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alternatively we could use a meaningful default
… style of .py files)
- leave out most multiline string for now (which need dedenting) - one whitespace update in tests
- sometime indent and dedent has to be used - one typo (altair plot, not plotly plot corrected) - new line before python code block in qmd files
- maybe 'Verschlimmbessern': footer can be hard to read (pdf)
- needed to use escaping of {} using unicode:
\u007b is { and \u007d is }
- 🐛 jupyter used relative import -> changed to URL link of LOGO
- unify MONA mentioning (pdf)
lazy logging is recommended (only a warning): https://pylint.readthedocs.io/en/latest/user_guide/messages/warning/logging-fstring-interpolation.html
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Pull Request Overview
This pull request makes widespread style and formatting improvements across the codebase, including updates to logging message formatting (switching from f‐strings to % formatting), use of textwrap for dedenting multiline strings, and minor refactorings to exception handling.
- Updated log messages for consistency and better readability
- Reformatted multiline strings using textwrap.dedent and adjusted error chaining
- Minor adjustments in variable naming and documentation for clarity
Reviewed Changes
Copilot reviewed 32 out of 32 changed files in this pull request and generated 1 comment.
Show a summary per file
| File | Description |
|---|---|
| tests/report_examples/…/quarto_report/*.qmd | Formatting improvements in Quarto report files with dedented multiline strings and updated iframe HTML markup. |
| tests/report_examples/…/streamlit_report/sections/*.py | Consistent reformatting of Streamlit sections using multiline dedent and updated logging message style. |
| src/vuegen/utils/init.py | Updated exception raising and logging; switched to chaining exceptions via “from e”. |
| src/vuegen/constants.py | Added project constants; note the use of curly braces in the GITHUB_ORG_URL_BRACKETS value. |
| Other source files | Similar reformatting and logging message updates across various modules (report_generator, report.py, etc.) for improved maintainability. |
Comments suppressed due to low confidence (1)
src/vuegen/constants.py:5
- Verify that the inclusion of curly braces in GITHUB_ORG_URL_BRACKETS is intentional; if not, update the string to match the expected URL format.
GITHUB_ORG_URL_BRACKETS = "{https://github.com/Multiomics-Analytics-Group}"
sayalaruano
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Jun 30, 2025
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The code looks better with the updates, all seems good, just committed a small fix for loading images from a URL in streamlit reports
…e config update config: - fixed line length to 88 as default - ensure line lenght is checked in tests
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I added the line length configuration to be 88 characters (black's default) and to check bugbear and other things using ruff.
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- dedent should be called only once - each block needs to be on the level of where it is supposed to be used (in the multiline f-string)
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Added updates to streamlit and quarto qmd files which were used for testing. But each commit should show the respective changes going through them: pull/131/commits
exc_info=Truein case an error is loggedfrom einstead of pasting it into a new error, see here