docs: add tutorial references and small syntax fix#3172
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📝 WalkthroughWalkthroughThe pull request introduces enhancements to the Snakemake documentation across several tutorial files. It elaborates on benchmarking capabilities, modularization of workflows, automatic deployment of software dependencies through Conda, and the use of tool wrappers. Additionally, a new tutorial focuses on interaction, visualization, and reporting, detailing the integration of Snakemake with Jupyter notebooks and data visualization tools. The changes aim to provide users with comprehensive guidance on utilizing Snakemake for data analysis workflows, including the generation of reports and interactive visualizations. Changes
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (1)
docs/tutorial/tutorial.rst (1)
33-34: LGTM with a minor suggestion for clarity.The addition of the follow-up tutorial reference is well-placed and properly formatted. However, consider rephrasing slightly for better clarity:
-As follow-up to this tutorial, we recommend to have a look at the :ref:`interaction, visualization and reporting tutorial <interaction_visualization_reporting_tutorial>`, which focuses on Snakemake's ability to cover the last mile of data analysis, i.e., the generation of publication ready reports and interactive visualizations. +As a follow-up to this tutorial, we recommend looking at the :ref:`interaction, visualization and reporting tutorial <interaction_visualization_reporting_tutorial>`, which focuses on Snakemake's ability to cover the last mile of data analysis: the generation of publication-ready reports and interactive visualizations.The suggested changes:
- Add article "a" before "follow-up"
- Remove "to" after "recommend"
- Replace "i.e.," with a colon for better readability
- Add hyphen in "publication-ready"
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📒 Files selected for processing (3)
- docs/tutorial/additional_features.rst (1 hunks)
- docs/tutorial/interaction_visualization_reporting/tutorial.rst (1 hunks)
- docs/tutorial/tutorial.rst (1 hunks)
🔇 Additional comments (2)
docs/tutorial/additional_features.rst (1)
225-226: LGTM! Well-structured tutorial reference addition.The added reference to the interaction, visualization, and reporting tutorial provides a natural progression for users learning Snakemake's features.
Let's verify that the referenced tutorial exists:
✅ Verification successful
The previous search might have been too specific. Let's try these broader searches to:
- Find the exact reference label
- Locate files with similar names
- Find mentions of this tutorial in table of contents or index files
This will help us verify if the tutorial exists and if the reference is correctly defined.
Reference link is valid and correctly used
The tutorial reference is properly defined and linked:
- The target tutorial exists at
docs/tutorial/interaction_visualization_reporting/tutorial.rst- The reference label
.. _interaction_visualization_reporting_tutorial:is correctly defined in the target file- The tutorial is properly included in the documentation structure via
docs/index.rst🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the existence of the referenced tutorial file # Test: Check if the referenced tutorial file exists fd --type f "interaction_visualization_reporting/tutorial.rst" docs/tutorial/Length of output: 77
Script:
#!/bin/bash # Let's try a broader search for the tutorial reference # First, search for any .rst files containing the reference label rg ".. _interaction_visualization_reporting_tutorial:" docs/ # Also search for files with similar naming patterns fd "interaction.*reporting.*\.rst$" docs/ # Check for any mentions of this tutorial in index or toc files rg "interaction.*visualization.*reporting" docs/ -g "*.rst"Length of output: 1193
docs/tutorial/interaction_visualization_reporting/tutorial.rst (1)
288-292: Consider adjusting the cylinder count domain range.The domain range of 0-16 for cylinder counts seems unnecessarily wide. Most cars typically have between 3-12 cylinders. Consider adjusting the domain to better match the actual data range for more effective visualization.
Let's verify the actual cylinder range in the data:
✅ Verification successful
From the context, I can see that the data comes from the
vega_datasets.data.cars()dataset, which is a well-known standard dataset. The domain range of 0-16 for cylinders is actually reasonable for this visualization because:
- It's a standard practice to start numeric domains at 0 for better visual interpretation
- The upper limit of 16 provides enough headroom for all possible cylinder counts in the dataset (typical cars in this dataset have 4-8 cylinders)
- The linear scale with this domain creates a proper visual representation of the relative differences between cylinder counts
The cylinder count domain range (0-16) is appropriate for this visualization.
The current configuration provides a clean and interpretable visualization where:
- The zero-point anchor helps establish a clear baseline
- The upper limit of 16 ensures no data point will be cut off
- The white-to-blue color scheme provides good contrast for the heatmap
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Check the range of cylinder values in the cars dataset cat resources/data/cars.tsv | awk -F'\t' 'NR>1 {print $3}' | sort -n | uniqLength of output: 133
Script:
#!/bin/bash # Let's first find the actual data file location fd -t f "cars" --full-path # Additionally, let's check the tutorial content to understand the data source rg -A 5 -B 5 "cars.*\.tsv" docs/tutorial/interaction_visualization_reporting/tutorial.rstLength of output: 3291
Script:
#!/bin/bash # Let's check the notebook that generates the data to understand the data source and ranges fd -t f "get_data.py.ipynb" --exec cat {} # Also check the datavzrd config to see if there are any comments about the cylinder range fd -t f "cars.yaml" --exec cat {}Length of output: 2429
🤖 I have created a release *beep* *boop* --- ## [8.25.0](v8.24.1...v8.25.0) (2024-10-29) ### Features * add first 5 rules to group name (used e.g. when naming cluster/cloud jobs or logfiles) ([#3168](#3168)) ([5657122](5657122)) * allow to mark input files of rules as ancient via the API or command line interface (and thereby also via workflow specific profiles). Putting this into a workflow specific profile (or specifying as argument) allows to overrule rerun triggers caused by file modification dates where the user knows better. ([#3171](#3171)) ([6f3aed3](6f3aed3)) ### Bug Fixes * skip storage object when cloning flags for shadowed IO ([#3174](#3174)) ([d733fed](d733fed)) * use permission safe copying when hidden conda files are already present in a workdir. This avoids problems in case multiple people use the same workdir and workflow. ([#3169](#3169)) ([c98b2e7](c98b2e7)) ### Documentation * add tutorial references and small syntax fix ([#3172](#3172)) ([6bee12a](6bee12a)) --- 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>



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
New Features
Documentation