update to main so passes test#69
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- Add parse_pdb_coords() to extract atom positions from PDB - Add charge_to_rdbu_hex() to map charges to RdBu diverging colormap - Generate 2D SVG structure with atoms colored by CHELPG charges - Blue for negative charges, red for positive, white for neutral - Atom size scales with charge magnitude - Includes colorbar legend matching bar chart colors - Redesign HTML layout: 3D viewer + 2D colored structure + bar chart - Smart text contrast for readability (white on dark, dark on light) - Color scheme matches bar chart for visual consistency
- Remove inversion (1-) from bar chart RdBu colormap - Remove inversion (1-) from 3D structure RdBu colormap - All three visualizations now consistent: red = negative charges, blue = positive - Improves visual clarity and consistency across all charge representations
Also, run ruff format on src dir.
Introduce helpers to significantly clean up from_json behavior. Notably, we provide full type checking for all input-output combinations. We also always return a list now in the case of a single path input, which is more consistent especially given the typing challenges with determining single-vs-many output types for file inputs. Also, update tests for the above and for latest upstream Rush.
fix: correct typing, addressing feedback, and smashing bugs
merging main changes to see if fixes tests
…snippets docs: add inline comments about STO-3G basis set limitations in code …
feat: script to run all examples for easier testing
feat: add charge-colored 2D aspirin structure to CHELPG output
Auto-attach metadata tags to every run submission for DAU/WAU/MAU tracking: - source=rushpy (always) - sdk_version (from pkg_version) - sdk_session_id (unique per process) - sdk_python (Python version) - sdk_platform (OS/arch) - sdk_function (inferred from call stack) Tags are merged with any user-provided tags (user tags take priority). Implementation at _submit_rex() with zero changes to module code.
feat: add changelog CI check and walk-up .env discovery
chore: bump version to 6.7.0 and update changelog
fix: try another method for docs pushing
feat: add manual trigger for docs deploy
feat: change where docs deploy
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Fix/docs chelpg html
feat: update docs style to match website and give more info on limita…
Add Auto3DResult/Auto3DStats dataclasses and save_outputs() for downloading and packaging multiple conformers per input. Bump auto3d_rex module revision and version to 6.8.0. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Generator requires 3 type args in 3.12; Iterator[T] is correct here since save_outputs only yields values. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
feat: auto3d multiple conformers with structured output
fix: project name
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