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build!: define in pyproject.toml #285

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Jul 16, 2024
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8 changes: 4 additions & 4 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -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.
Expand Down Expand Up @@ -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
2 changes: 1 addition & 1 deletion LICENSE
Original file line number Diff line number Diff line change
@@ -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
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2 changes: 1 addition & 1 deletion Procfile
Original file line number Diff line number Diff line change
@@ -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'
2 changes: 0 additions & 2 deletions server/curfu/version.py

This file was deleted.

71 changes: 69 additions & 2 deletions server/pyproject.toml
Original file line number Diff line number Diff line change
@@ -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
Expand Down
50 changes: 0 additions & 50 deletions server/setup.cfg

This file was deleted.

5 changes: 0 additions & 5 deletions server/setup.py

This file was deleted.

8 changes: 7 additions & 1 deletion server/curfu/__init__.py → server/src/curfu/__init__.py
Original file line number Diff line number Diff line change
@@ -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]
Expand Down
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2 changes: 1 addition & 1 deletion server/curfu/main.py → server/src/curfu/main.py
Original file line number Diff line number Diff line change
Expand Up @@ -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 (
Expand All @@ -19,7 +20,6 @@
utilities,
validate,
)
from curfu.version import __version__ as curfu_version

fastapi_app = FastAPI(
title="Fusion Curation API",
Expand Down
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Original file line number Diff line number Diff line change
Expand Up @@ -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()

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