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renumber headers in study notebook 04 - #249
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…d - References - Analysis - Summary pattern of notebooks 01 and 02
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #249 +/- ##
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+ Coverage 73.19% 73.92% +0.72%
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Files 35 36 +1
Lines 2067 2140 +73
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+ Hits 1513 1582 +69
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Sep 1, 2026
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sorry for missing your PR and opening another :)
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@vbrennsteiner @shanibmo which one is more up-to-date? |
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should be this one, I'll transfer the fixes from the other one (typos etc) and merge 👍 |
Follow-up cleanup on the header harmonization, addressing defects found while reconciling this PR with the duplicate #253: - Re-nest "Detailed sanity checks", "CV Analysis" and "Dimensionality Reduction" under "6. Biological validation and quality assessment", which previously had a single orphan subsection. Sections now run 1-9. - Fix the three duplicate "11.3" headers in the TF section (now 8.1-8.8). - Collapse the split "10. Recreating Study Figures:" header, whose title remainder had been stranded as body text. - Normalize subsection numbering to the dotted N.M. form used elsewhere in the notebook and in study 05. - Fix 27 typos, including the seven Copilot flagged on #253. - Set kernel display_name to "alphapept", matching studies 01-03. Markdown and notebook metadata only; no cells were re-executed. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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Purpose of this PR
To harmonize the header and subheader structure across all studies, this PR adjusts them in the 04 scDVP notebook according to notebooks 01 and 02. The goal is to have a (reasonably) uniform structure along the lines of Background - References - Analysis - Summary in all studies.