Virtool-workflow

[1.0.0](https://github.com/virtool/virtool-workflow/compare/0.6.0...1.0.0) (2021-10-18)


Bug Fixes

* use `create_redis_pool` ([adf7ec6](https://github.com/virtool/virtool-workflow/commit/adf7ec654686624c757e7bcd7b692420f0d30426))


chore

* downgrade to aioredis==1.3.1 from 2.0.0 ([e45548d](https://github.com/virtool/virtool-workflow/commit/e45548d4fad8d64193fec56082151e2e2f25566c))


BREAKING CHANGES

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

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](https://github.com/virtool/virtool-workflow/compare/0.5.2...0.5.3) (2021-10-18)


Bug Fixes

* use map for release types ([1ab47f7](https://github.com/virtool/virtool-workflow/commit/1ab47f71ec37a5cd889a0de1e8b57e0c05b0dc91))

[0.5.2](https://github.com/virtool/virtool-workflow/compare/0.5.1...0.5.2) (2021-10-18)


Bug Fixes

* add `jobs` key to semantic-release.yml ([072e949](https://github.com/virtool/virtool-workflow/commit/072e949291e5a28cd39dac500b167e9cb171af5a))
* Send error message as a JSON object. ([99ddc31](https://github.com/virtool/virtool-workflow/commit/99ddc319c813fdb3b3e9e7069ced36ad983fe83f))

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.

- 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