[codex] add fold03 agent evaluation bundle

evaluations/fold-03-holdout-4/AGENT_ACTION_LOG.failed-write-location.md

@@ -0,0 +1,50 @@
+2026-06-30T14:54:03-07:00 | shell_command | command=initialize\ AGENT_ACTION_LOG.md\ in\ sandbox | reason=create required action log before any inspection
+2026-06-30T14:54:03-07:00 | outcome | exit_status=0 | created action log
+2026-06-30T14:54:18-07:00 | shell_command | command=sed\ -n\ \'1\,240p\'\ AGENT_INSTRUCTIONS.md\ \&\&\ sed\ -n\ \'1\,240p\'\ MANIFEST.json | reason=read sandbox instructions and manifest
+2026-06-30T14:54:18-07:00 | outcome | exit_status=0 | read AGENT_INSTRUCTIONS.md and MANIFEST.json
+2026-06-30T14:54:28-07:00 | shell_command | command=find\ skills\ -maxdepth\ 4\ -type\ f\ \|\ sort\ \&\&\ find\ data\ -maxdepth\ 6\ -type\ f\ \|\ sort | reason=list sandbox-local skills and exemplar files
+2026-06-30T14:54:28-07:00 | outcome | exit_status=0 | listed sandbox skills and data files
+2026-06-30T14:54:38-07:00 | shell_command | command=sed\ -n\ \'1\,260p\'\ skills/essdive_sm_curator/SKILL.md\ \&\&\ sed\ -n\ \'1\,260p\'\ skills/essdive_sm_harmonizer/SKILL.md\ \&\&\ sed\ -n\ \'1\,260p\'\ skills/essdive_sm_harmonizer/soilmoisture_harmonization_general_insights.md | reason=read sandbox-local curator and harmonizer skill instructions
+2026-06-30T14:54:38-07:00 | outcome | exit_status=0 | read skill instructions and harmonization insights
+2026-06-30T14:54:44-07:00 | shell_command | command=sed\ -n\ \'261\,520p\'\ skills/essdive_sm_harmonizer/SKILL.md | reason=read remaining harmonizer skill instructions
+2026-06-30T14:54:44-07:00 | outcome | exit_status=0 | read remaining harmonizer skill instructions
+2026-06-30T14:54:50-07:00 | shell_command | command=sed\ -n\ \'521\,760p\'\ skills/essdive_sm_harmonizer/SKILL.md | reason=read final harmonizer skill instructions
+2026-06-30T14:54:50-07:00 | outcome | exit_status=0 | read final harmonizer skill instructions
+2026-06-30T14:55:01-07:00 | shell_command | command=python\ -c\ \'import\ json\;\ p=\"data/processed/ess-dive_wfsfa_soil_datasets/sm_data_harmonization_mapping.json\"\;\ data=json.load\(open\(p\)\)\;\ print\(type\(data\).__name__\,\ len\(data\)\)\;\ \[print\(e.get\(\"index\"\)\,\ e.get\(\"dataset_identifier\"\)\,\ e.get\(\"data_payload_files\"\)\,\ e.get\(\"location_metadata_files\"\)\)\ for\ e\ in\ data\]\' | reason=inspect fold-local mapping entries for schema examples and exemplar identifiers
+2026-06-30T14:55:01-07:00 | outcome | exit_status=0 | inspected fold-local mapping summary
+2026-06-30T14:55:10-07:00 | shell_command | command=find\ \'/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-6c7085e9c544cc6-20250424T164534831\'\ -maxdepth\ 4\ -type\ f\ \|\ sort | reason=list files in allowed held-out raw package only
+2026-06-30T14:55:10-07:00 | outcome | exit_status=0 | listed held-out raw package files
+2026-06-30T14:55:18-07:00 | shell_command | command=find\ data/external\ -maxdepth\ 3\ -type\ f\ \|\ sort | reason=check sandbox-local cached ESS-DIVE metadata availability
+2026-06-30T14:55:18-07:00 | outcome | exit_status=0 | checked sandbox-local cached metadata
+2026-06-30T14:55:31-07:00 | shell_command | command=sed\ -n\ \'1\,220p\'\ \'/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-6c7085e9c544cc6-20250424T164534831/Johnsen_Bi_2025_DAE_Manuscript_Data_Package/README.txt\'\ \&\&\ python\ -c\ \'import\ pandas\ as\ pd\,\ pathlib\;\ base=pathlib.Path\(\"\'/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-6c7085e9c544cc6-20250424T164534831/Johnsen_Bi_2025_DAE_Manuscript_Data_Package\'\"\)\;\ files=\[\"flmd.csv\"\,\"df_data_dd.csv\"\,\"df_meta_dd.csv\"\,\"df_meta.csv\"\,\"df_data.csv\"\]\;\\nfor\ f\ in\ files:\\n\ \ \ \ p=base/f\;\ print\(\"\\n###\"\,\ f\)\;\ df=pd.read_csv\(p\,\ nrows=8\)\;\ print\(\"shape_sample\"\,\ df.shape\)\;\ print\(\"columns\"\,\ list\(df.columns\)\)\;\ print\(df.head\(8\).to_string\(index=False\)\)\' | reason=read README and preview raw CSV/dictionary files for held-out package
+2026-06-30T14:55:31-07:00 | outcome | exit_status=1 | previewed README and raw CSV/dictionary files
+2026-06-30T14:55:43-07:00 | shell_command | command=python\ -c\ \'import\ pandas\ as\ pd\,\ pathlib\;\ base=pathlib.Path\(\"\'/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-6c7085e9c544cc6-20250424T164534831/Johnsen_Bi_2025_DAE_Manuscript_Data_Package\'\"\)\;\ files=\[\"flmd.csv\"\,\"df_data_dd.csv\"\,\"df_meta_dd.csv\"\,\"df_meta.csv\"\,\"df_data.csv\"\]\;\ \[\ \(print\(\"\\n###\"\,\ f\)\,\ \(lambda\ df:\ \(print\(\"sample_shape\"\,\ df.shape\)\,\ print\(\"columns\"\,\ list\(df.columns\)\)\,\ print\(df.head\(8\).to_string\(index=False\)\)\)\)\(pd.read_csv\(base/f\,\ nrows=8\)\)\)\ for\ f\ in\ files\ \]\' | reason=preview held-out raw CSV and data dictionary files after prior quoting failure
+2026-06-30T14:55:44-07:00 | outcome | exit_status=0 | previewed held-out raw CSV and dictionary files
+2026-06-30T14:55:57-07:00 | shell_command | command=sed\ -n\ \'1\,260p\'\ data/gold/expert_code/harmonize_sm/common.py\ \&\&\ sed\ -n\ \'1\,220p\'\ data/gold/expert_code/harmonize_sm/dataset_03.py\ \&\&\ sed\ -n\ \'1\,220p\'\ data/gold/expert_code/harmonize_sm/dataset_05.py\ \&\&\ sed\ -n\ \'1\,220p\'\ data/gold/expert_code/harmonize_sm/dataset_10.py | reason=read sandbox exemplar harmonizer code patterns for common helpers and similar soil moisture/potential datasets
+2026-06-30T14:55:57-07:00 | outcome | exit_status=0 | read exemplar harmonizer code patterns
+2026-06-30T14:56:11-07:00 | shell_command | command=python\ -c\ \'import\ pandas\ as\ pd\,\ pathlib\;\ base=pathlib.Path\(\"\'/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-6c7085e9c544cc6-20250424T164534831/Johnsen_Bi_2025_DAE_Manuscript_Data_Package\'\"\)\;\\nprint\(\"df_data_dd\"\)\;\ print\(pd.read_csv\(base/\"df_data_dd.csv\"\).to_string\(index=False\)\)\;\\nprint\(\"\\ndf_meta_dd\"\)\;\ print\(pd.read_csv\(base/\"df_meta_dd.csv\"\).to_string\(index=False\)\)\;\\nmeta=pd.read_csv\(base/\"df_meta.csv\"\)\;\ data=pd.read_csv\(base/\"df_data.csv\"\)\;\\nprint\(\"\\nrow_counts\"\,\ len\(meta\)\,\ len\(data\)\)\;\ print\(\"sites\"\,\ sorted\(meta\[\"site\"\].dropna\(\).unique\(\).tolist\(\)\)\)\;\ print\(\"date_min_max\"\,\ meta\[\"datetime\"\].min\(\)\,\ meta\[\"datetime\"\].max\(\)\)\;\ print\(\"data_nonnull\"\,\ data\[\[\"swc\"\,\"swp\"\,\"ET\"\]\].notna\(\).sum\(\).to_dict\(\)\)\;\ print\(\"duplicate_site_date\"\,\ int\(meta.duplicated\(\[\"site\"\,\"datetime\"\]\).sum\(\)\)\)\' | reason=read full data dictionaries and basic row alignment stats for held-out package
+2026-06-30T14:56:11-07:00 | outcome | exit_status=1 | inspected dictionaries and held-out row alignment
+2026-06-30T14:56:29-07:00 | shell_command | command=python\ -c\ \'import\ pandas\ as\ pd\,\ pathlib\;\ base=pathlib.Path\(\"\'/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-6c7085e9c544cc6-20250424T164534831/Johnsen_Bi_2025_DAE_Manuscript_Data_Package\'\"\)\;\ print\(\"df_data_dd\"\)\;\ print\(pd.read_csv\(base/\"df_data_dd.csv\"\).to_string\(index=False\)\)\;\ print\(\"\\ndf_meta_dd\"\)\;\ print\(pd.read_csv\(base/\"df_meta_dd.csv\"\).to_string\(index=False\)\)\;\ meta=pd.read_csv\(base/\"df_meta.csv\"\)\;\ data=pd.read_csv\(base/\"df_data.csv\"\)\;\ print\(\"\\nrow_counts\"\,\ len\(meta\)\,\ len\(data\)\)\;\ print\(\"sites\"\,\ sorted\(meta\[\"site\"\].dropna\(\).unique\(\).tolist\(\)\)\)\;\ print\(\"date_min_max\"\,\ meta\[\"datetime\"\].min\(\)\,\ meta\[\"datetime\"\].max\(\)\)\;\ print\(\"data_nonnull\"\,\ data\[\[\"swc\"\,\"swp\"\,\"ET\"\]\].notna\(\).sum\(\).to_dict\(\)\)\;\ print\(\"duplicate_site_date\"\,\ int\(meta.duplicated\(\[\"site\"\,\"datetime\"\]\).sum\(\)\)\)\' | reason=read full data dictionaries and basic row alignment stats for held-out package
+2026-06-30T14:56:29-07:00 | outcome | exit_status=0 | inspected dictionaries and held-out row alignment
+2026-06-30T14:56:50-07:00 | shell_command | command=python\ -c\ \'import\ pandas\ as\ pd\;\ p=\"\'/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive_b924ba040ecefee_20250707T154402200/data/East_Taylor_Watershed_Community_Observatory_Sites___Point_Locations__Surface_v3_2_20250327.csv\'\"\;\ df=pd.read_csv\(p\)\;\ print\(\"columns\"\,\ list\(df.columns\)\)\;\ print\(\"rows\"\,\ len\(df\)\)\;\ sites=\[\"ph1\"\,\"ph2\"\,\"sg5\"\,\"tb\"\,\"PHS1\"\,\"PHS2\"\,\"SG-EHS5\"\,\"TB\"\]\;\ mask=df.astype\(str\).apply\(lambda\ col:\ col.str.contains\(\"ph1\|ph2\|sg5\|tb\|PHS1\|PHS2\|SG-EHS5\|TB\"\,\ case=False\,\ na=False\)\).any\(axis=1\)\;\ print\(df.loc\[mask\].head\(40\).to_string\(index=False\)\)\' | reason=read shared raw location-reference CSV allowed by sandbox mapping entry 0 to resolve held-out site coordinates
+2026-06-30T14:56:50-07:00 | outcome | exit_status=0 | inspected shared location-reference rows for held-out site abbreviations
+2026-06-30T14:57:02-07:00 | shell_command | command=rg\ -n\ --ignore-case\ \'ph1\|ph2\|sg5\|tb\|pumphouse\|snodgrass\|taylor\'\ \'/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-6c7085e9c544cc6-20250424T164534831/Johnsen_Bi_2025_DAE_Manuscript_Data_Package/README.txt\'\ \'/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-6c7085e9c544cc6-20250424T164534831/Johnsen_Bi_2025_DAE_Manuscript_Data_Package/methods.py\'\ \'/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-6c7085e9c544cc6-20250424T164534831/Johnsen_Bi_2025_DAE_Manuscript_Data_Package/DAE_train.ipynb\'\ \'/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-6c7085e9c544cc6-20250424T164534831/Johnsen_Bi_2025_DAE_Manuscript_Data_Package/DAE_predict.ipynb\'\ \'/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-6c7085e9c544cc6-20250424T164534831/Johnsen_Bi_2025_DAE_Manuscript_Data_Package/ET_train.ipynb\'\ \'/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-6c7085e9c544cc6-20250424T164534831/Johnsen_Bi_2025_DAE_Manuscript_Data_Package/ET_predict.ipynb\' | reason=search held-out raw documentation/code for site abbreviation meanings
+2026-06-30T14:57:02-07:00 | outcome | exit_status=0 | searched held-out files for site abbreviation meanings
+2026-06-30T14:57:15-07:00 | shell_command | command=python\ -c\ \'import\ json\,\ pathlib\;\ base=pathlib.Path\(\"\'/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-6c7085e9c544cc6-20250424T164534831/Johnsen_Bi_2025_DAE_Manuscript_Data_Package\'\"\)\;\ files=\[\"DAE_train.ipynb\"\,\"DAE_predict.ipynb\"\,\"ET_train.ipynb\"\,\"ET_predict.ipynb\"\]\;\\nfor\ fn\ in\ files:\ nb=json.load\(open\(base/fn\)\)\;\\n\ for\ i\,c\ in\ enumerate\(nb.get\(\"cells\"\,\[\]\)\):\\n\ \ src=\"\".join\(c.get\(\"source\"\,\[\]\)\)\;\\n\ \ if\ \"if\ site\ in\ \[\\\\\'ph1\\\\\'\,\ \\\\\'ph2\\\\\'\,\ \\\\\'sg5\\\\\'\]\"\ in\ src\ or\ \"if\ site\ in\ \[\\\\\'tb\\\\\'\]\"\ in\ src:\ print\(\"###\"\,\ fn\,\ \"cell\"\,\ i\)\;\ print\(src\[:3000\]\)\' | reason=extract held-out notebook code cells that define site-specific behavior
+2026-06-30T14:57:15-07:00 | outcome | exit_status=1 | extracted relevant notebook code cells
+2026-06-30T14:57:28-07:00 | shell_command | command=python\ -c\ \'import\ json\,\ pathlib\;\ base=pathlib.Path\(\"\'/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive-6c7085e9c544cc6-20250424T164534831/Johnsen_Bi_2025_DAE_Manuscript_Data_Package\'\"\)\;\ files=\[\"DAE_train.ipynb\"\,\"DAE_predict.ipynb\"\,\"ET_train.ipynb\"\,\"ET_predict.ipynb\"\]\;\ \[\(print\(\"###\"\,\ fn\,\ \"cell\"\,\ i\)\,\ print\(src\[:3000\]\)\)\ for\ fn\ in\ files\ for\ i\,c\ in\ enumerate\(json.load\(open\(base/fn\)\).get\(\"cells\"\,\ \[\]\)\)\ for\ src\ in\ \[\"\".join\(c.get\(\"source\"\,\ \[\]\)\)\]\ if\ \(\"if\ site\ in\"\ in\ src\ and\ \(\"ph1\"\ in\ src\ or\ \"tb\"\ in\ src\)\)\]\' | reason=extract held-out notebook code cells that define site-specific behavior after prior quoting failure
+2026-06-30T14:57:28-07:00 | outcome | exit_status=0 | extracted relevant notebook code cells
+2026-06-30T14:57:41-07:00 | shell_command | command=python\ -c\ \'import\ pandas\ as\ pd\;\ df=pd.read_csv\(\"\'/h/jmc/ess-dive_wfsfa_soil_datasets/ess-dive_b924ba040ecefee_20250707T154402200/data/East_Taylor_Watershed_Community_Observatory_Sites___Point_Locations__Surface_v3_2_20250327.csv\'\"\)\;\ cols=\[\"Location_ID\"\,\"Location_Name\"\,\"Location_Alias\"\,\"Geographic_Region\"\,\"Parent_Location_ID\"\,\"Latitude\"\,\"Longitude\"\,\"Variables_Measured\"\,\"Description\"\]\;\ mask=df\[\"Location_ID\"\].astype\(str\).str.contains\(\"TB\|TBA\|TAYLOR\|Taylor\|tb\"\,\ case=False\,\ na=False\)\ \|\ df\[\"Location_Name\"\].astype\(str\).str.contains\(\"Taylor\|TB\|TBA\|tower\"\,\ case=False\,\ na=False\)\ \|\ df\[\"Location_Alias\"\].astype\(str\).str.contains\(\"\^tb\$\|TB\|TBA\"\,\ case=False\,\ na=False\)\;\ print\(df.loc\[mask\,\ cols\].head\(120\).to_string\(index=False\)\)\' | reason=search shared location-reference CSV for possible tb site coordinate match
+2026-06-30T14:57:42-07:00 | outcome | exit_status=0 | searched shared location-reference for tb candidates
+2026-06-30T14:58:19-07:00 | shell_command | command=mkdir\ -p\ agent_outputs | reason=create sandbox output directory
+2026-06-30T14:58:19-07:00 | outcome | exit_status=0 | created agent_outputs directory if absent
+2026-06-30T14:58:30-07:00 | shell_command | command=printf\ \'%s\ \|\ output_file_modify\ \|\ paths=%s\ \|\ reason=%s\\n\'\ \"2026-06-30T14:58:30-07:00\"\ \"agent_outputs/harmonize_heldout.py\,\ agent_outputs/mapping.json\,\ agent_outputs/mapping_notes.md\"\ \"prepare\ to\ create\ pilot\ harmonization\ script\ and\ mapping\ documentation\"\ \>\>\ AGENT_ACTION_LOG.md | reason=log upcoming output file creation before apply_patch edits
+2026-06-30T14:58:30-07:00 | output_file_modify | paths=agent_outputs/harmonize_heldout.py, agent_outputs/mapping.json, agent_outputs/mapping_notes.md | reason=prepare to create pilot harmonization script and mapping documentation
+2026-06-30T14:58:30-07:00 | outcome | exit_status=0 | logged upcoming output file creation
+2026-06-30T14:59:30-07:00 | shell_command | command=printf\ \'%s\ \|\ output_file_modify\ \|\ paths=%s\ \|\ reason=%s\\n\'\ \"2026-06-30T14:59:30-07:00\"\ \"agent_outputs/harmonize_heldout.py\,\ agent_outputs/mapping.json\,\ agent_outputs/mapping_notes.md\"\ \"created\ pilot\ harmonization\ script\ and\ mapping\ documentation\ via\ apply_patch\"\ \>\>\ AGENT_ACTION_LOG.md | reason=log completed output file creation after apply_patch edits
+2026-06-30T14:59:30-07:00 | output_file_modify | paths=agent_outputs/harmonize_heldout.py, agent_outputs/mapping.json, agent_outputs/mapping_notes.md | reason=created pilot harmonization script and mapping documentation via apply_patch
+2026-06-30T14:59:30-07:00 | outcome | exit_status=0 | logged completed output file creation
+2026-06-30T14:59:37-07:00 | shell_command | command=python\ agent_outputs/harmonize_heldout.py | reason=run pilot harmonization script to generate output CSVs
+2026-06-30T14:59:37-07:00 | output_file_modify | paths=agent_outputs/heldout_harmonized.csv, agent_outputs/heldout_locations.csv | reason=script is expected to write generated output CSVs
+2026-06-30T14:59:37-07:00 | outcome | exit_status=2 | ran pilot harmonization script
+2026-06-30T14:59:53-07:00 | violation | paths=/scratch/jmc/data-harmonization-eval/agent_outputs/harmonize_heldout.py, /scratch/jmc/data-harmonization-eval/agent_outputs/mapping.json, /scratch/jmc/data-harmonization-eval/agent_outputs/mapping_notes.md | reason=apply_patch created output files outside the fold sandbox; stopping immediately per anti-leak rule