From 7feec4859dec7e9cd47af9c4cbbebea719e61ac4 Mon Sep 17 00:00:00 2001 From: Garrett Stevens Date: Thu, 5 Oct 2023 20:42:24 -0600 Subject: [PATCH] Ensure consistent versions in monorepo deps --- .husky/pre-commit | 4 + .yarn/plugins/@yarnpkg/plugin-constraints.cjs | 52 + .yarnrc.yml | 2 + README.md | 14 +- constraints.pro | 9 + package.json | 5 +- .../apollo-collaboration-server/package.json | 12 +- packages/apollo-common/package.json | 26 +- packages/apollo-mst/package.json | 6 +- packages/apollo-schemas/package.json | 4 +- packages/apollo-shared/package.json | 24 +- packages/jbrowse-plugin-apollo/package.json | 35 +- yarn.lock | 2553 ++--------------- 13 files changed, 292 insertions(+), 2454 deletions(-) create mode 100755 .husky/pre-commit create mode 100644 .yarn/plugins/@yarnpkg/plugin-constraints.cjs create mode 100644 constraints.pro diff --git a/.husky/pre-commit b/.husky/pre-commit new file mode 100755 index 00000000..d8bf5c1f --- /dev/null +++ b/.husky/pre-commit @@ -0,0 +1,4 @@ +#!/usr/bin/env sh +. 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Le;(function(c){c.Dependencies="dependencies",c.DevDependencies="devDependencies",c.PeerDependencies="peerDependencies"})(Le||(Le={}));var ei=[Le.Dependencies,Le.DevDependencies,Le.PeerDependencies];function K(r){if(r instanceof Re.default.type.Num)return r.value;if(r instanceof Re.default.type.Term)switch(r.indicator){case"throw/1":return K(r.args[0]);case"error/1":return K(r.args[0]);case"error/2":if(r.args[0]instanceof Re.default.type.Term&&r.args[0].indicator==="syntax_error/1")return Object.assign(K(r.args[0]),...K(r.args[1]));{let u=K(r.args[0]);return u.message+=` (in ${K(r.args[1])})`,u}case"syntax_error/1":return new ae.ReportError(ae.MessageName.PROLOG_SYNTAX_ERROR,`Syntax error: ${K(r.args[0])}`);case"existence_error/2":return new ae.ReportError(ae.MessageName.PROLOG_EXISTENCE_ERROR,`Existence error: ${K(r.args[0])} ${K(r.args[1])} not found`);case"instantiation_error/0":return new ae.ReportError(ae.MessageName.PROLOG_INSTANTIATION_ERROR,"Instantiation error: an argument is variable when an instantiated argument was expected");case"line/1":return{line:K(r.args[0])};case"column/1":return{column:K(r.args[0])};case"found/1":return{found:K(r.args[0])};case"./2":return[K(r.args[0])].concat(K(r.args[1]));case"//2":return`${K(r.args[0])}/${K(r.args[1])}`;default:return r.id}throw`couldn't pretty print because of unsupported node ${r}`}function ri(r){let u;try{u=K(r)}catch(p){throw typeof p=="string"?new ae.ReportError(ae.MessageName.PROLOG_UNKNOWN_ERROR,`Unknown error: ${r} (note: ${p})`):p}return typeof u.line!="undefined"&&typeof u.column!="undefined"&&(u.message+=` at line ${u.line}, column ${u.column}`),u}var ti=class{constructor(u,p){let c=1e3*u.workspaces.length;this.session=Re.default.create(c),Kn(this.session,u),this.session.consult(":- use_module(library(lists))."),this.session.consult(p)}fetchNextAnswer(){return new Promise(u=>{this.session.answer(p=>{u(p)})})}async*makeQuery(u){let p=this.session.query(u);if(p!==!0)throw ri(p);for(;;){let c=await this.fetchNextAnswer();if(c===null)throw new ae.ReportError(ae.MessageName.PROLOG_LIMIT_EXCEEDED,"Resolution limit exceeded");if(!c)break;if(c.id==="throw")throw ri(c);yield c}}};function ke(r){return r.id==="null"?null:`${r.toJavaScript()}`}function Uo(r){if(r.id==="null")return null;{let u=r.toJavaScript();if(typeof u!="string")return JSON.stringify(u);try{return JSON.stringify(JSON.parse(u))}catch{return JSON.stringify(u)}}}var pe=class{constructor(u){this.source="";this.project=u;let p=u.configuration.get("constraintsPath");Ne.xfs.existsSync(p)&&(this.source=Ne.xfs.readFileSync(p,"utf8"))}static async find(u){return new pe(u)}getProjectDatabase(){let u="";for(let p of ei)u+=`dependency_type(${p}). +`;for(let p of this.project.workspacesByCwd.values()){let c=p.relativeCwd;u+=`workspace(${de(c)}). +`,u+=`workspace_ident(${de(c)}, ${de(le.structUtils.stringifyIdent(p.locator))}). +`,u+=`workspace_version(${de(c)}, ${de(p.manifest.version)}). +`;for(let w of ei)for(let _ of p.manifest[w].values())u+=`workspace_has_dependency(${de(c)}, ${de(le.structUtils.stringifyIdent(_))}, ${de(_.range)}, ${w}). +`}return u+=`workspace(_) :- false. +`,u+=`workspace_ident(_, _) :- false. +`,u+=`workspace_version(_, _) :- false. +`,u+=`workspace_has_dependency(_, _, _, _) :- false. +`,u}getDeclarations(){let u="";return u+=`gen_enforced_dependency(_, _, _, _) :- false. +`,u+=`gen_enforced_field(_, _, _) :- false. +`,u}get fullSource(){return`${this.getProjectDatabase()} +${this.source} +${this.getDeclarations()}`}createSession(){return new ti(this.project,this.fullSource)}async process(){let u=this.createSession();return{enforcedDependencies:await this.genEnforcedDependencies(u),enforcedFields:await this.genEnforcedFields(u)}}async genEnforcedDependencies(u){let p=[];for await(let c of u.makeQuery("workspace(WorkspaceCwd), dependency_type(DependencyType), gen_enforced_dependency(WorkspaceCwd, DependencyIdent, DependencyRange, DependencyType).")){let w=Ne.ppath.resolve(this.project.cwd,ke(c.links.WorkspaceCwd)),_=ke(c.links.DependencyIdent),v=ke(c.links.DependencyRange),g=ke(c.links.DependencyType);if(w===null||_===null)throw new Error("Invalid rule");let h=this.project.getWorkspaceByCwd(w),x=le.structUtils.parseIdent(_);p.push({workspace:h,dependencyIdent:x,dependencyRange:v,dependencyType:g})}return le.miscUtils.sortMap(p,[({dependencyRange:c})=>c!==null?"0":"1",({workspace:c})=>le.structUtils.stringifyIdent(c.locator),({dependencyIdent:c})=>le.structUtils.stringifyIdent(c)])}async genEnforcedFields(u){let p=[];for await(let c of u.makeQuery("workspace(WorkspaceCwd), gen_enforced_field(WorkspaceCwd, FieldPath, FieldValue).")){let w=Ne.ppath.resolve(this.project.cwd,ke(c.links.WorkspaceCwd)),_=ke(c.links.FieldPath),v=Uo(c.links.FieldValue);if(w===null||_===null)throw new Error("Invalid rule");let g=this.project.getWorkspaceByCwd(w);p.push({workspace:g,fieldPath:_,fieldValue:v})}return le.miscUtils.sortMap(p,[({workspace:c})=>le.structUtils.stringifyIdent(c.locator),({fieldPath:c})=>c])}async*query(u){let p=this.createSession();for await(let c of p.makeQuery(u)){let w={};for(let[_,v]of Object.entries(c.links))_!=="_"&&(w[_]=ke(v));yield w}}};function de(r){return typeof r=="string"?`'${r}'`:"[]"}var He=class extends ni.BaseCommand{constructor(){super(...arguments);this.json=We.Option.Boolean("--json",!1,{description:"Format the output as an NDJSON stream"});this.query=We.Option.String()}async execute(){let u=await ur.Configuration.find(this.context.cwd,this.context.plugins),{project:p}=await ur.Project.find(u,this.context.cwd),c=await pe.find(p),w=this.query;return w.endsWith(".")||(w=`${w}.`),(await ii.StreamReport.start({configuration:u,json:this.json,stdout:this.context.stdout},async v=>{for await(let g of c.query(w)){let h=Array.from(Object.entries(g)),x=h.length,T=h.reduce((b,[C])=>Math.max(b,C.length),0);for(let b=0;b{let v=new Set,g=[];for(let h=0,x=this.fix?10:1;h{await h.persistManifest()}));for(let[h,x]of g)_.reportError(h,x)});return w.hasErrors()?w.exitCode():0}};Ye.paths=[["constraints"]],Ye.usage=fr.Command.Usage({category:"Constraints-related commands",description:"check that the project constraints are met",details:` + This command will run constraints on your project and emit errors for each one that is found but isn't met. If any error is emitted the process will exit with a non-zero exit code. + + If the \`--fix\` flag is used, Yarn will attempt to automatically fix the issues the best it can, following a multi-pass process (with a maximum of 10 iterations). Some ambiguous patterns cannot be autofixed, in which case you'll have to manually specify the right resolution. + + For more information as to how to write constraints, please consult our dedicated page on our website: https://yarnpkg.com/features/constraints. + `,examples:[["Check that all constraints are satisfied","yarn constraints"],["Autofix all unmet constraints","yarn constraints --fix"]]});var qi=Ye;async function Pu(r,u,p,{configuration:c,fix:w}){let _=new Map,v=new Map;for(let{workspace:g,dependencyIdent:h,dependencyRange:x,dependencyType:T}of p){let b=v.get(g);typeof b=="undefined"&&v.set(g,b=new Map);let C=b.get(h.identHash);typeof C=="undefined"&&b.set(h.identHash,C=new Map);let N=C.get(T);typeof N=="undefined"&&C.set(T,N=new Set),_.set(h.identHash,h),N.add(x)}for(let[g,h]of v)for(let[x,T]of h){let b=_.get(x);if(typeof b=="undefined")throw new Error("Assertion failed: The ident should have been registered");for(let[C,N]of T){let L=N.has(null)?[null]:[...N];if(L.length>2)u.push([se.MessageName.CONSTRAINTS_AMBIGUITY,`${$.structUtils.prettyWorkspace(c,g)} must depend on ${$.structUtils.prettyIdent(c,b)} via conflicting ranges ${L.slice(0,-1).map(ee=>$.structUtils.prettyRange(c,String(ee))).join(", ")}, and ${$.structUtils.prettyRange(c,String(L[L.length-1]))} (in ${C})`]);else if(L.length>1)u.push([se.MessageName.CONSTRAINTS_AMBIGUITY,`${$.structUtils.prettyWorkspace(c,g)} must depend on ${$.structUtils.prettyIdent(c,b)} via conflicting ranges ${$.structUtils.prettyRange(c,String(L[0]))} and ${$.structUtils.prettyRange(c,String(L[1]))} (in ${C})`]);else{let ee=g.manifest[C].get(b.identHash),[te]=L;te!==null?ee?ee.range!==te&&(w?(g.manifest[C].set(b.identHash,$.structUtils.makeDescriptor(b,te)),r.add(g)):u.push([se.MessageName.CONSTRAINTS_INCOMPATIBLE_DEPENDENCY,`${$.structUtils.prettyWorkspace(c,g)} must depend on ${$.structUtils.prettyIdent(c,b)} via ${$.structUtils.prettyRange(c,te)}, but uses ${$.structUtils.prettyRange(c,ee.range)} instead (in ${C})`])):w?(g.manifest[C].set(b.identHash,$.structUtils.makeDescriptor(b,te)),r.add(g)):u.push([se.MessageName.CONSTRAINTS_MISSING_DEPENDENCY,`${$.structUtils.prettyWorkspace(c,g)} must depend on ${$.structUtils.prettyIdent(c,b)} (via ${$.structUtils.prettyRange(c,te)}), but doesn't (in ${C})`]):ee&&(w?(g.manifest[C].delete(b.identHash),r.add(g)):u.push([se.MessageName.CONSTRAINTS_EXTRANEOUS_DEPENDENCY,`${$.structUtils.prettyWorkspace(c,g)} has an extraneous dependency on ${$.structUtils.prettyIdent(c,b)} (in ${C})`]))}}}}async function Cu(r,u,p,{configuration:c,fix:w}){let _=new Map;for(let{workspace:v,fieldPath:g,fieldValue:h}of p){let x=Pe.miscUtils.getMapWithDefault(_,v);Pe.miscUtils.getSetWithDefault(x,g).add(h)}for(let[v,g]of _)for(let[h,x]of g){let T=[...x];if(T.length>2)u.push([se.MessageName.CONSTRAINTS_AMBIGUITY,`${$.structUtils.prettyWorkspace(c,v)} must have a field ${$.formatUtils.pretty(c,h,"cyan")} set to conflicting values ${T.slice(0,-1).map(b=>$.formatUtils.pretty(c,String(b),"magenta")).join(", ")}, or ${$.formatUtils.pretty(c,String(T[T.length-1]),"magenta")}`]);else if(T.length>1)u.push([se.MessageName.CONSTRAINTS_AMBIGUITY,`${$.structUtils.prettyWorkspace(c,v)} must have a field ${$.formatUtils.pretty(c,h,"cyan")} set to conflicting values ${$.formatUtils.pretty(c,String(T[0]),"magenta")} or ${$.formatUtils.pretty(c,String(T[1]),"magenta")}`]);else{let b=(0,Ni.default)(v.manifest.raw,h),[C]=T;C!==null?b===void 0?w?(await qr(v,h,C),r.add(v)):u.push([se.MessageName.CONSTRAINTS_MISSING_FIELD,`${$.structUtils.prettyWorkspace(c,v)} must have a field ${$.formatUtils.pretty(c,h,"cyan")} set to ${$.formatUtils.pretty(c,String(C),"magenta")}, but doesn't`]):JSON.stringify(b)!==C&&(w?(await qr(v,h,C),r.add(v)):u.push([se.MessageName.CONSTRAINTS_INCOMPATIBLE_FIELD,`${$.structUtils.prettyWorkspace(c,v)} must have a field ${$.formatUtils.pretty(c,h,"cyan")} set to ${$.formatUtils.pretty(c,String(C),"magenta")}, but is set to ${$.formatUtils.pretty(c,JSON.stringify(b),"magenta")} instead`])):b!=null&&(w?(await qr(v,h,null),r.add(v)):u.push([se.MessageName.CONSTRAINTS_EXTRANEOUS_FIELD,`${$.structUtils.prettyWorkspace(c,v)} has an extraneous field ${$.formatUtils.pretty(c,h,"cyan")} set to ${$.formatUtils.pretty(c,JSON.stringify(b),"magenta")}`]))}}}async function qr(r,u,p){p===null?(0,Mi.default)(r.manifest.raw,u):(0,Ri.default)(r.manifest.raw,u,JSON.parse(p))}var Iu={configuration:{constraintsPath:{description:"The path of the constraints file.",type:$i.SettingsType.ABSOLUTE_PATH,default:"./constraints.pro"}},commands:[si,oi,qi]},Eu=Iu;return Ou;})(); +return plugin; +} +}; diff --git a/.yarnrc.yml b/.yarnrc.yml index 0a626997..96955fc9 100644 --- a/.yarnrc.yml +++ b/.yarnrc.yml @@ -32,5 +32,7 @@ plugins: spec: "@yarnpkg/plugin-workspace-tools" - path: .yarn/plugins/@yarnpkg/plugin-version.cjs spec: "@yarnpkg/plugin-version" + - path: .yarn/plugins/@yarnpkg/plugin-constraints.cjs + spec: "@yarnpkg/plugin-constraints" yarnPath: .yarn/releases/yarn-3.6.4.cjs diff --git a/README.md b/README.md index 8891a52c..f4bd09b6 100644 --- a/README.md +++ b/README.md @@ -2,9 +2,11 @@ Monorepo for Apollo3 development -| Package | Description | -| ---------------------------------------------------------------------- | ---------------------------------------- | -| [apollo-collaboration-server](./packages/apollo-collaboration-server/) | Server-side code | -| [apollo-schemas](./packages/apollo-schemas/) | MongoDB schemas | -| [apollo-shared](./packages/apollo-shared/) | Code shared between server and client | -| [jbrowse-plugin-apollo](./packages/jbrowse-plugin-apollo/) | Client-side code (as a JBrowse 2 plugin) | +| Package | Description | +| ---------------------------------------------------------------------- | ---------------------------------------------------------- | +| [apollo-collaboration-server](./packages/apollo-collaboration-server/) | Server-side code | +| [apollo-common](./packages/apollo-common/) | Public base classes for developers creating Apollo plugins | +| [apollo-mst](./packages/apollo-mst/) | mobx-state-tree models | +| [apollo-schemas](./packages/apollo-schemas/) | MongoDB schemas | +| [apollo-shared](./packages/apollo-shared/) | Internal code shared between server and client | +| [jbrowse-plugin-apollo](./packages/jbrowse-plugin-apollo/) | Client-side code (as a JBrowse 2 plugin) | diff --git a/constraints.pro b/constraints.pro new file mode 100644 index 00000000..fbd0b210 --- /dev/null +++ b/constraints.pro @@ -0,0 +1,9 @@ +%gen_enforced_dependency(WorkspaceCwd, '@jbrowse/core', '^2.6.3', _) :- +% workspace_has_dependency(WorkspaceCwd, '@jbrowse/core', _, _). +%gen_enforced_dependency(WorkspaceCwd, 'typescript', '^5.1.6', devDependencies) :- +% workspace_has_dependency(WorkspaceCwd, 'typescript', _, devDependencies). + +gen_enforced_dependency(WorkspaceCwd, DependencyIdent, DependencyRange2, DependencyType) :- + workspace_has_dependency(WorkspaceCwd, DependencyIdent, DependencyRange, DependencyType), + workspace_has_dependency(OtherWorkspaceCwd, DependencyIdent, DependencyRange2, DependencyType2), + DependencyRange \= DependencyRange2. diff --git a/package.json b/package.json index 6e674cdb..bb9a3e3c 100644 --- a/package.json +++ b/package.json @@ -30,13 +30,14 @@ "eslint-plugin-sort-destructure-keys": "^1.5.0", "eslint-plugin-tsdoc": "^0.2.17", "eslint-plugin-unicorn": "^48.0.0", + "husky": "^8.0.3", "import-sort-parser-typescript": "^6.0.0", "import-sort-style-module": "^6.0.0", - "jest": "^29.6.1", + "jest": "^29.6.2", "npm-run-all": "^4.1.5", "prettier": "^3.0.0", "prettier-plugin-import-sort": "^0.0.7", - "react": "^17.0.2", + "react": "^18.2.0", "typescript": "^5.1.6" }, "private": true diff --git a/packages/apollo-collaboration-server/package.json b/packages/apollo-collaboration-server/package.json index 03805f4a..10610d93 100644 --- a/packages/apollo-collaboration-server/package.json +++ b/packages/apollo-collaboration-server/package.json @@ -28,7 +28,7 @@ "@emotion/styled": "^11.10.6", "@gmod/gff": "^1.2.0", "@gmod/indexedfasta": "^2.0.4", - "@jbrowse/core": "^2.3.4", + "@jbrowse/core": "2.6.3", "@mui/base": "^5.0.0-alpha.118", "@mui/material": "^5.11.10", "@nestjs/common": "^10.1.0", @@ -55,7 +55,7 @@ "mobx": "^6.6.1", "mobx-react": "^7.2.1", "mobx-state-tree": "^5.1.7", - "mongoose": "^6.2.6", + "mongoose": "^6.12.0", "mongoose-id-validator": "^0.6.0", "multer": "^1.4.4", "node-fetch": "^2.6.7", @@ -65,7 +65,7 @@ "passport-local": "^1.0.0", "passport-microsoft": "^1.0.0", "pm2": "^5.3.0", - "prop-types": "^15.0.0", + "prop-types": "^15.8.1", "react": "^18.2.0", "react-dom": "^18.2.0", "reflect-metadata": "^0.1.13", @@ -84,7 +84,7 @@ "@types/express-session": "^1", "@types/jest": "^27.0.1", "@types/multer": "^1.4.7", - "@types/node": "^18.11.9", + "@types/node": "^18.14.2", "@types/node-fetch": "^2.6.2", "@types/passport-google-oauth20": "^2.0.11", "@types/passport-jwt": "^3.0.6", @@ -93,9 +93,9 @@ "@types/react": "^17.0.34", "@types/supertest": "^2.0.11", "apollo-mst": "workspace:^", - "jest": "^27.0.6", + "jest": "^29.6.2", "mongodb": "^4.7.0", - "prettier": "^2.3.2", + "prettier": "^3.0.0", "rimraf": "^3.0.2", "source-map-support": "^0.5.20", "supertest": "^6.1.3", diff --git a/packages/apollo-common/package.json b/packages/apollo-common/package.json index 6eaf86b1..37745032 100644 --- a/packages/apollo-common/package.json +++ b/packages/apollo-common/package.json @@ -11,30 +11,30 @@ "build": "tsc" }, "dependencies": { - "@gmod/gff": "^1.3.0", - "@jbrowse/core": "^2.3.4", + "@gmod/gff": "^1.2.0", + "@jbrowse/core": "2.6.3", "apollo-schemas": "workspace:^", "bson-objectid": "^2.0.4", "tslib": "^2.3.1" }, "peerDependencies": { - "@mui/material": "^5.0.0", - "@mui/x-data-grid": "^5.0.0", - "mobx": "^6.0.0", - "mobx-react": "^7.0.0", - "mobx-state-tree": "^5.0.0", - "prop-types": "^15.0.0", - "react": ">=16.8.0", - "react-dom": ">=16.8.0", - "rxjs": "^7.0.0", - "tss-react": "^4.0.0" + "@mui/material": "^5.11.10", + "@mui/x-data-grid": "^6.0.1", + "mobx": "^6.6.1", + "mobx-react": "^7.2.1", + "mobx-state-tree": "^5.1.7", + "prop-types": "^15.8.1", + "react": "^18.2.0", + "react-dom": "^18.2.0", + "rxjs": "^7.4.0", + "tss-react": "^4.6.1" }, "devDependencies": { "@nestjs/common": "^10.1.0", "@nestjs/core": "^10.1.0", "@types/node": "^18.14.2", "apollo-mst": "workspace:^", - "mongoose": "^7.0.0", + "mongoose": "^6.12.0", "typescript": "^5.1.6" }, "private": true diff --git a/packages/apollo-mst/package.json b/packages/apollo-mst/package.json index bdea5a7b..9304bbd1 100644 --- a/packages/apollo-mst/package.json +++ b/packages/apollo-mst/package.json @@ -6,10 +6,10 @@ "build": "tsc" }, "dependencies": { - "@jbrowse/core": "^2.3.4", + "@jbrowse/core": "2.6.3", "mobx": "^6.6.1", - "mobx-state-tree": "^5.1.5", - "rxjs": "^6.0.0", + "mobx-state-tree": "^5.1.7", + "rxjs": "^7.4.0", "tslib": "^2.3.1" }, "devDependencies": { diff --git a/packages/apollo-schemas/package.json b/packages/apollo-schemas/package.json index 870770de..e9c7d788 100644 --- a/packages/apollo-schemas/package.json +++ b/packages/apollo-schemas/package.json @@ -9,14 +9,14 @@ "@nestjs/common": "^10.1.0", "@nestjs/core": "^10.1.0", "@nestjs/mongoose": "^10.0.0", - "mongoose": "^6.2.6", + "mongoose": "^6.12.0", "reflect-metadata": "^0.1.13", "regenerator-runtime": "^0.13.9", "rxjs": "^7.4.0", "tslib": "^2.3.1" }, "devDependencies": { - "@types/node": "^18.11.9", + "@types/node": "^18.14.2", "apollo-mst": "workspace:^", "typescript": "^5.1.6" }, diff --git a/packages/apollo-shared/package.json b/packages/apollo-shared/package.json index 55edcc3e..7fc74c34 100644 --- a/packages/apollo-shared/package.json +++ b/packages/apollo-shared/package.json @@ -10,11 +10,11 @@ "dependencies": { "@gmod/gff": "^1.2.0", "@gmod/indexedfasta": "^2.0.4", - "@jbrowse/core": "^2.3.4", + "@jbrowse/core": "2.6.3", "apollo-common": "workspace:^", "apollo-mst": "workspace:^", "apollo-schemas": "workspace:^", - "bson-objectid": "^2.0.3", + "bson-objectid": "^2.0.4", "generic-filehandle": "^3.0.0", "jwt-decode": "^3.1.2", "regenerator-runtime": "^0.13.9", @@ -24,24 +24,24 @@ "devDependencies": { "@nestjs/common": "^10.1.0", "@nestjs/core": "^10.1.0", - "@types/node": "^18.11.9", + "@types/node": "^18.14.2", "@types/rimraf": "^3", "mobx": "^6.6.1", - "mobx-state-tree": "^5.1.5", - "mongoose": "^6.2.10", + "mobx-state-tree": "^5.1.7", + "mongoose": "^6.12.0", "rimraf": "^3.0.2", "typescript": "^5.1.6" }, "peerDependencies": { - "@mui/material": "^5.9.1", - "@mui/x-data-grid": "^4.0.0", + "@mui/material": "^5.11.10", + "@mui/x-data-grid": "^6.0.1", "mobx": "^6.6.1", "mobx-react": "^7.2.1", - "mobx-state-tree": "^5.1.5", - "prop-types": "^15.0.0", - "react": "^17.0.0", - "react-dom": "^17.0.0", - "rxjs": "^6.0.0" + "mobx-state-tree": "^5.1.7", + "prop-types": "^15.8.1", + "react": "^18.2.0", + "react-dom": "^18.2.0", + "rxjs": "^7.4.0" }, "private": true } diff --git a/packages/jbrowse-plugin-apollo/package.json b/packages/jbrowse-plugin-apollo/package.json index 99e49cd3..aa2116d5 100644 --- a/packages/jbrowse-plugin-apollo/package.json +++ b/packages/jbrowse-plugin-apollo/package.json @@ -51,8 +51,8 @@ "name": "Apollo" }, "dependencies": { - "@emotion/react": "^11.9.3", - "@emotion/styled": "^11.9.3", + "@emotion/react": "^11.10.6", + "@emotion/styled": "^11.10.6", "@gmod/gff": "^1.2.0", "@jbrowse/plugin-authentication": "^2.0.1", "@jbrowse/plugin-linear-genome-view": "^2.0.1", @@ -62,7 +62,7 @@ "apollo-mst": "workspace:^", "apollo-shared": "workspace:^", "autosuggest-highlight": "^3.3.4", - "bson-objectid": "^2.0.3", + "bson-objectid": "^2.0.4", "clsx": "^1.1.1", "fast-deep-equal": "^3.1.3", "file-saver": "^2.0.5", @@ -71,32 +71,31 @@ "jsonpath": "^1.1.1", "nanoid": "^4.0.2", "regenerator-runtime": "^0.13.9", - "socket.io-client": "^4.5.3", - "tslib": "^2.0.3" + "socket.io-client": "^4.5.4", + "tslib": "^2.3.1" }, "peerDependencies": { - "@jbrowse/core": "^2.6.2", - "@mui/material": "^5.9.1", + "@jbrowse/core": "2.6.3", + "@mui/material": "^5.11.10", "mobx": "^6.6.1", "mobx-react": "^7.2.1", - "mobx-state-tree": "^5.1.5", + "mobx-state-tree": "^5.1.7", "prop-types": "^15.8.1", "react": "^18.2.0", "react-dom": "^18.2.0", - "rxjs": "^6.5.2", - "tss-react": "^3.7.1" + "rxjs": "^7.4.0", + "tss-react": "^4.6.1" }, "devDependencies": { "@jbrowse/cli": "^2.6.2", - "@jbrowse/core": "^2.6.2", + "@jbrowse/core": "2.6.3", "@jbrowse/development-tools": "^2.1.1", "@jest/globals": "^29.0.3", - "@mui/material": "^5.9.1", + "@mui/material": "^5.11.10", "@mui/x-data-grid": "^6.0.1", "@types/autosuggest-highlight": "^3", - "@types/cypress": "^1.1.3", "@types/file-saver": "^2", - "@types/node": "^18.11.9", + "@types/node": "^18.14.2", "@types/prop-types": "^15", "@types/react": "^17.0.34", "@types/react-dom": "^18", @@ -107,20 +106,20 @@ "jest-fetch-mock": "^3.0.3", "mobx": "^6.6.1", "mobx-react": "^7.2.1", - "mobx-state-tree": "^5.1.5", - "npm-run-all": "4.1.5", + "mobx-state-tree": "^5.1.7", + "npm-run-all": "^4.1.5", "prop-types": "^15.8.1", "react": "^18.2.0", "react-dom": "^18.2.0", "rimraf": "^3.0.2", "rollup": "^2.59.0", - "rxjs": "^6.5.2", + "rxjs": "^7.4.0", "serve": "^14.0.1", "shx": "^0.3.3", "start-server-and-test": "^1.11.7", "ts-jest": "^29.1.1", "ts-node": "^10.3.0", - 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languageName: node - linkType: hard - "cypress@npm:^12.17.2": version: 12.17.2 resolution: "cypress@npm:12.17.2" @@ -9154,17 +8345,6 @@ __metadata: languageName: node linkType: hard -"data-urls@npm:^2.0.0": - version: 2.0.0 - resolution: "data-urls@npm:2.0.0" - dependencies: - abab: ^2.0.3 - whatwg-mimetype: ^2.3.0 - whatwg-url: ^8.0.0 - checksum: 97caf828aac25e25e04ba6869db0f99c75e6859bb5b424ada28d3e7841941ebf08ddff3c1b1bb4585986bd507a5d54c2a716853ea6cb98af877400e637393e71 - languageName: node - linkType: hard - "dayjs@npm:^1.10.4": version: 1.11.4 resolution: "dayjs@npm:1.11.4" @@ -9186,13 +8366,6 @@ __metadata: languageName: node linkType: hard -"debounce@npm:^1.2.1": - version: 1.2.1 - resolution: "debounce@npm:1.2.1" - checksum: 682a89506d9e54fb109526f4da255c5546102fbb8e3ae75eef3b04effaf5d4853756aee97475cd4650641869794e44f410eeb20ace2b18ea592287ab2038519e - languageName: node - linkType: hard - "debug@npm:2.6.9": version: 2.6.9 resolution: "debug@npm:2.6.9" @@ -9235,13 +8408,6 @@ __metadata: languageName: node linkType: hard -"decimal.js@npm:^10.2.1": - 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languageName: node - linkType: hard - "depd@npm:2.0.0, depd@npm:~2.0.0": version: 2.0.0 resolution: "depd@npm:2.0.0" @@ -9615,15 +8767,6 @@ __metadata: languageName: node linkType: hard -"domexception@npm:^2.0.1": - version: 2.0.1 - resolution: "domexception@npm:2.0.1" - dependencies: - webidl-conversions: ^5.0.0 - checksum: d638e9cb05c52999f1b2eb87c374b03311ea5b1d69c2f875bc92da73e17db60c12142b45c950228642ff7f845c536b65305483350d080df59003a653da80b691 - languageName: node - linkType: hard - "dompurify@npm:^3.0.0": version: 3.0.0 resolution: "dompurify@npm:3.0.0" @@ -9732,13 +8875,6 @@ __metadata: languageName: node linkType: hard -"emittery@npm:^0.8.1": - version: 0.8.1 - resolution: "emittery@npm:0.8.1" - checksum: 2457e8c7b0688bb006126f2c025b2655abe682f66b184954122a8a065b5277f9813d49d627896a10b076b81c513ec5f491fd9c14fbd42c04b95ca3c9f3c365ee - languageName: node - linkType: hard - "emoji-regex@npm:^8.0.0": version: 8.0.0 resolution: "emoji-regex@npm:8.0.0" @@ -10088,25 +9224,6 @@ __metadata: languageName: node linkType: hard -"escodegen@npm:^2.0.0": - 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