Kmerdb

This is a very minor release cycle at this point on the 0.8 version. The project is still pre-alignment, pre-assembly and other milestones. The 0.8.13 focuses on making a minimizer index for beginning a discussion on minimizer exact matching or approximate matching between two sequences. Currently, only a stub for a minimizer-seeded alignment routine is implemented, and a utility for creating single minimizer subsets of a k-mer array.

On a personal note, I'm working on some personal things, considering deepseek R1, and trying to get a new job. That's my goal is earn some change, sadly.

Otherwise, I believe this is the direction the project needs to achieve its eventual goal of minimizer distances and interoperable minimizer and match index files and how they can be use to seed alignments and store those intermediary forms as well.

That's the direction I'm going in and excited for more time to work on this.

New features

- [x] average k-mer coverage, k-mer histogram
- [ ] strassen mulitplication, numpy delegations
- [ ] batched strassen
- [ ] regression and least-squares analysis

bugfixes and quality of life improvements.

Hotfix to the 0.8.4 release, which was said to be 'acceptance tested'. And then came the profile UI rework during the actual 0.8.4-0.8.5 interlude, and the 0.8.4 commit that was chosen needed to be yanked, and then UI fix is replaced here with hotfix. Currently writes correct counts (not zeros, see diff) to the file and not zeroes I'm glad I noticed, just a few days after the 0.8.4 patch.

This release includes the recent features:


- `graph` subcommand
- `usage|help` subcommands
- `--debug` for default error handling
- `-o|--output-name` revised usage patterns
- <samplesheet.txt|input_1.fa|input2_.fq.gz> samplesheet pattern.
- `--quiet` throughout verbose commands

Acceptance tested version v0.8. New features (vs 0.7.6+) include

* exit_summary
* graph subcommand
* usage/help subcommand
* Deprecations
* Improved logging
* Logfile
* --num-log-lines to display last X lines of log in the exit_summary error datastructure, upon raising an exception
* Command banner
* Fixed citation subcommand.

as well as a number of bugfixes




Notes

Acceptance tested 'stable' v0.8 release. Some regressions may remain silent in usage without the `--debug` feature, which skips a feature used to condense metadata, and help the developer collect and assess bugs with relevant feature/step metadata available, as well as traceback, feature description etc error information available at program exit. The structure is YAML/JSON.

The data structure schema is located at `config.exit_summary_schema`.

--debug flag introduced to skip error/exit handling module. In brief, errors are caught and processed differently under --debug modes. Convenience features have been added to the standard invocation to provide an "exit summary", describing (clearly) the 'last loggable line', abbreviates the logging to stderr, captures traceback objects, errors, program "steps" and "features" (described in config.py) where the program failed, and other relevant metadata.

Use --debug if the program exits early or with no logged information.

`kmerdb usage -m method` introduced

Revisions tested across the board.

profile, graph, usage, matrix, distance, kmeans, and hierarchical have been acceptance tested.

This release include the new `graph` command. Some homemaking/housekeeping. Some bona-fide regressions handled.

Maintenance release. New interface otw.