Enhance the Python typing for the files we touch

[mr-c]

1. Find a Python file we touch in https://github.com/common-workflow-lab/galaxy/pull/47 https://github.com/galaxyproject/galaxy/pull/12909 or https://github.com/common-workflow-language/galaxy/pull/123
2. Edit https://github.com/galaxyproject/galaxy/blob/dev/setup.cfg#L24 to remove the check_untyped_defs = False from underneath that filename
3. tox -e mypy
4. Fix/enhance types ; send PR to https://github.com/galaxyproject/galaxy/ against the dev branch
5. Repeat from 1 with another file

• [x] lib/galaxy/config/__init__.py
• [x] lib/galaxy/datatypes/data.py
• [x] lib/galaxy/job_execution/output_collect.py
• [x] lib/galaxy/jobs/__init__.py
• [x] lib/galaxy/jobs/command_factory.py
• [x] lib/galaxy/jobs/runners/local.py
• [x] lib/galaxy/managers/collections.py
• [x] lib/galaxy/managers/collections_util.py
• [x] lib/galaxy/managers/histories.py
• [x] lib/galaxy/managers/tools.py
• [x] lib/galaxy/managers/workflows.py
• [x] lib/galaxy/metadata/__init__.py
• [x] lib/galaxy/model/__init__.py
• [x] lib/galaxy/model/dataset_collections/builder.py
• [x] lib/galaxy/model/dataset_collections/matching.py
• [x] lib/galaxy/model/dataset_collections/registry.py
• [x] lib/galaxy/model/dataset_collections/type_description.py
• [x] lib/galaxy/model/dataset_collections/types/__init__.py
• [x] lib/galaxy/model/dataset_collections/types/list.py
• [x] lib/galaxy/model/dataset_collections/types/paired.py
• [x] lib/galaxy/schema/schema.py
• [x] lib/galaxy/tool_util/client/staging.py
• [x] lib/galaxy/tool_util/cwl/parser.py
• [x] lib/galaxy/tool_util/cwl/representation.py
• [x] lib/galaxy/tool_util/cwl/schema.py
• [x] lib/galaxy/tool_util/cwl/util.py
• [x] lib/galaxy/tool_util/output_checker.py
• [x] lib/galaxy/tool_util/parser/cwl.py
• [x] lib/galaxy/tool_util/parser/factory.py
• [x] lib/galaxy/tool_util/parser/interface.py
• [x] lib/galaxy/tool_util/parser/output_objects.py
• [x] lib/galaxy/tool_util/parser/yaml.py
• [x] lib/galaxy/tools/__init__.py
• [x] lib/galaxy/tools/actions/__init__.py
• [x] lib/galaxy/tools/evaluation.py
• [x] lib/galaxy/tools/execute.py
• [x] lib/galaxy/tools/parameters/basic.py
• [x] lib/galaxy/tools/parameters/grouping.py
• [x] lib/galaxy/tools/parameters/wrapped.py
• [x] lib/galaxy/tools/wrappers.py
• [x] lib/galaxy/util/compression_utils.py
• [x] lib/galaxy/webapps/galaxy/api/tools.py
• [x] lib/galaxy/webapps/galaxy/api/workflows.py
• [x] lib/galaxy/webapps/galaxy/controllers/tool_runner.py
• [x] lib/galaxy/webapps/galaxy/services/dataset_collections.py
• [x] lib/galaxy/workflow/modules.py
• [x] lib/galaxy/workflow/run.py
• [x] lib/galaxy/workflow/run_request.py
• [x] lib/galaxy/workflow/steps.py
• [x] lib/galaxy_test/api/test_dataset_collections.py
• [x] lib/galaxy_test/api/test_tools.py
• [x] lib/galaxy_test/driver/driver_util.py
• [x] test/integration/test_upload_configuration_options.py
• [x] test/unit/app/jobs/test_command_factory.py
• [x] test/unit/app/jobs/test_runner_local.py
• [x] test/unit/app/managers/test_HistoryManager.py
• [x] test/unit/tool_util/test_parsing.py

[mr-c]

I've assigned myself, but others are welcome as well

[dakariakin]

Started work in https://github.com/dakariakin/galaxy/commits/added_types

• [x] lib/galaxy/model/dataset_collections/registry.py
• [x] lib/galaxy/model/dataset_collections/matching.py (need to discuss)
• [x] lib/galaxy/job_execution/output_collect.py

[dakariakin]

Sent WIP PR https://github.com/galaxyproject/galaxy/pull/12884 Will continue with

• [x] lib/galaxy/jobs/__init__.py
• [x] lib/galaxy/jobs/runners/local.py

[mr-c]

Tomorrow I plan on working on

• [x] lib/galaxy/tools/__init__.py
• [x] lib/galaxy/tools/actions/__init__.py
• [x] lib/galaxy/tools/evaluation.py
• [x] lib/galaxy/tools/execute.py
• [x] lib/galaxy/tools/parameters/basic.py
• [x] lib/galaxy/tools/parameters/grouping.py

[dakariakin]

Fixed in https://github.com/galaxyproject/galaxy/pull/12884

• [x] lib/galaxy/tool_util/client/staging.py
• [x] lib/galaxy/tool_util/output_checker.py

Tomorrow I'll work on

• [x] lib/galaxy/tool_util/cwl/parser.py
• [x] lib/galaxy/tool_util/cwl/representation.py

[mr-c]

Next up for me:

• [x] lib/galaxy/managers/collections.py
• [x] lib/galaxy/managers/collections_util.py
• [x] lib/galaxy/managers/tools.py
• [x] lib/galaxy/managers/workflows.py

[dakariakin]

also done with

• [x] lib/galaxy/tool_util/parser/yaml.py
• [x] lib/galaxy/tool_util/parser/output_objects.py
• [x] lib/galaxy/metadata/__init__.py

I'll work on lib/galaxy/model/__init__.py on separate PR because it throws 119 errors

[mr-c]

Building off of @dakariakin 's https://github.com/galaxyproject/galaxy/pull/12884/ I will work on the following next:

• [x] lib/galaxy/tool_util/client/staging.py
• [x] lib/galaxy/tool_util/cwl/parser.py
• [x] lib/galaxy/tool_util/cwl/representation.py
• [x] lib/galaxy/tool_util/output_checker.py
• [x] lib/galaxy/tool_util/parser/cwl.py

[mr-c]

I updated the list at the top, and I'll be working on the new entries from the bottom up

[dakariakin]

I've just created an MR with typings for lib/galaxy/model/init.py https://github.com/galaxyproject/galaxy/pull/12971

Could you please review it?