Merge pull request #1 from abacusmodeling/develop

update from branch develop

.clang-format

@@ -0,0 +1,166 @@
+---
+Language:        Cpp
+# BasedOnStyle:  LLVM
+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
+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
+...
+

.clang-tidy

@@ -0,0 +1,5 @@
+---
+Checks: '-*,clang-diagnostic-*,clang-analyzer-*,google-*,llvm-header-guard,cppcoreguidelines-avoid-non-const-global-variables,cppcoreguidelines-init-variables,cppcoreguidelines-pro-type-member-init,fuchsia-multiple-inheritance,misc-non-private-member-variables-in-classes,readability-make-member-function-const,readability-function-size,misc-unused-parameters,readability-non-const-parameter,cppcoreguidelines-macro-usage,modernize-use-nullptr,modernize-deprecated-headers'
+FormatStyle: none
+CheckOptions:
+...

.devcontainer/Dockerfile

@@ -0,0 +1 @@
+FROM ghcr.io/deepmodeling/abacus-development-kit:gnu

.devcontainer/devcontainer.json

@@ -0,0 +1,32 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the README at:
+// https://github.com/microsoft/vscode-dev-containers/tree/v0.183.0/containers/docker-existing-dockerfile
+{
+	"name": "Existing Dockerfile",
+
+	// Sets the run context to one level up instead of the .devcontainer folder.
+	"context": "..",
+
+	// Update the 'dockerFile' property if you aren't using the standard 'Dockerfile' filename.
+	"dockerFile": "Dockerfile",
+
+	// Set *default* container specific settings.json values on container create.
+	"settings": {},
+
+	// Add the IDs of extensions you want installed when the container is created.
+	"extensions": []
+
+	// Use 'forwardPorts' to make a list of ports inside the container available locally.
+	// "forwardPorts": [],
+
+	// Uncomment the next line to run commands after the container is created - for example installing curl.
+	// "postCreateCommand": "apt-get update && apt-get install -y curl",
+
+	// Uncomment when using a ptrace-based debugger like C++, Go, and Rust
+	// "runArgs": [ "--cap-add=SYS_PTRACE", "--security-opt", "seccomp=unconfined" ],
+
+	// Uncomment to use the Docker CLI from inside the container. See https://aka.ms/vscode-remote/samples/docker-from-docker.
+	// "mounts": [ "source=/var/run/docker.sock,target=/var/run/docker.sock,type=bind" ],
+
+	// Uncomment to connect as a non-root user if you've added one. See https://aka.ms/vscode-remote/containers/non-root.
+	// "remoteUser": "vscode"
+}

.editorconfig

@@ -0,0 +1,12 @@
+root = true
+
+[*]
+indent_style = space
+indent_size = 4
+charset = utf-8
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+
+[*.yaml]
+indent_size = 2

.github/workflows/container.yml

@@ -0,0 +1,32 @@
+name: Container
+
+on:
+  push:
+    branches:
+      - develop
+      - reconstruction
+
+env:
+  CONTAINER: ghcr.io/deepmodeling/abacus-development-kit:gnu
+
+jobs:
+  build_container_and_push:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Setup Docker Buildx
+        uses: docker/setup-buildx-action@v1
+      - name: Login to GitHub Container Registry
+        uses: docker/login-action@v1
+        with:
+          registry: ghcr.io
+          username: ${{ secrets.OWNER }}
+          password: ${{ secrets.PAT }}
+      - name: Build and Push Container
+        uses: docker/build-push-action@v2
+        with:
+          tags: ${{ env.CONTAINER }}
+          cache-from: type=registry,ref=${{ env.CONTAINER }}
+          cache-to: type=inline
+          push: true

.github/workflows/dynamic.yml

@@ -0,0 +1,77 @@
+name: Dynamic Analysis
+
+on:
+  schedule:
+    - cron: '0 20 * * *'
+  workflow_dispatch:
+    inputs:
+      name:
+        description: 'Number of Cores to Run ABACUS'
+        required: false
+        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
+    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 --build build -j16
+          ctest --test-dir build --verbose
+      - 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

@@ -0,0 +1,46 @@
+name: Static Analysis
+
+on:
+  workflow_dispatch:
+
+jobs:
+  clang-tidy:
+    runs-on: ubuntu-20.04
+    container: ghcr.io/deepmodeling/abacus-development-kit:gnu
+    steps:
+      - name: Checkout Pull Request
+        uses: actions/checkout@v2
+        with:
+          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
+      - name: Generate Build Commands
+        run: |
+          cmake -B build -DCMAKE_EXPORT_COMPILE_COMMANDS=1 -DCMAKE_CXX_COMPILER=clang++-12
+      - 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`
+      - name: Run clang-tidy-pr-comments action
+        uses: deepmodeling/abacus-code-reviewer@master
+        with:
+          # The GitHub token (or a personal access token)
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          # The path to the clang-tidy fixes generated previously
+          clang_tidy_fixes: diagnostics.yaml
+          # Optionally set to true if you want the Action to request
+          # changes in case warnings are found
+          request_changes: true
+          # Optionally set the number of comments per review
+          # to avoid GitHub API timeouts for heavily loaded
+          # pull requests
+          suggestions_per_comment: 10