Refactoring: sr2silo #01

[gordonkoehn]

After this sprint until X-Mas some proper refactoring is necessary. Especially since we have decided that sr2silo will mostly be for v-pipe, not in general for imports of short reads to the silo.

Let's restructure the product to have sr2silo.vpipe. functions ?

Does any Object Orientation Make sense here ?

• perhaps organize an analysis as an object ?

Testing

• Add Start-to-End Test #66
• Add Unit-Tests for Functions
• Add Output verification to Start-to-End test
• Change Upload to Test S3 upload, not real AWS #72

Code Smells

• Ensure Type Safety #60

Restructuring

• Move V-Pipe specific functions into sr2slio #61
• Refactor to silo module wrangle stream_formater lapis_submitter
• Refactor to storage module with s3
• Add process module with convert, translator
• Refactor to utils module with logger compress configs serialize

Other

• Add proper logging / figlet welcome
• Remove AWS secrets from docker compose envs / move to .env #64
• Add an bash install to have the runs package installed and be able to test without Docker
• refactor: removing outdated and unused code #67
• Close unused stashes - Deamon PR