build!: define in pyproject.toml (#285)

* use `src/` layout
* define build configs in `pyproject.toml` using `setuptools-scm` rather than `version.py`
* update some associated metadata

.gitignore

@@ -91,7 +91,7 @@ ipython_config.py
 # pyenv
 #   For a library or package, you might want to ignore these files since the code is
 #   intended to run in multiple environments; otherwise, check them in:
-# .python-version
+**/.python-version
 
 # pipenv
 #   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
@@ -176,8 +176,8 @@ yarn-debug.log*
 yarn-error.log*
 frontend/public/
 frontend/node_modules
-node_modules/
+**/node_modules/
+**/.yarn
 
 # Data
-server/curfu/data
-client/node_modules
+server/src/curfu/data

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2021-2022 Alex H. Wagner
+Copyright (c) 2021-2024 Genomic Medicine Lab
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

Procfile

@@ -1 +1 @@
-web: sh -c 'cd ./server/ && gunicorn -k uvicorn.workers.UvicornWorker curfu.main:app --timeout 1000 --log-level debug'
+web: sh -c 'cd ./server/src/ && gunicorn -k uvicorn.workers.UvicornWorker curfu.main:app --timeout 1000 --log-level debug'

server/pyproject.toml

@@ -1,6 +1,73 @@
+[project]
+name = "curfu"
+authors = [
+    {name = "Alex Wagner", email = "[email protected]"},
+    {name = "Kori Kuzma", email = "[email protected]"},
+    {name = "James Stevenson", email = "[email protected]"},
+    {name = "Katie Stahl", email = "[email protected]"},
+    {name = "Jeremy Arbesfeld", email = "[email protected]"}
+]
+readme = "README.md"
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "Intended Audience :: Developers",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+]
+requires-python = ">=3.10"
+description = "Curation tool for gene fusions"
+license = {file = "../LICENSE"}
+dependencies = [
+    "fastapi >= 0.72.0",
+    "aiofiles",
+    "asyncpg",
+    "fusor ~= 0.0.30-dev1",
+    "sqlparse >= 0.4.2",
+    "urllib3 >= 1.26.5",
+    "click",
+    "jinja2",
+    "boto3",
+]
+dynamic = ["version"]
+
+[project.optional-dependencies]
+tests = [
+    "pytest",
+    "pytest-asyncio >= 0.19.0",
+    "pytest-cov",
+    "coverage",
+    "httpx",
+]
+dev = [
+    "psycopg2-binary",
+    "ruff",
+    "black",
+    "pre-commit>=3.7.1",
+    "gene-normalizer ~= 0.1.39",
+    "pydantic-to-typescript",
+]
+
+[project.scripts]
+curfu_devtools = "curfu.cli:devtools"
+curfu = "curfu.cli:serve"
+
 [build-system]
-requires = ["setuptools", "wheel"]
-build-backend = "setuptools.build_meta:__legacy__"
+requires = ["setuptools>=64", "setuptools_scm>=8"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools_scm]
+
+[tool.pytest.ini_options]
+addopts = "--cov=src --cov-report term-missing"
+testpaths = ["tests"]
 
 [tool.black]
 line-length = 88

server/curfu/__init__.py → server/src/curfu/__init__.py

@@ -1,9 +1,15 @@
 """Fusion curation interface."""
 import logging
+from importlib.metadata import PackageNotFoundError, version
 from os import environ
 from pathlib import Path
 
-from .version import __version__
+try:
+    __version__ = version("curfu")
+except PackageNotFoundError:
+    __version__ = "unknown"
+finally:
+    del version, PackageNotFoundError
 
 # provide consistent paths
 APP_ROOT = Path(__file__).resolve().parents[0]

server/curfu/main.py → server/src/curfu/main.py

@@ -7,6 +7,7 @@
 from starlette.templating import _TemplateResponse as TemplateResponse
 
 from curfu import APP_ROOT
+from curfu import __version__ as curfu_version
 from curfu.domain_services import DomainService
 from curfu.gene_services import GeneService
 from curfu.routers import (
@@ -19,7 +20,6 @@
     utilities,
     validate,
 )
-from curfu.version import __version__ as curfu_version
 
 fastapi_app = FastAPI(
     title="Fusion Curation API",

server/curfu/routers/meta.py → server/src/curfu/routers/meta.py

@@ -3,8 +3,8 @@
 from fastapi import APIRouter
 from fusor import __version__ as fusor_version
 
+from curfu import __version__ as curfu_version
 from curfu.schemas import RouteTag, ServiceInfoResponse
-from curfu.version import __version__ as curfu_version
 
 router = APIRouter()