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docs: refine deployment monitoring guidance - #153

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kopardev wants to merge 27 commits into
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issue_147
Open

kopardev wants to merge 27 commits into
mainfrom
issue_147

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Clarify the ASPEN deployment guide so users check the sidecar and pipeline.* status files first, with squeue and scontrol documented as advanced alternatives. Also fix the replicate guidance admonition formatting and include the generated console-output source assets used by the docs.

Issues

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PR Checklist

(Strikethrough any points that are not applicable.)

  • This comment contains a description of changes with justifications, with any relevant issues linked.
  • Update docs if there are any API changes.
  • Update CHANGELOG.md with a short description of any user-facing changes and reference the PR number. Guidelines: https://keepachangelog.com/en/1.1.0/
  • Test run completes successfully on biowulf.

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Add dry-run and run console output screenshots plus explanatory text for issue 147.

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Update the monitoring section to prefer the sidecar and pipeline.* files, and fix admonition formatting in the replicate guidance block.

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Tighten the ASPEN deployment guide so the monitoring section points users to the sidecar and pipeline.* files first, while keeping the Slurm commands as an advanced fallback. Include the generated console-output source assets alongside the docs update.

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@github-actions github-actions Bot added the ASPEN RepoName label Sep 25, 2026
pre-commit-ci Bot and others added 21 commits September 25, 2026 19:15
Indent the tip callout bodies so MkDocs renders them as proper admonitions on ghpages.

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Rewrite the spike-in normalization tip so the yes/no guidance renders as regular admonition text instead of a code-like block on ghpages.

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Indent the zero-spike-in warning body so it renders as a proper MkDocs admonition alongside the spike-in normalization tip.

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Indent MkDocs admonition bodies across the ASPEN docs so notes, tips, and warnings render consistently on ghpages.

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Make the orange spike-in warning render as a proper admonition by indenting its body in the overview docs.

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Make the remaining note and tip callouts in outputs.md render as proper MkDocs admonitions, including the consensus table and motif guidance.

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Indent the deployment note and warning bodies so the callouts render consistently on ghpages.

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Indent MkDocs admonition bodies across the documentation so notes, tips, and warnings render consistently on ghpages.

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Capture the remaining overview markdown change before syncing with the latest remote branch tip.

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Stop prettier from reformatting docs/*.md pages that use MkDocs admonition syntax requiring preserved indentation.

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Keep the overview markdown admonitions indented so they render correctly on ghpages and are not flattened into plain paragraphs.

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Keep MkDocs admonition bodies indented across the remaining documentation pages so ghpages renders the callouts correctly.

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@kopardev kopardev self-assigned this Sep 25, 2026

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