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

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.

PyPI serves billions of requests daily- but sustaining it isn’t free. The PSF joined the OpenSSF & others in calling for organizations to invest in sustainable open infrastructure. Learn what this means for #PyPI, the PSF, & how our community can pitch in:
https://pyfound.blogspot.com/2025/10/open-infrastructure-is-not-free-pypi.html

PyPI serves billions of requests daily- but sustaining it isn’t free. The PSF joined the OpenSSF & others in calling for organizations to invest in sustainable open infrastructure. Learn what this means for #PyPI, the PSF, & how our community can pitch in:
https://pyfound.blogspot.com/2025/10/open-infrastructure-is-not-free-pypi.html

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 1.9.2!

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/v1.9.2 for details. Here is the header of the changelog:

𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* logo: https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/367

And why is this called `hermetic-seal?` ? Well after searching for a perfect name I picked `hermetic`, which is 404 on pypi, free to take? Nope, if you register trusted publisher for that name #pypi says it is **taken**!

PyPI now checks for expired domains to prevent domain resurrection attacks, a type of supply-chain attack where someone buys an expired domain and uses it to take over #PyPI accounts through password resets. #Python#OpenSource#SupplyChain#Security
https://blog.pypi.org/posts/2025-08-18-preventing-domain-resurrections/

PyPI now checks for expired domains to prevent domain resurrection attacks, a type of supply-chain attack where someone buys an expired domain and uses it to take over #PyPI accounts through password resets. #Python#OpenSource#SupplyChain#Security
https://blog.pypi.org/posts/2025-08-18-preventing-domain-resurrections/

🚨 Be aware there's a potential phishing campaign likely targeting #PyPI / #Python package maintainers:

https://discuss.python.org/t/phishing-attack/100267

🚨 Be aware there's a potential phishing campaign likely targeting #PyPI / #Python package maintainers:

https://discuss.python.org/t/phishing-attack/100267