fix: ChimeraX --cmd quoting breaks rendering#110
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Pull request overview
This PR updates the ChimeraX plotting integration to build --cmd scripts using unquoted paths (to accommodate ChimeraX versions that reject quoted paths in ;-separated --cmd strings) and adds stricter path validation to prevent malformed scripts and command injection.
Changes:
- Switched ChimeraX
open/savecommand generation to interpolate paths unquoted in the--cmdscript. - Expanded path validation to reject additional characters (notably whitespace) that would break ChimeraX tokenization.
- Clarified inline documentation around subprocess execution vs. ChimeraX command parsing.
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PR #106 wrapped paths in double quotes inside the ChimeraX
--cmdscript to handle spaces. On some ChimeraX versions (e.g. 1.6.1) that quoting breaks the parser ("incomplete quoted text"), so every chimerax-plot render fails.Fix: drop the quoting and instead reject paths containing characters that would break or inject into the
;-separated command — space, tab,;,", newline, CR — surfacing a clear error rather than a broken/injected command.Also silences the expected
log(0)RuntimeWarning (zero-score positions) vianp.errstate; no behavioral change.