NEWS

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OmicsLake 0.99.3

• Standardized optional agent-context capture on the package-specific OL_PROMPT_ID, OL_AGENT_RUN_ID, and OL_AGENT_NAME environment variables.
• Replaced tool-specific labels in tests and documentation with neutral software-agent terminology.

OmicsLake 0.99.2

• Declared the optional xcms and Chromatograms adapter dependencies and aligned dependency-contract tests with the adapters' runtime behavior.
• Made path-normalization testing portable across Unix-like and Windows hosts.
• Expanded the package description and removed the premature package citation; a publication citation will be added when a stable DOI is available.

OmicsLake 0.99.1

• Prepared the public Bioconductor submission snapshot.
• Isolated test storage in a temporary directory for reliable package checks.
• Preserved callers' random-number state in evaluation helpers.
• Completed missing evaluation-topic return-value documentation.

OmicsLake 0.99.0

• Bioconductor submission preparation release.
• Added reproducibility hardening:
  • strict reproducibility mode (ol_enable_strict_repro_mode(), lake_strict_on())
  • automatic Git/renv/session metadata capture on commit/snapshot
  • optional clean-git guard and snapshot validation checks
• Added Bioconductor preflight tooling:
  • tools/check_bioc.sh
  • tools/check_bioc_readiness.R
  • GitHub Actions workflow .github/workflows/bioc-check.yml
• Expanded documentation and submission checklist in inst/bioc/BIOCONDUCTOR_SUBMISSION.md.