Merge pull request #110 from dyzheng/develop

update abacusmodeling/abacus-develop: develop from deepmodeling/abacus-develop: develop

Author: dyzheng

.clang-format

@@ -1,166 +1,37 @@
 ---
-Language:        Cpp
-# BasedOnStyle:  LLVM
-AccessModifierOffset: -2
+BasedOnStyle: Microsoft
+AccessModifierOffset: '-2'
 AlignAfterOpenBracket: Align
-AlignConsecutiveMacros: None
-AlignConsecutiveAssignments: None
-AlignConsecutiveBitFields: None
-AlignConsecutiveDeclarations: None
-AlignEscapedNewlines: Right
-AlignOperands:   Align
-AlignTrailingComments: true
-AllowAllArgumentsOnNextLine: true
-AllowAllConstructorInitializersOnNextLine: true
-AllowAllParametersOfDeclarationOnNextLine: true
-AllowShortEnumsOnASingleLine: true
-AllowShortBlocksOnASingleLine: Never
-AllowShortCaseLabelsOnASingleLine: false
-AllowShortFunctionsOnASingleLine: All
-AllowShortLambdasOnASingleLine: All
-AllowShortIfStatementsOnASingleLine: Never
-AllowShortLoopsOnASingleLine: false
-AlwaysBreakAfterDefinitionReturnType: None
-AlwaysBreakAfterReturnType: None
-AlwaysBreakBeforeMultilineStrings: false
-AlwaysBreakTemplateDeclarations: MultiLine
-AttributeMacros:
-  - __capability
-BinPackArguments: true
-BinPackParameters: true
-BraceWrapping:
-  AfterCaseLabel:  false
-  AfterClass:      false
-  AfterControlStatement: Never
-  AfterEnum:       false
-  AfterFunction:   false
-  AfterNamespace:  false
-  AfterObjCDeclaration: false
-  AfterStruct:     false
-  AfterUnion:      false
-  AfterExternBlock: false
-  BeforeCatch:     false
-  BeforeElse:      false
-  BeforeLambdaBody: false
-  BeforeWhile:     false
-  IndentBraces:    false
-  SplitEmptyFunction: true
-  SplitEmptyRecord: true
-  SplitEmptyNamespace: true
-BreakBeforeBinaryOperators: None
-BreakBeforeConceptDeclarations: true
-BreakBeforeBraces: Attach
-BreakBeforeInheritanceComma: false
-BreakInheritanceList: BeforeColon
-BreakBeforeTernaryOperators: true
-BreakConstructorInitializersBeforeComma: false
-BreakConstructorInitializers: BeforeColon
-BreakAfterJavaFieldAnnotations: false
-BreakStringLiterals: true
-ColumnLimit:     80
-CommentPragmas:  '^ IWYU pragma:'
-CompactNamespaces: false
-ConstructorInitializerAllOnOneLineOrOnePerLine: false
-ConstructorInitializerIndentWidth: 4
-ContinuationIndentWidth: 4
-Cpp11BracedListStyle: true
-DeriveLineEnding: true
-DerivePointerAlignment: false
-DisableFormat:   false
-EmptyLineBeforeAccessModifier: LogicalBlock
-ExperimentalAutoDetectBinPacking: false
-FixNamespaceComments: true
-ForEachMacros:
-  - foreach
-  - Q_FOREACH
-  - BOOST_FOREACH
-StatementAttributeLikeMacros:
-  - Q_EMIT
-IncludeBlocks:   Preserve
-IncludeCategories:
-  - Regex:           '^"(llvm|llvm-c|clang|clang-c)/'
-    Priority:        2
-    SortPriority:    0
-    CaseSensitive:   false
-  - Regex:           '^(<|"(gtest|gmock|isl|json)/)'
-    Priority:        3
-    SortPriority:    0
-    CaseSensitive:   false
-  - Regex:           '.*'
-    Priority:        1
-    SortPriority:    0
-    CaseSensitive:   false
-IncludeIsMainRegex: '(Test)?$'
-IncludeIsMainSourceRegex: ''
-IndentCaseLabels: false
-IndentCaseBlocks: false
-IndentGotoLabels: true
-IndentPPDirectives: None
-IndentExternBlock: AfterExternBlock
-IndentRequires:  false
-IndentWidth:     4
-IndentWrappedFunctionNames: false
-InsertTrailingCommas: None
-JavaScriptQuotes: Leave
-JavaScriptWrapImports: true
-KeepEmptyLinesAtTheStartOfBlocks: true
-MacroBlockBegin: ''
-MacroBlockEnd:   ''
-MaxEmptyLinesToKeep: 1
-NamespaceIndentation: None
-ObjCBinPackProtocolList: Auto
-ObjCBlockIndentWidth: 2
-ObjCBreakBeforeNestedBlockParam: true
-ObjCSpaceAfterProperty: false
-ObjCSpaceBeforeProtocolList: true
-PenaltyBreakAssignment: 2
-PenaltyBreakBeforeFirstCallParameter: 19
-PenaltyBreakComment: 300
-PenaltyBreakFirstLessLess: 120
-PenaltyBreakString: 1000
-PenaltyBreakTemplateDeclaration: 10
-PenaltyExcessCharacter: 1000000
-PenaltyReturnTypeOnItsOwnLine: 60
-PenaltyIndentedWhitespace: 0
+AlignConsecutiveMacros: 'true'
+AlignEscapedNewlines: Left
+AlignOperands: 'true'
+AlignTrailingComments: 'false'
+AllowAllArgumentsOnNextLine: 'false'
+AllowAllParametersOfDeclarationOnNextLine: 'false'
+BinPackArguments: 'false'
+BinPackParameters: 'false'
+BreakBeforeBinaryOperators: All
+BreakBeforeTernaryOperators: 'true'
+Cpp11BracedListStyle: 'true'
+DerivePointerAlignment: 'true'
+FixNamespaceComments: 'true'
+IncludeBlocks: Regroup
+IndentWidth: '4'
+Language: Cpp
 PointerAlignment: Right
-ReflowComments:  true
-SortIncludes:    true
-SortJavaStaticImport: Before
-SortUsingDeclarations: true
-SpaceAfterCStyleCast: false
-SpaceAfterLogicalNot: false
-SpaceAfterTemplateKeyword: true
-SpaceBeforeAssignmentOperators: true
-SpaceBeforeCaseColon: false
-SpaceBeforeCpp11BracedList: false
-SpaceBeforeCtorInitializerColon: true
-SpaceBeforeInheritanceColon: true
-SpaceBeforeParens: ControlStatements
-SpaceAroundPointerQualifiers: Default
-SpaceBeforeRangeBasedForLoopColon: true
-SpaceInEmptyBlock: false
-SpaceInEmptyParentheses: false
-SpacesBeforeTrailingComments: 1
-SpacesInAngles:  false
-SpacesInConditionalStatement: false
-SpacesInContainerLiterals: true
-SpacesInCStyleCastParentheses: false
-SpacesInParentheses: false
-SpacesInSquareBrackets: false
-SpaceBeforeSquareBrackets: false
-BitFieldColonSpacing: Both
-Standard:        Latest
-StatementMacros:
-  - Q_UNUSED
-  - QT_REQUIRE_VERSION
-TabWidth:        8
-UseCRLF:         false
-UseTab:          Never
-WhitespaceSensitiveMacros:
-  - STRINGIZE
-  - PP_STRINGIZE
-  - BOOST_PP_STRINGIZE
-  - NS_SWIFT_NAME
-  - CF_SWIFT_NAME
+ReflowComments: 'true'
+SortIncludes: 'true'
+SortUsingDeclarations: 'true'
+SpaceAfterCStyleCast: 'false'
+SpaceAfterLogicalNot: 'false'
+SpaceBeforeRangeBasedForLoopColon: 'false'
+SpaceInEmptyParentheses: 'false'
+SpacesInAngles: 'false'
+SpacesInCStyleCastParentheses: 'false'
+SpacesInContainerLiterals: 'false'
+SpacesInParentheses: 'false'
+SpacesInSquareBrackets: 'false'
+Standard: Cpp11
+TabWidth: '4'
+UseTab: Never
 ...
-

.devcontainer/devcontainer.json

@@ -1,5 +1,10 @@
-// For format details, see https://aka.ms/devcontainer.json.
+// To develop inside a pre-configured container, see https://code.visualstudio.com/docs/remote/containers .
+// For format details, see https://aka.ms/devcontainer.json .
 {
 	"image":"ghcr.io/deepmodeling/abacus-development-kit:gnu",
-	"extensions": ["ms-vscode.cpptools-extension-pack"]
-}
+	"extensions": [
+		"ms-vscode.cpptools-extension-pack",
+		"xaver.clang-format",
+		"cschlosser.doxdocgen"
+	]
+}

.editorconfig

@@ -10,3 +10,7 @@ trim_trailing_whitespace = true
 
 [*.yaml]
 indent_size = 2
+
+[CMakeLists.txt]
+indent_style = space
+indent_size = 2

.github/workflows/hosted_test.yml renamed to .github/workflows/build_test.yml

@@ -1,4 +1,4 @@
-name: Test
+name: Build Test
 on: push
 
 jobs:
@@ -27,5 +27,4 @@ jobs:
       - name: Build
         run: |
           cmake -B build -DBUILD_TESTING=ON ${{ matrix.build_args }}
-          cmake --build build -j4
-          cmake --install build
+          cmake --build build -j2

.github/workflows/container.yml

@@ -6,7 +6,7 @@ on:
       - develop
       - reconstruction
       - newelpa
-      
+
 jobs:
   build_container_and_push:
     runs-on: ubuntu-latest

.github/workflows/dynamic.yml

@@ -11,67 +11,23 @@ on:
         default: '2'
 
 jobs:
-  start-runner:
-    name: Start self-hosted EC2 runner
-    runs-on: ubuntu-latest
-    outputs:
-      label: ${{ steps.start-ec2-runner.outputs.label }}
-      ec2-instance-id: ${{ steps.start-ec2-runner.outputs.ec2-instance-id }}
-    steps:
-      - name: Configure AWS credentials
-        uses: aws-actions/configure-aws-credentials@v1
-        with:
-          aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}
-          aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
-          aws-region: ${{ secrets.AWS_REGION }}
-      - name: Start EC2 runner
-        id: start-ec2-runner
-        uses: machulav/ec2-github-runner@v2
-        with:
-          mode: start
-          github-token: ${{ secrets.PAT }}
-          ec2-image-id: ami-07758124f42f794bf
-          ec2-instance-type: c5.4xlarge
-          subnet-id: subnet-f7edb991
-          security-group-id: sg-fd5185e7
   test:
     name: Do the job on the runner
-    needs: start-runner # required to start the main job when the runner is ready
-    runs-on: ${{ needs.start-runner.outputs.label }} # run the job on the newly created runner
+    runs-on: self-hosted
     container: ghcr.io/deepmodeling/abacus-development-kit:gnu
     steps:
       - name: Checkout
         uses: actions/checkout@v2
       - name: Build and Test
         run: |
-          cmake -B build -DENABLE_ASAN=1
+          cmake -B build -DENABLE_ASAN=1 -DBUILD_TESTING=ON -DENABLE_DEEPKS=1
           cmake --build build -j16
-          ctest --test-dir build --verbose
+          cmake --install build
+          cmake --build build --target test ARGS="-V"
       - name: Publish Report to Dashboard
         uses: crazy-max/ghaction-github-pages@v2
         with:
           target_branch: dashboard
           build_dir: html
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-  stop-runner:
-    name: Stop self-hosted EC2 runner
-    needs:
-      - start-runner # required to get output from the start-runner job
-      - test # required to wait when the main job is done
-    runs-on: ubuntu-latest
-    if: ${{ always() }} # required to stop the runner even if the error happened in the previous jobs
-    steps:
-      - name: Configure AWS credentials
-        uses: aws-actions/configure-aws-credentials@v1
-        with:
-          aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}
-          aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
-          aws-region: ${{ secrets.AWS_REGION }}
-      - name: Stop EC2 runner
-        uses: machulav/ec2-github-runner@v2
-        with:
-          mode: stop
-          github-token: ${{ secrets.PAT }}
-          label: ${{ needs.start-runner.outputs.label }}
-          ec2-instance-id: ${{ needs.start-runner.outputs.ec2-instance-id }}

.github/workflows/static.yaml

@@ -5,7 +5,7 @@ on:
 
 jobs:
   clang-tidy:
-    runs-on: ubuntu-20.04
+    runs-on: self-hosted
     container: ghcr.io/deepmodeling/abacus-development-kit:gnu
     steps:
       - name: Checkout Pull Request
@@ -14,22 +14,17 @@ jobs:
           ref: ${{ github.event.pull_request.head.sha }}
       - name: Setup clang-tidy
         run: |
-          apt-get install -y --no-install-recommends gnupg ca-certificates
-          wget https://apt.llvm.org/llvm-snapshot.gpg.key --no-check-certificate && apt-key add llvm-snapshot.gpg.key
-          echo "deb http://apt.llvm.org/buster/ llvm-toolchain-buster-12 main" >> /etc/apt/sources.list
-          echo "deb-src http://apt.llvm.org/buster/ llvm-toolchain-buster-12 main" >> /etc/apt/sources.list
-          apt-get update
-          apt-get install -y --no-install-recommends clang-tidy-12
+          apt-get update && apt-get install -y --no-install-recommends clang-format clang-tidy
       - name: Generate Build Commands
         run: |
-          cmake -B build -DCMAKE_EXPORT_COMPILE_COMMANDS=1 -DCMAKE_CXX_COMPILER=clang++-12
+          cmake -B build -DCMAKE_EXPORT_COMPILE_COMMANDS=1
       - name: Checkout Changed Files
         id: files
         uses: deepmodeling/get-changed-files@master
       - name: Run clang-tidy
         run: |
           printf "%s\n" ${{ steps.files.outputs.added_modified }} | grep -E "^.*\.(cpp|h)$" > cppfiles.txt
-          clang-tidy-12 -p=build --export-fixes=diagnostics.yaml `cat cppfiles.txt`
+          clang-tidy -p=build --export-fixes=diagnostics.yaml `cat cppfiles.txt`
       - name: Run clang-tidy-pr-comments action
         uses: deepmodeling/abacus-code-reviewer@master
         with: