feat: Added database migration with alembic (#112)

* feat: alembic database migration config

* chore: PYTHONPATH app/ to make python app modules importable

* chore: github workflow placeholder for alembic db migration

* doc: alembic contributing link

* chore: move alembic to requirements-dev

* chore: remove gh workflow comments

* chore: remove useless alembic.ini comments

* docs: Fixed copyright + license notice

Co-authored-by: Jean <[email protected]>
Co-authored-by: frgfm <[email protected]>

CONTRIBUTING.md

@@ -60,3 +60,8 @@ To ensure that your incoming PR complies with the lint settings, you need to ins
 flake8 ./
 ```
 This will read the `.flake8` setting file and let you know whether your commits need some adjustments.
+
+
+### Database schema migration
+
+- See [Alembic](src/alembic) guide to create revision and run it locally. 

Dockerfile

@@ -6,6 +6,8 @@ WORKDIR /usr/src/app
 # set environment variables
 ENV PYTHONDONTWRITEBYTECODE 1
 ENV PYTHONUNBUFFERED 1
+ENV PYTHONPATH "${PYTHONPATH}:/app"
+
 
 # copy requirements file
 COPY ./requirements.txt /usr/src/app/requirements.txt

src/alembic.ini

@@ -0,0 +1,80 @@
+[alembic]
+# path to migration scripts
+script_location = alembic
+
+# template used to generate migration files
+# file_template = %%(rev)s_%%(slug)s
+
+# timezone to use when rendering the date
+# within the migration file as well as the filename.
+# string value is passed to dateutil.tz.gettz()
+# 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 alembic/versions.  When using multiple version
+# directories, initial revisions must be specified with --version-path
+# version_locations = %(here)s/bar %(here)s/bat alembic/versions
+
+# the output encoding used when revision files
+# are written from script.py.mako
+# output_encoding = utf-8
+
+[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
+
+# Logging configuration
+[loggers]
+keys = root,sqlalchemy,alembic
+
+[handlers]
+keys = console
+
+[formatters]
+keys = generic
+
+[logger_root]
+level = WARN
+handlers = console
+qualname =
+
+[logger_sqlalchemy]
+level = WARN
+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

src/alembic/README.md

@@ -0,0 +1,22 @@
+# Alembic main commands
+
+Following main guidelines, following commands should be run within a running container using docker-compose: `$ PORT=8002 docker-compose exec -T web alembic ...` 
+
+## Manually created revision
+
+-> `$ alembic revision -m "create account table"`<br/>
+generates template "alembic/{id}_create_account_table.py"
+
+-> implement `upgrade()` & `downgrade()` functions using SQLAlchemy operations (op.create_table, op.add_column, etc.)
+
+-> `$ alembic upgrade head`
+applies all pending revisions to database
+
+
+## Auto generated revision
+**Alternative** using auto generated revision (https://alembic.sqlalchemy.org/en/latest/autogenerate.html)
+
+-> `$ alembic revision --autogenerate -m "Add account ts column"`
+generates filled "alembic/{id}_add_account_ts_column.py"
+
+-> review and adjust generated script

src/alembic/env.py

@@ -0,0 +1,87 @@
+# Copyright (C) 2021, Pyronear contributors.
+
+# This program is licensed under the Apache License version 2.
+# See LICENSE or go to <https://www.apache.org/licenses/LICENSE-2.0.txt> for full license details.
+
+from logging.config import fileConfig
+
+from sqlalchemy import engine_from_config
+from sqlalchemy import pool
+
+from alembic import context
+
+from app import config as cfg
+from app.db import metadata
+
+# this is the Alembic Config object, which provides
+# access to the values within the .ini file in use.
+config = context.config
+
+# Interpret the config file for Python logging.
+# This line sets up loggers basically.
+fileConfig(config.config_file_name)
+
+# for 'autogenerate' support
+target_metadata = metadata
+
+# 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.
+
+
+def get_db_url():
+    return cfg.DATABASE_URL
+
+
+def run_migrations_offline():
+    """Run migrations in 'offline' mode.
+
+    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.
+
+    Calls to context.execute() here emit the given string to the
+    script output.
+
+    """
+    context.configure(
+        url=get_db_url(),
+        target_metadata=target_metadata,
+        literal_binds=True,
+        dialect_opts={"paramstyle": "named"},
+    )
+
+    with context.begin_transaction():
+        context.run_migrations()
+
+
+def run_migrations_online():
+    """Run migrations in 'online' mode.
+
+    In this scenario we need to create an Engine
+    and associate a connection with the context.
+
+    """
+    configuration = config.get_section(config.config_ini_section)
+    configuration["sqlalchemy.url"] = get_db_url()
+    connectable = engine_from_config(
+        configuration,
+        prefix="sqlalchemy.",
+        poolclass=pool.NullPool,
+    )
+
+    with connectable.connect() as connection:
+        context.configure(
+            connection=connection, target_metadata=target_metadata
+        )
+
+        with context.begin_transaction():
+            context.run_migrations()
+
+
+if context.is_offline_mode():
+    run_migrations_offline()
+else:
+    run_migrations_online()

src/alembic/script.py.mako

@@ -0,0 +1,24 @@
+"""${message}
+
+Revision ID: ${up_revision}
+Revises: ${down_revision | comma,n}
+Create Date: ${create_date}
+
+"""
+from alembic import op
+import sqlalchemy as sa
+${imports if imports else ""}
+
+# revision identifiers, used by Alembic.
+revision = ${repr(up_revision)}
+down_revision = ${repr(down_revision)}
+branch_labels = ${repr(branch_labels)}
+depends_on = ${repr(depends_on)}
+
+
+def upgrade():
+    ${upgrades if upgrades else "pass"}
+
+
+def downgrade():
+    ${downgrades if downgrades else "pass"}

src/requirements-dev.txt

@@ -4,3 +4,4 @@ asyncpg>=0.20.0
 coverage>=4.5.4
 aiosqlite>=0.16.0
 httpx>=0.16.1
+alembic==1.5.4