Rename application package to src from api (#146)

In PR #138 we renamed the route package to api, which makes it api.api.
This PR renames the top level package to src to avoid naming issues and
to represent the idea that the application contains other things like
CLI commands / background jobs. We considered naming it app, but that
would conflict with the app folder at the repo root, and it would also
create ambiguity with the flask app variable.

app/Dockerfile

@@ -34,4 +34,4 @@ ENV HOST=0.0.0.0
 # https://python-poetry.org/docs/basic-usage/#installing-dependencies
 RUN poetry install
 # Run the application.
-CMD ["poetry", "run", "python", "-m", "api"]
+CMD ["poetry", "run", "python", "-m", "src"]

app/Makefile

@@ -10,15 +10,15 @@ APP_NAME := main-app
 # Note that you can also change the LOG_FORMAT env var to switch
 # between JSON & human readable format. This is left in place
 # in the event JSON is output from a process we don't log.
-DECODE_LOG := 2>&1 | python3 -u api/logging/util/decodelog.py
+DECODE_LOG := 2>&1 | python3 -u src/logging/util/decodelog.py
 
 # A few commands need adjustments if they're run in CI, specify those here
 # TODO - when CI gets hooked up, actually test this.
 ifdef CI
  DOCKER_EXEC_ARGS := -T -e CI -e PYTEST_ADDOPTS="--color=yes"
- FLAKE8_FORMAT := '::warning file=api/%(path)s,line=%(row)d,col=%(col)d::%(path)s:%(row)d:%(col)d: %(code)s %(text)s'
+ FLAKE8_FORMAT := '::warning file=src/%(path)s,line=%(row)d,col=%(col)d::%(path)s:%(row)d:%(col)d: %(code)s %(text)s'
  MYPY_FLAGS := --no-pretty
- MYPY_POSTPROC := | perl -pe "s/^(.+):(\d+):(\d+): error: (.*)/::warning file=api\/\1,line=\2,col=\3::\4/"
+ MYPY_POSTPROC := | perl -pe "s/^(.+):(\d+):(\d+): error: (.*)/::warning file=src\/\1,line=\2,col=\3::\4/"
 else
  FLAKE8_FORMAT := default
 endif
@@ -92,7 +92,7 @@ db-recreate: clean-docker-volumes init-db
 # DB Migrations
 #########################
 
-alembic_config := ./api/db/migrations/alembic.ini
+alembic_config := ./src/db/migrations/alembic.ini
 alembic_cmd := $(PY_RUN_CMD) alembic --config $(alembic_config)
 
 db-upgrade: ## Apply pending migrations to db
@@ -139,7 +139,7 @@ test-watch:
 	$(PY_RUN_CMD) pytest-watch --clear $(args)
 
 test-coverage:
-	$(PY_RUN_CMD) coverage run --branch --source=api -m pytest -m "not audit" $(args)
+	$(PY_RUN_CMD) coverage run --branch --source=src -m pytest -m "not audit" $(args)
 	$(PY_RUN_CMD) coverage report
 
 test-coverage-report: ## Open HTML test coverage report
@@ -151,22 +151,22 @@ test-coverage-report: ## Open HTML test coverage report
 ##################################################
 
 format:
-	$(PY_RUN_CMD) isort --atomic api tests
-	$(PY_RUN_CMD) black api tests
+	$(PY_RUN_CMD) isort --atomic src tests
+	$(PY_RUN_CMD) black src tests
 
 format-check:
-	$(PY_RUN_CMD) isort --atomic --check-only api tests
-	$(PY_RUN_CMD) black --check api tests
+	$(PY_RUN_CMD) isort --atomic --check-only src tests
+	$(PY_RUN_CMD) black --check src tests
 
 lint: lint-py
 
 lint-py: lint-flake lint-mypy
 
 lint-flake:
-	$(PY_RUN_CMD) flake8 --format=$(FLAKE8_FORMAT) api tests
+	$(PY_RUN_CMD) flake8 --format=$(FLAKE8_FORMAT) src tests
 
 lint-mypy:
-	$(PY_RUN_CMD) mypy --show-error-codes $(MYPY_FLAGS) api $(MYPY_POSTPROC)
+	$(PY_RUN_CMD) mypy --show-error-codes $(MYPY_FLAGS) src $(MYPY_POSTPROC)
 
 lint-security: # https://bandit.readthedocs.io/en/latest/index.html
 	$(PY_RUN_CMD) bandit -c pyproject.toml -r . --number 3 --skip B101 -ll -x ./.venv

app/local.env

@@ -1,6 +1,6 @@
 # Local environment variables
 # Used by docker-compose and it can be loaded
-# by calling load_local_env_vars() from app/api/util/local.py
+# by calling load_local_env_vars() from app/src/util/local.py
 
 ENVIRONMENT=local
 PORT=8080
@@ -15,7 +15,7 @@ PYTHONPATH=/app/
 # commands that can run in or out
 # of the Docker container - defaults to outside
 
-FLASK_APP=api.app:create_app
+FLASK_APP=src.app:create_app
 
 ############################
 # Logging

app/pyproject.toml

@@ -2,7 +2,7 @@
 name = "template-application-flask"
 version = "0.1.0"
 description = "A template flask API for building ontop of"
-packages = [{ include = "api" }]
+packages = [{ include = "src" }]
 authors = ["Nava Engineering <[email protected]>"]
 
 [tool.poetry.dependencies]
@@ -44,9 +44,9 @@ requires = ["poetry-core>=1.0.0"]
 build-backend = "poetry.core.masonry.api"
 
 [tool.poetry.scripts]
-db-migrate-up = "api.db.migrations.run:up"
-db-migrate-down = "api.db.migrations.run:down"
-db-migrate-down-all = "api.db.migrations.run:downall"
+db-migrate-up = "src.db.migrations.run:up"
+db-migrate-down = "src.db.migrations.run:down"
+db-migrate-down-all = "src.db.migrations.run:downall"
 
 [tool.black]
 line-length = 100
@@ -85,14 +85,14 @@ plugins = ["sqlalchemy.ext.mypy.plugin"]
 
 [tool.bandit]
 # Ignore audit logging test file since test audit logging requires a lot of operations that trigger bandit warnings
-exclude_dirs = ["./tests/api/logging/test_audit.py"]
+exclude_dirs = ["./tests/src/logging/test_audit.py"]
 
 [[tool.mypy.overrides]]
 # Migrations are generated without "-> None"
 # for the returns. Rather than require manually
 # fixing this for every migration generated,
 # disable the check for that folder.
-module = "api.db.migrations.versions.*"
+module = "src.db.migrations.versions.*"
 disallow_untyped_defs = false
 
 [tool.pytest.ini_options]
@@ -108,5 +108,5 @@ markers = [
   "audit: mark a test as a security audit log test, to be run isolated from other tests"]
 
 [tool.coverage.run]
-omit = ["api/db/migrations/*.py"]
+omit = ["src/db/migrations/*.py"]
 

app/api/__main__.py → app/src/__main__.py

@@ -7,10 +7,10 @@
 
 import logging
 
-import api.app
-import api.logging
-from api.app_config import AppConfig
-from api.util.local import load_local_env_vars
+import src.app
+import src.logging
+from src.app_config import AppConfig
+from src.util.local import load_local_env_vars
 
 logger = logging.getLogger(__package__)
 
@@ -19,7 +19,7 @@ def main() -> None:
     load_local_env_vars()
     app_config = AppConfig()
 
-    app = api.app.create_app()
+    app = src.app.create_app()
 
     environment = app_config.environment
 

app/api/adapters/db/__init__.py → app/src/adapters/db/__init__.py

@@ -7,7 +7,7 @@
 To use this module with Flask, use the flask_db module.
 
 Usage:
-    import api.adapters.db as db
+    import src.adapters.db as db
 
     db_client = db.init()
 
@@ -23,7 +23,7 @@
 """
 
 # Re-export for convenience
-from api.adapters.db.client import Connection, DBClient, Session, init
+from src.adapters.db.client import Connection, DBClient, Session, init
 
 # Do not import flask_db here, because this module is not dependent on any specific framework.
 # Code can choose to use this module on its own or with the flask_db module depending on needs.

app/api/adapters/db/client.py → app/src/adapters/db/client.py

@@ -17,7 +17,7 @@
 import sqlalchemy.pool as pool
 from sqlalchemy.orm import session
 
-from api.adapters.db.config import DbConfig, get_db_config
+from src.adapters.db.config import DbConfig, get_db_config
 
 # Re-export the Connection type that is returned by the get_connection() method
 # to be used for type hints.

app/api/adapters/db/config.py → app/src/adapters/db/config.py

@@ -3,7 +3,7 @@
 
 from pydantic import Field
 
-from api.util.env_config import PydanticBaseEnvConfig
+from src.util.env_config import PydanticBaseEnvConfig
 
 logger = logging.getLogger(__name__)
 

app/api/adapters/db/flask_db.py → app/src/adapters/db/flask_db.py

@@ -5,8 +5,8 @@
 of a Flask app and an instance of a DBClient.
 
 Example:
-    import api.adapters.db as db
-    import api.adapters.db.flask_db as flask_db
+    import src.adapters.db as db
+    import src.adapters.db.flask_db as flask_db
 
     db_client = db.init()
     app = APIFlask(__name__)
@@ -16,8 +16,8 @@
 new database session that lasts for the duration of the request.
 
 Example:
-    import api.adapters.db as db
-    import api.adapters.db.flask_db as flask_db
+    import src.adapters.db as db
+    import src.adapters.db.flask_db as flask_db
 
     @app.route("/health")
     @flask_db.with_db_session
@@ -31,7 +31,7 @@ def health(db_session: db.Session):
 
 Example:
     from flask import current_app
-    import api.adapters.db.flask_db as flask_db
+    import src.adapters.db.flask_db as flask_db
 
     @app.route("/health")
     def health():
@@ -43,8 +43,8 @@ def health():
 
 from flask import Flask, current_app
 
-import api.adapters.db as db
-from api.adapters.db.client import DBClient
+import src.adapters.db as db
+from src.adapters.db.client import DBClient
 
 _FLASK_EXTENSION_KEY = "db"
 
@@ -67,7 +67,7 @@ def get_db(app: Flask) -> DBClient:
 
     Example:
         from flask import current_app
-        import api.adapters.db.flask_db as flask_db
+        import src.adapters.db.flask_db as flask_db
 
         @app.route("/health")
         def health():

app/api/api/healthcheck.py → app/src/api/healthcheck.py

@@ -6,9 +6,9 @@
 from sqlalchemy import text
 from werkzeug.exceptions import ServiceUnavailable
 
-import api.adapters.db.flask_db as flask_db
-from api.api import response
-from api.api.schemas import request_schema
+import src.adapters.db.flask_db as flask_db
+from src.api import response
+from src.api.schemas import request_schema
 
 logger = logging.getLogger(__name__)
 

app/api/api/response.py → app/src/api/response.py

@@ -1,8 +1,8 @@
 import dataclasses
 from typing import Optional
 
-from api.api.schemas import response_schema
-from api.db.models.base import Base
+from src.api.schemas import response_schema
+from src.db.models.base import Base
 
 
 @dataclasses.dataclass

app/api/api/schemas/response_schema.py → app/src/api/schemas/response_schema.py

@@ -1,6 +1,6 @@
 from apiflask import fields
 
-from api.api.schemas import request_schema
+from src.api.schemas import request_schema
 
 
 class ValidationErrorSchema(request_schema.OrderedSchema):

app/api/api/users/__init__.py → app/src/api/users/__init__.py

@@ -1,10 +1,10 @@
-from api.api.users.user_blueprint import user_blueprint
+from src.api.users.user_blueprint import user_blueprint
 
 # import user_commands module to register the CLI commands on the user_blueprint
-import api.api.users.user_commands  # noqa: F401 E402 isort:skip
+import src.api.users.user_commands  # noqa: F401 E402 isort:skip
 
 # import user_commands module to register the API routes on the user_blueprint
-import api.api.users.user_routes  # noqa: F401 E402 isort:skip
+import src.api.users.user_routes  # noqa: F401 E402 isort:skip
 
 
 __all__ = ["user_blueprint"]

app/api/api/users/user_commands.py → app/src/api/users/user_commands.py

@@ -4,11 +4,11 @@
 
 import click
 
-import api.adapters.db as db
-import api.adapters.db.flask_db as flask_db
-import api.services.users as user_service
-from api.api.users.user_blueprint import user_blueprint
-from api.util.datetime_util import utcnow
+import src.adapters.db as db
+import src.adapters.db.flask_db as flask_db
+import src.services.users as user_service
+from src.api.users.user_blueprint import user_blueprint
+from src.util.datetime_util import utcnow
 
 logger = logging.getLogger(__name__)
 

app/api/api/users/user_routes.py → app/src/api/users/user_routes.py

@@ -1,15 +1,15 @@
 import logging
 from typing import Any
 
-import api.adapters.db as db
-import api.adapters.db.flask_db as flask_db
-import api.api.response as response
-import api.api.users.user_schemas as user_schemas
-import api.services.users as user_service
-import api.services.users as users
-from api.api.users.user_blueprint import user_blueprint
-from api.auth.api_key_auth import api_key_auth
-from api.db.models.user_models import User
+import src.adapters.db as db
+import src.adapters.db.flask_db as flask_db
+import src.api.response as response
+import src.api.users.user_schemas as user_schemas
+import src.services.users as user_service
+import src.services.users as users
+from src.api.users.user_blueprint import user_blueprint
+from src.auth.api_key_auth import api_key_auth
+from src.db.models.user_models import User
 
 logger = logging.getLogger(__name__)
 

app/api/api/users/user_schemas.py → app/src/api/users/user_schemas.py

@@ -1,8 +1,8 @@
 from apiflask import fields
 from marshmallow import fields as marshmallow_fields
 
-from api.api.schemas import request_schema
-from api.db.models import user_models
+from src.api.schemas import request_schema
+from src.db.models import user_models
 
 
 class RoleSchema(request_schema.OrderedSchema):

app/api/app.py → app/src/app.py

@@ -6,22 +6,22 @@
 from flask import g
 from werkzeug.exceptions import Unauthorized
 
-import api.adapters.db as db
-import api.adapters.db.flask_db as flask_db
-import api.logging
-import api.logging.flask_logger as flask_logger
-from api.api.healthcheck import healthcheck_blueprint
-from api.api.schemas import response_schema
-from api.api.users import user_blueprint
-from api.auth.api_key_auth import User, get_app_security_scheme
+import src.adapters.db as db
+import src.adapters.db.flask_db as flask_db
+import src.logging
+import src.logging.flask_logger as flask_logger
+from src.api.healthcheck import healthcheck_blueprint
+from src.api.schemas import response_schema
+from src.api.users import user_blueprint
+from src.auth.api_key_auth import User, get_app_security_scheme
 
 logger = logging.getLogger(__name__)
 
 
 def create_app() -> APIFlask:
     app = APIFlask(__name__)
 
-    root_logger = api.logging.init(__package__)
+    root_logger = src.logging.init(__package__)
     flask_logger.init_app(root_logger, app)
 
     db_client = db.init()

app/api/app_config.py → app/src/app_config.py

@@ -1,4 +1,4 @@
-from api.util.env_config import PydanticBaseEnvConfig
+from src.util.env_config import PydanticBaseEnvConfig
 
 
 class AppConfig(PydanticBaseEnvConfig):

app/api/db/migrations/alembic.ini → app/src/db/migrations/alembic.ini

@@ -2,7 +2,7 @@
 
 [alembic]
 # path to migration scripts
-script_location = api/db/migrations
+script_location = src/db/migrations
 
 file_template = %%(year)d_%%(month).2d_%%(day).2d_%%(slug)s