BEEP, BEEP - I am your friendly #Snakemake release announcement bot.

There is a new release of Snakemake. Its version now is 9.14.3!

Give us some time, and you will automatically find it on #Bioconda and #Pypi.

If you want to discuss the release, you will find the maintainer here on Mastodon!
@johanneskoester

If you discover any issues, please report them on https://github.com/snakemake/snakemake/issues.

See https://github.com/snakemake/snakemake/releases/tag/v9.14.3 for details. Here is the header of the changelog:
𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* ensure that queue input jobs wait if the queue is still empty upon job creation: https://github.com/snakemake/snakemake/issues/3866
* fix issues with cyclic dependencies when using the update and before_update flag: https://github.com/snakemake/snakemake/issues/3857

🚀 dirval published on #PyPI!

My first official #Python package 🎉
#dirval can now be installed easily via:

pip install dirval

It is a core library of the #InfinitoNexus ecosystem and is used by backup, validation, and infrastructure tools to reliably detect directory structure changes.

Thanks to #pkgmgr, I can now release and publish packages much faster and more consistently.

Released under the #MIT License.

https://pypi.org/project/dirval/

#opensource #mitlicense #devtools #cli #automation

🚀 dirval published on #PyPI!

My first official #Python package 🎉
#dirval can now be installed easily via:

pip install dirval

It is a core library of the #InfinitoNexus ecosystem and is used by backup, validation, and infrastructure tools to reliably detect directory structure changes.

Thanks to #pkgmgr, I can now release and publish packages much faster and more consistently.

Released under the #MIT License.

https://pypi.org/project/dirval/

#opensource #mitlicense #devtools #cli #automation

Beep, Beep - I am your friendly #Snakemake release announcement bot.

There is a new release of the Snakemake executor for #SLURM on #HPC systems. Its version now is 2.0.2!

Give us some time, and you will automatically find the plugin on #Bioconda and #Pypi.

If you want to discuss the release, you will find the maintainers here on Mastodon!
@rupdecat and @johanneskoester

If you discover any issues, please report them on https://github.com/snakemake/snakemake-executor-plugin-slurm/issues.

See https://github.com/snakemake/snakemake-executor-plugin-slurm/releases/tag/v2.0.2 for details. Here is the header of the changelog:
𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* partition cluster selection: https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/385

Beep, Beep - I am your friendly #Snakemake release announcement bot.

There is a new release of the Snakemake executor for #SLURM on #HPC systems. Its version now is 2.0.2!

Give us some time, and you will automatically find the plugin on #Bioconda and #Pypi.

If you want to discuss the release, you will find the maintainers here on Mastodon!
@rupdecat and @johanneskoester

If you discover any issues, please report them on https://github.com/snakemake/snakemake-executor-plugin-slurm/issues.

See https://github.com/snakemake/snakemake-executor-plugin-slurm/releases/tag/v2.0.2 for details. Here is the header of the changelog:
𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* partition cluster selection: https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/385

BEEP, BEEP - I am your friendly #Snakemake release announcement bot.

There is a new release of Snakemake. Its version now is 9.14.3!

Give us some time, and you will automatically find it on #Bioconda and #Pypi.

If you want to discuss the release, you will find the maintainer here on Mastodon!
@johanneskoester

If you discover any issues, please report them on https://github.com/snakemake/snakemake/issues.

See https://github.com/snakemake/snakemake/releases/tag/v9.14.3 for details. Here is the header of the changelog:
𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* ensure that queue input jobs wait if the queue is still empty upon job creation: https://github.com/snakemake/snakemake/issues/3866
* fix issues with cyclic dependencies when using the update and before_update flag: https://github.com/snakemake/snakemake/issues/3857

Beep, Beep - I am your friendly #Snakemake release announcement bot.

There is a new release of the Snakemake executor for #SLURM on #HPC systems. Its version now is 2.0.1!

Give us some time, and you will automatically find the plugin on #Bioconda and #Pypi.

If you want to discuss the release, you will find the maintainers here on Mastodon!
@rupdecat and @johanneskoester

If you discover any issues, please report them on https://github.com/snakemake/snakemake-executor-plugin-slurm/issues.

See https://github.com/snakemake/snakemake-executor-plugin-slurm/releases/tag/v2.0.1 for details. Here is the header of the changelog:
𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* validator check for integers was broken.: https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/381

BEEP, BEEP - I am your friendly #Snakemake release announcement bot.

There is a new release of Snakemake. Its version now is 9.14.0!

Give us some time, and you will automatically find it on #Bioconda and #Pypi.

If you want to discuss the release, you will find the maintainer here on Mastodon!
@johanneskoester

If you discover any issues, please report them on https://github.com/snakemake/snakemake/issues.

See https://github.com/snakemake/snakemake/releases/tag/v9.14.0 for details. Here is the header of the changelog:
𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐅𝐞𝐚𝐭𝐮𝐫𝐞𝐬

* Support Hy in script directive: https://github.com/snakemake/snakemake/issues/3824

𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* Add support for pathlib in `notebook` field: https://github.com/snakemake/snakemake/issues/3811
* Addressed race condition in workdir_handler.py: https://github.com/snakemake/snakemake/issues/3844
* cleanup update-marked output files of failed jobs if there was no backup to restore them: https://github.com/snakemake/snakemake/issues/3843
* correct Windows callable path handling: https://github.com/snakemake/snakemake/issues/3832
* expand env vars on resources: https://github.com/snakemake/snakemake/issues/3823
* fix backup for output marked by `update`: https://github.com/snakemake/snakemake/issues/3839
* Minor fixes/additions to logging module.: https://github.com/snakemake/snakemake/issues/3802
* mount local storage prefix into containers: https://github.com/snakemake/snakemake/issues/3840
* proper...

Legacy Python Bootstrap Scripts Create Domain-Takeover Risk in Multiple PyPI Packages

Cybersecurity researchers have discovered vulnerable code in legacy Python packages that could potentially pave the way for a supply chain compromise on the Python Package Index (PyPI) via a domain takeover attack.

https://thehackernews.com/2025/11/legacy-python-bootstrap-scripts-create.html

#python #bootstrap #pypi #itsecurity #py #domaintakeover #domain #takeover #coding #cybersecurity #supplychain #attack #packaging #itsec #infosec

RE: https://hachyderm.io/@miketheman/115618016841703831

Use Trusted Publishing instead of long-lived PyPI tokens. For other things, here's how to use 1Password with direnv to set secrets in env vars.
https://hugovk.dev/blog/2025/secrets-in-env-vars/
#security #1Password #direnv #cli #PyPI

Beep, Beep - I am your friendly #Snakemake release announcement bot.

There is a new release of the Snakemake executor for #SLURM on #HPC systems. Its version now is 2.0.1!

Give us some time, and you will automatically find the plugin on #Bioconda and #Pypi.

If you want to discuss the release, you will find the maintainers here on Mastodon!
@rupdecat and @johanneskoester

If you discover any issues, please report them on https://github.com/snakemake/snakemake-executor-plugin-slurm/issues.

See https://github.com/snakemake/snakemake-executor-plugin-slurm/releases/tag/v2.0.1 for details. Here is the header of the changelog:
𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* validator check for integers was broken.: https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/381

BEEP, BEEP - I am your friendly #Snakemake release announcement bot.

There is a new release of Snakemake. Its version now is 9.14.0!

Give us some time, and you will automatically find it on #Bioconda and #Pypi.

If you want to discuss the release, you will find the maintainer here on Mastodon!
@johanneskoester

If you discover any issues, please report them on https://github.com/snakemake/snakemake/issues.

See https://github.com/snakemake/snakemake/releases/tag/v9.14.0 for details. Here is the header of the changelog:
𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐅𝐞𝐚𝐭𝐮𝐫𝐞𝐬

* Support Hy in script directive: https://github.com/snakemake/snakemake/issues/3824

𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* Add support for pathlib in `notebook` field: https://github.com/snakemake/snakemake/issues/3811
* Addressed race condition in workdir_handler.py: https://github.com/snakemake/snakemake/issues/3844
* cleanup update-marked output files of failed jobs if there was no backup to restore them: https://github.com/snakemake/snakemake/issues/3843
* correct Windows callable path handling: https://github.com/snakemake/snakemake/issues/3832
* expand env vars on resources: https://github.com/snakemake/snakemake/issues/3823
* fix backup for output marked by `update`: https://github.com/snakemake/snakemake/issues/3839
* Minor fixes/additions to logging module.: https://github.com/snakemake/snakemake/issues/3802
* mount local storage prefix into containers: https://github.com/snakemake/snakemake/issues/3840
* proper...

Legacy Python Bootstrap Scripts Create Domain-Takeover Risk in Multiple PyPI Packages

Cybersecurity researchers have discovered vulnerable code in legacy Python packages that could potentially pave the way for a supply chain compromise on the Python Package Index (PyPI) via a domain takeover attack.

https://thehackernews.com/2025/11/legacy-python-bootstrap-scripts-create.html

#python #bootstrap #pypi #itsecurity #py #domaintakeover #domain #takeover #coding #cybersecurity #supplychain #attack #packaging #itsec #infosec

RE: https://hachyderm.io/@miketheman/115618016841703831

Use Trusted Publishing instead of long-lived PyPI tokens. For other things, here's how to use 1Password with direnv to set secrets in env vars.
https://hugovk.dev/blog/2025/secrets-in-env-vars/
#security #1Password #direnv #cli #PyPI

Beep, Beep - I am your friendly #Snakemake release announcement bot.

There is a new release of the Snakemake executor for #SLURM on #HPC systems. Its version now is 2.0.0!

Give us some time, and you will automatically find the plugin on #Bioconda and #Pypi.

If you want to discuss the release, you will find the maintainers here on Mastodon!
@rupdecat and @johanneskoester

If you discover any issues, please report them on https://github.com/snakemake/snakemake-executor-plugin-slurm/issues.

See https://github.com/snakemake/snakemake-executor-plugin-slurm/releases/tag/v2.0.0 for details. Here is the header of the changelog:

𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
⚠ 𝐁𝐑𝐄𝐀𝐊𝐈𝐍𝐆 𝐂𝐇𝐀𝐍𝐆𝐄𝐒

* proposal for dynamic partition selection: https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/321

𝐅𝐞𝐚𝐭𝐮𝐫𝐞𝐬

* partition time handling: https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/378
* proposal for dynamic partition selection: https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/321

𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* naming SLURM logs, SLURM logs not just "log files": https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/372

𝐃𝐨𝐜𝐮𝐦𝐞𝐧𝐭𝐚𝐭𝐢𝐨𝐧

* Replace incorrect Markdown with a blockquote: https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/377

BEEP, BEEP - I am your friendly #Snakemake release announcement bot.

There is a new release of Snakemake. Its version now is 9.13.6!

Give us some time, and you will automatically find it on #Bioconda and #Pypi.

If you want to discuss the release, you will find the maintainer here on Mastodon!
@johanneskoester

If you discover any issues, please report them on https://github.com/snakemake/snakemake/issues.

See https://github.com/snakemake/snakemake/releases/tag/v9.13.6 for details. Here is the header of the changelog:

𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* only complain about mixed rules and functions for workflows that are not in a single snakefile; improve internal pathvar error handling: https://github.com/snakemake/snakemake/issues/3829

Even still, we’re raising the flag early: the PSF has only ~6 months of runway and needs your support to sustain essential #Python & #PyPI infrastructure, #PyConUS, and, hopefully, to reopen our Grants Program.

BEEP, BEEP - I am your friendly #Snakemake release announcement bot.

There is a new release of Snakemake. Its version now is 9.13.5!

Give us some time, and you will automatically find it on #Bioconda and #Pypi.

If you want to discuss the release, you will find the maintainer here on Mastodon!
@johanneskoester

If you discover any issues, please report them on https://github.com/snakemake/snakemake/issues.

See https://github.com/snakemake/snakemake/releases/tag/v9.13.5 for details. Here is the header of the changelog:

𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* cache wrapper files and wait for them in case of shared filesystem for sources: https://github.com/snakemake/snakemake/issues/3809
* correctly handle meta-wrapper tag replacement depending on the used snakemake-wrapper release: https://github.com/snakemake/snakemake/issues/3826
* ensure that flags are properly considered for input files before applying path modifiers: https://github.com/snakemake/snakemake/issues/3813
* ensure that tokens are not leaked when paths or uris of source files are logged: https://github.com/snakemake/snakemake/issues/3821
* print secs as numeric in jsonl benchmark format: https://github.com/snakemake/snakemake/issues/3814
* revert breaking change in 9.11.9 disallowing empty input files even when unused: https://github.com/snakemake/snakemake/issues/3810
* shorten report ids: https://github.com/snakemake/snakemake/issues/3822

BEEP, BEEP - I am your friendly #Snakemake release announcement bot.

There is a new release of Snakemake. Its version now is 9.13.5!

Give us some time, and you will automatically find it on #Bioconda and #Pypi.

If you want to discuss the release, you will find the maintainer here on Mastodon!
@johanneskoester

If you discover any issues, please report them on https://github.com/snakemake/snakemake/issues.

See https://github.com/snakemake/snakemake/releases/tag/v9.13.5 for details. Here is the header of the changelog:

𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* cache wrapper files and wait for them in case of shared filesystem for sources: https://github.com/snakemake/snakemake/issues/3809
* correctly handle meta-wrapper tag replacement depending on the used snakemake-wrapper release: https://github.com/snakemake/snakemake/issues/3826
* ensure that flags are properly considered for input files before applying path modifiers: https://github.com/snakemake/snakemake/issues/3813
* ensure that tokens are not leaked when paths or uris of source files are logged: https://github.com/snakemake/snakemake/issues/3821
* print secs as numeric in jsonl benchmark format: https://github.com/snakemake/snakemake/issues/3814
* revert breaking change in 9.11.9 disallowing empty input files even when unused: https://github.com/snakemake/snakemake/issues/3810
* shorten report ids: https://github.com/snakemake/snakemake/issues/3822