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


##
[9.6.0](v9.5.1...v9.6.0)
(2025-06-16)


### Features

* Prefer papermill to nbconvert
([#2857](#2857))
([4263b03](4263b03))


### Bug Fixes

* DeprecationWarning when using snakemake.utils.validate
([#3420](#3420))
([cf72427](cf72427))
* display group jobs on dryrun
([#3435](#3435))
([3bebef4](3bebef4))
* expandvars for special profile keys
([#3597](#3597))
([4020188](4020188))
* fix bug causing --precommand to not being executed before each remote
job ([#3625](#3625))
([e59d125](e59d125))
* improved toggle switch behavior in reports
([#3623](#3623))
([0c4bd23](0c4bd23))
* pass envvars defined via the envvars directive to remote jobs
([#3626](#3626))
([d4890b4](d4890b4))
* remove wms arg, update logging cli docs
([#3622](#3622))
([3a9a5ac](3a9a5ac))
* typo in CondaEnvDirSpec.__eq__ (issue
[#3192](#3192))
([#3613](#3613))
([f4c107f](f4c107f))
* Unclear handling of params overriding with inheritance
([#3624](#3624))
([077ac4a](077ac4a))


### Documentation

* Added snakemake command to execute the rule plot_with_python
([#3608](#3608))
([bd99c11](bd99c11))
* Updated Reporting Section of The Tutorial(Interaction, Visualization,
and Reporting with Snakemake)
([#3606](#3606))
([91e90ba](91e90ba))
* Updated Requirement Section of The Tutorial With Warning of Not
Installing The Tools Manually
([#3607](#3607))
([3bd114b](3bd114b))
* Updated Wrapper Version in Tutorial and Used Simple Rule For
Consistency & Ease
([#3605](#3605))
([b3bcc21](b3bcc21))

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

<!--Add a description of your PR here-->
Envvars on resources (e.g. `tmpdir`) are not expanded correctly (e.g.
runtime). This PR fixes that, as well as expansion of envvars on
profiles. For that reason, changes from PR #3597 were reverted.

Tests were also added for both cases.

### 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

* **New Features**
* Configuration values and resource expressions now expand environment
variables (e.g., $VAR) and user home (~), allowing dynamic paths and
settings.
* **Tests**
* Test workflows updated to validate environment-variable and
home-directory expansion in configs and resource handling.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

Fixes snakemake#3592 




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

* [ ] The PR contains a test case for the changes or the changes are
already covered by an existing test case.
* [ ] 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

- **Bug Fixes**
- Environment variables within profile configuration values are now
automatically expanded, ensuring correct values are used in
configurations.

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

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


##
[9.6.0](snakemake/snakemake@v9.5.1...v9.6.0)
(2025-06-16)


### Features

* Prefer papermill to nbconvert
([snakemake#2857](snakemake#2857))
([4263b03](snakemake@4263b03))


### Bug Fixes

* DeprecationWarning when using snakemake.utils.validate
([snakemake#3420](snakemake#3420))
([cf72427](snakemake@cf72427))
* display group jobs on dryrun
([snakemake#3435](snakemake#3435))
([3bebef4](snakemake@3bebef4))
* expandvars for special profile keys
([snakemake#3597](snakemake#3597))
([4020188](snakemake@4020188))
* fix bug causing --precommand to not being executed before each remote
job ([snakemake#3625](snakemake#3625))
([e59d125](snakemake@e59d125))
* improved toggle switch behavior in reports
([snakemake#3623](snakemake#3623))
([0c4bd23](snakemake@0c4bd23))
* pass envvars defined via the envvars directive to remote jobs
([snakemake#3626](snakemake#3626))
([d4890b4](snakemake@d4890b4))
* remove wms arg, update logging cli docs
([snakemake#3622](snakemake#3622))
([3a9a5ac](snakemake@3a9a5ac))
* typo in CondaEnvDirSpec.__eq__ (issue
[snakemake#3192](snakemake#3192))
([snakemake#3613](snakemake#3613))
([f4c107f](snakemake@f4c107f))
* Unclear handling of params overriding with inheritance
([snakemake#3624](snakemake#3624))
([077ac4a](snakemake@077ac4a))


### Documentation

* Added snakemake command to execute the rule plot_with_python
([snakemake#3608](snakemake#3608))
([bd99c11](snakemake@bd99c11))
* Updated Reporting Section of The Tutorial(Interaction, Visualization,
and Reporting with Snakemake)
([snakemake#3606](snakemake#3606))
([91e90ba](snakemake@91e90ba))
* Updated Requirement Section of The Tutorial With Warning of Not
Installing The Tools Manually
([snakemake#3607](snakemake#3607))
([3bd114b](snakemake@3bd114b))
* Updated Wrapper Version in Tutorial and Used Simple Rule For
Consistency & Ease
([snakemake#3605](snakemake#3605))
([b3bcc21](snakemake@b3bcc21))

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

<!--Add a description of your PR here-->
Envvars on resources (e.g. `tmpdir`) are not expanded correctly (e.g.
runtime). This PR fixes that, as well as expansion of envvars on
profiles. For that reason, changes from PR snakemake#3597 were reverted.

Tests were also added for both cases.

### 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

* **New Features**
* Configuration values and resource expressions now expand environment
variables (e.g., $VAR) and user home (~), allowing dynamic paths and
settings.
* **Tests**
* Test workflows updated to validate environment-variable and
home-directory expansion in configs and resource handling.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->