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Flatten data/readings/ → data/

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Remove the intermediate readings/ subdirectory level — dataset naming
(synthetic_YYYYMMDD, manual_YYYYMMDD) already encodes what the data is.
Update all path references across scripts and docs accordingly.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
This commit is contained in:
Nathan Schneider
2026-03-20 17:46:23 -06:00
parent 1a80219a25
commit 60e83783ec
533 changed files with 97 additions and 97 deletions
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12
analysis/TEST_COMMANDS.md
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@@ -7,7 +7,7 @@ Run these tests in order to verify the refactored code works correctly.
Test that prompts are generated correctly with protocol context:
```bash
python3 scripts/bicorder_query.py data/readings/synthetic_20251116/protocols_edited.csv 1 --dry-run | head -80
python3 scripts/bicorder_query.py data/synthetic_20251116/protocols_edited.csv 1 --dry-run | head -80
```
**Expected result:**
@@ -21,7 +21,7 @@ python3 scripts/bicorder_query.py data/readings/synthetic_20251116/protocols_edi
Check that the analyze script still creates proper CSV structure:
```bash
python3 scripts/bicorder_analyze.py data/readings/synthetic_20251116/protocols_edited.csv -o test_output.csv
python3 scripts/bicorder_analyze.py data/synthetic_20251116/protocols_edited.csv -o test_output.csv
head -1 test_output.csv | tr ',' '\n' | grep -E "(explicit|precise|elite)" | head -5
```
@@ -76,7 +76,7 @@ llm logs list | grep -i bicorder
Test batch processing on rows 1-3:
```bash
python3 scripts/bicorder_batch.py data/readings/synthetic_20251116/protocols_edited.csv -o test_batch_output.csv --start 1 --end 3 -m gpt-4o-mini
python3 scripts/bicorder_batch.py data/synthetic_20251116/protocols_edited.csv -o test_batch_output.csv --start 1 --end 3 -m gpt-4o-mini
```
**Expected result:**
@@ -106,7 +106,7 @@ with open('test_batch_output.csv') as f:
Test that model parameter works in dry run:
```bash
python3 scripts/bicorder_query.py data/readings/synthetic_20251116/protocols_edited.csv 5 --dry-run -m mistral | head -50
python3 scripts/bicorder_query.py data/synthetic_20251116/protocols_edited.csv 5 --dry-run -m mistral | head -50
```
**Expected result:**
@@ -129,11 +129,11 @@ Compare the new standalone prompts vs old system prompt approach:
```bash
# New approach - protocol context in each prompt
python3 scripts/bicorder_query.py data/readings/synthetic_20251116/protocols_edited.csv 1 --dry-run | grep -A 5 "Analyze this protocol"
python3 scripts/bicorder_query.py data/synthetic_20251116/protocols_edited.csv 1 --dry-run | grep -A 5 "Analyze this protocol"
# Old approach would have had protocol in system prompt only (no longer used)
# Verify that protocol context appears in EVERY gradient prompt
python3 scripts/bicorder_query.py data/readings/synthetic_20251116/protocols_edited.csv 1 --dry-run | grep -c "Analyze this protocol"
python3 scripts/bicorder_query.py data/synthetic_20251116/protocols_edited.csv 1 --dry-run | grep -c "Analyze this protocol"
```
**Expected result:**