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Enhance the Python typing for the files we touch #137

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mr-c opened this issue Nov 8, 2021 · 10 comments
Closed
57 tasks done

Enhance the Python typing for the files we touch #137

mr-c opened this issue Nov 8, 2021 · 10 comments
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@mr-c
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mr-c commented Nov 8, 2021

  1. Find a Python file we touch in Implement a subset of the Common Workflow Language. #47 Implement a subset of the Common Workflow Language galaxyproject/galaxy#12909 or [WIP] Implement conditionals. #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
  • lib/galaxy/config/__init__.py
  • lib/galaxy/datatypes/data.py
  • lib/galaxy/job_execution/output_collect.py
  • lib/galaxy/jobs/__init__.py
  • lib/galaxy/jobs/command_factory.py
  • lib/galaxy/jobs/runners/local.py
  • lib/galaxy/managers/collections.py
  • lib/galaxy/managers/collections_util.py
  • lib/galaxy/managers/histories.py
  • lib/galaxy/managers/tools.py
  • lib/galaxy/managers/workflows.py
  • lib/galaxy/metadata/__init__.py
  • lib/galaxy/model/__init__.py
  • lib/galaxy/model/dataset_collections/builder.py
  • lib/galaxy/model/dataset_collections/matching.py
  • lib/galaxy/model/dataset_collections/registry.py
  • lib/galaxy/model/dataset_collections/type_description.py
  • lib/galaxy/model/dataset_collections/types/__init__.py
  • lib/galaxy/model/dataset_collections/types/list.py
  • lib/galaxy/model/dataset_collections/types/paired.py
  • lib/galaxy/schema/schema.py
  • lib/galaxy/tool_util/client/staging.py
  • lib/galaxy/tool_util/cwl/parser.py
  • lib/galaxy/tool_util/cwl/representation.py
  • lib/galaxy/tool_util/cwl/schema.py
  • lib/galaxy/tool_util/cwl/util.py
  • lib/galaxy/tool_util/output_checker.py
  • lib/galaxy/tool_util/parser/cwl.py
  • lib/galaxy/tool_util/parser/factory.py
  • lib/galaxy/tool_util/parser/interface.py
  • lib/galaxy/tool_util/parser/output_objects.py
  • lib/galaxy/tool_util/parser/yaml.py
  • lib/galaxy/tools/__init__.py
  • lib/galaxy/tools/actions/__init__.py
  • lib/galaxy/tools/evaluation.py
  • lib/galaxy/tools/execute.py
  • lib/galaxy/tools/parameters/basic.py
  • lib/galaxy/tools/parameters/grouping.py
  • lib/galaxy/tools/parameters/wrapped.py
  • lib/galaxy/tools/wrappers.py
  • lib/galaxy/util/compression_utils.py
  • lib/galaxy/webapps/galaxy/api/tools.py
  • lib/galaxy/webapps/galaxy/api/workflows.py
  • lib/galaxy/webapps/galaxy/controllers/tool_runner.py
  • lib/galaxy/webapps/galaxy/services/dataset_collections.py
  • lib/galaxy/workflow/modules.py
  • lib/galaxy/workflow/run.py
  • lib/galaxy/workflow/run_request.py
  • lib/galaxy/workflow/steps.py
  • lib/galaxy_test/api/test_dataset_collections.py
  • lib/galaxy_test/api/test_tools.py
  • lib/galaxy_test/driver/driver_util.py
  • test/integration/test_upload_configuration_options.py
  • test/unit/app/jobs/test_command_factory.py
  • test/unit/app/jobs/test_runner_local.py
  • test/unit/app/managers/test_HistoryManager.py
  • test/unit/tool_util/test_parsing.py
@mr-c mr-c self-assigned this Nov 8, 2021
@mr-c
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mr-c commented Nov 8, 2021

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

@dakariakin
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dakariakin commented Nov 8, 2021

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

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

@dakariakin
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dakariakin commented Nov 9, 2021

Sent WIP PR galaxyproject#12884
Will continue with

  • lib/galaxy/jobs/__init__.py
  • lib/galaxy/jobs/runners/local.py

@mr-c
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mr-c commented Nov 9, 2021

Tomorrow I plan on working on

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

@dakariakin
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dakariakin commented Nov 10, 2021

Fixed in galaxyproject#12884

  • lib/galaxy/tool_util/client/staging.py
  • lib/galaxy/tool_util/output_checker.py

Tomorrow I'll work on

  • lib/galaxy/tool_util/cwl/parser.py
  • lib/galaxy/tool_util/cwl/representation.py

@mr-c
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mr-c commented Nov 11, 2021

Next up for me:

  • lib/galaxy/managers/collections.py
  • lib/galaxy/managers/collections_util.py
  • lib/galaxy/managers/tools.py
  • lib/galaxy/managers/workflows.py

@dakariakin
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dakariakin commented Nov 11, 2021

also done with

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

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

@mr-c
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mr-c commented Nov 12, 2021

Building off of @dakariakin 's galaxyproject#12884 I will work on the following next:

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

@mr-c
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mr-c commented Nov 12, 2021

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

@dakariakin
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I've just created an MR with typings for lib/galaxy/model/init.py
galaxyproject#12971

Could you please review it?

@mr-c mr-c closed this as completed Oct 7, 2022
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