fix: surface ChimeraX failures and cap +inf scores before plotting

[St3451]

Two independent plot-script robustness fixes that share the same file area:

1. ChimeraX subprocess failures were silent. subprocess.run(...) had no check and no capture_output. When ChimeraX errored out (e.g., the $HOME read-only issue), the script logged "Generating 3D images..", moved on, and produced no PNG with no warning. Replaced with a _run_chimerax() helper that captures stderr and logs a WARNING on non-zero return, matching the existing pattern in pdb_tool.py.

2. +inf in Score_obs_sim broke downstream plots. Extreme hotspots (e.g., NOTCH1 in some cohorts) make the observed anomaly score saturate to +inf even after the high-precision Decimal fallback. That +inf then leaked into the gene plot (normalization via sum=inf zeroed the track), summary plot (wild y-axis), and chimerax-plot (np.log(+inf)). Added cap_inf_scores() in scripts/plotting/utils.py and call it right after loading pos_result in both plot entry points. +inf is replaced with 1.5 * max(finite) with a WARNING log.

[Copilot]

Pull request overview

Improves robustness of plotting scripts by (1) preventing +inf score values from breaking downstream plots and (2) surfacing ChimeraX subprocess failures instead of failing silently.

Changes:

• Add cap_inf_scores() utility to replace +inf score values with a finite capped value for plotting.
• Apply cap_inf_scores() immediately after loading position-level results in both plot.py and chimerax_plot.py.
• Introduce _run_chimerax() to capture ChimeraX stderr and log warnings on non-zero exit codes.

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 4 comments.

File	Description
scripts/plotting/utils.py	Adds cap_inf_scores() to cap inf scores prior to plotting.
scripts/plotting/plot.py	Calls cap_inf_scores() after loading pos_result.
scripts/plotting/chimerax_plot.py	Calls cap_inf_scores(), and replaces silent ChimeraX calls with _run_chimerax() warnings.

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[Copilot]

Pull request overview

Copilot reviewed 3 out of 3 changed files in this pull request and generated 1 comment.

Comments suppressed due to low confidence (1)

scripts/plotting/chimerax_plot.py:134

• The ChimeraX --cmd script embeds file paths unquoted (e.g., open {pdb_path} / open {attr_file_path} / save {output_path}). If any of these paths contain spaces, ChimeraX will likely split them into multiple tokens and fail to open/save. Consider quoting/escaping these paths inside the ChimeraX script (and update the comment about “paths with spaces” accordingly).

    chimerax_script = (
        f"open {pdb_path}; "
        "set bgColor white; "
        "color lightgray; "
        f"open {attr_file_path}; "
        f"color byattribute {attribute} palette {palette}; "

[Copilot]

Pull request overview

Copilot reviewed 3 out of 3 changed files in this pull request and generated 1 comment.