Update Module

Update Module

Check for newer versions of bioconda tools used in Bactopia modules and apply updates.

Steps

1. Run bactopia-update via the wrapper script, saving the JSON to a timestamped record so /release-checklist can later confirm module versions were checked this cycle:

   mkdir -p /home/rpetit3/repos/bactopia/bactopia/logs/module-updates
   TS=$(date +%Y%m%d_%H%M%S)
   bash .agents/skills/update-module/scripts/run-bactopia-update.sh --bactopia-path /home/rpetit3/repos/bactopia/bactopia --json --silent \
       | tee /home/rpetit3/repos/bactopia/bactopia/logs/module-updates/$TS.json
   

   Parse the JSON from that file. If the user specified a module name, add --module <name> to the command and do not write the record (a filtered run is not a full-repo check — only an unfiltered scan is a valid /release-checklist freshness record). logs/ is gitignored, so the record is scratch, not a tracked file.

2. Parse the JSON output. Separate entries into three categories:

   • Needs update (needs_update: true): ready for automatic update
   • Needs user review (needs_user_review: true): multi-package toolName, cannot auto-update
   • Up to date (needs_update: false): no action needed

3. Present results as a clean summary:

   • For updatable modules, show a table: tool, config path, installed version -> latest version
   • For user-review modules, list them separately with config path and a note that they require manual review
   • If nothing needs updating and nothing needs review, report "All modules are up to date" and stop

4. Ask the user which updates to apply (all or a subset). Do NOT proceed without confirmation.

5. For each confirmed update, read the module.config file at the path given by the config field, then edit three lines per module:

   ext.toolName -- Replace the conda spec string (the text between the first " and the " before .replace) with the latest_toolName value. Keep the .replace() chain untouched.

   // Before:
   ext.toolName = "bioconda::bakta=1.11.4".replace("=", "-").replace(":", "-").replace(" ", "-")
   // After (latest_toolName = "bioconda::bakta=1.12.0"):
   ext.toolName = "bioconda::bakta=1.12.0".replace("=", "-").replace(":", "-").replace(" ", "-")
   

   ext.docker -- Replace the entire quoted value with latest_docker.

   // Before:
   ext.docker = "biocontainers/bakta:1.11.4--pyhdfd78af_0"
   // After:
   ext.docker = "biocontainers/bakta:1.12.0--pyhdfd78af_0"
   

   ext.image -- Replace the entire quoted value with latest_image.

   // Before:
   ext.image = "https://depot.galaxyproject.org/singularity/bakta:1.11.4--pyhdfd78af_0"
   // After:
   ext.image = "https://depot.galaxyproject.org/singularity/bakta:1.12.0--pyhdfd78af_0"
   

   For multi-process config files (e.g., genotyphi/parse has both genotyphi and mykrobe), use the tool field to match the correct ext.toolName line containing that tool name.

6. Update CHANGELOG.md. Under ## Unreleased Changes > ### \Added``:

   • Look for an existing - bump program versions in modules line
   • If found, merge new entries into the indented list below it
   • If not found, add the block at the end of the ### \Added`` section
   • Format each entry as: - \tool`: old_version -> new_version`
   • One entry per tool (not per module) -- deduplicate shared tools (e.g., bakta_run and bakta_download both use bakta)
   • Sort entries alphabetically by tool name
   • Use the tool field (bioconda package name) as the display name

Notes

• The wrapper script auto-discovers bactopia-update (checks PATH, then conda envs)
• Multi-package toolName modules (pirate, lissero, clonalframeml) have needs_user_review: true and no latest_* fields -- present them for manual review, do not auto-edit
• If latest_version is null for an entry (API failure), skip it and note the failure
• The --module flag filters by tool name prefix (e.g., bakta matches both bakta_run and bakta_download)
• Ignore list: filter these entries out before presenting results -- Anaconda metadata quirks, not real updates:
  • tool == "aria2" && module == "checkm2_download" -- Anaconda reports 1.34.0 as "latest" while 1.36.0 is installed (spurious downgrade)

JSON Output Fields

Standard update entry:

• tool -- bioconda package name
• module -- Bactopia module name (underscores)
• config -- relative path to module.config
• installed_version -- current version from module.config
• latest_version -- latest version from Anaconda API
• latest_build -- build string from Anaconda API
• needs_update -- true if versions differ
• latest_toolName -- new conda spec for ext.toolName
• latest_docker -- new docker image path for ext.docker
• latest_image -- new singularity image URL for ext.image

User review entry (multi-package):

• tool, module, config, installed_version -- same as above
• needs_user_review -- true (no latest_* fields provided)