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Postgres back-end

mwham requested to merge postgres into master
  • Version 1.0 🎉
  • Postgres backend:
    • isaric schema name
    • isaric_admin read/write role
    • drops known data linkage tables before doing a new release
      • database versioning with pg_dump exports
    • Renaming WP5 RNA-seq report columns - Postgres didn't like some of them
    • New environment variables: PGPASSFILE (optional), ISARIC_LINKAGE_CREDENTIALS
    • New CI system
      • Docker executor
  • Generic SQLite/Postgres-compatible function for day comparisons
  • Lazy-loading configs
  • Cleaning up circular imports in index table queries
  • Assays done report:
    • ported to SQLAlchemy
    • sample_assays is now a SQL table, not a WITH statement
  • New Conda dependency: postgresql=12.3 (client binaries)
  • Closes #10 (closed)

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