Docker deployment

.dockerignore

@@ -0,0 +1 @@
+.venv

.gitattributes

@@ -0,0 +1 @@
+*.sh text eol=lf

.gitignore

@@ -24,5 +24,4 @@ migrate.sh
 
 
 # deployment files
-app.yaml
-alembic.ini
+app.yaml

.pre-commit-config.yaml

@@ -0,0 +1,21 @@
+repos:
+  - repo: https://github.com/psf/black
+    rev: 24.4.2
+    hooks:
+      - id: black
+
+  - repo: https://github.com/pycqa/flake8
+    rev: 7.0.0
+    hooks:
+      - id: flake8
+        args: [
+          '--count',
+          '--select=E9,F63,F7,F82,F401,F541,F631,F634,F701,F702',
+          '--show-source',
+          '--statistics'
+          ]
+
+  # - repo: https://github.com/pre-commit/mirrors-mypy
+  #   rev: v1.10.0  # Use the latest stable version or pin to your preference
+  #   hooks:
+  #     - id: mypy

README.md

@@ -43,6 +43,9 @@ uv venv
 source .venv/bin/activate
 uv pip install -r requirements.txt
 
+# Set up pre-commit hooks
+pre-commit install
+
 # Set up environment variables
 cp .env.example .env
 # Edit `.env` to configure database connection and app settings

alembic.ini

@@ -0,0 +1,141 @@
+# A generic, single database configuration.
+
+[alembic]
+# path to migration scripts.
+# this is typically a path given in POSIX (e.g. forward slashes)
+# format, relative to the token %(here)s which refers to the location of this
+# ini file
+script_location = %(here)s/alembic
+
+# template used to generate migration file names; The default value is %%(rev)s_%%(slug)s
+# Uncomment the line below if you want the files to be prepended with date and time
+# see https://alembic.sqlalchemy.org/en/latest/tutorial.html#editing-the-ini-file
+# for all available tokens
+# file_template = %%(year)d_%%(month).2d_%%(day).2d_%%(hour).2d%%(minute).2d-%%(rev)s_%%(slug)s
+
+# sys.path path, will be prepended to sys.path if present.
+# defaults to the current working directory.  for multiple paths, the path separator
+# is defined by "path_separator" below.
+prepend_sys_path = .
+
+
+# timezone to use when rendering the date within the migration file
+# as well as the filename.
+# If specified, requires the python>=3.9 or backports.zoneinfo library and tzdata library.
+# Any required deps can installed by adding `alembic[tz]` to the pip requirements
+# string value is passed to ZoneInfo()
+# leave blank for localtime
+# timezone =
+
+# max length of characters to apply to the "slug" field
+# truncate_slug_length = 40
+
+# set to 'true' to run the environment during
+# the 'revision' command, regardless of autogenerate
+# revision_environment = false
+
+# set to 'true' to allow .pyc and .pyo files without
+# a source .py file to be detected as revisions in the
+# versions/ directory
+# sourceless = false
+
+# version location specification; This defaults
+# to <script_location>/versions.  When using multiple version
+# directories, initial revisions must be specified with --version-path.
+# The path separator used here should be the separator specified by "path_separator"
+# below.
+# version_locations = %(here)s/bar:%(here)s/bat:%(here)s/alembic/versions
+
+# path_separator; This indicates what character is used to split lists of file
+# paths, including version_locations and prepend_sys_path within configparser
+# files such as alembic.ini.
+# The default rendered in new alembic.ini files is "os", which uses os.pathsep
+# to provide os-dependent path splitting.
+#
+# Note that in order to support legacy alembic.ini files, this default does NOT
+# take place if path_separator is not present in alembic.ini.  If this
+# option is omitted entirely, fallback logic is as follows:
+#
+# 1. Parsing of the version_locations option falls back to using the legacy
+#    "version_path_separator" key, which if absent then falls back to the legacy
+#    behavior of splitting on spaces and/or commas.
+# 2. Parsing of the prepend_sys_path option falls back to the legacy
+#    behavior of splitting on spaces, commas, or colons.
+#
+# Valid values for path_separator are:
+#
+# path_separator = :
+# path_separator = ;
+# path_separator = space
+# path_separator = newline
+#
+# Use os.pathsep. Default configuration used for new projects.
+path_separator = os
+
+# set to 'true' to search source files recursively
+# in each "version_locations" directory
+# new in Alembic version 1.10
+# recursive_version_locations = false
+
+# the output encoding used when revision files
+# are written from script.py.mako
+# output_encoding = utf-8
+
+# database URL.  This is consumed by the user-maintained env.py script only.
+# other means of configuring database URLs may be customized within the env.py
+# file.
+sqlalchemy.url = 
+
+
+[post_write_hooks]
+# post_write_hooks defines scripts or Python functions that are run
+# on newly generated revision scripts.  See the documentation for further
+# detail and examples
+
+# format using "black" - use the console_scripts runner, against the "black" entrypoint
+# hooks = black
+# black.type = console_scripts
+# black.entrypoint = black
+# black.options = -l 79 REVISION_SCRIPT_FILENAME
+
+# lint with attempts to fix using "ruff" - use the exec runner, execute a binary
+# hooks = ruff
+# ruff.type = exec
+# ruff.executable = %(here)s/.venv/bin/ruff
+# ruff.options = check --fix REVISION_SCRIPT_FILENAME
+
+# Logging configuration.  This is also consumed by the user-maintained
+# env.py script only.
+[loggers]
+keys = root,sqlalchemy,alembic
+
+[handlers]
+keys = console
+
+[formatters]
+keys = generic
+
+[logger_root]
+level = WARNING
+handlers = console
+qualname =
+
+[logger_sqlalchemy]
+level = WARNING
+handlers =
+qualname = sqlalchemy.engine
+
+[logger_alembic]
+level = INFO
+handlers =
+qualname = alembic
+
+[handler_console]
+class = StreamHandler
+args = (sys.stderr,)
+level = NOTSET
+formatter = generic
+
+[formatter_generic]
+format = %(levelname)-5.5s [%(name)s] %(message)s
+datefmt = %H:%M:%S

alembic/README

@@ -1 +1 @@
-pyproject configuration, based on the generic configuration.
+Generic single-database configuration.

alembic/env.py

@@ -1,9 +1,10 @@
+from alembic import context
+from dotenv import load_dotenv
 from logging.config import fileConfig
-
+from os import environ
 from sqlalchemy import engine_from_config
 from sqlalchemy import pool
 
-from alembic import context
 
 # this is the Alembic Config object, which provides
 # access to the values within the .ini file in use.
@@ -19,35 +20,46 @@
 # from myapp import mymodel
 
 # from db import Base  # Import your Base from models/__init__.py
-from db import *
+from db import Base
 
 # target_metadata = mymodel.Base.metadata
 target_metadata = Base.metadata
+model_tables = set(target_metadata.tables.keys())
 
 # other values from the config, defined by the needs of env.py,
 # can be acquired:
 # my_important_option = config.get_main_option("my_important_option")
 # ... etc.
 
+load_dotenv()
 
-def run_migrations_offline() -> None:
-    """Run migrations in 'offline' mode.
+# Fallback to environment variables for PostgreSQL connection
+user = environ.get("POSTGRES_USER", None)
+password = environ.get("POSTGRES_PASSWORD", None)
+db = environ.get("POSTGRES_DB", None)
+host = environ.get("POSTGRES_HOST", None)
+port = environ.get("POSTGRES_PORT", None)
+SQLALCHEMY_DATABASE_URL = f"postgresql+psycopg2://{user}:{password}@{host}:{port}/{db}"
 
-    This configures the context with just a URL
-    and not an Engine, though an Engine is acceptable
-    here as well.  By skipping the Engine creation
-    we don't even need a DBAPI to be available.
+config.set_main_option("sqlalchemy.url", SQLALCHEMY_DATABASE_URL)
 
-    Calls to context.execute() here emit the given string to the
-    script output.
 
-    """
+def include_object(object, name, type_, reflected, compare_to):
+    # only include tables in sql alchemy model, not auto-generated tables from PostGIS or TIGER
+    if type_ == "table":
+        return name in model_tables
+    return True
+
+
+def run_migrations_offline() -> None:
+    """Run migrations in 'offline' mode."""
     url = config.get_main_option("sqlalchemy.url")
     context.configure(
         url=url,
         target_metadata=target_metadata,
         literal_binds=True,
         dialect_opts={"paramstyle": "named"},
+        include_object=include_object,
     )
 
     with context.begin_transaction():
@@ -68,8 +80,11 @@ def run_migrations_online() -> None:
     )
 
     with connectable.connect() as connection:
-        context.configure(connection=connection, target_metadata=target_metadata)
-
+        context.configure(
+            connection=connection,
+            target_metadata=target_metadata,
+            include_object=include_object,
+        )
         with context.begin_transaction():
             context.run_migrations()
 

alembic/script.py.mako

@@ -8,12 +8,14 @@ Create Date: ${create_date}
 from typing import Sequence, Union
 
 from alembic import op
+import geoalchemy2
 import sqlalchemy as sa
+import sqlalchemy_utils
 ${imports if imports else ""}
 
 # revision identifiers, used by Alembic.
 revision: str = ${repr(up_revision)}
-down_revision: Union[str, None] = ${repr(down_revision)}
+down_revision: Union[str, Sequence[str], None] = ${repr(down_revision)}
 branch_labels: Union[str, Sequence[str], None] = ${repr(branch_labels)}
 depends_on: Union[str, Sequence[str], None] = ${repr(depends_on)}