This is the first iteration of PRs to start enforcing type annotations. 

The move to the src layout also helps with the finicky nature of
pytest-cov

While mypy type-checking is possible, there are currently ~50 issues to
be addressed

<details>
<summary>mypy output</summary>



```console
➜ pixi run type-check
✨ Pixi task (type-check in dev): mypy src/
src/snakemake_interface_common/settings.py:15: error: Need type annotation for "skip"  [var-annotated]
src/snakemake_interface_common/settings.py:16: error: Generator has incompatible item type "SettingsEnumBase"; expected "TSettingsEnumBase"  [misc]
src/snakemake_interface_common/settings.py:20: error: Argument 1 to "_parse_choices_into" of "SettingsEnumBase" has incompatible type "list[str]"; expected "str"  [arg-type]
src/snakemake_interface_common/settings.py:24: error: Incompatible return value type (got "list[Never]", expected "set[TSettingsEnumBase]")  [return-value]
src/snakemake_interface_common/settings.py:24: error: Argument 1 to "_parse_choices_into" of "SettingsEnumBase" has incompatible type "list[str]"; expected "str"  [arg-type]
src/snakemake_interface_common/settings.py:27: error: Function is missing a type annotation for one or more arguments  [no-untyped-def]
src/snakemake_interface_common/settings.py:31: error: A function returning TypeVar should receive at least one argument containing the same TypeVar  [type-var]
src/snakemake_interface_common/settings.py:31: note: Consider using the upper bound "SettingsEnumBase" instead
src/snakemake_interface_common/settings.py:32: error: Incompatible return value type (got "SettingsEnumBase", expected "TSettingsEnumBase")  [return-value]
src/snakemake_interface_common/settings.py:42: error: Function is missing a type annotation  [no-untyped-def]
src/snakemake_interface_common/logging.py:7: error: Function is missing a return type annotation  [no-untyped-def]
src/snakemake_interface_common/plugin_registry/attribute_types.py:23: error: Function is missing a return type annotation  [no-untyped-def]
src/snakemake_interface_common/plugin_registry/attribute_types.py:27: error: Function is missing a return type annotation  [no-untyped-def]
src/snakemake_interface_common/plugin_registry/attribute_types.py:30: error: Function is missing a return type annotation  [no-untyped-def]
src/snakemake_interface_common/exceptions.py:19: error: Function is missing a type annotation  [no-untyped-def]
src/snakemake_interface_common/exceptions.py:39: error: Function is missing a type annotation for one or more arguments  [no-untyped-def]
src/snakemake_interface_common/exceptions.py:50: error: Incompatible types in assignment (expression has type "int | None", variable has type "int")  [assignment]
src/snakemake_interface_common/exceptions.py:51: error: Incompatible types in assignment (expression has type "Path | None", variable has type "Path")  [assignment]
src/snakemake_interface_common/exceptions.py:58: error: Incompatible types in assignment (expression has type "list[Any]", variable has type "tuple[Any, ...]")  [assignment]
src/snakemake_interface_common/exceptions.py:63: error: Function is missing a type annotation  [no-untyped-def]
src/snakemake_interface_common/utils.py:7: error: Function is missing a type annotation  [no-untyped-def]
src/snakemake_interface_common/utils.py:19: error: Function is missing a type annotation  [no-untyped-def]
src/snakemake_interface_common/utils.py:22: error: Function is missing a type annotation  [no-untyped-def]
src/snakemake_interface_common/utils.py:27: error: Function is missing a type annotation  [no-untyped-def]
src/snakemake_interface_common/utils.py:38: error: Function is missing a type annotation for one or more arguments  [no-untyped-def]
src/snakemake_interface_common/utils.py:56: error: Function is missing a type annotation  [no-untyped-def]
src/snakemake_interface_common/utils.py:72: error: Function is missing a type annotation  [no-untyped-def]
src/snakemake_interface_common/utils.py:77: error: Function is missing a type annotation  [no-untyped-def]
src/snakemake_interface_common/plugin_registry/plugin.py:28: error: Function is missing a return type annotation  [no-untyped-def]
src/snakemake_interface_common/plugin_registry/plugin.py:41: error: Function is missing a return type annotation  [no-untyped-def]
src/snakemake_interface_common/plugin_registry/plugin.py:42: error: Invalid index type "str | None" for "dict[str, SettingsBase]"; expected type "str"  [index]
src/snakemake_interface_common/plugin_registry/plugin.py:45: error: Argument 1 to "get" of "dict" has incompatible type "str | None"; expected "str"  [arg-type]
src/snakemake_interface_common/plugin_registry/plugin.py:48: error: No overload variant of "get" of "dict" matches argument type "None"  [call-overload]
src/snakemake_interface_common/plugin_registry/plugin.py:48: note: Possible overload variants:
src/snakemake_interface_common/plugin_registry/plugin.py:48: note:     def get(self, str, /) -> SettingsBase | None
src/snakemake_interface_common/plugin_registry/plugin.py:48: note:     def get(self, str, SettingsBase, /) -> SettingsBase
src/snakemake_interface_common/plugin_registry/plugin.py:48: note:     def [_T] get(self, str, _T, /) -> SettingsBase | _T
src/snakemake_interface_common/plugin_registry/plugin.py:57: error: Function is missing a type annotation  [no-untyped-def]
src/snakemake_interface_common/plugin_registry/plugin.py:78: error: Function is missing a return type annotation  [no-untyped-def]
src/snakemake_interface_common/plugin_registry/plugin.py:87: error: Function is missing a type annotation  [no-untyped-def]
src/snakemake_interface_common/plugin_registry/plugin.py:113: error: Function is missing a type annotation  [no-untyped-def]
src/snakemake_interface_common/plugin_registry/plugin.py:172: error: Function is missing a type annotation  [no-untyped-def]
src/snakemake_interface_common/plugin_registry/plugin.py:173: error: Function is missing a type annotation  [no-untyped-def]
src/snakemake_interface_common/plugin_registry/plugin.py:195: error: Function is missing a type annotation for one or more arguments  [no-untyped-def]
src/snakemake_interface_common/plugin_registry/plugin.py:211: error: Function is missing a type annotation  [no-untyped-def]
src/snakemake_interface_common/plugin_registry/plugin.py:217: error: Need type annotation for "kwargs_tagged"  [var-annotated]
src/snakemake_interface_common/plugin_registry/plugin.py:232: error: Function is missing a type annotation  [no-untyped-def]
src/snakemake_interface_common/plugin_registry/plugin.py:300: error: Function is missing a type annotation  [no-untyped-def]
src/snakemake_interface_common/plugin_registry/plugin.py:301: error: Function is missing a type annotation  [no-untyped-def]
src/snakemake_interface_common/plugin_registry/__init__.py:22: error: Function is missing a return type annotation  [no-untyped-def]
src/snakemake_interface_common/plugin_registry/__init__.py:27: error: Function is missing a return type annotation  [no-untyped-def]
src/snakemake_interface_common/plugin_registry/__init__.py:27: note: Use "-> None" if function does not return a value
src/snakemake_interface_common/plugin_registry/__init__.py:56: error: Function is missing a type annotation  [no-untyped-def]
src/snakemake_interface_common/plugin_registry/__init__.py:62: error: Function is missing a return type annotation  [no-untyped-def]
src/snakemake_interface_common/plugin_registry/__init__.py:62: note: Use "-> None" if function does not return a value
src/snakemake_interface_common/plugin_registry/__init__.py:80: error: Function is missing a return type annotation  [no-untyped-def]
src/snakemake_interface_common/plugin_registry/__init__.py:95: error: Function is missing a return type annotation  [no-untyped-def]
Found 50 errors in 7 files (checked 11 source files)
```

</details>

I've also realized that there are some inconsistencies between some of
the abstract classes and their concrete implementations in the
`snakemake-interface-*-plugins` repos which need to be addressed.

I will begin addressing these in a set of separate PRs and iterate over
them.




<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->

## Summary by CodeRabbit

- **Chores**
- Streamlined CI/CD workflows for package publishing and testing by
updating dependency management and automation steps.
- Enhanced repository configurations and ignore rules to support new
build environments.

- **Refactor**
- Simplified internal method structures to boost maintainability without
impacting functionality.

- **Tests**
- Improved quality control checks within test workflows for more
consistent formatting and linting results.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

🤖 I have created a release *beep* *boop*
---


##
[1.18.0](v1.17.4...v1.18.0)
(2025-03-27)


### Features

* setup pixi, move to src layout, run ruff format once
([#58](#58))
([95d1d8d](95d1d8d))

---
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