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v1.6.5: Deprecate console db (#841)
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@tanghaibao tanghaibao tagged this 31 Mar 05:15 
* Remove deprecated jcvi.utils.console and jcvi.utils.db modules

Remove the console module (thin wrapper around rich.Console) and the db
module (legacy JCVI database connectors for Sybase/MySQL/PostgreSQL/Oracle).
Replace console imports with direct rich.console.Console usage in aws.py,
fetch.py, and formats/base.py. Remove the now-unused set_db_opts method
from OptionParser.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

* Remove deprecated modules: formats.cdt, formats.contig, formats.coords,
variation.deconvolute, assembly.syntenypath, annotation.ahrd, apps.emboss,
apps.gbsubmit

Relocate reusable code to consuming modules:
- CoordsLine, Coords, Overlap_types, get_coords_stats -> formats.blast
- CDT class -> compara.pad
- ContigFile/ContigLine/ReadLine -> assembly.postprocess
- read_interpro -> projects.pineapple
- needle/NeedleHeader -> annotation.reformat
Also fix remaining utils.console references in formats.fasta and
algorithms.ec from prior deprecation.

* Remove deprecated modules: apps.blastplus, apps.bowtie, apps.lastz,
utils.ez_setup

Relocate reusable code to consuming modules:
- Bowtie2 wrappers (BowtieLogFile, check_index, align) -> apps.align
- Download utilities (ALL_DOWNLOADERS, get_best_downloader) -> apps.base
- LASTZ score conversion functions -> formats.maf

* Style fixes by Black

* Update src/jcvi/formats/blast.py

* Update src/jcvi/projects/pineapple.py

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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