Add expand modifier to pipeline#6
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Core engine: - Thin-instance rendering with ImpostorState GPU buffer management - Command system with full undo/redo (DrawFrame, UpdateFrame, Clear, etc.) - 5 interaction modes: View, Select, Edit, Manipulate, Measure - Modifier pipeline: expression select, color-by-property, hide/delete, transparency, wrap PBC - Smart trajectory playback with FrameDiff (position-only vs full rebuild) - Ribbon rendering for protein secondary structure (PDB HELIX/SHEET) - Bond order display (single/double/triple as parallel cylinders) - Picker system with ID-pass off-screen rendering File format support: - PDB, XYZ, LAMMPS data/dump via @molcrafts/molrs WASM - Export to XYZ Web app (React 19): - Three-panel layout with resizable panels - Analysis tools: RDF, MSD, cluster, topology, scatter plot, histogram - Per-atom labels, data inspector, property coloring - Fence (lasso) selection, expression-based selection VSCode extension: - Custom editor for .pdb/.xyz/.data files - Standalone viewer panel with message-based communication Infrastructure: - Monorepo with npm workspaces (core, page, vsc-ext, python, electron) - CI pipeline: parallel lint/test/build with GitHub Actions - Pre-commit hooks via Python pre-commit framework - Biome for linting and formatting - rstest for testing (287 tests)
Roy-Kid
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master's PR #6 (v0.0.3) is a squash of earlier dev history; dev already contains that content as individual commits plus later features. Using -s ours to retain dev's newer tree while recording master as a parent, making dev fast-forwardable to master.
Roy-Kid
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Phase 1, task #5 of multi-data-source-pipeline spec. Two new public methods on MolvisApp: - `addDataSource(ds)`: appends a DataSourceModifier to the pipeline. TrajectoryDataSource frame counts must match every existing TrajectoryDataSource (throws with concrete numbers otherwise); FrameDataSource is always safe to append (it broadcasts across the system's frame count). When the new DS is the first TrajectoryDataSource, System adopts its trajectory so navigation events keep flowing. applyAutoAttach runs against the DS's frame 0 to install default Draw modifiers (DrawAtom / DrawBond / DrawBox) for new block kinds the source contributes. - `removeDataSource(id)`: cascade-removes via the existing pipeline.removeModifier path, calls dispose() on each removed DS to free WASM resources. Removing a TrajectoryDataSource re-derives System: if another TrajectoryDataSource remains, System adopts it; otherwise System collapses to a single empty frame so navigation state stays consistent. Per the spec's 1a "delete = rebuild" semantics, applyPipeline runs after. Both methods route through applyPipeline at the end so the rendered scene stays in sync. The pipeline's phase A handles the actual block merge; these methods just manage DS lifecycle around it. Task #6 wires the io loaders to use addDataSource for second-and-later file loads (the multi-DS user flow). For now, existing legacy paths (setTrajectory + ensureDataSource) remain untouched and keep producing single-DS pipelines. All 445 core tests pass.
Roy-Kid
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Phase 1, task #6 of multi-data-source-pipeline spec. `loadFileContent` and `loadFileStream` gain an optional `mode` parameter (`"replace" | "append"`, default `"replace"` to preserve existing UX). In append mode they apply the spec's load decision tree: - Single-frame file (`N_file === 1`) → wrap as `FrameDataSource` and broadcast across whatever trajectory length the pipeline already has (or stay at 1 if there's no trajectory yet). - Multi-frame file matching the existing trajectory length (or no existing trajectory) → wrap as `TrajectoryDataSource` so phase A index-aligns frame-by-frame. - Frame-count mismatch → throw `Cannot append "<filename>": file has N frame(s); existing trajectory has M. File must be single-frame (topology) or match existing frame count.` A new internal helper `appendTrajectoryAsDataSource` runs the decision tree and adds an atom-count consistency check: if both the existing system and the new file contribute an `atoms` block, their atom counts must match (otherwise downstream bonds/selection indices would dangle). Then forwards to `MolvisApp.addDataSource`, which performs the redundant frame-count check and runs auto-attach. Trajectory disposal on error stays correct: append mode disposes the trajectory if validation throws, so failed loads don't leak WASM. Replace mode is unchanged — keeps using `ensureDataSource` + `setTrajectory`, which after task #3+#4 also routes through a TrajectoryDataSource transparently. Page UI stays single-DS until the phase-3 "Add Data Source" button passes `mode: "append"`. All 445 core tests pass.
Roy-Kid
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…s, append on drop
Phase 3 of multi-data-source-pipeline spec.
Sidebar / pipeline list:
- New "Add Data Source" button next to the "Add modifier" dropdown.
Opens the format picker (same as drag-drop / per-DS panel) and calls
loadFileSmart in append mode if the pipeline already has a DS,
replace otherwise. First-load case routes through replace transparently.
- Each pipeline tree row for a DataSourceModifier now shows
`<filename> · Trajectory · N frames` or `<filename> · Topology · 1 frame`
so the user can tell trajectory vs topology DSs at a glance.
Drag-drop:
- MolvisWrapper drag-drop handler checks whether any DataSourceModifier
is already in the pipeline and switches between replace (empty
system, first load) and append (additive) automatically.
Per-DS panel (DataSourceModifier.tsx):
- Removed the deprecated showAtoms/showBonds/showBox visibility
toggles. Their job is now done by the auto-attached DrawAtom /
DrawBond / DrawBox children's `enabled` checkboxes (phase 2 nests
them under the DS in the pipeline tree).
- New compact summary card shows kind badge, sourceType label,
filename, and the contributedBlocks list ("atoms, bonds (default)"
fallback when not explicitly set).
- New per-DS Remove button calls `app.removeDataSource(modifier.id)`
via the lifecycle method introduced in phase 1 task #5 (cascade-
removes child Draws, disposes WASM, re-derives system trajectory).
Plumbing:
- `loadFileSmart` / `loadFileWithFormatPrompt` /
`loadFileStreamWithFormatPrompt` gain a `mode: "replace" | "append"`
parameter, default `"replace"`. Threads through to the core io
loaders' append branch (introduced in phase 1 task #6).
No core test changes — page UI doesn't have a unit-test harness.
Page typecheck clean (the pre-existing `FileSystemSyncAccessHandle`
errors in OPFS streaming code are unrelated). Core 474 tests still pass.
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Summary
Testing
npm test -w core(fails: Module @swc/jest in the transform option was not found)https://chatgpt.com/codex/tasks/task_e_68499033cf5c8324be267d6a8505ef8b