Skip to content

[codex] add fold06 agent evaluation bundle #26

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Draft
jmchandonia wants to merge 1 commit into
base: main
Choose a base branch
from
Draft

[codex] add fold06 agent evaluation bundle #26

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
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
74 changes: 74 additions & 0 deletions evaluations/fold-06-holdout-8/AGENT_ACTION_LOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,74 @@
- 2026-06-30T15:54:54-07:00 | action=init_log | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-06-holdout-8/AGENT_ACTION_LOG.md | reason=initialize mandatory trace log before benchmark actions
- 2026-06-30T15:54:54-07:00 | action=mkdir | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-06-holdout-8/agent_outputs | reason=initialize output directory for required artifacts
- 2026-06-30T15:54:54-07:00 | action=command | subject=bootstrap log and output directory | reason=complete workflow initialization
- 2026-06-30T15:55:04-07:00 | action=command | subject=read benchmark instructions, manifest, and fold-local skills | reason=load required task context
- 2026-06-30T15:55:04-07:00 | action=read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-06-holdout-8/AGENT_INSTRUCTIONS.md | reason=required benchmark workflow instructions
- 2026-06-30T15:55:04-07:00 | action=read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-06-holdout-8/MANIFEST.json | reason=required fold manifest and allowed paths
- 2026-06-30T15:55:04-07:00 | action=read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-06-holdout-8/skills/essdive_sm_curator/SKILL.md | reason=required fold-local curator skill
- 2026-06-30T15:55:04-07:00 | action=read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-06-holdout-8/skills/essdive_sm_harmonizer/SKILL.md | reason=required fold-local harmonizer skill
- 2026-06-30T15:55:12-07:00 | action=command | subject=read remaining fold-local harmonizer skill | reason=complete required skill read before task actions
- 2026-06-30T15:55:12-07:00 | action=read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-06-holdout-8/skills/essdive_sm_harmonizer/SKILL.md lines 321-520 | reason=finish fold-local harmonizer instructions
- 2026-06-30T15:55:18-07:00 | action=command | subject=read final fold-local harmonizer skill chunk | reason=complete example and QA instructions
- 2026-06-30T15:55:18-07:00 | action=read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-06-holdout-8/skills/essdive_sm_harmonizer/SKILL.md lines 521-760 | reason=finish fold-local harmonizer instructions
- 2026-06-30T15:55:27-07:00 | action=command | subject=list fold-local sandbox files | reason=identify allowed exemplar and output structure
- 2026-06-30T15:55:27-07:00 | action=list | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-06-holdout-8 | reason=inspect fold-local sandbox top-level contents
- 2026-06-30T15:55:27-07:00 | action=list | subject=/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-61a0ecd70856892-20230808T205724993 | reason=inspect allowed raw held-out package files
- 2026-06-30T15:55:35-07:00 | action=command | subject=list fold-local sandbox deeper structure | reason=locate allowed exemplar mapping and code copies
- 2026-06-30T15:55:35-07:00 | action=list | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-06-holdout-8/data | reason=inspect fold-local data directories only
- 2026-06-30T15:55:44-07:00 | action=command | subject=read fold-local mapping and common helper code | reason=understand allowed schema and code conventions
- 2026-06-30T15:55:44-07:00 | action=read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-06-holdout-8/data/processed/ess-dive_wfsfa_soil_datasets/sm_data_harmonization_mapping.json | reason=allowed fold-local mapping examples with held-out removed
- 2026-06-30T15:55:44-07:00 | action=read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-06-holdout-8/data/gold/expert_code/harmonize_sm/common.py | reason=allowed fold-local harmonizer helper functions
- 2026-06-30T15:56:34-07:00 | action=command | subject=list fold-local metadata cache | reason=find allowed cached ESS-DIVE metadata for held-out package
- 2026-06-30T15:56:34-07:00 | action=list | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-06-holdout-8/data/external/ess-dive_meta | reason=confirm fold-local metadata cache absent
- 2026-06-30T15:56:34-07:00 | action=command | subject=inspect raw held-out CSV headers and counts | reason=classify payload and metadata files
- 2026-06-30T15:56:34-07:00 | action=read | subject=/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-61a0ecd70856892-20230808T205724993/SLT_OBJ2_SoilSensors_2018_InstallationMethods.csv first 8 lines | reason=inspect raw held-out CSV structure
- 2026-06-30T15:56:34-07:00 | action=command | subject=wc -l /h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-61a0ecd70856892-20230808T205724993/SLT_OBJ2_SoilSensors_2018_InstallationMethods.csv | reason=count rows in raw held-out file
- 2026-06-30T15:56:34-07:00 | action=read | subject=/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-61a0ecd70856892-20230808T205724993/SLT_OBJ2_SoilSensors_2018_data.csv first 8 lines | reason=inspect raw held-out CSV structure
- 2026-06-30T15:56:34-07:00 | action=command | subject=wc -l /h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-61a0ecd70856892-20230808T205724993/SLT_OBJ2_SoilSensors_2018_data.csv | reason=count rows in raw held-out file
- 2026-06-30T15:56:34-07:00 | action=read | subject=/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-61a0ecd70856892-20230808T205724993/SLT_OBJ2_SoilSensors_2019_InstallationMethods.csv first 8 lines | reason=inspect raw held-out CSV structure
- 2026-06-30T15:56:34-07:00 | action=command | subject=wc -l /h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-61a0ecd70856892-20230808T205724993/SLT_OBJ2_SoilSensors_2019_InstallationMethods.csv | reason=count rows in raw held-out file
- 2026-06-30T15:56:34-07:00 | action=read | subject=/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-61a0ecd70856892-20230808T205724993/SLT_OBJ2_SoilSensors_2019_data.csv first 8 lines | reason=inspect raw held-out CSV structure
- 2026-06-30T15:56:34-07:00 | action=command | subject=wc -l /h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-61a0ecd70856892-20230808T205724993/SLT_OBJ2_SoilSensors_2019_data.csv | reason=count rows in raw held-out file
- 2026-06-30T15:56:34-07:00 | action=read | subject=/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-61a0ecd70856892-20230808T205724993/SLT_OBJ2_SoilSensors_2020_InstallationMethods.csv first 8 lines | reason=inspect raw held-out CSV structure
- 2026-06-30T15:56:34-07:00 | action=command | subject=wc -l /h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-61a0ecd70856892-20230808T205724993/SLT_OBJ2_SoilSensors_2020_InstallationMethods.csv | reason=count rows in raw held-out file
- 2026-06-30T15:56:34-07:00 | action=read | subject=/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-61a0ecd70856892-20230808T205724993/SLT_OBJ2_SoilSensors_2020_data.csv first 8 lines | reason=inspect raw held-out CSV structure
- 2026-06-30T15:56:34-07:00 | action=command | subject=wc -l /h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-61a0ecd70856892-20230808T205724993/SLT_OBJ2_SoilSensors_2020_data.csv | reason=count rows in raw held-out file
- 2026-06-30T15:56:34-07:00 | action=read | subject=/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-61a0ecd70856892-20230808T205724993/SLT_OBJ2_SoilSensors_2021_InstallationMethods.csv first 8 lines | reason=inspect raw held-out CSV structure
- 2026-06-30T15:56:34-07:00 | action=command | subject=wc -l /h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-61a0ecd70856892-20230808T205724993/SLT_OBJ2_SoilSensors_2021_InstallationMethods.csv | reason=count rows in raw held-out file
- 2026-06-30T15:56:34-07:00 | action=read | subject=/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-61a0ecd70856892-20230808T205724993/SLT_OBJ2_SoilSensors_2021_data.csv first 8 lines | reason=inspect raw held-out CSV structure
- 2026-06-30T15:56:34-07:00 | action=command | subject=wc -l /h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-61a0ecd70856892-20230808T205724993/SLT_OBJ2_SoilSensors_2021_data.csv | reason=count rows in raw held-out file
- 2026-06-30T15:56:57-07:00 | action=command | subject=search fold-local exemplar scripts for wide soil moisture patterns | reason=choose structurally relevant exemplar code without leaving fold sandbox
- 2026-06-30T15:56:57-07:00 | action=search | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-06-holdout-8/data/gold/expert_code/harmonize_sm | reason=find allowed examples containing melt or soil moisture wide columns
- 2026-06-30T15:57:09-07:00 | action=command | subject=read selected fold-local wide-format exemplar scripts | reason=reuse allowed implementation patterns for held-out harmonizer
- 2026-06-30T15:57:09-07:00 | action=read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-06-holdout-8/data/gold/expert_code/harmonize_sm/dataset_01.py | reason=selected allowed exemplar script for wide-to-long harmonization pattern
- 2026-06-30T15:57:09-07:00 | action=read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-06-holdout-8/data/gold/expert_code/harmonize_sm/dataset_02.py | reason=selected allowed exemplar script for wide-to-long harmonization pattern
- 2026-06-30T15:57:09-07:00 | action=read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-06-holdout-8/data/gold/expert_code/harmonize_sm/dataset_24.py | reason=selected allowed exemplar script for wide-to-long harmonization pattern
- 2026-06-30T15:57:09-07:00 | action=read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-06-holdout-8/data/gold/expert_code/harmonize_sm/dataset_27.py | reason=selected allowed exemplar script for wide-to-long harmonization pattern
- 2026-06-30T15:57:19-07:00 | action=command | subject=curl -sS https://api.ess-dive.lbl.gov/packages/ess-dive-61a0ecd70856892-20230808T205724993 | reason=retrieve public package metadata because fold-local cache is absent
- 2026-06-30T15:57:31-07:00 | action=command | subject=curl -sS https://api.ess-dive.lbl.gov/packages/ess-dive-61a0ecd70856892-20230808T205724993 | reason=retry public package metadata retrieval after sandbox DNS failure
- 2026-06-30T15:57:50-07:00 | action=command | subject=python profile raw held-out CSVs | reason=verify columns, depth patterns, sentinels, intervals, and coordinates
- 2026-06-30T15:57:51.395802-07:00 | action=read | subject=/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-61a0ecd70856892-20230808T205724993/SLT_OBJ2_SoilSensors_2018_InstallationMethods.csv | reason=profile raw held-out CSV with pandas
- 2026-06-30T15:57:51.402352-07:00 | action=read | subject=/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-61a0ecd70856892-20230808T205724993/SLT_OBJ2_SoilSensors_2018_data.csv | reason=profile raw held-out CSV with pandas
- 2026-06-30T15:57:51.417475-07:00 | action=read | subject=/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-61a0ecd70856892-20230808T205724993/SLT_OBJ2_SoilSensors_2019_InstallationMethods.csv | reason=profile raw held-out CSV with pandas
- 2026-06-30T15:57:51.423217-07:00 | action=read | subject=/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-61a0ecd70856892-20230808T205724993/SLT_OBJ2_SoilSensors_2019_data.csv | reason=profile raw held-out CSV with pandas
- 2026-06-30T15:57:51.498040-07:00 | action=read | subject=/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-61a0ecd70856892-20230808T205724993/SLT_OBJ2_SoilSensors_2020_InstallationMethods.csv | reason=profile raw held-out CSV with pandas
- 2026-06-30T15:57:51.502806-07:00 | action=read | subject=/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-61a0ecd70856892-20230808T205724993/SLT_OBJ2_SoilSensors_2020_data.csv | reason=profile raw held-out CSV with pandas
- 2026-06-30T15:57:51.552658-07:00 | action=read | subject=/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-61a0ecd70856892-20230808T205724993/SLT_OBJ2_SoilSensors_2021_InstallationMethods.csv | reason=profile raw held-out CSV with pandas
- 2026-06-30T15:57:51.557056-07:00 | action=read | subject=/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-61a0ecd70856892-20230808T205724993/SLT_OBJ2_SoilSensors_2021_data.csv | reason=profile raw held-out CSV with pandas
- 2026-06-30T15:59:39-07:00 | action=command | subject=generate curator_bundle.json mapping.json mapping_notes.md harmonize_heldout.py | reason=write required benchmark outputs from inspected allowed inputs
- 2026-06-30T15:59:39.361929-07:00 | action=write | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-06-holdout-8/agent_outputs/curator_bundle.json | reason=write required benchmark artifact
- 2026-06-30T15:59:39.362336-07:00 | action=write | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-06-holdout-8/agent_outputs/mapping.json | reason=write required benchmark artifact
- 2026-06-30T15:59:39.362603-07:00 | action=write | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-06-holdout-8/agent_outputs/mapping_notes.md | reason=write required benchmark artifact
- 2026-06-30T15:59:39.362764-07:00 | action=write | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-06-holdout-8/agent_outputs/harmonize_heldout.py | reason=write required benchmark artifact
- 2026-06-30T15:59:46-07:00 | action=command | subject=python /scratch/jmc/data-harmonization-eval/.runs/fold-06-holdout-8/agent_outputs/harmonize_heldout.py | reason=run required harmonization script to produce heldout_harmonized.csv
- 2026-06-30T15:59:47.365101-07:00 | action=read | subject=/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-61a0ecd70856892-20230808T205724993/SLT_OBJ2_SoilSensors_2018_data.csv | reason=read raw held-out data payload for harmonization
- 2026-06-30T15:59:47.695558-07:00 | action=read | subject=/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-61a0ecd70856892-20230808T205724993/SLT_OBJ2_SoilSensors_2019_data.csv | reason=read raw held-out data payload for harmonization
- 2026-06-30T15:59:48.309096-07:00 | action=read | subject=/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-61a0ecd70856892-20230808T205724993/SLT_OBJ2_SoilSensors_2020_data.csv | reason=read raw held-out data payload for harmonization
- 2026-06-30T15:59:49.150184-07:00 | action=read | subject=/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-61a0ecd70856892-20230808T205724993/SLT_OBJ2_SoilSensors_2021_data.csv | reason=read raw held-out data payload for harmonization
- 2026-06-30T15:59:49.593905-07:00 | action=write | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-06-holdout-8/agent_outputs/heldout_harmonized.csv | reason=write required held-out harmonized CSV
- 2026-06-30T16:00:18-07:00 | action=command | subject=validate generated benchmark outputs and scan action log | reason=confirm required artifacts, schema, row count, and anti-leakage compliance
- 2026-06-30T16:00:18-07:00 | action=list | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-06-holdout-8/agent_outputs | reason=list final output artifacts
- 2026-06-30T16:00:18.685329-07:00 | action=read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-06-holdout-8/agent_outputs/curator_bundle.json | reason=validate required JSON artifact
- 2026-06-30T16:00:18.685508-07:00 | action=read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-06-holdout-8/agent_outputs/mapping.json | reason=validate required JSON artifact
- 2026-06-30T16:00:18.685640-07:00 | action=read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-06-holdout-8/agent_outputs/heldout_harmonized.csv | reason=validate held-out harmonized CSV schema and row count
- 2026-06-30T16:00:18.859573-07:00 | action=read | subject=/scratch/jmc/data-harmonization-eval/.runs/fold-06-holdout-8/AGENT_ACTION_LOG.md | reason=scan mandatory trace for forbidden path patterns
10 changes: 10 additions & 0 deletions evaluations/fold-06-holdout-8/AGENT_INSTRUCTIONS.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,10 @@
# Run environment — leave-one-cluster-out

Harmonize the held-out dataset(s) below using ONLY:
- the skills in `skills/`,
- the exemplars in `data/processed/.../sm_data_harmonization_mapping.json` and the code patterns in `data/gold/expert_code/harmonize_sm/` (both have the held-out cluster removed),
- the shared raw inputs under `~/ess-dive_wfsfa_soil_datasets/` and the cached metadata under `data/external/ess-dive_meta/`.

Do NOT look up the held-out dataset's existing harmonized output, expert code, or mapping entry from any other location. The held-out datasets are:

- `ess-dive-61a0ecd70856892-20230808T205724993`
52 changes: 52 additions & 0 deletions evaluations/fold-06-holdout-8/EVALUATION.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,52 @@
# fold-06-holdout-8 Agent Evaluation

## Scope

This directory records one sandboxed sub-agent attempt for held-out dataset indices `[8]`.

- Sandbox: `.runs/fold-06-holdout-8`
- Tracked artifact copy: `evaluations/fold-06-holdout-8`
- Successful agent trace: `AGENT_ACTION_LOG.md`

## Anti-Leakage Audit

The successful trace was scanned for root gold data, root processed data, other fold sandboxes, held-out expert module names, and explicit `violation` markers. Result: `0` matches.

## Output Equivalence Against Gold

| Metric | Agent | Gold |
| --- | ---: | ---: |
| Rows | 195,524 | 195,446 |
| Target columns present | 9 / 9 | 9 / 9 |
| Schema exact match | true | n/a |
| Unique keyed rows recovered | 194,255 | 195,438 |
| Missing gold keyed rows | 1,183 | n/a |
| Extra agent keyed rows | 1,269 | n/a |
| Row precision | 0.994 | n/a |
| Gold recall | 0.994 | n/a |

Shared-row value matches after key merge:

| Column | Matched rows |
| --- | ---: |
| `interval_min` | 194247/194263 |
| `volumetric_water_content_m3_m3` | 191225/194263 |
| `gravimetric_water_content_gH2O_gs` | 194263/194263 |
| `water_potential_kPa` | 178229/194263 |
| `is_timeseries` | 194263/194263 |

## JSON Mapping Match

- Summary: `{"extra_agent_categories": [], "field_exact_matches_by_name": {"destination_variable": "8/8", "source_files": "6/8", "source_pattern": "4/8", "transformation": "0/8", "unit_conversion": "6/8"}, "field_level_exact_matches": "24/40", "gold_mapping_categories_present": "8/8", "missing_gold_categories": [], "top_level_exact_matches": "6/7", "top_level_matches": {"archive_repository": true, "data_payload_files": true, "dataset_identifier": true, "doi": true, "index": true, "location_metadata_files": true, "sensor_metadata_files": false}}`

| Field | Exact matches |
| --- | ---: |
| `destination_variable` | 8/8 |
| `source_pattern` | 4/8 |
| `source_files` | 6/8 |
| `transformation` | 0/8 |
| `unit_conversion` | 6/8 |

## Overall Assessment

See `evaluation_metrics.json` for machine-readable details. The run passed the targeted local no-gold path audit. Output equivalence should be interpreted with the key policy recorded in the metrics (`key_includes_dataset_index=False`).
35 changes: 35 additions & 0 deletions evaluations/fold-06-holdout-8/MANIFEST.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,35 @@
{
"name": "fold-06-holdout-8",
"holdout_indices": [
8
],
"holdout_identifiers": [
"ess-dive-61a0ecd70856892-20230808T205724993"
],
"exemplar_indices": [
1,
2,
3,
4,
5,
6,
7,
9,
10,
15,
16,
17,
18,
23,
24,
25,
26,
27
],
"n_exemplars": 27,
"sources": {
"package": "data/gold/expert_code/harmonize_sm",
"mapping": "data/gold/sm_data_harmonization_mapping.json",
"skills": "skills"
}
}
Loading
Loading