diff --git a/.clang-format b/.clang-format
new file mode 100644
index 0000000000000000000000000000000000000000..77aee75e10e7d5682421b91bc758a4d7add82bf3
--- /dev/null
+++ b/.clang-format
@@ -0,0 +1,4 @@
+Language: Cpp
+BasedOnStyle: LLVM
+BreakBeforeBraces: Allman
+IndentCaseLabels: true
diff --git a/.gitignore b/.gitignore
index 4581ef2eeefc7832704f4a78f3018455f7a06178..6848b4f0086e8a453c1561cf0442635f4a87f13d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,29 +1,5 @@
-# Compiled Object files
-*.slo
-*.lo
-*.o
-*.obj
+# Vi(m) temporary buffer files
+*.sw?
-# Precompiled Headers
-*.gch
-*.pch
-
-# Compiled Dynamic libraries
-*.so
-*.dylib
-*.dll
-
-# Fortran module files
-*.mod
-*.smod
-
-# Compiled Static libraries
-*.lai
-*.la
-*.a
-*.lib
-
-# Executables
-*.exe
-*.out
-*.app
+# Emacs temporary files
+*~
diff --git a/CMakeLists.txt b/CMakeLists.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1a689cc48d05da8394bfaba5c5f00cb4bbea154d
--- /dev/null
+++ b/CMakeLists.txt
@@ -0,0 +1,85 @@
+#------------------------------------------------------------------------------#
+# Distributed under the OSI-approved Apache License, Version 2.0. See
+# accompanying file Copyright.txt for details.
+#------------------------------------------------------------------------------#
+
+cmake_minimum_required(VERSION 3.7)
+project(ADIOS VERSION 2.0.a)
+
+#------------------------------------------------------------------------------#
+# Some boilerplate to setup nice output directories
+#------------------------------------------------------------------------------#
+
+include(GNUInstallDirs)
+
+list(INSERT CMAKE_MODULE_PATH 0 "${ADIOS_SOURCE_DIR}/cmake")
+if(NOT CMAKE_ARCHIVE_OUTPUT_DIRECTORY)
+ set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY
+ ${ADIOS_BINARY_DIR}/${CMAKE_INSTALL_LIBDIR})
+endif()
+if(NOT CMAKE_LIBRARY_OUTPUT_DIRECTORY)
+ set(CMAKE_LIBRARY_OUTPUT_DIRECTORY
+ ${ADIOS_BINARY_DIR}/${CMAKE_INSTALL_LIBDIR})
+endif()
+if(NOT CMAKE_RUNTIME_OUTPUT_DIRECTORY)
+ set(CMAKE_RUNTIME_OUTPUT_DIRECTORY
+ ${ADIOS_BINARY_DIR}/${CMAKE_INSTALL_BINDIR})
+endif()
+
+#------------------------------------------------------------------------------#
+# Top level options
+#------------------------------------------------------------------------------#
+
+# Force C++11
+set(CMAKE_CXX_STANDARD 11)
+set(CMAKE_CXX_STANDARD_REQUIRED True)
+
+include(CMakeDependentOption)
+
+# Setup shared library / -fPIC stuff
+get_property(SHARED_LIBS_SUPPORTED GLOBAL PROPERTY TARGET_SUPPORTS_SHARED_LIBS)
+cmake_dependent_option(BUILD_SHARED_LIBS
+ "Whether or not to build shared libraries" ON
+ "SHARED_LIBS_SUPPORTED" OFF)
+if(SHARED_LIBS_SUPPORTED)
+ cmake_dependent_option(ADIOS_ENABLE_PIC
+ "Build with Position Independent Code" ON
+ "NOT BUILD_SHARED_LIBS" ON)
+endif()
+if(ADIOS_ENABLE_PIC)
+ set(CMAKE_POSITION_INDEPENDENT_CODE ON)
+endif()
+
+#------------------------------------------------------------------------------#
+# Main library source
+#------------------------------------------------------------------------------#
+add_subdirectory(source)
+
+#------------------------------------------------------------------------------#
+# Examples
+#------------------------------------------------------------------------------#
+option(ADIOS_BUILD_EXAMPLES "Build ADIOS examples" ON)
+if(ADIOS_BUILD_EXAMPLES)
+ add_subdirectory(examples)
+endif()
+
+#------------------------------------------------------------------------------#
+# Testing
+#------------------------------------------------------------------------------#
+include(CTest)
+option(ADIOS_ENABLE_TESTING "Enable ADIOS Testing" ON)
+set(ENABLE_TESTING ${ADIOS_ENABLE_TESTING} CACHE INTERNAL "" FORCE)
+mark_as_advanced(ENABLE_TESTING)
+if(ADIOS_ENABLE_TESTING)
+ enable_testing()
+ add_subdirectory(testing)
+endif()
+
+#------------------------------------------------------------------------------#
+# Installation
+#------------------------------------------------------------------------------#
+install(DIRECTORY include/
+ DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
+ FILES_MATCHING PATTERN "*.h"
+)
+
diff --git a/Copyright.txt b/Copyright.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f8ad35da7be7ffd7734b6ba94cbd9ff9387ac6f9
--- /dev/null
+++ b/Copyright.txt
@@ -0,0 +1,32 @@
+Copyright Oak Ridge National Laboratory and Contributors
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+------------------------------------------------------------------------------
+
+The following individuals and institutions are among the Contributors:
+
+* Chuck Atkins <chuck.atkins@kitware.com>
+* Greg S. Eisenhauer <eisen@cc.gatech.edu>
+* William F. Goody <godoywf@ornl.gov>
+* Norbert Podhorszki <pnorbert@ornl.gov>
+
+See version control history for details of individual contributions.
+
+------------------------------------------------------------------------------
+
+The above copyright and license notice applies to distributions of
+ADIOS in source and binary form. Third-party software packages supplied
+with ADIOS under compatible licenses provide their own copyright notices
+documented in corresponding subdirectories or source files.
+
diff --git a/LICENSE-2.0 b/LICENSE-2.0
new file mode 100644
index 0000000000000000000000000000000000000000..d645695673349e3947e8e5ae42332d0ac3164cd7
--- /dev/null
+++ b/LICENSE-2.0
@@ -0,0 +1,202 @@
+
+ Apache License
+ Version 2.0, January 2004
+ http://www.apache.org/licenses/
+
+ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+ 1. Definitions.
+
+ "License" shall mean the terms and conditions for use, reproduction,
+ and distribution as defined by Sections 1 through 9 of this document.
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+ "Licensor" shall mean the copyright owner or entity authorized by
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+ "Work" shall mean the work of authorship, whether in Source or
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+ "Derivative Works" shall mean any work, whether in Source or Object
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+ of this License, Derivative Works shall not include works that remain
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+ "Contribution" shall mean any work of authorship, including
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+ to that Work or Derivative Works thereof, that is intentionally
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+ "Contributor" shall mean Licensor and any individual or Legal Entity
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+ 2. Grant of Copyright License. Subject to the terms and conditions of
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+ meet the following conditions:
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+
+ (b) You must cause any modified files to carry prominent notices
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+
+ (c) You must retain, in the Source form of any Derivative Works
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+ You may add Your own copyright statement to Your modifications and
+ may provide additional or different license terms and conditions
+ for use, reproduction, or distribution of Your modifications, or
+ for any such Derivative Works as a whole, provided Your use,
+ reproduction, and distribution of the Work otherwise complies with
+ the conditions stated in this License.
+
+ 5. Submission of Contributions. Unless You explicitly state otherwise,
+ any Contribution intentionally submitted for inclusion in the Work
+ by You to the Licensor shall be under the terms and conditions of
+ this License, without any additional terms or conditions.
+ Notwithstanding the above, nothing herein shall supersede or modify
+ the terms of any separate license agreement you may have executed
+ with Licensor regarding such Contributions.
+
+ 6. Trademarks. This License does not grant permission to use the trade
+ names, trademarks, service marks, or product names of the Licensor,
+ except as required for reasonable and customary use in describing the
+ origin of the Work and reproducing the content of the NOTICE file.
+
+ 7. Disclaimer of Warranty. Unless required by applicable law or
+ agreed to in writing, Licensor provides the Work (and each
+ Contributor provides its Contributions) on an "AS IS" BASIS,
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+ PARTICULAR PURPOSE. You are solely responsible for determining the
+ appropriateness of using or redistributing the Work and assume any
+ risks associated with Your exercise of permissions under this License.
+
+ 8. Limitation of Liability. In no event and under no legal theory,
+ whether in tort (including negligence), contract, or otherwise,
+ unless required by applicable law (such as deliberate and grossly
+ negligent acts) or agreed to in writing, shall any Contributor be
+ liable to You for damages, including any direct, indirect, special,
+ incidental, or consequential damages of any character arising as a
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+ Work (including but not limited to damages for loss of goodwill,
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+ has been advised of the possibility of such damages.
+
+ 9. Accepting Warranty or Additional Liability. While redistributing
+ the Work or Derivative Works thereof, You may choose to offer,
+ and charge a fee for, acceptance of support, warranty, indemnity,
+ or other liability obligations and/or rights consistent with this
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+ on Your own behalf and on Your sole responsibility, not on behalf
+ of any other Contributor, and only if You agree to indemnify,
+ defend, and hold each Contributor harmless for any liability
+ incurred by, or claims asserted against, such Contributor by reason
+ of your accepting any such warranty or additional liability.
+
+ END OF TERMS AND CONDITIONS
+
+ APPENDIX: How to apply the Apache License to your work.
+
+ To apply the Apache License to your work, attach the following
+ boilerplate notice, with the fields enclosed by brackets "[]"
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+ Copyright [yyyy] [name of copyright owner]
+
+ Licensed under the Apache License, Version 2.0 (the "License");
+ you may not use this file except in compliance with the License.
+ You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
diff --git a/Readme.txt b/Readme.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c19f2000bb24e2f4788bd2d0a619d40a241c8113
--- /dev/null
+++ b/Readme.txt
@@ -0,0 +1,29 @@
+# Adaptable Input / Output System (ADIOS) v2.0
+
+This is v2.0 of the ADIOS I/O system, developed as part of the DoE. Exascale
+Computing Program.
+
+## License
+ADIOS >= 2.0 is licensed under the Apache License v2.0. See the accompanying
+Copyright.txt for more details.
+
+## Directory layout
+
+/cmake : Project specific CMake modules
+/examples : ADIOS Examples
+/include : Public header files
+/scripts : Project maintenance and development scripts
+source : Main ADIOS source
+-- /foo : Source and private header files for the "foo" component
+testing : Tests
+
+## Developers
+
+###Getting started
+
+Uppon cloning this repo, you will need to run the scripts/developer/setup.sh
+script. This will perform the following:
+
+ * Validate that clang-format is available
+ * Setup formatting commit hooks
+
diff --git a/examples/CMakeLists.txt b/examples/CMakeLists.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/scripts/developer/git/git-clang-format b/scripts/developer/git/git-clang-format
new file mode 100755
index 0000000000000000000000000000000000000000..74fd451a847be8cbbff6873fe2251f4315de7758
--- /dev/null
+++ b/scripts/developer/git/git-clang-format
@@ -0,0 +1,542 @@
+#!/usr/bin/env python
+#
+#===- git-clang-format - ClangFormat Git Integration ---------*- python -*--===#
+#
+# The LLVM Compiler Infrastructure
+#
+# This file is distributed under the University of Illinois Open Source
+# License. See LICENSE.TXT for details.
+#
+#===------------------------------------------------------------------------===#
+
+r"""
+clang-format git integration
+============================
+
+This file provides a clang-format integration for git. Put it somewhere in your
+path and ensure that it is executable. Then, "git clang-format" will invoke
+clang-format on the changes in current files or a specific commit.
+
+For further details, run:
+git clang-format -h
+
+Requires Python 2.7
+"""
+
+import argparse
+import collections
+import contextlib
+import errno
+import os
+import re
+import subprocess
+import sys
+
+usage = 'git clang-format [OPTIONS] [<commit>] [<commit>] [--] [<file>...]'
+
+desc = '''
+If zero or one commits are given, run clang-format on all lines that differ
+between the working directory and <commit>, which defaults to HEAD. Changes are
+only applied to the working directory.
+
+If two commits are given (requires --diff), run clang-format on all lines in the
+second <commit> that differ from the first <commit>.
+
+The following git-config settings set the default of the corresponding option:
+ clangFormat.binary
+ clangFormat.commit
+ clangFormat.extension
+ clangFormat.style
+'''
+
+# Name of the temporary index file in which save the output of clang-format.
+# This file is created within the .git directory.
+temp_index_basename = 'clang-format-index'
+
+
+Range = collections.namedtuple('Range', 'start, count')
+
+
+def main():
+ config = load_git_config()
+
+ # In order to keep '--' yet allow options after positionals, we need to
+ # check for '--' ourselves. (Setting nargs='*' throws away the '--', while
+ # nargs=argparse.REMAINDER disallows options after positionals.)
+ argv = sys.argv[1:]
+ try:
+ idx = argv.index('--')
+ except ValueError:
+ dash_dash = []
+ else:
+ dash_dash = argv[idx:]
+ argv = argv[:idx]
+
+ default_extensions = ','.join([
+ # From clang/lib/Frontend/FrontendOptions.cpp, all lower case
+ 'c', 'h', # C
+ 'm', # ObjC
+ 'mm', # ObjC++
+ 'cc', 'cp', 'cpp', 'c++', 'cxx', 'hpp', # C++
+ # Other languages that clang-format supports
+ 'proto', 'protodevel', # Protocol Buffers
+ 'java', # Java
+ 'js', # JavaScript
+ 'ts', # TypeScript
+ ])
+
+ p = argparse.ArgumentParser(
+ usage=usage, formatter_class=argparse.RawDescriptionHelpFormatter,
+ description=desc)
+ p.add_argument('--binary',
+ default=config.get('clangformat.binary', 'clang-format'),
+ help='path to clang-format'),
+ p.add_argument('--commit',
+ default=config.get('clangformat.commit', 'HEAD'),
+ help='default commit to use if none is specified'),
+ p.add_argument('--diff', action='store_true',
+ help='print a diff instead of applying the changes')
+ p.add_argument('--extensions',
+ default=config.get('clangformat.extensions',
+ default_extensions),
+ help=('comma-separated list of file extensions to format, '
+ 'excluding the period and case-insensitive')),
+ p.add_argument('-f', '--force', action='store_true',
+ help='allow changes to unstaged files')
+ p.add_argument('-p', '--patch', action='store_true',
+ help='select hunks interactively')
+ p.add_argument('-q', '--quiet', action='count', default=0,
+ help='print less information')
+ p.add_argument('--style',
+ default=config.get('clangformat.style', None),
+ help='passed to clang-format'),
+ p.add_argument('-v', '--verbose', action='count', default=0,
+ help='print extra information')
+ # We gather all the remaining positional arguments into 'args' since we need
+ # to use some heuristics to determine whether or not <commit> was present.
+ # However, to print pretty messages, we make use of metavar and help.
+ p.add_argument('args', nargs='*', metavar='<commit>',
+ help='revision from which to compute the diff')
+ p.add_argument('ignored', nargs='*', metavar='<file>...',
+ help='if specified, only consider differences in these files')
+ opts = p.parse_args(argv)
+
+ opts.verbose -= opts.quiet
+ del opts.quiet
+
+ commits, files = interpret_args(opts.args, dash_dash, opts.commit)
+ if len(commits) > 1:
+ if not opts.diff:
+ die('--diff is required when two commits are given')
+ else:
+ if len(commits) > 2:
+ die('at most two commits allowed; %d given' % len(commits))
+ changed_lines = compute_diff_and_extract_lines(commits, files)
+ if opts.verbose >= 1:
+ ignored_files = set(changed_lines)
+ filter_by_extension(changed_lines, opts.extensions.lower().split(','))
+ if opts.verbose >= 1:
+ ignored_files.difference_update(changed_lines)
+ if ignored_files:
+ print 'Ignoring changes in the following files (wrong extension):'
+ for filename in ignored_files:
+ print ' ', filename
+ if changed_lines:
+ print 'Running clang-format on the following files:'
+ for filename in changed_lines:
+ print ' ', filename
+ if not changed_lines:
+ print 'no modified files to format'
+ return
+ # The computed diff outputs absolute paths, so we must cd before accessing
+ # those files.
+ cd_to_toplevel()
+ if len(commits) > 1:
+ old_tree = commits[1]
+ new_tree = run_clang_format_and_save_to_tree(changed_lines,
+ revision=commits[1],
+ binary=opts.binary,
+ style=opts.style)
+ else:
+ old_tree = create_tree_from_workdir(changed_lines)
+ new_tree = run_clang_format_and_save_to_tree(changed_lines,
+ binary=opts.binary,
+ style=opts.style)
+ if opts.verbose >= 1:
+ print 'old tree:', old_tree
+ print 'new tree:', new_tree
+ if old_tree == new_tree:
+ if opts.verbose >= 0:
+ print 'clang-format did not modify any files'
+ elif opts.diff:
+ print_diff(old_tree, new_tree)
+ else:
+ changed_files = apply_changes(old_tree, new_tree, force=opts.force,
+ patch_mode=opts.patch)
+ if (opts.verbose >= 0 and not opts.patch) or opts.verbose >= 1:
+ print 'changed files:'
+ for filename in changed_files:
+ print ' ', filename
+
+
+def load_git_config(non_string_options=None):
+ """Return the git configuration as a dictionary.
+
+ All options are assumed to be strings unless in `non_string_options`, in which
+ is a dictionary mapping option name (in lower case) to either "--bool" or
+ "--int"."""
+ if non_string_options is None:
+ non_string_options = {}
+ out = {}
+ for entry in run('git', 'config', '--list', '--null').split('\0'):
+ if entry:
+ name, value = entry.split('\n', 1)
+ if name in non_string_options:
+ value = run('git', 'config', non_string_options[name], name)
+ out[name] = value
+ return out
+
+
+def interpret_args(args, dash_dash, default_commit):
+ """Interpret `args` as "[commits] [--] [files]" and return (commits, files).
+
+ It is assumed that "--" and everything that follows has been removed from
+ args and placed in `dash_dash`.
+
+ If "--" is present (i.e., `dash_dash` is non-empty), the arguments to its
+ left (if present) are taken as commits. Otherwise, the arguments are checked
+ from left to right if they are commits or files. If commits are not given,
+ a list with `default_commit` is used."""
+ if dash_dash:
+ if len(args) == 0:
+ commits = [default_commit]
+ else:
+ commits = args
+ for commit in commits:
+ object_type = get_object_type(commit)
+ if object_type not in ('commit', 'tag'):
+ if object_type is None:
+ die("'%s' is not a commit" % commit)
+ else:
+ die("'%s' is a %s, but a commit was expected" % (commit, object_type))
+ files = dash_dash[1:]
+ elif args:
+ commits = []
+ while args:
+ if not disambiguate_revision(args[0]):
+ break
+ commits.append(args.pop(0))
+ if not commits:
+ commits = [default_commit]
+ files = args
+ else:
+ commits = [default_commit]
+ files = []
+ return commits, files
+
+
+def disambiguate_revision(value):
+ """Returns True if `value` is a revision, False if it is a file, or dies."""
+ # If `value` is ambiguous (neither a commit nor a file), the following
+ # command will die with an appropriate error message.
+ run('git', 'rev-parse', value, verbose=False)
+ object_type = get_object_type(value)
+ if object_type is None:
+ return False
+ if object_type in ('commit', 'tag'):
+ return True
+ die('`%s` is a %s, but a commit or filename was expected' %
+ (value, object_type))
+
+
+def get_object_type(value):
+ """Returns a string description of an object's type, or None if it is not
+ a valid git object."""
+ cmd = ['git', 'cat-file', '-t', value]
+ p = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+ stdout, stderr = p.communicate()
+ if p.returncode != 0:
+ return None
+ return stdout.strip()
+
+
+def compute_diff_and_extract_lines(commits, files):
+ """Calls compute_diff() followed by extract_lines()."""
+ diff_process = compute_diff(commits, files)
+ changed_lines = extract_lines(diff_process.stdout)
+ diff_process.stdout.close()
+ diff_process.wait()
+ if diff_process.returncode != 0:
+ # Assume error was already printed to stderr.
+ sys.exit(2)
+ return changed_lines
+
+
+def compute_diff(commits, files):
+ """Return a subprocess object producing the diff from `commits`.
+
+ The return value's `stdin` file object will produce a patch with the
+ differences between the working directory and the first commit if a single
+ one was specified, or the difference between both specified commits, filtered
+ on `files` (if non-empty). Zero context lines are used in the patch."""
+ git_tool = 'diff-index'
+ if len(commits) > 1:
+ git_tool = 'diff-tree'
+ cmd = ['git', git_tool, '-p', '-U0'] + commits + ['--']
+ cmd.extend(files)
+ p = subprocess.Popen(cmd, stdin=subprocess.PIPE, stdout=subprocess.PIPE)
+ p.stdin.close()
+ return p
+
+
+def extract_lines(patch_file):
+ """Extract the changed lines in `patch_file`.
+
+ The return value is a dictionary mapping filename to a list of (start_line,
+ line_count) pairs.
+
+ The input must have been produced with ``-U0``, meaning unidiff format with
+ zero lines of context. The return value is a dict mapping filename to a
+ list of line `Range`s."""
+ matches = {}
+ for line in patch_file:
+ match = re.search(r'^\+\+\+\ [^/]+/(.*)', line)
+ if match:
+ filename = match.group(1).rstrip('\r\n')
+ match = re.search(r'^@@ -[0-9,]+ \+(\d+)(,(\d+))?', line)
+ if match:
+ start_line = int(match.group(1))
+ line_count = 1
+ if match.group(3):
+ line_count = int(match.group(3))
+ if line_count > 0:
+ matches.setdefault(filename, []).append(Range(start_line, line_count))
+ return matches
+
+
+def filter_by_extension(dictionary, allowed_extensions):
+ """Delete every key in `dictionary` that doesn't have an allowed extension.
+
+ `allowed_extensions` must be a collection of lowercase file extensions,
+ excluding the period."""
+ allowed_extensions = frozenset(allowed_extensions)
+ for filename in dictionary.keys():
+ base_ext = filename.rsplit('.', 1)
+ if len(base_ext) == 1 or base_ext[1].lower() not in allowed_extensions:
+ del dictionary[filename]
+
+
+def cd_to_toplevel():
+ """Change to the top level of the git repository."""
+ toplevel = run('git', 'rev-parse', '--show-toplevel')
+ os.chdir(toplevel)
+
+
+def create_tree_from_workdir(filenames):
+ """Create a new git tree with the given files from the working directory.
+
+ Returns the object ID (SHA-1) of the created tree."""
+ return create_tree(filenames, '--stdin')
+
+
+def run_clang_format_and_save_to_tree(changed_lines, revision=None,
+ binary='clang-format', style=None):
+ """Run clang-format on each file and save the result to a git tree.
+
+ Returns the object ID (SHA-1) of the created tree."""
+ def index_info_generator():
+ for filename, line_ranges in changed_lines.iteritems():
+ if revision:
+ git_metadata_cmd = ['git', 'ls-tree',
+ '%s:%s' % (revision, os.path.dirname(filename)),
+ os.path.basename(filename)]
+ git_metadata = subprocess.Popen(git_metadata_cmd, stdin=subprocess.PIPE,
+ stdout=subprocess.PIPE)
+ stdout = git_metadata.communicate()[0]
+ mode = oct(int(stdout.split()[0], 8))
+ else:
+ mode = oct(os.stat(filename).st_mode)
+ blob_id = clang_format_to_blob(filename, line_ranges,
+ revision=revision,
+ binary=binary,
+ style=style)
+ yield '%s %s\t%s' % (mode, blob_id, filename)
+ return create_tree(index_info_generator(), '--index-info')
+
+
+def create_tree(input_lines, mode):
+ """Create a tree object from the given input.
+
+ If mode is '--stdin', it must be a list of filenames. If mode is
+ '--index-info' is must be a list of values suitable for "git update-index
+ --index-info", such as "<mode> <SP> <sha1> <TAB> <filename>". Any other mode
+ is invalid."""
+ assert mode in ('--stdin', '--index-info')
+ cmd = ['git', 'update-index', '--add', '-z', mode]
+ with temporary_index_file():
+ p = subprocess.Popen(cmd, stdin=subprocess.PIPE)
+ for line in input_lines:
+ p.stdin.write('%s\0' % line)
+ p.stdin.close()
+ if p.wait() != 0:
+ die('`%s` failed' % ' '.join(cmd))
+ tree_id = run('git', 'write-tree')
+ return tree_id
+
+
+def clang_format_to_blob(filename, line_ranges, revision=None,
+ binary='clang-format', style=None):
+ """Run clang-format on the given file and save the result to a git blob.
+
+ Runs on the file in `revision` if not None, or on the file in the working
+ directory if `revision` is None.
+
+ Returns the object ID (SHA-1) of the created blob."""
+ clang_format_cmd = [binary]
+ if style:
+ clang_format_cmd.extend(['-style='+style])
+ clang_format_cmd.extend([
+ '-lines=%s:%s' % (start_line, start_line+line_count-1)
+ for start_line, line_count in line_ranges])
+ if revision:
+ clang_format_cmd.extend(['-assume-filename='+filename])
+ git_show_cmd = ['git', 'cat-file', 'blob', '%s:%s' % (revision, filename)]
+ git_show = subprocess.Popen(git_show_cmd, stdin=subprocess.PIPE,
+ stdout=subprocess.PIPE)
+ git_show.stdin.close()
+ clang_format_stdin = git_show.stdout
+ else:
+ clang_format_cmd.extend([filename])
+ git_show = None
+ clang_format_stdin = subprocess.PIPE
+ try:
+ clang_format = subprocess.Popen(clang_format_cmd, stdin=clang_format_stdin,
+ stdout=subprocess.PIPE)
+ if clang_format_stdin == subprocess.PIPE:
+ clang_format_stdin = clang_format.stdin
+ except OSError as e:
+ if e.errno == errno.ENOENT:
+ die('cannot find executable "%s"' % binary)
+ else:
+ raise
+ clang_format_stdin.close()
+ hash_object_cmd = ['git', 'hash-object', '-w', '--path='+filename, '--stdin']
+ hash_object = subprocess.Popen(hash_object_cmd, stdin=clang_format.stdout,
+ stdout=subprocess.PIPE)
+ clang_format.stdout.close()
+ stdout = hash_object.communicate()[0]
+ if hash_object.returncode != 0:
+ die('`%s` failed' % ' '.join(hash_object_cmd))
+ if clang_format.wait() != 0:
+ die('`%s` failed' % ' '.join(clang_format_cmd))
+ if git_show and git_show.wait() != 0:
+ die('`%s` failed' % ' '.join(git_show_cmd))
+ return stdout.rstrip('\r\n')
+
+
+@contextlib.contextmanager
+def temporary_index_file(tree=None):
+ """Context manager for setting GIT_INDEX_FILE to a temporary file and deleting
+ the file afterward."""
+ index_path = create_temporary_index(tree)
+ old_index_path = os.environ.get('GIT_INDEX_FILE')
+ os.environ['GIT_INDEX_FILE'] = index_path
+ try:
+ yield
+ finally:
+ if old_index_path is None:
+ del os.environ['GIT_INDEX_FILE']
+ else:
+ os.environ['GIT_INDEX_FILE'] = old_index_path
+ os.remove(index_path)
+
+
+def create_temporary_index(tree=None):
+ """Create a temporary index file and return the created file's path.
+
+ If `tree` is not None, use that as the tree to read in. Otherwise, an
+ empty index is created."""
+ gitdir = run('git', 'rev-parse', '--git-dir')
+ path = os.path.join(gitdir, temp_index_basename)
+ if tree is None:
+ tree = '--empty'
+ run('git', 'read-tree', '--index-output='+path, tree)
+ return path
+
+
+def print_diff(old_tree, new_tree):
+ """Print the diff between the two trees to stdout."""
+ # We use the porcelain 'diff' and not plumbing 'diff-tree' because the output
+ # is expected to be viewed by the user, and only the former does nice things
+ # like color and pagination.
+ #
+ # We also only print modified files since `new_tree` only contains the files
+ # that were modified, so unmodified files would show as deleted without the
+ # filter.
+ subprocess.check_call(['git', 'diff', '--diff-filter=M', old_tree, new_tree,
+ '--'])
+
+
+def apply_changes(old_tree, new_tree, force=False, patch_mode=False):
+ """Apply the changes in `new_tree` to the working directory.
+
+ Bails if there are local changes in those files and not `force`. If
+ `patch_mode`, runs `git checkout --patch` to select hunks interactively."""
+ changed_files = run('git', 'diff-tree', '--diff-filter=M', '-r', '-z',
+ '--name-only', old_tree,
+ new_tree).rstrip('\0').split('\0')
+ if not force:
+ unstaged_files = run('git', 'diff-files', '--name-status', *changed_files)
+ if unstaged_files:
+ print >>sys.stderr, ('The following files would be modified but '
+ 'have unstaged changes:')
+ print >>sys.stderr, unstaged_files
+ print >>sys.stderr, 'Please commit, stage, or stash them first.'
+ sys.exit(2)
+ if patch_mode:
+ # In patch mode, we could just as well create an index from the new tree
+ # and checkout from that, but then the user will be presented with a
+ # message saying "Discard ... from worktree". Instead, we use the old
+ # tree as the index and checkout from new_tree, which gives the slightly
+ # better message, "Apply ... to index and worktree". This is not quite
+ # right, since it won't be applied to the user's index, but oh well.
+ with temporary_index_file(old_tree):
+ subprocess.check_call(['git', 'checkout', '--patch', new_tree])
+ index_tree = old_tree
+ else:
+ with temporary_index_file(new_tree):
+ run('git', 'checkout-index', '-a', '-f')
+ return changed_files
+
+
+def run(*args, **kwargs):
+ stdin = kwargs.pop('stdin', '')
+ verbose = kwargs.pop('verbose', True)
+ strip = kwargs.pop('strip', True)
+ for name in kwargs:
+ raise TypeError("run() got an unexpected keyword argument '%s'" % name)
+ p = subprocess.Popen(args, stdout=subprocess.PIPE, stderr=subprocess.PIPE,
+ stdin=subprocess.PIPE)
+ stdout, stderr = p.communicate(input=stdin)
+ if p.returncode == 0:
+ if stderr:
+ if verbose:
+ print >>sys.stderr, '`%s` printed to stderr:' % ' '.join(args)
+ print >>sys.stderr, stderr.rstrip()
+ if strip:
+ stdout = stdout.rstrip('\r\n')
+ return stdout
+ if verbose:
+ print >>sys.stderr, '`%s` returned %s' % (' '.join(args), p.returncode)
+ if stderr:
+ print >>sys.stderr, stderr.rstrip()
+ sys.exit(2)
+
+
+def die(message):
+ print >>sys.stderr, 'error:', message
+ sys.exit(2)
+
+
+if __name__ == '__main__':
+ main()
diff --git a/scripts/developer/git/setup-aliases b/scripts/developer/git/setup-aliases
new file mode 100755
index 0000000000000000000000000000000000000000..11b43d53f0060d90312a33fe8b75b3863742e925
--- /dev/null
+++ b/scripts/developer/git/setup-aliases
@@ -0,0 +1,16 @@
+#!/usr/bin/env bash
+
+if ! which clang-format 2>1 1>/dev/null
+then
+ echo "ADIOS development requires clang-format to be available in your path."
+ exit 1
+fi
+
+echo "Adding 'git clang-format' alias"
+if ! git config alias.clang-format "!bash scripts/git/git-clang-format"
+then
+ echo "Error adding clang-format alias"
+ exit 2
+fi
+
+exit 0
diff --git a/scripts/developer/git/setup-hooks b/scripts/developer/git/setup-hooks
new file mode 100755
index 0000000000000000000000000000000000000000..c07985ae5661658139ae7aff4353cfb374c35bc1
--- /dev/null
+++ b/scripts/developer/git/setup-hooks
@@ -0,0 +1,63 @@
+#!/usr/bin/env bash
+#=============================================================================
+# Copyright 2010-2012 Kitware, Inc.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#=============================================================================
+
+# Run this script to set up local Git hooks for this project.
+
+# Project configuration instructions:
+#
+# - Publish a "hooks" branch in the project repository such that
+# clones will have "refs/remotes/origin/hooks".
+#
+# - Populate adjacent "config" file with:
+# hooks.url = Repository URL publishing "hooks" branch
+# hooks.branch = Repository branch instead of "hooks"
+
+egrep-q() {
+ egrep "$@" >/dev/null 2>/dev/null
+}
+
+die() {
+ echo 1>&2 "$@" ; exit 1
+}
+
+# Make sure we are inside the repository.
+cd "${BASH_SOURCE%/*}" &&
+
+# Select a hooks branch.
+if url=$(git config --get hooks.url); then
+ # Fetch hooks from locally configured repository.
+ branch=$(git config hooks.branch || echo hooks)
+elif git for-each-ref refs/remotes/origin/hooks 2>/dev/null |
+ egrep-q 'refs/remotes/origin/hooks$'; then
+ # Use hooks cloned from origin.
+ url=.. && branch=remotes/origin/hooks
+elif url=$(git config -f config --get hooks.url); then
+ # Fetch hooks from project-configured repository.
+ branch=$(git config -f config hooks.branch || echo hooks)
+else
+ die 'This project is not configured to install local hooks.'
+fi &&
+
+# Populate ".git/hooks".
+echo 'Setting up git hooks...' &&
+git_dir=$(git rev-parse --git-dir) &&
+cd "$git_dir/hooks" &&
+if ! test -e .git; then
+ git init -q || die 'Could not run git init for hooks.'
+fi &&
+git fetch -q "$url" "$branch" &&
+git reset -q --hard FETCH_HEAD || die 'Failed to install hooks'
diff --git a/scripts/developer/setup.sh b/scripts/developer/setup.sh
new file mode 100644
index 0000000000000000000000000000000000000000..bd3bed7aec4c84b30efc81a16ee1bf12097f8c95
--- /dev/null
+++ b/scripts/developer/setup.sh
@@ -0,0 +1,18 @@
+#!/usr/bin/env bash
+
+test_cmd {
+ if ! $1 ;
+ then
+ echo "Error: $2";
+ exit $3
+ fi
+}
+
+cd "${BASH_SOURCE%/*}"
+
+test_cmd scripts/git/setup-alias \
+ "Failed to setup git aliases" 2
+
+test_cmd scripts/git/setup-hooks \
+ "Failed to setup git hooks" 1
+git config hooks.clang-format true
diff --git a/source/CMakeLists.txt b/source/CMakeLists.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/testing/CMakeLists.txt b/testing/CMakeLists.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391