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mecfs_bio.figures.key_scripts.publish_figures

End-to-end "the figure system is out of date" workflow.

Runs the four steps a contributor wants in sequence: 1. pull_figures --- download any figures listed in the manifest that are missing or out-of-date locally. This ensures that generate_new_figures only triggers the build system for genuinely new tasks, not for every figure the collaborator hasn't pulled yet. 2. generate_new_figures --- invoke the build system for any figure task in ALL_FIGURE_TASKS whose output is not yet on disk, and copy the results into the figure directory. 3. prune_orphan_figures --- drop manifest entries (and local files) for figures no task in ALL_FIGURE_TASKS produces. If any such entry is still referenced in the documentation, the script raises before touching anything; the user resolves the conflict by restoring the task or removing the doc reference. 4. push_figures --- rehash the figure directory, update the committed manifest, and upload any new content-addressed blobs to the GitHub release.

After this script finishes, commit the updated mecfs_bio/figures/figures_manifest.json to record the change.

Functions:

Attributes:

logger module-attribute 

logger = get_logger()

publish_figures 

publish_figures() -> None
Source code in mecfs_bio/figures/key_scripts/publish_figures.py 
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def publish_figures() -> None:
    logger.info("Pulling existing figures from the GitHub release.")
    pull_figures()
    logger.info("Generating any missing figures from ALL_FIGURE_TASKS.")
    generate_new_figures(
        all_figure_tasks=ALL_FIGURE_TASKS,
        fig_dir=FIGURE_DIRECTORY,
        exporter=FIGURE_EXPORTER,
    )
    logger.info("Pruning orphan figures (entries not produced by ALL_FIGURE_TASKS).")
    prune_orphan_figures(
        manifest_path=FIGURE_MANIFEST_PATH,
        docs_dir=DOCS_DIRECTORY,
        fig_dir=FIGURE_DIRECTORY,
        figure_tasks=ALL_FIGURE_TASKS,
    )
    logger.info("Updating manifest and pushing new blobs to the GitHub release.")
    push_figures(figure_tasks=ALL_FIGURE_TASKS)
    logger.info(
        "Done. Commit mecfs_bio/figures/figures_manifest.json to record the change."
    )