Skip to content
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
27 commits
Select commit Hold shift + click to select a range
9f04fd5
Merge branch 'main' of github.com:CCBR/ASPEN
kopardev Sep 25, 2026
d438f18
Merge branch 'main' of github.com:CCBR/ASPEN
kopardev Sep 25, 2026
d589c9b
Merge branch 'main' of github.com:CCBR/ASPEN
kopardev Sep 25, 2026
27df9ed
docs(deployment): add console output examples
kopardev Sep 25, 2026
06ae3a1
docs(deployment): clarify status and replicate guidance
kopardev Sep 25, 2026
331bd44
docs(deployment): refine monitoring and replicate guidance
kopardev Sep 25, 2026
bb4eb03
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 25, 2026
e2a8c54
docs(overview): fix admonition formatting
kopardev Sep 25, 2026
1f7065b
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 25, 2026
3b1ed81
docs(overview): fix spike-in callout formatting
kopardev Sep 25, 2026
8add0f7
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 25, 2026
b71d738
docs(overview): fix spike-in warning formatting
kopardev Sep 25, 2026
280ddac
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 25, 2026
8a93c6d
docs: fix admonition indentation in markdown docs
kopardev Sep 25, 2026
0a13d3b
ci: 🤖 format everything with pre-commit
github-actions[bot] Sep 25, 2026
7aa301d
docs(overview): indent spike-in warning body
kopardev Sep 25, 2026
5942e96
ci: 🤖 format everything with pre-commit
github-actions[bot] Sep 25, 2026
eed7f41
docs(outputs): indent remaining admonitions
kopardev Sep 25, 2026
2af0268
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 25, 2026
dfc810f
docs(deployment): indent note callouts
kopardev Sep 25, 2026
fbe8e22
ci: 🤖 format everything with pre-commit
github-actions[bot] Sep 25, 2026
66da879
docs: fix markdown admonition rendering
kopardev Sep 25, 2026
0486819
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 25, 2026
ea6bb02
docs(overview): update rendered callout markup
kopardev Sep 25, 2026
f175f5e
ci(prettier): ignore MkDocs markdown pages
kopardev Sep 25, 2026
1448e23
docs(overview): preserve MkDocs admonition indentation
kopardev Sep 25, 2026
1c2957f
docs: preserve admonition indentation
kopardev Sep 25, 2026
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions .prettierignore
Original file line number Diff line number Diff line change
Expand Up @@ -6,3 +6,4 @@ results/
.DS_Store
*.code-workspace
assets/*.html
docs/*.md
1 change: 1 addition & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
## ASPEN development version

- Document successful `dryrun` and `run` console output in `docs/deployment.md`, including example screenshots, an explanation of `STEP`/`OK`/`INFO`/`NEXT`, and explicit links between wrapper messages and `WORKDIR` status files. (#147, @kopardev)
- Add attempt-aware resource scaling for the main Snakemake rules, document how baseline `cluster.json` resources interact with retry-based `resources.gres` scaling, and fix dry-run failure handling so failed dry-runs now exit non-zero instead of reporting success. (#152, @kopardev)
- Detect SLURM-killed Snakemake child jobs in classic cluster mode by adding a `--cluster-status` hook and `scancel` integration, so timed out, OOM-killed, cancelled, or otherwise failed child jobs now retry/fail cleanly instead of leaving the master workflow hanging indefinitely. (#148, @kopardev)
- Clarify motif enrichment outputs and interpretation in the documentation: fix the reported location of HOMER/AME result folders, explain how ASPEN reuses HOMER-generated `target.fa`/`background.fa` in AME, document the AME parallelization strategy, and add simpler guidance for interpreting `knownResults.txt` and `ame_results.txt`. (#146, @kopardev)
Expand Down
210 changes: 210 additions & 0 deletions docs/assets/images/aspen_console_output_examples.html
Original file line number Diff line number Diff line change
@@ -0,0 +1,210 @@
<!doctype html>
<html lang="en">
<head>
<meta charset="UTF-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>ASPEN Console Output Examples</title>
<style>
:root {
--page-bg: #f3efe3;
--frame: #d9cfb8;
--terminal-bg: #111315;
--terminal-top: #1f2328;
--terminal-border: #2f353d;
--text: #e8edf2;
--muted: #b4bec8;
--ok: #81d979;
--info: #7dcfff;
--step: #ffd166;
--next: #ff9e64;
--prompt: #c6a0f6;
}

* {
box-sizing: border-box;
}

body {
margin: 0;
background:
radial-gradient(circle at top left, #fffaf0 0%, transparent 32%),
linear-gradient(180deg, #f6f1e4 0%, var(--page-bg) 100%);
color: #1a1f24;
font-family: "IBM Plex Sans", "Segoe UI", sans-serif;
}

main {
width: 1240px;
margin: 0 auto;
padding: 48px 32px 64px;
}

.header {
margin-bottom: 28px;
}

.eyebrow {
display: inline-block;
padding: 6px 10px;
border: 1px solid #cdbf9e;
border-radius: 999px;
font-size: 12px;
letter-spacing: 0.08em;
text-transform: uppercase;
color: #5b5a53;
background: rgba(255, 252, 244, 0.75);
}

h1 {
margin: 12px 0 8px;
font-size: 42px;
line-height: 1.08;
}

.subtitle {
margin: 0;
font-size: 18px;
line-height: 1.5;
color: #4e5560;
max-width: 920px;
}

.shot {
margin-top: 28px;
padding: 18px;
border: 1px solid var(--frame);
border-radius: 24px;
background: rgba(255, 250, 240, 0.78);
box-shadow: 0 16px 40px rgba(56, 46, 24, 0.08);
}

.caption {
display: flex;
align-items: baseline;
justify-content: space-between;
gap: 16px;
margin-bottom: 14px;
padding: 0 4px;
}

.caption h2 {
margin: 0;
font-size: 24px;
line-height: 1.2;
}

.caption p {
margin: 0;
font-size: 14px;
color: #616873;
}

.terminal {
overflow: hidden;
border: 1px solid var(--terminal-border);
border-radius: 20px;
background: var(--terminal-bg);
box-shadow: 0 20px 36px rgba(0, 0, 0, 0.22);
}

.terminal-topbar {
display: flex;
align-items: center;
gap: 14px;
padding: 14px 18px;
border-bottom: 1px solid #343a43;
background: var(--terminal-top);
}

.traffic {
display: flex;
gap: 8px;
}

.traffic span {
width: 12px;
height: 12px;
border-radius: 50%;
}

.traffic span:nth-child(1) { background: #ff5f57; }
.traffic span:nth-child(2) { background: #febc2e; }
.traffic span:nth-child(3) { background: #28c840; }

.title {
font-size: 14px;
color: var(--muted);
}

pre {
margin: 0;
padding: 22px 24px 26px;
white-space: pre-wrap;
font: 15px/1.6 "IBM Plex Mono", "Cascadia Code", Consolas, monospace;
color: var(--text);
}

.prompt { color: var(--prompt); }
.step { color: var(--step); font-weight: 600; }
.ok { color: var(--ok); font-weight: 600; }
.info { color: var(--info); font-weight: 600; }
.next { color: var(--next); font-weight: 600; }
.dim { color: var(--muted); }
.rule { color: #7a828e; }
</style>
</head>
<body>
<main>
<div class="header">
<div class="eyebrow">ASPEN Docs Assets</div>
<h1>ASPEN console output examples</h1>
<p class="subtitle">Terminal-style screenshots for the deployment docs, showing what successful <code>dryrun</code> and <code>run</code> wrapper output look like in practice.</p>
</div>

<section class="shot" id="dryrun-shot">
<div class="caption">
<h2>Successful dry-run summary</h2>
<p>Use in deployment docs near the <code>aspen -m=dryrun</code> example.</p>
</div>
<div class="terminal">
<div class="terminal-topbar">
<div class="traffic"><span></span><span></span><span></span></div>
<div class="title">bash • ASPEN dryrun example</div>
</div>
<pre><span class="prompt">$</span> aspen --workdir=&lt;WORKDIR&gt; --runmode=dryrun
<span class="step">STEP</span> [dryrun] Running preflight checks
<span class="info">INFO</span> Validating config, samples, and runtime dependencies
<span class="info">INFO</span> Rendering the planned Snakemake DAG without execution
<span class="ok">OK</span> Dry-run completed.
<span class="info">INFO</span> Full dry-run output captured in &lt;WORKDIR&gt;/dryrun.log
<span class="next">NEXT</span> Submit run with: aspen --workdir=&lt;WORKDIR&gt; --runmode=run</pre>
</div>
</section>

<section class="shot" id="run-shot">
<div class="caption">
<h2>Successful run submission summary</h2>
<p>Use in deployment docs near the <code>aspen -m=run</code> and monitoring guidance.</p>
</div>
<div class="terminal">
<div class="terminal-topbar">
<div class="traffic"><span></span><span></span><span></span></div>
<div class="title">bash • ASPEN run example</div>
</div>
<pre><span class="prompt">$</span> aspen --workdir=&lt;WORKDIR&gt; --runmode=run
<span class="ok">OK</span> Dry-run was successful.
<span class="step">STEP</span> [run] Preparing workdir for new execution
<span class="ok">OK</span> Created &lt;WORKDIR&gt;/submit_script.sbatch
<span class="info">INFO</span> State marker updated: pipeline.running <span class="dim">(reason=submission_started, slurm_job_id=NA)</span>
<span class="info">INFO</span> State marker updated: pipeline.running <span class="dim">(reason=sbatch_submitted, slurm_job_id=&lt;jobid&gt;)</span>
<span class="rule">---------------------------------------------------------------------</span>
<span class="ok">OK</span> Job submitted successfully <span class="dim">(SLURM job ID: &lt;jobid&gt;)</span>
<span class="next">NEXT</span> Monitor: squeue -u $USER
<span class="next">NEXT</span> Progress: tail -f &lt;WORKDIR&gt;/snakemake.log
<span class="next">NEXT</span> Status: ls -1 &lt;WORKDIR&gt;/pipeline.*
<span class="next">NEXT</span> Sidecar: &lt;WORKDIR&gt;/pipeline.status.json</pre>
</div>
</section>
</main>
</body>
</html>
Binary file added docs/assets/images/aspen_dryrun_console.jpeg
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
55 changes: 55 additions & 0 deletions docs/assets/images/aspen_dryrun_console.svg
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added docs/assets/images/aspen_run_console.jpeg
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
62 changes: 62 additions & 0 deletions docs/assets/images/aspen_run_console.svg
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Loading