Refactored frontend setup configuration

frontend/MANIFEST.in

@@ -9,13 +9,8 @@ include requirements.txt
 include requirements-dev.txt
 
 # server
-recursive-include gens/templates/ *.html
-recursive-include gens/static/**/ *
-recursive-include scout/blueprints/**/templates/ *.html
-recursive-include scout/blueprints/**/static/ *
-
-# api
-include gens/openapi/openapi.yaml
+recursive-include app/templates/ *.html
+recursive-include app/static/**/ *
 
 # excluding
 recursive-exclude * *.py[co]

frontend/app/__init__.py

@@ -1,2 +1 @@
-from .__version__ import VERSION as version
-from .app import create_app
+from .__version__ import VERSION as __version__

frontend/app/blueprints/gens/views.py

@@ -5,7 +5,7 @@
 
 from flask import Blueprint, abort, current_app, render_template, request
 
-from app import version
+from app import __version__ as version
 from app.api import get_sample
 from app.io import parse_region_str
 

frontend/app/blueprints/home/views.py

@@ -6,7 +6,7 @@
 
 from flask import Blueprint, current_app, render_template, request
 
-from app import version
+from app import __version__ as version
 from app.api import get_samples, get_timestamps
 
 LOG = logging.getLogger(__name__)

frontend/pyproject.toml

@@ -0,0 +1,7 @@
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+[tool.isort]
+profile = "black"
+src_paths = ["app"]

frontend/requirements.txt

@@ -1,2 +1 @@
-gunicorn
 .

frontend/setup.cfg

@@ -1,8 +1,41 @@
-[bumpversion]
-current_version = 2.1.1
-
 [metadata]
-description-file = README.md
+name = gens_app
+version = attr: app.__version__
+author = Markus Johansson
+author_email = [email protected]
+classifiers =
+    Development Status :: 5 - Production/Stable
+    License :: OSI Approved :: MIT License
+    Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
+    Programming Language :: Python :: 3.12
+
+[options]
+packages = find:
+zip_safe = True
+include_package_data = True
+python_requires = >=3.10
+install_requires =
+    setuptools
+    wheel
+    flask
+    gunicorn
+    flask-compress
+    requests
+    pydantic
+    tabulate
+
+[options.package_data]
+app = *.css, *js
+
+[options.extras_require]
+dev = 
+    black
+    isort
+    mypy
+    pytest
+    pytest-cov
+    pytest-flask
 
 [isort]
 profile=black

frontend/setup.py

@@ -1,53 +1,9 @@
-# coding: utf-8
+#!/usr/bin/env python
+"""Build frontend with setuptools.
 
-from os import path
+Build is defined in setup.cfg"""
 
-from setuptools import find_packages, setup
+import setuptools
 
-setup(
-    name="gens",
-    version="2.1.1",
-    description="Gens is a web-based interactive tool to visualize genomic copy number profiles from WGS data.",
-    license="MIT",
-    author="Ronja, Markus Johansson",
-    classifiers=[
-        "Development Status :: 5 - Production/Stable",
-        "Intended Audience :: Developers",
-        "License :: OSI Approved :: MIT License",
-        "Programming Language :: Python",
-        "Programming Language :: Python :: 3.5",
-        "Programming Language :: Python :: 3.6",
-        "Programming Language :: Python :: 3.7",
-        "Programming Language :: Python :: 3.8",
-        "Programming Language :: Python :: 3.9",
-    ],
-    keywords=["Flask", "Genomics", "WGS"],
-    packages=find_packages(),
-    zip_safe=False,
-    install_requires=[
-        "Flask",
-        "pydantic",
-        "gtfparse>=1.2.0",
-        "pysam>=0.15.4",
-        "pyyaml",
-        "flask-compress",
-        "tabulate",
-        "requests",
-    ],
-    setup_requires=["pytest-runner"],
-    tests_require=["pytest", "mongomock"],
-    entry_points={
-        "console_scripts": ["gens=gens.commands:cli"],
-    },
-    package_data={
-        "gens": [
-            "gens/templates/*.html",
-            "gens/static/**/*",
-            "gens/static/**/*",
-            "scout/blueprints/**/templates/*.html",
-            "scout/blueprints/**/static/*",
-            "gens/openapi/openapi.yaml",
-        ]
-    },
-    include_package_data=True,
-)
+if __name__ == "__main__":
+    setuptools.setup()