Add SCimilarity

[lazappi]

Describe your changes

Add SCimilarity as a method. Requires adding a new test dataset as SCimilarity can only be run on human data.

Checklist before requesting a review

• I have performed a self-review of my code

• Check the correct box. Does this PR contain:

  • Breaking changes
  • New functionality
  • Major changes
  • Minor changes
  • Bug fixes

• Proposed changes are described in the CHANGELOG.md

• CI Tests succeed and look good!

[lazappi]

@rcannood I am relatively confident the component works but we need to work out how to handle the model input. At the moment the component tests fail because there is no example file and they model is not downloaded anywhere.

[rcannood]

minor comments

[rcannood]

You can add a value for model here

Suggested change

	scimilarity,
	scimilarity.run(
	args: [model: file("https://path/to/model")]
	),

[lazappi]

This doesn't quite work, you get ERROR ~ No such variable: scimilarity from Nextflow (I guess because it's not defined yet)

[rcannood]

this could be used to not let the CI run the scimilarity unit test for now:

src/api/base_method.yaml:

namespace: methods
info:
  type: method
  type_info:
    label: Method
    summary: A method for the batch integration task.
    description: |
      A batch integration method which integrates multiple datasets.
arguments:
  - name: --input
    __merge__: file_dataset.yaml
    direction: input
    required: true
  - name: --output
    __merge__: file_integrated.yaml
    direction: output
    required: true
test_resources:
  - type: python_script
    path: /common/component_tests/check_config.py

src/api/comp_method.yaml:

__merge__: base_method.yaml
test_resources:
  - type: python_script
    path: /common/component_tests/run_and_check_output.py
  - path: /resources_test/task_batch_integration/cxg_mouse_pancreas_atlas
    dest: resources_test/task_batch_integration/cxg_mouse_pancreas_atlas

[lazappi]

Replaced by #3