First commit

.clang-format

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+BasedOnStyle: LLVM
+
+AccessModifierOffset: 0
+AlignAfterOpenBracket: Align
+AlignConsecutiveAssignments: true
+AlignConsecutiveDeclarations: false
+AlignEscapedNewlinesLeft: false
+AlignOperands: false
+AlignTrailingComments: true
+AllowAllParametersOfDeclarationOnNextLine: false
+AllowShortBlocksOnASingleLine: true
+AllowShortCaseLabelsOnASingleLine: true
+AllowShortFunctionsOnASingleLine: All
+AllowShortIfStatementsOnASingleLine: true
+AllowShortLoopsOnASingleLine: true
+AlwaysBreakBeforeMultilineStrings: true
+AlwaysBreakTemplateDeclarations: false
+BinPackArguments: true
+BinPackParameters: true 
+BreakBeforeBinaryOperators: NonAssignment
+BreakBeforeBraces: Attach
+BreakBeforeTernaryOperators: false
+BreakConstructorInitializersBeforeComma: false
+BreakStringLiterals: false
+ColumnLimit: 150
+ConstructorInitializerAllOnOneLineOrOnePerLine: true
+ConstructorInitializerIndentWidth: 3
+ContinuationIndentWidth: 3
+Cpp11BracedListStyle: true
+DerivePointerBinding : false
+IndentCaseLabels: true
+IndentWidth: 2
+Language: Cpp
+MaxEmptyLinesToKeep: 1
+NamespaceIndentation : All
+PointerAlignment: Right
+ReflowComments: false
+SortIncludes: false
+SpaceAfterControlStatementKeyword: true
+SpaceBeforeAssignmentOperators: true
+SpaceInEmptyParentheses: false
+SpacesInParentheses: false
+Standard: Cpp11
+TabWidth: 2
+UseTab: Never

.clang-tidy

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+Checks: '-*,modernize-*,cppcoreguidelines-*,-cppcoreguidelines-init*, -modernize-use-trailing-return-type,op-check, -cppcoreguidelines-non-private-member-variables-in-classes'

.dockerignore

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+.travis.yml
+Dockerfile
+Jenkinsfile
+.git/objects/pack
+build*

.github/ISSUE_TEMPLATE/bug.md

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+---
+name: Bug report
+about: Create a report to help us improve
+title: Bug report
+labels: bug
+
+---
+
+### Prerequisites
+
+* Please check that a similar issue isn't already filed: https://github.com/flatironinstitute/clair/issues
+
+### Description
+
+[Description of the issue]
+
+### Steps to Reproduce
+
+1. [First Step]
+2. [Second Step]
+3. [and so on...]
+
+or paste a minimal code example to reproduce the issue.
+
+**Expected behavior:** [What you expect to happen]
+
+**Actual behavior:** [What actually happens]
+
+### Versions
+
+Please provide the application version that you used.
+
+Also, please include the OS you are running and its version.
+
+### Formatting
+
+Please use markdown in your issue message. A useful summary of commands can be found [here](https://guides.github.com/pdfs/markdown-cheatsheet-online.pdf).
+
+### Additional Information
+
+Any additional information, configuration or data that might be necessary to reproduce the issue.

.github/ISSUE_TEMPLATE/feature.md

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+---
+name: Feature request
+about: Suggest an idea for this project
+title: Feature request
+labels: feature
+
+---
+
+### Summary
+
+One paragraph explanation of the feature.
+
+### Motivation
+
+Why is this feature of general interest?
+
+### Implementation
+
+What user interface do you suggest?
+
+### Formatting
+
+Please use markdown in your issue message. A useful summary of commands can be found [here](https://guides.github.com/pdfs/markdown-cheatsheet-online.pdf).

.github/workflows/build.yml

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+name: build
+
+on:
+  push:
+    branches: [ unstable ]
+  pull_request:
+    branches: [ unstable ]
+
+jobs:
+  build:
+
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - {os: ubuntu-18.04, cc: clang-11, cxx: clang++-11}
+          - {os: ubuntu-20.04, cc: clang-10, cxx: clang++-10}
+          - {os: ubuntu-20.04, cc: clang-11, cxx: clang++-11}
+            #- {os: macos-10.15, cc: /usr/local/opt/llvm/bin/clang, cxx: /usr/local/opt/llvm/bin/clang++}
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Install ubuntu 20.04 clang-10 dependencies
+      if: matrix.os == 'ubuntu-20.04' && matrix.cc == 'clang-10'
+      run: >
+        sudo apt-get update &&
+        sudo apt-get install
+        clang-10
+        clang-tools-10
+        libclang-10-dev
+        libhdf5-dev
+        python3-dev
+        python3-numpy
+
+    - name: Install dependencies for ubuntu 18.04 and 20.04 builds with clang-11
+      if: (matrix.os == 'ubuntu-18.04' || matrix.os == 'ubuntu-20.04') && matrix.cc == 'clang-11'
+      run: |
+        sudo bash -c "$(wget -O - https://apt.llvm.org/llvm.sh)"
+        sudo apt-get install libclang-11-dev libhdf5-dev python3-dev python3-numpy
+
+    - name: Install homebrew dependencies
+      if: matrix.os == 'macos-10.15'
+      run: |
+        brew install llvm hdf5
+        pip3 install numpy
+
+    - name: Build clair
+      env:
+        CC: ${{ matrix.cc }}
+        CXX: ${{ matrix.cxx }}
+        LIBRARY_PATH: /usr/local/opt/llvm/lib
+        CMAKE_PREFIX_PATH: /usr/lib/llvm-11/lib/cmake/clang:/usr/lib/llvm-10/lib/cmake/clang
+      run: |
+        mkdir build && cmake -B build -DCMAKE_INSTALL_PREFIX=/opt/clair
+        cmake --build build -j2
+
+    - name: Test clair
+      env:
+        DYLD_FALLBACK_LIBRARY_PATH: /usr/local/opt/llvm/lib
+      run: |
+        cd build
+        ctest -j2 --output-on-failure

.gitignore

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+compile_commands.json
+.*.sw?
+code.vim
+.cache
+.vscode
+.clangd
+deps/c2py
+deps/nda
+#c2py_src
+#c2py_test
+compile_commands*
+howto*
+*.cxx
+*.hxx
+*.so
+

.mailmap

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+Olivier Parcollet <[email protected]> <[email protected]>
+