docs: various documentation fixes#3052
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johanneskoester merged 8 commits intosnakemake:mainfrom Aug 28, 2024
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Fixed links, text references and download links. Download links required "Miniforge3" instead of "Miniforge".
Now included in sphinxawesome-theme by default - Changelog entry: https://sphinxawesome.xyz/changelog/#version-5-2 - Docs: https://sphinxawesome.xyz/how-to/configure/#syntax-highlighting
This commit contains only fixes to obvious internal links. Links I was not sure about or where text needed to be reworded are in a separate commits. API links also in a separate commit.
I assumed the intended link destination was the tutorial section about cluster or cloud execution in additional_features.rst.
…of `_` Adding a second underscore makes the links anonymous and silence warnings. Not critical, but adds a lot of noise when checking documentation issues. Ref: sphinx-doc/sphinx#3921
Wrong level for bash headings in `rules.rst` and not enough characters in `additional_features`
…rial I wanted to fix the broken link and realized the sub-workflow docs were gone.
Contributor
WalkthroughThe changes encompass updates to the Snakemake documentation, including modifications to hyperlink formatting, reference updates, and terminology clarifications. Notably, there is a removal of an extension from the Sphinx configuration, updates to the command line interface, and adjustments to references for improved clarity. These alterations collectively enhance the documentation's accuracy and consistency without impacting the underlying functionality. Changes
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Files selected for processing (16)
- docs/conf.py (1 hunks)
- docs/executing/caching.rst (1 hunks)
- docs/executing/cli.rst (1 hunks)
- docs/getting_started/migration.rst (3 hunks)
- docs/project_info/contributing.rst (1 hunks)
- docs/project_info/faq.rst (6 hunks)
- docs/snakefiles/best_practices.rst (1 hunks)
- docs/snakefiles/configuration.rst (2 hunks)
- docs/snakefiles/foreign_wms.rst (1 hunks)
- docs/snakefiles/modularization.rst (2 hunks)
- docs/snakefiles/reporting.rst (3 hunks)
- docs/snakefiles/rules.rst (6 hunks)
- docs/snakefiles/utils.rst (1 hunks)
- docs/tutorial/additional_features.rst (2 hunks)
- docs/tutorial/basics.rst (2 hunks)
- docs/tutorial/setup.rst (5 hunks)
Files skipped from review due to trivial changes (15)
- docs/conf.py
- docs/executing/caching.rst
- docs/executing/cli.rst
- docs/project_info/contributing.rst
- docs/project_info/faq.rst
- docs/snakefiles/best_practices.rst
- docs/snakefiles/configuration.rst
- docs/snakefiles/foreign_wms.rst
- docs/snakefiles/modularization.rst
- docs/snakefiles/reporting.rst
- docs/snakefiles/rules.rst
- docs/snakefiles/utils.rst
- docs/tutorial/additional_features.rst
- docs/tutorial/basics.rst
- docs/tutorial/setup.rst
Additional comments not posted (3)
docs/getting_started/migration.rst (3)
28-33: LGTM!The documentation updates are clear and provide useful information about the migration of remote providers to storage plugins.
The code changes are approved.
45-52: LGTM!The documentation updates are clear and provide useful information about the renaming of execution backends and the deprecation of certain command flags.
The code changes are approved.
581-581: LGTM!The documentation updates are clear and provide useful information about the complete rewrite of the Snakemake API using a modern dataclass approach.
The code changes are approved.
johanneskoester
approved these changes
Aug 28, 2024
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Thank you so much! |
Contributor
|
This is highly appreciated! |
johanneskoester
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Aug 29, 2024
🤖 I have created a release *beep* *boop* --- ## [8.19.0](v8.18.2...v8.19.0) (2024-08-29) ### Features * check consistency of output file mtimes (must be newer than input files) ([#3050](#3050)) ([666cf62](666cf62)) * print host name when executing workflow ([#3048](#3048)) ([b0ff787](b0ff787)) ### Bug Fixes * `mem` and `disk` inference fixes ([#3040](#3040)) ([7530794](7530794)) * avoid error accessing superclass in ioutils ([#3056](#3056)) ([a66a5f5](a66a5f5)) * disable execute after print compilation ([#3041](#3041)) ([86ed3cd](86ed3cd)) * download report assets upon package build such that reports become possible offline (cont. of [#2904](#2904)) ([#3026](#3026)) ([e8dad4b](e8dad4b)) ### Documentation * Add 'Editor integrations' section to Installation page ([#3045](#3045)) ([9a4006d](9a4006d)) * Fix typo (seesee to see) ([#3037](#3037)) ([de201fb](de201fb)) * various documentation fixes ([#3052](#3052)) ([b11460c](b11460c)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
vandalt
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🤖 I have created a release *beep* *boop* --- ## [8.19.0](snakemake/snakemake@v8.18.2...v8.19.0) (2024-08-29) ### Features * check consistency of output file mtimes (must be newer than input files) ([snakemake#3050](snakemake#3050)) ([666cf62](snakemake@666cf62)) * print host name when executing workflow ([snakemake#3048](snakemake#3048)) ([b0ff787](snakemake@b0ff787)) ### Bug Fixes * `mem` and `disk` inference fixes ([snakemake#3040](snakemake#3040)) ([7530794](snakemake@7530794)) * avoid error accessing superclass in ioutils ([snakemake#3056](snakemake#3056)) ([a66a5f5](snakemake@a66a5f5)) * disable execute after print compilation ([snakemake#3041](snakemake#3041)) ([86ed3cd](snakemake@86ed3cd)) * download report assets upon package build such that reports become possible offline (cont. of [snakemake#2904](snakemake#2904)) ([snakemake#3026](snakemake#3026)) ([e8dad4b](snakemake@e8dad4b)) ### Documentation * Add 'Editor integrations' section to Installation page ([snakemake#3045](snakemake#3045)) ([9a4006d](snakemake@9a4006d)) * Fix typo (seesee to see) ([snakemake#3037](snakemake#3037)) ([de201fb](snakemake@de201fb)) * various documentation fixes ([snakemake#3052](snakemake#3052)) ([b11460c](snakemake@b11460c)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
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I initially wanted to fix only the Mambaforge mentions in the Setup tutorial, but then noticed several warnings when building the docs so I tried tackling those as well. Here is a list:
sphinxawesome_theme.highlightingextensionLet me know if these are too unrelated for a single PR and you want me to split it.
Thank you!
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