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


##
[9.14.0](v9.13.7...v9.14.0)
(2025-11-27)


### Features

* Support Hy in script directive
([#3824](#3824))
([2329c9e](2329c9e))


### Bug Fixes

* Add support for pathlib in `notebook` field
([#3811](#3811))
([7b2180a](7b2180a))
* Addressed race condition in workdir_handler.py
([#3844](#3844))
([8dbfcfb](8dbfcfb))
* cleanup update-marked output files of failed jobs if there was no
backup to restore them
([#3843](#3843))
([41f1ce8](41f1ce8))
* correct Windows callable path handling
([#3832](#3832))
([5caad70](5caad70))
* expand env vars on resources
([#3823](#3823))
([fcfa1bc](fcfa1bc))
* fix backup for output marked by `update`
([#3839](#3839))
([09c64b7](09c64b7))
* Minor fixes/additions to logging module.
([#3802](#3802))
([3b3986d](3b3986d))
* mount local storage prefix into containers
([#3840](#3840))
([f1e8b62](f1e8b62))
* properly format input/output files in case of missing rule to produce
them ([#3849](#3849))
([69d5d24](69d5d24))
* Unpack AnnotatedString in _apply_wildcards
([#3798](#3798))
([7886508](7886508))


### Performance Improvements

* retrieve storage inputs immediately before scheduling jobs instead of
before running the entire workflow
([#3850](#3850))
([4ac6cda](4ac6cda))

---
This PR was generated with [Release
Please](https://github.com/googleapis/release-please). See
[documentation](https://github.com/googleapis/release-please#release-please).

Race condition existed in workdir_handler.py when for some reason (such
as testing suites that might run in parallel) snakemake is run in
parallel, and change_to is called, an exception is called, though
control-flow can continue as normal without any issues.

Here is a more thorough description of how the race condition can occur

For reference, take a look at mkdir from pathlib

```python
    def mkdir(self, mode=0o777, parents=False, exist_ok=False):
        """
        Create a new directory at this given path.
        """
        try:
            os.mkdir(self, mode)
        except FileNotFoundError:
            if not parents or self.parent == self:
                raise
            self.parent.mkdir(parents=True, exist_ok=True)
            self.mkdir(mode, parents=False, exist_ok=exist_ok)
        except OSError:
            # Cannot rely on checking for EEXIST, since the operating system
            # could give priority to other errors like EACCES or EROFS
            if not exist_ok or not self.is_dir():
                raise
```

Take two threads that are run on snakemake, and both try to cd into
"/fake/address"

Thread 1 and 2:
checks if "/fake/address" (returns False)
calls self.workdir.mkdir(parents=True) (with exists_ok defaulting to
false)
inside the try block: tries to mkdir "/fake/address" which fails with
FileNotFoundError because "/fake" does not exist
catches exception

Thread 1:
calls `self.parent.mkdir(parents=True, exist_ok=True)`
successfully creates "/fake"

Thread 2:
calls  `self.parent.mkdir(parents=True, exist_ok=True)`
"/fake" already exists, but that is not a problem
calls `self.mkdir(mode, parents=False, exist_ok=exist_ok)` to create
"/fake/address"
succeeds

Thread 1:
calls `self.mkdir(mode, parents=False, exist_ok=exist_ok)` to create
"/fake/address"
fails because "/fake/address" exists

Whereby there is no problem here that "/fake/address" exists. 

Not sure if I should write a test for this, I personally wouldn't even
know how to begin testing this issue, but it seems to have already been
solved by pathlib, so just adding this small param should fix this niche
issue.

This PR does not change intended behavior.


### QC
<!-- Make sure that you can tick the boxes below. -->

* [x] The PR contains a test case for the changes or the changes are
already covered by an existing test case.
* [x] The documentation (`docs/`) is updated to reflect the changes or
this is not necessary (e.g. if the change does neither modify the
language nor the behavior or functionalities of Snakemake).


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

## Summary by CodeRabbit

# Release Notes

* **Bug Fixes**
* Enhanced working directory handling to gracefully manage scenarios
where directories already exist, improving reliability during concurrent
operations and preventing unnecessary errors.

<sub>✏️ Tip: You can customize this high-level summary in your review
settings.</sub>

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

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


##
[9.14.0](snakemake/snakemake@v9.13.7...v9.14.0)
(2025-11-27)


### Features

* Support Hy in script directive
([snakemake#3824](snakemake#3824))
([2329c9e](snakemake@2329c9e))


### Bug Fixes

* Add support for pathlib in `notebook` field
([snakemake#3811](snakemake#3811))
([7b2180a](snakemake@7b2180a))
* Addressed race condition in workdir_handler.py
([snakemake#3844](snakemake#3844))
([8dbfcfb](snakemake@8dbfcfb))
* cleanup update-marked output files of failed jobs if there was no
backup to restore them
([snakemake#3843](snakemake#3843))
([41f1ce8](snakemake@41f1ce8))
* correct Windows callable path handling
([snakemake#3832](snakemake#3832))
([5caad70](snakemake@5caad70))
* expand env vars on resources
([snakemake#3823](snakemake#3823))
([fcfa1bc](snakemake@fcfa1bc))
* fix backup for output marked by `update`
([snakemake#3839](snakemake#3839))
([09c64b7](snakemake@09c64b7))
* Minor fixes/additions to logging module.
([snakemake#3802](snakemake#3802))
([3b3986d](snakemake@3b3986d))
* mount local storage prefix into containers
([snakemake#3840](snakemake#3840))
([f1e8b62](snakemake@f1e8b62))
* properly format input/output files in case of missing rule to produce
them ([snakemake#3849](snakemake#3849))
([69d5d24](snakemake@69d5d24))
* Unpack AnnotatedString in _apply_wildcards
([snakemake#3798](snakemake#3798))
([7886508](snakemake@7886508))


### Performance Improvements

* retrieve storage inputs immediately before scheduling jobs instead of
before running the entire workflow
([snakemake#3850](snakemake#3850))
([4ac6cda](snakemake@4ac6cda))

---
This PR was generated with [Release
Please](https://github.com/googleapis/release-please). See
[documentation](https://github.com/googleapis/release-please#release-please).