Improve plotting code - robustness, unification, remove code repetition#574

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keiran-rowell-unsw wants to merge 43 commits intonf-core:devfrom

Australian-Structural-Biology-Computing:improve_plotting

Commits on Mar 31, 2026

common plotting util that reports can leverage
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A common generate_report that leverages plot_utils
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remove bs4 since HTML replace is so simple now
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separate MSA and PAE DUMMY files to avoid clashes and check generically
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remove matcher because sort_structures_by_rank() in plot_utils.py handles this more robusts on a per-program basis, can be source of truth
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remove hard to read inconsistent whitespace in channel construction
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remove blank divs in the report is the metrics aren't there
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simplify post_processing by not having a seq_coverage.png
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remove write_html since I don't think the intermediates have advantage of plotly saving from the actual report
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remove unused multiqc channel which used to just plot plddt, and blocks the way for PR #450
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Use modeChannel() everywhere to stop exploding verbosity just to map meta.mode to each output
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radically reduce post_processing put channels by just accessing params directly
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Use modeChannel to create list even for single files, god I love modeChannel to simpligy everything
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newline replacement might be causing mis-rendered PDB structure
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trailing whitespace.......
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make boltz follow non _raw .tsv naming convention and use _npz for unprocessed files #487
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emit ordering conistency
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update snapshots; fix Boltz plddt stub naming exception
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prettify seq coverage plot and drop uneeded y-axis 2
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lock seq cov axes
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remove odd nxf-tmp file
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Set max PAE, plots autosize to div
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Chain, residue, atom, only heavy-atoms. Reverting to v2.0 main as comment by tlitfin on draft PR #574
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stub no longer calls obselete generate_comparison_report.py
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Commits on Apr 2, 2026