
+IndentWrappedFunctionNames: false
+JavaScriptQuotes: Leave
+JavaScriptWrapImports: true
+KeepEmptyLinesAtTheStartOfBlocks: false
+MacroBlockBegin: ''
+MacroBlockEnd:   ''
+MaxEmptyLinesToKeep: 1
+NamespaceIndentation: None
+ObjCBinPackProtocolList: Never
+ObjCBlockIndentWidth: 2
+ObjCSpaceAfterProperty: false
+ObjCSpaceBeforeProtocolList: true
+PenaltyBreakAssignment: 2
+PenaltyBreakBeforeFirstCallParameter: 1
+PenaltyBreakComment: 300
+PenaltyBreakFirstLessLess: 120
+PenaltyBreakString: 1000
+PenaltyBreakTemplateDeclaration: 10
+PenaltyExcessCharacter: 1000000
+PenaltyReturnTypeOnItsOwnLine: 200
+PointerAlignment: Left
+RawStringFormats:
+  - Language: Cpp
+    Delimiters:
+      - cc
+      - CC
+      - cpp
+      - Cpp
+      - CPP
+      - 'c++'
+      - 'C++'
+    CanonicalDelimiter: ''
+  - Language: TextProto
+    Delimiters:
+      - pb
+      - PB
+      - proto
+      - PROTO
+    EnclosingFunctions:
+      - EqualsProto
+      - EquivToProto
+      - PARSE_PARTIAL_TEXT_PROTO
+      - PARSE_TEST_PROTO
+      - PARSE_TEXT_PROTO
+      - ParseTextOrDie
+      - ParseTextProtoOrDie
+    CanonicalDelimiter: ''
+    BasedOnStyle: google
+# Enabling comment reflow causes doxygen comments to be messed up in their formats!
+ReflowComments: true
+SortIncludes: true
+SortUsingDeclarations: true
+SpaceAfterCStyleCast: false
+SpaceAfterTemplateKeyword: true
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeCpp11BracedList: false
+SpaceBeforeCtorInitializerColon: true
+SpaceBeforeInheritanceColon: true
+SpaceBeforeParens: ControlStatements
+SpaceBeforeRangeBasedForLoopColon: true
+SpaceInEmptyParentheses: false
+SpacesBeforeTrailingComments: 2
+SpacesInAngles: false
+SpacesInContainerLiterals: true
+SpacesInCStyleCastParentheses: false
+SpacesInParentheses: false
+SpacesInSquareBrackets: false
+Standard: Cpp11
+StatementMacros:
+  - Q_UNUSED
+  - QT_REQUIRE_VERSION
+# Be consistent with indent-width, even for people who use tab for indentation!
+TabWidth: 2
+UseTab: Never
+

cpp/CMakeLists.txt

@@ -171,46 +171,6 @@ if(BUILD_TESTS)
     endif(GTEST_FOUND)
 endif(BUILD_TESTS)
 
-###################################################################################################
-# - NVStrings -------------------------------------------------------------------------------------
-
-find_path(NVSTRINGS_INCLUDE "nvstrings"
-          HINTS "$ENV{NVSTRINGS_ROOT}/include"
-                "$ENV{CONDA_PREFIX}/include/nvstrings"
-                "$ENV{CONDA_PREFIX}/include")
-
-find_library(NVSTRINGS_LIBRARY "NVStrings"
-             HINTS "$ENV{NVSTRINGS_ROOT}/lib"
-                   "$ENV{CONDA_PREFIX}/lib")
-
-find_library(NVCATEGORY_LIBRARY "NVCategory"
-             HINTS "$ENV{NVSTRINGS_ROOT}/lib"
-                   "$ENV{CONDA_PREFIX}/lib")
-
-find_library(NVTEXT_LIBRARY "NVText"
-             HINTS "$ENV{NVSTRINGS_ROOT}/lib"
-                   "$ENV{CONDA_PREFIX}/lib")
-
-message(STATUS "NVSTRINGS: NVSTRINGS_INCLUDE set to ${NVSTRINGS_INCLUDE}")
-message(STATUS "NVSTRINGS: NVSTRINGS_LIBRARY set to ${NVSTRINGS_LIBRARY}")
-message(STATUS "NVSTRINGS: NVCATEGORY_LIBRARY set to ${NVCATEGORY_LIBRARY}")
-message(STATUS "NVSTRINGS: NVTEXT_LIBRARY set to ${NVTEXT_LIBRARY}")
-
-add_library(NVStrings SHARED IMPORTED ${NVSTRINGS_LIBRARY})
-if (NVSTRINGS_INCLUDE AND NVSTRINGS_LIBRARY)
-    set_target_properties(NVStrings PROPERTIES IMPORTED_LOCATION ${NVSTRINGS_LIBRARY})
-endif (NVSTRINGS_INCLUDE AND NVSTRINGS_LIBRARY)
-
-add_library(NVCategory SHARED IMPORTED ${NVCATEGORY_LIBRARY})
-if (NVSTRINGS_INCLUDE AND NVCATEGORY_LIBRARY)
-    set_target_properties(NVCategory PROPERTIES IMPORTED_LOCATION ${NVCATEGORY_LIBRARY})
-endif (NVSTRINGS_INCLUDE AND NVCATEGORY_LIBRARY)
-
-add_library(NVText SHARED IMPORTED ${NVTEXT_LIBRARY})
-if (NVSTRINGS_INCLUDE AND NVTEXT_LIBRARY)
-    set_target_properties(NVText PROPERTIES IMPORTED_LOCATION ${NVTEXT_LIBRARY})
-endif (NVSTRINGS_INCLUDE AND NVTEXT_LIBRARY)
-
 ###################################################################################################
 # - cudf ------------------------------------------------------------------------------------------
 
@@ -350,16 +310,11 @@ add_library(cugraph SHARED
     src/community/ECG.cu
     src/cores/core_number.cu
     src/traversal/two_hop_neighbors.cu
-    src/snmg/blas/spmv.cu
-    src/snmg/link_analysis/pagerank.cu
     src/utilities/cusparse_helper.cu
     src/utilities/graph_utils.cu
-    src/snmg/utils.cu
     src/components/connectivity.cu
     src/centrality/katz_centrality.cu
     src/centrality/betweenness_centrality.cu
-    src/snmg/degree/degree.cu
-    src/snmg/COO2CSR/COO2CSR.cu
     src/nvgraph/arnoldi.cu
     src/nvgraph/bfs.cu
     src/nvgraph/bfs2d.cu