Release v1.0.0 - Streamlined Workflow, Unauthenticated Access, and Performance Improvements

[himal2007]

Release v1.0.0

Summary

Major release introducing the streamlined connect + update workflow, replacing the previous fetch-first approach. The update command now works out of the box with a built-in curated scheme list of ~300 MLST schemes from both PubMLST and Pasteur.

What's changed

New features

• mlstdb connect command for one-time OAuth credential setup
• Built-in curated scheme list — no fetch step needed for standard usage (Add curated APIs input file to be used for mlstdb update #10)
• --no-auth flag for unauthenticated access to public APIs
• --resume flag to recover from interrupted downloads
• --threads for parallel downloads (both fetch and update)
• Session reuse and connection pooling for faster API calls
• Restrictive permissions (0600) on stored credential files

Bug fixes

• Fetch looping error at 76% (initial fetch doesn't work looping error at 76% #19)
• Missing scheme URI resolution errors (mlstdb fetch - Error: The following URIs have missing schemes #18)
• 401 errors on unregistered databases no longer crash the process — skipped schemes are reported at the end (mlstdb fetch 401 - Ribosomal MLST databases #17)

Breaking changes

• fetch is now an advanced command; the recommended workflow is connect → update (Refactor: Deprecate 'fetch' in favor of 'connect' and 'update' subcommands (Feature Enhancement) #25)
• update --input is now optional (defaults to built-in scheme list)

Documentation

• Complete README rewrite focused on the two-command workflow
• New MkDocs documentation site with getting started guide, detailed command references, and troubleshooting

Closes

• Refactor: Deprecate 'fetch' in favor of 'connect' and 'update' subcommands (Feature Enhancement) #25 — Refactor: Deprecate 'fetch' in favour of 'connect' and 'update'
• initial fetch doesn't work looping error at 76% #19 — Initial fetch doesn't work, looping error at 76%
• mlstdb fetch - Error: The following URIs have missing schemes #18 — mlstdb fetch: missing schemes error
• mlstdb fetch 401 - Ribosomal MLST databases #17 — mlstdb fetch 401 on Ribosomal MLST databases
• Add curated APIs input file to be used for mlstdb update #10 — Add curated APIs input file for mlstdb update

How to test

pip install mlstdb==1.0.0
mlstdb connect --db pubmlst
mlstdb connect --db pasteur
mlstdb update
mlst --blastdb blast/mlst.fa --datadir pubmlst test.fasta