slow5lib-v1.3.0

What's Changed

• new signal compression method ex-zd
• new low-level API function: slow5_set_skip_rid()
• using $(MAKE) by @sashajenner in #93
• pyslow5 could handle new enum values in end_reason aux attribute "api_request" and"device_data_error" by @Psy-Fer

Full Changelog: v1.2.0...v1.3.0

slow5lib-v1.2.0

What's Changed

• big-endian support (request by #88) added - for all features except for svb-zd compression that uses StreamVByte which does not support big-endian
• slow5lib easy multi-thread API is no-longer beta and is fully documented now at here. Examples at here
• new low-level API function slow5_idx_load_with added (for use in slow5curl)
• update cmake to work with add_subdirectory by @hiruna72 (address #91)
• many improvements to documentation and examples

slow5lib-v1.1.0

Major improvements from v1.0.0 are:

slow5lib:

• slow5_idx_load_with() function added to the low-level API
• improved error handling in slow5 index-related functions (fixes hasindu2008/slow5tools#88)

pyslow5

• binary wheels for Linux will now be on pypi
• pyslow5 now compiles smoothly on ARM Macs
• BLOW5 writing in pyslow5 is 57X faster
• pyslow5 can handle new fields (tracked_scaling_shift, tracked_scaling_scale, predicted_scaling_shift, predicted_scaling_scale, num_reads_since_mux_change, time_since_mux_change, num_minknow_events) that will be in S/BLOW5 files converted from POD5s
• new API function get_num_read_groups() added

and many documentation improvements.

slow5lib-v1.0.0

No changes from the previous version. Marking the fact that slow5lib is feature complete and stable.

slow5lib-v0.9.0

• only documentation improvements

slow5lib-v0.8.0

• adding the high-level muti-threading API for slow5lib in C (still beta and not yet documented). See examples here
• API functions to write enum aux fields added to both C and Python APIs

slow5lib-v0.7.0

• briefly document the slow5 low-level API
• advanced examples demonstrating the use of low-level API added
• fix a minor error that prevented writing slow5 files to stdout

slow5lib-v0.6.0

Major improvements are:

• added the slow5lib high-level writing API (examples and the documentation!)
• improvements to documentation, error checking, examples etc.
• pyslow5 can now write zstd files

slow5lib-v0.5.1

• improvements to the make file and cmake files

slow5lib-v0.5.0

slow5lib:

• indexing zlib compressed BLOW5 is made significantly faster using partial decompression
• improvement to documentation
• added slow5lib C benchmarks to mirror ONT's Python-only POD5 benchmarks. summary: in hour hands slow5lib C API is a few times more efficient than pod5 c_api (and pyslow5 API obviously). Users are encouraged to run these benchmarks themselves on their systems. We will put the results of a comprehensive benchmark when the POD5 API is stable and mature.

pyslow5: mostly by @Psy-Fer

• new API calls to pyslow5 to get a batch using multiple threads
• writing API added (thanks @mattloose for requesting this and experimenting with it)
• fix some memory leaks in cython side
• supports optional zstd compression