chore(docs): run sphinx-apidocs

[JaeAeich]

Summary by Sourcery

Enhance documentation formatting and readability, add resource limits and security context configurations to Kubernetes templates, update ingress configuration to 'networking.k8s.io/v1', and introduce new unit tests, OpenAPI specification, Python models, Kubernetes client wrapper, taskmaster script, and example input JSON file.

Enhancements:

• Update documentation formatting in 'local_ftp.md' and 'README.md' for better readability and consistency.
• Add resource limits and security context configurations to the Kubernetes deployment templates.
• Update Kubernetes ingress configuration to use the 'networking.k8s.io/v1' API version.

Documentation:

• Add badges to 'README.md' for code coverage, documentation status, license, Python version, development status, contributors, and security tools.
• Update 'README.md' to improve structure and readability, including better formatting and links.

Tests:

• Add unit tests for the 'Job' class in 'tests/test_unit/test_services/test_job.py'.

Chores:

• Add OpenAPI specification file 'task_execution_service.117cd92.openapi.yaml' for the Task Execution Service API.
• Add new Python models for the TES API in 'tesk/api/ga4gh/tes/models.py'.
• Add new Kubernetes client wrapper in 'tesk/api/kubernetes/wrapper.py'.
• Add new taskmaster script in 'tesk/services/taskmaster.py'.
• Add example input JSON file 'docs/examples/inputHelloWorld.json'.

[sourcery-ai]

Reviewer's Guide by Sourcery

This pull request primarily focuses on updating documentation for better readability and consistency, adding new badges to the README, and enhancing the Helm chart configurations with resource limits, security contexts, and updated ingress settings. Additionally, it introduces new API specifications, models, and services for TESK, along with corresponding unit tests and example JSON files.

File-Level Changes

Files	Changes
deployment/documentation/local_ftp.md README.md	Updated documentation files for better readability, consistency, and added badges for project status.
deployment/charts/tesk/values.yaml deployment/charts/tesk/templates/common/tesk-deployment.yaml deployment/charts/tesk/templates/ingress/ingress-rules.yaml deployment/charts/tesk/templates/openshift/oc-route.yaml deployment/charts/tesk/templates/storage/openstack.yaml	Updated Helm chart configurations to include resource limits, security contexts, and updated ingress settings.
tesk/api/specs/task_execution_service.117cd92.openapi.yaml tesk/api/ga4gh/tes/models.py tesk/api/kubernetes/wrapper.py	Added new API specifications, models, and Kubernetes client wrapper for TESK.
tesk/services/filer.py tesk/services/taskmaster.py	Added new services for file handling and task management in TESK.
tests/test_unit/test_services/test_job.py	Added new unit tests for Job service.
docs/examples/localftp/taskWithIO.json docs/examples/inputHelloWorld.json	Added new example JSON files for task execution.

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[JaeAeich]

#201 should be merged first.

[uniqueg]

I suppose if you remove all the changes in the tesk package, this PR will probably be good to go once the other stuff is merged, which - as you say - should happen first.

[uniqueg]

The docs stuff looks fine, but not sure why there are the other files (constants, wrapper, exceptions) in this PR. Just remove it. Then, when #201 is merged, you can just update the branch and all will be fine, I think (or otherwise, merge the updated main into your feature branch).

Also, not sure about the PR title: I don't see any code that runs the API docs build, but rather only changes to the pages. So shouldn't it be something like docs: add API docs pages or docs: extend API docs or something like that?

[JaeAeich]

closing as #201 got this covered.