[workspace]
name = "bttoxin-pipeline"
channels = ["conda-forge", "bioconda", "bioconda/label/cf201901"]
platforms = ["linux-64"]
version = "0.1.0"
channel-priority = "disabled"

# =========================
# digger 环境：bioconda 依赖
# =========================
[feature.digger.dependencies]
bttoxin_digger = "==1.0.10"
perl = "==5.26.2"
perl-file-tee = "==0.07"
perl-list-util = "==1.38"
blast = "==2.16.0"

# =========================
# pipeline 环境：Python 分析依赖
# =========================
[feature.pipeline.dependencies]
python = ">=3.9"
pandas = ">=2.0.0"
matplotlib = ">=3.7.0"
seaborn = ">=0.12.2"

# =========================
# frontend 环境：Node.js 前端依赖
# =========================
[feature.frontend.dependencies]
nodejs = ">=20"
pnpm = ">=10"

# =========================
# webbackend 环境：FastAPI 后端依赖
# =========================
[feature.webbackend.dependencies]
python = ">=3.11"
fastapi = "*"
uvicorn = "*"
pydantic = "*"
pydantic-settings = "*"
python-dotenv = "*"
httpx = "*"
pytest = "*"

# =========================
# 环境定义
# =========================
[environments]
digger = ["digger"]
pipeline = ["pipeline"]
frontend = ["frontend"]
webbackend = ["webbackend"]

# =========================
# pixi tasks
# =========================
[feature.pipeline.tasks]
# 完整 pipeline（三阶段）
pipeline = "python scripts/run_single_fna_pipeline.py"
# 单独阶段
digger-only = "python scripts/run_digger_stage.py"
shotter = "python scripts/bttoxin_shoter.py"
plot = "python scripts/plot_shotter.py"

# =========================
# frontend tasks
# =========================
[feature.frontend.tasks]
fe-install = { cmd = "pnpm install", cwd = "frontend" }
fe-dev = { cmd = "pnpm dev", cwd = "frontend" }
fe-build = { cmd = "pnpm build", cwd = "frontend" }
fe-test = { cmd = "pnpm test:unit --run", cwd = "frontend" }
fe-lint = { cmd = "pnpm lint", cwd = "frontend" }

# =========================
# webbackend tasks
# =========================
[feature.webbackend.tasks]
api-dev = "uvicorn web.backend.main:app --reload --host 0.0.0.0 --port 8000"
api-test = "pytest web/backend/ -v"