fix: remove wms arg, update logging cli docs#3622
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📝 Walkthrough""" WalkthroughReferences to the deprecated Panoptes monitoring system and related command-line options ( Changes
Sequence Diagram(s)sequenceDiagram
participant User
participant Snakemake CLI
participant Logger Plugin
User->>Snakemake CLI: snakemake --logger <plugin>
Snakemake CLI->>Logger Plugin: Initialize and configure
Snakemake CLI->>Logger Plugin: Send job execution events (timings, errors, resources)
Logger Plugin-->>Snakemake CLI: Log data to monitoring system(s)
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docs/executing/monitoring.rst (2)
7-15: Consider adding a short note on plugin installationReaders new to logger plugins may not realise they have to install the plugin package (e.g.
pip install snakemake-logger-<name>) before the--loggerflag works. A one-sentence hint here would avoid confusion.
24-27: Provide concrete example for enabling multiple loggersThe text says the option can be repeated, but an explicit example improves clarity. Suggested diff:
-Multiple logger plugins can be used simultaneously by specifying the ``--logger`` option multiple times. +Multiple logger plugins can be enabled simultaneously by repeating the ``--logger`` option: + +.. code-block:: console + + $ snakemake --logger plugin1 --logger plugin2 --cores 4 + +Ensure the desired plugins are installed first, e.g.: + +.. code-block:: console + + $ pip install snakemake-logger-plugin1 snakemake-logger-plugin2
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src/snakemake/cli.py
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src/snakemake/cli.py (1)
886-886: Nothing to review – only a blank line addedThe sole change in this file is an added blank line, so there is no functional impact.
m-jahn
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m-jahn
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🤖 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).
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Removed wms monitor arg and updated monitoring docs. closes snakemake#3620 snakemake#3619 ### 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 ## Summary by CodeRabbit - **Documentation** - Updated monitoring documentation to introduce logger plugins as the new monitoring mechanism, replacing previous references to Panoptes and the `--wms-monitor` flag. Added instructions for using logger plugins and linked to the plugin catalog. - **Bug Fixes** - Removed obsolete `--wms-monitor` and `--wms-monitor-arg` command-line options and related configuration support. <!-- end of auto-generated comment: release notes by coderabbit.ai -->
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🤖 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).
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Removed wms monitor arg and updated monitoring docs.
closes #3620 #3619
QC
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).Summary by CodeRabbit
Summary by CodeRabbit
Documentation
--wms-monitorflag. Added instructions for using logger plugins and linked to the plugin catalog.Bug Fixes
--wms-monitorand--wms-monitor-argcommand-line options and related configuration support.