day-ec_scripts.log

# DAY-EC Conda Environment Script Analysis
# Generated: 2026-02-05
# Updated: 2026-02-05 - Added consistent DAY-EC environment checks to all scripts
# Repository: daylily-ephemeral-cluster

## Implementation Summary

All scripts now use consistent DAY-EC environment checking via:
- **Python scripts**: Import `ensure_dayec` from `bin/helpers/ensure_dayec.py`
- **Bash scripts**: Source `bin/helpers/ensure_dayec.sh` and call `ensure_dayec`

The check logic:
1. Checks if DAY-EC is already active
2. If not active, attempts to activate it
3. If activation fails or environment doesn't exist, provides clear error message and exits

## Scripts Updated with DAY-EC Environment Checks

### Python Scripts (17 scripts)
1. **bin/aws_deets.py** - AWS instance details and metadata
2. **bin/calc_daylily_aws_cost_estimates.py** - AWS cost estimates for genomics
3. **bin/calcuate_spotprice_for_cluster_yaml.py** - Spot price insertion
4. **bin/check_current_spot_market_by_zones.py** - Spot market pricing
5. **bin/check_current_spot_market_by_zones_wcapacity.py** - Spot market with capacity
6. **bin/check_instance_az_presence.py** - Instance AZ presence check
7. **bin/daylily-analysis-samples-to-manifest-new.py** - Sample manifest conversion
8. **bin/daylily-export-fsx-to-s3-from-local** - FSx export to S3
9. **bin/daylily-grant-admin** - Admin privilege management
10. **bin/daylily-run-omics-analysis-headnode** - Launch omics analysis
11. **bin/daylily-stage-samples-from-local-to-headnode** - Stage samples remotely
12. **bin/estimate-daylily-ephemeral-compute-cost.py** - Compute cost estimation
13. **bin/generate-report-of-aws-tagged-resources.py** - Tagged resource reports
14. **bin/helpers/setup_cluster_heartbeat.py** - SNS heartbeat setup
15. **bin/helpers/teardown_cluster_heartbeat.py** - Heartbeat teardown
16. **bin/helpers/watch_cluster_status.py** - Cluster status monitoring

### Bash Scripts (12 scripts)
1. **bin/daylily-cfg-headnode** - Headnode configuration
2. **bin/daylily-create-ephemeral-cluster** - Cluster creation
3. **bin/daylily-delete-ephemeral-cluster** - Cluster deletion
4. **bin/daylily-ensure-sns-permissions** - SNS permissions setup
5. **bin/daylily-export-fsx-to-s3** - FSx export
6. **bin/daylily-iam-smoke-test** - IAM permissions test
7. **bin/daylily-return-fsx-filesystem-for-cluster** - FSx filesystem lookup
8. **bin/daylily-run-ephemeral-cluster-remote-tests** - Remote tests
9. **bin/daylily-ssh-into-headnode** - SSH into headnode
10. **bin/daylily-stage-analysis-samples-headnode** - Stage samples on headnode
11. **bin/daylily-stage-analysis-samples-local-experimental** - Local staging
12. **bin/init_dayec** - DAY-EC environment initialization (special case)

## Helper Modules Created

### bin/helpers/ensure_dayec.py
Python module providing `ensure_dayec(quiet=False)` function.
- Checks `CONDA_DEFAULT_ENV` environment variable
- Provides clear error messages with activation instructions
- Can be imported by any Python script

### bin/helpers/ensure_dayec.sh
Bash function library providing `ensure_dayec` function.
- Sources conda if not available
- Attempts automatic activation if environment exists
- Provides clear error messages with creation/activation instructions
- Can be sourced by any bash script

## Usage

### In Python scripts:
```python
import os
import sys
sys.path.insert(0, os.path.join(os.path.dirname(os.path.abspath(__file__)), "helpers"))
from ensure_dayec import ensure_dayec
ensure_dayec(quiet=True)
```

### In Bash scripts:
```bash
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
source "${SCRIPT_DIR}/helpers/ensure_dayec.sh"
ensure_dayec || exit 1
```

## Key Dependencies Provided by DAY-EC
- Python 3.11
- Bash 5.2.37
- aws-parallelcluster==3.13.2
- awscli==2.22.4
- boto3 (via aws-parallelcluster)
- tabulate, colr, rich
- ruamel.yaml (via dependencies)
- jq, yq, rclone
- daylib (local package, installed in editable mode)

## Commands

Activate DAY-EC:
```bash
conda activate DAY-EC
```

Create DAY-EC if it doesn't exist:
```bash
./bin/init_dayec
```