molstar 2.3.6 → 2.4.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "2.3.6",
+  "version": "2.4.0",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {
@@ -89,52 +89,51 @@
   "license": "MIT",
   "devDependencies": {
     "@graphql-codegen/add": "^3.1.0",
-    "@graphql-codegen/cli": "^2.2.0",
+    "@graphql-codegen/cli": "^2.3.0",
     "@graphql-codegen/time": "^3.1.0",
-    "@graphql-codegen/typescript": "^2.2.2",
+    "@graphql-codegen/typescript": "^2.4.1",
     "@graphql-codegen/typescript-graphql-files-modules": "^2.1.0",
-    "@graphql-codegen/typescript-graphql-request": "^4.1.4",
-    "@graphql-codegen/typescript-operations": "^2.1.6",
+    "@graphql-codegen/typescript-graphql-request": "^4.3.1",
+    "@graphql-codegen/typescript-operations": "^2.2.1",
     "@types/cors": "^2.8.12",
     "@types/gl": "^4.1.0",
-    "@types/jest": "^27.0.2",
-    "@typescript-eslint/eslint-plugin": "^4.32.0",
-    "@typescript-eslint/parser": "^4.32.0",
+    "@types/jest": "^27.0.3",
+    "@typescript-eslint/eslint-plugin": "^5.4.0",
+    "@typescript-eslint/parser": "^5.4.0",
     "benchmark": "^2.1.4",
-    "concurrently": "^6.3.0",
+    "concurrently": "^6.4.0",
     "cpx2": "^4.0.0",
     "crypto-browserify": "^3.12.0",
-    "css-loader": "^6.3.0",
-    "eslint": "^7.32.0",
+    "css-loader": "^6.5.1",
+    "eslint": "^8.3.0",
     "extra-watch-webpack-plugin": "^1.0.3",
     "file-loader": "^6.2.0",
     "fs-extra": "^10.0.0",
-    "graphql": "^15.6.0",
-    "http-server": "^13.0.2",
-    "jest": "^27.2.4",
-    "mini-css-extract-plugin": "^2.3.0",
-    "node-sass": "^6.0.1",
+    "graphql": "^15.7.2",
+    "http-server": "^14.0.0",
+    "jest": "^27.3.1",
+    "mini-css-extract-plugin": "^2.4.5",
     "path-browserify": "^1.0.1",
     "raw-loader": "^4.0.2",
-    "sass-loader": "^12.1.0",
-    "simple-git": "^2.46.0",
+    "sass": "^1.43.5",
+    "sass-loader": "^12.3.0",
+    "simple-git": "^2.47.0",
     "stream-browserify": "^3.0.0",
-    "style-loader": "^3.3.0",
-    "ts-jest": "^27.0.5",
-    "typescript": "^4.4.3",
-    "webpack": "^5.56.0",
-    "webpack-cli": "^4.8.0",
-    "webpack-version-file-plugin": "^0.4.0"
+    "style-loader": "^3.3.1",
+    "ts-jest": "^27.0.7",
+    "typescript": "^4.5.2",
+    "webpack": "^5.64.4",
+    "webpack-cli": "^4.9.1"
   },
   "dependencies": {
     "@types/argparse": "^2.0.10",
     "@types/benchmark": "^2.1.1",
     "@types/compression": "1.7.2",
     "@types/express": "^4.17.13",
-    "@types/node": "^16.10.2",
+    "@types/node": "^16.11.10",
     "@types/node-fetch": "^2.5.12",
-    "@types/react": "^17.0.27",
-    "@types/react-dom": "^17.0.9",
+    "@types/react": "^17.0.37",
+    "@types/react-dom": "^17.0.11",
     "@types/swagger-ui-dist": "3.30.1",
     "argparse": "^2.0.1",
     "body-parser": "^1.19.0",
@@ -142,13 +141,13 @@
     "cors": "^2.8.5",
     "express": "^4.17.1",
     "h264-mp4-encoder": "^1.0.12",
-    "immer": "^9.0.6",
+    "immer": "^9.0.7",
     "immutable": "^3.8.2",
     "node-fetch": "^2.6.2",
     "react": "^17.0.2",
     "react-dom": "^17.0.2",
-    "rxjs": "^7.3.1",
-    "swagger-ui-dist": "^3.52.3",
+    "rxjs": "^7.4.0",
+    "swagger-ui-dist": "^4.1.1",
     "tslib": "^2.3.1",
     "util.promisify": "^1.1.1",
     "xhr2": "^0.2.1"

package/CHANGELOG.md

@@ -1,191 +0,0 @@
-# Change Log
-All notable changes to this project will be documented in this file, following the suggestions of [Keep a CHANGELOG](http://keepachangelog.com/). This project adheres to [Semantic Versioning](http://semver.org/) for its most widely used - and defacto - public interfaces.
-
-Note that since we don't clearly distinguish between a public and private interfaces there will be changes in non-major versions that are potentially breaking. If we make breaking changes to less used interfaces we will highlight it in here.
-
-
-## [Unreleased]
-
-- Added ``ViewerOptions.collapseRightPanel``
-- Added ``Viewer.loadTrajectory`` to support loading "composed" trajectories (e.g. from gro + xtc)
-- Fix: handle parent in Structure.remapModel
-- Add ``rounded`` and ``square`` helix profile options to Cartoon representation (in addition to the default ``elliptical``)
-
-## [v2.3.6] - 2021-11-8
-
-- Add additional measurement controls: orientation (box, axes, ellipsoid) & plane (best fit)
-- Improve aromatic bond visuals (add ``aromaticScale``, ``aromaticSpacing``, ``aromaticDashCount`` params)
-- [Breaking] Change ``adjustCylinderLength`` default to ``false`` (set to true for focus representation)
-- Fix marker highlight color overriding select color
-- CellPack extension update
-    - add binary model support
-    - add compartment (including membrane) geometry support
-    - add latest mycoplasma model example
-- Prefer WebGL1 in Safari 15.1.
-
-## [v2.3.5] - 2021-10-19
-
-- Fix sequence viewer for PDB files with COMPND record and multichain entities.
-- Fix index pair bonds order assignment
-
-## [v2.3.4] - 2021-10-12
-
-- Fix pickScale not taken into account in line/point shader
-- Add pixel-scale, pick-scale & pick-padding GET params to Viewer app
-- Fix selecting bonds not adding their atoms in selection manager
-- Add ``preferAtoms`` option to SelectLoci/HighlightLoci behaviors
-- Make the implicit atoms of bond visuals pickable
-    - Add ``preferAtomPixelPadding`` to Canvas3dInteractionHelper
-- Add points & crosses visuals to Line representation
-- Add ``pickPadding`` config option (look around in case target pixel is empty)
-- Add ``multipleBonds`` param to bond visuals with options: off, symmetric, offset
-- Fix ``argparse`` config in servers.
-
-## [v2.3.3] - 2021-10-01
-
-- Fix direct volume shader
-
-## [v2.3.2] - 2021-10-01
-
-- Prefer WebGL1 on iOS devices until WebGL2 support has stabilized.
-
-## [v2.3.1] - 2021-09-28
-
-- Add Charmm saccharide names
-- Treat missing occupancy column as occupancy of 1
-- Fix line shader not accounting for aspect ratio
-- [Breaking] Fix point repr & shader
-    - Was unusable with ``wboit``
-    - Replaced ``pointFilledCircle`` & ``pointEdgeBleach`` params by ``pointStyle`` (square, circle, fuzzy)
-    - Set ``pointSizeAttenuation`` to false by default
-    - Set ``sizeTheme`` to ``uniform`` by default
-- Add ``markerPriority`` option to Renderer (useful in combination with edges of marking pass)
-- Add support support for ``chem_comp_bond`` and ``struct_conn`` categories (fixes ModelServer behavior where these categories should have been present)
-- Model and VolumeServer: fix argparse config
-
-## [v2.3.0] - 2021-09-06
-
-- Take include/exclude flags into account when displaying aromatic bonds
-- Improve marking performance
-    - Avoid unnecessary draw calls/ui updates when marking
-    - Check if loci is superset of visual
-    - Check if loci overlaps with unit visual
-    - Ensure ``Interval`` is used for ranges instead of ``SortedArray``
-    - Add uniform marker type
-    - Special case for reversing previous mark
-- Add optional marking pass
-    - Outlines visible and hidden parts of highlighted/selected groups
-    - Add highlightStrength/selectStrength renderer params
-
-## [v2.2.3] - 2021-08-25
-
-- Add ``invertCantorPairing`` helper function
-- Add ``Mesh`` processing helper ``.smoothEdges``
-- Smooth border of molecular-surface with ``includeParent`` enabled
-- Hide ``includeParent`` option from gaussian-surface visuals (not particularly useful)
-- Improved ``StructureElement.Loci.size`` performance (for marking large cellpack models)
-- Fix new ``TransformData`` issues (camera/bounding helper not showing up)
-- Improve marking performance (avoid superfluous calls to ``StructureElement.Loci.isWholeStructure``)
-
-## [v2.2.2] - 2021-08-11
-
-- Fix ``TransformData`` issues [#133](https://github.com/molstar/molstar/issues/133)
-- Fix ``mol-script`` query compiler const expression recognition.
-
-## [v2.2.1] - 2021-08-02
-
-- Add surrounding atoms (5 Angstrom) structure selection query
-- [Breaking] Add maxDistance prop to ``IndexPairBonds``
-- Fix coordinateSystem not handled in ``Structure.asParent``
-- Add ``dynamicBonds`` to ``Structure`` props (force re-calc on model change)
-    - Expose as optional param in root structure transform helper
-- Add overpaint support to geometry exporters
-- ``InputObserver`` improvements
-  - normalize wheel speed across browsers/platforms
-  - support Safari gestures (used by ``TrackballControls``)
-  - ``PinchInput.fractionDelta`` and use it in ``TrackballControls``
-
-## [v2.2.0] - 2021-07-31
-
-- Add ``tubularHelices`` parameter to Cartoon representation
-- Add ``SdfFormat`` and update SDF parser to be able to parse data headers according to spec (hopefully :)) #230
-- Fix mononucleotides detected as polymer components (#229)
-- Set default outline scale back to 1
-- Improved DCD reader cell angle handling (interpret near 0 angles as 90 deg)
-- Handle more residue/atom names commonly used in force-fields
-- Add USDZ support to ``geo-export`` extension.
-- Fix ``includeParent`` support for multi-instance bond visuals.
-- Add ``operator`` Loci granularity, selecting everything with the same operator name.
-- Prefer ``_label_seq_id`` fields in secondary structure assignment.
-- Support new EMDB API (https://www.ebi.ac.uk/emdb/api/entry/map/[EMBD-ID]) for EM volume contour levels.
-- ``Canvas3D`` tweaks:
-    - Update ``forceDraw`` logic.
-    - Ensure the scene is re-rendered when viewport size changes.
-    - Support ``noDraw`` mode in ``PluginAnimationLoop``.
-
-## [v2.1.0] - 2021-07-05
-
-- Add parameter for to display aromatic bonds as dashes next to solid cylinder/line.
-- Add backbone representation
-- Fix outline in orthographic mode and set default scale to 2.
-
-## [v2.0.7] - 2021-06-23
-
-- Add ability to specify ``volumeIndex`` in ``Viewer.loadVolumeFromUrl`` to better support Volume Server inputs.
-- Support in-place reordering for trajectory ``Frame.x/y/z`` arrays for better memory efficiency.
-- Fixed text CIF encoder edge cases (most notably single whitespace not being escaped).
-
-## [v2.0.6] - 2021-06-01
-
-- Add glTF (GLB) and STL support to ``geo-export`` extension.
-- Protein crosslink improvements
-    - Change O-S bond distance to allow for NOS bridges (doi:10.1038/s41586-021-03513-3)
-    - Added NOS-bridges query & improved disulfide-bridges query
-- Fix #178: ``IndexPairBonds`` for non-single residue structures (bug due to atom reordering).
-- Add volumetric color smoothing for MolecularSurface and GaussianSurface representations (#173)
-- Fix nested 3d grid lookup that caused results being overwritten in non-covalent interactions computation.
-- Basic implementation of ``BestDatabaseSequenceMapping`` (parse from CIF, color theme, superposition).
-- Add atom id ranges support to Selection UI.
-
-## [v2.0.5] - 2021-04-26
-
-- Ability to pass ``Canvas3DContext`` to ``PluginContext.fromCanvas``.
-- Relative frame support for ``Canvas3D`` viewport.
-- Fix bug in screenshot copy UI.
-- Add ability to select residues from a list of identifiers to the Selection UI.
-- Fix SSAO bugs when used with ``Canvas3D`` viewport.
-- Support for  full pausing (no draw) rendering: ``Canvas3D.pause(true)``.
-- Add ``MeshBuilder.addMesh``.
-- Add ``Torus`` primitive.
-- Lazy volume loading support.
-- [Breaking] ``Viewer.loadVolumeFromUrl`` signature change.
-    - ``loadVolumeFromUrl(url, format, isBinary, isovalues, entryId)`` => ``loadVolumeFromUrl({ url, format, isBinary }, isovalues, { entryId, isLazy })``
-- Add ``TextureMesh`` support to ``geo-export`` extension.
-
-## [v2.0.4] - 2021-04-20
-
-- [WIP] Mesh export extension
-- ``Structure.eachAtomicHierarchyElement`` (#161)
-- Fixed reading multi-line values in SDF format
-- Fixed Measurements UI labels (#166)
-
-## [v2.0.3] - 2021-04-09
-
-- Add support for ``ColorTheme.palette`` designed for providing gradient-like coloring.
-- [Breaking] The ``zip`` function is now asynchronous and expects a ``RuntimeContext``. Also added ``Zip()`` returning a ``Task``.
-- [Breaking] Add ``CubeGridFormat`` in ``alpha-orbitals`` extension.
-
-## [v2.0.2] - 2021-03-29
-
-- Add ``Canvas3D.getRenderObjects``.
-- [WIP] Animate state interpolating, including model trajectories
-- Recognise MSE, SEP, TPO, PTR and PCA as non-standard amino-acids.
-- Fix VolumeFromDensityServerCif transform label
-
-## [v2.0.1] - 2021-03-23
-
-- Exclude tsconfig.commonjs.tsbuildinfo from npm bundle
-
-## [v2.0.0] - 2021-03-23
-
-Too many changes to list as this is the start of the changelog... Notably, default exports are now forbidden.