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

0.2.4

[0.2.4] 2023-07-13

Changed

• Increased numpy minimum version to >= 1.21.0
• Improved performance of subset, filter and merge tools.
• Repacker.wait and Repacker.waiter parameters

Deprecated

• Repacker.wait and Repacker.waiter some parameters are deprecated and issue FutureWarning

Fixed

• Repacker.is_complete returning True when work is queued.

0.2.3

[0.2.3] 2023-06-26

Added

• Add API (pod5_open_file_options) to prevent pod5 from opening a file using mmap, instead using direct file IO.
• Default field values (empty string) when converting fast5 files with missing fields

Changed

• Corrected Oxford Nanopore Technologies company name in package metadata to use Public Limited Company (Plc) instead of Limited (Ltd)
• Limited the number of processes created when specifying --threads to the number of cpu cores available os.cpu_count()
• Reduced the default value for --threads from 8 to 4 to improve stability on resource constrained systems

0.2.2

[0.2.2] 2023-06-0

Fixed

• Add API error when adding reads with invalid end reason, pore type or run info.

Changed

• Update internal arrow lib to not export flatbuffers symbols.

0.2.0

[0.2.0] 2023-05-18

Added

• pod5 view tool to view / inspect pod5 files as tables. Gives a >200x speed improvement compared to pod5 inspect reads
• pod5 recover tool to recover data from corrupted / truncated pod5 files
• pod5 update documentation
• source distributions to pypi

Changed

• pod5 subset and pod5 filter uses polars to parse inputs
• pod5 subset and pod5 filter csv formatting requirements tightened
• pod5 tools which use multiple pod5 file inputs now accept directories which can be searched recursively with -r/--recursive
• pod5 subset --read-id-column argument abbreviateion -r change to -R to allow -r/--recursive to be consistent for all tools
• pod5 tools use hyphens in all arguments (e.g. --force-overwrite and --read-id-column)
• pod5 merge and pod5 update uses named -o/--output argument instead of positional output argument to standardise tools
• pod5 update progress bar and better detection of name conflicts
• Minimised number of open file handles in tools to prevent Too many open files error
• Logging added to view, merge, filter and subset. Enabled with POD5_DEBUG=1

Deprecated

• pod5 inspect reads deprecated in-favour of pod5 view

Fixed

• Exception raised when calling pod5 without any arguments
• Exception raised in pod5 convert fast5 where closed writers were reopened after being closed by a caught exception
• Fixed Gitlab 38, pod5_get_end_reason and pod5_get_pore_type ignoring input string length checks.

Removed

• pod5 subset --json mapping arguments
• pod5 merge --chunk-size argument
• ReadTableVersion replaced with an integer value