updates for 0.4.0 release (#389)

* updated release notes for 0.4.0 * update copyright header to 2019 * update version number to 0.4.0 * add new valgrind sup case for macOS
LLNL · Mar 2, 2019 · ec67a2e · ec67a2e
1 parent d9cf601
commit ec67a2e
Show file tree

Hide file tree

Showing 326 changed files with 442 additions and 346 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,9 +2,10 @@
 Notable changes to Conduit are documented in this file.
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
-and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+and this project aspires to adhere to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [Unreleased]
+
+## [0.4.0] - Released 2019-03-01
 
 ### Added
 - Added Generic IO Handle class (relay::io::IOHandle) with C++ and Python APIs, tests, and docs.
@@ -17,24 +18,31 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Added C bindings for relay IO
 - Added several more functions to conduit node python interfaces
 
+
 - Blueprint: Added implicit point topology docs and example
 - Blueprint: Added julia and spiral mesh bp examples
 - Blueprint: Added mesh topology transformations to blueprint
 - Blueprint: Added polygonal mesh support to mesh blueprint
 - Blueprint: Added verify method for mesh blueprint nestset
 
-- Relay: Added ADIOS Support
+
+- Relay: Added ADIOS Support, enabling ADIOS read and write of Node objects.
+- Relay: Added a relay::mpi::io library that mirrors the API of relay::io, except  that all functions take an MPI communicator. The functions are implemented in parallel for the ADIOS protocol. For other protocols, they will behave the same as the serial functions in relay::io. For the ADIOS protocol, the save() and save_merged() functions operate collectively within a communicator to enable multiple MPI ranks to save data to a single file as separate "domains".
+- Relay: Added an add_time_step() function to that lets the caller append data collectively to an existing  ADIOS file
+- Relay: Added a function to query the number of time steps and the number of domains in a  ADIOS file.
 - Relay: Added versions of save and save_merged that take an options node. 
 - Relay: Added C API for new save, save_merged functions.
 - Relay: Added method to list an HDF5 group's child names
 - Relay: Added save and append methods to the HDF5 I/O interface
 - Relay: Added docs and examples for relay io
 
+
 ### Changed
 - Changed mapping of c types to bit-width style to be compatible with C++11 std bit-width types when C++11 is enabled
 - Several improvements to uberenv, our automated build process, and building directions
 - Upgraded the type system with more explicit signed support
 
+
 - Relay: Improvements to the Silo mesh writer
 - Relay: Refactor to support both relay::io and relay::mpi::io namespaces. 
 - Relay: Refactor to add support for steps and domains to I/O interfaces
@@ -47,9 +55,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Fixed issue with Node::diff failing for string data with offsets
 - Fixes for building on BlueOS with the xl compiler
 
+
 - Blueprint: Fixed validity status for blueprint functions
 - Blueprint: Fixed improper error reporting for Blueprint references
 
+
 - Relay: Relay I/O exceptions are now forwarded to python  
 - Relay: Fixed MPI send_with_schema bug when data was compact but not contiguous  
 - Relay: Switched to use MPI bit-width style data type enums in ``relay::mpi``
@@ -61,6 +71,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Expanded the Node Python Capsule API
 - Added Python version of basic tutorial
 
+
 - Blueprint: Added Multi-level Array Protocol (conduit::blueprint::mlarray)
 
 
@@ -72,6 +83,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Various Python API bug fixes
 - Fixed API exports for static libs on Windows
 
+
 - Relay: Bug fixes for HDF5 support on Windows
 
 ### Removed
@@ -82,9 +94,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Added 
 - Exposed more of the Conduit API in Python
 
+
 - Blueprint: Added support for multi-material fields via *matsets* (volume fractions and per-material values)
 - Blueprint: Added initial support for domain boundary info via *adjsets* for distributed-memory unstructured meshes  
 
+
 - Relay: Added support for MPI reductions and broadcast
 - Relay: Added support zero-copy pass to MPI for a wide set of calls
 - Relay: Hardened notion of `known schema` vs `generic` MPI support
@@ -94,6 +108,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Moved to use BLT (https://github.com/llnl/blt) as our core CMake-based build system
 - Use ints instead of bools in the Conduit C-APIs for wider compiler compatibility
 
+
 - Relay: Improved error checking and error messages for HDF5 I/O support
 
 ### Fixed
@@ -117,8 +132,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Added fixes to support static builds on BGQ using xlc and gcc
 - Fixed missing install of fortran module files
 
+
 - Blueprint: Fixed bug with verify of mesh/coords for rectilinear case
 
+
 - Relay: Updated the version of civetweb used to avoid dlopen issues with SSL for static builds
 
 ## [0.2.0] - Released 2016-11-03
@@ -128,11 +145,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Added support for building on Windows 
 - Added more Python, C, and Fortran API support
 
+
 - Blueprint: Added verify support for the mcarray and mesh protocols
 - Blueprint: Added functions that create examples instances of mcarrays and meshes
 - Blueprint: Added memory layout transform helpers for mcarrays
 - Blueprint: Added a helper that creates a mesh blueprint index from a valid mesh
 
+
 - Relay: Added entangle, a python script ssh tunneling solution
 - Relay: Added extensive HDF5 I/O support for reading and writing between HDF5 files and conduit Node trees
 
@@ -141,6 +160,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Improved unit test coverage
 - Renamed source and header files for clarity and to avoid potential conflicts with other projects 
 
+
 - Relay: Changed I/O protocol string names for clarity 
 - Relay: Refactored the relay::WebServer and the Conduit Node Viewer application 
 
@@ -153,7 +173,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Added
 - Initial Open Source Release on GitHub
 
-[Unreleased]: https://github.com/llnl/conduit/compare/v0.3.1...HEAD
+[Unreleased]: https://github.com/llnl/conduit/compare/v0.4.0...HEAD
+[0.4.0]: https://github.com/llnl/conduit/compare/v0.3.1...v0.4.0
 [0.3.1]: https://github.com/llnl/conduit/compare/v0.3.0...v0.3.1
 [0.3.0]: https://github.com/llnl/conduit/compare/v0.2.1...v0.3.0
 [0.2.1]: https://github.com/llnl/conduit/compare/v0.2.0...v0.2.1

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -57,7 +57,7 @@ endif()
 # Conduit
 ################################
 
-project(conduit VERSION "0.3.2")
+project(conduit VERSION "0.4.0")
 
 ################################
 # Build Options

diff --git a/src/cmake/BasicTypeChecks.cmake b/src/cmake/BasicTypeChecks.cmake
@@ -1,5 +1,5 @@
 ###############################################################################
-# Copyright (c) 2014-2018, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2014-2019, Lawrence Livermore National Security, LLC.
 # 
 # Produced at the Lawrence Livermore National Laboratory
 # 

diff --git a/src/cmake/CMakeBasics.cmake b/src/cmake/CMakeBasics.cmake
@@ -1,5 +1,5 @@
 ###############################################################################
-# Copyright (c) Copyright (c) 2015-2018, Lawrence Livermore National Security, LLC.
+# Copyright (c) Copyright (c) 2015-2019, Lawrence Livermore National Security, LLC.
 #
 # Produced at the Lawrence Livermore National Laboratory
 #

diff --git a/src/cmake/Setup3rdParty.cmake b/src/cmake/Setup3rdParty.cmake
@@ -1,5 +1,5 @@
 ###############################################################################
-# Copyright (c) Copyright (c) 2015-2018, Lawrence Livermore National Security, LLC.
+# Copyright (c) Copyright (c) 2015-2019, Lawrence Livermore National Security, LLC.
 #
 # Produced at the Lawrence Livermore National Laboratory
 #

diff --git a/src/cmake/SetupFortran.cmake b/src/cmake/SetupFortran.cmake
@@ -1,5 +1,5 @@
 ###############################################################################
-# Copyright (c) 2014-2018, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2014-2019, Lawrence Livermore National Security, LLC.
 # 
 # Produced at the Lawrence Livermore National Laboratory
 # 

diff --git a/src/cmake/SetupIncludes.cmake b/src/cmake/SetupIncludes.cmake
@@ -1,5 +1,5 @@
 ###############################################################################
-# Copyright (c) 2014-2018, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2014-2019, Lawrence Livermore National Security, LLC.
 # 
 # Produced at the Lawrence Livermore National Laboratory
 # 

diff --git a/src/cmake/SetupTests.cmake b/src/cmake/SetupTests.cmake
@@ -1,5 +1,5 @@
 ###############################################################################
-# Copyright (c) Copyright (c) 2015-2018, Lawrence Livermore National Security, LLC.
+# Copyright (c) Copyright (c) 2015-2019, Lawrence Livermore National Security, LLC.
 #
 # Produced at the Lawrence Livermore National Laboratory
 #

diff --git a/src/cmake/conduit-config.cmake.in b/src/cmake/conduit-config.cmake.in
@@ -1,5 +1,5 @@
 ###############################################################################
-# Copyright (c) 2014-2018, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2014-2019, Lawrence Livermore National Security, LLC.
 # 
 # Produced at the Lawrence Livermore National Laboratory
 # 

diff --git a/src/cmake/conduit-deps-paths.cmake.in b/src/cmake/conduit-deps-paths.cmake.in
@@ -1,5 +1,5 @@
 ###############################################################################
-# Copyright (c) 2014-2018, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2014-2019, Lawrence Livermore National Security, LLC.
 # 
 # Produced at the Lawrence Livermore National Laboratory
 # 

diff --git a/src/cmake/tests/fortran_test_obj_support.f90 b/src/cmake/tests/fortran_test_obj_support.f90
@@ -1,5 +1,5 @@
 !*~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~*!
-!* Copyright (c) Copyright (c) 2015-2018, Lawrence Livermore National Security, LLC.
+!* Copyright (c) Copyright (c) 2015-2019, Lawrence Livermore National Security, LLC.
 !* 
 !* Produced at the Lawrence Livermore National Laboratory
 !* 

diff --git a/src/cmake/thirdparty/FindNumPy.cmake b/src/cmake/thirdparty/FindNumPy.cmake
@@ -1,5 +1,5 @@
 ###############################################################################
-# Copyright (c) 2014-2018, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2014-2019, Lawrence Livermore National Security, LLC.
 # 
 # Produced at the Lawrence Livermore National Laboratory
 # 

diff --git a/src/cmake/thirdparty/SetupADIOS.cmake b/src/cmake/thirdparty/SetupADIOS.cmake
@@ -1,5 +1,5 @@
 ###############################################################################
-# Copyright (c) 2014-2018, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2014-2019, Lawrence Livermore National Security, LLC.
 # 
 # Produced at the Lawrence Livermore National Laboratory
 # 

diff --git a/src/cmake/thirdparty/SetupHDF5.cmake b/src/cmake/thirdparty/SetupHDF5.cmake
@@ -1,5 +1,5 @@
 ###############################################################################
-# Copyright (c) 2014-2018, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2014-2019, Lawrence Livermore National Security, LLC.
 # 
 # Produced at the Lawrence Livermore National Laboratory
 # 

diff --git a/src/cmake/thirdparty/SetupPython.cmake b/src/cmake/thirdparty/SetupPython.cmake
@@ -1,5 +1,5 @@
 ###############################################################################
-# Copyright (c) 2014-2018, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2014-2019, Lawrence Livermore National Security, LLC.
 # 
 # Produced at the Lawrence Livermore National Laboratory
 # 

diff --git a/src/cmake/thirdparty/SetupRapidJSON.cmake b/src/cmake/thirdparty/SetupRapidJSON.cmake
@@ -1,5 +1,5 @@
 ###############################################################################
-# Copyright (c) 2014-2018, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2014-2019, Lawrence Livermore National Security, LLC.
 # 
 # Produced at the Lawrence Livermore National Laboratory
 # 

diff --git a/src/cmake/thirdparty/SetupSilo.cmake b/src/cmake/thirdparty/SetupSilo.cmake
@@ -1,5 +1,5 @@
 ###############################################################################
-# Copyright (c) 2014-2018, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2014-2019, Lawrence Livermore National Security, LLC.
 # 
 # Produced at the Lawrence Livermore National Laboratory
 # 

diff --git a/src/cmake/valgrind.supp b/src/cmake/valgrind.supp
@@ -531,5 +531,13 @@
    obj:/bin/bash
 }
 
+{
+   MacoOS_LauncherLeak
+   Memcheck:Leak
+   fun:calloc
+   fun:map_images_nolock
+   ...
+   fun:libSystem_initializer
+}
 
 
diff --git a/src/config/CMakeLists.txt b/src/config/CMakeLists.txt
@@ -1,5 +1,5 @@
 ###############################################################################
-# Copyright (c) 2015-2018, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2015-2019, Lawrence Livermore National Security, LLC.
 #
 # Produced at the Lawrence Livermore National Laboratory
 #

diff --git a/src/config/conduit_config.mk.in b/src/config/conduit_config.mk.in
@@ -1,5 +1,5 @@
 ###############################################################################
-# Copyright (c) 2015-2018, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2015-2019, Lawrence Livermore National Security, LLC.
 #
 # Produced at the Lawrence Livermore National Laboratory
 #

diff --git a/src/docs/doxygen/CMakeLists.txt b/src/docs/doxygen/CMakeLists.txt
@@ -1,5 +1,5 @@
 ###############################################################################
-# Copyright (c) 2014-2018, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2014-2019, Lawrence Livermore National Security, LLC.
 # 
 # Produced at the Lawrence Livermore National Laboratory
 # 

diff --git a/src/docs/doxygen/Doxyfile.in b/src/docs/doxygen/Doxyfile.in
@@ -1,5 +1,5 @@
 ###############################################################################
-# Copyright (c) 2014-2018, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2014-2019, Lawrence Livermore National Security, LLC.
 # 
 # Produced at the Lawrence Livermore National Laboratory
 # 

diff --git a/src/docs/sphinx/CMakeLists.txt b/src/docs/sphinx/CMakeLists.txt
@@ -1,5 +1,5 @@
 ###############################################################################
-# Copyright (c) 2014-2018, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2014-2019, Lawrence Livermore National Security, LLC.
 # 
 # Produced at the Lawrence Livermore National Laboratory
 # 

diff --git a/src/docs/sphinx/blueprint.rst b/src/docs/sphinx/blueprint.rst
@@ -1,5 +1,5 @@
 .. ############################################################################
-.. # Copyright (c) 2014-2018, Lawrence Livermore National Security, LLC.
+.. # Copyright (c) 2014-2019, Lawrence Livermore National Security, LLC.
 .. # 
 .. # Produced at the Lawrence Livermore National Laboratory
 .. # 

diff --git a/src/docs/sphinx/blueprint_mcarray.rst b/src/docs/sphinx/blueprint_mcarray.rst
@@ -1,5 +1,5 @@
 .. ############################################################################
-.. # Copyright (c) 2014-2018, Lawrence Livermore National Security, LLC.
+.. # Copyright (c) 2014-2019, Lawrence Livermore National Security, LLC.
 .. # 
 .. # Produced at the Lawrence Livermore National Laboratory
 .. # 

diff --git a/src/docs/sphinx/blueprint_mesh.rst b/src/docs/sphinx/blueprint_mesh.rst
@@ -1,5 +1,5 @@
 .. ############################################################################
-.. # Copyright (c) 2014-2018, Lawrence Livermore National Security, LLC.
+.. # Copyright (c) 2014-2019, Lawrence Livermore National Security, LLC.
 .. # 
 .. # Produced at the Lawrence Livermore National Laboratory
 .. # 

diff --git a/src/docs/sphinx/conduit.rst b/src/docs/sphinx/conduit.rst
@@ -1,5 +1,5 @@
 .. ############################################################################
-.. # Copyright (c) 2014-2018, Lawrence Livermore National Security, LLC.
+.. # Copyright (c) 2014-2019, Lawrence Livermore National Security, LLC.
 .. # 
 .. # Produced at the Lawrence Livermore National Laboratory
 .. # 

diff --git a/src/docs/sphinx/conduit_cpp_api.rst b/src/docs/sphinx/conduit_cpp_api.rst
@@ -1,5 +1,5 @@
 .. ############################################################################
-.. # Copyright (c) 2014-2018, Lawrence Livermore National Security, LLC.
+.. # Copyright (c) 2014-2019, Lawrence Livermore National Security, LLC.
 .. # 
 .. # Produced at the Lawrence Livermore National Laboratory
 .. # 

diff --git a/src/docs/sphinx/conf.py b/src/docs/sphinx/conf.py
@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
 #
 ###############################################################################
-# Copyright (c) Copyright (c) 2015-2018, Lawrence Livermore National Security, LLC.
+# Copyright (c) Copyright (c) 2015-2019, Lawrence Livermore National Security, LLC.
 #
 # Produced at the Lawrence Livermore National Laboratory
 #
@@ -101,16 +101,16 @@
 
 # General information about the project.
 project = u'Conduit'
-copyright = u'Copyright (c) 2015-2018, LLNS'
+copyright = u'Copyright (c) 2015-2019, LLNS'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = '0.4.0-pre'
+version = '0.4.0'
 # The full version, including alpha/beta/rc tags.
-release = '0.4.0-pre'
+release = '0.4.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/src/docs/sphinx/developer.rst b/src/docs/sphinx/developer.rst
@@ -1,5 +1,5 @@
 .. ############################################################################
-.. # Copyright (c) 2014-2018, Lawrence Livermore National Security, LLC.
+.. # Copyright (c) 2014-2019, Lawrence Livermore National Security, LLC.
 .. # 
 .. # Produced at the Lawrence Livermore National Laboratory
 .. # 

diff --git a/src/docs/sphinx/glossary.rst b/src/docs/sphinx/glossary.rst
@@ -1,5 +1,5 @@
 .. ############################################################################
-.. # Copyright (c) 2014-2018, Lawrence Livermore National Security, LLC.
+.. # Copyright (c) 2014-2019, Lawrence Livermore National Security, LLC.
 .. # 
 .. # Produced at the Lawrence Livermore National Laboratory
 .. # 

diff --git a/src/docs/sphinx/index.rst b/src/docs/sphinx/index.rst
@@ -1,5 +1,5 @@
 .. ############################################################################
-.. # Copyright (c) 2014-2018, Lawrence Livermore National Security, LLC.
+.. # Copyright (c) 2014-2019, Lawrence Livermore National Security, LLC.
 .. # 
 .. # Produced at the Lawrence Livermore National Laboratory
 .. # 

diff --git a/src/docs/sphinx/licenses.rst b/src/docs/sphinx/licenses.rst
@@ -1,5 +1,5 @@
 .. ############################################################################
-.. # Copyright (c) Copyright (c) 2015-2018, Lawrence Livermore National Security, LLC.
+.. # Copyright (c) Copyright (c) 2015-2019, Lawrence Livermore National Security, LLC.
 .. #
 .. # Produced at the Lawrence Livermore National Laboratory
 .. #

diff --git a/src/docs/sphinx/presentations.rst b/src/docs/sphinx/presentations.rst
@@ -1,5 +1,5 @@
 .. ############################################################################
-.. # Copyright (c) Copyright (c) 2015-2018, Lawrence Livermore National Security, LLC.
+.. # Copyright (c) Copyright (c) 2015-2019, Lawrence Livermore National Security, LLC.
 .. #
 .. # Produced at the Lawrence Livermore National Laboratory
 .. #