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@cyrush cyrush released this 03 Nov 00:54
· 277 commits to develop since this release
dcab780

0.6.0 Release Highlights

(adapted from Conduit's Changelog)

Added

General

  • Added support for children with names that include /. Since slashes are part of Conduit's hierarchical path mechanism, you must use explicit methods (add_child(), child(), etc) to create and access children with these types of names. These names are also supported in all basic i/o cases (JSON, YAML, Conduit Binary).
  • Added Node::child and Schema::child methods, which provide access to existing children by name.
  • Added Node::fetch_existing and Schema::fetch_existing methods, which provide access to existing paths or error when given a bad path.
  • Added Node::add_child() and Node::remove_child() to support direct operations and cases where names have / s.
  • Added a set of conduit::utils::log::remove_* filtering functions, which process conduit log/info nodes and strip out the requested information (useful for focusing the often verbose output in log/info nodes).
  • Added to_string() and to_string_default() methods to Node, Schema, DataType, and DataArray. These methods alias either to_yaml() or to_json(). Long term yaml will be preferred over json.
  • Added helper script (scripts/regen_docs_outputs.py) that regenerates all example outputs used Conduit's Sphinx docs.
  • Added to_yaml() and to_yaml_stream methods() to Schema, DataType, and DataArray.
  • Added support for C++-style iterators on node children. You can now do for (Node &node : node.children()) {}. You can also do node.children.begin() and node.children.end() to work with the iterators directly.

Relay

  • Added an open mode option to Relay IOHandle. See Relay IOHandle docs (https://llnl-conduit.readthedocs.io/en/latest/relay_io.html#relay-i-o-handle-interface) for more details.
  • Added the conduit.relay.mpi Python module to support Relay MPI in Python.
  • Added support to write and read Conduit lists to HDF5 files. Since HDF5 Groups do not support unnamed indexed children, each list child is written using a string name that represents its index and a special attribute is written to the HDF5 group to mark the list case. On read, the special attribute is used to detect and read this style of group back into a Conduit list.
  • Added preliminary support to read Sidre Datastore-style HDF5 using Relay IOHandle, those grouped with a root file.
  • Added conduit::relay::io::blueprint::read_mesh functions, were pulled in from Ascent's Blueprint import logic.
  • Added conduit::relay::mpi::wait and conduit::relay::mpi::wait_all functions. These functions consolidate the logic supporting both isend and irecv requests. wait_all supports cases where both sends and receives were posted, which is a common for non-trivial point-to-point communication use cases.

Blueprint

  • Added support for sparse one-to-many relationships with the new blueprint::o2mrelation protocol. See the blueprint::o2mrelation::examples::uniform example for details.
  • Added sparse one-to-many, uni-buffer, and material-dominant specification support to Material sets. See the Material sets documentation
    (https://llnl-conduit.readthedocs.io/en/latest/blueprint_mesh.html#material-sets) for more details.
  • Added support for Adjacency sets for Structured Mesh Topologies. See the blueprint::mesh::examples::adjset_uniform example.
  • Added blueprint::mesh::examples::julia_nestsets_simple and blueprint::mesh::examples::julia_nestsets_complex examples represent Julia set fractals using patch-based AMR meshes and the Mesh Blueprint Nesting Set protocol. See the Julia AMR Blueprint docs
    (https://llnl-conduit.readthedocs.io/en/latest/blueprint_mesh.html#julia-amr-examples) for more details.
  • Added blueprint::mesh::examples::venn example that demonstrates different ways to encode volume fraction based multi-material fields. See the Venn Blueprint docs
    (https://llnl-conduit.readthedocs.io/en/latest/blueprint_mesh.html#venn) for more details.
  • Added blueprint::mesh::number_of_domains property method for trees that conform to the mesh blueprint.
  • Added MPI mesh blueprint methods, blueprint::mpi::mesh::verify and blueprint::mpi::mesh::number_of_domains (available in the conduit_blueprint_mpi library)
  • Added blueprint::mpi::mesh::examples::braid_uniform_multi_domain and blueprint::mpi::mesh::examples::spiral_round_robin distributed-memory mesh examples to the conduit_blueprint_mpi library.
  • Added state/path to the Mesh Blueprint index, needed for consumers to know the proper path to read extended state info (such as domain_id)

Fixed

General

  • Updated to newer BLT to resolve BLT/FindMPI issues with rpath linking commands when using OpenMPI.
  • Fixed internal object name string for the Python Iterator object. It used to report Schema, which triggered both puzzling and concerned emotions.
  • Fixed a bug with Node.set in the Python API that undermined setting NumPy arrays with sliced views and complex striding. General slices should now work with set. No changes to the set_external case, which requires 1-D effective striding and throws an exception when more complex strides are presented.
  • Fixed a bug with auto detect of protocol for Node.load
  • Fixed bugs with auto detect of protocol for Node.load and Node.save in the Python interface

Relay

  • Use H5F_ACC_RDONLY in relay::io::is_hdf5_file to avoid errors when checking files that already have open HDF5 handles.
  • Fixed compatibility check for empty Nodes against HDF5 files with existing paths

Changed

General

  • Conduit's main git branch was renamed from master to develop. To allow time for folks to migrate, the master branch is active but frozen and will be removed during the 0.7.0 release.
  • We recommend a C++11 (or newer) compiler, support for older C++ standards is deprecated and will be removed in a future release.
  • Node::fetch_child and Schema::fetch_child are deprecated in favor of the more clearly named Node::fetch_existing and Schema::fetch_existing. fetch_child variants still exist, but will be removed in a future release.
  • Python str() methods for Node, Schema, and DataType now use their new to_string() methods.
  • DataArray::to_json(std::ostring &) is deprecated in favor DataArray::to_json_stream. to_json(std::ostring &) will be removed in a future release.
  • Schema::to_json and Schema::save variants with detailed (bool) arg are deprecated. The detailed arg was never used. These methods will be removed in a future release.
  • Node::print() now prints yaml instead of json.
  • The string return variants of about methods now return yaml strings instead of json strings.
  • Sphinx Docs code examples and outputs are now included using start-after and end-before style includes.
  • Schema to_json() and to_json_stream() methods were expanded to support indent, depth, pad and end-of-element args.
  • In Python, conduit.Node() repr now returns the YAML string representation of the Node. Perviously verbose conduit_json was used, which was overwhelming.
  • conduit.about() now reports the git tag if found, and version was changed to add git sha and status (dirty) info to avoid confusion between release and development installs.

Relay

  • Provide more context when a Conduit Node cannot be written to a HDF5 file because it is incompatible with the existing HDF5 tree. Error messages now provide the full path and details about the incompatibility.
  • conduit::relay::io_blueprint::save functions are deprecated in favor of conduit::relay::io::blueprint::write_mesh
  • conduit::relay::io::blueprint::write_mesh functions were pulled in from Ascent's Blueprint export logic.
  • conduit_relay_io_mpi lib now depends on conduit_relay_io. Due to this change, a single build supports either ADIOS serial (no-mpi) or ADIOS with MPI support, but not both. If conduit is configured with MPI support, ADIOS MPI is used.
  • The functions conduit::relay::mpi::wait_send and conduit::relay::mpi::wait_recv now use conduit::relay::mpi::wait. The functions wait_send and wait_recv exist to preserve the old API, there is no benefit to use them over wait.
  • The functions conduit::relay::mpi::wait_all_send and conduit::relay::mpi::wait_all_recv now use conduit::relay::mpi::wait_all. The functions wait_all_send and wait_all_recv exist to preserve the old API, there is no benefit to use them over wait_all.

Blueprint

  • Refactored the Polygonal and Polyhedral mesh blueprint specification to leverage one-to-many concepts and to allow more zero-copy use cases.
  • The conduit_blueprint_mpi library now depends on conduit_relay_mpi.
  • The optional Mesh Blueprint structured topology logical element origin is now specified using {i,j,k} instead of {i0,j0,k0}.