Feature/comp 114 python code quality

Various python code quality and readability improvements Noteworthy are:

• The db model upgrade to the sqlalchemy2 syntax, giving full type information. NB the package types-sqlalchemy has to be removed, potentially also from the servers if it doesnt happen automatically (this package is only intended for sqlalchemy 1.4, sqlalchemy2 has its type info included).
• The use of a new package sphinxcontrib-httpdomain for more conveniently documenting the api endpoints in sphinx
• SURVEY_DATABASE_URI is still a required config entry, but as the format isn't checked, it can be left empty, as in the config-example.json file. Should be clear enough.

compendium_v2/background_task/parse_excel_data.py

+import logging
 import openpyxl
 import os
-import logging
 
 from compendium_v2.db.model import FeeType
 from compendium_v2.environment import setup_logging
@@ -9,9 +9,7 @@ setup_logging()
 
 logger = logging.getLogger(__name__)
 
-EXCEL_FILE = os.path.join(
-    os.path.dirname(__file__), "xlsx",
-    "2021_Organisation_DataSeries.xlsx")
+EXCEL_FILE = os.path.join(os.path.dirname(__file__), "xlsx", "2021_Organisation_DataSeries.xlsx")
 
 
 def fetch_budget_excel_data():
@@ -32,12 +30,7 @@ def fetch_budget_excel_data():
             if budget is not None:
                 budget = round(budget / 1000000, 2)
                 if budget > 200:
-                    logger.info(
-                        f'{nren} has budget set to '
-                        f'>200M EUR for {year}. ({budget})')
-
-                # process the data (e.g. save to database)
-                # print(f"NREN: {nren}, Budget: {budget}, Year: {year}")
+                    logger.info(f'{nren} has budget set to >200M EUR for {year}. ({budget})')
 
                 yield nren.upper(), budget, year
 
@@ -52,17 +45,12 @@ def fetch_funding_excel_data():
 
     def hard_number_convert(s, source_name, nren, year):
         if s is None:
-            logger.info(
-                f'Invalid Value :{nren} has empty value for {source_name}.'
-                + f'for year ({year})')
+            logger.info(f'Invalid Value :{nren} has empty value for {source_name} for year ({year})')
             return float(0)
-        """ Returns True if string is a number. """
         try:
             return float(s)
         except ValueError:
-            logger.info(
-                f'Invalid Value :{nren} has empty value for {source_name}.'
-                + f'for year ({year}) with value ({s})')
+            logger.info(f'Invalid Value :{nren} has empty value for {source_name} for year ({year}) with value ({s})')
             return float(0)
 
     # iterate over the rows in the worksheet
@@ -76,7 +64,6 @@ def fetch_funding_excel_data():
             gov_public_bodies = ws.cell(row=row, column=col_start + 3).value
             other_european_funding = ws.cell(row=row, column=col_start + 4).value
             other = ws.cell(row=row, column=col_start + 5).value
-            print(nren, client_institution, commercial, geant_subsidy, gov_public_bodies, other_european_funding, other)
 
             client_institution = hard_number_convert(client_institution, "client institution", nren, year)
             commercial = hard_number_convert(commercial, "commercial", nren, year)
@@ -89,10 +76,7 @@ def fetch_funding_excel_data():
 
             # process the data (e.g. save to database)
             if nren is not None:
-                yield (nren.upper(), year, client_institution,
-                       european_funding,
-                       gov_public_bodies,
-                       commercial, other)
+                yield (nren.upper(), year, client_institution, european_funding, gov_public_bodies, commercial, other)
 
     def create_points_for_year_from_2018(start_row, end_row, year, col_start):
         for row in range(start_row, end_row):
@@ -112,10 +96,7 @@ def fetch_funding_excel_data():
 
             # process the data (e.g. save to database)
             if nren is not None:
-                yield (nren.upper(), year, client_institution,
-                       european_funding,
-                       gov_public_bodies,
-                       commercial, other)
+                yield (nren.upper(), year, client_institution, european_funding, gov_public_bodies, commercial, other)
 
     # For 2016
     yield from create_points_for_year_until_2017(8, 50, 2016, 43, 45)
@@ -147,26 +128,22 @@ def fetch_charging_structure_excel_data():
             # extract the data from the row
             nren = ws.cell(row=row, column=col_start).value
             charging_structure = ws.cell(row=row, column=col_start + 1).value
-            logger.info(
-                f'NREN: {nren}, Charging Structure: {charging_structure},'
-                f' Year: {year}')
+            logger.info(f'NREN: {nren}, Charging Structure: {charging_structure}, Year: {year}')
             if charging_structure is not None:
                 if "do not charge" in charging_structure:
-                    charging_structure = FeeType.no_charge.value
+                    charging_structure = FeeType.no_charge
                 elif "combination" in charging_structure:
-                    charging_structure = FeeType.combination.value
+                    charging_structure = FeeType.combination
                 elif "flat" in charging_structure:
-                    charging_structure = FeeType.flat_fee.value
+                    charging_structure = FeeType.flat_fee
                 elif "usage-based" in charging_structure:
-                    charging_structure = FeeType.usage_based_fee.value
+                    charging_structure = FeeType.usage_based_fee
                 elif "Other" in charging_structure:
-                    charging_structure = FeeType.other.value
+                    charging_structure = FeeType.other
                 else:
                     charging_structure = None
 
-                logger.info(
-                    f'NREN: {nren}, Charging Structure: {charging_structure},'
-                    f' Year: {year}')
+                logger.info(f'NREN: {nren}, Charging Structure: {charging_structure}, Year: {year}')
 
                 yield nren.upper(), year, charging_structure