feat(fusion): parameter sweep for doctor validation by adamrtalbot · Pull Request #44 · seqeralabs/nf-canary

adamrtalbot · 2026-03-12T18:50:33Z

Why

Instead of maintaining separate low/recommended/high threshold profiles per cloud provider, we can validate fusion doctor across a range of parameter values using a single sweep. This simplifies configuration and provides broader test coverage.

What

Replace 12 tiered cloud profiles (low/recommended/high x 4 clouds) with 3 simple cloud profiles (AWS/GCP/Azure)
Add parameter sweep support: comma-separated values for kernel version, memory, disk, CPU, and open files are expanded into all combinations
Add comprehensive nf-test suite covering the parameter sweep workflow
Expose sweep parameters in nextflow_schema.json with descriptions and defaults
Refactor main.nf to generate parameter combinations and run fusion doctor across the full matrix

Generated with Claude Code

Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

…3b0a0e59d95a6` Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

…tion - Add --template argument to generate_fusion_report.py - Update TEST_FUSION_REPORT process to pass template file path directly - Removes need to copy template to /usr/local/assets/templates - Makes template handling more flexible and container-agnostic

The real `fusion doctor` binary outputs a different JSON schema than the mock: `checks` as a list (not a dict), `check_summary.overall` instead of `summary.status`, and `fusion_version` instead of `version`. The template and merge logic now handle both formats. Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

…urce sections Display rich system environment, storage, and resource limit data from fusion doctor JSON. Improve UX with native details/summary elements, structured check details, filesystem filtering/sorting, thousands separators, copy-to-clipboard buttons, and localized timestamps. Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

Rewrite HTML template (v3) adopting Seqera Platform design tokens, card-based layout, and kv-grid patterns. Add Instance card with cloud metadata, humanized check names, bucket URI in check titles, trimmed sub-check messages, consistent used/total usage framing, and clean Jinja whitespace output. Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

Add check label mappings for nvme, cpu_cores, open_files, and kernel_version checks introduced in fusion doctor schema 1.2. Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

Add three new reference profile parameters for fusion doctor checks: - nvme_required: false (low), true (recommended/high) - cpu_cores_min: 2/4/16 matching target instance vCPU counts - open_files_min: 65536/131072/1048576 (high matches docs ulimit) Bump AWS high tier disk_gb_min from 474 to 950 to align with .4xlarge instances (16 vCPUs) instead of .2xlarge (8 vCPUs). Wire new params through nextflow.config defaults and main.nf YAML builder. Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

Add validation logic to prevent multiple Fusion profiles from being specified simultaneously. When multiple fusion_* profiles are detected, the pipeline now exits with a clear error message. This ensures that the reference profile passed to the fusion doctor process contains consistent, non-conflicting thresholds from a single well-defined profile (e.g., fusion_aws_recommended) rather than merged parameters from multiple profiles that could overwrite each other. The validation: - Parses workflow.profile to identify all fusion_* profiles - Exits with error if more than one Fusion profile is detected - Provides helpful guidance on correct usage - Allows normal operation with 0 or 1 Fusion profile

Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

Use brand color (#160f26) background with white text and icons, consistent with cloud.seqera.io top nav style. Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

- Passed card gets green background/text, failed gets red (when > 0) - Overall status badge moved into the overview grid as first tile - Total and skipped cards stay neutral Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

…details Replace check-item cards with a compact table (Status, Check, Category, Message) and a toggle button to expand/collapse technical details per row. Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

- Remove duplicate status badge from header (now in overview grid) - Add subtle row tinting for warn/fail checks in validation table - Rename "Category" column to "Severity" for clarity - Make entire check row clickable to toggle details (not just button) - Animate expand button rotation on toggle Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

Rebuild the HTML report with Seqera Platform design tokens, split check tables (system/storage/bucket), overview metrics, collapsible environment cards, FontAwesome icons, access tags, and remediation callouts. Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

Add keyboard navigation, ARIA attributes, screen reader support, semantic heading hierarchy, warn badge WCAG AA contrast, Jinja2 `check_row` macro deduplication, and `humanize` package integration. Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

- Full-bleed header/footer backgrounds with content constrained to 1200px - Resource limits: replace hardcoded open_files threshold with dynamic check data from doctor JSON - Generalize resource limit rows with collapsible details, status colors, and expand chevron matching the check-row pattern - Fix mobile: use col-expand class instead of generic last-child hiding Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

Match the common Linux default soft limit so vanilla systems are not flagged at the lowest validation tier. Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

Example JSON profiles (passed, degraded, failed) and corresponding generated HTML reports for development and review. Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

The collapsible details and remediation are already shown in the System Checks section; resource limits now only shows values with status color and Low tag. Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

Adds a boolean parameter (disabled by default) that passes --redact to fusion doctor, stripping hostnames, IPs, bucket names, etc. from the diagnostic output. Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

… boundary Let errors propagate from library code instead of returning error dicts. Bad file paths now fail fast with a clean error message instead of producing partial results. Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

Replace tiered fusion profiles (low/recommended/high per cloud) with simple per-cloud profiles and comma-separated sweep parameters. The FUSION_DOCTOR workflow builds a Cartesian product of all sweep values (kernel, memory, disk, NVMe, CPU, open files) and runs fusion doctor once per combination, collecting all reports into a single consolidated HTML/JSON output. Generated by Claude Code

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>

adamrtalbot · 2026-04-28T18:46:56Z

@copilot resolve the merge conflicts in this pull request

alberto-miranda · 2026-04-28T18:55:21Z

@adamrtalbot I noticed that you are updating this branch and this line in the description concerns me:

Replace 12 tiered cloud profiles (low/recommended/high x 4 clouds) with 3 simple cloud profiles (AWS/GCP/Azure)

Please do not remove the tiered profiles, because we rely on them in the public Fusion docs. It would not be a problem to do the parameter sweep in addition to that if you think it's valuable. Thanks!

…ML report changes Co-authored-by: adamrtalbot <12817534+adamrtalbot@users.noreply.github.com>

Copilot · 2026-04-28T18:59:40Z

@copilot resolve the merge conflicts in this pull request

Merge conflicts resolved in commit 5e234d4. The branch now incorporates:

Dedicated fusion-doctor container image (cr.seqera.io/public/fusion/doctor:1.0.0-dev-260420150843)
Updated HTML report template and generator from main
Pinned GitHub Actions hashes
Correct test task counts (15/14 for non-fusion tests)

Our parameter sweep logic (3 simple cloud profiles, Cartesian product sweep) is preserved.

adamrtalbot · 2026-07-22T12:59:55Z

@copilot resolve the merge conflicts in this pull request

- Resolve nextflow.config: add gpu_container, rename fusion params to match updated fusion-doctor schema (memory_capacity_gb_min, disk_capacity_gb_min, vcpus_min), keep sweep defaults - Resolve main.nf: use fusion-doctor:1.0.0 container, add gpu_container to NF_CANARY workflow signature and call, add onComplete handler from main - Update FUSION_DOCTOR workflow YAML keys to new schema names - Update nextflow_schema.json with renamed param keys - Replace simplified fusion profiles with full tiered profiles from main - Update test comment labels for renamed parameters

Copilot · 2026-07-22T13:10:01Z

@copilot resolve the merge conflicts in this pull request

Merge conflicts resolved in commit fix: resolve merge conflicts with origin/main. The resolution incorporates:

fusion-doctor:1.0.0 container (bumped from dev version)
gpu_container parameter added to nextflow.config, NF_CANARY workflow signature, and the workflow {} entrypoint
onComplete handler from main
Renamed fusion params to align with the updated fusion-doctor schema: fusion_memory_capacity_gb_min, fusion_disk_capacity_gb_min, fusion_vcpus_min (and corresponding YAML keys in the sweep)
Tiered cloud profiles (fusion_aws_low/recommended/high, etc.) restored from main
New logo SVGs, updated HTML report generator, and CI workflow changes from main

alberto-miranda added 30 commits February 25, 2026 07:58

feat(fusion-doctor): Add Python report generator and HTML template

b19e7be

Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

test(fusion-doctor): Add unit tests for report generation

05b3ff7

Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

feat(fusion-doctor): Add FUSION_DOCTOR_GENERATE_REPORT process

ab418fb

Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

chore: Update test snapshots

b150c34

Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

ci: Integrate Python tests in CI pipelines

02a8dad

Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

fix: Make fusion_report_template.html conformant with prettier

fc6768e

Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

fix: Add uv container for FUSION_DOCTOR_GENERATE_REPORT

33ea648

Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

fix: Replace uv:0.10.6 container with uv:python3.12-bookworm-slim

8d0d96d

Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

ci: Add setup-uv to nf-test job

e814e44

Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

fix: Replace uv:python3.12-bookworm-slim with `jinja2_python_uv:711…

53afe7e

…3b0a0e59d95a6` Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

chore: Rename HTML report to fusion-report.html

047347b

Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

feat(fusion-doctor): Split profiles into tiers

09220c1

Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

fix: Stage report template file as an input

676f39c

Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

fix: Ensure uv does not check for project files

6b77f7f

Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

fix: Fix report generation

d581249

Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

fix: Add humanized labels for new fusion doctor checks

0e37e90

Add check label mappings for nvme, cpu_cores, open_files, and kernel_version checks introduced in fusion doctor schema 1.2. Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

fix: Update report names in tests

6b74eb6

Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

feat: Dark header matching Seqera Platform navigation bar

c9af456

Use brand color (#160f26) background with white text and icons, consistent with cloud.seqera.io top nav style. Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

feat: Allow TEST_FUSION_DOCTOR to continue with exit codes 1 and 3

c785947

Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

alberto-miranda and others added 13 commits March 9, 2026 11:37

fix(fusion): Lower open_files_min to 65535 in low-tier profiles

26a60ea

Match the common Linux default soft limit so vanilla systems are not flagged at the lowest validation tier. Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

feat(fusion): Add example doctor report fixtures and generator script

acfd727

Example JSON profiles (passed, degraded, failed) and corresponding generated HTML reports for development and review. Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

refactor(fusion): Remove duplicate details from resource limits table

bffe20e

The collapsible details and remediation are already shown in the System Checks section; resource limits now only shows values with status color and Low tag. Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

feat(fusion): Add fusion_redact param to mask PII in diagnostics

90b8b8c

Adds a boolean parameter (disabled by default) that passes --redact to fusion doctor, stripping hostnames, IPs, bucket names, etc. from the diagnostic output. Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

chore: Leave profile handling to Nextflow

0766a8e

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

chore: Replace horizontal dividers with subheadings

18f2a2d

Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

fix: Clarify NVMe auto-selection for AWS CEs

f887634

Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

fix: Make path mandatory in load_json_report

01ccfe5

Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

refactor(tests): Convert fusion doctor report test to process-level

0e7735d

Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

chore: Remove example report fixtures

66e90f8

Signed-off-by: Alberto Miranda <alberto.miranda@seqera.io>

adamrtalbot requested a review from alberto-miranda March 13, 2026 09:45

Base automatically changed from COMP-1319/generate-doctor-html-report to main March 13, 2026 16:23

alberto-miranda mentioned this pull request Mar 16, 2026

refactor: Adapt HTML report generator to fusion doctor schema v2.0 #47

Merged

4 tasks

adamrtalbot commented Apr 28, 2026

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1e4a587

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>

Copilot started work on behalf of adamrtalbot April 28, 2026 18:47 View session

Merge origin/main: integrate dedicated fusion-doctor container and HT…

5e234d4

…ML report changes Co-authored-by: adamrtalbot <12817534+adamrtalbot@users.noreply.github.com>

Copilot finished work on behalf of adamrtalbot April 28, 2026 19:00

Copilot started work on behalf of adamrtalbot July 22, 2026 13:00 View session

Copilot AI added 2 commits July 22, 2026 13:04

chore: initial plan for merge conflict resolution

3116670

Copilot finished work on behalf of adamrtalbot July 22, 2026 13:10

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feat(fusion): parameter sweep for doctor validation - #44

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