Merge pull request #329 from CodeForPhilly/update_setup

Update setup

Author: quinn-dougherty

Dockerfile

@@ -2,6 +2,7 @@ FROM python:3.7.7-slim-buster
 RUN mkdir /app
 WORKDIR /app
 COPY README.md .
+COPY setup.cfg .
 COPY setup.py .
 COPY requirements.txt .
 # Creating an empty src dir is a (hopefully) temporary hack to improve layer caching and speed up image builds

setup.cfg

@@ -0,0 +1,65 @@
+[metadata]
+long_description = file: README.md
+long_description_content_type = text/markdown
+
+[options]
+# tests_require is a list of dependencies that are *absolutely required*
+# to run the tests. tests_require is used when running tests from your
+# *current* Python environment (that is, not using tox).
+# tests_require is ignored by tox.
+#
+# As such, you can usually get away with neglecting tests_require ---
+# it's not a big deal if some of the dependencies get left out.
+#
+# If you're running tests from your current environment, it's because
+# you're actively developing, in which case you usually have an
+# environment you built for development. But if you have to change
+# environments mid-development for any reason, tests_require can save you
+# from getting tripped up.
+#
+# tests_require is used when running tests and debugging through an IDE like
+# PyCharm, to ensure the environment the IDE is using has the requirements.
+#
+# Unless you're in one of those situations, you can simply ignore this.
+tests_require = pytest
+
+[aliases]
+# Alias `setup.py test` to `setup.py pytest`
+test = pytest
+
+[flake8]
+max-complexity = 10
+
+[mypy]
+follow_imports = normal
+ignore_missing_imports = True
+
+[tool:pytest]
+# If a pytest section is found in one of the possible config files
+# (pytest.ini, tox.ini or setup.cfg), then pytest will not look for any others,
+# so if you add a pytest config section elsewhere,
+# you will need to delete this section from setup.cfg.
+log_cli=true
+log_level=NOSET
+norecursedirs =
+    .git
+    .tox
+    .env
+    dist
+    build
+python_files =
+    test_*.py
+    *_test.py
+    tests.py
+addopts =
+    -ra
+    --cov=penn_chime
+    --cov-report=term-missing
+    --strict
+    --ignore=ci
+    --ignore=.eggs
+    --doctest-modules
+    --doctest-glob=\*.rst
+    --tb=short
+testpaths =
+    test

setup.py

@@ -1,23 +1,18 @@
 """Setup file for chime
 """
-__version__ = "0.1.0"
+__version__ = "0.2.0"
 __author__ = "Predictive Healthcare @ Penn Medicine"
 
-import io
 from os import path
 from setuptools import setup, find_packages, find_namespace_packages
 
-with io.open("README.md", "r") as inp:
-    LONG_DESCRIPTION = inp.read()
-    
+
 setup(
     name="penn_chime",
     version=__version__,
     author=__author__,
     author_email="",
     description="COVID-19 Hospital Impact Model for Epidemics",
-    long_description=LONG_DESCRIPTION,
-    long_description_content_type="text/markdown",
     url="https://github.com/CodeForPhilly/chime",
     project_urls={
         "Bug Reports": "https://github.com/CodeForPhilly/chime/issues",
@@ -32,17 +27,17 @@
         "numpy",
         "altair",
         "pytest",
-        "dash", 
-        "dash_bootstrap_components", 
-        "pyyaml", 
+        "dash",
+        "dash_bootstrap_components",
+        "pyyaml",
         "gunicorn"
     ],
     classifiers=[
         "Programming Language :: Python :: 3",
         "License :: OSI Approved :: MIT License",
         "Operating System :: OS Independent",
     ],
-    python_requires='>=3.6',
+    python_requires='>=3.7',
     entry_points = {
         'console_scripts': ['penn_chime=penn_chime.cli:main'],
     },

src/penn_chime/__init__.py

@@ -1 +1 @@
-x = 1
+"""Penn Chime."""

src/penn_chime/charts.py

@@ -2,8 +2,8 @@
 from math import ceil
 import datetime
 
-from altair import Chart  # type: ignore
-import pandas as pd  # type: ignore
+from altair import Chart
+import pandas as pd
 import numpy as np
 
 from .parameters import Parameters

src/penn_chime/models.py

@@ -9,8 +9,8 @@
 
 from typing import Dict, Generator, Tuple
 
-import numpy as np  # type: ignore
-import pandas as pd  # type: ignore
+import numpy as np
+import pandas as pd
 
 from .parameters import Parameters
 

src/penn_chime/presentation.py

@@ -1,7 +1,7 @@
 """effectful functions for streamlit io"""
 
-import numpy as np  # type: ignore
-import pandas as pd  # type: ignore
+import numpy as np
+import pandas as pd
 
 from .defaults import Constants, RateLos
 from .utils import add_date_column, dataframe_to_base64

src/penn_chime/utils.py

@@ -5,10 +5,8 @@
 from typing import Optional
 from base64 import b64encode
 
-import numpy as np  # type: ignore
-import pandas as pd  # type: ignore
-
-# from .parameters import Parameters
+import numpy as np
+import pandas as pd
 
 
 # (0.02, 7) is 2%, 7 days