[Done] Initial migration + migrate friction type 4 to 2 (#80)

CHANGES.rst

@@ -13,6 +13,13 @@ Changelog of threedi-modelchecker
 
 - Removed the summarize (--sum, --no-sum) option from the command-line interface.
 
+- Complete run through of the checks.
+
+- Added an initial migration (0200) that adds the tables only when necessary. In
+  this way, empty and existing sqlite files can be initialized.
+
+- Added a migration (0201) that replaces friction_type=4 with 2.
+
 
 0.14 (2021-07-29)
 -----------------

README.rst

@@ -52,11 +52,21 @@ Command-line interface
 
 Use the modelchecker from the command line as follows::
 
-    threedi-modelchecker -l warning sqlite -s path/to/model.sqlite
+    threedi_modelchecker -s path/to/model.sqlite check -l warning 
 
 By default, WARNING and INFO checks are ignored.
 
 
+Migrations
+----------
+
+Migrate the schematisation file to the latest version as follows::
+
+    threedi_modelchecker -s path/to/model.sqlite migrate
+
+The file will be change in-place.
+
+
 Development
 -----------
 

alembic.ini

@@ -0,0 +1,91 @@
+# A generic, single database configuration.
+
+[alembic]
+# path to migration scripts
+script_location = threedi_modelchecker/migrations
+
+
+version_table = schema_version
+# template used to generate migration files
+# file_template = %%(rev)s_%%(slug)s
+
+# sys.path path, will be prepended to sys.path if present.
+# defaults to the current working directory.
+prepend_sys_path = .
+
+# 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
+
+sqlalchemy.url = sqlite:///
+
+
+[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
+
+# 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

setup.py

@@ -47,7 +47,7 @@
     python_requires='>=3.6',
     entry_points={
         "console_scripts": [
-            "threedi-modelchecker = threedi_modelchecker.scripts:check_model"
+            "threedi_modelchecker = threedi_modelchecker.scripts:threedi_modelchecker"
         ]
     },
 )

tests/test_schema.py

@@ -122,7 +122,7 @@ def test_upgrade_with_preexisting_version(in_memory_sqlite):
     schema = ModelSchema(in_memory_sqlite)
 
     with mock.patch.object(schema, "get_version", return_value=199):
-        schema.upgrade(backup=False)
+        schema.upgrade(backup=False, revision="0201")
 
     assert in_memory_sqlite.get_engine().has_table("v2_connection_nodes")
 

threedi_modelchecker/migrations/env.py

@@ -1,18 +1,33 @@
 from alembic import context
+from sqlalchemy import create_engine
 from threedi_modelchecker.threedi_model.models import Base
 
+import os
+import threedi_modelchecker.threedi_model.models  # NOQA needed for autogenerate
+
 
 target_metadata = Base.metadata
 config = context.config
 
 
+def get_url():
+    db_url = os.environ.get("DB_URL")
+    if not db_url:
+        raise RuntimeError(
+            "Database URL must be specified using the environment variable DB_URL"
+        )
+    return db_url
+
+
 def run_migrations_online():
     """Run migrations in 'online' mode.
 
     Note: SQLite does not (completely) support transactions, so, backup the
     SQLite before running migrations.
     """
     connectable = config.attributes.get("connection")
+    if connectable is None:
+        connectable = create_engine(get_url())
 
     with connectable.connect() as connection:
         context.configure(connection=connection, target_metadata=target_metadata)