build: clean up project configuration (#41)

* move coverage.py and mypy config to pyproject.toml

* remove travis config

* move project metadata from setup.py to pyproject.toml

* add  missing newline

* fix version reading in api docs

* move flake8 config to pyproject and move version to pyproject.toml

* fix version dependency

* fix formatting

* fix dependency error

* fix toml dependency

Dockerfile

@@ -14,8 +14,7 @@ COPY ./ /app
 
 ## Install app
 RUN cd /app \
-  && python setup.py develop \
-  && pip install -r requirements.txt \
+  && pip install -e . \
   && cd / \
   && chmod g+w /app/cloud_registry/api/ \
   && pip install yq

docs/api/conf.py

@@ -12,14 +12,17 @@
 #
 from pathlib import Path
 import sys
+import toml
 
 from sphinx.ext import apidoc
 
 root_dir = Path.cwd().resolve().parents[1]
 
 sys.path.insert(0, root_dir)
 
-exec(open(root_dir / "cloud_registry" / "version.py").read())
+with open(root_dir / "pyproject.toml", "r") as f:
+    config = toml.load(f)
+    __version__ = config["project"]["version"]
 
 
 # -- Project information -----------------------------------------------------

docs/api/requirements.txt

@@ -1,3 +1,4 @@
 Sphinx==7.2.6
 readthedocs-sphinx-ext==2.2.3
-sphinx-rtd-theme==1.3.0
+sphinx-rtd-theme==1.3.0
+toml==0.10.0

pyproject.toml

@@ -3,3 +3,55 @@ max-line-length = 88
 target-version = ["py310"]
 workers = 1
 
+[tool.mypy]
+ignore_missing_imports = true
+
+[tool.coverage.run]
+source = ["cloud_registry"]
+omit = ["cloud_registry/app.py"]
+
+[tool.flake8]
+exclude = [".git", ".eggs", "build", "venv", "env"]
+max-line-length = 88
+extend-ignore = "E203"
+
+[project]
+name ="cloud-registry"
+version="0.2.0"
+authors = [{name = "ELIXIR Cloud & AAI"}, {email = "[email protected]"}]
+keywords = [
+    "ga4gh", "service", "registry", "elixir", "cloud", "rest", "restful", 
+    "api", "app", "server", "openapi", "swagger", "mongodb", "python", "flask"
+]
+classifiers = [
+    "License :: OSI Approved :: Apache Software License",
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Natural Language :: English",
+    "Programming Language :: Python :: 3.8",
+]
+description = "GA4GH Service Registry API implementation for the ELIXIR Cloud"
+dynamic = ["dependencies"]
+
+[project.license]
+text = "Apache License 2.0"
+
+[project.readme]
+file = "README.md"
+content-type = "text/markdown"
+
+[project.urls]
+homepage = "https://github.com/elixir-cloud-aai/cloud-registry.git"
+
+[tool.setuptools.dynamic.version]
+file = ["cloud_registry/version"]
+
+[tool.setuptools.packages.find]
+exclude = ["deployment", "docs"]
+
+[tool.setuptools.dynamic.dependencies]
+file = ["requirements.txt"]
+
+[tool.setuptools.dynamic.optional-dependencies]
+dev = { file = ["requirements_dev.txt"] }

requirements.txt

@@ -1 +1,2 @@
+connexion>=2.11.2,<3.0.0
 foca==0.12.1

requirements_dev.txt

@@ -1,5 +1,6 @@
 coverage==6.3.2
-flake8==4.0.1
+Flake8-pyproject==1.2.3
+flake8==6.1.0
 mongomock==4.0.0
 mypy==0.971
 pytest==7.1.1