Merge branch 'feature/COMP-114_python_code_quality' into 'develop'

Feature/comp 114 python code quality

See merge request !12

compendium_v2/__init__.py

@@ -17,6 +17,22 @@ def migrate_database(config: dict) -> None:
     migration_utils.upgrade(dsn)
 
 
+def _create_app(app_config) -> Flask:
+    # used by sphinx to create documentation without config and db migrations
+    app = Flask(__name__)
+    CORS(app)
+
+    app.config['CONFIG_PARAMS'] = app_config
+
+    from compendium_v2.routes import default
+    app.register_blueprint(default.routes, url_prefix='/')
+
+    from compendium_v2.routes import api
+    app.register_blueprint(api.routes, url_prefix='/api')
+
+    return app
+
+
 def create_app() -> Flask:
     """
     overrides default settings with those found
@@ -25,22 +41,12 @@ def create_app() -> Flask:
     :return: a new flask app instance
     """
 
-    assert 'SETTINGS_FILENAME' in os.environ, \
-        "environment variable 'SETTINGS_FILENAME' is required"
+    assert 'SETTINGS_FILENAME' in os.environ, "environment variable 'SETTINGS_FILENAME' is required"
 
     with open(os.environ['SETTINGS_FILENAME']) as f:
         app_config = config.load(f)
 
-    app = Flask(__name__)
-    CORS(app)
-
-    app.config['CONFIG_PARAMS'] = app_config
-
-    from compendium_v2.routes import default
-    app.register_blueprint(default.routes, url_prefix='/')
-
-    from compendium_v2.routes import api
-    app.register_blueprint(api.routes, url_prefix='/api')
+    app = _create_app(app_config)
 
     logging.info('Flask app initialized')
 

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
 

compendium_v2/config.py

 import json
-
 import jsonschema
 
+
 CONFIG_SCHEMA = {
     '$schema': 'http://json-schema.org/draft-07/schema#',
     'type': 'object',
-
-    'definitions': {
-        'database-uri': {
-            'type': 'string'
-        }
-    },
-
     'properties': {
-        'SQLALCHEMY_DATABASE_URI': {
-            'type': 'string',
-            'properties': {
-                'database-uri': {'$ref': '#definitions/database-uri'}
-            },
-            'additionalProperties': False
-        },
-        'SURVEY_DATABASE_URI': {
-            'type': 'string',
-            'properties': {
-                'database-uri': {'$ref': '#definitions/database-uri'}
-            },
-            'additionalProperties': False
-        }
+        'SQLALCHEMY_DATABASE_URI': {'type': 'string', 'format': 'database-uri'},
+        'SURVEY_DATABASE_URI': {'type': 'string', 'format': 'database-uri'}
     },
     'required': ['SQLALCHEMY_DATABASE_URI', 'SURVEY_DATABASE_URI'],
     'additionalProperties': False

compendium_v2/db/model.py

 import logging
-import sqlalchemy as sa
+from decimal import Decimal
 from enum import Enum
+from typing import Optional
+from typing_extensions import Annotated
 
-from typing import Any
+from sqlalchemy import MetaData, String
+from sqlalchemy.orm import DeclarativeBase, Mapped, mapped_column, relationship
+from sqlalchemy.schema import ForeignKey
 
-from sqlalchemy import MetaData
-from sqlalchemy.ext.declarative import declarative_base
-from sqlalchemy.orm import relationship
 
 logger = logging.getLogger(__name__)
 
@@ -20,37 +21,42 @@ convention = {
 
 metadata_obj = MetaData(naming_convention=convention)
 
-# https://github.com/python/mypy/issues/2477
-base_schema: Any = declarative_base(metadata=metadata_obj)
+str128 = Annotated[str, 128]
+int_pk = Annotated[int, mapped_column(primary_key=True)]
+int_pk_fkNREN = Annotated[int, mapped_column(ForeignKey("nren.id"), primary_key=True)]
 
 
-class NREN(base_schema):
+class Base(DeclarativeBase):
+    metadata = metadata_obj
+    type_annotation_map = {
+        str128: String(128),
+    }
+
+
+class NREN(Base):
     __tablename__ = 'nren'
-    id = sa.Column(sa.Integer, primary_key=True)
-    name = sa.Column(sa.String(128), nullable=False)
+    id: Mapped[int_pk]
+    name: Mapped[str128]
 
 
-class BudgetEntry(base_schema):
+class BudgetEntry(Base):
     __tablename__ = 'budgets'
-    nren_id = sa.Column(
-        sa.Integer, sa.schema.ForeignKey(NREN.id), primary_key=True)
-    nren = relationship(NREN, lazy='joined')
-    year = sa.Column(sa.Integer, primary_key=True)
-    budget = sa.Column(sa.Numeric(asdecimal=False), nullable=False)
+    nren_id: Mapped[int_pk_fkNREN]
+    nren: Mapped[NREN] = relationship(lazy='joined')
+    year: Mapped[int_pk]
+    budget: Mapped[Decimal]
 
 
-class FundingSource(base_schema):
+class FundingSource(Base):
     __tablename__ = 'funding_source'
-    nren_id = sa.Column(
-        sa.Integer, sa.schema.ForeignKey(NREN.id), primary_key=True)
-    nren = relationship(NREN, lazy='joined')
-    year = sa.Column(sa.Integer, primary_key=True)
-    client_institutions = sa.Column(
-        sa.Numeric(asdecimal=False), nullable=False)
-    european_funding = sa.Column(sa.Numeric(asdecimal=False), nullable=False)
-    gov_public_bodies = sa.Column(sa.Numeric(asdecimal=False), nullable=False)
-    commercial = sa.Column(sa.Numeric(asdecimal=False), nullable=False)
-    other = sa.Column(sa.Numeric(asdecimal=False), nullable=False)
+    nren_id: Mapped[int_pk_fkNREN]
+    nren: Mapped[NREN] = relationship(lazy='joined')
+    year: Mapped[int_pk]
+    client_institutions: Mapped[Decimal]
+    european_funding: Mapped[Decimal]
+    gov_public_bodies: Mapped[Decimal]
+    commercial: Mapped[Decimal]
+    other: Mapped[Decimal]
 
 
 class FeeType(Enum):
@@ -61,49 +67,45 @@ class FeeType(Enum):
     other = "other"
 
 
-class ChargingStructure(base_schema):
+class ChargingStructure(Base):
     __tablename__ = 'charging_structure'
-    nren_id = sa.Column(
-        sa.Integer, sa.schema.ForeignKey(NREN.id), primary_key=True)
-    nren = relationship(NREN, lazy='joined')
-    year = sa.Column(sa.Integer, primary_key=True)
-    fee_type = sa.Column('fee_type', sa.Enum("flat_fee", "usage_based_fee",
-                                             "combination", "no_charge",
-                                             "other",
-                                             name="fee_type"), nullable=True)
+    nren_id: Mapped[int_pk_fkNREN]
+    nren: Mapped[NREN] = relationship(lazy='joined')
+    year: Mapped[int_pk]
+    fee_type: Mapped[Optional[FeeType]]
 
 
-class NrenStaff(base_schema):
+class NrenStaff(Base):
     __tablename__ = 'nren_staff'
-    nren_id = sa.Column(sa.Integer, sa.schema.ForeignKey(NREN.id), primary_key=True)
-    nren = relationship(NREN, lazy='joined')
-    year = sa.Column(sa.Integer, primary_key=True)
-    permanent_fte = sa.Column(sa.Numeric(asdecimal=False), nullable=False)
-    subcontracted_fte = sa.Column(sa.Numeric(asdecimal=False), nullable=False)
-    technical_fte = sa.Column(sa.Numeric(asdecimal=False), nullable=False)
-    non_technical_fte = sa.Column(sa.Numeric(asdecimal=False), nullable=False)
+    nren_id: Mapped[int_pk_fkNREN]
+    nren: Mapped[NREN] = relationship(lazy='joined')
+    year: Mapped[int_pk]
+    permanent_fte: Mapped[Decimal]
+    subcontracted_fte: Mapped[Decimal]
+    technical_fte: Mapped[Decimal]
+    non_technical_fte: Mapped[Decimal]
 
 
-class ParentOrganization(base_schema):
+class ParentOrganization(Base):
     __tablename__ = 'parent_organization'
-    nren_id = sa.Column(sa.Integer, sa.schema.ForeignKey(NREN.id), primary_key=True)
-    nren = relationship(NREN, lazy='joined')
-    year = sa.Column(sa.Integer, primary_key=True)
-    organization = sa.Column(sa.String(128), nullable=False)
+    nren_id: Mapped[int_pk_fkNREN]
+    nren: Mapped[NREN] = relationship(lazy='joined')
+    year: Mapped[int_pk]
+    organization: Mapped[str128]
 
 
-class SubOrganization(base_schema):
+class SubOrganization(Base):
     __tablename__ = 'sub_organization'
-    nren_id = sa.Column(sa.Integer, sa.schema.ForeignKey(NREN.id), primary_key=True)
-    nren = relationship(NREN, lazy='joined')
-    year = sa.Column(sa.Integer, primary_key=True)
-    organization = sa.Column(sa.String(128), primary_key=True)
-    role = sa.Column(sa.String(128), nullable=False)
+    nren_id: Mapped[int_pk_fkNREN]
+    nren: Mapped[NREN] = relationship(lazy='joined')
+    year: Mapped[int_pk]
+    organization: Mapped[str128] = mapped_column(primary_key=True)
+    role: Mapped[str128]
 
 
-class ECProject(base_schema):
+class ECProject(Base):
     __tablename__ = 'ec_project'
-    nren_id = sa.Column(sa.Integer, sa.schema.ForeignKey(NREN.id), primary_key=True)
-    nren = relationship(NREN, lazy='joined')
-    year = sa.Column(sa.Integer, primary_key=True)
-    project = sa.Column(sa.String(256), primary_key=True)
+    nren_id: Mapped[int_pk_fkNREN]
+    nren: Mapped[NREN] = relationship(NREN, lazy='joined')
+    year: Mapped[int_pk]
+    project: Mapped[str] = mapped_column(String(256), primary_key=True)

compendium_v2/environment.py

@@ -7,8 +7,7 @@ LOGGING_DEFAULT_CONFIG = {
     'disable_existing_loggers': False,
     'formatters': {
         'simple': {
-            'format': '%(asctime)s - %(name)s '
-                      '(%(lineno)d) - %(levelname)s - %(message)s'
+            'format': '%(asctime)s - %(name)s (%(lineno)d) - %(levelname)s - %(message)s'
         }
     },
 

compendium_v2/migrations/README

-Single-database configuration for Flask.

compendium_v2/migrations/env.py

@@ -4,7 +4,7 @@ from sqlalchemy import engine_from_config
 from sqlalchemy import pool
 
 from alembic import context
-from compendium_v2.db.model import base_schema
+from compendium_v2.db.model import metadata_obj
 
 # this is the Alembic Config object, which provides
 # access to the values within the .ini file in use.
@@ -18,7 +18,7 @@ logging.basicConfig(level=logging.INFO)
 # for 'autogenerate' support
 # from myapp import mymodel
 # target_metadata = mymodel.Base.metadata
-target_metadata = base_schema.metadata
+target_metadata = metadata_obj
 
 # other values from the config, defined by the needs of env.py,
 # can be acquired:

compendium_v2/publishers/survey_publisher_2022.py

+"""
+survey_publisher_2022
+=========================
+
+This module loads the survey data from 2022 from the survey database.
+Registered as click cli command when installing compendium-v2.
+
+"""
 import logging
 import click
 import enum
@@ -136,15 +144,11 @@ def transfer_budget():
             try:
                 budget = float(_budget.replace('"', '').replace(',', ''))
             except ValueError:
-                logger.info(
-                    f'{nren_name} has no budget for 2022. Skipping.'
-                    f' ({_budget}))')
+                logger.info(f'{nren_name} has no budget for 2022. Skipping. ({_budget}))')
                 continue
 
             if budget > 200:
-                logger.info(
-                    f'{nren_name} has budget set to >200M EUR for 2022.'
-                    f' ({budget})')
+                logger.info(f'{nren_name} has budget set to >200M EUR for 2022. ({budget})')
 
             if nren_name not in nren_dict:
                 logger.info(f'{nren_name} unknown. Skipping.')
@@ -172,9 +176,7 @@ def transfer_funding_sources():
                     value = float(_value.replace('"', '').replace(',', ''))
                 except ValueError:
                     name = source.name
-                    logger.info(
-                        f'{nren_name} has invalid value for {name}.'
-                        + f' ({_value}))')
+                    logger.info(f'{nren_name} has invalid value for {name}. ({_value}))')
                     value = 0
 
                 nren_info = sourcedata.setdefault(
@@ -196,8 +198,7 @@ def transfer_funding_sources():
             funding_source = model.FundingSource(
                 nren=nren_dict[nren_name],
                 year=2022,
-                client_institutions=nren_info[
-                    FundingSource.CLIENT_INSTITUTIONS],
+                client_institutions=nren_info[FundingSource.CLIENT_INSTITUTIONS],
                 european_funding=nren_info[FundingSource.EUROPEAN_FUNDING],
                 gov_public_bodies=nren_info[FundingSource.GOV_PUBLIC_BODIES],
                 commercial=nren_info[FundingSource.COMMERCIAL],
@@ -241,11 +242,8 @@ def transfer_staff_data():
 
             employed = nren_info[StaffQuestion.PERMANENT_FTE] + nren_info[StaffQuestion.SUBCONTRACTED_FTE]
             technical = nren_info[StaffQuestion.TECHNICAL_FTE] + nren_info[StaffQuestion.NON_TECHNICAL_FTE]
-            if not math.isclose(
-                    employed,
-                    technical,
-                    abs_tol=0.01,
-            ):
+
+            if not math.isclose(employed, technical, abs_tol=0.01):
                 logger.info(f'{nren_name} FTE do not equal across employed/technical categories.'
                             f' ({employed} != {technical})')
 
@@ -354,15 +352,15 @@ def transfer_charging_structure():
                 continue
 
             if "do not charge" in value:
-                charging_structure = FeeType.no_charge.value
+                charging_structure = FeeType.no_charge
             elif "combination" in value:
-                charging_structure = FeeType.combination.value
+                charging_structure = FeeType.combination
             elif "flat" in value:
-                charging_structure = FeeType.flat_fee.value
+                charging_structure = FeeType.flat_fee
             elif "usage-based" in value:
-                charging_structure = FeeType.usage_based_fee.value
+                charging_structure = FeeType.usage_based_fee
             elif "Other" in value:
-                charging_structure = FeeType.other.value
+                charging_structure = FeeType.other
             else:
                 charging_structure = None
 

compendium_v2/publishers/survey_publisher_v1.py

+"""
+survey_publisher_v1
+=========================
+
+This module loads the survey data from before 2022 from and excel file.
+Missing info is filled in from the survey db for some questions.
+Registered as click cli command when installing compendium-v2.
+
+"""
 import logging
 import math
 import click
@@ -29,10 +38,7 @@ def db_budget_migration():
                 year = budget.year
 
                 if float(budget.budget) > 200:
-                    logger.info(
-                        f'Incorrect Data: '
-                        f'{abbrev} has budget set to '
-                        f'>200M EUR for {year}. ({budget.budget})')
+                    logger.info(f'Incorrect Data: {abbrev} has budget set to >200M EUR for {year}. ({budget.budget})')
 
                 if abbrev not in nren_dict:
                     logger.info(f'{abbrev} unknown. Skipping.')
@@ -53,8 +59,7 @@ def db_budget_migration():
                 logger.info(f'{abbrev} unknown. Skipping.')
                 continue
 
-            budget_entry = model.BudgetEntry(
-                nren=nren_dict[abbrev], budget=budget, year=year)
+            budget_entry = model.BudgetEntry(nren=nren_dict[abbrev], budget=budget, year=year)
             session.merge(budget_entry)
         session.commit()
 
@@ -71,13 +76,10 @@ def db_funding_migration():
              gov_public_bodies,
              commercial, other) in data:
 
-            _data = [client_institution, european_funding,
-                     gov_public_bodies, commercial, other]
+            _data = [client_institution, european_funding, gov_public_bodies, commercial, other]
             total = sum(_data)
             if not math.isclose(total, 100, abs_tol=0.01):
-                logger.info(
-                    f'{abbrev} funding sources for {year}'
-                    f' do not sum to 100% ({total})')
+                logger.info(f'{abbrev} funding sources for {year} do not sum to 100% ({total})')
 
             if abbrev not in nren_dict:
                 logger.info(f'{abbrev} unknown. Skipping.')

compendium_v2/routes/api.py

-"""
-API Endpoints
-=========================
-
-.. contents:: :local:
-
-/api/
----------------------
-
-
-
-"""
 import logging
 
 from flask import Blueprint

compendium_v2/routes/charging.py

@@ -57,7 +57,7 @@ def charging_structure_view() -> Any:
         return {
             'NREN': entry.nren.name,
             'YEAR': int(entry.year),
-            'FEE_TYPE': entry.fee_type,
+            'FEE_TYPE': entry.fee_type.value if entry.fee_type is not None else None,
         }
 
     with db.session_scope() as session:

compendium_v2/routes/default.py

-"""
-Default Endpoints
-=========================
-
-.. contents:: :local:
-
-/version
----------------------
-
-.. autofunction:: compendium_v2.routes.default.version
-
-"""
 import pkg_resources
 from flask import Blueprint, jsonify, render_template, Response
 

compendium_v2/routes/funding.py

@@ -62,7 +62,7 @@ def funding_source_view() -> Any:
     def _extract_data(entry: model.FundingSource):
         return {
             'NREN': entry.nren.name,
-            'YEAR': int(entry.year),
+            'YEAR': entry.year,
             'CLIENT_INSTITUTIONS': float(entry.client_institutions),
             'EUROPEAN_FUNDING': float(entry.european_funding),
             'GOV_PUBLIC_BODIES': float(entry.gov_public_bodies),

compendium_v2/routes/staff.py

@@ -61,10 +61,10 @@ def staff_view() -> Any:
         return {
             'nren': entry.nren.name,
             'year': entry.year,
-            'permanent_fte': entry.permanent_fte,
-            'subcontracted_fte': entry.subcontracted_fte,
-            'technical_fte': entry.technical_fte,
-            'non_technical_fte': entry.non_technical_fte
+            'permanent_fte': float(entry.permanent_fte),
+            'subcontracted_fte': float(entry.subcontracted_fte),
+            'technical_fte': float(entry.technical_fte),
+            'non_technical_fte': float(entry.non_technical_fte)
         }
 
     with db.session_scope() as session:

compendium_v2/survey_db/model.py

 import logging
-import sqlalchemy as sa
+from typing import List, Optional
 
-from typing import Any
-
-from sqlalchemy.ext.declarative import declarative_base
-from sqlalchemy.orm import relationship
+from sqlalchemy.orm import DeclarativeBase, Mapped, mapped_column, relationship
+from sqlalchemy.schema import ForeignKey
 
 logger = logging.getLogger(__name__)
 
-# https://github.com/python/mypy/issues/2477
-base_schema: Any = declarative_base()
+
+class Base(DeclarativeBase):
+    pass
 
 
-class Budgets(base_schema):
+class Budgets(Base):
     __tablename__ = 'budgets'
-    id = sa.Column(sa.Integer, primary_key=True)
-    budget = sa.Column(sa.String)
-    year = sa.Column(sa.Integer)
-    country_code = sa.Column('country_code', sa.String,
-                             sa.ForeignKey('nrens.country_code'))
-    nren = relationship('Nrens', back_populates='budgets')
+    id: Mapped[int] = mapped_column(primary_key=True)
+    budget: Mapped[Optional[str]]
+    year: Mapped[Optional[int]]
+    country_code: Mapped[Optional[str]] = mapped_column(ForeignKey('nrens.country_code'))
+    nren: Mapped[Optional['Nrens']] = relationship(back_populates='budgets')
 
 
-class Nrens(base_schema):
+class Nrens(Base):
     __tablename__ = 'nrens'
-    id = sa.Column(sa.Integer, primary_key=True)
-    abbreviation = sa.Column(sa.String)
-    country_code = sa.Column(sa.String)
-    budgets = relationship('Budgets', back_populates='nren')
+    id: Mapped[int] = mapped_column(primary_key=True)
+    abbreviation: Mapped[Optional[str]]
+    country_code: Mapped[Optional[str]]
+    budgets: Mapped[List['Budgets']] = relationship(back_populates='nren')

docs/source/api.rst

@@ -9,14 +9,8 @@ Responses to valid requests are returned as JSON messages.
 The server will therefore return an error unless
 `application/json` is in the `Accept` request header field.
 
-HTTP communication and JSON grammar details are
-beyond the scope of this document.
-Please refer to [RFC 2616](https://tools.ietf.org/html/rfc2616)
-and www.json.org for more details.
-
-.. contents:: :local:
-
-.. automodule:: compendium_v2.routes.default
-
-.. automodule:: compendium_v2.routes.api
+.. qrefflask:: compendium_v2:_create_app(None)
+   :autoquickref:
 
+.. autoflask:: compendium_v2:_create_app(None)
+   :undoc-static:

docs/source/conf.py

@@ -73,7 +73,9 @@ release = '0.0'
 extensions = [
   'sphinx_rtd_theme',
   'sphinx.ext.autodoc',
-  'sphinx.ext.coverage'
+  'sphinx.ext.coverage',
+  'sphinxcontrib.autohttp.flask',
+  'sphinxcontrib.autohttp.flaskqref'
 ]
 
 # Add any paths that contain templates here, relative to this directory.

docs/source/index.rst

@@ -11,3 +11,4 @@ a React web application that consumes and renders the json data.
 
    api
    development
+   publishers

docs/source/publishers.rst

+.. api intro
+
+Publishers
+===============
+
+
+.. contents:: :local:
+
+.. automodule:: compendium_v2.publishers.survey_publisher_v1
+    :members:
+
+.. automodule:: compendium_v2.publishers.survey_publisher_2022
+    :members:

requirements.txt

@@ -6,19 +6,19 @@ flask-cors
 psycopg2-binary
 cryptography
 SQLAlchemy
+openpyxl
 pytest
 pytest-mock
 python-dotenv
 
 sphinx
 sphinx-rtd-theme
+sphinxcontrib-httpdomain
 tox
 
 mypy
 types-docutils
 types-jsonschema
 types-Flask-Cors
+types-openpyxl
 types-setuptools
-types-sqlalchemy
-
-openpyxl