1.0.1

1.0.1 (2021-10-27)

Bug Fixes

• use "subtractions" key, not "subtraction_id" (a7aafed)

1.0.0

1.0.0 (2021-10-18)

Bug Fixes

• use create_redis_pool (adf7ec6)

chore

• downgrade to aioredis==1.3.1 from 2.0.0 (e45548d)

BREAKING CHANGES

• rediss connection strings are no longer supported,
  use ssl=true query parameter instead.

0.6.0

Added

• fixture_context, a context manager which creates a new context for fixtures
• config fixture, a dictionary containing all of the command line option values
• Sphinx plugin autofixture to provide special rendering for fixture functions

Removed

• 'config fixtures' removed in favor of single fixture config
• FixtureGroup removed in favor of fixture_context
• The abstract classes for data provider classes Abstract*Provider

0.5.3

0.5.3 (2021-10-18)

Bug Fixes

• use map for release types (1ab47f7)

0.5.2

0.5.2 (2021-10-18)

Bug Fixes

• add jobs key to semantic-release.yml (072e949)
• Send error message as a JSON object. (99ddc31)

0.5.1

Added

• Add indexes fixture and tests
• Add integration tests against Virtool's jobs API
• Add provider abstract classes
  • Avoid accessing the database directly
  • Simplify testing by allowing for alternate implementations
• Add FixtureGroup
• Add dataclasses for various domain objects
  • Jobs
  • Subtractions
  • Indexes
  • References
  • ...
• Github action for testing the docker build
• Github action for testing the PyPi package validity
• Github action for verifying this changelog
• Move virtool/workflow Dockerfile to repository root
• Github action to create github releases
• Github action to perform a a nightly build
• Github action to create a release branch
• Github action to run integration tests
• Github action to performa a nightly build
  • Releases virtool/workflow:nightly docker image
• workflow test subcommand
  • Runs a workflow in a test environment using docker-compose
• Github action to push changes from master branch to develop branch

Changed

• Switch back to Sphinx for documentation
• Rename temp_path to work_path
• Improve error handling and exception messages
  • WorkflowFixtureNotAvailable replaced by FixtureNotFound and FixtureBindingError
  • Proper use of exception chaining
• Implements provider abstract classes using the Virtool Jobs API
• Removes code relating to MongoDB from virtool_worlflow
• Improves configuration fixtures
• Moves most functionality from virtool_workflow_runtime to virtool_workflow
  • virtool_workflow_runtime now contains code relating to the standalone runner process for workflows.
• Switches to poetry for dependency and build management
• Re-implement read trimming + caching
• Support colored logging
• Move virtool/workflow Dockerfile to repository root
• Run integration tests
• Config fixtures are funtions instead of ConfigFixture instances
• CLI options such as --dev-mode are now flags instead of boolean options.

0.5.0

• Switch back to Sphinx for documentation
• Add indexes fixture and tests
• Rename temp_path to work_path
• Add provider abstract classes
• Avoid accessing the database directly
• Simplify testing by allowing for alternate implementations
• Improve error handling and exception messages
• WorkflowFixtureNotAvailable replaced by FixtureNotFound and FixtureBindingError
• Proper use of exception chaining
• Introduce FixtureGroup
• Add dataclasses for various domain objects
  • Jobs
  • Subtractions
  • Indexes
  • References
• Implements provider abstract classes using the Virtool Jobs API
• Removes code relating to MongoDB from virtool_worlflow
• Improves configuration fixtures
• Moves most functionality from virtool_workflow_runtime to virtool_workflow
• virtool_workflow_runtime now contains code relating to the standalone runner process for workflows.
• Switches to poetry for dependency and build management
• Re-implement read trimming + caching
• Support coloured logging
• Add integration tests against Virtool's jobs API

0.4.0

Added

• add analysis fixture to provide file upload capability (#91)
• add indexes fixture to provide simple access to reference indexes used in an analysis workflow (#94)

Changed

• provide more discrete fixtures instead of analysis_args (#90)
• rename temp_path fixture to work_path
• remove temp_analysis_path fixture
• update fixtures documentation (#90)

0.3.0

Added

• implement logging (#66)
• add runtime pytest fixture to simplify workflow step testing (#84)
• add hmms workflow fixture

Changed

• remove direct database access to make move to database-less workflows smoother (#69)
• greatly improved documentation fixtures and hooks (#74)

Removed

• drop run-local sub-command

0.2.0

Added

• add reads fixture for using prepared sequencing read data used in an analysis workflow
• add run_subprocess fixture for executing command line tools
• add subtractions fixture for accessing subtractions selected by the user when the workflow job was created

Changed

• update documentation