0.1.5

• OSX Python 3.11 Wheels.
• Fixed issue where closing many pod5 files while repacking is slow.
• Fixed incorrect python types and adopted python type-checking.
• Explicitly re-exported lib-pod5 public symbols and added py.typed marker file to support type-checking.

0.1.4

Bug fixes since the 0.1.0 release.

Changed

• Linux python 3.11 wheels
• OSX arm64 wheel naming corrections - works with wider set of python executables
• rtd support
• Fixed osx arm64 wheel compatibility for older python versions.
• Fixed EndReason type errors.
• Renamed EndReason.name to EndReason.reason to access the inner enum and added
  EndReason.name as a property to return the string representation of this enum value.
• Fixed EndReason in pod5 to fast5 conversion.
• Removed deprecated Writer functions.
• BaseRead, Read, CompressedRead, Calibration and Pore dataclasses are now mutable.
• Added Reader.__iter__ method.
• Optimised the file writing utilities
• Restricted exported boost dependencies of conan package to just the boost::headers component.

v0.1.0

Changed

• Fixed name of internal utils - "pad_file".
• Fixed spelling of various internal variables.
• Documentation edits
• Deprecated Writer methods add_read_object and add_read_objects for add_read and add_reads respectively.
• Writer.add_reads now handles both Read and CompressedRead.
• Removed direct pod5 tool scripts.
• Fixed pod5 convert to_fast5

0.0.43

Added

• Added pod5 tools entry-point
• Added api to query file version information as written on disk.

Changed

• Fixed name of internal utils - "pad_file".
• Fixed spelling of various internal variables.
• Reformat c++ code with more consistent format file.
• Fixed signal_chunk_size type error in convert-from-fast5
• Replaced ont_fast5_api dependency with vbz_h5py_plugin
• Restructured Python packaging to include lib_pod5 which contains the native bindings build from pybind11.
• pod5_format and pod5_format_tools are now pure python packages which depend on lib_pod5
• Python packages pod5_format and pod5_format_tools have been merged into single pod5 pure-python package.
• pod5-convert-from-fast5 --output-one-to-one reworked so that output files maintain the input structure making this argument more flexible and avoid filename clobbering.
• Added missing lib_pod5.update_file function to pyi.
• pod5-convert-from-fast5 output now takes existing directories and writes output.pod5 (current behaviour) or creates a new file with the given name if it doesn't exist.
• Renamed arguments in tools relating to multi-processing / multi-threading from -p/--processes to the mode common -t/--threads.

0.0.41

Changed since 0.0.32

• Fixed pod5-inspect erroring when loading data.
• Fixed issue where some files inbetween 0.34 - 0.38 wouldn't load correctly.
• Fixed migrating of large files from older versions.
• Fixed building against the c++ api - previously missing include files.
• Support for opening and writing "split" pod5 files. All API's now expect and return combined pod5 files.
• All data in the read table that was previously contained in dictionaries of structs is now stored in the read table, or a new "run info" table. This change simplifies data access into the pod5 files, and helps users who want to convert the pod5 data to pandas or other arrow-compatible reader formats. Old data is migrated on load, and will continue to work, data can be permanently migrated using the tool pod5-migrate
• Updated Conan recipe to support building without specifying C++ standard version.
• Bump the Boost and Arrow versions to pick up latest changes.
• Support C++17 + C++20 with the conan package pod5 generates.
• Modified pod5_format_tools/pod5_convert_to_fast5.py to separate pod5_convert_to_fast5_argparser() and convert_from_fast5() out from pod5_convert_from_fast5.main().
• File version is now V2, due to the addition of num_samples.
• Added num_samples field to read table, containing the total number of samples a read contains. The field is filled in by API if it doesn't exist.

0.0.32

Changed since 0.0.31

• Fixed an issue where multi-threaded access to a single batch could cause a crash discovered by dorado testing.
• Fixed help text in convert to fast5 script.

0.0.31

Update POD5Version.cmake

Python API improvements

0.0.23

Update POD5Version.cmake

0.0.20

• Fix bug reading data via C API

0.0.19

• Further OSX python packages