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Use diff reg plots - #94

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enryH wants to merge 4 commits into
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use_diff_reg_plots
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enryH wants to merge 4 commits into
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use_diff_reg_plots

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@enryH

@enryH enryH commented Oct 9, 2026 •

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Summary

Use the latest vuecore release 0.3.0 for differential regulation plots.

List of changes proposed in this PR (pull-request)

  • fix doc version of vuecore to 0.3.0
  • switch to vuecore.interactive.get_enrichment_plot in examples instead of basic scatter plot

Checks

In case you add a new module or update one, please check the following tasks:

  • The folder names defines the name of the subpackage (module)
  • Add the user-facing functions to the __init__.py in the new folder, so that
    they are available when the subpackage is imported.
  • Create Pandera schema in a file with subpackage name in the src/acore/types folder.
    Optimal is to have only one output schema of results per subpackage or module.
  • Add a relatively small and public dataset to the data folder, or reuse an existing one for testing
  • Create an api example jupyter notebook in the docs/api_examples_module folder with that data
  • Use jupytext to sync the Jupyter notebook with a Python script
  • Update index.md file in the docs folder with the new example
  • Create test script in the /tests folder with the name of the subpackage or module
    using pytest or unittests to test your new functionality.

@enryH
enryH marked this pull request as ready for review October 12, 2026 08:50
@chatgpt-codex-connector

chatgpt-codex-connector Bot commented Oct 12, 2026 •

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Codex Review Summary

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Review Status Commit Review trigger
📝 Code Review ✅ Completed 2026-10-12T08:52:33.851607Z 7f58f0f Draft marked ready
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💡 Codex Review

Here are some automated review suggestions for this pull request.

Reviewed commit: 7f58f0f31f

ℹ️ About Codex in GitHub

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Comment thread pyproject.toml Outdated
"sphinx-llms-txt",
# Multi-Omics-Analysis group package for visualisation of results in the documentation
"vuecore",
"vuecore>=0.2.1",

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P1 Badge Require a published VueCore version

The public PyPI release history currently only provides VueCore through 0.2.0, so pip install .[docs] cannot satisfy this new >=0.2.1 constraint. This blocks creation of the documentation environment and Read the Docs/CI builds; publish the intended release first or reference an available version that contains the new plotting API.

Useful? React with 👍 / 👎.

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