0.1.12

• Fixed file handle leak in repacker
• Added readthedocs documentation links in README.md
• Updated developer installation instructions to use conan<2
• Reworked pod5 convert fast5 to tolerate runtime exceptions
• Added --output argument to pod5 convert fast5 and to_fast5 replacing positional argument of the same name
• Added --strict argument to pod5 convert fast5 to promptly stop on exceptions
• Use same type run_info_index_t for pod5_get_file_run_info_count and pod5_get_file_run_info.

0.1.11

• Python API supports python 3.11
• Changed python API dependency version pyarrow~=11.0.0 from 8.0.0 to support python 3.11
• Changed python API dependency version hdf5~=8.0.0 from v7.0.0 to support python 3.11
• Added missing python API wheels on windows

0.1.10

• Added pod5_get_read_count to find the count of all reads in file
• Added pod5_get_read_ids to retrieve all read id's in file
• Added pod5_get_file_run_info to retrieve a run info at an absolute index in the file
• Added pod5_free_run_info to free run info's (replaces pod5_release_run_info)
• Deprecated pod5_release_run_info (see pod5_free_run_info)
• Added pod5_get_file_run_info_count to find the number of run info's in a file
• Added pod5 filter tool to subset pod5 files with simple list of read ids
• Reworked pod5 subset to give better control over resources used
• Added tqdm progress bar to pod5 subset (disable with POD5_PBAR=0)
• pod5 subset can now parse csv and tsv tables / summaries
• Removed filepath header line from pod5 inspect reads
• pod5 repack now repacks all inputs one-to-one
• Versioning now controlled by VCS inspection using setuptools_scm
• Added version attributes to lib-pod5

0.1.8

• Update to zlib 1.2.13
• Update to zstd 1.5.4
• Pinned pre-commit=v2.21.0 while supporting python3.7
• Added more read_id getter methods to Reader
• Fixed pod5 inspect read
• Reworked pod5 convert to_fast5 output filenames to allow for 1-1 mapping
• Fixed pod5 convert to_fast5 creating an empty fast5 output
• Fixed pod5 convert to_fast5 ignoring the --force_overwrite argument
• Fixed issue where thread_pool.h wasn't shipped.
• Added support for python 3.8 + 3.10 on windows
• Added gcc7 linux build of pod5

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.