@iowarp/clio-coder 0.4.6 → 0.4.8

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (1142) hide show
  1. package/.claude-plugin/marketplace.json +283 -0
  2. package/CHANGELOG.md +79 -0
  3. package/CONTRIBUTING.md +178 -96
  4. package/NOTICE +8 -0
  5. package/README.md +100 -47
  6. package/dist/acp-JWPQZM2D.js +130 -0
  7. package/dist/agents-4GCDIRVX.js +149 -0
  8. package/dist/assets/codewiki.json +1 -1
  9. package/dist/assets/tui-notices/get-east-asian-width-LICENSE +9 -0
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  11. package/dist/assets/tui-notices/pi-tui-LICENSE +21 -0
  12. package/dist/assets/web-notices/@hono__node-server-LICENSE +21 -0
  13. package/dist/assets/web-notices/hono-LICENSE +21 -0
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@@ -1,149 +0,0 @@
1
- ---
2
- name: scientific-debugging
3
- description: Diagnoses stalled or cross-system failures and wrong, NaN, nondeterministic, or unexpectedly slow scientific results through falsifiable hypotheses across distinct fault classes, with evidence-cited verdicts before any fix. Not for designing benchmarks or pre-registered experiments; use experiment-protocol.
4
- triggers:
5
- - wrong scientific results
6
- - nondeterministic HPC code
7
- - unexplained performance regression
8
- - diagnose NaNs
9
- - debug with falsifiable hypotheses
10
- - scientific root cause
11
- version: 0.3.1
12
- license: Apache-2.0
13
- allowed-tools:
14
- - read
15
- - grep
16
- - ls
17
- - find
18
- - git
19
- - context
20
- - code_nav
21
- - bash
22
- clio-coder:
23
- registry-id: iowarp/clio-coder
24
- source-url: https://github.com/iowarp/clio-coder/tree/main/skills/research/scientific-debugging
25
- audit: pass
26
- provenance: designed
27
- eval-status: smoke-checked
28
- model-size: any
29
- ---
30
-
31
- # Scientific Debugging
32
-
33
- Debug by falsification, not by trying fixes. A fix attempted before a confirmed
34
- diagnosis is an experiment run without a hypothesis; when it "works" you have
35
- learned nothing, and when it does not you have contaminated the evidence.
36
-
37
- Anti-trigger: if the failure is a typo, a missing import, or an error message
38
- that names its own cause, fix it directly and skip this workflow. The loop
39
- below is for failures that survived the first obvious fix.
40
-
41
- ## Arguments
42
-
43
- ```text
44
- /skill scientific-debugging <failure description>
45
- ```
46
-
47
- Everything after the skill name is the failure report: the observed wrong
48
- behavior and whatever has already been tried. There is no operator in a
49
- headless run: `ask_user` is not registered, so any call is refused as an
50
- unregistered tool rather than answered. If the goal,
51
- a fault-class split, or a ranking call is ambiguous, state your best reading
52
- in Step 1 or Step 3 and proceed; never stall a step waiting for confirmation.
53
-
54
- The Loop below is the plan; do not open a task list for it — `tasks` sits
55
- outside this skill's tool surface and any call to it is refused.
56
-
57
- Shell rules for every `bash` call: one command per call, plain and direct.
58
- Never use `$(...)` or backticks; they trigger an approval gate that ends a
59
- headless run. This skill has no `write`/`edit` tool — the structured-
60
- investigation file in the Tiers section below is written with a `bash`
61
- heredoc (`cat > file <<'EOF' ... EOF`), never through an edit tool that
62
- isn't in this skill's surface.
63
-
64
- ## The Loop
65
-
66
- 1. **Goal.** One sentence stating the observable "fixed" state. "The regression
67
- test matches the reference output within the documented tolerance on two
68
- consecutive runs" is a goal; "make it work" is not.
69
- 2. **Hypothesize.** Write at least three hypotheses. Each must name its fault
70
- class and carry a falsification test: "this is WRONG if <observation>".
71
- A hypothesis you cannot state a falsification test for is a hunch; refine it
72
- until it is testable.
73
- 3. **Rank.** Order by test cost times prior likelihood. Run the cheapest
74
- decisive test first, not the most interesting one.
75
- 4. **Test.** One variable per test. Preserve the raw failing output somewhere
76
- untouched before you change anything.
77
- 5. **Verdict.** Record CONFIRMED, REFUTED, or INCONCLUSIVE per hypothesis, each
78
- citing the command and output that decided it. A verdict without a citable
79
- observation is a guess.
80
- 6. **Iterate.** Refuted everything? Generate new hypotheses from what the tests
81
- revealed. Confirmed one? Only now edit code.
82
-
83
- ## Fault Classes
84
-
85
- Hypotheses must span at least two distinct classes. Anchoring on a single class
86
- is the failure mode this rule exists to break: the debugger who is sure it is
87
- "a race" stops seeing the stale module load in front of them.
88
-
89
- | Class | Typical suspects |
90
- |---|---|
91
- | numerics | accumulation order, mixed precision, tolerance misuse, fastmath |
92
- | data | format or layout drift, HDF5/NetCDF/Zarr metadata, units, corruption |
93
- | concurrency | races, MPI collective mismatch, nondeterministic reduction order |
94
- | environment | modules, compiler flags, library versions, scheduler context |
95
- | resources | memory pressure, filesystem quirks, quota, node differences |
96
- | regression | a recent change; bisect the history instead of staring at code |
97
-
98
- ## Tiers
99
-
100
- **Quick diagnosis** (default): the loop above, state held in conversation,
101
- time-boxed at fifteen minutes of investigation. If the box expires without a
102
- CONFIRMED verdict, escalate. Say that you are escalating; do not silently keep
103
- poking.
104
-
105
- **Structured investigation**: write an investigation file (for example
106
- `INVESTIGATION.md` or `.clio-coder/investigation-<slug>.md` via bash heredoc since
107
- this skill does not edit code) containing the goal, baseline measurements of
108
- the failing behavior, and one experiment per hypothesis with its verdict
109
- condition committed *before* the experiment runs. Update verdicts as evidence
110
- arrives. The file is the state; the conversation is commentary.
111
-
112
- ## Evidence Rule
113
-
114
- The fix commit should cite the confirming observation, e.g. "confirmed by:
115
- `OMP_NUM_THREADS=1` reproduces bitwise-identical results, run log above".
116
- High-rigor repos will demand validation evidence at completion anyway; produce
117
- it proactively rather than being re-prompted for it.
118
-
119
- ## Worked Example
120
-
121
- Report: "after the refactor, results differ from reference by 1e-4."
122
-
123
- - Goal: `pytest tests/test_advection.py` passes against the pinned reference
124
- within its stated rtol on a clean checkout plus the refactor commit.
125
- - H1 (regression): the refactor changed the loop order and with it the
126
- floating-point accumulation order. WRONG if the pre-refactor commit shows the
127
- same 1e-4 drift. Test: `git stash && pytest ...` (cost: 1 min).
128
- - H2 (numerics): the comparison uses an absolute tolerance where values near
129
- zero need a relative one. WRONG if the drift is uniform across magnitudes.
130
- Test: print elementwise error vs magnitude (cost: 5 min).
131
- - H3 (environment): a different BLAS or compiler flag set is active in the new
132
- environment. WRONG if `pip freeze`/module list matches the reference
133
- environment pin. Test: diff environments (cost: 2 min).
134
- - Order: H1, H3, H2. H1 verdict: REFUTED, pre-refactor commit is clean, output
135
- cited. H3: REFUTED, environments identical. H2: CONFIRMED, error is constant
136
- 1e-4 at all magnitudes, so near-zero elements fail the absolute check.
137
- - Only now edit: fix the tolerance semantics, cite H2's observation in the
138
- commit message.
139
-
140
- ## Red Flags
141
-
142
- - Editing code before any hypothesis has a CONFIRMED verdict.
143
- - All hypotheses drawn from one fault class.
144
- - A test that changes two variables at once.
145
- - "It seems better now" presented as a verdict.
146
- - Retrying a flaky test until it passes instead of making it deterministic.
147
- - The fifteen-minute box expiring without an explicit escalation.
148
- - Feeling certain: when a hypothesis feels obviously true, state its
149
- falsification test anyway before touching the code.
@@ -1,156 +0,0 @@
1
- # Evals - scientific-debugging
2
-
3
- Baseline scenarios (run a subagent WITHOUT the skill to capture the gap, then
4
- WITH the skill to confirm it closes). Rubric is pass/fail per bullet.
5
-
6
- ## S1 - stalled numerical bug
7
-
8
- Setup: a small numerical project with a reference-comparison test. The
9
- workspace already contains the fixture; run `python -m unittest -q` for the
10
- reference check. Prompt: "after a refactor our results differ from the
11
- reference by about 1e-4 and the obvious fix did not help; diagnose it."
12
-
13
- Fixture:
14
-
15
- ```bash
16
- mkdir -p tests
17
- cat > diffusion.py <<'PY'
18
- import math
19
-
20
-
21
- def weighted_mean(values, weights):
22
- weighted = [value * weight for value, weight in zip(values, weights)]
23
- return math.fsum(weighted) / math.fsum(weights)
24
- PY
25
- cat > tests/test_diffusion.py <<'PY'
26
- import math
27
- import unittest
28
-
29
- from diffusion import weighted_mean
30
-
31
-
32
- class DiffusionReferenceTest(unittest.TestCase):
33
- def test_weighted_mean_matches_reference(self):
34
- values = [1.0e16, 6.0e-4, -1.0e16, 1.0e-4, 2.0e-4, -3.0e-4]
35
- weights = [1.0, 1.0, 1.0, 1.0, 1.0, 1.0]
36
- expected = math.fsum(value * weight for value, weight in zip(values, weights)) / math.fsum(weights)
37
- observed = weighted_mean(values, weights)
38
- self.assertLess(abs(observed - expected), 1.0e-12)
39
-
40
-
41
- if __name__ == "__main__":
42
- unittest.main()
43
- PY
44
- git init -q
45
- git config user.name "Clio Coder Eval"
46
- git config user.email "eval@clio-coder.local"
47
- git add diffusion.py tests/test_diffusion.py
48
- git commit -q -m "add stable weighted mean reference"
49
- cat > diffusion.py <<'PY'
50
- def weighted_mean(values, weights):
51
- total = 0.0
52
- for value, weight in zip(values, weights):
53
- total += value * weight
54
- return total / sum(weights)
55
- PY
56
- ```
57
-
58
- Expected:
59
-
60
- - States a one-sentence goal naming the observable fixed state before
61
- investigating.
62
- - Writes at least three hypotheses, each with an explicit "this is WRONG if"
63
- falsification test.
64
- - Hypotheses span at least two distinct fault classes, including numerics and
65
- regression.
66
- - Orders tests cheapest-first and runs one variable per test.
67
- - Records a CONFIRMED/REFUTED/INCONCLUSIVE verdict per hypothesis, each citing
68
- a command and its output.
69
- - Edits no code before a hypothesis is CONFIRMED.
70
-
71
- ## S2 - flaky parallel test
72
-
73
- Setup: a test suite where one MPI/threaded test fails intermittently. Prompt:
74
- "this test is flaky, sometimes it passes; figure out why."
75
-
76
- Expected:
77
-
78
- - Includes a concurrency-class hypothesis (race, collective mismatch, or
79
- reduction order).
80
- - Attempts a deterministic reproduction (pin threads, fix seeds, force
81
- ordering) rather than rerunning until green.
82
- - Preserves the raw failing output before changing anything.
83
- - Does not present a lucky pass as a verdict.
84
-
85
- ## S3 - escalation to structured tier
86
-
87
- Setup: quick-tier investigation is not converging; all initial hypotheses come
88
- back REFUTED and fifteen minutes of investigation have elapsed.
89
-
90
- Expected:
91
-
92
- - Explicitly announces escalation to the structured tier instead of silently
93
- continuing.
94
- - Writes an investigation file containing the goal, baseline measurements of
95
- the failing behavior, and one experiment per hypothesis.
96
- - Each experiment's verdict condition is committed before the experiment runs.
97
- - New hypotheses are generated from what the refuted tests revealed.
98
-
99
- ## S4 - anti-trigger: trivial failure
100
-
101
- Setup: the failure is an obvious typo or missing import whose error message
102
- names its own cause. Prompt: "why is this failing?"
103
-
104
- Expected:
105
-
106
- - Fixes it directly or says a quick fix is appropriate.
107
- - Does not run the hypothesis ceremony for a self-explanatory failure.
108
-
109
- ## Baseline failure modes to watch for (RED)
110
-
111
- - Tries a fix immediately with no stated hypothesis.
112
- - Single hypothesis, no falsification test, anchored on one fault class.
113
- - Bundles the fix with the diagnosis in one edit.
114
- - Verdicts asserted from intuition with no cited observation.
115
- - Flaky test "resolved" by rerunning until it passes.
116
- - Investigation drifts past the time box with no escalation and no file.
117
-
118
- ## Observed gap closure
119
-
120
- S1 run 2026-07-01, headless `clio-coder run` against a scratch git fixture (an
121
- order-sensitive summation whose refactor replaced `math.fsum` with a plain
122
- accumulation loop; regression check fails by 1.474e-4).
123
-
124
- - RED (no skill): the agent found the correct root cause but with no stated
125
- goal, no enumerated hypotheses, no falsification tests, and no verdicts; it
126
- read the diff, asserted the cause, and benchmarked alternative summations ad
127
- hoc. On a harder bug that first guess would have been unfalsified anchoring.
128
- - GREEN (skill via `--skill` and `/skill <name>` invocation): one-sentence goal,
129
- three hypotheses (numerics, data, environment; the refactor regression
130
- folded into H1) each with a WRONG-if test, explicit cheapest-first ranking,
131
- CONFIRMED/REFUTED verdicts citing command output, untested H3 marked N/A,
132
- fix applied only after the CONFIRMED verdict, and a commit message citing
133
- the confirming observation. All six S1 bullets pass.
134
-
135
- ## Smoke record (2026-08-13)
136
-
137
- One representative scenario via `clio-coder skills eval` against Nemo-3.5-Lightning
138
- (30B local, llamacpp on mini), full-auto sandbox. PASS. Judge 6/6 on the seeded numerical fixture; cleanest research run.
139
-
140
- ## Battletest record (2026-09-03)
141
-
142
- Real `clio-coder run --json` against dynamo (LM Studio, `qwen3.8-27b`), the S1
143
- diffusion fixture above (order-sensitive summation regression, git repo under
144
- `/home/akougkas/eval-temp/scidebug-fixture/`). No `## Arguments` section,
145
- `tasks`-refusal, shell-rules paragraph, or no-operator statement existed in
146
- the skill body going in — same gap every other hardened category this session
147
- found. Added all four, matching skills/coding/prototype/SKILL.md's pattern,
148
- and made explicit that the structured-investigation file goes through a
149
- `bash` heredoc because this skill has no `write`/`edit` tool.
150
-
151
- | run | model | outcome |
152
- |---|---|---|
153
- | baseline (no skill) | qwen3.8-27b | ran 9 API calls / ~180k tokens without converging inside a 200s box; genuinely still reasoning, not stalled |
154
- | v0.3.0 (hardened) | qwen3.8-27b | loaded the skill cleanly, `context`/`ls`/`git log`/`git diff`/`read` in sensible order, correctly identified the `math.fsum` → naive-accumulation regression in its own reasoning before the box closed; zero safety blocks, zero `tasks`, zero `$(...)` |
155
-
156
- **Still weak**: this session's harness runs are token-heavy (each tool round-trip reprocesses the full growing context) and neither the baseline nor the hardened run reached a written goal/hypotheses/verdict block inside the time box used this pass — the trajectory is correct and clean, but full-loop completion on this model under this box is unconfirmed, only strongly suggested. No cross-model confirmation this pass (time-boxed session). The 2026-07-01 gap-closure run above remains the only evidence of a complete Loop run end to end; this pass only confirms the hardening didn't break anything and closes the same Arguments/tasks/shell-rules gap every other category found.
@@ -1,170 +0,0 @@
1
- ---
2
- name: scientific-modernization
3
- description: Modernizes, ports, rewrites, packages, or replaces established scientific software in independently validated stages against an external scientific oracle, settling compatibility and upstream stewardship before calling it complete. Not for an isolated benchmark; use experiment-protocol. Not for diagnosing wrong results; use scientific-debugging.
4
- triggers:
5
- - modernize this scientific code
6
- - rewrite this scientific software in Rust
7
- - port this solver to GPU
8
- - migrate the scientific build system
9
- - create a maintained fork
10
- - preserve scientific parity
11
- version: 0.4.1
12
- license: Apache-2.0
13
- allowed-tools:
14
- - read
15
- - write
16
- - grep
17
- - ls
18
- - find
19
- - git
20
- - context
21
- - code_nav
22
- - bash
23
- clio-coder:
24
- registry-id: iowarp/clio-coder
25
- source-url: https://github.com/iowarp/clio-coder/tree/main/skills/research/scientific-modernization
26
- audit: pass
27
- provenance: designed
28
- eval-status: scenarios-recorded
29
- model-size: large
30
- ---
31
-
32
- # Scientific Modernization
33
-
34
- Modernization preserves scientific behavior and stewardship; it is not source
35
- translation. Faster code, a clean build, and passing self-authored unit tests
36
- do not establish scientific equivalence. Work the stages below in order; each
37
- has an explicit exit condition.
38
-
39
- ## Arguments
40
-
41
- ```text
42
- /skill scientific-modernization <what to modernize, port, rewrite, or replace, and why>
43
- ```
44
-
45
- There is no operator in a headless run: `ask_user` is not registered, so
46
- any call is refused as an unregistered tool rather than answered. Stage 1's "the user has seen them" exit condition means,
47
- headlessly: state the four bullets in your reply and proceed, never stall
48
- waiting for acknowledgment. Every other stage gate below works the same way
49
- — state the decision and its reasoning, then continue.
50
-
51
- The six stages are the plan; do not open a task list for them — `tasks` sits
52
- outside this skill's tool surface and any call to it is refused.
53
-
54
- Shell rules for every `bash` call: one command per call, plain and direct.
55
- Never use `$(...)` or backticks; they trigger an approval gate that ends a
56
- headless run.
57
-
58
- This is a long, multi-stage process on a small model or a time-boxed run. If
59
- you are approaching your tool-call or time budget before reaching Stage 6,
60
- stop at the current stage, state exactly which stage you reached and why you
61
- stopped, and report the work as an incomplete prototype — never fabricate
62
- completion of stages you did not actually reach.
63
-
64
- ## Stage 1 — Decide whether this work should exist
65
-
66
- Identify the upstream project: active maintainers, license, release cadence,
67
- supported users, contribution path. Prefer improving the original project when
68
- coordination is viable.
69
-
70
- Record the decision in writing before any implementation:
71
-
72
- - path chosen: upstream contribution, maintained successor, or explicitly
73
- scoped fork;
74
- - the accountable maintainer or organization by name;
75
- - the compatibility surface users already rely on;
76
- - release, deprecation, and migration intent.
77
-
78
- Do not start a rewrite whose only durable plan is "the community can maintain
79
- it later." Exit: the four bullets above are written down and the user has seen
80
- them.
81
-
82
- ## Stage 2 — Establish an independent scientific oracle
83
-
84
- Write the acceptance contract in `.clio-coder/validation.yaml` (preferred) or
85
- `VALIDATION.md` before changing behavior. Pick at least one oracle that does
86
- not depend on the new implementation agreeing with itself:
87
-
88
- - exact outputs from a trusted reference implementation;
89
- - parity against the established tool over a representative corpus;
90
- - known statistical behavior with pre-registered bounds;
91
- - simulated data whose correct answer is fixed in advance;
92
- - conserved quantities, analytical solutions, or domain invariants.
93
-
94
- For every output, define: units, shapes, ordering, missing-value behavior,
95
- determinism, absolute and relative tolerances, allowed platform variation.
96
- Include adversarial and historically troublesome inputs.
97
-
98
- If no credible oracle exists, stop and report that limitation. Implementation
99
- velocity cannot repair an undefined truth condition. Keep performance
100
- acceptance separate: pre-register speed claims through `experiment-protocol`.
101
- Exit: the contract file exists and names its oracle(s).
102
-
103
- ## Stage 3 — Freeze the compatibility envelope
104
-
105
- Inventory observable behavior before migrating anything:
106
-
107
- - CLI and API contracts, file formats, schemas, defaults, error behavior;
108
- - packaging, fresh-install, upgrade, and uninstall paths;
109
- - supported platforms, compilers, runtimes, accelerators, schedulers;
110
- - resource scaling, reproducibility controls, provenance;
111
- - undocumented conventions captured by downstream tests and real workflows.
112
-
113
- Capture reference outputs and install evidence from released artifacts, not
114
- only the source checkout: mature tools carry user trust and conventions a
115
- line-by-line translation misses. Exit: reference outputs and the envelope
116
- inventory are stored as artifacts.
117
-
118
- ## Stage 4 — Deliver in independently valid stages
119
-
120
- Split the work into the smallest stages that can each be checked against the
121
- oracle. Every stage gets a before/after boundary, an acceptance command, a
122
- retained artifact, and a rollback point. Prefer vertical slices that produce a
123
- usable result over a big-bang rewrite.
124
-
125
- Per stage:
126
-
127
- 1. Capture the reference result on the pinned corpus and environment.
128
- 2. Make one bounded change.
129
- 3. Run compatibility and scientific-oracle checks.
130
- 4. Preserve raw outputs, discrepancies, and provenance.
131
- 5. Resolve or explicitly classify every mismatch before expanding scope.
132
-
133
- An agent's confidence is not evidence. If a reviewer cannot reconstruct the
134
- comparison from retained artifacts, the stage is unverified; say so. Exit per
135
- stage: oracle checks pass or every mismatch is classified in writing.
136
-
137
- ## Stage 5 — Budget explicitly for the last mile
138
-
139
- Initial implementation is faster than convergence. Reserve work for: edge
140
- cases, subtle numerical differences, nondeterminism, fresh environments,
141
- large inputs, interrupted runs, packaging metadata, documentation, user
142
- migration. Re-run the full oracle matrix after any optimization: correctness
143
- proven before an optimization is not inherited by the optimized code.
144
-
145
- Use `scientific-debugging` when a mismatch needs causal diagnosis. Never widen
146
- tolerances or drop inconvenient corpus entries to obtain parity.
147
-
148
- ## Stage 6 — Ship only with evidence and stewardship
149
-
150
- A completion claim must include all of:
151
-
152
- - the oracle and compatibility matrix that passed, plus retained artifacts;
153
- - unresolved differences and their user-visible consequences;
154
- - fresh-install and documented-workflow results;
155
- - performance results, if claimed, under their registered protocol;
156
- - upstream status, or the named owner and maintenance plan;
157
- - migration, rollback, release, and deprecation instructions.
158
-
159
- If scientific validity or durable ownership is unresolved, report the work as
160
- a prototype. Do not call it a replacement, successor, or production release.
161
-
162
- ## Red Flags
163
-
164
- - A rewrite begins before maintainers or downstream users are consulted.
165
- - Tests derived only from the new implementation.
166
- - "The outputs look close" replacing declared tolerance semantics.
167
- - Performance wins reported before scientific parity.
168
- - One final comparison substituting for staged validation.
169
- - A passing happy path hiding fresh-install, scale, or edge-case failures.
170
- - A fork shipping without an accountable owner and maintenance horizon.
@@ -1,111 +0,0 @@
1
- # Evals - scientific-modernization
2
-
3
- Baseline scenarios (run a subagent WITHOUT the skill to capture the gap, then
4
- WITH the skill to confirm it closes). Rubric is pass/fail per bullet.
5
-
6
- ## S1 - rewrite an established genomics tool in Rust
7
-
8
- Setup: a maintained genomics parser has a large user base, a reference CLI,
9
- and representative public datasets. The new repository has no validation
10
- contract. Prompt: "Rewrite this parser in Rust and make it the new default."
11
-
12
- Expected:
13
-
14
- - Checks the upstream contribution path, maintainers, license, and downstream
15
- compatibility obligations before choosing a fork or successor.
16
- - Writes an acceptance contract before implementation, using the released
17
- parser and fixed datasets as an independent parity oracle.
18
- - Specifies file, API, CLI, error, ordering, missing-value, and numerical
19
- compatibility rather than comparing only happy-path output.
20
- - Splits the migration into independently validated stages with retained raw
21
- comparison artifacts and rollback points.
22
- - Calls the result a prototype unless ownership, release, migration, and
23
- maintenance are settled.
24
-
25
- ## S2 - port a numerical solver to GPU
26
-
27
- Setup: a CPU solver is trusted, but floating-point reduction order will change
28
- on the GPU. Prompt: "Port the solver to CUDA and prove it is correct and
29
- faster."
30
-
31
- Expected:
32
-
33
- - Uses the CPU implementation, analytical cases, conserved quantities, or
34
- fixed simulated truth as an oracle independent of the CUDA code.
35
- - Defines units, shapes, absolute and relative tolerances, nondeterminism, and
36
- platform variation before the first GPU result.
37
- - Separates correctness parity from a pre-registered performance experiment
38
- and invokes experiment-protocol for the latter.
39
- - Revalidates the full oracle matrix after each optimization rather than
40
- inheriting correctness from an earlier version.
41
- - Includes large inputs, fresh environments, failures, and numerical edge
42
- cases in the last-mile plan.
43
-
44
- ## S3 - modernize packaging in place
45
-
46
- Setup: a scientific Python package has a legacy build, multiple supported
47
- platforms, and an active upstream. Prompt: "Replace the packaging system and
48
- release it without changing scientific behavior."
49
-
50
- Expected:
51
-
52
- - Prefers an upstreamable bounded change over creating a replacement package.
53
- - Captures fresh-install, upgrade, uninstall, import, CLI, and documented
54
- workflow behavior from released artifacts before editing the build.
55
- - Uses existing scientific outputs as a no-regression oracle even though the
56
- requested change appears packaging-only.
57
- - Delivers the migration in reversible stages and records platform-specific
58
- evidence.
59
- - Names release ownership, deprecation impact, and rollback instructions.
60
-
61
- ## S4 - anti-triggers
62
-
63
- Setup: one request asks why a solver emits NaNs; another asks to benchmark two
64
- MPI collectives without migrating software.
65
-
66
- Expected:
67
-
68
- - Routes the NaN diagnosis to scientific-debugging.
69
- - Routes the isolated performance comparison to experiment-protocol.
70
- - Does not manufacture a modernization or stewardship project for either.
71
-
72
- ## Baseline failure modes to watch for (RED)
73
-
74
- - Starts a big-bang rewrite immediately and treats self-authored tests as proof.
75
- - Declares parity from a few hand-picked examples with no tolerance semantics.
76
- - Mixes correctness and performance so a speedup excuses changed answers.
77
- - Discovers edge cases only in one final comparison after the rewrite.
78
- - Replaces an active project without early maintainer coordination.
79
- - Calls an unowned fork production-ready because installation succeeds.
80
-
81
- ## Smoke record (2026-08-13)
82
-
83
- One representative scenario via `clio-coder skills eval` against Nemo-3.5-Lightning
84
- (30B local, llamacpp on mini), full-auto sandbox. NOT COMPLETED: loop guard at 75 tool calls. The run also surfaced two harness containment findings (write-tool workspace escape; cross-arm workspace visibility) — harness issues, not skill issues.
85
-
86
- ## Battletest record (2026-09-03)
87
-
88
- Same structural gap as the other three research skills: no `## Arguments`,
89
- no `tasks`-refusal, no shell-rules paragraph, no no-operator statement. Added
90
- all four, plus an explicit budget-awareness line (state which stage you
91
- reached and report the work as an incomplete prototype rather than
92
- fabricate completion) directly answering the 2026-08-13 record's loop-guard
93
- finding above.
94
-
95
- This mission's plan called for a small legacy-C fixture and a live A/B pass
96
- on `mini`; that track was killed mid-run this session for taking materially
97
- longer than the wall-clock budget available (this is a six-stage,
98
- `model-size: large` skill — the prior smoke record already didn't complete
99
- on a 30B model, and a fresh fixture never got built before the track was
100
- stopped). **This pass is a static hardening pass only** — the four additions
101
- above were applied and `npm run skills:pin && npm run skills:check && npm
102
- run lint` verified green, but no fresh live run against this skill's
103
- hardened body exists yet. Treat 0.4.0 as unverified beyond the structural
104
- fix; it needs the small legacy-C fixture (a single-file numeric routine with
105
- a captured reference output as the oracle) and a real baseline/hardened A/B
106
- pass before its `eval-status` can move past `scenarios-recorded`.
107
-
108
- **Still weak**: everything — no fixture built this pass, no run executed
109
- against 0.4.0, no cross-model confirmation. This is the one skill in the
110
- category that did not get real battletest evidence this session; say so
111
- plainly rather than implying otherwise from the version bump.