apply mypy and fix minor issues

CONTRIBUTING.rst

@@ -289,7 +289,7 @@ to ``upstream/develop``, so you have to branch-off from it too.
 There is one exception: If you
 want to suggest a change to the docs in the folder
 ``app/docs/`` (e. g. fix a typo in
-:ref:`User Guide - Basic Usage <user_basic-usage>`),
+:ref:`Installation <user_installation>`),
 you can also pull to ``upstream/master``. This means, you have also to
 branch-off from the ``master`` branch.
 

app/config.py

@@ -1,7 +1,7 @@
 import os
-from typing import Type
-from typing import Union
+from typing import Any
 
+from flask import Flask
 from pydantic import BaseSettings
 
 
@@ -47,7 +47,7 @@ class Config:
         env_file = os.path.join(ROOT_DIR, "env/development.env")
 
     @classmethod
-    def init_app(cls, app):
+    def init_app(cls, app: Flask):
         BaseConfig.init_app(app)
 
         from flask_debugtoolbar import DebugToolbarExtension
@@ -144,27 +144,8 @@ def init_app(cls, app):
         DockerConfig.init_app(app)
 
 
-ConfigTypes: Type[
-    Union[
-        DevelopmentConfig,
-        TestingConfig,
-        ProductionConfig,
-        UnixConfig,
-        DockerConfig,
-        DockerComposeConfig,
-    ]
-] = Union[
-    DevelopmentConfig,
-    TestingConfig,
-    ProductionConfig,
-    UnixConfig,
-    DockerConfig,
-    DockerComposeConfig,
-]
-
-
-def get_config_class(config_name: str = "default") -> ConfigTypes:
-    configs = {
+def get_config_class(config_name: str = "default",) -> Any:
+    configs: dict = {
         "development": DevelopmentConfig,
         "testing": TestingConfig,
         "production": ProductionConfig,

app/crud.py

@@ -14,11 +14,11 @@
 from app.models import Url
 
 
-DatabaseModels = Type[Union[Import, Doi, Url, Request, FBRequest]]
+DatabaseModelTypes = Type[Union[Import, Doi, Url, Request, FBRequest]]
 
 
 def get_all(
-    db: Session, model: DatabaseModels, skip: int = 0, limit: int = 100,
+    db: Session, model: DatabaseModelTypes, skip: int = 0, limit: int = 100,
 ) -> Query:
     """Get all entries of a model.
 
@@ -42,7 +42,7 @@ def get_all(
     return db.session.query(model).offset(skip).limit(limit).all()
 
 
-def get_first(db: Session, model: DatabaseModels, kwargs: dict) -> Query:
+def get_first(db: Session, model: DatabaseModelTypes, kwargs: dict) -> Query:
     """Get first entry of a model.
 
     Parameters
@@ -62,8 +62,8 @@ def get_first(db: Session, model: DatabaseModels, kwargs: dict) -> Query:
 
 
 def create_entity(
-    db: Session, model: DatabaseModels, kwargs: dict = {}
-) -> DatabaseModels:
+    db: Session, model: DatabaseModelTypes, kwargs: dict = {}
+) -> DatabaseModelTypes:
     """Create one entry of a model.
 
     Parameters
@@ -85,8 +85,8 @@ def create_entity(
 
 
 def create_entities(
-    db: Session, model: DatabaseModels, iterable: list, kwargs: dict = {},
-) -> DatabaseModels:
+    db: Session, model: DatabaseModelTypes, iterable: list, kwargs: dict = {},
+) -> DatabaseModelTypes:
     """Create entities of a model.
 
     Parameters

app/db.py

@@ -4,43 +4,46 @@
 import os
 from datetime import datetime
 from json import dumps
+from typing import Any
 from typing import List
+from urllib.parse import quote
 
 from flask import g
 from flask_sqlalchemy import SQLAlchemy
 from pandas import read_csv
 from tqdm import tqdm
 
-try:
-    from urllib.parse import quote
-except ImportError:
-    from urlparse import quote
-
-from app.config import get_config_class, ConfigTypes
-from app.crud import create_entity, create_entities, get_all
-from app.models import db, Doi, Import, Url, Request, FBRequest
-from app.requests import (
-    request_doi_landingpage,
-    request_ncbi_api,
-    request_unpaywall_api,
-    get_graph_api,
-    get_graph_api_urls,
-    get_graph_api_token,
-)
+from app.config import get_config_class
+from app.crud import create_entities
+from app.crud import create_entity
+from app.crud import get_all
+from app.models import db
+from app.models import Doi
+from app.models import FBRequest
+from app.models import Import
+from app.models import Request
+from app.models import Url
+from app.requests import get_graph_api
+from app.requests import get_graph_api_token
+from app.requests import get_graph_api_urls
+from app.requests import request_doi_landingpage
+from app.requests import request_ncbi_api
+from app.requests import request_unpaywall_api
 from app.utils import is_valid_doi
 
 
-def get_config() -> ConfigTypes:
+DATABASE = db
+
+
+def get_config() -> Any:
     """Get config."""
     config_name = os.getenv("FLASK_CONFIG") or "default"
     config_class = get_config_class(config_name)
 
     if os.getenv("ENV_FILE"):
-        config = config_class(_env_file=os.getenv("ENV_FILE"))
+        return config_class(_env_file=os.getenv("ENV_FILE"))
     else:
-        config = config_class()
-
-    return config
+        return config_class()
 
 
 def get_db() -> SQLAlchemy:
@@ -51,7 +54,7 @@ def get_db() -> SQLAlchemy:
     again.
     """
     if "db" not in g:
-        g.db = db
+        g.db = DATABASE
     return g.db
 
 
@@ -68,14 +71,14 @@ def close_db(e=None) -> None:
 
 def init_db() -> None:
     """Connect to database and create new tables."""
-    db = get_db()
-    db.create_all()
+    database = get_db()
+    database.create_all()
 
 
 def drop_db() -> None:
     """Drop database."""
-    db = get_db()
-    db.drop_all()
+    database = get_db()
+    database.drop_all()
 
 
 def dev() -> None:
@@ -412,15 +415,15 @@ def create_unpaywall_urls() -> None:
     """
     num_urls_unpaywall_added = 0
     num_requests_added = 0
-    urls_added = []
+    urls_added: List[str] = []
 
-    db = get_db()
+    database = get_db()
     config = get_config()
     # batch_size = config.URL_BATCH_SIZE # TODO: identify default and best practice values
     email = config.APP_EMAIL
     batch_size = 20
 
-    url_list = [url.url for url in get_all(db, Url)]
+    url_list = [url.url for url in get_all(database, Url)]
 
     list_dois = Doi.query.filter(Doi.url_unpaywall is False).all()
     print("Found DOI's: {0}".format(len(list_dois)))
@@ -468,8 +471,8 @@ def create_unpaywall_urls() -> None:
                     url_dict = {"url": url, "doi": row.doi, "url_type": url_type}
                     urls_added.append(url)
                     db_urls_added.append(url_dict)
-        create_entities(db, Request, db_requests_added)
-        create_entities(db, Url, db_urls_added)
+        create_entities(database, Request, db_requests_added)
+        create_entities(database, Url, db_urls_added)
         num_urls_unpaywall_added += len(db_urls_added)
         num_requests_added += len(db_requests_added)
     print('{0} "Unpaywall" URL\'s added to database.'.format(num_urls_unpaywall_added))

app/main.py

@@ -27,7 +27,6 @@
 from app.db import create_unpaywall_urls
 from app.db import dev
 from app.db import drop_db
-from app.db import get_config
 from app.db import get_fb_data
 from app.db import import_basedata
 from app.db import init_db
@@ -43,7 +42,7 @@ def create_app() -> Flask:
     print("* Start FHE Collector...")
 
     app = Flask("fhe_collector", root_path=ROOT_DIR)
-    env_name = os.getenv("FLASK_ENV")
+    env_name = os.getenv("FLASK_ENV", "default")
     config = get_config_class(env_name)
     app.config.from_object(config())
     config.init_app(app)

app/models.py

@@ -5,13 +5,15 @@
 from datetime import timezone
 
 from flask_sqlalchemy import SQLAlchemy
+from flask_sqlalchemy.model import DefaultMeta
 from sqlalchemy.exc import IntegrityError
 
 
 db = SQLAlchemy()
+BaseModelType: DefaultMeta = db.Model
 
 
-class BaseModel(db.Model):
+class BaseModel(BaseModelType):
     __abstract__ = True
 
     created_at = db.Column(db.DateTime, default=lambda: datetime.now(timezone.utc))

app/utils.py

@@ -5,6 +5,7 @@
 from csv import DictReader
 from csv import DictWriter
 from csv import reader
+from csv import writer
 from json import dump
 from json import dumps
 from json import load
@@ -171,9 +172,9 @@ def write_csv(
 
     """
     with open(filename, "w", newline=newline, encoding=encoding) as csvfile:
-        writer = writer(csvfile, delimiter=delimiter, quotechar=quotechar)
+        csv_writer = writer(csvfile, delimiter=delimiter, quotechar=quotechar)
         for row in data:
-            writer.writerow(row)
+            csv_writer.writerow(row)
 
 
 def read_csv_as_dicts(

setup.cfg

@@ -36,3 +36,6 @@ exclude =
 
 [pylint]
 max-line-length = 88
+
+[mypy]
+ignore_missing_imports = True

setup.py

@@ -5,6 +5,7 @@
 import os
 import re
 import sys
+from typing import List
 
 from setuptools import find_packages
 from setuptools import setup
@@ -46,8 +47,7 @@ def run_tests(self):
         # import here, cause outside the eggs aren't loaded
         import tox
 
-        errcode = tox.cmdline(self.test_args)
-        sys.exit(errcode)
+        tox.cmdline(self.test_args)
 
 
 INSTALL_REQUIREMENTS = [
@@ -65,7 +65,7 @@ def run_tests(self):
     "pydantic==1.7.2",
 ]
 
-TESTS_REQUIREMENTS = []
+TESTS_REQUIREMENTS: List = []
 
 CLASSIFIERS = [
     # How mature is this project? Common values are

tox.ini

@@ -1,5 +1,5 @@
 [tox]
-envlist = py36,py37,py38,coverage,docs,packaging,dist_install
+envlist = py36,py37,py38,mypy,docs
 skip_missing_interpreters = True
 ignore_basepython_conflict = True