.env.example

# Copy to `.env` in the repo root (loaded automatically by the app and CLI; not committed).
# Shell-exported variables still win over `.env`. Never commit real secrets.

# Slurm defaults (optional). Empty / omitted → partition falls back to "gpu"; no account line in batch scripts.
# SCFMS_SLURM_PARTITION=gpu
# SCFMS_SLURM_ACCOUNT=your_slurm_account
# Hugging Face: required for some gated models (e.g. xTrimo download).
# HF_TOKEN=

# Optional: override default public model repos / URLs (see scripts/download_weights.py).
# GENEFORMER_REPO=ctheodoris/Geneformer
# SCGPT_URL=https://drive.google.com/drive/folders/...
# XTRIMO_REPO=TencentAILabHealthcare/xTrimoGene-356M-Entrez
# TranscriptFormer: which CZI S3 bundle download-weights fetches (tf-sapiens | tf-exemplar | tf-metazoa).
# TRANSCRIPTFORMER_VARIANT=tf-sapiens

# After download-weights, point the app at local checkpoints (or use --env-file .scfms.env).
# GENEFORMER_MODEL=/path/to/repo/models/geneformer
# TRANSCRIPTFORMER_MODEL=/path/to/repo/models/transcriptformer/tf_sapiens
# SCGPT_CKPT_DIR=/path/to/repo/models/scgpt/whole-human

# Restrict which server paths the UI may load (pipe-separated absolute prefixes).
# SCFMS_ALLOWED_PATH_PREFIXES=/scratch/mygroup|/project/shared

# Session folders (plots, session_meta.json): default ``<repo>/.assets/<first path segment>/<timestamp>_…/``.
# Set to use a single directory instead (no .assets grouping):
# SCFMS_SESSION_DIR=/path/to/sessions

# Optional: move job store / reports (defaults under repo).
# SCFMS_JOB_DIR=/path/to/job_store
# SCFMS_SLURM_EMBED_BASE=/path/to/slurm_embeddings
# SCFMS_COMPAT_REPORT_DIR=/path/to/reports

# Weights & Biases (benchmark flows): use `wandb login` or:
# WANDB_API_KEY=

# Embedding token cap for some HF models (optional).
# SCFMS_SCFM_MAX_TOKENS=2048