0.3.23

Added

• ArrowTableHandle stream member to store the BatchFileReader backend
• ArrowTableHandle options argument to pass in IpcReadOptions
• pod5::default_memory_pool function which selects an appropriate memory pool even on large page systems.

Changed

• Refactored Multi-threading in DatasetReader to prevent too many open files errors
• Updated dependency to pyarrow~=18.0.0 for python>=3.9
• Relaxed h5py python dependency
• Removed use of python build when building wheel in cmake.

0.3.21

[0.3.21]

Added

• Support for python 3.13.
• New end reason for reads terminated due to an analysis configuration change.
• Ability to disable flushing on batch complete
• Use new LinuxOutputStream to cache allocations and reduce memory when writing many files.
• svb16 headers packaged with pod5

Changed

• Removed use of Boost. This does not affect the C interface, but may require changes to
  consumers of the C++ headers.
• Refactored directio writing engine to open up async io support.
• Fixed Boost version compatibility checking in Conan packages.
• Reduced allocations when compressing signal.
• Directio output now writes on batch complete without flushing explicitly.

Fixed

• Crash when searching empty file for reads.

0.3.15

Added

• Added new end reasons "api_request" and "device_data_error" to allow for new read end reasons future minknow versions will generate.
• Allow directio to specify the chunk size directly.
• gcc8 builds

Fixed

• Instability when creating a pod5 writer fails.
• Issue with directio mode where space is over reserved.

0.3.12

Fixed

• Fixed issues reading signal from uncompressed pod5 files.

0.3.11

Added

• Typechecking on Writer.add_reads to inform users incorrectly passing ReadRecords
• Compatibility with numpy 2.0.

Fixed

• DatasetReader correctly handles string paths

0.3.10

[0.3.10]

Added

• Required pypa project metadata.

Changed

• Updated pre-commit to clang-format-17.
• Updated Arrow to 12.0.0

Fixed

• ReadRecord.to_read() missing fields
• Conan windows upload jobs failure due to using different line endings.
• CI package uploading to PyPi following API token migration.
• Documentation for some functions.
• Explicitly sized type in pod5_vbz_decompress_signal().
• CI execution of tests.

Removed

• Dropped support OSX builds for XCode < 14.2.

0.3.6

Merge branch 'rh/fix_polars_column_not_found_on_not_set' into 'master'

Rh/fix polars column not found on not set

See merge request minknow/pod5-file-format!320

0.3.2

• Add 3.12 Python Support.

0.3.1

Fixed

• Logging no longer calls basicConfig which may unintentionally edit users logging configuration
• Fix a crash in repacker code where multiple threads interacted with the per thread state.
• Repacker reads content from source files before batches are complete to avoid a deadlock when limiting open input files.

0.3.0

Added

• DatasetReader class for reading collections of pod5 files
• Return index errors when querying invalid errors from API's
• Added compression status to pod5 inspect summary <file>
• Added environment override POD5_DISABLE_MMAP_OPEN to force non-mmapped opening of files.

Changed

• Transfers dataframes used in subsetting / filter use categorical fields to reduce memory consumption
• Polars version increased to ~=0.19
• Documentation regarding positional arguments
• Recursive search for files now traverses symbolic links and ignores hidden files
• Write pod5 files using DirectIO on Linux platforms (performance)

Fixed

• Fixed a bug in the build scripts that prevented iOS and Windows Conan packages from being uploaded.
• convert to_fast5 writes byte encoded read_ids to match MinKNOW (was str)
• Corrected the visibility of dependencies when building pod5 as a shared library.
• num_minknow_events field description from int8 to uint64
• ReadRecord.num_minknow_events return type-hint from float to int

Removed

• Removed python3.7 support