Make skills aggregator-compatible: co-located evals + self-contain complexa-sweep - #57

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Make skills aggregator-compatible: co-located evals + self-contain complexa-sweep#57
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@trvachovtrvachov commented Jul 16, 2026

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What

Makes the Proteina-Complexa skills cleanly aggregatable by bionemo-agent-toolkit
(and NVIDIA/skills), fixing two concrete compatibility issues:

  1. Co-located evals (SRC-10) — adds evals/evals.json for all 5 skills
    (complexa-design, complexa-evaluate-pdbs, complexa-setup,
    complexa-sweep, complexa-target). These currently live only in the
    aggregator catalog; since these are sourced skills, the sync overwrites the
    catalog from this repo, so the evals belong here or they're lost on sync.
    (Copied from bionemo-agent-toolkit@main; please verify they match current
    skill behavior.)

  2. Self-contained complexa-sweep (SRC-4) — complexa-sweep/SKILL.md
    referenced ../../../docs/SWEEP.md, which is outside the vendored
    .claude/skills/ subtree, so the link breaks once aggregated. Copied
    docs/SWEEP.md into complexa-sweep/reference/SWEEP.md and repointed the
    link. (The other two refs — to ../complexa-design/SKILL.md and
    ../_shared/reference/hardware.md — stay inside the subtree and are fine.)

Not done here — needs owner decisions

  • 🔶 complexa-slurm: this skill exists in the aggregator catalog but is
    absent on dev. I did not add it back — please confirm whether it was
    intentionally removed or should be restored to this repo.
  • 🔹 .claude/skills/README.md: gets vendored into the catalog as a stray
    non-skill file (SRC-9). Minor; remove or keep as you prefer.
  • 🔹 .gitignore ignores .claude/: the skills here are force-tracked, so
    new skill files (like these evals) are silently ignored unless git add -f.
    Consider un-ignoring .claude/skills/ so future skill additions aren't dropped.

🤖 Generated with Claude Code

@trvachov@claude
Make skills aggregator-compatible: co-located evals + self-contain co…
5391310
…mplexa-sweep
- Add evals/evals.json for all 5 skills (were catalog-only; sourced skills are
overwritten from this repo on sync, so evals belong here — SRC-10).
- complexa-sweep referenced ../../../docs/SWEEP.md (outside .claude/skills/,
breaks when aggregated); copied it into complexa-sweep/reference/SWEEP.md and
repointed the link (SRC-4).
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@trvachovtrvachov mentioned this pull request Aug 4, 2026
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Make skills aggregator-compatible: co-located evals + self-contain complexa-sweep - #57
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Make skills aggregator-compatible: co-located evals + self-contain complexa-sweep#57
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@trvachov
@trvachovtrvachov
commented
Jul 16, 2026

Copy link


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What
Makes the Proteina-Complexa skills cleanly aggregatable by bionemo-agent-toolkit

(and NVIDIA/skills), fixing two concrete compatibility issues:
  1. Co-located evals (SRC-10) — adds evals/evals.json for all 5 skills
    
(complexa-design, complexa-evaluate-pdbs, complexa-setup,
    complexa-sweep, complexa-target). These currently live only in the
    
aggregator catalog; since these are sourced skills, the sync overwrites the
    
catalog from this repo, so the evals belong here or they're lost on sync.
    
(Copied from bionemo-agent-toolkit@main; please verify they match current
    
skill behavior.)
  2. Self-contained complexa-sweep (SRC-4) — complexa-sweep/SKILL.md
    
referenced ../../../docs/SWEEP.md, which is outside the vendored
    .claude/skills/ subtree, so the link breaks once aggregated. Copied
    docs/SWEEP.md into complexa-sweep/reference/SWEEP.md and repointed the
    
link. (The other two refs — to ../complexa-design/SKILL.md and
    ../_shared/reference/hardware.md — stay inside the subtree and are fine.)
Not done here — needs owner decisions
  • 🔶 complexa-slurm: this skill exists in the aggregator catalog but is
    absent on dev. I did not add it back — please confirm whether it was
    
intentionally removed or should be restored to this repo.
  • 🔹 .claude/skills/README.md: gets vendored into the catalog as a stray
    
non-skill file (SRC-9). Minor; remove or keep as you prefer.
  • 🔹 .gitignore ignores .claude/: the skills here are force-tracked, so
    new skill files (like these evals) are silently ignored unless git add -f.
    
Consider un-ignoring .claude/skills/ so future skill additions aren't dropped.
🤖 Generated with Claude Code
@trvachov@claude
Make skills aggregator-compatible: co-located evals + self-contain co…
5391310
…mplexa-sweep
- Add evals/evals.json for all 5 skills (were catalog-only; sourced skills are
overwritten from this repo on sync, so evals belong here — SRC-10).
- complexa-sweep referenced ../../../docs/SWEEP.md (outside .claude/skills/,
breaks when aggregated); copied it into complexa-sweep/reference/SWEEP.md and
repointed the link (SRC-4).
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@trvachovtrvachov
mentioned this pull request
Aug 4, 2026
 Open

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Make skills aggregator-compatible: co-located evals + self-contain complexa-sweep - #57
Open
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Make skills aggregator-compatible: co-located evals + self-contain complexa-sweep#57
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@trvachov
@trvachovtrvachov
commented
Jul 16, 2026

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What
Makes the Proteina-Complexa skills cleanly aggregatable by bionemo-agent-toolkit

(and NVIDIA/skills), fixing two concrete compatibility issues:
  1. Co-located evals (SRC-10) — adds evals/evals.json for all 5 skills
    
(complexa-design, complexa-evaluate-pdbs, complexa-setup,
    complexa-sweep, complexa-target). These currently live only in the
    
aggregator catalog; since these are sourced skills, the sync overwrites the
    
catalog from this repo, so the evals belong here or they're lost on sync.
    
(Copied from bionemo-agent-toolkit@main; please verify they match current
    
skill behavior.)
  2. Self-contained complexa-sweep (SRC-4) — complexa-sweep/SKILL.md
    
referenced ../../../docs/SWEEP.md, which is outside the vendored
    .claude/skills/ subtree, so the link breaks once aggregated. Copied
    docs/SWEEP.md into complexa-sweep/reference/SWEEP.md and repointed the
    
link. (The other two refs — to ../complexa-design/SKILL.md and
    ../_shared/reference/hardware.md — stay inside the subtree and are fine.)
Not done here — needs owner decisions
  • 🔶 complexa-slurm: this skill exists in the aggregator catalog but is
    absent on dev. I did not add it back — please confirm whether it was
    
intentionally removed or should be restored to this repo.
  • 🔹 .claude/skills/README.md: gets vendored into the catalog as a stray
    
non-skill file (SRC-9). Minor; remove or keep as you prefer.
  • 🔹 .gitignore ignores .claude/: the skills here are force-tracked, so
    new skill files (like these evals) are silently ignored unless git add -f.
    
Consider un-ignoring .claude/skills/ so future skill additions aren't dropped.
🤖 Generated with Claude Code
@trvachov@claude
Make skills aggregator-compatible: co-located evals + self-contain co…
5391310
…mplexa-sweep
- Add evals/evals.json for all 5 skills (were catalog-only; sourced skills are
overwritten from this repo on sync, so evals belong here — SRC-10).
- complexa-sweep referenced ../../../docs/SWEEP.md (outside .claude/skills/,
breaks when aggregated); copied it into complexa-sweep/reference/SWEEP.md and
repointed the link (SRC-4).
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@trvachovtrvachov
mentioned this pull request
Aug 4, 2026
 Open

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, 'i');
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(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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Make skills aggregator-compatible: co-located evals + self-contain complexa-sweep - #57
Open
trvachov wants to merge 1 commit into
devfrom 
aggregator-compat
Open
Make skills aggregator-compatible: co-located evals + self-contain complexa-sweep#57
trvachov wants to merge 1 commit into
devfrom 
aggregator-compat
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@trvachov
@trvachovtrvachov
commented
Jul 16, 2026

Copy link


Copy Markdown

What
Makes the Proteina-Complexa skills cleanly aggregatable by bionemo-agent-toolkit

(and NVIDIA/skills), fixing two concrete compatibility issues:
  1. Co-located evals (SRC-10) — adds evals/evals.json for all 5 skills
    
(complexa-design, complexa-evaluate-pdbs, complexa-setup,
    complexa-sweep, complexa-target). These currently live only in the
    
aggregator catalog; since these are sourced skills, the sync overwrites the
    
catalog from this repo, so the evals belong here or they're lost on sync.
    
(Copied from bionemo-agent-toolkit@main; please verify they match current
    
skill behavior.)
  2. Self-contained complexa-sweep (SRC-4) — complexa-sweep/SKILL.md
    
referenced ../../../docs/SWEEP.md, which is outside the vendored
    .claude/skills/ subtree, so the link breaks once aggregated. Copied
    docs/SWEEP.md into complexa-sweep/reference/SWEEP.md and repointed the
    
link. (The other two refs — to ../complexa-design/SKILL.md and
    ../_shared/reference/hardware.md — stay inside the subtree and are fine.)
Not done here — needs owner decisions
  • 🔶 complexa-slurm: this skill exists in the aggregator catalog but is
    absent on dev. I did not add it back — please confirm whether it was
    
intentionally removed or should be restored to this repo.
  • 🔹 .claude/skills/README.md: gets vendored into the catalog as a stray
    
non-skill file (SRC-9). Minor; remove or keep as you prefer.
  • 🔹 .gitignore ignores .claude/: the skills here are force-tracked, so
    new skill files (like these evals) are silently ignored unless git add -f.
    
Consider un-ignoring .claude/skills/ so future skill additions aren't dropped.
🤖 Generated with Claude Code
@trvachov@claude
Make skills aggregator-compatible: co-located evals + self-contain co…
5391310
…mplexa-sweep
- Add evals/evals.json for all 5 skills (were catalog-only; sourced skills are
overwritten from this repo on sync, so evals belong here — SRC-10).
- complexa-sweep referenced ../../../docs/SWEEP.md (outside .claude/skills/,
breaks when aggregated); copied it into complexa-sweep/reference/SWEEP.md and
repointed the link (SRC-4).
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@trvachovtrvachov
mentioned this pull request
Aug 4, 2026
 Open

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try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

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Make skills aggregator-compatible: co-located evals + self-contain complexa-sweep - #57
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Make skills aggregator-compatible: co-located evals + self-contain complexa-sweep#57
trvachov wants to merge 1 commit into
devfrom 
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@trvachov
@trvachovtrvachov
commented
Jul 16, 2026

Copy link


Copy Markdown

What
Makes the Proteina-Complexa skills cleanly aggregatable by bionemo-agent-toolkit

(and NVIDIA/skills), fixing two concrete compatibility issues:
  1. Co-located evals (SRC-10) — adds evals/evals.json for all 5 skills
    
(complexa-design, complexa-evaluate-pdbs, complexa-setup,
    complexa-sweep, complexa-target). These currently live only in the
    
aggregator catalog; since these are sourced skills, the sync overwrites the
    
catalog from this repo, so the evals belong here or they're lost on sync.
    
(Copied from bionemo-agent-toolkit@main; please verify they match current
    
skill behavior.)
  2. Self-contained complexa-sweep (SRC-4) — complexa-sweep/SKILL.md
    
referenced ../../../docs/SWEEP.md, which is outside the vendored
    .claude/skills/ subtree, so the link breaks once aggregated. Copied
    docs/SWEEP.md into complexa-sweep/reference/SWEEP.md and repointed the
    
link. (The other two refs — to ../complexa-design/SKILL.md and
    ../_shared/reference/hardware.md — stay inside the subtree and are fine.)
Not done here — needs owner decisions
  • 🔶 complexa-slurm: this skill exists in the aggregator catalog but is
    absent on dev. I did not add it back — please confirm whether it was
    
intentionally removed or should be restored to this repo.
  • 🔹 .claude/skills/README.md: gets vendored into the catalog as a stray
    
non-skill file (SRC-9). Minor; remove or keep as you prefer.
  • 🔹 .gitignore ignores .claude/: the skills here are force-tracked, so
    new skill files (like these evals) are silently ignored unless git add -f.
    
Consider un-ignoring .claude/skills/ so future skill additions aren't dropped.
🤖 Generated with Claude Code
@trvachov@claude
Make skills aggregator-compatible: co-located evals + self-contain co…
5391310
…mplexa-sweep
- Add evals/evals.json for all 5 skills (were catalog-only; sourced skills are
overwritten from this repo on sync, so evals belong here — SRC-10).
- complexa-sweep referenced ../../../docs/SWEEP.md (outside .claude/skills/,
breaks when aggregated); copied it into complexa-sweep/reference/SWEEP.md and
repointed the link (SRC-4).
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@trvachovtrvachov
mentioned this pull request
Aug 4, 2026
 Open

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, 'i');
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Skip to content
Make skills aggregator-compatible: co-located evals + self-contain complexa-sweep - #57
Open
trvachov wants to merge 1 commit into
devfrom 
aggregator-compat
Open
Make skills aggregator-compatible: co-located evals + self-contain complexa-sweep#57
trvachov wants to merge 1 commit into
devfrom 
aggregator-compat
Conversation
@trvachov
@trvachovtrvachov
commented
Jul 16, 2026

Copy link


Copy Markdown

What
Makes the Proteina-Complexa skills cleanly aggregatable by bionemo-agent-toolkit

(and NVIDIA/skills), fixing two concrete compatibility issues:
  1. Co-located evals (SRC-10) — adds evals/evals.json for all 5 skills
    
(complexa-design, complexa-evaluate-pdbs, complexa-setup,
    complexa-sweep, complexa-target). These currently live only in the
    
aggregator catalog; since these are sourced skills, the sync overwrites the
    
catalog from this repo, so the evals belong here or they're lost on sync.
    
(Copied from bionemo-agent-toolkit@main; please verify they match current
    
skill behavior.)
  2. Self-contained complexa-sweep (SRC-4) — complexa-sweep/SKILL.md
    
referenced ../../../docs/SWEEP.md, which is outside the vendored
    .claude/skills/ subtree, so the link breaks once aggregated. Copied
    docs/SWEEP.md into complexa-sweep/reference/SWEEP.md and repointed the
    
link. (The other two refs — to ../complexa-design/SKILL.md and
    ../_shared/reference/hardware.md — stay inside the subtree and are fine.)
Not done here — needs owner decisions
  • 🔶 complexa-slurm: this skill exists in the aggregator catalog but is
    absent on dev. I did not add it back — please confirm whether it was
    
intentionally removed or should be restored to this repo.
  • 🔹 .claude/skills/README.md: gets vendored into the catalog as a stray
    
non-skill file (SRC-9). Minor; remove or keep as you prefer.
  • 🔹 .gitignore ignores .claude/: the skills here are force-tracked, so
    new skill files (like these evals) are silently ignored unless git add -f.
    
Consider un-ignoring .claude/skills/ so future skill additions aren't dropped.
🤖 Generated with Claude Code
@trvachov@claude
Make skills aggregator-compatible: co-located evals + self-contain co…
5391310
…mplexa-sweep
- Add evals/evals.json for all 5 skills (were catalog-only; sourced skills are
overwritten from this repo on sync, so evals belong here — SRC-10).
- complexa-sweep referenced ../../../docs/SWEEP.md (outside .claude/skills/,
breaks when aggregated); copied it into complexa-sweep/reference/SWEEP.md and
repointed the link (SRC-4).
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@trvachovtrvachov
mentioned this pull request
Aug 4, 2026
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Make skills aggregator-compatible: co-located evals + self-contain complexa-sweep - #57
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aggregator-compat
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Make skills aggregator-compatible: co-located evals + self-contain complexa-sweep#57
trvachov wants to merge 1 commit into
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@trvachov
@trvachovtrvachov
commented
Jul 16, 2026

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What
Makes the Proteina-Complexa skills cleanly aggregatable by bionemo-agent-toolkit

(and NVIDIA/skills), fixing two concrete compatibility issues:
  1. Co-located evals (SRC-10) — adds evals/evals.json for all 5 skills
    
(complexa-design, complexa-evaluate-pdbs, complexa-setup,
    complexa-sweep, complexa-target). These currently live only in the
    
aggregator catalog; since these are sourced skills, the sync overwrites the
    
catalog from this repo, so the evals belong here or they're lost on sync.
    
(Copied from bionemo-agent-toolkit@main; please verify they match current
    
skill behavior.)
  2. Self-contained complexa-sweep (SRC-4) — complexa-sweep/SKILL.md
    
referenced ../../../docs/SWEEP.md, which is outside the vendored
    .claude/skills/ subtree, so the link breaks once aggregated. Copied
    docs/SWEEP.md into complexa-sweep/reference/SWEEP.md and repointed the
    
link. (The other two refs — to ../complexa-design/SKILL.md and
    ../_shared/reference/hardware.md — stay inside the subtree and are fine.)
Not done here — needs owner decisions
  • 🔶 complexa-slurm: this skill exists in the aggregator catalog but is
    absent on dev. I did not add it back — please confirm whether it was
    
intentionally removed or should be restored to this repo.
  • 🔹 .claude/skills/README.md: gets vendored into the catalog as a stray
    
non-skill file (SRC-9). Minor; remove or keep as you prefer.
  • 🔹 .gitignore ignores .claude/: the skills here are force-tracked, so
    new skill files (like these evals) are silently ignored unless git add -f.
    
Consider un-ignoring .claude/skills/ so future skill additions aren't dropped.
🤖 Generated with Claude Code
@trvachov@claude
Make skills aggregator-compatible: co-located evals + self-contain co…
5391310
…mplexa-sweep
- Add evals/evals.json for all 5 skills (were catalog-only; sourced skills are
overwritten from this repo on sync, so evals belong here — SRC-10).
- complexa-sweep referenced ../../../docs/SWEEP.md (outside .claude/skills/,
breaks when aggregated); copied it into complexa-sweep/reference/SWEEP.md and
repointed the link (SRC-4).
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@trvachovtrvachov
mentioned this pull request
Aug 4, 2026
 Open

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Skip to content
Make skills aggregator-compatible: co-located evals + self-contain complexa-sweep - #57
Open
trvachov wants to merge 1 commit into
devfrom 
aggregator-compat
Open
Make skills aggregator-compatible: co-located evals + self-contain complexa-sweep#57
trvachov wants to merge 1 commit into
devfrom 
aggregator-compat
Conversation
@trvachov
@trvachovtrvachov
commented
Jul 16, 2026

Copy link


Copy Markdown

What
Makes the Proteina-Complexa skills cleanly aggregatable by bionemo-agent-toolkit

(and NVIDIA/skills), fixing two concrete compatibility issues:
  1. Co-located evals (SRC-10) — adds evals/evals.json for all 5 skills
    
(complexa-design, complexa-evaluate-pdbs, complexa-setup,
    complexa-sweep, complexa-target). These currently live only in the
    
aggregator catalog; since these are sourced skills, the sync overwrites the
    
catalog from this repo, so the evals belong here or they're lost on sync.
    
(Copied from bionemo-agent-toolkit@main; please verify they match current
    
skill behavior.)
  2. Self-contained complexa-sweep (SRC-4) — complexa-sweep/SKILL.md
    
referenced ../../../docs/SWEEP.md, which is outside the vendored
    .claude/skills/ subtree, so the link breaks once aggregated. Copied
    docs/SWEEP.md into complexa-sweep/reference/SWEEP.md and repointed the
    
link. (The other two refs — to ../complexa-design/SKILL.md and
    ../_shared/reference/hardware.md — stay inside the subtree and are fine.)
Not done here — needs owner decisions
  • 🔶 complexa-slurm: this skill exists in the aggregator catalog but is
    absent on dev. I did not add it back — please confirm whether it was
    
intentionally removed or should be restored to this repo.
  • 🔹 .claude/skills/README.md: gets vendored into the catalog as a stray
    
non-skill file (SRC-9). Minor; remove or keep as you prefer.
  • 🔹 .gitignore ignores .claude/: the skills here are force-tracked, so
    new skill files (like these evals) are silently ignored unless git add -f.
    
Consider un-ignoring .claude/skills/ so future skill additions aren't dropped.
🤖 Generated with Claude Code
@trvachov@claude
Make skills aggregator-compatible: co-located evals + self-contain co…
5391310
…mplexa-sweep
- Add evals/evals.json for all 5 skills (were catalog-only; sourced skills are
overwritten from this repo on sync, so evals belong here — SRC-10).
- complexa-sweep referenced ../../../docs/SWEEP.md (outside .claude/skills/,
breaks when aggregated); copied it into complexa-sweep/reference/SWEEP.md and
repointed the link (SRC-4).
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@trvachovtrvachov
mentioned this pull request
Aug 4, 2026
 Open

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@trvachov