• New pre-commit hook: ccbr-hooks sync-nextflow-version. Syncs manifest.version in nextflow.config from the repo VERSION file. (#193, @kelly-sovacool, @copilot)

Bug fixes for two critical issues in the ccbr_tools install command: (#191, @kopardev, @copilot)

1. Mamba Activation Error Suppression — Suppress misleading error messages when mamba environment activation fails (non-critical operation)
2. Fix Permissions Scope — Apply chown and chmod only to the newly-installed version folder, not the entire parent directory

• ccbr_tools install: Add latest symlink support and final read-only permission model. Creates complete symlink chain (latest → v{major}.{minor} → .v{version}) and applies read-only permissions (u-w,g-w,o-w,a+rX) to deployed code. Uses atomic symlink operations to prevent race conditions. (#187, @kopardev)

• pkg_util: Lazy-import cffconvert to fix rpds ABI mismatch on Python 3.12. (#182, @kopardev)
• ccbr-hooks detect-absolute-paths: Reduce false positives caused by /dev/null. (#174, @kelly-sovacool)

• ccbr-hooks detect-absolute-paths: Reduce false positives caused by /dev/shm and language comments. (#157, @kelly-sovacool)

• New arguments for ccbr-hooks detect-absolute-paths: --ignore-paths and --ignore-paths-file. (#154, @kelly-sovacool)

• Add parkit to the list of CCBR software. (#144, @kelly-sovacool)
• New pre-commit hook: ccbr-hooks detect-absolute-paths. (#147, @kelly-sovacool)
• Do not include app/bot contributors in github.get_repo_contributors(). (#148, @kelly-sovacool)

• When an invalid GitHub user is passed to github.get_user_info(), raise a warning and return a dict with "name": None. (#135, @kelly-sovacool)

• Fix how jobby parses slurm stdout/stderr files. (#122, @kopardev, @kelly-sovacool)
• The run_jobby_on_* scripts are now deprecated in favor of using jobby directly. (#123, @kelly-sovacool)
• Use miniforge3 installation on biowulf. (#124, @kelly-sovacool)

• Fixes for ccbr_tools install: (#98, @kelly-sovacool)
  • Correct installation method for spacesavers2.
  • Change symlink permissions so group members can edit them.
• Allow nextflow pipelines to specify walltime & memory usage for the slurm submission template. (#116, @kelly-sovacool)