Merge pull request #421 from epam/maintenance

Maintenance update, part 1

.appveyor.yml

@@ -1,7 +1,7 @@
 version: "{build}"
 environment:
   matrix:
-    - nodejs_version: "14"
+    - nodejs_version: "16"
 cache:
   - "%LOCALAPPDATA%\\Yarn"
 init:

.eslintrc

@@ -31,7 +31,8 @@
     "@typescript-eslint/no-var-requires": "off"
   },
   "env": {
+    "browser": true,
     "jest": true,
     "mocha": true
   }
-}
+}

.gitattributes

@@ -0,0 +1,6 @@
+# https://docs.github.com/en/get-started/getting-started-with-git/configuring-git-to-handle-line-endings
+* text=auto
+
+*.png binary
+*.jpg binary
+*.ico binary

.github/workflows/ci.yml

@@ -19,7 +19,7 @@ jobs:
 
     strategy:
       matrix:
-        node-version: [14.x]
+        node-version: [16.x]
         # See supported Node.js release schedule at https://nodejs.org/en/about/releases/
 
     steps:

.prettierrc.js

@@ -1,3 +1,4 @@
 module.exports = {
-  ...require('prettier-config-standard')
+  ...require('prettier-config-standard'),
+  endOfLine: 'auto'
 }

.travis.yml

@@ -1,7 +1,7 @@
 language: node_js
 version: 1.0
 node_js:
-  - "14"
+  - "16"
 cache:
   yarn: true
   directories:
@@ -44,15 +44,15 @@ deploy:
     tag: latest
     on:
       tags: true
-      node: "14"
+      node: "16"
       condition: $TRAVIS_TAG =~ ^v[0-9]+\.[0-9]+\.[0-9]+$
   - provider: script
     edge: true
     cleanup: false
     script: "chmod +x ./tools/deploy.sh && ./tools/deploy.sh"
     on:
       all_branches: true
-      node: "14"
+      node: "16"
 notifications:
   slack:
     secure: 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

.yarnrc.yml

@@ -3,5 +3,7 @@ nodeLinker: node-modules
 plugins:
   - path: .yarn/plugins/@yarnpkg/plugin-workspace-tools.cjs
     spec: "@yarnpkg/plugin-workspace-tools"
+  - path: .yarn/plugins/@yarnpkg/plugin-interactive-tools.cjs
+    spec: "@yarnpkg/plugin-interactive-tools"
 
 yarnPath: .yarn/releases/yarn-3.1.1.cjs

Dockerfile

@@ -1,4 +1,4 @@
-FROM node:14 AS build
+FROM node:16 AS build
 COPY . /miew
 RUN cd /miew \
     && yarn install \

package.json

@@ -61,5 +61,10 @@
     "webpack": "^4.43.0",
     "webpack-cli": "^3.3.11"
   },
-  "packageManager": "yarn@3.1.1"
+  "packageManager": "yarn@3.1.1",
+  "resolutions": {
+    "eventsource": "1.1.1",
+    "minimist": "1.2.6",
+    "url-parse": "1.5.10"
+  }
 }

packages/miew-cli/src/Miew-cli.js

@@ -44,7 +44,7 @@ class RepresentationMap {
     }
 
     if (index !== undefined) {
-      if (!this.representationMap.hasOwnProperty(strId)) {
+      if (!Object.hasOwn(this.representationMap, strId)) {
         this.representationMap[strId.toString()] = index
         this.representationID[index] = strId.toString()
       } else {
@@ -55,14 +55,14 @@ class RepresentationMap {
   }
 
   remove(index) {
-    if (index && this.representationID.hasOwnProperty(index)) {
+    if (index && Object.hasOwn(this.representationID, index)) {
       delete this.representationMap[this.representationID[index]]
       delete this.representationID[index]
     }
 
     const sortedKeys = Object.keys(this.representationID).sort()
     for (const i in sortedKeys) {
-      if (sortedKeys.hasOwnProperty(i)) {
+      if (Object.hasOwn(sortedKeys, i)) {
         const id = sortedKeys[i]
         if (id > index) {
           this.representationID[id - 1] = this.representationID[id]
@@ -145,7 +145,7 @@ class CLIUtils {
     let ret = ''
 
     for (const k in context) {
-      if (context.hasOwnProperty(k)) {
+      if (Object.hasOwn(context, k)) {
         ret += `${k} : "${context[k]}"\n`
       }
     }

packages/miew-cli/src/MiewCLIParser.js

@@ -2276,7 +2276,7 @@ var parser = (function () {
       var lexer = Object.create(this.lexer)
       var sharedState = { yy: {} }
       for (var k in this.yy) {
-        if (Object.prototype.hasOwnProperty.call(this.yy, k)) {
+        if (Object.hasOwn(this.yy, k)) {
           sharedState.yy[k] = this.yy[k]
         }
       }

packages/miew-cli/src/utils.js

@@ -339,7 +339,7 @@ function isAlmostPlainObject(o) {
   const proto = o && Object.getPrototypeOf(o)
   return (
     !!proto &&
-    !proto.hasOwnProperty('constructor') &&
+    !Object.hasOwn(proto, 'constructor') &&
     isAlmostPlainObject(proto)
   )
 }

packages/miew-react/src/Viewer.tsx

@@ -135,7 +135,7 @@ const Viewer = ({
 
     const callbacks = addListeners(miew, dispatch)
     return () => removeListeners(miew, callbacks)
-  }, [options, onInit])
+  }, [options, onInit, dispatch])
 
   return (
     <ThemeProvider theme={merge(muiTheme, { miew: viewerTheme })}>

packages/miew-react/src/typings.d.ts

@@ -2,6 +2,7 @@ import { MiewTheme } from 'theming'
 
 declare module '*.svg' {
   import * as React from 'react'
+  import { ReactComponent } from 'react'
 
   export const ReactComponent: React.FunctionComponent<
     React.SVGProps<SVGSVGElement> & { title?: string }

packages/miew/package.json

@@ -16,6 +16,9 @@
     "directory": "packages/miew"
   },
   "license": "MIT",
+  "engines": {
+    "node": ">=16.9.0"
+  },
   "scripts": {
     "ci": "run-s clean test-cover build",
     "eslint": "eslint . --ext .ts,.tsx,.js,.jsx",

packages/miew/src/ComplexVisual.js

@@ -201,7 +201,7 @@ class ComplexVisual extends Visual {
       if (!isEmpty(diff)) {
         target.needsRebuild = true
         for (const key in diff) {
-          if (diff.hasOwnProperty(key)) {
+          if (Object.hasOwn(diff, key)) {
             desc[key] = diff[key]
             logger.debug(`rep[${index}].${key} changed to ${diff[key]}`)
           }
@@ -655,6 +655,7 @@ class ComplexVisual extends Visual {
               }
             }
 
+            /* global DEBUG:false */
             if (DEBUG && !errorOccured) {
               logger.debug(
                 `Triangles count: ${meshutils.countTriangles(repr.geo)}`
@@ -755,7 +756,7 @@ class ComplexVisual extends Visual {
       }
       if (Object.keys(residues).length > 0) {
         for (const ch in residues) {
-          if (residues.hasOwnProperty(ch)) {
+          if (Object.hasOwn(residues, ch)) {
             selector = selectors.and(
               selectors.chain(ch),
               selectors.residx(optimizeList(residues[ch]))

packages/miew/src/ComplexVisualEdit.js

@@ -102,7 +102,7 @@ class ComplexComponentEditor extends ComplexEditor {
       reprNode = selection.children[i]
       for (j = 0; j < reprNode.children.length; ++j) {
         geo = reprNode.children[j]
-        if (geo.hasOwnProperty('_component') && geo._component === component) {
+        if (Object.hasOwn(geo, '_component') && geo._component === component) {
           res.objects.push(geo)
         }
       }
@@ -178,7 +178,7 @@ class ComplexComponentEditor extends ComplexEditor {
       reprNode = visual.children[i]
       for (j = 0; j < reprNode.children.length; ++j) {
         geo = reprNode.children[j]
-        if (geo.hasOwnProperty('_component')) {
+        if (Object.hasOwn(geo, '_component')) {
           geo.position.set(0, 0, 0)
           geo.quaternion.set(0, 0, 0, 1)
         }
@@ -190,7 +190,7 @@ class ComplexComponentEditor extends ComplexEditor {
       reprNode = selection.children[i]
       for (j = 0; j < reprNode.children.length; ++j) {
         geo = reprNode.children[j]
-        if (geo.hasOwnProperty('_component')) {
+        if (Object.hasOwn(geo, '_component')) {
           geo.position.set(0, 0, 0)
           geo.quaternion.set(0, 0, 0, 1)
         }

packages/miew/src/Miew.ts

@@ -1,3 +1,4 @@
+/* global DEBUG:false, PACKAGE_VERSION:false */
 // eslint-disable-next-line
 //@ts-nocheck
 import { Spinner } from 'spin.js'
@@ -1031,7 +1032,7 @@ export class Miew extends EventDispatcher {
 
     let name = baseName
     let suffix = 1
-    while (this._visuals.hasOwnProperty(name)) {
+    while (Object.hasOwn(this._visuals, name)) {
       name = `${baseName} (${suffix.toString()})`
       suffix++
     }
@@ -1078,7 +1079,7 @@ export class Miew extends EventDispatcher {
 
     if (
       !obj ||
-      !this._visuals.hasOwnProperty(name) ||
+      !Object.hasOwn(this._visuals, name) ||
       this._visuals[name] !== obj
     ) {
       return
@@ -1100,7 +1101,7 @@ export class Miew extends EventDispatcher {
    */
   _forEachVisual(callback) {
     for (const name in this._visuals) {
-      if (this._visuals.hasOwnProperty(name)) {
+      if (Object.hasOwn(this._visuals, name)) {
         callback(this._visuals[name])
       }
     }
@@ -1116,7 +1117,7 @@ export class Miew extends EventDispatcher {
     }
 
     for (const name in this._visuals) {
-      if (this._visuals.hasOwnProperty(name)) {
+      if (Object.hasOwn(this._visuals, name)) {
         this._visuals[name].release()
       }
     }
@@ -1135,7 +1136,7 @@ export class Miew extends EventDispatcher {
 
     for (const name in this._visuals) {
       if (
-        this._visuals.hasOwnProperty(name) &&
+        Object.hasOwn(this._visuals, name) &&
         this._visuals[name] instanceof ComplexVisual
       ) {
         callback(this._visuals[name])

packages/miew/src/chem/Complex.js

@@ -685,7 +685,7 @@ class Complex {
   }
 
   getAtomNames() {
-    if (this.hasOwnProperty('_atomNames')) {
+    if (Object.hasOwn(this, '_atomNames')) {
       return this._atomNames
     }
 
@@ -699,7 +699,7 @@ class Complex {
   }
 
   getElements() {
-    if (this.hasOwnProperty('_elements')) {
+    if (Object.hasOwn(this, '_elements')) {
       return this._elements
     }
 
@@ -713,7 +713,7 @@ class Complex {
   }
 
   getResidueNames() {
-    if (this.hasOwnProperty('_residueNames')) {
+    if (Object.hasOwn(this, '_residueNames')) {
       return this._residueNames
     }
 
@@ -727,7 +727,7 @@ class Complex {
   }
 
   getChainNames() {
-    if (this.hasOwnProperty('_chainNames')) {
+    if (Object.hasOwn(this, '_chainNames')) {
       return this._chainNames
     }
 
@@ -741,7 +741,7 @@ class Complex {
   }
 
   getAltLocNames() {
-    if (this.hasOwnProperty('_altlocNames')) {
+    if (Object.hasOwn(this, '_altlocNames')) {
       return this._altlocNames
     }
 
@@ -755,7 +755,7 @@ class Complex {
   }
 
   getVoxelWorld() {
-    if (!this.hasOwnProperty('_voxelWorld')) {
+    if (!Object.hasOwn(this, '_voxelWorld')) {
       try {
         this._voxelWorld = new VoxelWorld(
           this.getDefaultBoundaries().boundingBox,
@@ -854,7 +854,7 @@ class Complex {
       this.addElement(c.structures, this.structures, 0, doNothing)
       // merge residue types
       for (const rt in c._residueTypes) {
-        if (c._residueTypes.hasOwnProperty(rt)) {
+        if (Object.hasOwn(c._residueTypes, rt)) {
           this._residueTypes[rt] = c._residueTypes[rt]
         }
       }

packages/miew/src/chem/VoxelWorld.js

@@ -458,7 +458,7 @@ class VoxelWorld {
 
     // for each marked voxel
     for (voxel in voxels) {
-      if (voxels.hasOwnProperty(voxel)) {
+      if (Object.hasOwn(voxels, voxel)) {
         self._forEachAtomInVoxel(voxel, processIfWithin)
       }
     }

packages/miew/src/chem/selectors.js

@@ -230,7 +230,7 @@ selectors.InfixOperator = InfixOperator
 selectors.Context = Object.create({})
 
 selectors.GetSelector = function (key) {
-  if (!selectors.Context.hasOwnProperty(key)) {
+  if (!Object.hasOwn(selectors.Context, key)) {
     const exc = { message: `selector ${key} is not registered` }
     throw exc
   }

packages/miew/src/gfx/geometries/ChunkedObjectsGeometry.js

@@ -70,7 +70,7 @@ class ChunkedObjectsGeometry extends BufferGeometry {
     mesh.raycast(raycaster, inters)
     const facesPerChunk = this._chunkGeo.index.count / 3
     for (let i = 0, n = inters.length; i < n; ++i) {
-      if (!inters[i].hasOwnProperty('faceIndex')) {
+      if (!Object.hasOwn(inters[i], 'faceIndex')) {
         continue
       }
       inters[i].chunkIdx = Math.floor(inters[i].faceIndex / facesPerChunk)

packages/miew/src/gfx/gfxutils.js

@@ -318,7 +318,7 @@ function _calcChunkMatrix(eye, target, up, rad) {
 function _groupHasGeometryToRender(group) {
   let hasGeoms = false
   group.traverse((node) => {
-    if (node.hasOwnProperty('geometry') || node instanceof CSS2DObject) {
+    if (Object.hasOwn(node, 'geometry') || node instanceof CSS2DObject) {
       hasGeoms = true
     }
   })

packages/miew/src/gfx/meshutils.js

@@ -209,7 +209,7 @@ function _countMeshTriangles(mesh) {
     const attribs = geom.attributes
     for (const property in attribs) {
       if (
-        attribs.hasOwnProperty(property) &&
+        Object.hasOwn(attribs, property) &&
         attribs[property] instanceof InstancedBufferAttribute
       ) {
         const currAttr = attribs[property]

packages/miew/src/gfx/modes/groups/AtomsGroup.js

@@ -8,7 +8,7 @@ class AtomsGroup extends ChemGroup {
     const atomsIdc = this._chunksIdc
     // process inters array - arr object references
     for (let i = 0, n = inters.length; i < n; ++i) {
-      if (!inters[i].hasOwnProperty('chunkIdx')) {
+      if (!Object.hasOwn(inters[i], 'chunkIdx')) {
         continue
       }
       const atomIdx = atomsIdc[inters[i].chunkIdx]