Linux Build/Install/Test CI, Docs, and Coding Standard Script

.clang-format

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+---
+Language:        Cpp
+BasedOnStyle:  LLVM
+AlignConsecutiveAssignments: true
+#llvm11: AlignConsecutiveBitFields: false
+AlignConsecutiveDeclarations: true
+AlignConsecutiveMacros: true
+#llvm10-11: AlignOperands:   true - Align
+#llvm11: AllowShortEnumsOnASingleLine: true
+AllowShortFunctionsOnASingleLine: None
+AlwaysBreakAfterReturnType: AllDefinitions
+BraceWrapping:
+  AfterFunction:   true
+  #llvm10-11: AfterControlStatement: false - Never
+  BeforeCatch:     true
+  BeforeElse:      true
+  #llvm11:   BeforeLambdaBody: false
+  #llvm11:   BeforeWhile:     false
+BreakBeforeBraces: Stroustrup
+BreakAfterJavaFieldAnnotations: true
+BreakStringLiterals: true
+ColumnLimit:     110    # Update $max_trace_macro_line_len in bin/trace also
+IncludeCategories:
+  - Regex:           '^"(llvm|llvm-c|clang|clang-c)/'
+    Priority:        3
+    SortPriority:    0
+  - Regex:           '^(<|"(gtest|gmock|isl|json)/)'
+    Priority:        4
+    SortPriority:    0
+  - Regex:           '.*'
+    Priority:        0
+    SortPriority:    0
+  - Regex:           '^PDC*.*'
+    Priority:        1
+    SortPriority:    0
+  - Regex:           'private.*'
+    Priority:        2
+    SortPriority:    0
+IncludeIsMainRegex: '(public)?$'
+IndentCaseLabels: true
+#llvm11: IndentCaseBlocks: false
+IndentGotoLabels: false
+#llvm11: IndentExternBlock: AfterExternBlock
+IndentWidth:     4
+#llvm11: InsertTrailingCommas: None
+# MacroBlockBegin: "^BEGIN_FUNC"
+# MacroBlockEnd: "^END_FUNC"
+ObjCBlockIndentWidth: 4
+#llvm11: ObjCBreakBeforeNestedBlockParam: true
+ReflowComments:  true
+SortIncludes:    false
+StatementMacros:
+#llvm10: TypenameMacros:
+#llvm10:   - STACK_OF
+#llvm10:   - LIST
+#llvm11: WhitespaceSensitiveMacros:
+#llvm11:   - STRINGIZE
+#llvm11:   - PP_STRINGIZE

.github/workflows/clang-format-check.yml

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+name: clang-format Check
+on:
+  pull_request:
+jobs:
+  formatting-check:
+    name: Formatting Check
+    runs-on: ubuntu-latest
+    if: "!contains(github.event.head_commit.message, 'skip-ci')"
+    steps:
+    - uses: actions/checkout@v2
+    - name: Run clang-format style check for C programs.
+      uses: DoozyX/clang-format-lint-action@v0.11
+      with:
+        source: '.'
+        extensions: 'c,h,cpp,hpp'
+        clangFormatVersion: 10
+        style: file
+        # exclude: './config'

.github/workflows/clang-format-fix.yml

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+name: clang-format Check
+on: 
+  workflow_dispatch:
+  push:
+jobs:
+  formatting-check:
+    name: Formatting Check
+    runs-on: ubuntu-latest
+    if: "!contains(github.event.head_commit.message, 'skip-ci')"
+    steps:
+    - uses: actions/checkout@v2
+    - name: Run clang-format style check for C programs.
+      uses: DoozyX/clang-format-lint-action@v0.11
+      with:
+        source: '.'
+        extensions: 'c,h,cpp,hpp'
+        clangFormatVersion: 10
+        inplace: True
+        style: file
+        # exclude: './config '
+    - uses: EndBug/add-and-commit@v7
+      with:
+          author_name: github-actions
+          author_email: github-actions[bot]@users.noreply.github.com
+          message: 'Committing clang-format changes'

.github/workflows/linux.yml

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+name: linux 
+
+on:
+  pull_request:
+    branches: [ develop ]
+
+  # Allows to run this workflow manually from the Actions tab
+  workflow_dispatch:
+jobs:
+  vol-async:
+    runs-on: ubuntu-latest
+    timeout-minutes: 60
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Checkout submodule argobots
+        run: git submodule update --init --recursive
+
+
+      - name: Dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install libtool
+          # hdf5
+          git clone https://github.com/HDFGroup/hdf5.git
+          # mpi
+          sudo apt-get install libopenmpi-dev
+          # zlib
+          sudo apt-get install zlib1g-dev 
+          # python3
+          sudo apt-get install python3
+
+      - name: Installation
+        run: |
+          mydir="$PWD"
+          export HDF5_DIR=$mydir/hdf5/install
+          export ABT_DIR=$mydir/argobots
+          export VOL_DIR=$mydir
+
+          mkdir $HDF5_DIR
+          # Compile HDF5
+          cd hdf5
+          export HDF5_LIBTOOL=/usr/bin/libtoolize
+          ./autogen.sh
+          ./configure --prefix=$HDF5_DIR --enable-parallel --enable-threadsafe --enable-unsupported
+          make && make install
+
+          # Compile Argobots
+          cd $ABT_DIR
+          ./autogen.sh
+          ./configure --prefix=$ABT_DIR
+          make && make install
+
+          # Compile Asynchronous VOL connector
+          cd $VOL_DIR/src
+          tail -n 48 Makefile.summit > Makefile
+          make
+
+      - name: Compile and Test Vol-Async
+        run: |
+          # Compile vol-async tests
+          mydir="$PWD"
+          cd $mydir
+          cd test
+
+          # Set Environmental Variables
+          export H5_DIR=$mydir/hdf5
+          export VOL_DIR=$mydir/
+          export ABT_DIR=$mydir/argobots
+          export ASYNC_DIR=$mydir/src
+          export HDF5_DIR=$mydir/hdf5/install
+          export LD_LIBRARY_PATH=$VOL_DIR/src:$H5_DIR/install/lib:$ABT_DIR/lib:$LD_LIBRARY_PATH
+          export HDF5_PLUGIN_PATH="$VOL_DIR/src"
+          export HDF5_VOL_CONNECTOR="async under_vol=0;under_info={}"
+
+          # Makefile
+          tail -n 47 Makefile.summit > Makefile
+          export LD_PRELOAD=$mydir/argobots/lib/libabt.so
+          make
+
+          # Run serial and parallel tests
+          make check
+
+          # Run serial tests only
+          make check_serial
+

docs/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/make.bat

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+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/conf.py

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+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'HDF5 Asynchronous I/O VOL Connector'
+copyright = '2021, Houjun Tang, Quincey Koziol, Suren Byna, John Mainzer, Tonglin Li'
+author = 'Houjun Tang, Quincey Koziol, Suren Byna, John Mainzer, Tonglin Li'
+
+# The full version, including alpha/beta/rc tags
+release = '0.1'
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = []
+
+pygments_style = 'sphinx'
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = []
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'sphinx_rtd_theme'
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']

docs/source/copyright.rst

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+Copyright
+===================================
+
+Asynchronous I/O VOL Connector (AsyncVOL) Copyright (c) 2020, The
+Regents of the University of California, through Lawrence Berkeley
+National Laboratory (subject to receipt of any required approvals from
+the U.S. Dept. of Energy).  All rights reserved.
+
+If you have questions about your rights to use or distribute this software,
+please contact Berkeley Lab's Intellectual Property Office at
+IPO@lbl.gov.
+
+NOTICE.  This Software was developed under funding from the U.S. Department
+of Energy and the U.S. Government consequently retains certain rights.  As
+such, the U.S. Government has been granted for itself and others acting on
+its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the
+Software to reproduce, distribute copies to the public, prepare derivative 
+works, and perform publicly and display publicly, and to permit others to do so.