update release notes for 0.8.0 (#890)

* changelog updates for 0.8.0 rel

* rel notes updates for 0.8.0 rel

* pin spack fork for 0.8.0 rel

.uberenv_config.json

@@ -6,7 +6,7 @@
 "spack_configs_path": "scripts/uberenv_configs/spack_configs",
 "spack_packages_path": "scripts/uberenv_configs/packages",
 "spack_url": "https://github.com/alpine-DAV/spack",
-"spack_branch": "ascent/develop",
+"spack_branch": "conduit/releases/v0.8.0",
 "spack_activate" : {"py-numpy" : ["+python"], 
                     "py-sphinx": ["+python","+doc"], 
                     "py-mpi4py" : ["+python", "+mpi"],

CHANGELOG.md

@@ -4,7 +4,7 @@ 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 aspires to adhere to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## Unreleased
+## [0.8.0] - Released 2021-12-20
 
 
 ### Added
@@ -15,17 +15,22 @@ and this project aspires to adhere to [Semantic Versioning](https://semver.org/s
 - Added support to register custom memory allocators and a custom data movement handler. This allows conduit to move trees of data between heterogenous memory spaces (e.g. CPU and GPU memory). See conduit_utils.hpp for API details.
 
 #### Blueprint
-- Added the `blueprint::mesh::examples::polychain` example. It is an example of a polyhedral mesh. See Mesh Blueprint Examples docs (https://llnl-conduit.readthedocs.io/en/latest/blueprint_mesh.html#polychain) for more details.
-- Added to the `blueprint::mesh::examples::polytess` example. Now `polytess` takes a new argument, called `nz`, which allows it to be extended into 3 dimensions. See Mesh Blueprint Examples docs (https://llnl-conduit.readthedocs.io/en/latest/blueprint_mesh.html#polytess) for more details.
+- Added `conduit::blueprint::{mpi}::partition` function that provides a general N-to-M partition capability for Blueprint Meshes. This helps with load balancing and other use cases, including fusing multi-domain data to simplifying post processing. This capability supports several options, see (https://llnl-conduit.readthedocs.io/en/latest/blueprint_mesh_partition.html) for more details.
+- Added a `Table` blueprint used to represent tables of numeric data. See (https://llnl-conduit.readthedocs.io/en/latest/blueprint_table.html) more details.
+- Added `conduit::blueprint::{mpi}::flatten` which transforms Blueprint Meshes into Blueprint Tables. This transforms Mesh Blueprint data into a form that is more easily digestible in machine learning applications.
+- Added `conduit::blueprint::mpi::generate_partition_field`, which uses Parmetis to create a field that identifies how to load balance an input mesh elements.  This field can be used as a Field selection input to `conduit::blueprint::mpi::partition` function.
+- Added the`blueprint::mesh::examples::polychain` example. It is an example of a polyhedral mesh. See Mesh Blueprint Examples docs (https://llnl-conduit.readthedocs.io/en/latest/blueprint_mesh.html#polychain) for more details.
 - Added a new function signature for `blueprint::mesh::topology::unstructured::generate_sides`, which performs the same task as the original and also takes fields from the original topology and maps them onto the new topology.
+- Added `blueprint::mpi::mesh::to_polygonal`, which provides a MPI aware conversion Blueprint Structured AMR meshes to a Blueprint Polyhedral meshes.
 - Added a host of `conduit::blueprint::mpi::mesh::generate_*` methods, which are the MPI parallel equivalents of the `conduit::blueprint::mesh::topology::unstructured::generate_*` functions.
 - Added the `conduit::blueprint::mpi::mesh::find_delegate_domain` function, which returns a single delegate domain for the given mesh across MPI ranks (useful when all ranks need mesh information and some ranks can have empty meshes).
 - Added check and transform functions for the newly-designated `pairwise` and `maxshare` variants of `adjsets`. For more information, see the `conduit::blueprint::mesh::adjset` namespace.
 - Added `mesh::topology::unstructured::to_polytopal` as an alias to `mesh::topology::unstructured::to_polygonal`, to reflect that both polygonal and polyhedral are supported.
 - Added `conduit::blueprint::mpi::mesh::to_polytopal` as an alias to `conduit::blueprint::mpi::mesh::to_polygonal` and `conduit::blueprint::mpi::mesh::to_polyhedral`.
 
+
 #### Relay
-- Added `conduit::relay::io::hdf5_identifier_report` methods, which creates a conduit node that describes active hdf5 resource handles.
+- Added `conduit::relay::io::hdf5_identifier_report` methods, which create conduit nodes that describes active hdf5 resource handles.
 
 
 ### Changed
@@ -36,6 +41,7 @@ and this project aspires to adhere to [Semantic Versioning](https://semver.org/s
 - `conduit::Node::print()` and in Python Node `repr` and `str` now use `to_summary_string()`. This reduces the output for large Nodes. Full output is still supported via `to_string()`, `to_yaml()`, etc methods.
 
 #### Blueprint
+- The `blueprint::mesh::examples::polytess` function now takes a new argument, called `nz`, which allows it to be extended into 3 dimensions. See Mesh Blueprint Examples docs (https://llnl-conduit.readthedocs.io/en/latest/blueprint_mesh.html#polytess) for more details.
 - Added support for both `const` and non-`const` inputs to the `conduit::blueprint::mesh::domains` function.
 - Improved mesh blueprint index generation logic (local and MPI) to support domains with different topos, fields, etc. 
 - Deprecated accepting `npts_z !=0` for 2D shape types in `conduit::blueprint::mesh::examples::{braid,basic,grid}`. They issue a `CONDUIT_INFO` message when this detected and future versions will issue a `CONDUIT_ERROR`.
@@ -53,7 +59,7 @@ and this project aspires to adhere to [Semantic Versioning](https://semver.org/s
 #### General
 - Avoid compile issue with using `_Pragma()` with Python 3.8 on Windows
 - `conduit_node` and `conduit_datatype` in the C API are no longer aliases to `void` so that callers cannot pass just any pointer to the APIs.
-- Fixed overread issue with Fortran API due to int vs bool binding error. Fortran API still provides logical returns for methods like conduit_node_has_path() however the binding implementation now properly translates C_INT return codes into logical values.
+- Fixed memory over read issue with Fortran API due to int vs bool binding error. Fortran API still provides logical returns for methods like conduit_node_has_path() however the binding implementation now properly translates C_INT return codes into logical values.
 - Fixed a subtle bug with Node fetch and Object role initialization.
 
 #### Blueprint
@@ -556,7 +562,9 @@ and this project aspires to adhere to [Semantic Versioning](https://semver.org/s
 ### Added
 - Initial Open Source Release on GitHub
 
-[Unreleased]: https://github.com/llnl/conduit/compare/v0.7.1...HEAD
+[Unreleased]: https://github.com/llnl/conduit/compare/v0.8.0...HEAD
+[0.8.0]: https://github.com/llnl/conduit/compare/v0.7.2...v0.8.0
+[0.7.2]: https://github.com/llnl/conduit/compare/v0.7.1...v0.7.2
 [0.7.1]: https://github.com/llnl/conduit/compare/v0.7.0...v0.7.1
 [0.7.0]: https://github.com/llnl/conduit/compare/v0.6.0...v0.7.0
 [0.6.0]: https://github.com/llnl/conduit/compare/v0.5.1...v0.6.0

azure-pipelines.yml

@@ -316,6 +316,9 @@ stages:
            export APT_PKGS="$APT_PKGS libbz2-dev"
            export APT_PKGS="$APT_PKGS openmpi-bin"
            export APT_PKGS="$APT_PKGS libopenmpi-dev"
+           # display packages
+           echo "Installing APT_PKGS:"
+           echo $APT_PKGS
            # install pkgs we need
            sudo apt-get -y install $APT_PKGS
         displayName: 'Prepare build env'
@@ -355,6 +358,7 @@ stages:
            # silo constraints
            if [ $ENABLE_SILO = 'ON' ]; then export SPACK_SPEC="${SPACK_SPEC} ^silo~mpi"; fi
            # show final spec
+           echo "Spack Spec:"
            echo $SPACK_SPEC
            # run uber to build tpls
            python scripts/uberenv/uberenv.py -k --pull --spec "${SPACK_SPEC}" --spack-config-dir=scripts/uberenv_configs/spack_configs/configs/alpinedav/ubuntu_18_devel/

src/docs/sphinx/conf.py

@@ -62,16 +62,16 @@
 
 # General information about the project.
 project = u'Conduit'
-copyright = u'Copyright (c) 2015-2020, LLNS'
+copyright = u'Copyright (c) 2015-2021, 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 = '0.7.2'
+version = '0.8.0'
 # The full version, including alpha/beta/rc tags.
-release = '0.7.2'
+release = '0.8.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

src/docs/sphinx/releases.rst

@@ -12,6 +12,93 @@ https://github.com/LLNL/conduit/releases
 
 .. note:: Conduit uses `BLT <https://github.com/LLNL/blt>`__ as its core CMake build system. We leverage BLT as a git submodule, however github does not include submodule contents in its automatically created source tarballs. To avoid confusion, starting with v0.3.0 we provide our own source tarballs that include BLT. 
 
+v0.8.0
+---------------------------------
+
+* `Source Tarball <https://github.com/LLNL/conduit/releases/download/v0.8.0/conduit-v0.8.0-src-with-blt.tar.gz>`__
+
+Highlights
+++++++++++++++++++++++++++++++++++++
+
+(Extracted from Conduit's :download:`Changelog <../../../CHANGELOG.md>`)
+
+
+Added
+~~~~~
+
+
+* **General**
+
+ * Added ``setup.py`` for building and installing Conduit and its Python module via pip
+ * Added DataAccessor class that helps write generic algorithms that consume data arrays using expected types.
+ * Added support to register custom memory allocators and a custom data movement handler. This allows conduit to move trees of data between heterogenous memory spaces (e.g. CPU and GPU memory). See conduit_utils.hpp for API details.
+
+* **Blueprint**
+
+ * Added ``conduit::blueprint::{mpi}::partition`` function that provides a general N-to-M partition capability for Blueprint Meshes. This helps with load balancing and other use cases, including fusing multi-domain data to simplifying post processing. This capability supports several options, see (https://llnl-conduit.readthedocs.io/en/latest/blueprint_mesh_partition.html) for more details.
+ * Added a ``Table`` blueprint used to represent tables of numeric data. See (https://llnl-conduit.readthedocs.io/en/latest/blueprint_table.html) more details.
+ * Added ``conduit::blueprint::{mpi}::flatten`` which transforms Blueprint Meshes into Blueprint Tables. This transforms Mesh Blueprint data into a form that is more easily digestible in machine learning applications.
+ * Added ``conduit::blueprint::mpi::generate_partition_field``, which uses Parmetis to create a field that identifies how to load balance an input mesh elements.  This field can be used as a Field selection input to ``conduit::blueprint::mpi::partition`` function.
+ * Added the``blueprint::mesh::examples::polychain`` example. It is an example of a polyhedral mesh. See Mesh Blueprint Examples docs (https://llnl-conduit.readthedocs.io/en/latest/blueprint_mesh.html#polychain) for more details.
+ * Added a new function signature for ``blueprint::mesh::topology::unstructured::generate_sides``, which performs the same task as the original and also takes fields from the original topology and maps them onto the new topology.
+ * Added ``blueprint::mpi::mesh::to_polygonal``, which provides a MPI aware conversion Blueprint Structured AMR meshes to a Blueprint Polyhedral meshes.
+ * Added a host of ``conduit::blueprint::mpi::mesh::generate_*`` methods, which are the MPI parallel equivalents of the ``conduit::blueprint::mesh::topology::unstructured::generate_*`` functions.
+ * Added the ``conduit::blueprint::mpi::mesh::find_delegate_domain`` function, which returns a single delegate domain for the given mesh across MPI ranks (useful when all ranks need mesh information and some ranks can have empty meshes).
+ * Added check and transform functions for the newly-designated ``pairwise`` and ``maxshare`` variants of ``adjsets``. For more information, see the ``conduit::blueprint::mesh::adjset`` namespace.
+ * Added ``mesh::topology::unstructured::to_polytopal`` as an alias to ``mesh::topology::unstructured::to_polygonal``, to reflect that both polygonal and polyhedral are supported.
+ * Added ``conduit::blueprint::mpi::mesh::to_polytopal`` as an alias to ``conduit::blueprint::mpi::mesh::to_polygonal`` and ``conduit::blueprint::mpi::mesh::to_polyhedral``.
+
+* **Relay**
+
+ * Added ``conduit::relay::io::hdf5_identifier_report`` methods, which create conduit nodes that describes active hdf5 resource handles.
+
+Changed
+~~~~~~~
+
+
+* **General**
+
+ * Updated CMake logic to provide more robust Python detection and better support for HDF5 installs that were built with CMake.
+ * Improved Node::diff and Node::diff_compatible to show string values when strings differ.
+ * ``conduit::Node::print()`` and in Python Node ``repr`` and ``str`` now use ``to_summary_string()``. This reduces the output for large Nodes. Full output is still supported via ``to_string()``, ``to_yaml()``, etc methods.
+
+* **Blueprint**
+
+ * The ``blueprint::mesh::examples::polytess`` function now takes a new argument, called ``nz``, which allows it to be extended into 3 dimensions. See Mesh Blueprint Examples docs (https://llnl-conduit.readthedocs.io/en/latest/blueprint_mesh.html#polytess) for more details.
+ * Added support for both ``const`` and non-``const`` inputs to the ``conduit::blueprint::mesh::domains`` function.
+ * Improved mesh blueprint index generation logic (local and MPI) to support domains with different topos, fields, etc.
+ * Deprecated accepting ``npts_z !=0`` for 2D shape types in ``conduit::blueprint::mesh::examples::{braid,basic,grid}``. They issue a ``CONDUIT_INFO`` message when this detected and future versions will issue a ``CONDUIT_ERROR``.
+ * An empty Conduit Node is now considered a valid multi-domain mesh. This change was made to make serial uses cases better match sparse MPI multi-domain use cases. Existing code that relied ``mesh::verify`` to exclude empty Nodes will now need an extra check to see if an input mesh has data.
+ * Added MPI communicator argument to ``conduit::blueprint::mpi::mesh::to_polygonal`` and ``conduit::blueprint::mpi::mesh::to_polyhedral``.
+
+* **Relay**
+
+ * Added CMake option (``ENABLE_RELAY_WEBSERVER``, default = ``ON``) to control if Conduit's Relay Web Server support is built. Down stream codes can check for support via header ifdef ``CONDUIT_RELAY_WEBSERVER_ENABLED`` or at runtime in ``conduit::relay::about``.
+ * Added support to compile against HDF5 1.12.
+
+Fixed
+~~~~~
+
+
+* **General**
+
+ * Avoid compile issue with using ``_Pragma()`` with Python 3.8 on Windows
+ * ``conduit_node`` and ``conduit_datatype`` in the C API are no longer aliases to ``void`` so that callers cannot pass just any pointer to the APIs.
+ * Fixed memory over read issue with Fortran API due to int vs bool binding error. Fortran API still provides logical returns for methods like conduit_node_has_path() however the binding implementation now properly translates C_INT return codes into logical values.
+ * Fixed a subtle bug with Node fetch and Object role initialization.
+
+* **Blueprint**
+
+ * Fixed a bug that was causing the ``conduit::blueprint::mesh::topology::unstructured::generate_*`` functions to produce bad results for polyhedral input topologies with heterogeneous elements (e.g. tets and hexs).
+ * Fixed a bug with ``conduit::relay::io::blueprint::write_mesh`` that undermined ``truncate=true`` option for root-only style output.
+ * Fixed options parsing bugs and improved error messages for the ``conduit_blueprint_verify`` exe.
+
+* **Relay**
+
+ * Changed HDF5 offset support to use 64-bit unsigned integers for offsets, strides, and sizes.
+ * Fixed a bug with ``conduit::relay::mpi::io::blueprint::save_mesh`` where ``file_style=root_only`` could crash or truncate output files.
+ * Fixed a bug with inconsistent HDF5 handles being used in some cases when converting existing HDF5 Datasets from fixed to extendable.
+
 
 v0.7.2
 ---------------------------------

src/tests/relay/python/t_python_relay_mpi.py

@@ -1,48 +1,6 @@
-###############################################################################
-# Copyright (c) 2015-2020, Lawrence Livermore National Security, LLC.
-#
-# Produced at the Lawrence Livermore National Laboratory
-#
-# LLNL-CODE-716457
-#
-# All rights reserved.
-#
-# This file is part of Ascent.
-#
-# For details, see: http://ascent.readthedocs.io/.
-#
-# Please also read ascent/LICENSE
-#
-# Redistribution and use in source and binary forms, with or without
-# modification, are permitted provided that the following conditions are met:
-#
-# * Redistributions of source code must retain the above copyright notice,
-#   this list of conditions and the disclaimer below.
-#
-# * Redistributions in binary form must reproduce the above copyright notice,
-#   this list of conditions and the disclaimer (as noted below) in the
-#   documentation and/or other materials provided with the distribution.
-#
-# * Neither the name of the LLNS/LLNL nor the names of its contributors may
-#   be used to endorse or promote products derived from this software without
-#   specific prior written permission.
-#
-# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-# ARE DISCLAIMED. IN NO EVENT SHALL LAWRENCE LIVERMORE NATIONAL SECURITY,
-# LLC, THE U.S. DEPARTMENT OF ENERGY OR CONTRIBUTORS BE LIABLE FOR ANY
-# DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-# DAMAGES  (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
-# OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
-# HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
-# STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
-# IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
-# POSSIBILITY OF SUCH DAMAGE.
-#
-###############################################################################
-
-
+# Copyright (c) Lawrence Livermore National Security, LLC and other Conduit
+# Project developers. See top-level LICENSE AND COPYRIGHT files for dates and
+# other details. No copyright assignment is required to contribute to Conduit.
 """
  file: t_python_relay_mpi.py
  description: Unit tests for relay mpi