fix: update and dedupe dependencies (#1383)

cheminfo · Feb 25, 2022 · 4995931 · 4995931
1 parent 44698cb
commit 4995931
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Showing 14 changed files with 455 additions and 676 deletions.
diff --git a/.ncurc.json b/.ncurc.json
@@ -3,8 +3,6 @@
   "reject": [
     "react-color",
     "// TODO: Migrate to v6",
-    "react-router-dom",
-    "// TODO: Migrate out of reactstrap",
-    "reactstrap"
+    "react-router-dom"
   ]
 }
diff --git a/package-lock.json b/package-lock.json
diff --git a/package.json b/package.json
@@ -45,10 +45,10 @@
     "react-dom": ">=16.0.0"
   },
   "dependencies": {
-    "@emotion/react": "^11.7.1",
-    "analysis-ui-components": "^0.10.1",
+    "@emotion/react": "^11.8.1",
+    "analysis-ui-components": "^0.10.2",
     "cheminfo-font": "^1.8.1",
-    "cheminfo-types": "^0.9.1",
+    "cheminfo-types": "^1.0.0",
     "d3": "^7.3.0",
     "eventemitter3": "^4.0.7",
     "file-saver": "^2.0.5",
@@ -64,22 +64,22 @@
     "ml-array-xy-equally-spaced": "^1.2.1",
     "ml-baseline-correction-regression": "^1.0.0",
     "ml-conrec": "^3.2.1",
-    "ml-gsd": "^9.1.0",
-    "ml-spectra-processing": "^10.1.2",
+    "ml-gsd": "^10.1.2",
+    "ml-spectra-processing": "^11.0.0",
     "ml-stat": "^1.3.3",
     "multiplet-analysis": "^2.0.0",
-    "nmr-correlation": "^2.2.0",
+    "nmr-correlation": "^2.2.5",
     "nmr-parser": "^1.7.2",
-    "nmr-processing": "^6.0.8",
+    "nmr-processing": "^7.0.1",
     "nmredata": "^0.6.1",
     "numeral": "^2.0.6",
     "openchemlib": "^7.4.3",
     "openchemlib-utils": "^1.9.0",
-    "re-resizable": "^6.9.1",
+    "re-resizable": "^6.9.2",
     "react-color": "2.17.2",
     "react-d3-utils": "^0.5.0",
     "react-draggable": "^4.4.4",
-    "react-dropzone": "^11.5.3",
+    "react-dropzone": "^12.0.4",
     "react-error-boundary": "^3.1.4",
     "react-icons": "^4.3.1",
     "react-inspector": "^5.1.1",
@@ -99,11 +99,11 @@
     "@babel/plugin-transform-modules-commonjs": "^7.16.8",
     "@babel/preset-react": "^7.16.7",
     "@babel/preset-typescript": "^7.16.7",
-    "@playwright/test": "^1.19.1",
+    "@playwright/test": "^1.19.2",
     "@simbathesailor/use-what-changed": "^2.0.0",
     "@types/d3": "^7.1.0",
-    "@types/jest": "^27.4.0",
-    "@types/node": "^17.0.18",
+    "@types/jest": "^27.4.1",
+    "@types/node": "^17.0.21",
     "@types/react": "^17.0.39",
     "@types/react-dom": "^17.0.11",
     "@types/react-router-dom": "^5.3.3",
@@ -118,7 +118,6 @@
     "react": "^17.0.2",
     "react-dom": "^17.0.2",
     "react-router-dom": "^5.3.0",
-    "reactstrap": "^8.10.1",
     "rimraf": "^3.0.2",
     "rollup-plugin-analyzer": "^4.0.0",
     "serve": "^13.0.2",

diff --git a/src/component/panels/SummaryPanel/CorrelationTable/AdditionalColumnField.tsx b/src/component/panels/SummaryPanel/CorrelationTable/AdditionalColumnField.tsx
@@ -1,4 +1,4 @@
-import { buildLink, Types } from 'nmr-correlation';
+import { buildLink, Link, Correlation } from 'nmr-correlation';
 import { useCallback, useMemo, useRef } from 'react';
 
 import { buildID } from '../../../../data/utilities/Concatenation';
@@ -68,16 +68,16 @@ function AdditionalColumnField({
   );
 
   const handleEditPseudoHSQC = useCallback(
-    (action: 'add' | 'remove', link?: Types.Link) => {
+    (action: 'add' | 'remove', link?: Link) => {
       const pseudoLinkCountHSQC = rowCorrelation.link.filter(
         (_link) =>
           (_link.experimentType === 'hsqc' ||
             _link.experimentType === 'hmqc') &&
           _link.pseudo === true,
       ).length;
 
-      let _correlationDim1: Types.Correlation;
-      let _correlationDim2: Types.Correlation;
+      let _correlationDim1: Correlation;
+      let _correlationDim2: Correlation;
       if (action === 'add') {
         const commonPseudoLink = buildLink({
           experimentType: 'hsqc',

diff --git a/src/component/panels/SummaryPanel/CorrelationTable/CorrelationTableRow.tsx b/src/component/panels/SummaryPanel/CorrelationTable/CorrelationTableRow.tsx
@@ -3,7 +3,7 @@ import {
   getCorrelationDelta,
   getLabel,
   getLinkDim,
-  Types,
+  Link,
 } from 'nmr-correlation';
 import { CSSProperties, useCallback, useMemo, useRef } from 'react';
 
@@ -83,7 +83,7 @@ function CorrelationTableRow({
 
   const additionalColumnFields = useMemo(() => {
     return additionalColumnData.map((_correlation) => {
-      const commonLinks: Types.Link[] = [];
+      const commonLinks: Link[] = [];
       correlation.link.forEach((link) => {
         _correlation.link.forEach((_link) => {
           if (

diff --git a/src/component/panels/SummaryPanel/CorrelationTable/editLink/MoveLink.tsx b/src/component/panels/SummaryPanel/CorrelationTable/editLink/MoveLink.tsx
@@ -1,6 +1,6 @@
 /** @jsxImportSource @emotion/react */
 import { css } from '@emotion/react';
-import { getCorrelationDelta, Types } from 'nmr-correlation';
+import { getCorrelationDelta, Correlation, Link } from 'nmr-correlation';
 import { useCallback, useState } from 'react';
 
 import Select from '../../../../elements/Select';
@@ -38,10 +38,10 @@ const moveLinkStyles = css`
 `;
 
 interface MoveLinkProps {
-  correlationDim1: Types.Correlation;
-  correlationDim2: Types.Correlation;
-  link: Types.Link;
-  correlations: Types.Correlation[];
+  correlationDim1: Correlation;
+  correlationDim2: Correlation;
+  link: Link;
+  correlations: Correlation[];
   onEdit: (
     action: string,
     valueDim1: string,
@@ -61,13 +61,13 @@ function MoveLink({
   const [selectedCorrelationIdDim2, setSelectedCorrelationIdDim2] =
     useState<string>(correlationDim2?.id || undefined);
 
-  function getCorrelationLabel(correlation: Types.Correlation) {
+  function getCorrelationLabel(correlation: Correlation) {
     const delta = getCorrelationDelta(correlation);
     return `${delta ? delta.toFixed(2) : '?'}`;
   }
 
   const getSelection = useCallback(
-    (correlation: Types.Correlation, dim: 0 | 1) => {
+    (correlation: Correlation, dim: 0 | 1) => {
       const selectionData = correlations.reduce((arr, _correlation) => {
         if (
           _correlation.pseudo === false &&

diff --git a/src/component/panels/SummaryPanel/SummaryPanel.tsx b/src/component/panels/SummaryPanel/SummaryPanel.tsx
@@ -1,6 +1,13 @@
 /** @jsxImportSource @emotion/react */
 import { css } from '@emotion/react';
-import { getLinkDelta, getLinkDim, Types } from 'nmr-correlation';
+import {
+  getLinkDelta,
+  getLinkDim,
+  Correlation,
+  Values as CorrelationValues,
+  Options as CorrelationOptions,
+  Link,
+} from 'nmr-correlation';
 import { memo, useCallback, useEffect, useMemo, useState } from 'react';
 import { FaFlask, FaSlidersH } from 'react-icons/fa';
 
@@ -95,7 +102,7 @@ function SummaryPanel() {
   const [filterIsActive, setFilterIsActive] = useState(false);
 
   const filteredCorrelationsData = useMemo(() => {
-    const isInView = (correlation: Types.Correlation): boolean => {
+    const isInView = (correlation: Correlation): boolean => {
       if (correlation.pseudo === true) {
         return false;
       }
@@ -381,7 +388,7 @@ function SummaryPanel() {
   );
 
   const setCorrelationsHandler = useCallback(
-    (correlations: Types.Values, options?: Types.Options) => {
+    (correlations: CorrelationValues, options?: CorrelationOptions) => {
       dispatch({
         type: SET_CORRELATIONS,
         payload: {
@@ -394,7 +401,7 @@ function SummaryPanel() {
   );
 
   const deleteCorrelationHandler = useCallback(
-    (correlation: Types.Correlation) => {
+    (correlation: Correlation) => {
       dispatch({
         type: DELETE_CORRELATION,
         payload: {
@@ -407,7 +414,7 @@ function SummaryPanel() {
   );
 
   const deleteSignalHandler = useCallback(
-    (link: Types.Link) => {
+    (link: Link) => {
       // remove linking signal in spectrum
       const linkDim = getLinkDim(link);
       if (linkDim === 1) {
@@ -453,10 +460,10 @@ function SummaryPanel() {
 
   const editCorrelationTableCellHandler = useCallback(
     (
-      editedCorrelations: Types.Correlation[],
+      editedCorrelations: Correlation[],
       action: string,
-      link?: Types.Link,
-      options?: Types.Options,
+      link?: Link,
+      options?: CorrelationOptions,
     ) => {
       if (
         action === 'add' ||

diff --git a/src/component/panels/SummaryPanel/Utilities.ts b/src/component/panels/SummaryPanel/Utilities.ts
@@ -6,7 +6,8 @@ import {
   buildLink,
   getLinkDim,
   removeLink,
-  Types,
+  Link,
+  Correlation,
 } from 'nmr-correlation';
 
 import { Datum2D } from '../../../data/types/data2d';
@@ -44,7 +45,7 @@ function getLabelColor(correlationData, correlation) {
 
 function findSignalMatch1D(
   spectrum: Datum2D,
-  link: Types.Link,
+  link: Link,
   factor: number,
   xDomain0: number,
   xDomain1: number,
@@ -64,7 +65,7 @@ function findSignalMatch1D(
 
 function findSignalMatch2D(
   spectrum: Datum2D,
-  link: Types.Link,
+  link: Link,
   factor: number,
   xDomain0: number,
   xDomain1: number,
@@ -85,7 +86,7 @@ function findSignalMatch2D(
   return false;
 }
 
-function getAbbreviation(link: Types.Link): string {
+function getAbbreviation(link: Link): string {
   if (link.experimentType === 'hsqc' || link.experimentType === 'hmqc') {
     return !link.signal || link.signal.sign === 0
       ? 'S'
@@ -120,7 +121,7 @@ function buildNewLink1D(link) {
   });
 }
 
-function buildNewLink2D(link: Types.Link, axis: 'x' | 'y') {
+function buildNewLink2D(link: Link, axis: 'x' | 'y') {
   const linkIDs = link.id.split('_');
   return buildLink({
     ...link,
@@ -135,11 +136,11 @@ function buildNewLink2D(link: Types.Link, axis: 'x' | 'y') {
 }
 
 function cloneCorrelationAndEditLink(
-  correlation: Types.Correlation,
-  link: Types.Link,
+  correlation: Correlation,
+  link: Link,
   axis: 'x' | 'y',
   action: 'add' | 'remove' | 'unmove',
-): Types.Correlation {
+): Correlation {
   const linkDim = getLinkDim(link);
   const _correlation = lodashCloneDeep(correlation);
   const split = link.id.split('_');
@@ -175,7 +176,7 @@ function getEditedCorrelations({
     correlationDim2 && selectedCorrelationDim2?.id !== correlationDim2?.id;
   const linkDim = getLinkDim(link);
 
-  const editedCorrelations: Types.Correlation[] = [];
+  const editedCorrelations: Correlation[] = [];
   const buildCorrelationDataOptions: {
     skipDataUpdate?: boolean;
   } = {};
@@ -190,7 +191,7 @@ function getEditedCorrelations({
         'remove',
       );
       // modify selected correlation
-      let newCorrelationDim1: Types.Correlation;
+      let newCorrelationDim1: Correlation;
       if (selectedCorrelationDim1) {
         newCorrelationDim1 = cloneCorrelationAndEditLink(
           hasChangedDim1 ? selectedCorrelationDim1 : _correlationDim1,

diff --git a/src/component/reducer/Reducer.ts b/src/component/reducer/Reducer.ts
@@ -1,5 +1,5 @@
 import { Draft, produce } from 'immer';
-import { buildCorrelationData, Types } from 'nmr-correlation';
+import { buildCorrelationData, CorrelationData } from 'nmr-correlation';
 
 import { predictSpectra } from '../../data/PredictionManager';
 import * as SpectraManager from '../../data/SpectraManager';
@@ -274,7 +274,7 @@ export interface State {
   /**
    * Correlation data
    */
-  correlations: Types.CorrelationData;
+  correlations: CorrelationData;
 
   /**
    * Zoom Manager for vertical scale for spectra, integral, And undo zoom in per tab (nucleus)

diff --git a/src/component/reducer/actions/CorrelationsActions.ts b/src/component/reducer/actions/CorrelationsActions.ts
@@ -1,6 +1,13 @@
 import { original, Draft } from 'immer';
 import lodashCloneDeep from 'lodash/cloneDeep';
-import { buildCorrelationData, setCorrelation, Types } from 'nmr-correlation';
+import {
+  buildCorrelationData,
+  setCorrelation,
+  Tolerance,
+  Options as CorrelationOptions,
+  Correlation,
+  Values as CorrelationValues,
+} from 'nmr-correlation';
 
 import { Datum1D } from '../../../data/types/data1d';
 import { Datum2D } from '../../../data/types/data2d';
@@ -18,7 +25,7 @@ import { handleDeleteSignal as handleDeleteSignal2D } from './ZonesActions';
 
 function handleUpdateCorrelations(draft: Draft<State>) {
   const { data: spectra, correlations } = draft;
-  draft.correlations = buildCorrelationData(spectra as Types.Spectra, {
+  draft.correlations = buildCorrelationData(spectra, {
     ...correlations.options,
     values: lodashCloneDeep(correlations.values),
   });
@@ -30,7 +37,7 @@ function handleSetMF(draft: Draft<State>, payload: { mf: string }) {
   const { mf } = payload;
   // update of correlation data is needed only if the following is true
   if (correlations.options.mf === '' || correlations.options.mf !== mf) {
-    draft.correlations = buildCorrelationData(spectra as Types.Spectra, {
+    draft.correlations = buildCorrelationData(spectra, {
       ...correlations.options,
       mf,
       values: lodashCloneDeep(correlations.values),
@@ -40,12 +47,12 @@ function handleSetMF(draft: Draft<State>, payload: { mf: string }) {
 
 function handleSetTolerance(
   draft: Draft<State>,
-  payload: { tolerance: Types.Tolerance },
+  payload: { tolerance: Tolerance },
 ) {
   const state = original(draft) as State;
   const { data: spectra, correlations } = state;
   const { tolerance } = payload;
-  draft.correlations = buildCorrelationData(spectra as Types.Spectra, {
+  draft.correlations = buildCorrelationData(spectra, {
     ...correlations.options,
     tolerance,
     values: lodashCloneDeep(correlations.values),
@@ -56,8 +63,8 @@ function handleSetCorrelation(
   draft: Draft<State>,
   payload: {
     id: string;
-    correlation: Types.Correlation;
-    options: Types.Options;
+    correlation: Correlation;
+    options: CorrelationOptions;
   },
 ) {
   const state = original(draft) as State;
@@ -76,8 +83,8 @@ function handleSetCorrelation(
 function handleSetCorrelations(
   draft: Draft<State>,
   payload: {
-    correlations: Types.Values;
-    options: Types.Options;
+    correlations: CorrelationValues;
+    options: CorrelationOptions;
   },
 ) {
   const { correlations, options } = payload;
@@ -102,7 +109,7 @@ function handleSetCorrelations(
 
 function handleDeleteCorrelation(
   draft: Draft<State>,
-  payload: { correlation: Types.Correlation; assignmentData },
+  payload: { correlation: Correlation; assignmentData },
 ) {
   const { correlation, assignmentData } = payload;
   // delete all signals linked to the correlation