docs: Updated Requirement Section of The Tutorial With Warning of Not Installing The Tools Manually#3607
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johanneskoester merged 1 commit intoJun 12, 2025
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…ait for installation of required tools. Fixes snakemake#3582
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📝 WalkthroughWalkthroughThe tutorial setup documentation was revised to clarify that users should not install prerequisite software immediately. The instructions now prominently advise readers to wait for the tutorial's installation guidance, while maintaining the list of required tools and removing redundant warnings. Changes
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docs/tutorial/setup.rst (1)
41-42: Consider using a Sphinx warning admonition for clarity
The inline bold callout works, but switching to a.. warning::block will be more consistent with the rest of the tutorial and better highlight the “wait to install” instruction. You can also streamline the wording slightly:-**Please wait to install the tools listed below, as this tutorial will guide you through better and more reliable setup processes in the next sections.** +.. warning:: + Please wait to install the required tools listed below. This tutorial will guide you through more reliable setup methods in the next sections. -For your reference, the following tools will be used: +For your reference, the following tools will be used:
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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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… Installing The Tools Manually (snakemake#3607) Updated requirement section docs in the tutorial, to guide the user to wait for preferred ways of installation of required tools to appear in the following sections and not to install the tools one by one by yourself through the terminal manually etc. This was important as some users could do that as the warning may be hidden as in the original version of docs and secondly had grammatical mistake. Fixes snakemake#3582 <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **Documentation** - Improved setup instructions in the tutorial to more clearly advise users to wait for guided installation steps, enhancing clarity and reducing confusion. <!-- end of auto-generated comment: release notes by coderabbit.ai --> Co-authored-by: rohan-ibn-tariq <your-username@users.noreply.github.com>
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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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Updated requirement section docs in the tutorial, to guide the user to wait for preferred ways of installation of required tools to appear in the following sections and not to install the tools one by one by yourself through the terminal manually etc.
This was important as some users could do that as the warning may be hidden as in the original version of docs and secondly had grammatical mistake.
Fixes #3582
Summary by CodeRabbit