CHANGELOG.md

Changelog

0.7.0

Added

• HDF5 C library can now be built from source and linked in statically, enabled via hdf5-sys/static feature (as of this release, the version of the bundled sources of the library is 1.10.6). CMake is required for building. For further details, see the docs for hdf5-sys.
• Thanks to static build option, the documentation will now be built on docs.rs; if it builds successfully, this will be the official documentation source from now on.
• Add support for HDF5 1.12 on all platforms and include it in CI.

Changed

• Switched CI from Travis/AppVeyor to GitHub Actions; for each pull request, we now run around 30 concurrent builds which provides with a much wider coverage than previously and has already revealed some issues that have been fixed. Platforms covered: macOS 10.15, Windows Server 2019, Ubuntu 16.04/18.04/20.04; HDF5 installation methods covered: conda, apt, homebrew, also official binaries on Windows. We now also test MPI versions of the library for both MPICH and OpenMPI on macOS / Linux.

Fixed

• We now force the variable-length allocator that HDF5 uses when reading data to use libc::malloc and libc::free, so that they can be deallocated properly by VarLenString and VarLenArray in hdf5-types. Previously, this could cause a rare but serious failure for Windows builds when the default allocator used for vlen types by HDF5 was not matching the libc deallocator.
• Use std::panic::catch_unwind in all cases where we uses extern C callbacks, so that they are panic-safe.
• Reader::read_raw and Reader::read_slice should now be Drop-safe in the event where the read operation fails and the destination type is not trivial.

0.6.1

Added

• Implement Default for H5D_layout_t, H5D_alloc_time_t, H5T_cset_t, H5D_fill_time_t, H5D_fill_value_t (based on what their values are set to in default property lists).
• Derive Debug for ErrorFrame and ErrorStack.
• Implement Display for TypeDescriptor.
• Implement Dimension for [Ix], &[Ix], [Ix; N] and &[Ix; N].

Changed

• h5check!, h5lock!, h5try!, h5call! and h5check() are now public.
• globals module containing HDF5 runtime constants is now also public.
• Switch to using 1.0 versions of syn, quote and proc-macro2 (which required a bit of a rewrite of hdf5-derive).
• Bump ascii to 1.0, update hdf5-types to be compatible.
• Bump other dependencies to their latest versions (parking_lot to 0.10, ndarray to 0.13, bitflags to 1.2, lazy_static to 1.4, libloading to 0.6, winreg to 0.7).
• Remove implementations of deprecated Error::description().
• Switch to trybuild instead of compiletest_rs for derive-macro testing; enable full tests (including hdf5-derive) on both AppVeyor and Travis.
• Update the minimum Rust version to 1.40 (because of ndarray and libloading).

Fixed

• Use H5_free_memory() instead of libc::free() to free HDF5-allocated resources if possible (1.8.13+); this fixes some deallocation errors.
• Fix wrong H5D_DONT_FILTER_PARTIAL_CHUNKS constant value.
• H5Z_filter_t is changed to c_int (was wrongfully set to hid_t).

0.6.0

Added

• Added support for HDF5 1.10.5 with bindings for new functions.
• File::access_plist() or File::fapl() to get file access plist.
• File::create_plist() or File::fcpl() to get file creation plist.
• Added high-level wrappers for dataset access H5P API (plist::DatasetAccess).
• Added hdf5::is_library_threadsafe() function.
• Added Group::member_names().
• Added Datatype::byte_order().
• Added Dataset::num_chunks() (1.10.5+).
• Added Dataset::chunk_info() (1.10.5+).

Changed

• Changed File constructors, getting rid of string access modes:
  • File::open(path, "r") is now File::open(path)
  • File::open(path, "r+") is now File::open_rw(path)
  • File::open(path, "w") is now File::create(path)
  • File::open(path, "x" | "w-") is now File::create_excl(path)
  • File::open(path, "a") is now File::append(path)
• Also added File::open_as(path, mode) which accepts the mode enum.
• Rewritten FileBuilder: it no longer accepts userblock, driver etc; all of these parameters can be set in the corresponding FAPL / FCPL:
  • FileBuilder::set_access_plist() or FileBuilder::set_fapl() to set the active file access plist to a given one.
  • FileBuilder::access_plist() or FileBuilder::fapl() to get a mutable reference to the FAPL builder - any parameter of it can then be tweaked as desired.
  • FileBuilder::with_access_plist() or FileBuilder::with_fapl() to get access to the FAPL builder in an inline way via a closure.
  • Same as the three above for create_plist / fcpl.
• As a result, all of the newly added FAPL / FCPL functionality is fully accessible in the new FileBuilder. Also, driver strings are gone, everything is strongly typed now.
• It's no longer prohibited to set FCPL options when opening a file and not creating it -- it will simply be silently ignored (this simplifies the behavior and allows using a single file builder).
• Added an explicit hdf5_types::string::StringError error type, as a result error-chain dependency has been dropped.
• hdf5::Error is now convertible from ndarray::ShapeError; hdf5::ResultExt trait has been removed.
• Renamed hdf5::hdf5_version() to hdf5::library_version().

Fixed

• Replaced deprecated std::mem::uninitialized with std::mem::MaybeUninit.
• Fixed a serde-related problem with building hdf5-sys on Windows.

0.5.2

Changed

• Allow chunk dimensions to exceed dataset dimensions for resizable datasets.
• Default HDF5 location should now be detected automatically on Fedora Linux.

0.5.1

Added

• Added Group::link_exists().
• Re-export silence_errors() at the crate root.
• Added from_id() unsafe method at the crate root.

Changed

• Using #[derive(H5Type)] no longer requires adding hdf5-types as a dependency.

0.5.0

Added

• Added support for HDF5 1.10.
• Added Rust equivalents of HDF5 primitives: arrays, Unicode strings and ASCII strings – all of them available in both fixed-size or variable-length flavours (hdf5-types crate).
• Added H5Type trait that unifies the types that can be handled by the HDF5 library. This trait is implemented by default for all scalar types, tuples, fixed-size arrays and all types in hdf5-types and can be used to create Datatype objects.
• Implemented #[derive(H5Type)] proc macro that allows for seamless mapping of user-defined structs and enums to their HDF5 counterparts.
• Added high-level wrappers for file-creation H5P API (plist::FileCreate) and file-access H5P API (plist::FileAccess), covering almost the entirety of FCPL and FAPL property list functionality.
• Various improvements and additions to PropertyList type.
• Added support for various file drivers (sec2/stdio/core/family/multi/split/log).
• Added support for MPIO driver (HDF5 has to be built with H5_HAVE_PARALLEL and the crate has to be built with "mpio" feature enabled).
• Added support for direct VFD driver (HDF5 has to be built with H5_HAVE_DIRECT).
• Added some missing bindings to hdf5-sys: driver-related FAPL bindings in h5p/h5fd (including MPIO and direct VFD drivers), MPIO bindings in h5p/h5f/h5fd.
• Added core reading/writing API in Container, with support for reading/writing scalars, 1-d, 2-d, and dynamic-dimensional arrays, and raw slices. As a side effect, the main crate now depends on ndarray. Dataset now dereferences to Container.
• Added basic support for reading and writing dataset slices.
• When creating datasets, in-memory type layouts are normalized (converted to C repr).
• Added packed option to DatasetBuilder (for creating packed HDF5 datasets).
• All high-level objects now implement Clone (shallow copy, increases refcount).

Changed

• Renamed hdf5-rs crate (importable as h5) to hdf5 (importable simply as hdf5).
• Renamed libhdf5-sys crate to hdf5-sys (importable as hdf5_sys).
• Renamed GitHub repository to aldanor/hdf5-rust.
• Updated the bindings and tests to the latest HDF5 versions (1.10.4 and 1.8.21).
• The build system has been reworked from the ground up:
  • hdf5-lib crate has been removed; all of the build-time logic now resides in the build script of hdf5-sys.
  • The environment variables the build script reacts to are now HDF5_DIR and HDF5_VERSION.
  • pkg-config is now only launched on Linux.
  • On macOS, the build scripts detects Homebrew installations, for both 1.8 and 1.10 versions.
  • On Windows, we now scan the registry to detect official system-wide installations.
  • Dynamic linking now works with conda envs; HDF5_DIR can be now pointed to a conda env.
  • A few definitions from H5pubconf.h are now exposed as cfg definitions, like h5_have_parallel, h5_have_threadsafe and h5_have_direct (this requires us to locate the include folder and parse the header at build time).
• Various clean ups in hdf5-sys: implemented Default and Clone where applicable, moved a few types and methods to matching parent modules.
• Major refactor: trait-based type hierarchy has been replaced with a Deref-based hierarchy instead (53eff4f). ID and FromID traits have been removed. Traits like Location, Object and a few other have been replaced with real types (wrappers around HDF5 handles, same as the concrete types like File). Subtypes then dereference into parent types, so the user can user methods of the parent type without having to import any traits into scope (for instance, File dereferences into Group, which dereferences into Location, which dereferences into Object).
• Dataspaces and property lists can now be copied via .copy() method (instead of .clone()).

Fixed

• hbool_t is now mapped to unsigned integer of proper size (either 1 byte or 4 bytes), depending on how the HDF5 library was built and on which platform.
• Added missing bindings for previous versions (mostly in h5p and h5fd modules).
• Querying the HDF5 error stack is now thread-safe.
• Error silencing (silence_errors()) is now thread-safe.
• Fixed wrong bindings for H5AC_cache_config_t.

Removed

• Removed hdf5-lib crate (merged it into hdf5-sys, see above).
• Removed remutex crate, using locking primitives from parking_lot crate instead.
• Container trait has been removed, all of its functionality merged into Group type.

Notes

• The version number jump is due to renaming crates hdf5-rs and libhdf5-sys to hdf5 and hdf5-sys, respectively. Since there were already published crates with those names and the crates registry is meant to be immutable even if the crates are yanked, we had to bump the version so that it shadows all of the older versions.

0.2.0 (Apr 17, 2016)

Added

• Full support of msvc target on Windows. CI tests on AppVeyor now use official reeases of HDF5 binaries (1.8.16, VS2015, x86_x64). The gnu target are still unofficially supported but won't be tested.
• If HDF5_LIBDIR is not specified when building on Windows and PATH contains what looks like the bin folder of HDF5 installation, the library directory will be inferred automatically. The official HDF5 installers add the bin folder to user path, so the official MSVC releases should just work out of the box without having to set any environment variables.
• The library is now split into three crates: hdf5-lib (requests linkage to HDF5), hdf5-sys (contains bindings, requires hdf5-lib at build time in order to conditionally enable or disable certain HDF5 functionality), and hdf5 (the user-facing crate, requires both lower-level crates at build time).
• Added hdf5::hdf5_version function.
• The minimum required version of the HDF5 library is now 1.8.4.
• Both hdf5-sys and hdf5 crates can now use version attributes at compile time to enable/disable/change functionality. All functions and definitions that appeared in HDF5 versions past 1.8.4 are now conditionally enabled in hdf5-sys.
• Added bindings for HDF5 functions that were added in releases 1.8.15 and 1.8.16.
• Static global variables in HDF5 (H5E, H5P, H5T) are now linked based on HDF5 version and not the target platform (_ID_g variables were introduced in 1.8.14). When msvc target is used, the dllimport stub prefixes are also accounted for. The constants exposed by hdf5-sys are now of reference type and need to be dereferenced upon use (for msvc, they have to be dereferenced twice).

Changed

• API simplification: many methods previously expecting Into<String> inputs now just take &str.
• util::to_cstring now takes Borrow<str> instead of Into<String> so as to avoid unnecessary allocations, and the return value is now wrapped in Result so that interior null bytes in input strings trigger an error.

Fixed

• Fixed dangling pointer problems when strings were being passed as pointers to the C API.
• Fixed target path not being passed correctly in Container::link_soft.

0.1.1 (July 2015)

Initial public version.