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docs: add tutorial references and small syntax fix#3172

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johanneskoester merged 1 commit intomainfrom
docs/tutorials
Oct 28, 2024
Merged

docs: add tutorial references and small syntax fix#3172
johanneskoester merged 1 commit intomainfrom
docs/tutorials

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@johanneskoester johanneskoester commented Oct 28, 2024

QC

  • The PR contains a test case for the changes or the changes are already covered by an existing test case.
  • 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).

Summary by CodeRabbit

  • New Features

    • Enhanced documentation on benchmarking capabilities, modularization, and automatic deployment of software dependencies.
    • Introduced a comprehensive tutorial on interaction, visualization, and reporting with Snakemake, including integration with Jupyter notebooks and Datavzrd.
    • Added new rules for data retrieval and visualization in Snakemake workflows.
  • Documentation

    • Improved clarity and detail in tutorials to facilitate user understanding and workflow integration.

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coderabbitai bot commented Oct 28, 2024

📝 Walkthrough

Walkthrough

The 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

File Path Change Summary
docs/tutorial/additional_features.rst Enhanced documentation on benchmarking, modularization, Conda environments, tool wrappers, and executor plugins.
docs/tutorial/interaction_visualization_reporting/tutorial.rst Added a detailed tutorial on using Snakemake for data analysis workflows with Jupyter, R, Python, and Datavzrd.
docs/tutorial/tutorial.rst Added a recommendation for further learning on generating publication-ready reports and visualizations.

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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"
📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between c98b2e7 and 08f0b29.

📒 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:

  1. Find the exact reference label
  2. Locate files with similar names
  3. 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:

  1. It's a standard practice to start numeric domains at 0 for better visual interpretation
  2. 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)
  3. 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 | uniq

Length 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.rst

Length 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

@johanneskoester johanneskoester merged commit 6bee12a into main Oct 28, 2024
@johanneskoester johanneskoester deleted the docs/tutorials branch October 28, 2024 12:43
johanneskoester pushed a commit that referenced this pull request Oct 29, 2024
🤖 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>
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