style: add typing to pass mypy and pyright in snakemake.io.__init__ and snakemake.io.container by Hocnonsense · Pull Request #4082 · snakemake/snakemake

Hocnonsense · 2026-03-13T09:33:37Z

fix bugs introduced in #4032

QC

The PR contains a test case for the changes or the changes are already covered by an existing test case.
The change does neither modify the language nor the behavior or functionalities of Snakemake.

Summary by CodeRabbit

Bug Fixes
- Improved handling of function-based file paths and wildcard resolution for more reliable IO behavior.
New Features
- Added a property to report temporary file sizes for input collections, aiding cleanup and monitoring.
Chores
- Strengthened internal type hints and typing consistency to improve reliability and maintainability.

coderabbitai · 2026-03-13T09:33:58Z

No actionable comments were generated in the recent review. 🎉

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Run ID: b4afab24-181c-4015-a792-96a5b0af89ee

📥 Commits

Reviewing files that changed from the base of the PR and between e1d19b8 and 80d9518.

📒 Files selected for processing (1)

src/snakemake/io/container.py

📝 Walkthrough

Walkthrough

Tightened and modernized type annotations in io modules: added a TypeVar and Coroutine typing for iocache, introduced forward references and relaxed return types for Namedlist/ReportHref and _IOFile, changed wait_for_files default to frozenset(), and added InputFiles.size_tempfiles.

Changes

Cohort / File(s)	Summary
Typing & iocache `src/snakemake/io/__init__.py`	Added `TypeVar T` and `Coroutine` imports; updated `iocache` signature to `Callable[..., Coroutine[Any,Any,T]]`; generalized async cache typing.
_IOFile & property typings `src/snakemake/io/__init__.py`	Widened `_IOFile._file` to a forward-referenced `Callable[\"Namedlist\", str]`; annotated `storage_object -> Any` and `file -> str
wait_for_files, flag, apply_wildcards, flatten `src/snakemake/io/__init__.py`	Changed `wait_for_files` `consider_local` default to `frozenset()` (with `# type: ignore[assignment]`); `flag()` `flag_value` typed as `Any`; added lazy `Namedlist` import in `apply_wildcards`; simplified `flatten` typing and removed several list-item ignores.
Namedlist generics & ReportHref forward refs `src/snakemake/io/container.py`	Removed key TypeVar from `Namedlist`, now `Generic[_TNamedList]`; `fromdict` expects `Dict[str, _TNamedList]`; `items()` yields `(str, value)`; `ReportHref` uses `parent: Optional[\"ReportHref\"]` and constructs returns via `self.__class__`.
InputFiles & optional deps handling `src/snakemake/io/container.py`	Added `InputFiles.size_tempfiles` property using `is_flagged`; adjusted `_safely_store_params`/params logic to initialize optional deps (`pd`, `np`, `pl`) with `# type: ignore` where needed and other small typing cleanups.

Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~20 minutes

🚥 Pre-merge checks | ✅ 1 | ❌ 2

❌ Failed checks (1 warning, 1 inconclusive)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 10.34% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.
Description check	❓ Inconclusive	The description is incomplete. It mentions fixing bugs from `#4032` and adding typing, but lacks detail on what bugs were fixed and why the changes are necessary.	Provide more context about the bugs introduced in `#4032` and explain how the typing changes address them.

✅ Passed checks (1 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title accurately describes the main change: adding typing annotations to pass mypy and pyright in specific modules.

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Commit unit tests in branch style/post-4032

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coderabbitai

Actionable comments posted: 1

🤖 Prompt for all review comments with AI agents

Verify each finding against the current code and only fix it if needed.

Inline comments:
In `@src/snakemake/io/__init__.py`:
- Around line 791-799: In the except MissingOutputException block, preserve the
original exception context by chaining the new WorkflowError from the caught
exception (use "raise WorkflowError(... ) from e") and avoid shadowing the
built-in by renaming the local variable dir to dirpath (update the assignment
"dir = _file if self.is_directory else os.path.dirname(_file)" to use dirpath).
Keep references to _file, is_directory, and the is_callable(self._file) check
unchanged and ensure the new WorkflowError is raised using "from e".

ℹ️ Review info

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Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: 247f5fa0-2360-4902-92cb-da773ec49db1

📥 Commits

Reviewing files that changed from the base of the PR and between e8ad771 and 1528efa.

📒 Files selected for processing (2)

src/snakemake/io/__init__.py
src/snakemake/io/container.py

src/snakemake/io/__init__.py

coderabbitai

Actionable comments posted: 1

🤖 Prompt for all review comments with AI agents

Verify each finding against the current code and only fix it if needed.

Inline comments:
In `@src/snakemake/io/__init__.py`:
- Around line 461-463: Fix the misspelling in the inline comment inside the
storage_object method: change "silance" to "silence" in the comment that starts
with "assume that all .storage_object is called after .is_storage check..." near
the storage_object function (which returns get_flag_value(self._file,
"storage_object")). Ensure only the comment text is updated and no code behavior
is changed.

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Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: 567b8dff-42a1-46fa-8cf4-0193779e24bd

📥 Commits

Reviewing files that changed from the base of the PR and between 1528efa and e510316.

📒 Files selected for processing (1)

src/snakemake/io/__init__.py

src/snakemake/io/__init__.py

coderabbitai

🧹 Nitpick comments (1)

src/snakemake/io/__init__.py (1)
1046-1046: Use collections.abc.Set annotation to match immutable default value.

Line 1046 annotates consider_local as Set[_IOFile] (mutable protocol) but defaults to frozenset() (immutable), requiring # type: ignore[assignment]. Since this parameter is used only for membership checks, annotate it as collections.abc.Set[_IOFile] to properly reflect its immutable usage and eliminate the ignore comment.
♻️ Proposed typing-only adjustment
-    consider_local: Set[_IOFile] = frozenset(),  # type: ignore[assignment]
+    consider_local: collections.abc.Set[_IOFile] = frozenset(),
🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed.

In `@src/snakemake/io/__init__.py` at line 1046, The parameter annotation for
consider_local currently uses typing.Set[_IOFile] but the default is an
immutable frozenset() and the value is only used for membership checks; change
the annotation to collections.abc.Set[_IOFile] (import collections.abc as
needed) on the function or variable where consider_local is declared and remove
the trailing "# type: ignore[assignment]" so the type matches the immutable
default and eliminates the ignore; reference the consider_local parameter and
the _IOFile element type when making this edit.

🤖 Prompt for all review comments with AI agents

Verify each finding against the current code and only fix it if needed.

Nitpick comments:
In `@src/snakemake/io/__init__.py`:
- Line 1046: The parameter annotation for consider_local currently uses
typing.Set[_IOFile] but the default is an immutable frozenset() and the value is
only used for membership checks; change the annotation to
collections.abc.Set[_IOFile] (import collections.abc as needed) on the function
or variable where consider_local is declared and remove the trailing "# type:
ignore[assignment]" so the type matches the immutable default and eliminates the
ignore; reference the consider_local parameter and the _IOFile element type when
making this edit.

ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: 6b56a6f4-c7d2-459c-aad7-0567059f9fd6

📥 Commits

Reviewing files that changed from the base of the PR and between e510316 and e1d19b8.

📒 Files selected for processing (1)

src/snakemake/io/__init__.py

src/snakemake/io/container.py

Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>

style: add typing to pass mypy and pyright

19ae60f

Hocnonsense requested a review from johanneskoester as a code owner March 13, 2026 09:33

Merge branch 'main' into style/post-4032

1528efa

fix

e510316

coderabbitai bot reviewed Mar 13, 2026

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Hocnonsense and others added 2 commits March 13, 2026 17:50

fix

cdc1554

Merge branch 'main' into style/post-4032

e1d19b8

Hocnonsense changed the title ~~style: add typing to pass mypy and pyright~~ style: add typing to pass mypy and pyright in snakemake.io.__init__ and snakemake.io.container Mar 13, 2026

Hocnonsense added this to Snakemake Hackathon 2026 Mar 13, 2026

Hocnonsense moved this to In review in Snakemake Hackathon 2026 Mar 13, 2026

fgvieira assigned Hocnonsense Mar 13, 2026

fgvieira added the bug Something isn't working label Mar 13, 2026

coderabbitai bot reviewed Mar 13, 2026

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Merge branch 'main' into style/post-4032

8d18b7c

johanneskoester reviewed Mar 13, 2026

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johanneskoester approved these changes Mar 13, 2026

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Update src/snakemake/io/container.py

c01e326

Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>

johanneskoester enabled auto-merge (squash) March 13, 2026 13:22

Hocnonsense added 2 commits March 13, 2026 21:22

Merge branch 'main' into style/post-4032

80d9518

Merge branch 'main' into style/post-4032

fb3d8f0

johanneskoester merged commit a554741 into main Mar 13, 2026
59 checks passed

johanneskoester deleted the style/post-4032 branch March 13, 2026 19:41

github-project-automation bot moved this from In review to Done in Snakemake Hackathon 2026 Mar 13, 2026

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style: add typing to pass mypy and pyright in snakemake.io.init and snakemake.io.container#4082

style: add typing to pass mypy and pyright in snakemake.io.init and snakemake.io.container#4082
johanneskoester merged 9 commits intomainfrom
style/post-4032

Hocnonsense commented Mar 13, 2026 •

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Hocnonsense commented Mar 13, 2026 •

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