bootstap script (#145)

## Description
Removing the git controlled `.env` file and automating the dev setup
process with `scripts/bootstrap.sh`.

## Additional Notes
Developers should be able to customize the .env file to their
environment, and not have to worry about it changing whenever they pull
new code. To make the developer setup process easy, the new bootstrap
script will create a .env file if it doesn't exist, initialize a virtual
environment if it doesn't exist, activate the virtual env and install
the development python requirements.

- Connection pooling parameters now have their default values set to
None, so it will work with sqlite:///:memory:
- The sessionmaker autocommit parameter was removed in sqlalchemy 2.0

.gitignore

@@ -31,6 +31,9 @@ temp/
 # ignore all files ending in .DS_Store
 **/.DS_Store
 
+# Project environment files
+.env
+
 # Python-Virtual Environments
 .venv
 .python-version

README.md

@@ -20,19 +20,17 @@ The RecordLinker is a service that links records from two datasets based on a se
 ### Initial Setup
 
 Set up a Python virtual environment and install the required development dependencies:
-NOTE: The `-e` flag is used to install the package in "src/" in editable mode. This allows
-the package to be imported in other modules without needing to re-install the package.
+NOTE: Sourcing the script is recommended over simply executing the script. This allows
+the virtual environment to stay active in your shell.
 ```bash
-python -m venv .venv
-source .venv/bin/activate
-pip install -e '.[dev]'
+source scripts/bootstrap.sh
 ```
 
 ### Running the API
 
 To run the API locally, use the following command:
 ```bash
-./scripts/local_server.sh 8000
+./scripts/local_server.sh
 ```
 
 The API will be available at `http://localhost:8000`. Visit `http://localhost:8000/redocs` to view the API documentation.
@@ -49,6 +47,20 @@ To run a single unit test, use the following command:
 pytest tests/unit/test_utils.py::test_bind_functions
 ```
 
+### Running type checks
+
+To run type checks, use the following command:
+```bash
+mypy
+```
+
+### Running code formatting checks
+
+To run code formatting checks, use the following command:
+```bash
+ruff check
+```
+
 For more information on developer workflows, see the [Developer Guide](docs/developer_guide.md).
 
 ## Standard Notices

pyproject.toml

@@ -101,6 +101,7 @@ filterwarnings = [
     "ignore:typing.io is deprecated, import directly from typing instead:DeprecationWarning"
 ]
 env = [
+    "DB_URI=sqlite:///:memory:",
     "INITIAL_ALGORITHMS=",
 ]
 

scripts/bootstrap.sh

@@ -0,0 +1,32 @@
+#!/bin/bash
+
+# Use this script to initialize the development environment.
+#
+# Usage: source bootstrap.sh
+# Requires: python3
+
+cd "$(dirname "$0")/.."
+
+# Create a default .env file if it doesn't exist
+if [ ! -f .env ]; then
+    echo "Creating a default .env file..."
+    echo "DB_URI=sqlite:///db.sqlite3" > .env
+else
+    echo "Default .env file already exists."
+fi
+
+# Create a virtual environment if it doesn't exist
+if [ ! -d .venv ]; then
+    echo "Creating a virtual environment..."
+    python3 -m venv .venv
+else
+    echo "Virtual environment already exists."
+fi
+
+# Activate the virtual environment
+echo "Activating the virtual environment..."
+source .venv/bin/activate
+# Install the development requirements
+echo "Installing the development requirements..."
+pip install --upgrade pip > /dev/null
+pip install '.[dev]' > /dev/null

src/recordlinker/config.py

@@ -33,12 +33,12 @@ class Settings(pydantic_settings.BaseSettings):
     )
     connection_pool_size: typing.Optional[int] = pydantic.Field(
         description="The number of MPI database connections in the connection pool",
-        default=5,
+        default=None,
     )
     connection_pool_max_overflow: typing.Optional[int] = pydantic.Field(
         description="The maximum number of MPI database connections that can be opened "
         "above the connection pool size",
-        default=10,
+        default=None,
     )
     log_config: typing.Optional[str] = pydantic.Field(
         description="The path to the logging configuration file",

src/recordlinker/database/__init__.py

@@ -19,14 +19,15 @@ def create_sessionmaker(init_tables: bool = True) -> orm.sessionmaker:
     """
     Create a new sessionmaker for the database connection.
     """
-    engine = create_engine(
-        settings.db_uri,
-        pool_size=settings.connection_pool_size,
-        max_overflow=settings.connection_pool_max_overflow,
-    )
+    kwargs: dict[str, typing.Any] = {}
+    if settings.connection_pool_size is not None:
+        kwargs["pool_size"] = settings.connection_pool_size
+    if settings.connection_pool_max_overflow is not None:
+        kwargs["max_overflow"] = settings.connection_pool_max_overflow
+    engine = create_engine(settings.db_uri, **kwargs)
     if init_tables:
         models.Base.metadata.create_all(engine)
-    return orm.sessionmaker(autocommit=False, bind=engine)
+    return orm.sessionmaker(bind=engine)
 
 
 def get_session() -> typing.Iterator[orm.Session]:

tests/unit/database/test_base.py

@@ -0,0 +1,31 @@
+"""
+unit.database.test_base.py
+~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+This module contains the unit tests for the recordlinker.database module.
+"""
+
+import unittest.mock
+
+from recordlinker.config import settings
+from recordlinker.database import create_sessionmaker
+
+
+def test_create_sessionmaker():
+    """
+    Test the create_sessionmaker function.
+    """
+    with unittest.mock.patch.dict(
+        "os.environ",
+        {
+            "DB_URI": "sqlite:///test.db",
+            "CONNECTION_POOL_SIZE": "10",
+            "CONNECTION_POOL_MAX_OVERFLOW": "20",
+        },
+    ):
+        settings.__init__()
+        session = create_sessionmaker()()
+        assert str(session.bind.url) == "sqlite:///test.db"
+        assert session.bind.pool.size() == 10
+        assert session.bind.pool._max_overflow == 20
+    settings.__init__()