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

There is a new release of Snakemake. Its version now is 9.15.0!

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/v9.15.0 for details. Here is the header of the changelog:
𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐅𝐞𝐚𝐭𝐮𝐫𝐞𝐬

* expose logger plugin handlers via get_log_handlers: https://github.com/snakemake/snakemake/issues/3897

𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* catch OSError raised during benchmarking: https://github.com/snakemake/snakemake/issues/3931
* ensure that fetching of remote git repo updates properly handles commit ids: https://github.com/snakemake/snakemake/issues/3933

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

There is a new release of Snakemake. Its version now is 9.15.0!

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/v9.15.0 for details. Here is the header of the changelog:
𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐅𝐞𝐚𝐭𝐮𝐫𝐞𝐬

* expose logger plugin handlers via get_log_handlers: https://github.com/snakemake/snakemake/issues/3897

𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* catch OSError raised during benchmarking: https://github.com/snakemake/snakemake/issues/3931
* ensure that fetching of remote git repo updates properly handles commit ids: https://github.com/snakemake/snakemake/issues/3933

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

There is a new release of Snakemake. Its version now is 9.14.6!

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/v9.14.6 for details. Here is the header of the changelog:
𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* create local clone of git repos for source files from hosting providers: https://github.com/snakemake/snakemake/issues/3643
* create potentially missing .snakemake folder in case of very long command lines for spawned jobs: https://github.com/snakemake/snakemake/issues/3894
* make ilp solver enumeration lazy: https://github.com/snakemake/snakemake/issues/3900
* Prevent broken report_href links by using deterministic report IDs with fixed prefix length: https://github.com/snakemake/snakemake/issues/3889
* refactor LoggerManager setup and scope: https://github.com/snakemake/snakemake/issues/3851
* yield proper error message in case a local git source file is not retrievable: https://github.com/snakemake/snakemake/issues/3892

𝐃𝐨𝐜𝐮𝐦𝐞𝐧𝐭𝐚𝐭𝐢𝐨𝐧

* explain how to pass nested config via CLI: https://github.com/snakemake/snakemake/issues/3885

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

There is a new release of Snakemake. Its version now is 9.14.6!

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/v9.14.6 for details. Here is the header of the changelog:
𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* create local clone of git repos for source files from hosting providers: https://github.com/snakemake/snakemake/issues/3643
* create potentially missing .snakemake folder in case of very long command lines for spawned jobs: https://github.com/snakemake/snakemake/issues/3894
* make ilp solver enumeration lazy: https://github.com/snakemake/snakemake/issues/3900
* Prevent broken report_href links by using deterministic report IDs with fixed prefix length: https://github.com/snakemake/snakemake/issues/3889
* refactor LoggerManager setup and scope: https://github.com/snakemake/snakemake/issues/3851
* yield proper error message in case a local git source file is not retrievable: https://github.com/snakemake/snakemake/issues/3892

𝐃𝐨𝐜𝐮𝐦𝐞𝐧𝐭𝐚𝐭𝐢𝐨𝐧

* explain how to pass nested config via CLI: https://github.com/snakemake/snakemake/issues/3885

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

The last blog post I wrote was about Life Science Support on HPC clusters. Honestly? It was more of a rant. Not a good blog post.

So, someone suggested I delete it, which I did. It took me a long time to recover. Now, I have re-written this blog post. I think it is better. I weighted every phrase. It still has some rant flavour.

Here it is: https://blogs.fediscience.org/rupture-de-catenaire/2025/12/15/empowering-life-scientists-what-hpc-support-should-look-like/

The upcoming articles will have more of an example character. But I still will not be able to update on a regular basis.

#Bioinformatics #HPC #ReproducibleComputing #Snakemake #Nextflow

@tkuhn perhaps, I should do a few #nanopub onboarding sessions embedded with my planned #Snakemake Hackathon and the Snakemake implementation for nanopubs in a workshop (for which I still need to do some work) next year.

I'm not sure, I followed you with your remark - is this better? https://w3id.org/np/RAADhF-xHWOeATa1pKZelZ2Jwbpjxrxn8Md-yKVRxdHho

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

@Dutch_Reproducibility_Network

In fact, I am a #Snakemake co-maintainer and teacher. I was not aware of WorkflowHub - and that was an omission on my part. We actually support and favour this kind of registration: https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#uploading-workflows-to-workflowhub

In my original post, I also neglected to mention the integration of WorkflowHub with #RO-Crate and in turn, the integration of RO-Crates with nanopubs. I am actively working on a better support for #nanopub and RO-Crates with @fbartusch. The question, how I teach that stands: The #HPC world (at least my bubble) is not really supportive for #ReproducibleComputing . All #OpenScience shenanigans are frowned upon. And PIs in my vicinity are still on this level: https://phdcomics.com/comics/archive.php?comicid=1531 - so, how do we educate the educators?

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...

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...

rOpenSci will be participating in @latinr_conf!

Here is the key data for your participation:

🎙️ Keynotes

- Heather Turner: Lowering Barriers to Contributing to R.

- Stephanie Zimmer: Transforming a team to open-source first.

- TRACE-LAC Team. Lo invisible del código abierto: Lecciones desde el proyecto TRACE-LAC / Epiverso para conectar el desarrollo de software con la salud pública

🎓 Tutorials by rOpenSci members:

📌 ¡Miércoles, Git! Manejo de errores en Git y no morir en el intento — @maelle , @yabellini. Registration: https://www.eventbrite.cl/e/miercoles-git-manejo-de-errores-en-git-y-no-morir-en-el-intento-tickets-1937068908249

📌 Introducción a #Tidymodels — Francisco Cardozo & Edgar Ruiz. Registration: https://www.eventbrite.cl/e/introducion-a-tidymodels-tickets-1962543491413

📌 Automatización de workflows en R y Python con #targets y #Snakemake — Diana García. Registration: https://www.eventbrite.cl/e/automatizacion-de-workflows-en-r-y-python-con-targets-y-snakemake-tickets-1936131664929

📌 ¿Qué historia vas a contar hoy Herramientas para una comunicación eficaz — Alejandra Bellini. Registration: https://www.eventbrite.cl/e/que-historia-vas-a-contar-hoy-herramientas-para-una-comunicacion-eficaz-tickets-1891497192019

📌 Coding with #AI in RStudio — Juan Cruz Rodríguez & @LuisDVerde. Registration: https://www.eventbrite.cl/e/coding-with-ai-in-rstudio-tickets-1962817615325

List with all tutorials here: https://latinr.org/en/

#RStats #RStatsES #openScience #RSE #OpenData #FOSS #DataScience #Analytics

1/2

RE: https://fediscience.org/@snakemake/115611862667755622

Now, this is huge!

Thanks to a contribution from Cade Mirchandani (Santa Cruz, CA), whom I met at this year's #SnakemakeHackathon users can now supply a partition profile. So, instead of wrangling #SLURM partition information into a workflow profile (indicated with --workflow-profile), we can now have a global file to contain this information.

I added a time conversion function, such that the SLURM time format is obeyed, too.

There are several other development needs, before we continue in this direction (e.g. parsing SLURM partition information directly). But a task to be done is summing this up for non-users, e.g. administrators, is due too.

In any case, I think this merits a new major version.

#Snakemake #HPC #ReproducibleComputing

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

rOpenSci will be participating in @latinr_conf!

Here is the key data for your participation:

🎙️ Keynotes

- Heather Turner: Lowering Barriers to Contributing to R.

- Stephanie Zimmer: Transforming a team to open-source first.

- TRACE-LAC Team. Lo invisible del código abierto: Lecciones desde el proyecto TRACE-LAC / Epiverso para conectar el desarrollo de software con la salud pública

🎓 Tutorials by rOpenSci members:

📌 ¡Miércoles, Git! Manejo de errores en Git y no morir en el intento — @maelle , @yabellini. Registration: https://www.eventbrite.cl/e/miercoles-git-manejo-de-errores-en-git-y-no-morir-en-el-intento-tickets-1937068908249

📌 Introducción a #Tidymodels — Francisco Cardozo & Edgar Ruiz. Registration: https://www.eventbrite.cl/e/introducion-a-tidymodels-tickets-1962543491413

📌 Automatización de workflows en R y Python con #targets y #Snakemake — Diana García. Registration: https://www.eventbrite.cl/e/automatizacion-de-workflows-en-r-y-python-con-targets-y-snakemake-tickets-1936131664929

📌 ¿Qué historia vas a contar hoy Herramientas para una comunicación eficaz — Alejandra Bellini. Registration: https://www.eventbrite.cl/e/que-historia-vas-a-contar-hoy-herramientas-para-una-comunicacion-eficaz-tickets-1891497192019

📌 Coding with #AI in RStudio — Juan Cruz Rodríguez & @LuisDVerde. Registration: https://www.eventbrite.cl/e/coding-with-ai-in-rstudio-tickets-1962817615325

List with all tutorials here: https://latinr.org/en/

#RStats #RStatsES #openScience #RSE #OpenData #FOSS #DataScience #Analytics

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