build!: define in pyproject.toml

.github/workflows/backend_checks.yml

@@ -7,8 +7,8 @@ jobs:
     strategy:
       fail-fast: false
     steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
         with:
           python-version: 3.11
 
@@ -18,7 +18,7 @@ jobs:
     name: lint
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v3
 
       - name: black
         uses: psf/black@stable

.gitignore

@@ -179,5 +179,5 @@ frontend/node_modules
 node_modules/
 
 # Data
-server/curfu/data
+server/src/curfu/data
 client/node_modules

server/pyproject.toml

@@ -1,6 +1,69 @@
+[project]
+name = "curfu"
+authors = [
+    {name = "Wagner Lab"},
+]
+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("{{ cookiecutter.project_slug }}")
+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",