Type hinting and misc changes #417

mranst · 2024-09-11T22:40:30Z

Description

Adds type hinting for all python modules (#349)

renamed datetime.py to datetime_util.py to avoid confusion with baseline package

SLES15 is now default platform (#407)

updated docs to reflect this, along with a few additions which may help new users

If specified in config and a valid location, appropriate tasks will now source from swell_static_files_user (#360)

GenerateBCClimatology
StageJedi
GetGeosRestart
PrepGeosRunDir

Addressed a potential error when trying to abort in observing_system_records.py

…er additions (GEOS-ESM#407)

…-ESM#360)

…, added type hinting (GEOS-ESM#349)

asewnath

@mranst Thanks for all of these type hint changes and catches

src/swell/deployment/create_experiment.py

src/swell/tasks/run_geos_executable.py

src/swell/utilities/data_assimilation_window_params.py

src/swell/utilities/exceptions.py

src/swell/utilities/render_jedi_interface_files.py

src/swell/utilities/run_jedi_executables.py

src/swell/utilities/scripts/task_question_dicts_defaults.py

src/swell/utilities/shell_commands.py

…nd copy_eva_files

…typing.Optional used where appropriate

ashiklom

Excellent work! I just had a few minor suggestions, but overall, this is well done. Having type hints everywhere will be a huge quality of life improvement for Swell developers, especially around some of our weirder functions.

Did you also try running Swell through a static type checker like mypy or Pyright?

docs/configuring_cylc.md

src/swell/deployment/create_experiment.py

src/swell/deployment/prepare_config_and_suite/question_and_answer_defaults.py

src/swell/swell.py

src/swell/tasks/base/task_base.py

src/swell/utilities/filehandler.py

src/swell/utilities/gsi_record_parser.py

src/swell/utilities/jinja2.py

src/swell/utilities/gsi_record_parser.py

src/swell/utilities/observing_system_records.py

Dooruk

Thank you, this is colossal work @mranst! Just a few minor comments following others.

I made a copy of your branch to run Tier1 tests (which they run succesfully)

https://github.com/GEOS-ESM/swell/actions/runs/10850825590

Are you part of GEOS-ESM and push changes to and create branches on Swell repo? I think we need to add you.

src/swell/utilities/shell_commands.py

src/swell/utilities/scripts/task_question_dicts_defaults.py

src/swell/utilities/run_jedi_executables.py

src/swell/utilities/dictionary.py

Co-authored-by: Alexey Shiklomanov <[email protected]>

ashiklom · 2024-09-13T15:43:49Z

@asewnath @Dooruk Thanks both for the thorough reviews!

We should probably come to some consensus on the use of Forward References in type hints (i.e., logger: "Logger") vs. direct class references (from swell.logger import Logger; logger: Logger), so @mranst can just resolve all of those without our individual approval.

I don't have very strong feelings about this. My mild preference is:

Accept Forward References for "Logger" because it's relatively obvious what that is and where it comes from (and, I think our Logger class should be more-or-less interchangeable with the logging.Logger from the Python standard library), but...
Prefer direct class references + imports for more specialized classes (e.g., FileCollection, JediConfigRendering) so that it's easier for future developers to jump to those definitions.

What do you two think?

mranst · 2024-09-13T15:53:34Z

Thanks for the comments everyone! I have added direct type hinting for Logger everywhere, unless we do want to go back to the forward references. I'm looking through for other object instance calls so I can type them directly, as well.

…hinting-misc

… typing functions

…hinting-misc

asewnath · 2024-09-13T20:33:28Z

What do you two think?

@ashiklom I'm inclined to sticking with direct class references for now. Seeing both forward references and direct class references may be confusing for new users and developers. If we wanted to use both approaches, we should document our type hinting methodology for clarification.

Dooruk · 2024-09-16T13:50:15Z

What do you two think?

@ashiklom I'm inclined to sticking with direct class references for now. Seeing both forward references and direct class references may be confusing for new users and developers. If we wanted to use both approaches, we should document our type hinting methodology for clarification.

I agree with @asewnath on this one. I think many Python users (myself included) aren't familiar with typehinting and forward refence is one step beyond that. Direct class reference is more straightforward.

Dooruk

This is all good, thanks again @mranst! I will wait on others approval before merging.

ashiklom

Changes look good! However, when I ran this through a type checker locally (mypy), it turned up a bunch of errors. We don't have to address all (or even most, and perhaps not any) of them now...but I recommend taking a look through this list and deciding consciously which of the errors are worth fixing now and which ones we can wait on for a future PR.

@mranst I leave this up to your judgment. Let me know when you think we've hit a reasonably stopping point for this PR.

Full mypy output is in the Details below.

src/swell/deployment/platforms/platforms.py:12: error: Library stubs not installed for "yaml"  [import-untyped]
src/swell/deployment/platforms/platforms.py:12: note: Hint: "python3 -m pip install types-PyYAML"
src/swell/deployment/platforms/platforms.py:12: note: (or run "mypy --install-types" to install all missing stub packages)
src/swell/deployment/platforms/platforms.py:12: note: See https://mypy.readthedocs.io/en/stable/running_mypy.html#missing-imports
src/swell/utilities/slurm.py:13: error: Library stubs not installed for "yaml"  [import-untyped]
src/swell/utilities/slurm.py:201: error: Item "None" of "Match[str] | None" has no attribute "group"  [union-attr]
src/swell/utilities/shell_commands.py:39: error: Item "None" of "IO[bytes] | None" has no attribute "readline"  [union-attr]
src/swell/utilities/shell_commands.py:71: error: Argument "stdout" to "run_subprocess" has incompatible type "int"; expected "str | None"  [arg-type]
src/swell/utilities/shell_commands.py:71: error: Argument "stderr" to "run_subprocess" has incompatible type "int"; expected "str | None"  [arg-type]
src/swell/utilities/shell_commands.py:86: error: Argument "stdout" to "run" has incompatible type "str | None"; expected "int | IO[Any] | None"  [arg-type]
src/swell/utilities/shell_commands.py:86: error: Argument "stderr" to "run" has incompatible type "str | None"; expected "int | IO[Any] | None"  [arg-type]
src/swell/utilities/observations.py:11: error: Library stubs not installed for "yaml"  [import-untyped]
src/swell/utilities/netcdf_files.py:12: error: Cannot find implementation or library stub for module named "xarray"  [import-not-found]
src/swell/utilities/get_channels.py:10: error: Library stubs not installed for "yaml"  [import-untyped]
src/swell/utilities/get_channels.py:54: error: Incompatible return value type (got "str", expected "list[Any]")  [return-value]
src/swell/utilities/get_channels.py:59: error: Missing return statement  [return]
src/swell/utilities/get_channels.py:110: error: Incompatible return value type (got "tuple[list[Any], list[int]]", expected "tuple[str, list[Any]]")  [return-value]
src/swell/utilities/get_channels.py:113: error: Incompatible return value type (got "tuple[None, None]", expected "tuple[str, list[Any]]")  [return-value]
src/swell/utilities/get_channels.py:134: error: No return value expected  [return-value]
src/swell/utilities/exceptions.py:25: error: "Logger" not callable  [operator]
src/swell/utilities/dictionary.py:10: error: Library stubs not installed for "yaml"  [import-untyped]
src/swell/utilities/dictionary.py:19: error: Missing return statement  [return]
src/swell/utilities/config.py:11: error: Library stubs not installed for "yaml"  [import-untyped]
src/swell/utilities/config.py:68: error: Incompatible types in assignment (expression has type "None", variable has type "list[Any]")  [assignment]
src/swell/utilities/scripts/check_jedi_interface_templates.py:71: error: Need type annotation for "templates" (hint: "templates: list[<type>] = ...")  [var-annotated]
src/swell/utilities/git_utils.py:28: error: Argument 2 to "run_subprocess_dev_null" has incompatible type "list[str]"; expected "str"  [arg-type]
src/swell/utilities/git_utils.py:51: error: Argument 2 to "run_subprocess_dev_null" has incompatible type "list[str]"; expected "str"  [arg-type]
src/swell/utilities/git_utils.py:75: error: Argument 2 to "run_subprocess_dev_null" has incompatible type "list[str]"; expected "str"  [arg-type]
src/swell/utilities/git_utils.py:85: error: Argument 2 to "run_subprocess_dev_null" has incompatible type "list[str]"; expected "str"  [arg-type]
src/swell/utilities/geos.py:11: error: Skipping analyzing "f90nml": module is installed, but missing library stubs or py.typed marker  [import-untyped]
src/swell/utilities/geos.py:13: error: Skipping analyzing "isodate": module is installed, but missing library stubs or py.typed marker  [import-untyped]
src/swell/utilities/geos.py:14: error: Skipping analyzing "netCDF4": module is installed, but missing library stubs or py.typed marker  [import-untyped]
src/swell/utilities/geos.py:110: error: Argument 2 to "run_subprocess" has incompatible type "list[str]"; expected "str"  [arg-type]
src/swell/utilities/geos.py:172: error: Incompatible default for argument "dst_dir" (default has type "None", argument has type "str")  [assignment]
src/swell/utilities/geos.py:172: note: PEP 484 prohibits implicit Optional. Accordingly, mypy has changed its default to no_implicit_optional=True
src/swell/utilities/geos.py:172: note: Use https://github.com/hauntsaninja/no_implicit_optional to automatically upgrade your codebase
src/swell/utilities/geos.py:279: error: Incompatible types in assignment (expression has type "list[str]", variable has type "str")  [assignment]
src/swell/utilities/data_assimilation_window_params.py:11: error: Skipping analyzing "isodate": module is installed, but missing library stubs or py.typed marker  [import-untyped]
src/swell/utilities/data_assimilation_window_params.py:66: error: Incompatible return value type (got "datetime", expected "str")  [return-value]
src/swell/test/code_tests/slurm_test.py:54: error: Argument 1 to "prepare_scheduling_dict" has incompatible type "logging.Logger"; expected "swell.utilities.logger.Logger"  [arg-type]
src/swell/test/code_tests/slurm_test.py:60: error: Argument 1 to "prepare_scheduling_dict" has incompatible type "logging.Logger"; expected "swell.utilities.logger.Logger"  [arg-type]
src/swell/test/code_tests/slurm_test.py:68: error: Argument 1 to "prepare_scheduling_dict" has incompatible type "logging.Logger"; expected "swell.utilities.logger.Logger"  [arg-type]
src/swell/deployment/launch_experiment.py:58: error: Argument 2 to "run_subprocess" has incompatible type "list[str]"; expected "str"  [arg-type]
src/swell/deployment/launch_experiment.py:60: error: Argument 2 to "run_subprocess" has incompatible type "list[str]"; expected "str"  [arg-type]
src/swell/deployment/launch_experiment.py:67: error: Argument 2 to "run_subprocess" has incompatible type "list[str]"; expected "str"  [arg-type]
src/swell/deployment/launch_experiment.py:72: error: Argument 2 to "run_subprocess" has incompatible type "list[str]"; expected "str"  [arg-type]
src/swell/deployment/launch_experiment.py:97: error: Argument 2 to "run_subprocess" has incompatible type "list[str]"; expected "str"  [arg-type]
src/swell/utilities/gsi_record_parser.py:1: error: Library stubs not installed for "pandas"  [import-untyped]
src/swell/utilities/gsi_record_parser.py:1: note: Hint: "python3 -m pip install pandas-stubs"
src/swell/utilities/gsi_record_parser.py:28: error: "None" has no attribute "loc"  [attr-defined]
src/swell/utilities/gsi_record_parser.py:28: error: Value of type "None" is not indexable  [index]
src/swell/utilities/gsi_record_parser.py:43: error: "None" has no attribute "iloc"  [attr-defined]
src/swell/utilities/gsi_record_parser.py:44: error: "None" has no attribute "iloc"  [attr-defined]
src/swell/utilities/gsi_record_parser.py:51: error: Value of type "None" is not indexable  [index]
src/swell/utilities/gsi_record_parser.py:54: error: "None" has no attribute "loc"  [attr-defined]
src/swell/utilities/gsi_record_parser.py:54: error: Value of type "None" is not indexable  [index]
src/swell/utilities/gsi_record_parser.py:65: error: "None" has no attribute "loc"  [attr-defined]
src/swell/utilities/gsi_record_parser.py:65: error: Value of type "None" is not indexable  [index]
src/swell/utilities/gsi_record_parser.py:101: error: "None" has no attribute "loc"  [attr-defined]
src/swell/utilities/gsi_record_parser.py:101: error: Value of type "None" is not indexable  [index]
src/swell/utilities/observing_system_records.py:2: error: Library stubs not installed for "yaml"  [import-untyped]
src/swell/utilities/observing_system_records.py:3: error: Library stubs not installed for "pandas"  [import-untyped]
src/swell/utilities/observing_system_records.py:94: error: Need type annotation for "column_names" (hint: "column_names: list[<type>] = ...")  [var-annotated]
src/swell/utilities/observing_system_records.py:97: error: Need type annotation for "obs_registry" (hint: "obs_registry: list[<type>] = ...")  [var-annotated]
src/swell/utilities/observing_system_records.py:169: error: Value of type "None" is not indexable  [index]
src/swell/utilities/observing_system_records.py:171: error: "None" has no attribute "loc"  [attr-defined]
src/swell/utilities/observing_system_records.py:171: error: Value of type "None" is not indexable  [index]
src/swell/utilities/observing_system_records.py:172: error: "None" has no attribute "loc"  [attr-defined]
src/swell/utilities/observing_system_records.py:172: error: Value of type "None" is not indexable  [index]
src/swell/utilities/filehandler.py:113: error: Need type annotation for "listing" (hint: "listing: list[<type>] = ...")  [var-annotated]
src/swell/utilities/filehandler.py:137: error: "FileHandler" has no attribute "list"  [attr-defined]
src/swell/utilities/filehandler.py:172: error: "FileHandler" has no attribute "list"  [attr-defined]
src/swell/utilities/filehandler.py:274: error: Argument 1 to "FileCollection" has incompatible type "dict[str, bool]"; expected "list[Any]"  [arg-type]
src/swell/utilities/filehandler.py:341: error: Argument 1 to "FileCollection" has incompatible type "dict[Any, Any]"; expected "list[Any]"  [arg-type]
src/swell/utilities/filehandler.py:355: error: Incompatible types in assignment (expression has type "Literal[True] | list[Any]", variable has type "bool")  [assignment]
src/swell/utilities/filehandler.py:392: error: Need type annotation for "listing" (hint: "listing: list[<type>] = ...")  [var-annotated]
src/swell/utilities/filehandler.py:393: error: "list[Any]" has no attribute "get"  [attr-defined]
src/swell/utilities/filehandler.py:394: error: "list[Any]" has no attribute "get"  [attr-defined]
src/swell/utilities/filehandler.py:395: error: "list[Any]" has no attribute "get"  [attr-defined]
src/swell/utilities/file_system_operations.py:54: error: Argument 2 to "info" of "Logger" has incompatible type "list[Any]"; expected "bool"  [arg-type]
src/swell/utilities/file_system_operations.py:93: error: Missing return statement  [return]
src/swell/utilities/build.py:13: error: Cannot find implementation or library stub for module named "jedi_bundle.bin.jedi_bundle"  [import-not-found]
src/swell/utilities/build.py:14: error: Cannot find implementation or library stub for module named "jedi_bundle.config.config"  [import-not-found]
src/swell/utilities/build.py:33: error: Incompatible return value type (got "tuple[str, str]", expected "str")  [return-value]
src/swell/utilities/scripts/task_question_dicts_defaults.py:14: error: Library stubs not installed for "yaml"  [import-untyped]
src/swell/utilities/scripts/task_question_dicts_defaults.py:42: error: Item "list[Any]" of "list[Any] | dict[Any, Any]" has no attribute "items"  [union-attr]
src/swell/utilities/scripts/task_question_dicts_defaults.py:59: error: Need type annotation for "jedi_tq_dict"  [var-annotated]
src/swell/utilities/scripts/task_question_dicts_defaults.py:104: error: Item "list[Any]" of "list[Any] | dict[Any, Any]" has no attribute "items"  [union-attr]
src/swell/utilities/scripts/task_question_dicts_defaults.py:110: error: Need type annotation for "platform_tq_dict"  [var-annotated]
src/swell/utilities/scripts/task_question_dicts.py:15: error: Library stubs not installed for "yaml"  [import-untyped]
src/swell/utilities/jinja2.py:37: error: Signature of "__getitem__" incompatible with supertype "Undefined"  [override]
src/swell/utilities/jinja2.py:37: note:      Superclass:
src/swell/utilities/jinja2.py:37: note:          def (self: Undefined, *args: Any, **kwargs: Any) -> Never
src/swell/utilities/jinja2.py:37: note:      Subclass:
src/swell/utilities/jinja2.py:37: note:          def __getitem__(self, str | int, /) -> SilentUndefined
src/swell/utilities/render_jedi_interface_files.py:11: error: Library stubs not installed for "yaml"  [import-untyped]
src/swell/utilities/render_jedi_interface_files.py:48: error: "str" has no attribute "dto"  [attr-defined]
src/swell/utilities/render_jedi_interface_files.py:60: error: Incompatible types in assignment (expression has type "str | None", target has type "str")  [assignment]
src/swell/utilities/render_jedi_interface_files.py:132: error: Incompatible types in assignment (expression has type "object", target has type "str")  [assignment]
src/swell/utilities/render_jedi_interface_files.py:163: error: Incompatible return value type (got "object", expected "dict[Any, Any]")  [return-value]
src/swell/utilities/render_jedi_interface_files.py:176: error: Argument 3 to "join" has incompatible type "str | None"; expected "str"  [arg-type]
src/swell/utilities/render_jedi_interface_files.py:180: error: Incompatible return value type (got "object", expected "dict[Any, Any]")  [return-value]
src/swell/utilities/render_jedi_interface_files.py:189: error: Incompatible types in assignment (expression has type "str", variable has type "None")  [assignment]
src/swell/utilities/render_jedi_interface_files.py:191: error: Incompatible types in assignment (expression has type "str", variable has type "None")  [assignment]
src/swell/utilities/render_jedi_interface_files.py:204: error: Argument 3 to "join" has incompatible type "str | None"; expected "str"  [arg-type]
src/swell/utilities/render_jedi_interface_files.py:228: error: Incompatible return value type (got "object", expected "dict[Any, Any]")  [return-value]
src/swell/utilities/render_jedi_interface_files.py:239: error: Incompatible types in assignment (expression has type "str | dict[Any, Any]", variable has type "str | None")  [assignment]
src/swell/utilities/render_jedi_interface_files.py:247: error: Argument 3 to "join" has incompatible type "str | None"; expected "str"  [arg-type]
src/swell/utilities/render_jedi_interface_files.py:251: error: Incompatible return value type (got "object", expected "dict[Any, Any]")  [return-value]
src/swell/tasks/base/task_base.py:50: error: Argument 2 to "info" of "Logger" has incompatible type "type[Logger]"; expected "bool"  [arg-type]
src/swell/tasks/base/task_base.py:98: error: Item "None" of "Datetime | None" has no attribute "string_directory"  [union-attr]
src/swell/tasks/base/task_base.py:107: error: Argument 4 to "JediConfigRendering" has incompatible type "str | None"; expected "str"  [arg-type]
src/swell/tasks/base/task_base.py:108: error: Argument 5 to "JediConfigRendering" has incompatible type "Datetime | None"; expected "str | None"  [arg-type]
src/swell/tasks/base/task_base.py:112: error: Argument 2 to "Geos" has incompatible type "str | None"; expected "str"  [arg-type]
src/swell/tasks/base/task_base.py:164: error: Incompatible return value type (got "str | None", expected "str")  [return-value]
src/swell/tasks/base/task_base.py:194: error: Item "None" of "Datetime | None" has no attribute "string_directory"  [union-attr]
src/swell/tasks/base/task_base.py:205: error: Argument 1 to "makedirs" has incompatible type "str | None"; expected "str | bytes | PathLike[str] | PathLike[bytes]"  [arg-type]
src/swell/tasks/base/task_base.py:219: error: Argument 1 to "join" has incompatible type "str | None"; expected "str"  [arg-type]
src/swell/tasks/base/task_base.py:221: error: Incompatible return value type (got "str | None", expected "str")  [return-value]
src/swell/tasks/base/task_base.py:227: error: Item "None" of "Datetime | None" has no attribute "dto"  [union-attr]
src/swell/tasks/base/task_base.py:233: error: Item "None" of "Datetime | None" has no attribute "string_iso"  [union-attr]
src/swell/utilities/run_jedi_executables.py:12: error: Skipping analyzing "netCDF4": module is installed, but missing library stubs or py.typed marker  [import-untyped]
src/swell/utilities/run_jedi_executables.py:88: error: Item "str" of "str | None" has no attribute "copy"  [union-attr]
src/swell/utilities/run_jedi_executables.py:88: error: Item "None" of "str | None" has no attribute "copy"  [union-attr]
src/swell/utilities/run_jedi_executables.py:91: error: Argument 1 to "check_obs" has incompatible type "None"; expected "str"  [arg-type]
src/swell/utilities/run_jedi_executables.py:92: error: Argument 4 to "check_obs" has incompatible type "str | None"; expected "str"  [arg-type]
src/swell/utilities/run_jedi_executables.py:97: error: Item "str" of "str | None" has no attribute "remove"  [union-attr]
src/swell/utilities/run_jedi_executables.py:97: error: Item "None" of "str | None" has no attribute "remove"  [union-attr]
src/swell/utilities/run_jedi_executables.py:101: error: Argument 1 to "render_interface_model" of "JediConfigRendering" has incompatible type "str | None"; expected "str"  [arg-type]
src/swell/utilities/run_jedi_executables.py:129: error: Argument 2 to "run_track_log_subprocess" has incompatible type "list[str]"; expected "str"  [arg-type]
src/swell/tasks/store_background.py:12: error: Skipping analyzing "isodate": module is installed, but missing library stubs or py.typed marker  [import-untyped]
src/swell/tasks/store_background.py:14: error: Cannot find implementation or library stub for module named "r2d2"  [import-not-found]
src/swell/tasks/stage_jedi.py:77: error: Argument 1 to "get_file_handler" has incompatible type "dict[Any, Any]"; expected "list[Any]"  [arg-type]
src/swell/tasks/run_geos_executable.py:26: error: Argument 1 to "forecast_dir" of "taskBase" has incompatible type "str"; expected "list[Any]"  [arg-type]
src/swell/tasks/run_geos_executable.py:31: error: Argument 1 to "forecast_dir" of "taskBase" has incompatible type "str"; expected "list[Any]"  [arg-type]
src/swell/tasks/run_geos_executable.py:32: error: Argument 1 to "forecast_dir" of "taskBase" has incompatible type "str"; expected "list[Any]"  [arg-type]
src/swell/tasks/run_geos_executable.py:36: error: Argument 1 to "forecast_dir" of "taskBase" has incompatible type "str"; expected "list[Any]"  [arg-type]
src/swell/tasks/run_geos_executable.py:83: error: Argument 2 to "run_track_log_subprocess" has incompatible type "list[str]"; expected "str"  [arg-type]
src/swell/tasks/prepare_analysis.py:11: error: Skipping analyzing "netCDF4": module is installed, but missing library stubs or py.typed marker  [import-untyped]
src/swell/tasks/prepare_analysis.py:51: error: "str" has no attribute "hour"  [attr-defined]
src/swell/tasks/prepare_analysis.py:51: error: "str" has no attribute "minute"  [attr-defined]
src/swell/tasks/prepare_analysis.py:51: error: "str" has no attribute "second"  [attr-defined]
src/swell/tasks/prepare_analysis.py:63: error: "object" has no attribute "strftime"  [attr-defined]
src/swell/tasks/prepare_analysis.py:65: error: "object" has no attribute "strftime"  [attr-defined]
src/swell/tasks/prepare_analysis.py:78: error: Argument 1 to "forecast_dir" of "taskBase" has incompatible type "str"; expected "list[Any]"  [arg-type]
src/swell/tasks/prepare_analysis.py:81: error: "str" has no attribute "strftime"  [attr-defined]
src/swell/tasks/prepare_analysis.py:133: error: Argument 2 to "run_subprocess" has incompatible type "list[str]"; expected "str"  [arg-type]
src/swell/tasks/prepare_analysis.py:142: error: Name "ana_path" is not defined  [name-defined]
src/swell/tasks/prep_geos_run_dir.py:12: error: Library stubs not installed for "yaml"  [import-untyped]
src/swell/tasks/prep_geos_run_dir.py:69: error: Argument 1 to "forecast_dir" of "taskBase" has incompatible type "str"; expected "list[Any]"  [arg-type]
src/swell/tasks/prep_geos_run_dir.py:70: error: Argument 1 to "forecast_dir" of "taskBase" has incompatible type "str"; expected "list[Any]"  [arg-type]
src/swell/tasks/prep_geos_run_dir.py:75: error: Argument 1 to "forecast_dir" of "taskBase" has incompatible type "str"; expected "list[Any]"  [arg-type]
src/swell/tasks/prep_geos_run_dir.py:76: error: Argument 1 to "forecast_dir" of "taskBase" has incompatible type "str"; expected "list[Any]"  [arg-type]
src/swell/tasks/prep_geos_run_dir.py:95: error: Argument 1 to "forecast_dir" of "taskBase" has incompatible type "str"; expected "list[Any]"  [arg-type]
src/swell/tasks/prep_geos_run_dir.py:96: error: Argument 1 to "forecast_dir" of "taskBase" has incompatible type "str"; expected "list[Any]"  [arg-type]
src/swell/tasks/prep_geos_run_dir.py:98: error: Argument 1 to "forecast_dir" of "taskBase" has incompatible type "str"; expected "list[Any]"  [arg-type]
src/swell/tasks/prep_geos_run_dir.py:114: error: Argument 1 to "forecast_dir" of "taskBase" has incompatible type "str"; expected "list[Any]"  [arg-type]
src/swell/tasks/prep_geos_run_dir.py:118: error: Argument 1 to "forecast_dir" of "taskBase" has incompatible type "str"; expected "list[Any]"  [arg-type]
src/swell/tasks/prep_geos_run_dir.py:123: error: Argument 1 to "forecast_dir" of "taskBase" has incompatible type "str"; expected "list[Any]"  [arg-type]
src/swell/tasks/prep_geos_run_dir.py:133: error: Argument 1 to "forecast_dir" of "taskBase" has incompatible type "str"; expected "list[Any]"  [arg-type]
src/swell/tasks/prep_geos_run_dir.py:156: error: Argument 1 to "forecast_dir" of "taskBase" has incompatible type "str"; expected "list[Any]"  [arg-type]
src/swell/tasks/prep_geos_run_dir.py:173: error: Argument 1 to "forecast_dir" of "taskBase" has incompatible type "str"; expected "list[Any]"  [arg-type]
src/swell/tasks/prep_geos_run_dir.py:174: error: Argument 1 to "forecast_dir" of "taskBase" has incompatible type "str"; expected "list[Any]"  [arg-type]
src/swell/tasks/prep_geos_run_dir.py:190: error: Argument 1 to "forecast_dir" of "taskBase" has incompatible type "str"; expected "list[Any]"  [arg-type]
src/swell/tasks/prep_geos_run_dir.py:195: error: Argument 1 to "forecast_dir" of "taskBase" has incompatible type "str"; expected "list[Any]"  [arg-type]
src/swell/tasks/prep_geos_run_dir.py:233: error: Argument 1 to "forecast_dir" of "taskBase" has incompatible type "str"; expected "list[Any]"  [arg-type]
src/swell/tasks/prep_geos_run_dir.py:234: error: Argument 1 to "forecast_dir" of "taskBase" has incompatible type "str"; expected "list[Any]"  [arg-type]
src/swell/tasks/prep_geos_run_dir.py:303: error: Argument 1 to "forecast_dir" of "taskBase" has incompatible type "str"; expected "list[Any]"  [arg-type]
src/swell/tasks/prep_geos_run_dir.py:338: error: Argument 1 to "forecast_dir" of "taskBase" has incompatible type "str"; expected "list[Any]"  [arg-type]
src/swell/tasks/prep_geos_run_dir.py:429: error: Argument 1 to "forecast_dir" of "taskBase" has incompatible type "str"; expected "list[Any]"  [arg-type]
src/swell/tasks/prep_geos_run_dir.py:434: error: Argument 1 to "forecast_dir" of "taskBase" has incompatible type "str"; expected "list[Any]"  [arg-type]
src/swell/tasks/prep_geos_run_dir.py:442: error: Argument 1 to "forecast_dir" of "taskBase" has incompatible type "str"; expected "list[Any]"  [arg-type]
src/swell/tasks/move_forecast_restart.py:70: error: Argument 1 to "forecast_dir" of "taskBase" has incompatible type "str"; expected "list[Any]"  [arg-type]
src/swell/tasks/move_forecast_restart.py:84: error: Argument 1 to "forecast_dir" of "taskBase" has incompatible type "str"; expected "list[Any]"  [arg-type]
src/swell/tasks/move_da_restart.py:79: error: Argument 1 to "forecast_dir" of "taskBase" has incompatible type "str"; expected "list[Any]"  [arg-type]
src/swell/tasks/move_da_restart.py:84: error: Argument 1 to "forecast_dir" of "taskBase" has incompatible type "str"; expected "list[Any]"  [arg-type]
src/swell/tasks/move_da_restart.py:91: error: "str" has no attribute "strftime"  [attr-defined]
src/swell/tasks/move_da_restart.py:105: error: Argument 1 to "forecast_dir" of "taskBase" has incompatible type "str"; expected "list[Any]"  [arg-type]
src/swell/tasks/move_da_restart.py:120: error: "str" has no attribute "hour"  [attr-defined]
src/swell/tasks/move_da_restart.py:120: error: "str" has no attribute "minute"  [attr-defined]
src/swell/tasks/move_da_restart.py:120: error: "str" has no attribute "second"  [attr-defined]
src/swell/tasks/move_da_restart.py:122: error: "str" has no attribute "strftime"  [attr-defined]
src/swell/tasks/move_da_restart.py:130: error: "str" has no attribute "strftime"  [attr-defined]
src/swell/tasks/link_geos_output.py:11: error: Skipping analyzing "netCDF4": module is installed, but missing library stubs or py.typed marker  [import-untyped]
src/swell/tasks/link_geos_output.py:13: error: Cannot find implementation or library stub for module named "xarray"  [import-not-found]
src/swell/tasks/link_geos_output.py:65: error: "object" has no attribute "strftime"  [attr-defined]
src/swell/tasks/link_geos_output.py:80: error: "str" has no attribute "hour"  [attr-defined]
src/swell/tasks/link_geos_output.py:80: error: "str" has no attribute "minute"  [attr-defined]
src/swell/tasks/link_geos_output.py:80: error: "str" has no attribute "second"  [attr-defined]
src/swell/tasks/link_geos_output.py:89: error: Argument 1 to "forecast_dir" of "taskBase" has incompatible type "str"; expected "list[Any]"  [arg-type]
src/swell/tasks/link_geos_output.py:92: error: "str" has no attribute "strftime"  [attr-defined]
src/swell/tasks/gsi_ncdiag_to_ioda.py:18: error: Cannot find implementation or library stub for module named "pyiodaconv.gsi_ncdiag"  [import-not-found]
src/swell/tasks/gsi_ncdiag_to_ioda.py:18: error: Cannot find implementation or library stub for module named "pyiodaconv"  [import-not-found]
src/swell/tasks/gsi_ncdiag_to_ioda.py:19: error: Cannot find implementation or library stub for module named "pyiodaconv.combine_obsspace"  [import-not-found]
src/swell/tasks/gsi_ncdiag_to_ioda.py:73: error: Need type annotation for "ioda_to_gsi_dict" (hint: "ioda_to_gsi_dict: dict[<type>, <type>] = ...")  [var-annotated]
src/swell/tasks/gsi_ncdiag_to_ioda.py:95: error: Argument 1 to "strftime" of "date" has incompatible type "object"; expected "date"  [arg-type]
src/swell/tasks/gsi_bc_to_ioda.py:14: error: Cannot find implementation or library stub for module named "generate_aircraft_bias_csv"  [import-not-found]
src/swell/tasks/gsi_bc_to_ioda.py:112: error: Invalid index type "int | None" for "list[str]"; expected type "SupportsIndex"  [index]
src/swell/tasks/gsi_bc_to_ioda.py:113: error: Invalid index type "int | None" for "list[str]"; expected type "SupportsIndex"  [index]
src/swell/tasks/gsi_bc_to_ioda.py:144: error: Incompatible types in assignment (expression has type "list[str]", target has type "str")  [assignment]
src/swell/tasks/gsi_bc_to_ioda.py:157: error: Incompatible types in assignment (expression has type "list[dict[str, Any]]", target has type "str")  [assignment]
src/swell/tasks/gsi_bc_to_ioda.py:167: error: Argument 2 to "run_track_log_subprocess" has incompatible type "list[str]"; expected "str"  [arg-type]
src/swell/tasks/gsi_bc_to_ioda.py:185: error: Invalid index type "int | None" for "list[str]"; expected type "SupportsIndex"  [index]
src/swell/tasks/gsi_bc_to_ioda.py:205: error: No overload variant of "join" matches argument types "str", "object"  [call-overload]
src/swell/tasks/gsi_bc_to_ioda.py:205: note: Possible overload variants:
src/swell/tasks/gsi_bc_to_ioda.py:205: note:     def join(str, /, *paths: str) -> str
src/swell/tasks/gsi_bc_to_ioda.py:205: note:     def join(str | PathLike[str], /, *paths: str | PathLike[str]) -> str
src/swell/tasks/gsi_bc_to_ioda.py:205: note:     def join(bytes | PathLike[bytes], /, *paths: bytes | PathLike[bytes]) -> bytes
src/swell/tasks/get_observations.py:10: error: Skipping analyzing "isodate": module is installed, but missing library stubs or py.typed marker  [import-untyped]
src/swell/tasks/get_observations.py:13: error: Skipping analyzing "netCDF4": module is installed, but missing library stubs or py.typed marker  [import-untyped]
src/swell/tasks/get_observations.py:20: error: Cannot find implementation or library stub for module named "r2d2"  [import-not-found]
src/swell/tasks/get_observations.py:125: error: Argument 3 to "create_obs_time_list" of "GetObservations" has incompatible type "str"; expected "datetime"  [arg-type]
src/swell/tasks/get_observations.py:258: error: "object" has no attribute "__iter__"; maybe "__dir__" or "__str__"? (not iterable)  [attr-defined]
src/swell/tasks/get_observations.py:281: error: Return value expected  [return-value]
src/swell/tasks/get_observations.py:285: error: Return value expected  [return-value]
src/swell/tasks/get_observations.py:289: error: Return value expected  [return-value]
src/swell/tasks/get_observations.py:296: error: Return value expected  [return-value]
src/swell/tasks/get_gsi_ncdiag.py:31: error: "object" has no attribute "strftime"  [attr-defined]
src/swell/tasks/get_gsi_bc.py:12: error: Skipping analyzing "isodate": module is installed, but missing library stubs or py.typed marker  [import-untyped]
src/swell/tasks/get_geovals.py:15: error: Cannot find implementation or library stub for module named "r2d2"  [import-not-found]
src/swell/tasks/get_geos_restart.py:40: error: Argument 1 to "forecast_dir" of "taskBase" has incompatible type "str"; expected "list[Any]"  [arg-type]
src/swell/tasks/get_geos_restart.py:41: error: Argument 1 to "forecast_dir" of "taskBase" has incompatible type "str"; expected "list[Any]"  [arg-type]
src/swell/tasks/get_geos_restart.py:64: error: Argument 1 to "forecast_dir" of "taskBase" has incompatible type "str"; expected "list[Any]"  [arg-type]
src/swell/tasks/get_geos_restart.py:75: error: Argument 1 to "forecast_dir" of "taskBase" has incompatible type "str"; expected "list[Any]"  [arg-type]
src/swell/tasks/get_geos_adas_background.py:48: error: Item "None" of "Match[str] | None" has no attribute "group"  [union-attr]
src/swell/tasks/get_ensemble.py:36: error: "object" has no attribute "strftime"  [attr-defined]
src/swell/tasks/get_background_geos_experiment.py:12: error: Skipping analyzing "isodate": module is installed, but missing library stubs or py.typed marker  [import-untyped]
src/swell/tasks/get_background.py:14: error: Skipping analyzing "isodate": module is installed, but missing library stubs or py.typed marker  [import-untyped]
src/swell/tasks/get_background.py:16: error: Cannot find implementation or library stub for module named "r2d2"  [import-not-found]
src/swell/tasks/eva_jedi_log.py:12: error: Library stubs not installed for "yaml"  [import-untyped]
src/swell/tasks/eva_jedi_log.py:14: error: Cannot find implementation or library stub for module named "eva.eva_driver"  [import-not-found]
src/swell/tasks/eva_increment.py:12: error: Library stubs not installed for "yaml"  [import-untyped]
src/swell/tasks/eva_increment.py:14: error: Cannot find implementation or library stub for module named "eva.eva_driver"  [import-not-found]
src/swell/tasks/eva_increment.py:45: error: "object" has no attribute "strftime"  [attr-defined]
src/swell/tasks/eva_increment.py:48: error: "str" has no attribute "strftime"  [attr-defined]
src/swell/tasks/eva_increment.py:64: error: "object" has no attribute "strftime"  [attr-defined]
src/swell/tasks/clone_jedi.py:13: error: Cannot find implementation or library stub for module named "jedi_bundle.bin.jedi_bundle"  [import-not-found]
src/swell/tasks/clone_jedi.py:34: error: Unpacking a string is disallowed  [misc]
src/swell/tasks/clone_jedi.py:41: error: Cannot determine type of "jedi_bundle_source_path"  [has-type]
src/swell/tasks/clone_jedi.py:61: error: Cannot determine type of "jedi_bundle_source_path"  [has-type]
src/swell/tasks/clone_jedi.py:62: error: Cannot determine type of "jedi_bundle_build_path"  [has-type]
src/swell/tasks/clone_geos.py:32: error: Unpacking a string is disallowed  [misc]
src/swell/tasks/clone_geos.py:39: error: Cannot determine type of "geos_gcm_source_path"  [has-type]
src/swell/tasks/clone_geos.py:59: error: Argument 2 to "run_subprocess" has incompatible type "list[str]"; expected "str"  [arg-type]
src/swell/tasks/clone_geos.py:64: error: Name "geos_build_method" is not defined  [name-defined]
src/swell/tasks/build_jedi_by_linking.py:31: error: Unpacking a string is disallowed  [misc]
src/swell/tasks/build_jedi_by_linking.py:53: error: Cannot determine type of "jedi_bundle_build_path"  [has-type]
src/swell/tasks/build_jedi.py:13: error: Cannot find implementation or library stub for module named "jedi_bundle.bin.jedi_bundle"  [import-not-found]
src/swell/tasks/build_jedi.py:32: error: Unpacking a string is disallowed  [misc]
src/swell/tasks/build_jedi.py:54: error: Cannot determine type of "jedi_bundle_source_path"  [has-type]
src/swell/tasks/build_jedi.py:55: error: Cannot determine type of "jedi_bundle_build_path"  [has-type]
src/swell/tasks/build_geos_by_linking.py:31: error: Unpacking a string is disallowed  [misc]
src/swell/tasks/build_geos_by_linking.py:53: error: Cannot determine type of "geos_gcm_build_path"  [has-type]
src/swell/tasks/build_geos.py:32: error: Unpacking a string is disallowed  [misc]
src/swell/tasks/build_geos.py:33: error: Cannot determine type of "geos_gcm_build_path"  [has-type]
src/swell/tasks/build_geos.py:38: error: Name "jedi_build_method" is not defined  [name-defined]
src/swell/tasks/build_geos.py:43: error: Cannot determine type of "geos_gcm_build_path"  [has-type]
src/swell/tasks/build_geos.py:46: error: Cannot determine type of "geos_gcm_source_path"  [has-type]
src/swell/tasks/build_geos.py:52: error: Cannot determine type of "geos_gcm_build_path"  [has-type]
src/swell/tasks/build_geos.py:56: error: Cannot determine type of "geos_gcm_source_path"  [has-type]
src/swell/test/code_tests/missing_obs_test.py:30: error: Argument 5 to "JediConfigRendering" has incompatible type "Datetime"; expected "str | None"  [arg-type]
src/swell/test/code_tests/missing_obs_test.py:43: error: Argument 4 to "check_obs" has incompatible type "datetime"; expected "str"  [arg-type]
src/swell/test/code_tests/missing_obs_test.py:51: error: Argument 4 to "check_obs" has incompatible type "datetime"; expected "str"  [arg-type]
src/swell/test/code_tests/missing_obs_test.py:59: error: Argument 4 to "check_obs" has incompatible type "datetime"; expected "str"  [arg-type]
src/swell/test/code_tests/missing_obs_test.py:67: error: Argument 4 to "check_obs" has incompatible type "datetime"; expected "str"  [arg-type]
src/swell/test/code_tests/missing_obs_test.py:75: error: Argument 4 to "check_obs" has incompatible type "datetime"; expected "str"  [arg-type]
src/swell/tasks/save_obs_diags.py:12: error: Cannot find implementation or library stub for module named "r2d2"  [import-not-found]
src/swell/tasks/save_obs_diags.py:60: error: Argument 1 to "check_obs" has incompatible type "None"; expected "str"  [arg-type]
src/swell/tasks/save_obs_diags.py:61: error: Argument 4 to "check_obs" has incompatible type "object"; expected "str"  [arg-type]
src/swell/tasks/run_jedi_variational_executable.py:12: error: Library stubs not installed for "yaml"  [import-untyped]
src/swell/tasks/run_jedi_variational_executable.py:117: error: Argument 5 to "jedi_dictionary_iterator" has incompatible type "object"; expected "str | None"  [arg-type]
src/swell/tasks/run_jedi_ufo_tests_executable.py:13: error: Library stubs not installed for "yaml"  [import-untyped]
src/swell/tasks/run_jedi_ufo_tests_executable.py:68: error: Argument 5 to "jedi_dictionary_iterator" has incompatible type "object"; expected "str | None"  [arg-type]
src/swell/tasks/run_jedi_ufo_tests_executable.py:105: error: Incompatible types in assignment (expression has type "bool", target has type "str")  [assignment]
src/swell/tasks/run_jedi_local_ensemble_da_executable.py:12: error: Library stubs not installed for "yaml"  [import-untyped]
src/swell/tasks/run_jedi_local_ensemble_da_executable.py:152: error: Argument 5 to "jedi_dictionary_iterator" has incompatible type "object"; expected "str | None"  [arg-type]
src/swell/tasks/run_jedi_local_ensemble_da_executable.py:206: error: Unsupported operand types for + ("str" and overloaded function)  [operator]
src/swell/tasks/run_jedi_local_ensemble_da_executable.py:210: error: Argument 4 to "run_executable" has incompatible type overloaded function; expected "str"  [arg-type]
src/swell/tasks/run_jedi_hofx_executable.py:13: error: Library stubs not installed for "yaml"  [import-untyped]
src/swell/tasks/run_jedi_hofx_executable.py:119: error: Argument 5 to "jedi_dictionary_iterator" has incompatible type "object"; expected "str | None"  [arg-type]
src/swell/tasks/run_jedi_hofx_executable.py:205: error: Argument 5 to "jedi_dictionary_iterator" has incompatible type "object"; expected "str | None"  [arg-type]
src/swell/tasks/run_jedi_ensemble_mean_variance.py:12: error: Library stubs not installed for "yaml"  [import-untyped]
src/swell/tasks/run_jedi_ensemble_mean_variance.py:91: error: Argument 5 to "jedi_dictionary_iterator" has incompatible type "object"; expected "str | None"  [arg-type]
src/swell/tasks/run_jedi_convert_state_soca2cice_executable.py:12: error: Library stubs not installed for "yaml"  [import-untyped]
src/swell/tasks/generate_b_climatology.py:9: error: Library stubs not installed for "yaml"  [import-untyped]
src/swell/tasks/generate_b_climatology.py:104: error: Argument 2 to "run_track_log_subprocess" has incompatible type "list[str]"; expected "str"  [arg-type]
src/swell/tasks/generate_b_climatology.py:157: error: Argument 2 to "run_subprocess" has incompatible type "list[str]"; expected "str"  [arg-type]
src/swell/tasks/generate_b_climatology.py:215: error: Argument 2 to "run_track_log_subprocess" has incompatible type "list[str]"; expected "str"  [arg-type]
src/swell/tasks/eva_observations.py:13: error: Library stubs not installed for "yaml"  [import-untyped]
src/swell/tasks/eva_observations.py:15: error: Cannot find implementation or library stub for module named "eva.eva_driver"  [import-not-found]
src/swell/tasks/eva_observations.py:99: error: Argument 1 to "check_obs" has incompatible type "None"; expected "str"  [arg-type]
src/swell/tasks/eva_observations.py:100: error: Argument 4 to "check_obs" has incompatible type "object"; expected "str"  [arg-type]
src/swell/tasks/eva_observations.py:151: error: Incompatible types in assignment (expression has type "bool", target has type "str")  [assignment]
src/swell/tasks/eva_observations.py:156: error: Incompatible types in assignment (expression has type "list[int]", target has type "str")  [assignment]
src/swell/deployment/prepare_config_and_suite/question_and_answer_cli.py:40: error: Incompatible types in assignment (expression has type "str | list[Any]", variable has type "str")  [assignment]
src/swell/deployment/prepare_config_and_suite/question_and_answer_cli.py:42: error: Incompatible types in assignment (expression has type "bool", variable has type "str")  [assignment]
src/swell/deployment/prepare_config_and_suite/question_and_answer_cli.py:64: error: Function "questionary.prompts.text.text" is not valid as a type  [valid-type]
src/swell/deployment/prepare_config_and_suite/question_and_answer_cli.py:64: note: Perhaps you need "Callable[...]" or a callback protocol?
src/swell/deployment/prepare_config_and_suite/question_and_answer_cli.py:65: error: questionary.text? not callable  [misc]
src/swell/deployment/prepare_config_and_suite/question_and_answer_cli.py:71: error: Function "questionary.prompts.text.text" is not valid as a type  [valid-type]
src/swell/deployment/prepare_config_and_suite/question_and_answer_cli.py:71: note: Perhaps you need "Callable[...]" or a callback protocol?
src/swell/deployment/prepare_config_and_suite/question_and_answer_cli.py:73: error: questionary.text? not callable  [misc]
src/swell/deployment/prepare_config_and_suite/question_and_answer_cli.py:86: error: Function "questionary.prompts.text.text" is not valid as a type  [valid-type]
src/swell/deployment/prepare_config_and_suite/question_and_answer_cli.py:86: note: Perhaps you need "Callable[...]" or a callback protocol?
src/swell/deployment/prepare_config_and_suite/question_and_answer_cli.py:89: error: questionary.text? not callable  [misc]
src/swell/deployment/prepare_config_and_suite/question_and_answer_cli.py:104: error: Function "questionary.prompts.text.text" is not valid as a type  [valid-type]
src/swell/deployment/prepare_config_and_suite/question_and_answer_cli.py:104: note: Perhaps you need "Callable[...]" or a callback protocol?
src/swell/deployment/prepare_config_and_suite/question_and_answer_cli.py:109: error: questionary.text? not callable  [misc]
src/swell/deployment/prepare_config_and_suite/question_and_answer_cli.py:119: error: Function "questionary.prompts.text.text" is not valid as a type  [valid-type]
src/swell/deployment/prepare_config_and_suite/question_and_answer_cli.py:119: note: Perhaps you need "Callable[...]" or a callback protocol?
src/swell/deployment/prepare_config_and_suite/question_and_answer_cli.py:122: error: questionary.text? not callable  [misc]
src/swell/deployment/prepare_config_and_suite/question_and_answer_cli.py:132: error: Function "questionary.prompts.text.text" is not valid as a type  [valid-type]
src/swell/deployment/prepare_config_and_suite/question_and_answer_cli.py:132: note: Perhaps you need "Callable[...]" or a callback protocol?
src/swell/deployment/prepare_config_and_suite/question_and_answer_cli.py:145: error: questionary.text? not callable  [misc]
src/swell/deployment/prepare_config_and_suite/question_and_answer_cli.py:156: error: Function "questionary.prompts.text.text" is not valid as a type  [valid-type]
src/swell/deployment/prepare_config_and_suite/question_and_answer_cli.py:156: note: Perhaps you need "Callable[...]" or a callback protocol?
src/swell/deployment/prepare_config_and_suite/question_and_answer_cli.py:183: error: questionary.text? not callable  [misc]
src/swell/deployment/prepare_config_and_suite/question_and_answer_cli.py:195: error: Function "questionary.prompts.text.text" is not valid as a type  [valid-type]
src/swell/deployment/prepare_config_and_suite/question_and_answer_cli.py:195: note: Perhaps you need "Callable[...]" or a callback protocol?
src/swell/deployment/prepare_config_and_suite/question_and_answer_cli.py:206: error: Incompatible types in assignment (expression has type "None", variable has type "str | list[Any]")  [assignment]
src/swell/deployment/prepare_config_and_suite/question_and_answer_cli.py:208: error: questionary.text? not callable  [misc]
src/swell/tasks/run_jedi_hofx_ensemble_executable.py:12: error: Library stubs not installed for "yaml"  [import-untyped]
src/swell/tasks/run_jedi_hofx_ensemble_executable.py:27: error: Signature of "execute" incompatible with supertype "RunJediHofxExecutable"  [override]
src/swell/tasks/run_jedi_hofx_ensemble_executable.py:27: note:      Superclass:
src/swell/tasks/run_jedi_hofx_ensemble_executable.py:27: note:          def execute(self, ensemble_members: list[Any] | None = ...) -> None
src/swell/tasks/run_jedi_hofx_ensemble_executable.py:27: note:      Subclass:
src/swell/tasks/run_jedi_hofx_ensemble_executable.py:27: note:          def execute(self) -> None
src/swell/tasks/run_jedi_hofx_ensemble_executable.py:133: error: Argument 5 to "jedi_dictionary_iterator" has incompatible type "object"; expected "str | None"  [arg-type]
src/swell/deployment/prepare_config_and_suite/prepare_config_and_suite.py:13: error: Library stubs not installed for "yaml"  [import-untyped]
src/swell/deployment/prepare_config_and_suite/prepare_config_and_suite.py:69: error: Incompatible types in assignment (expression has type "GetAnswerDefaults", variable has type "GetAnswerCli")  [assignment]
src/swell/deployment/prepare_config_and_suite/prepare_config_and_suite.py:73: error: Need type annotation for "experiment_dict" (hint: "experiment_dict: dict[<type>, <type>] = ...")  [var-annotated]
src/swell/deployment/prepare_config_and_suite/prepare_config_and_suite.py:74: error: Need type annotation for "questions_dict" (hint: "questions_dict: dict[<type>, <type>] = ...")  [var-annotated]
src/swell/deployment/create_experiment.py:16: error: Library stubs not installed for "yaml"  [import-untyped]
src/swell/deployment/create_experiment.py:63: error: Missing positional argument "slurm" in call to "prepare_config"  [call-arg]
src/swell/deployment/create_experiment.py:212: error: Argument 1 to "copy_platform_files" has incompatible type "str"; expected "Logger"  [arg-type]
src/swell/deployment/create_experiment.py:305: error: Value of type variable "AnyOrLiteralStr" of "split" cannot be "str | None"  [type-var]
src/swell/deployment/create_experiment.py:417: error: Argument 4 to "dict_get" has incompatible type "list[Never]"; expected "str"  [arg-type]
src/swell/deployment/create_experiment.py:425: error: Need type annotation for "cycle_times" (hint: "cycle_times: list[<type>] = ...")  [var-annotated]
src/swell/test/suite_tests/suite_tests.py:2: error: Library stubs not installed for "yaml"  [import-untyped]
src/swell/test/suite_tests/suite_tests.py:56: error: Argument 2 to "update_dict" has incompatible type "Path"; expected "dict[Any, Any]"  [arg-type]
src/swell/test/suite_tests/suite_tests.py:80: error: Argument 6 to "create_experiment_directory" has incompatible type "None"; expected "str"  [arg-type]
src/swell/swell.py:116: error: Argument 4 to "create_experiment_directory" has incompatible type "dict[Any, Any] | str | None"; expected "str"  [arg-type]
src/swell/swell.py:151: error: Missing positional arguments "method", "platform", "override", "advanced", "slurm" in call to "create_experiment_directory"  [call-arg]
src/swell/swell.py:204: error: Argument 4 to "task_wrapper" has incompatible type "str | None"; expected "str"  [arg-type]
Found 318 errors in 69 files (checked 104 source files)

mranst · 2024-09-17T14:38:16Z

Changes look good! However, when I ran this through a type checker locally (mypy), it turned up a bunch of errors. We don't have to address all (or even most, and perhaps not any) of them now...but I recommend taking a look through this list and deciding consciously which of the errors are worth fixing now and which ones we can wait on for a future PR.

@mranst I leave this up to your judgment. Let me know when you think we've hit a reasonably stopping point for this PR.

Full mypy output is in the Details below.

I've gone through the output of mypy and revised many of the more obvious mistypes I had, although there's still a lot of errors. A lot of them don't seem to necessarily be related to mistakes in type hinting, for instance it doesn't like any action being done on an optional parameter, although as far as I can tell most instances are valid per expected behavior. I feel like I've addressed most of the low-hanging fruit, but if you think I should go deeper, let me know

src/swell/utilities/exceptions.py

src/swell/utilities/render_jedi_interface_files.py

Updated type hint to optional for consistency Co-authored-by: Alexey Shiklomanov <[email protected]>

mranst added 5 commits September 11, 2024 17:32

sles15 is now default platform, added to docs reflecting this and oth…

b62be29

…er additions (GEOS-ESM#407)

swell_static_files_user in config now used in appropriate tasks (GEOS…

c2a77f4

…-ESM#360)

addressed potential error on abort caused by undefined logger call

f9b50f2

renamed datetime utility to avoid hinting confusion with base package…

ccb93d6

…, added type hinting (GEOS-ESM#349)

type hinting for all python methods (GEOS-ESM#349)

d03c7ed

mranst requested review from ashiklom, asewnath and Dooruk September 11, 2024 22:40

ashiklom self-assigned this Sep 13, 2024

asewnath reviewed Sep 13, 2024

View reviewed changes

mranst added 2 commits September 13, 2024 10:22

removed unnecessary pass of logger to functions copy_platform_files a…

99b5f6d

…nd copy_eva_files

type hinting in run_geos_executable uses Optional

e277b8a

This was linked to issues Sep 13, 2024

(SE) Make SLES15 the default platform #407

Closed

(SE) Use swell_static_files_user as an alternate location for all tasks #360

Closed

SE: Add type hints throughout #349

Closed

Hinting changes, Logger properly type hinted, pd.DataFrame now used, …

5b000ff

…typing.Optional used where appropriate

ashiklom requested changes Sep 13, 2024

View reviewed changes

Dooruk requested changes Sep 13, 2024

View reviewed changes

mranst and others added 2 commits September 13, 2024 11:38

Update docs/configuring_cylc.md

dc846ce

Co-authored-by: Alexey Shiklomanov <[email protected]>

added proper hinting for SilentUndefined instance in jinja2.py

ee9852b

proper syntax for linking docs

3fab899

mranst added 7 commits September 13, 2024 11:59

Merge remote-tracking branch 'refs/remotes/origin/hinting-misc' into …

69a7d6d

…hinting-misc

direct type hinting for FileHandler objects

a8ff454

added Optional typing where appropriate

a7655d1

added missing type hint in run_jedi_hofx_executable.py, fixed missing…

5f93e20

… typing functions

Merge branch 'GEOS-ESM:develop' into hinting-misc

2895e5e

more types in hint

256595d

more precise type hinting

27ad6ce

mranst added 2 commits September 13, 2024 15:17

Merge remote-tracking branch 'refs/remotes/origin/hinting-misc' into …

4ff8fe8

…hinting-misc

Resolved code test error

ba8b009

mranst requested review from ashiklom and Dooruk September 16, 2024 12:57

Dooruk previously approved these changes Sep 16, 2024

View reviewed changes

ashiklom reviewed Sep 16, 2024

View reviewed changes

mranst added 5 commits September 16, 2024 14:26

more specific type hinting per mypy

e4d5cf1

corrected logger instance in type hint

50bd771

Revised type hinting

812990d

Revised datetime typing, other refinements

c109c28

Further revised type hinting

f4903b4

mranst dismissed Dooruk’s stale review via f4903b4 September 17, 2024 14:16

ashiklom reviewed Sep 17, 2024

View reviewed changes

src/swell/utilities/exceptions.py Show resolved Hide resolved

ashiklom reviewed Sep 17, 2024

View reviewed changes

src/swell/utilities/render_jedi_interface_files.py Outdated Show resolved Hide resolved

ashiklom previously approved these changes Sep 17, 2024

View reviewed changes

Update src/swell/utilities/render_jedi_interface_files.py

5173bcb

Updated type hint to optional for consistency Co-authored-by: Alexey Shiklomanov <[email protected]>

mranst dismissed ashiklom’s stale review via 5173bcb September 17, 2024 15:41

ashiklom approved these changes Sep 17, 2024

View reviewed changes

ashiklom merged commit 5ca0051 into GEOS-ESM:develop Sep 17, 2024
2 checks passed

mranst deleted the hinting-misc branch October 10, 2024 19:07

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Type hinting and misc changes #417

Type hinting and misc changes #417

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Type hinting and misc changes #417

Type hinting and misc changes #417

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mranst commented Sep 11, 2024

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