Pod5

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.

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

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.

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 `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

Fixed

- Repacker `reads_completed` value while copying a selection of reads.
- Fixed crash when trying to load files with a bad footer.