From 65b16bff1e8cd07a3d20ed932f4a91cd52acfe3b Mon Sep 17 00:00:00 2001 From: Garrett Stevens Date: Thu, 14 Nov 2024 20:40:14 +0000 Subject: [PATCH 01/12] Use depcheck to remove unused dependencies --- package.json | 5 - packages/apollo-common/package.json | 1 - packages/apollo-schemas/package.json | 1 - packages/apollo-shared/package.json | 3 - packages/jbrowse-plugin-apollo/package.json | 1 - yarn.lock | 179 +------------------- 6 files changed, 3 insertions(+), 187 deletions(-) diff --git a/package.json b/package.json index 52eedd208..21817a42b 100644 --- a/package.json +++ b/package.json @@ -30,7 +30,6 @@ "eslint-import-resolver-typescript": "^3.5.5", "eslint-plugin-cypress": "^2.13.3", "eslint-plugin-import": "^2.27.5", - "eslint-plugin-jest": "^27.2.3", "eslint-plugin-jsx-a11y": "^6.7.1", "eslint-plugin-react": "^7.32.2", "eslint-plugin-react-hooks": "^4.6.0", @@ -38,14 +37,10 @@ "eslint-plugin-tsdoc": "^0.2.17", "eslint-plugin-unicorn": "^48.0.0", "husky": "^9.0.11", - "import-sort-parser-typescript": "^6.0.0", - "import-sort-style-module": "^6.0.0", - "jest": "^29.6.2", "lint-staged": "^15.2.2", "npm-run-all": "^4.1.5", "prettier": "^3.3.2", "prettier-plugin-packagejson": "^2.5.2", - "react": "^18.2.0", "semver": "^7.6.3", "tslib": "^2.3.1", "tsx": "^4.6.2", diff --git a/packages/apollo-common/package.json b/packages/apollo-common/package.json index 3b1f9dd62..1b592a1a9 100644 --- a/packages/apollo-common/package.json +++ b/packages/apollo-common/package.json @@ -12,7 +12,6 @@ }, "dependencies": { "@apollo-annotation/schemas": "workspace:^", - "@gmod/gff": "1.2.0", "@jbrowse/core": "^2.13.1", "bson-objectid": "^2.0.4", "tslib": "^2.3.1" diff --git a/packages/apollo-schemas/package.json b/packages/apollo-schemas/package.json index 9681352b5..1bce71c8d 100644 --- a/packages/apollo-schemas/package.json +++ b/packages/apollo-schemas/package.json @@ -11,7 +11,6 @@ "@nestjs/mongoose": "^10.0.0", "mongoose": "^6.12.0", "reflect-metadata": "^0.1.13", - "regenerator-runtime": "^0.13.9", "rxjs": "^7.4.0", "tslib": "^2.3.1" }, diff --git a/packages/apollo-shared/package.json b/packages/apollo-shared/package.json index 22f74de40..0b1f3ba96 100644 --- a/packages/apollo-shared/package.json +++ b/packages/apollo-shared/package.json @@ -19,8 +19,6 @@ "bson-objectid": "^2.0.4", "generic-filehandle": "^3.0.0", "jwt-decode": "^3.1.2", - "regenerator-runtime": "^0.13.9", - "socket.io-client": "^4.5.4", "tslib": "^2.3.1" }, "devDependencies": { @@ -28,7 +26,6 @@ "@nestjs/core": "^10.1.0", "@types/chai": "^4.3.19", "@types/node": "^18.14.2", - "@types/rimraf": "^3", "chai": "^5.1.1", "chai-exclude": "^3.0.0", "glob": "^11.0.0", diff --git a/packages/jbrowse-plugin-apollo/package.json b/packages/jbrowse-plugin-apollo/package.json index b848dddf2..be858503a 100644 --- a/packages/jbrowse-plugin-apollo/package.json +++ b/packages/jbrowse-plugin-apollo/package.json @@ -67,7 +67,6 @@ "idb": "^7.1.1", "jsonpath": "^1.1.1", "nanoid": "^4.0.2", - "regenerator-runtime": "^0.13.9", "socket.io-client": "^4.5.4", "tslib": "^2.3.1" }, diff --git a/yarn.lock b/yarn.lock index ae9e89930..45069aa01 100644 --- a/yarn.lock +++ b/yarn.lock @@ -450,7 +450,6 @@ __metadata: dependencies: "@apollo-annotation/mst": "workspace:^" "@apollo-annotation/schemas": "workspace:^" - "@gmod/gff": "npm:1.2.0" "@jbrowse/core": "npm:^2.13.1" "@nestjs/common": "npm:^10.1.0" "@nestjs/core": "npm:^10.1.0" @@ -522,7 +521,6 @@ __metadata: prop-types: "npm:^15.8.1" react: "npm:^18.2.0" react-dom: "npm:^18.2.0" - regenerator-runtime: "npm:^0.13.9" rimraf: "npm:^3.0.2" rollup: "npm:^2.59.0" rxjs: "npm:^7.4.0" @@ -574,7 +572,6 @@ __metadata: "@types/node": "npm:^18.14.2" mongoose: "npm:^6.12.0" reflect-metadata: "npm:^0.1.13" - regenerator-runtime: "npm:^0.13.9" rxjs: "npm:^7.4.0" tslib: "npm:^2.3.1" typescript: "npm:^5.5.3" @@ -595,7 +592,6 @@ __metadata: "@nestjs/core": "npm:^10.1.0" "@types/chai": "npm:^4.3.19" "@types/node": "npm:^18.14.2" - "@types/rimraf": "npm:^3" bson-objectid: "npm:^2.0.4" chai: "npm:^5.1.1" chai-exclude: "npm:^3.0.0" @@ -606,10 +602,8 @@ __metadata: mobx-state-tree: "npm:^5.1.7" mongoose: "npm:^6.12.0" react-dom: "npm:^18.2.0" - regenerator-runtime: "npm:^0.13.9" rimraf: "npm:^3.0.2" rxjs: "npm:^7.4.0" - socket.io-client: "npm:^4.5.4" tslib: "npm:^2.3.1" tsx: "npm:^4.6.2" typescript: "npm:^5.5.3" @@ -9536,16 +9530,6 @@ __metadata: languageName: node linkType: hard -"@types/glob@npm:*": - version: 8.1.0 - resolution: "@types/glob@npm:8.1.0" - dependencies: - "@types/minimatch": "npm:^5.1.2" - "@types/node": "npm:*" - checksum: 10c0/ded07aa0d7a1caf3c47b85e262be82989ccd7933b4a14712b79c82fd45a239249811d9fc3a135b3e9457afa163e74a297033d7245b0dc63cd3d032f3906b053f - languageName: node - linkType: hard - "@types/graceful-fs@npm:^4.1.3": version: 4.1.7 resolution: "@types/graceful-fs@npm:4.1.7" @@ -9752,13 +9736,6 @@ __metadata: languageName: node linkType: hard -"@types/minimatch@npm:^5.1.2": - version: 5.1.2 - resolution: "@types/minimatch@npm:5.1.2" - checksum: 10c0/83cf1c11748891b714e129de0585af4c55dd4c2cafb1f1d5233d79246e5e1e19d1b5ad9e8db449667b3ffa2b6c80125c429dbee1054e9efb45758dbc4e118562 - languageName: node - linkType: hard - "@types/mocha@npm:^10": version: 10.0.6 resolution: "@types/mocha@npm:10.0.6" @@ -10098,16 +10075,6 @@ __metadata: languageName: node linkType: hard -"@types/rimraf@npm:^3": - version: 3.0.2 - resolution: "@types/rimraf@npm:3.0.2" - dependencies: - "@types/glob": "npm:*" - "@types/node": "npm:*" - checksum: 10c0/08beaf5d5ac6d6ecb76df74e3f873453feab079b5993f7cdd00bf2789bc2dea6917d5d24e75a5346fe201f396fa8a6eccb1291f97695997e34733f9663228a86 - languageName: node - linkType: hard - "@types/sax@npm:^1.2.1": version: 1.2.7 resolution: "@types/sax@npm:1.2.7" @@ -10131,7 +10098,7 @@ __metadata: languageName: node linkType: hard -"@types/semver@npm:^7.3.12, @types/semver@npm:^7.5.0": +"@types/semver@npm:^7.5.0": version: 7.5.3 resolution: "@types/semver@npm:7.5.3" checksum: 10c0/1dedcf5f50a5a345e817fdf1273a14d0c57de80eb1d47bf3f17563062be53a2c99b78755a8c88c794a03757f9cd05da61b2849bf109e1b71e30fca895529c2b0 @@ -10399,16 +10366,6 @@ __metadata: languageName: node linkType: hard -"@typescript-eslint/scope-manager@npm:5.62.0": - version: 5.62.0 - resolution: "@typescript-eslint/scope-manager@npm:5.62.0" - dependencies: - "@typescript-eslint/types": "npm:5.62.0" - "@typescript-eslint/visitor-keys": "npm:5.62.0" - checksum: 10c0/861253235576c1c5c1772d23cdce1418c2da2618a479a7de4f6114a12a7ca853011a1e530525d0931c355a8fd237b9cd828fac560f85f9623e24054fd024726f - languageName: node - linkType: hard - "@typescript-eslint/scope-manager@npm:6.14.0": version: 6.14.0 resolution: "@typescript-eslint/scope-manager@npm:6.14.0" @@ -10446,13 +10403,6 @@ __metadata: languageName: node linkType: hard -"@typescript-eslint/types@npm:5.62.0": - version: 5.62.0 - resolution: "@typescript-eslint/types@npm:5.62.0" - checksum: 10c0/7febd3a7f0701c0b927e094f02e82d8ee2cada2b186fcb938bc2b94ff6fbad88237afc304cbaf33e82797078bbbb1baf91475f6400912f8b64c89be79bfa4ddf - languageName: node - linkType: hard - "@typescript-eslint/types@npm:6.14.0": version: 6.14.0 resolution: "@typescript-eslint/types@npm:6.14.0" @@ -10467,24 +10417,6 @@ __metadata: languageName: node linkType: hard -"@typescript-eslint/typescript-estree@npm:5.62.0": - version: 5.62.0 - resolution: "@typescript-eslint/typescript-estree@npm:5.62.0" - dependencies: - "@typescript-eslint/types": "npm:5.62.0" - "@typescript-eslint/visitor-keys": "npm:5.62.0" - debug: "npm:^4.3.4" - globby: "npm:^11.1.0" - is-glob: "npm:^4.0.3" - semver: "npm:^7.3.7" - tsutils: "npm:^3.21.0" - peerDependenciesMeta: - typescript: - optional: true - checksum: 10c0/d7984a3e9d56897b2481940ec803cb8e7ead03df8d9cfd9797350be82ff765dfcf3cfec04e7355e1779e948da8f02bc5e11719d07a596eb1cb995c48a95e38cf - languageName: node - linkType: hard - "@typescript-eslint/typescript-estree@npm:6.14.0": version: 6.14.0 resolution: "@typescript-eslint/typescript-estree@npm:6.14.0" @@ -10536,24 +10468,6 @@ __metadata: languageName: node linkType: hard -"@typescript-eslint/utils@npm:^5.10.0": - version: 5.62.0 - resolution: "@typescript-eslint/utils@npm:5.62.0" - dependencies: - "@eslint-community/eslint-utils": "npm:^4.2.0" - "@types/json-schema": "npm:^7.0.9" - "@types/semver": "npm:^7.3.12" - "@typescript-eslint/scope-manager": "npm:5.62.0" - "@typescript-eslint/types": "npm:5.62.0" - "@typescript-eslint/typescript-estree": "npm:5.62.0" - eslint-scope: "npm:^5.1.1" - semver: "npm:^7.3.7" - peerDependencies: - eslint: ^6.0.0 || ^7.0.0 || ^8.0.0 - checksum: 10c0/f09b7d9952e4a205eb1ced31d7684dd55cee40bf8c2d78e923aa8a255318d97279825733902742c09d8690f37a50243f4c4d383ab16bd7aefaf9c4b438f785e1 - languageName: node - linkType: hard - "@typescript-eslint/utils@npm:^6.13.0": version: 6.14.0 resolution: "@typescript-eslint/utils@npm:6.14.0" @@ -10571,16 +10485,6 @@ __metadata: languageName: node linkType: hard -"@typescript-eslint/visitor-keys@npm:5.62.0": - version: 5.62.0 - resolution: "@typescript-eslint/visitor-keys@npm:5.62.0" - dependencies: - "@typescript-eslint/types": "npm:5.62.0" - eslint-visitor-keys: "npm:^3.3.0" - checksum: 10c0/7c3b8e4148e9b94d9b7162a596a1260d7a3efc4e65199693b8025c71c4652b8042501c0bc9f57654c1e2943c26da98c0f77884a746c6ae81389fcb0b513d995d - languageName: node - linkType: hard - "@typescript-eslint/visitor-keys@npm:6.14.0": version: 6.14.0 resolution: "@typescript-eslint/visitor-keys@npm:6.14.0" @@ -11288,7 +11192,6 @@ __metadata: eslint-import-resolver-typescript: "npm:^3.5.5" eslint-plugin-cypress: "npm:^2.13.3" eslint-plugin-import: "npm:^2.27.5" - eslint-plugin-jest: "npm:^27.2.3" eslint-plugin-jsx-a11y: "npm:^6.7.1" eslint-plugin-react: "npm:^7.32.2" eslint-plugin-react-hooks: "npm:^4.6.0" @@ -11296,14 +11199,10 @@ __metadata: eslint-plugin-tsdoc: "npm:^0.2.17" eslint-plugin-unicorn: "npm:^48.0.0" husky: "npm:^9.0.11" - import-sort-parser-typescript: "npm:^6.0.0" - import-sort-style-module: "npm:^6.0.0" - jest: "npm:^29.6.2" lint-staged: "npm:^15.2.2" npm-run-all: "npm:^4.1.5" prettier: "npm:^3.3.2" prettier-plugin-packagejson: "npm:^2.5.2" - react: "npm:^18.2.0" semver: "npm:^7.6.3" tslib: "npm:^2.3.1" tsx: "npm:^4.6.2" @@ -15952,24 +15851,6 @@ __metadata: languageName: node linkType: hard -"eslint-plugin-jest@npm:^27.2.3": - version: 27.4.2 - resolution: "eslint-plugin-jest@npm:27.4.2" - dependencies: - "@typescript-eslint/utils": "npm:^5.10.0" - peerDependencies: - "@typescript-eslint/eslint-plugin": ^5.0.0 || ^6.0.0 - eslint: ^7.0.0 || ^8.0.0 - jest: "*" - peerDependenciesMeta: - "@typescript-eslint/eslint-plugin": - optional: true - jest: - optional: true - checksum: 10c0/5a69e3b1bc0efdf3f826a8b7b686942e06476027cb7884559ae713edd259d01a6f31c6e7728806866e5073f2cb62b66360bf91f6efc5481fc95407c084586edb - languageName: node - linkType: hard - "eslint-plugin-jsx-a11y@npm:^6.7.1": version: 6.7.1 resolution: "eslint-plugin-jsx-a11y@npm:6.7.1" @@ -16103,7 +15984,7 @@ __metadata: languageName: node linkType: hard -"eslint-scope@npm:5.1.1, eslint-scope@npm:^5.1.1": +"eslint-scope@npm:5.1.1": version: 5.1.1 resolution: "eslint-scope@npm:5.1.1" dependencies: @@ -18761,22 +18642,6 @@ __metadata: languageName: node linkType: hard -"import-sort-parser-typescript@npm:^6.0.0": - version: 6.0.0 - resolution: "import-sort-parser-typescript@npm:6.0.0" - dependencies: - typescript: "npm:^3.2.4" - checksum: 10c0/e50b30b072b5291981e3b96a85c1b503f196269ebe2542ea9461d140e6cf1bf2a9f7a66ffd6b3745f3af9dabc5e80bb59d300395eb49c086eae5907687dfe18a - languageName: node - linkType: hard - -"import-sort-style-module@npm:^6.0.0": - version: 6.0.0 - resolution: "import-sort-style-module@npm:6.0.0" - checksum: 10c0/13b5854f0bf2aa2c677977a4f7cbf4fff6f7c30d65c674020c7a7cfe158add503c3cb67daf3e938eb3735dc86ffe59ec0e4913d6e939dd1904668e62a5438382 - languageName: node - linkType: hard - "imurmurhash@npm:^0.1.4": version: 0.1.4 resolution: "imurmurhash@npm:0.1.4" @@ -26311,13 +26176,6 @@ __metadata: languageName: node linkType: hard -"regenerator-runtime@npm:^0.13.9": - version: 0.13.11 - resolution: "regenerator-runtime@npm:0.13.11" - checksum: 10c0/12b069dc774001fbb0014f6a28f11c09ebfe3c0d984d88c9bced77fdb6fedbacbca434d24da9ae9371bfbf23f754869307fb51a4c98a8b8b18e5ef748677ca24 - languageName: node - linkType: hard - "regenerator-runtime@npm:^0.14.0": version: 0.14.0 resolution: "regenerator-runtime@npm:0.14.0" @@ -29223,7 +29081,7 @@ __metadata: languageName: node linkType: hard -"tslib@npm:^1.11.1, tslib@npm:^1.8.1": +"tslib@npm:^1.11.1": version: 1.14.1 resolution: "tslib@npm:1.14.1" checksum: 10c0/69ae09c49eea644bc5ebe1bca4fa4cc2c82b7b3e02f43b84bd891504edf66dbc6b2ec0eef31a957042de2269139e4acff911e6d186a258fb14069cd7f6febce2 @@ -29258,17 +29116,6 @@ __metadata: languageName: node linkType: hard -"tsutils@npm:^3.21.0": - version: 3.21.0 - resolution: "tsutils@npm:3.21.0" - dependencies: - tslib: "npm:^1.8.1" - peerDependencies: - typescript: ">=2.8.0 || >= 3.2.0-dev || >= 3.3.0-dev || >= 3.4.0-dev || >= 3.5.0-dev || >= 3.6.0-dev || >= 3.6.0-beta || >= 3.7.0-dev || >= 3.7.0-beta" - checksum: 10c0/02f19e458ec78ead8fffbf711f834ad8ecd2cc6ade4ec0320790713dccc0a412b99e7fd907c4cda2a1dc602c75db6f12e0108e87a5afad4b2f9e90a24cabd5a2 - languageName: node - linkType: hard - "tsx@npm:^4.6.2": version: 4.6.2 resolution: "tsx@npm:4.6.2" @@ -29476,16 +29323,6 @@ __metadata: languageName: node linkType: hard -"typescript@npm:^3.2.4": - version: 3.9.10 - resolution: "typescript@npm:3.9.10" - bin: - tsc: bin/tsc - tsserver: bin/tsserver - checksum: 10c0/863cc06070fa18a0f9c6a83265fb4922a8b51bf6f2c6760fb0b73865305ce617ea4bc6477381f9f4b7c3a8cb4a455b054f5469e6e41307733fe6a2bd9aae82f8 - languageName: node - linkType: hard - "typescript@npm:^5.5.3": version: 5.5.3 resolution: "typescript@npm:5.5.3" @@ -29506,16 +29343,6 @@ __metadata: languageName: node linkType: hard -"typescript@patch:typescript@npm%3A^3.2.4#optional!builtin": - version: 3.9.10 - resolution: "typescript@patch:typescript@npm%3A3.9.10#optional!builtin::version=3.9.10&hash=3bd3d3" - bin: - tsc: bin/tsc - tsserver: bin/tsserver - checksum: 10c0/9041fb3886e7d6a560f985227b8c941d17a750f2edccb5f9b3a15a2480574654d9be803ad4a14aabcc2f2553c4d272a25fd698a7c42692f03f66b009fb46883c - languageName: node - linkType: hard - "typescript@patch:typescript@npm%3A^5.5.3#optional!builtin": version: 5.5.3 resolution: "typescript@patch:typescript@npm%3A5.5.3#optional!builtin::version=5.5.3&hash=379a07" From 2806881e007306eac6dbbc1b1776f91254dd7d64 Mon Sep 17 00:00:00 2001 From: Garrett Stevens Date: Fri, 15 Nov 2024 16:35:17 -0700 Subject: [PATCH 02/12] Remove eslint-plugin-sort-destructure-keys --- .eslintrc.js | 4 +--- package.json | 1 - yarn.lock | 12 ------------ 3 files changed, 1 insertion(+), 16 deletions(-) diff --git a/.eslintrc.js b/.eslintrc.js index c3f71924d..cd9855c2e 100644 --- a/.eslintrc.js +++ b/.eslintrc.js @@ -9,7 +9,7 @@ module.exports = { 'plugin:@typescript-eslint/strict-type-checked', 'plugin:@typescript-eslint/stylistic-type-checked', ], - plugins: ['import', 'tsdoc', 'sort-destructure-keys'], + plugins: ['import', 'tsdoc'], parser: '@typescript-eslint/parser', parserOptions: { project: true, @@ -75,8 +75,6 @@ module.exports = { 'import/no-duplicates': 'warn', 'import/no-extraneous-dependencies': 'error', 'import/no-named-as-default': 'warn', - // eslint-plugin-sort-destructure-keys rules - 'sort-destructure-keys/sort-destructure-keys': 'warn', // eslint-plugin-tsdoc rules 'tsdoc/syntax': 'warn', // eslint-plugin-unicorn rules (override recommended) diff --git a/package.json b/package.json index 21817a42b..1d4ef1972 100644 --- a/package.json +++ b/package.json @@ -33,7 +33,6 @@ "eslint-plugin-jsx-a11y": "^6.7.1", "eslint-plugin-react": "^7.32.2", "eslint-plugin-react-hooks": "^4.6.0", - "eslint-plugin-sort-destructure-keys": "^1.5.0", "eslint-plugin-tsdoc": "^0.2.17", "eslint-plugin-unicorn": "^48.0.0", "husky": "^9.0.11", diff --git a/yarn.lock b/yarn.lock index 45069aa01..4814503f6 100644 --- a/yarn.lock +++ b/yarn.lock @@ -11195,7 +11195,6 @@ __metadata: eslint-plugin-jsx-a11y: "npm:^6.7.1" eslint-plugin-react: "npm:^7.32.2" eslint-plugin-react-hooks: "npm:^4.6.0" - eslint-plugin-sort-destructure-keys: "npm:^1.5.0" eslint-plugin-tsdoc: "npm:^0.2.17" eslint-plugin-unicorn: "npm:^48.0.0" husky: "npm:^9.0.11" @@ -15938,17 +15937,6 @@ __metadata: languageName: node linkType: hard -"eslint-plugin-sort-destructure-keys@npm:^1.5.0": - version: 1.5.0 - resolution: "eslint-plugin-sort-destructure-keys@npm:1.5.0" - dependencies: - natural-compare-lite: "npm:^1.4.0" - peerDependencies: - eslint: 3 - 8 - checksum: 10c0/1ab8ff259cca162344f09a47b6bdeccf03a6780771e70bd750c9a41a3f0ebb8935a631bd0712492fd49ba3e8a40c8016aec0aa525bd5b896dfef7461c6cdd335 - languageName: node - linkType: hard - "eslint-plugin-tsdoc@npm:^0.2.17": version: 0.2.17 resolution: "eslint-plugin-tsdoc@npm:0.2.17" From 1644cecf83fb1c32317197c3427ec71d991aa304 Mon Sep 17 00:00:00 2001 From: Garrett Stevens Date: Fri, 15 Nov 2024 17:01:40 -0700 Subject: [PATCH 03/12] eslint packages minor version updates --- package.json | 20 +- .../FeatureDetailsWidget/NumberTextField.tsx | 1 + .../FeatureDetailsWidget/StringTextField.tsx | 1 + .../TabularEditor/HybridGrid/NumberCell.tsx | 1 + .../src/components/AddChildFeature.tsx | 1 + .../src/components/AddFeature.tsx | 1 + .../src/components/AddRefSeqAliases.tsx | 1 + .../src/components/CopyFeature.tsx | 1 + .../src/components/DeleteAssembly.tsx | 1 + .../src/components/DeleteFeature.tsx | 1 + .../src/components/LogOut.tsx | 1 + .../src/components/ManageUsers.tsx | 1 + .../components/OntologyTermMultiSelect.tsx | 1 + .../src/components/OpenLocalFile.tsx | 1 + .../src/components/ViewChangeLog.tsx | 1 + .../src/components/ViewCheckResults.tsx | 1 + yarn.lock | 1137 ++++++++++++----- 17 files changed, 864 insertions(+), 308 deletions(-) diff --git a/package.json b/package.json index 1d4ef1972..4f440c070 100644 --- a/package.json +++ b/package.json @@ -21,20 +21,20 @@ "@types/node": "^18.14.2", "@types/semver": "^7", "@types/yargs": "^17.0.32", - "@typescript-eslint/eslint-plugin": "^7.16.0", - "@typescript-eslint/parser": "^7.16.0", + "@typescript-eslint/eslint-plugin": "^7.18.0", + "@typescript-eslint/parser": "^7.18.0", "@yarnpkg/types": "^4.0.0", "cross-env": "^7.0.3", "cross-spawn": "^7.0.3", - "eslint": "^8.57.0", - "eslint-import-resolver-typescript": "^3.5.5", - "eslint-plugin-cypress": "^2.13.3", - "eslint-plugin-import": "^2.27.5", - "eslint-plugin-jsx-a11y": "^6.7.1", - "eslint-plugin-react": "^7.32.2", - "eslint-plugin-react-hooks": "^4.6.0", + "eslint": "^8.57.1", + "eslint-import-resolver-typescript": "^3.6.3", + "eslint-plugin-cypress": "^2.15.2", + "eslint-plugin-import": "^2.31.0", + "eslint-plugin-jsx-a11y": "^6.10.2", + "eslint-plugin-react": "^7.37.2", + "eslint-plugin-react-hooks": "^4.6.2", "eslint-plugin-tsdoc": "^0.2.17", - "eslint-plugin-unicorn": "^48.0.0", + "eslint-plugin-unicorn": "^48.0.1", "husky": "^9.0.11", "lint-staged": "^15.2.2", "npm-run-all": "^4.1.5", diff --git a/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/NumberTextField.tsx b/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/NumberTextField.tsx index 7ef32d7ac..1901ffec5 100644 --- a/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/NumberTextField.tsx +++ b/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/NumberTextField.tsx @@ -1,3 +1,4 @@ +/* eslint-disable @typescript-eslint/unbound-method */ /* eslint-disable @typescript-eslint/no-unsafe-argument */ import { TextField, TextFieldProps } from '@mui/material' import { observer } from 'mobx-react' diff --git a/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/StringTextField.tsx b/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/StringTextField.tsx index 9d5f1d55d..3877a34dc 100644 --- a/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/StringTextField.tsx +++ b/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/StringTextField.tsx @@ -1,3 +1,4 @@ +/* eslint-disable @typescript-eslint/unbound-method */ /* eslint-disable @typescript-eslint/no-unsafe-argument */ import { TextField, TextFieldProps } from '@mui/material' import { observer } from 'mobx-react' diff --git a/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/NumberCell.tsx b/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/NumberCell.tsx index c6636e765..4421739c9 100644 --- a/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/NumberCell.tsx +++ b/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/NumberCell.tsx @@ -1,3 +1,4 @@ +/* eslint-disable @typescript-eslint/unbound-method */ /* eslint-disable @typescript-eslint/use-unknown-in-catch-callback-variable */ import { observer } from 'mobx-react' import React, { useEffect, useState } from 'react' diff --git a/packages/jbrowse-plugin-apollo/src/components/AddChildFeature.tsx b/packages/jbrowse-plugin-apollo/src/components/AddChildFeature.tsx index 4a049bc16..e2a8e4274 100644 --- a/packages/jbrowse-plugin-apollo/src/components/AddChildFeature.tsx +++ b/packages/jbrowse-plugin-apollo/src/components/AddChildFeature.tsx @@ -1,3 +1,4 @@ +/* eslint-disable @typescript-eslint/unbound-method */ /* eslint-disable @typescript-eslint/no-misused-promises */ import { AnnotationFeature } from '@apollo-annotation/mst' import { AddFeatureChange } from '@apollo-annotation/shared' diff --git a/packages/jbrowse-plugin-apollo/src/components/AddFeature.tsx b/packages/jbrowse-plugin-apollo/src/components/AddFeature.tsx index 375214474..71d11fe5b 100644 --- a/packages/jbrowse-plugin-apollo/src/components/AddFeature.tsx +++ b/packages/jbrowse-plugin-apollo/src/components/AddFeature.tsx @@ -1,3 +1,4 @@ +/* eslint-disable @typescript-eslint/unbound-method */ /* eslint-disable @typescript-eslint/no-unnecessary-condition */ /* eslint-disable @typescript-eslint/no-misused-promises */ import { AddFeatureChange } from '@apollo-annotation/shared' diff --git a/packages/jbrowse-plugin-apollo/src/components/AddRefSeqAliases.tsx b/packages/jbrowse-plugin-apollo/src/components/AddRefSeqAliases.tsx index 9373573d1..f08352fdb 100644 --- a/packages/jbrowse-plugin-apollo/src/components/AddRefSeqAliases.tsx +++ b/packages/jbrowse-plugin-apollo/src/components/AddRefSeqAliases.tsx @@ -1,3 +1,4 @@ +/* eslint-disable @typescript-eslint/unbound-method */ import { ChangeManager } from '../ChangeManager' import { ApolloSessionModel } from '../session' import { Dialog } from './Dialog' diff --git a/packages/jbrowse-plugin-apollo/src/components/CopyFeature.tsx b/packages/jbrowse-plugin-apollo/src/components/CopyFeature.tsx index c9d67755a..6807aff88 100644 --- a/packages/jbrowse-plugin-apollo/src/components/CopyFeature.tsx +++ b/packages/jbrowse-plugin-apollo/src/components/CopyFeature.tsx @@ -1,3 +1,4 @@ +/* eslint-disable @typescript-eslint/unbound-method */ /* eslint-disable @typescript-eslint/use-unknown-in-catch-callback-variable */ /* eslint-disable @typescript-eslint/no-unsafe-argument */ /* eslint-disable @typescript-eslint/no-misused-promises */ diff --git a/packages/jbrowse-plugin-apollo/src/components/DeleteAssembly.tsx b/packages/jbrowse-plugin-apollo/src/components/DeleteAssembly.tsx index 71114b67a..9fdae2f14 100644 --- a/packages/jbrowse-plugin-apollo/src/components/DeleteAssembly.tsx +++ b/packages/jbrowse-plugin-apollo/src/components/DeleteAssembly.tsx @@ -1,3 +1,4 @@ +/* eslint-disable @typescript-eslint/unbound-method */ /* eslint-disable @typescript-eslint/no-misused-promises */ import { DeleteAssemblyChange } from '@apollo-annotation/shared' import { Assembly } from '@jbrowse/core/assemblyManager/assembly' diff --git a/packages/jbrowse-plugin-apollo/src/components/DeleteFeature.tsx b/packages/jbrowse-plugin-apollo/src/components/DeleteFeature.tsx index 722f6cca7..0c20d51aa 100644 --- a/packages/jbrowse-plugin-apollo/src/components/DeleteFeature.tsx +++ b/packages/jbrowse-plugin-apollo/src/components/DeleteFeature.tsx @@ -1,3 +1,4 @@ +/* eslint-disable @typescript-eslint/unbound-method */ /* eslint-disable @typescript-eslint/no-misused-promises */ import { AnnotationFeature } from '@apollo-annotation/mst' import { DeleteFeatureChange } from '@apollo-annotation/shared' diff --git a/packages/jbrowse-plugin-apollo/src/components/LogOut.tsx b/packages/jbrowse-plugin-apollo/src/components/LogOut.tsx index 52969ddcd..c4d0a07d2 100644 --- a/packages/jbrowse-plugin-apollo/src/components/LogOut.tsx +++ b/packages/jbrowse-plugin-apollo/src/components/LogOut.tsx @@ -1,3 +1,4 @@ +/* eslint-disable @typescript-eslint/unbound-method */ import { Button, DialogActions, diff --git a/packages/jbrowse-plugin-apollo/src/components/ManageUsers.tsx b/packages/jbrowse-plugin-apollo/src/components/ManageUsers.tsx index 0b6e87579..c3047d3ae 100644 --- a/packages/jbrowse-plugin-apollo/src/components/ManageUsers.tsx +++ b/packages/jbrowse-plugin-apollo/src/components/ManageUsers.tsx @@ -1,3 +1,4 @@ +/* eslint-disable @typescript-eslint/unbound-method */ /* eslint-disable @typescript-eslint/use-unknown-in-catch-callback-variable */ /* eslint-disable @typescript-eslint/no-unnecessary-condition */ /* eslint-disable @typescript-eslint/no-misused-promises */ diff --git a/packages/jbrowse-plugin-apollo/src/components/OntologyTermMultiSelect.tsx b/packages/jbrowse-plugin-apollo/src/components/OntologyTermMultiSelect.tsx index 6445b2188..01700490e 100644 --- a/packages/jbrowse-plugin-apollo/src/components/OntologyTermMultiSelect.tsx +++ b/packages/jbrowse-plugin-apollo/src/components/OntologyTermMultiSelect.tsx @@ -1,3 +1,4 @@ +/* eslint-disable @typescript-eslint/unbound-method */ /* eslint-disable @typescript-eslint/use-unknown-in-catch-callback-variable */ /* eslint-disable @typescript-eslint/no-unnecessary-condition */ import { isAbortException } from '@jbrowse/core/util' diff --git a/packages/jbrowse-plugin-apollo/src/components/OpenLocalFile.tsx b/packages/jbrowse-plugin-apollo/src/components/OpenLocalFile.tsx index 22a08a596..28ac3f24a 100644 --- a/packages/jbrowse-plugin-apollo/src/components/OpenLocalFile.tsx +++ b/packages/jbrowse-plugin-apollo/src/components/OpenLocalFile.tsx @@ -1,3 +1,4 @@ +/* eslint-disable @typescript-eslint/unbound-method */ /* eslint-disable @typescript-eslint/no-unnecessary-condition */ /* eslint-disable @typescript-eslint/no-misused-promises */ import { AbstractSessionModel, isElectron } from '@jbrowse/core/util' diff --git a/packages/jbrowse-plugin-apollo/src/components/ViewChangeLog.tsx b/packages/jbrowse-plugin-apollo/src/components/ViewChangeLog.tsx index ee507f7ff..e046be36a 100644 --- a/packages/jbrowse-plugin-apollo/src/components/ViewChangeLog.tsx +++ b/packages/jbrowse-plugin-apollo/src/components/ViewChangeLog.tsx @@ -1,3 +1,4 @@ +/* eslint-disable @typescript-eslint/unbound-method */ /* eslint-disable @typescript-eslint/use-unknown-in-catch-callback-variable */ /* eslint-disable @typescript-eslint/no-unnecessary-condition */ /* eslint-disable @typescript-eslint/no-unsafe-assignment */ diff --git a/packages/jbrowse-plugin-apollo/src/components/ViewCheckResults.tsx b/packages/jbrowse-plugin-apollo/src/components/ViewCheckResults.tsx index 67e1d3238..7754ee99d 100644 --- a/packages/jbrowse-plugin-apollo/src/components/ViewCheckResults.tsx +++ b/packages/jbrowse-plugin-apollo/src/components/ViewCheckResults.tsx @@ -1,3 +1,4 @@ +/* eslint-disable @typescript-eslint/unbound-method */ /* eslint-disable @typescript-eslint/use-unknown-in-catch-callback-variable */ /* eslint-disable @typescript-eslint/no-unsafe-assignment */ /* eslint-disable @typescript-eslint/no-unsafe-argument */ diff --git a/yarn.lock b/yarn.lock index 4814503f6..100ee75e8 100644 --- a/yarn.lock +++ b/yarn.lock @@ -4495,7 +4495,7 @@ __metadata: languageName: node linkType: hard -"@babel/runtime@npm:^7.10.2, @babel/runtime@npm:^7.12.5, @babel/runtime@npm:^7.17.9, @babel/runtime@npm:^7.18.3, @babel/runtime@npm:^7.20.6, @babel/runtime@npm:^7.20.7, @babel/runtime@npm:^7.23.1, @babel/runtime@npm:^7.5.5, @babel/runtime@npm:^7.8.4, @babel/runtime@npm:^7.8.7": +"@babel/runtime@npm:^7.10.2, @babel/runtime@npm:^7.12.5, @babel/runtime@npm:^7.17.9, @babel/runtime@npm:^7.18.3, @babel/runtime@npm:^7.20.6, @babel/runtime@npm:^7.23.1, @babel/runtime@npm:^7.5.5, @babel/runtime@npm:^7.8.4, @babel/runtime@npm:^7.8.7": version: 7.23.1 resolution: "@babel/runtime@npm:7.23.1" dependencies: @@ -5588,10 +5588,10 @@ __metadata: languageName: node linkType: hard -"@eslint/js@npm:8.57.0": - version: 8.57.0 - resolution: "@eslint/js@npm:8.57.0" - checksum: 10c0/9a518bb8625ba3350613903a6d8c622352ab0c6557a59fe6ff6178bf882bf57123f9d92aa826ee8ac3ee74b9c6203fe630e9ee00efb03d753962dcf65ee4bd94 +"@eslint/js@npm:8.57.1": + version: 8.57.1 + resolution: "@eslint/js@npm:8.57.1" + checksum: 10c0/b489c474a3b5b54381c62e82b3f7f65f4b8a5eaaed126546520bf2fede5532a8ed53212919fed1e9048dcf7f37167c8561d58d0ba4492a4244004e7793805223 languageName: node linkType: hard @@ -5741,14 +5741,14 @@ __metadata: languageName: node linkType: hard -"@humanwhocodes/config-array@npm:^0.11.14": - version: 0.11.14 - resolution: "@humanwhocodes/config-array@npm:0.11.14" +"@humanwhocodes/config-array@npm:^0.13.0": + version: 0.13.0 + resolution: "@humanwhocodes/config-array@npm:0.13.0" dependencies: - "@humanwhocodes/object-schema": "npm:^2.0.2" + "@humanwhocodes/object-schema": "npm:^2.0.3" debug: "npm:^4.3.1" minimatch: "npm:^3.0.5" - checksum: 10c0/66f725b4ee5fdd8322c737cb5013e19fac72d4d69c8bf4b7feb192fcb83442b035b92186f8e9497c220e58b2d51a080f28a73f7899bc1ab288c3be172c467541 + checksum: 10c0/205c99e756b759f92e1f44a3dc6292b37db199beacba8f26c2165d4051fe73a4ae52fdcfd08ffa93e7e5cb63da7c88648f0e84e197d154bbbbe137b2e0dd332e languageName: node linkType: hard @@ -5759,7 +5759,7 @@ __metadata: languageName: node linkType: hard -"@humanwhocodes/object-schema@npm:^2.0.2": +"@humanwhocodes/object-schema@npm:^2.0.3": version: 2.0.3 resolution: "@humanwhocodes/object-schema@npm:2.0.3" checksum: 10c0/80520eabbfc2d32fe195a93557cef50dfe8c8905de447f022675aaf66abc33ae54098f5ea78548d925aa671cd4ab7c7daa5ad704fe42358c9b5e7db60f80696c @@ -7132,6 +7132,13 @@ __metadata: languageName: node linkType: hard +"@nolyfill/is-core-module@npm:1.0.39": + version: 1.0.39 + resolution: "@nolyfill/is-core-module@npm:1.0.39" + checksum: 10c0/34ab85fdc2e0250879518841f74a30c276bca4f6c3e13526d2d1fe515e1adf6d46c25fcd5989d22ea056d76f7c39210945180b4859fc83b050e2da411aa86289 + languageName: node + linkType: hard + "@npmcli/arborist@npm:^4.0.4": version: 4.3.1 resolution: "@npmcli/arborist@npm:4.3.1" @@ -7844,6 +7851,13 @@ __metadata: languageName: node linkType: hard +"@rtsao/scc@npm:^1.1.0": + version: 1.1.0 + resolution: "@rtsao/scc@npm:1.1.0" + checksum: 10c0/b5bcfb0d87f7d1c1c7c0f7693f53b07866ed9fec4c34a97a8c948fb9a7c0082e416ce4d3b60beb4f5e167cbe04cdeefbf6771320f3ede059b9ce91188c409a5b + languageName: node + linkType: hard + "@sideway/address@npm:^4.1.3": version: 4.1.4 resolution: "@sideway/address@npm:4.1.4" @@ -10325,15 +10339,15 @@ __metadata: languageName: node linkType: hard -"@typescript-eslint/eslint-plugin@npm:^7.16.0": - version: 7.16.0 - resolution: "@typescript-eslint/eslint-plugin@npm:7.16.0" +"@typescript-eslint/eslint-plugin@npm:^7.18.0": + version: 7.18.0 + resolution: "@typescript-eslint/eslint-plugin@npm:7.18.0" dependencies: "@eslint-community/regexpp": "npm:^4.10.0" - "@typescript-eslint/scope-manager": "npm:7.16.0" - "@typescript-eslint/type-utils": "npm:7.16.0" - "@typescript-eslint/utils": "npm:7.16.0" - "@typescript-eslint/visitor-keys": "npm:7.16.0" + "@typescript-eslint/scope-manager": "npm:7.18.0" + "@typescript-eslint/type-utils": "npm:7.18.0" + "@typescript-eslint/utils": "npm:7.18.0" + "@typescript-eslint/visitor-keys": "npm:7.18.0" graphemer: "npm:^1.4.0" ignore: "npm:^5.3.1" natural-compare: "npm:^1.4.0" @@ -10344,25 +10358,25 @@ __metadata: peerDependenciesMeta: typescript: optional: true - checksum: 10c0/a6c4c93bd7ec1604079018b95416d8ac28af3345d50620f815ffd36e705c4964d88edc434e710ef8722690497f1eeab1e9a0f48faa6d448405980f5d05c888b7 + checksum: 10c0/2b37948fa1b0dab77138909dabef242a4d49ab93e4019d4ef930626f0a7d96b03e696cd027fa0087881c20e73be7be77c942606b4a76fa599e6b37f6985304c3 languageName: node linkType: hard -"@typescript-eslint/parser@npm:^7.16.0": - version: 7.16.0 - resolution: "@typescript-eslint/parser@npm:7.16.0" +"@typescript-eslint/parser@npm:^7.18.0": + version: 7.18.0 + resolution: "@typescript-eslint/parser@npm:7.18.0" dependencies: - "@typescript-eslint/scope-manager": "npm:7.16.0" - "@typescript-eslint/types": "npm:7.16.0" - "@typescript-eslint/typescript-estree": "npm:7.16.0" - "@typescript-eslint/visitor-keys": "npm:7.16.0" + "@typescript-eslint/scope-manager": "npm:7.18.0" + "@typescript-eslint/types": "npm:7.18.0" + "@typescript-eslint/typescript-estree": "npm:7.18.0" + "@typescript-eslint/visitor-keys": "npm:7.18.0" debug: "npm:^4.3.4" peerDependencies: eslint: ^8.56.0 peerDependenciesMeta: typescript: optional: true - checksum: 10c0/bf809c5a59dddc72fc2f11a5d10c78825fa2ffbec72a711e3f783b022d77266a1b709ad450912ebbff24ca9ac20c6baae1d12477735e00aafce662fdbdfa66ef + checksum: 10c0/370e73fca4278091bc1b657f85e7d74cd52b24257ea20c927a8e17546107ce04fbf313fec99aed0cc2a145ddbae1d3b12e9cc2c1320117636dc1281bcfd08059 languageName: node linkType: hard @@ -10376,22 +10390,22 @@ __metadata: languageName: node linkType: hard -"@typescript-eslint/scope-manager@npm:7.16.0": - version: 7.16.0 - resolution: "@typescript-eslint/scope-manager@npm:7.16.0" +"@typescript-eslint/scope-manager@npm:7.18.0": + 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is-regex: "npm:^1.1.4" + checksum: 10c0/900bf7c98dc58f08d8523b7012b468e4eb757afa624f198902c0643d7008ba777b0bdc35810ba0b758671ce887617295fb742b3f3968991b178ceca54cb07603 + languageName: node + linkType: hard + "safer-buffer@npm:>= 2.1.2 < 3, safer-buffer@npm:>= 2.1.2 < 3.0.0, safer-buffer@npm:^2.0.2, safer-buffer@npm:^2.1.0, safer-buffer@npm:~2.1.0": version: 2.1.2 resolution: "safer-buffer@npm:2.1.2" @@ -27272,6 +27654,18 @@ __metadata: languageName: node linkType: hard +"set-function-name@npm:^2.0.2": + version: 2.0.2 + resolution: "set-function-name@npm:2.0.2" + dependencies: + define-data-property: "npm:^1.1.4" + es-errors: "npm:^1.3.0" + functions-have-names: "npm:^1.2.3" + has-property-descriptors: "npm:^1.0.2" + checksum: 10c0/fce59f90696c450a8523e754abb305e2b8c73586452619c2bad5f7bf38c7b6b4651895c9db895679c5bef9554339cf3ef1c329b66ece3eda7255785fbe299316 + languageName: node + linkType: hard + "setprototypeof@npm:1.1.0": version: 1.1.0 resolution: "setprototypeof@npm:1.1.0" @@ -27389,6 +27783,18 @@ __metadata: languageName: node linkType: hard +"side-channel@npm:^1.0.6": + version: 1.0.6 + resolution: "side-channel@npm:1.0.6" + dependencies: + call-bind: "npm:^1.0.7" + es-errors: "npm:^1.3.0" + get-intrinsic: "npm:^1.2.4" + object-inspect: "npm:^1.13.1" + checksum: 10c0/d2afd163dc733cc0a39aa6f7e39bf0c436293510dbccbff446733daeaf295857dbccf94297092ec8c53e2503acac30f0b78830876f0485991d62a90e9cad305f + languageName: node + linkType: hard + "sift@npm:16.0.1": version: 16.0.1 resolution: "sift@npm:16.0.1" @@ -28086,20 +28492,34 @@ __metadata: languageName: node linkType: hard -"string.prototype.matchall@npm:^4.0.8": - version: 4.0.10 - resolution: "string.prototype.matchall@npm:4.0.10" +"string.prototype.includes@npm:^2.0.1": + version: 2.0.1 + resolution: "string.prototype.includes@npm:2.0.1" dependencies: - call-bind: "npm:^1.0.2" - define-properties: "npm:^1.2.0" - es-abstract: "npm:^1.22.1" - get-intrinsic: "npm:^1.2.1" + call-bind: "npm:^1.0.7" + define-properties: "npm:^1.2.1" + es-abstract: "npm:^1.23.3" + checksum: 10c0/25ce9c9b49128352a2618fbe8758b46f945817a58a4420f4799419e40a8d28f116e176c7590d767d5327a61e75c8f32c86171063f48e389b9fdd325f1bd04ee5 + languageName: node + linkType: hard + +"string.prototype.matchall@npm:^4.0.11": + version: 4.0.11 + resolution: "string.prototype.matchall@npm:4.0.11" + dependencies: + call-bind: "npm:^1.0.7" + define-properties: "npm:^1.2.1" + es-abstract: "npm:^1.23.2" + es-errors: "npm:^1.3.0" + es-object-atoms: "npm:^1.0.0" + get-intrinsic: "npm:^1.2.4" + gopd: "npm:^1.0.1" has-symbols: "npm:^1.0.3" - internal-slot: "npm:^1.0.5" - regexp.prototype.flags: "npm:^1.5.0" - set-function-name: "npm:^2.0.0" - side-channel: "npm:^1.0.4" - checksum: 10c0/cd7495fb0de16d43efeee3887b98701941f3817bd5f09351ad1825b023d307720c86394d56d56380563d97767ab25bf5448db239fcecbb85c28e2180f23e324a + internal-slot: "npm:^1.0.7" + regexp.prototype.flags: "npm:^1.5.2" + set-function-name: "npm:^2.0.2" + side-channel: "npm:^1.0.6" + checksum: 10c0/915a2562ac9ab5e01b7be6fd8baa0b2b233a0a9aa975fcb2ec13cc26f08fb9a3e85d5abdaa533c99c6fc4c5b65b914eba3d80c4aff9792a4c9fed403f28f7d9d languageName: node linkType: hard @@ -28114,6 +28534,16 @@ __metadata: languageName: node linkType: hard +"string.prototype.repeat@npm:^1.0.0": + version: 1.0.0 + resolution: "string.prototype.repeat@npm:1.0.0" + dependencies: + define-properties: "npm:^1.1.3" + es-abstract: "npm:^1.17.5" + checksum: 10c0/94c7978566cffa1327d470fd924366438af9b04b497c43a9805e476e2e908aa37a1fd34cc0911156c17556dab62159d12c7b92b3cc304c3e1281fe4c8e668f40 + languageName: node + linkType: hard + "string.prototype.trim@npm:^1.2.8": version: 1.2.8 resolution: "string.prototype.trim@npm:1.2.8" @@ -28125,6 +28555,18 @@ __metadata: languageName: node linkType: hard +"string.prototype.trim@npm:^1.2.9": + version: 1.2.9 + resolution: "string.prototype.trim@npm:1.2.9" + dependencies: + call-bind: "npm:^1.0.7" + define-properties: "npm:^1.2.1" + es-abstract: "npm:^1.23.0" + es-object-atoms: "npm:^1.0.0" + checksum: 10c0/dcef1a0fb61d255778155006b372dff8cc6c4394bc39869117e4241f41a2c52899c0d263ffc7738a1f9e61488c490b05c0427faa15151efad721e1a9fb2663c2 + languageName: node + linkType: hard + "string.prototype.trimend@npm:^1.0.7": version: 1.0.7 resolution: "string.prototype.trimend@npm:1.0.7" @@ -28136,6 +28578,17 @@ __metadata: languageName: node linkType: hard +"string.prototype.trimend@npm:^1.0.8": + version: 1.0.8 + resolution: "string.prototype.trimend@npm:1.0.8" + dependencies: + call-bind: "npm:^1.0.7" + define-properties: "npm:^1.2.1" + es-object-atoms: "npm:^1.0.0" + checksum: 10c0/0a0b54c17c070551b38e756ae271865ac6cc5f60dabf2e7e343cceae7d9b02e1a1120a824e090e79da1b041a74464e8477e2da43e2775c85392be30a6f60963c + languageName: node + linkType: hard + "string.prototype.trimstart@npm:^1.0.7": version: 1.0.7 resolution: "string.prototype.trimstart@npm:1.0.7" @@ -28147,6 +28600,17 @@ __metadata: languageName: node linkType: hard +"string.prototype.trimstart@npm:^1.0.8": + version: 1.0.8 + resolution: "string.prototype.trimstart@npm:1.0.8" + dependencies: + call-bind: "npm:^1.0.7" + define-properties: "npm:^1.2.1" + es-object-atoms: "npm:^1.0.0" + checksum: 10c0/d53af1899959e53c83b64a5fd120be93e067da740e7e75acb433849aa640782fb6c7d4cd5b84c954c84413745a3764df135a8afeb22908b86a835290788d8366 + languageName: node + linkType: hard + "string_decoder@npm:^1.1.1, string_decoder@npm:^1.3.0": version: 1.3.0 resolution: "string_decoder@npm:1.3.0" @@ -29038,7 +29502,7 @@ __metadata: languageName: node linkType: hard -"tsconfig-paths@npm:^3.11.0, tsconfig-paths@npm:^3.14.2": +"tsconfig-paths@npm:^3.11.0": version: 3.14.2 resolution: "tsconfig-paths@npm:3.14.2" dependencies: @@ -29050,6 +29514,18 @@ __metadata: languageName: node linkType: hard +"tsconfig-paths@npm:^3.15.0": + version: 3.15.0 + resolution: "tsconfig-paths@npm:3.15.0" + dependencies: + "@types/json5": "npm:^0.0.29" + json5: "npm:^1.0.2" + minimist: "npm:^1.2.6" + strip-bom: "npm:^3.0.0" + checksum: 10c0/5b4f301a2b7a3766a986baf8fc0e177eb80bdba6e396792ff92dc23b5bca8bb279fc96517dcaaef63a3b49bebc6c4c833653ec58155780bc906bdbcf7dda0ef5 + languageName: node + linkType: hard + "tsconfig@npm:^7.0.0": version: 7.0.0 resolution: "tsconfig@npm:7.0.0" @@ -29242,6 +29718,17 @@ __metadata: languageName: node linkType: hard +"typed-array-buffer@npm:^1.0.2": + version: 1.0.2 + resolution: "typed-array-buffer@npm:1.0.2" + dependencies: + call-bind: "npm:^1.0.7" + es-errors: "npm:^1.3.0" + is-typed-array: "npm:^1.1.13" + checksum: 10c0/9e043eb38e1b4df4ddf9dde1aa64919ae8bb909571c1cc4490ba777d55d23a0c74c7d73afcdd29ec98616d91bb3ae0f705fad4421ea147e1daf9528200b562da + languageName: node + linkType: hard + "typed-array-byte-length@npm:^1.0.0": version: 1.0.0 resolution: "typed-array-byte-length@npm:1.0.0" @@ -29254,6 +29741,19 @@ __metadata: languageName: node linkType: hard +"typed-array-byte-length@npm:^1.0.1": + version: 1.0.1 + resolution: "typed-array-byte-length@npm:1.0.1" + dependencies: + call-bind: "npm:^1.0.7" + for-each: "npm:^0.3.3" + gopd: "npm:^1.0.1" + has-proto: "npm:^1.0.3" + is-typed-array: "npm:^1.1.13" + checksum: 10c0/fcebeffb2436c9f355e91bd19e2368273b88c11d1acc0948a2a306792f1ab672bce4cfe524ab9f51a0505c9d7cd1c98eff4235c4f6bfef6a198f6cfc4ff3d4f3 + languageName: node + linkType: hard + "typed-array-byte-offset@npm:^1.0.0": version: 1.0.0 resolution: "typed-array-byte-offset@npm:1.0.0" @@ -29267,6 +29767,20 @@ __metadata: languageName: node linkType: hard +"typed-array-byte-offset@npm:^1.0.2": + version: 1.0.2 + resolution: "typed-array-byte-offset@npm:1.0.2" + dependencies: + available-typed-arrays: "npm:^1.0.7" + call-bind: "npm:^1.0.7" + for-each: "npm:^0.3.3" + gopd: "npm:^1.0.1" + has-proto: "npm:^1.0.3" + is-typed-array: "npm:^1.1.13" + checksum: 10c0/d2628bc739732072e39269389a758025f75339de2ed40c4f91357023c5512d237f255b633e3106c461ced41907c1bf9a533c7e8578066b0163690ca8bc61b22f + languageName: node + linkType: hard + "typed-array-length@npm:^1.0.4": version: 1.0.4 resolution: "typed-array-length@npm:1.0.4" @@ -29278,6 +29792,20 @@ __metadata: languageName: node linkType: hard +"typed-array-length@npm:^1.0.6": + version: 1.0.6 + resolution: "typed-array-length@npm:1.0.6" + dependencies: + call-bind: "npm:^1.0.7" + for-each: "npm:^0.3.3" + gopd: "npm:^1.0.1" + has-proto: "npm:^1.0.3" + is-typed-array: "npm:^1.1.13" + possible-typed-array-names: "npm:^1.0.0" + checksum: 10c0/74253d7dc488eb28b6b2711cf31f5a9dcefc9c41b0681fd1c178ed0a1681b4468581a3626d39cd4df7aee3d3927ab62be06aa9ca74e5baf81827f61641445b77 + languageName: node + linkType: hard + "typedarray-to-buffer@npm:^3.1.5": version: 3.1.5 resolution: "typedarray-to-buffer@npm:3.1.5" @@ -30398,6 +30926,19 @@ __metadata: languageName: node linkType: hard +"which-typed-array@npm:^1.1.14, which-typed-array@npm:^1.1.15": + version: 1.1.15 + resolution: "which-typed-array@npm:1.1.15" + dependencies: + available-typed-arrays: "npm:^1.0.7" + call-bind: "npm:^1.0.7" + for-each: "npm:^0.3.3" + gopd: "npm:^1.0.1" + has-tostringtag: "npm:^1.0.2" + checksum: 10c0/4465d5348c044032032251be54d8988270e69c6b7154f8fcb2a47ff706fe36f7624b3a24246b8d9089435a8f4ec48c1c1025c5d6b499456b9e5eff4f48212983 + languageName: node + linkType: hard + "which@npm:^1.2.9, which@npm:^1.3.1": version: 1.3.1 resolution: "which@npm:1.3.1" From fadd7fc200bbb7e547d363dffbe47ce0096d9d60 Mon Sep 17 00:00:00 2001 From: Garrett Stevens Date: Fri, 15 Nov 2024 17:31:45 -0700 Subject: [PATCH 04/12] typescript-eslint major version updates --- .eslintrc.js | 12 +- package.json | 10 +- packages/apollo-cli/src/utils.ts | 6 +- .../src/files/FileStorageEngine.ts | 1 + .../src/files/filesUtil.ts | 14 +- .../src/plugins/plugins.service.ts | 3 +- .../apollo-mst/src/AnnotationFeatureModel.ts | 6 +- packages/apollo-mst/src/ApolloAssembly.ts | 4 +- packages/apollo-mst/src/ApolloRefSeq.ts | 4 +- packages/apollo-mst/src/CheckResult.ts | 4 +- .../src/Changes/DeleteUserChange.ts | 2 +- .../jbrowse-plugin-apollo/cypress.config.js | 7 +- packages/jbrowse-plugin-apollo/jestSetup.js | 3 +- .../components/AuthTypeSelector.tsx | 4 +- .../src/ApolloInternetAccount/configSchema.ts | 2 +- .../src/ApolloInternetAccount/model.ts | 11 +- .../ApolloRefNameAliasAdapter.ts | 2 +- .../src/BackendDrivers/DesktopFileDriver.ts | 5 +- .../src/FeatureDetailsWidget/model.ts | 8 +- .../components/LinearApolloDisplay.tsx | 1 + .../LinearApolloDisplay/stateModel/index.ts | 2 +- .../stateModel/mouseEvents.ts | 2 +- .../stateModel/rendering.ts | 2 +- .../OntologyManager/OntologyStore/index.ts | 12 +- .../src/OntologyManager/index.ts | 4 +- .../src/SixFrameFeatureDisplay/stateModel.ts | 2 +- .../TabularEditor/HybridGrid/HybridGrid.tsx | 1 + .../src/TabularEditor/model.ts | 2 +- .../components/OntologyTermAutocomplete.tsx | 9 +- .../src/components/OpenLocalFile.tsx | 3 +- .../src/extensions/annotationFromPileup.ts | 2 +- .../src/session/session.ts | 2 +- .../src/components/HomepageFeatures/index.tsx | 12 +- packages/website/src/pages/index.tsx | 2 +- yarn.lock | 219 ++++++++---------- 35 files changed, 187 insertions(+), 198 deletions(-) diff --git a/.eslintrc.js b/.eslintrc.js index cd9855c2e..1ac1038c5 100644 --- a/.eslintrc.js +++ b/.eslintrc.js @@ -52,11 +52,6 @@ module.exports = { { line: { markers: ['/'] } }, ], // @typescript-eslint/eslint-plugin rules (override recommended) - '@typescript-eslint/lines-between-class-members': [ - 'warn', - 'always', - { exceptAfterSingleLine: true }, - ], '@typescript-eslint/no-extraneous-class': [ 'error', { allowWithDecorator: true }, @@ -149,5 +144,12 @@ module.exports = { 'tsdoc/syntax': 'off', }, }, + // Temporary override + { + files: ['packages/apollo-cli/src/**/*.ts'], + rules: { + '@typescript-eslint/no-deprecated': 'off', + }, + }, ], } diff --git a/package.json b/package.json index 4f440c070..5c6bcc247 100644 --- a/package.json +++ b/package.json @@ -21,19 +21,19 @@ "@types/node": "^18.14.2", "@types/semver": "^7", "@types/yargs": "^17.0.32", - "@typescript-eslint/eslint-plugin": "^7.18.0", - "@typescript-eslint/parser": "^7.18.0", + "@typescript-eslint/eslint-plugin": "^8.14.0", + "@typescript-eslint/parser": "^8.14.0", "@yarnpkg/types": "^4.0.0", "cross-env": "^7.0.3", "cross-spawn": "^7.0.3", "eslint": "^8.57.1", "eslint-import-resolver-typescript": "^3.6.3", - "eslint-plugin-cypress": "^2.15.2", + "eslint-plugin-cypress": "^4.1.0", "eslint-plugin-import": "^2.31.0", "eslint-plugin-jsx-a11y": "^6.10.2", "eslint-plugin-react": "^7.37.2", - "eslint-plugin-react-hooks": "^4.6.2", - "eslint-plugin-tsdoc": "^0.2.17", + "eslint-plugin-react-hooks": "^5.0.0", + "eslint-plugin-tsdoc": "^0.3.0", "eslint-plugin-unicorn": "^48.0.1", "husky": "^9.0.11", "lint-staged": "^15.2.2", diff --git a/packages/apollo-cli/src/utils.ts b/packages/apollo-cli/src/utils.ts index 897dd5749..ba494b34e 100644 --- a/packages/apollo-cli/src/utils.ts +++ b/packages/apollo-cli/src/utils.ts @@ -347,7 +347,11 @@ export const waitFor = ( ): Promise => { const promise = new Promise((resolve, reject) => { const handleEvent = (eventData: T): void => { - eventData instanceof Error ? reject(eventData) : resolve(eventData) + if (eventData instanceof Error) { + reject(eventData) + } else { + resolve(eventData) + } emitter.removeListener(eventName, handleEvent) } diff --git a/packages/apollo-collaboration-server/src/files/FileStorageEngine.ts b/packages/apollo-collaboration-server/src/files/FileStorageEngine.ts index de8de219a..7ee1f13f9 100644 --- a/packages/apollo-collaboration-server/src/files/FileStorageEngine.ts +++ b/packages/apollo-collaboration-server/src/files/FileStorageEngine.ts @@ -15,6 +15,7 @@ export interface UploadedFile extends Express.Multer.File { export class FileStorageEngine implements StorageEngine { private readonly logger = new Logger(FileStorageEngine.name) + // eslint-disable-next-line @typescript-eslint/no-misused-promises async _handleFile( req: Express.Request, file: Express.Multer.File, diff --git a/packages/apollo-collaboration-server/src/files/filesUtil.ts b/packages/apollo-collaboration-server/src/files/filesUtil.ts index 31c6f416e..85ec3ef04 100644 --- a/packages/apollo-collaboration-server/src/files/filesUtil.ts +++ b/packages/apollo-collaboration-server/src/files/filesUtil.ts @@ -128,15 +128,15 @@ export class LocalFileGzip implements GenericFilehandle { return { bytesRead, buffer } } - public async readFile(): Promise - public async readFile(options: BufferEncoding): Promise - public async readFile( - options: + public async readFile( + options?: | Omit - | (Omit & { encoding: T }), + | (Omit & { encoding: undefined }), ): Promise - public async readFile( - options: Omit & { encoding: T }, + public async readFile( + options: + | BufferEncoding + | (Omit & { encoding: BufferEncoding }), ): Promise public async readFile( diff --git a/packages/apollo-collaboration-server/src/plugins/plugins.service.ts b/packages/apollo-collaboration-server/src/plugins/plugins.service.ts index ec5b64e23..53c5f5da8 100644 --- a/packages/apollo-collaboration-server/src/plugins/plugins.service.ts +++ b/packages/apollo-collaboration-server/src/plugins/plugins.service.ts @@ -1,3 +1,4 @@ +/* eslint-disable @typescript-eslint/no-unsafe-call */ import { ApolloPlugin } from '@apollo-annotation/common' import { Inject, Injectable } from '@nestjs/common' @@ -5,7 +6,7 @@ import { APOLLO_PLUGINS } from './plugins.constants' @Injectable() export class PluginsService { - // eslint-disable-next-line @typescript-eslint/ban-types + // eslint-disable-next-line @typescript-eslint/no-unsafe-function-type extensionPoints = new Map() constructor(@Inject(APOLLO_PLUGINS) private plugins: ApolloPlugin[]) { diff --git a/packages/apollo-mst/src/AnnotationFeatureModel.ts b/packages/apollo-mst/src/AnnotationFeatureModel.ts index 49ce671ac..94e26d344 100644 --- a/packages/apollo-mst/src/AnnotationFeatureModel.ts +++ b/packages/apollo-mst/src/AnnotationFeatureModel.ts @@ -264,7 +264,7 @@ export const AnnotationFeatureModel = types self.max = max } }, - setStrand(strand?: 1 | -1 | undefined) { + setStrand(strand?: 1 | -1) { self.strand = strand }, addChild(childFeature: AnnotationFeatureSnapshot) { @@ -345,7 +345,7 @@ export type Children = IMSTMap | undefined // eslint disables because of // https://mobx-state-tree.js.org/tips/typescript#using-a-mst-type-at-design-time -// eslint-disable-next-line @typescript-eslint/no-empty-interface +// eslint-disable-next-line @typescript-eslint/no-empty-object-type interface AnnotationFeatureRaw extends Instance {} // This type isn't exactly right, since "children" is actually an IMSTMap and @@ -354,7 +354,7 @@ export interface AnnotationFeature extends Omit { children?: Map } -// eslint-disable-next-line @typescript-eslint/no-empty-interface +// eslint-disable-next-line @typescript-eslint/no-empty-object-type interface AnnotationFeatureSnapshotRaw extends SnapshotIn {} export interface AnnotationFeatureSnapshot diff --git a/packages/apollo-mst/src/ApolloAssembly.ts b/packages/apollo-mst/src/ApolloAssembly.ts index 7a06b7f1a..eae3146d7 100644 --- a/packages/apollo-mst/src/ApolloAssembly.ts +++ b/packages/apollo-mst/src/ApolloAssembly.ts @@ -37,8 +37,8 @@ export const ApolloAssembly = types // eslint disables because of // https://mobx-state-tree.js.org/tips/typescript#using-a-mst-type-at-design-time -// eslint-disable-next-line @typescript-eslint/no-empty-interface +// eslint-disable-next-line @typescript-eslint/no-empty-object-type export interface ApolloAssemblyI extends Instance {} -// eslint-disable-next-line @typescript-eslint/no-empty-interface +// eslint-disable-next-line @typescript-eslint/no-empty-object-type export interface ApolloAssemblySnapshot extends SnapshotIn {} diff --git a/packages/apollo-mst/src/ApolloRefSeq.ts b/packages/apollo-mst/src/ApolloRefSeq.ts index 8c6145c20..94ec57190 100644 --- a/packages/apollo-mst/src/ApolloRefSeq.ts +++ b/packages/apollo-mst/src/ApolloRefSeq.ts @@ -114,7 +114,7 @@ export const ApolloRefSeq = types // eslint disables because of // https://mobx-state-tree.js.org/tips/typescript#using-a-mst-type-at-design-time -// eslint-disable-next-line @typescript-eslint/no-empty-interface +// eslint-disable-next-line @typescript-eslint/no-empty-object-type export interface ApolloRefSeqI extends Instance {} -// eslint-disable-next-line @typescript-eslint/no-empty-interface +// eslint-disable-next-line @typescript-eslint/no-empty-object-type export interface ApolloRefSeqSnapshot extends SnapshotIn {} diff --git a/packages/apollo-mst/src/CheckResult.ts b/packages/apollo-mst/src/CheckResult.ts index 1616a1401..cf8ef4360 100644 --- a/packages/apollo-mst/src/CheckResult.ts +++ b/packages/apollo-mst/src/CheckResult.ts @@ -15,7 +15,7 @@ export const CheckResult = types.model('CheckResult', { // eslint disables because of // https://mobx-state-tree.js.org/tips/typescript#using-a-mst-type-at-design-time -// eslint-disable-next-line @typescript-eslint/no-empty-interface +// eslint-disable-next-line @typescript-eslint/no-empty-object-type export interface CheckResultI extends Instance {} -// eslint-disable-next-line @typescript-eslint/no-empty-interface +// eslint-disable-next-line @typescript-eslint/no-empty-object-type export interface CheckResultSnapshot extends SnapshotIn {} diff --git a/packages/apollo-shared/src/Changes/DeleteUserChange.ts b/packages/apollo-shared/src/Changes/DeleteUserChange.ts index 8c1b09364..d1589e245 100644 --- a/packages/apollo-shared/src/Changes/DeleteUserChange.ts +++ b/packages/apollo-shared/src/Changes/DeleteUserChange.ts @@ -13,7 +13,7 @@ export interface SerializedDeleteUserChangeBase extends SerializedChange { userId: string } -// eslint-disable-next-line @typescript-eslint/no-empty-interface +// eslint-disable-next-line @typescript-eslint/no-empty-object-type export interface DeleteUserChangeDetails {} interface SerializedDeleteUserChangeSingle diff --git a/packages/jbrowse-plugin-apollo/cypress.config.js b/packages/jbrowse-plugin-apollo/cypress.config.js index b3bf4ed03..3e308d85e 100644 --- a/packages/jbrowse-plugin-apollo/cypress.config.js +++ b/packages/jbrowse-plugin-apollo/cypress.config.js @@ -1,10 +1,11 @@ +/* eslint-disable @typescript-eslint/no-require-imports */ /* eslint-disable @typescript-eslint/unbound-method */ /* eslint-disable @typescript-eslint/no-unsafe-argument */ -// eslint-disable-next-line @typescript-eslint/no-var-requires + const { defineConfig } = require('cypress') -// eslint-disable-next-line @typescript-eslint/no-var-requires + const { configurePlugin } = require('cypress-mongodb') -// eslint-disable-next-line @typescript-eslint/no-var-requires + const fs = require('node:fs') module.exports = defineConfig({ diff --git a/packages/jbrowse-plugin-apollo/jestSetup.js b/packages/jbrowse-plugin-apollo/jestSetup.js index f822ec40b..0a36090e2 100644 --- a/packages/jbrowse-plugin-apollo/jestSetup.js +++ b/packages/jbrowse-plugin-apollo/jestSetup.js @@ -1,3 +1,4 @@ +/* eslint-disable @typescript-eslint/no-require-imports */ /* eslint-disable @typescript-eslint/no-unsafe-call */ -/* eslint-disable @typescript-eslint/no-var-requires */ + require('jest-fetch-mock').enableMocks() diff --git a/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/components/AuthTypeSelector.tsx b/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/components/AuthTypeSelector.tsx index 135cc5fb8..2361f003c 100644 --- a/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/components/AuthTypeSelector.tsx +++ b/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/components/AuthTypeSelector.tsx @@ -51,7 +51,9 @@ export const AuthTypeSelector = ({ setLoginTypes(data) } getAuthTypes().catch((error) => { - isAbortException(error) ? '' : setErrorMessage(String(error)) + if (!isAbortException(error)) { + setErrorMessage(String(error)) + } }) return () => { controller.abort() diff --git a/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/configSchema.ts b/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/configSchema.ts index dfbaec3c8..040ab008f 100644 --- a/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/configSchema.ts +++ b/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/configSchema.ts @@ -23,7 +23,7 @@ export type ApolloInternetAccountConfigModel = typeof ApolloConfigSchema // eslint disable because of // https://mobx-state-tree.js.org/tips/typescript#using-a-mst-type-at-design-time -// eslint-disable-next-line @typescript-eslint/no-empty-interface +// eslint-disable-next-line @typescript-eslint/no-empty-object-type export interface ApolloInternetAccountConfig extends Instance {} export default ApolloConfigSchema diff --git a/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/model.ts b/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/model.ts index 0cc8fd0ea..2b7d4fbe0 100644 --- a/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/model.ts +++ b/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/model.ts @@ -345,14 +345,9 @@ const stateModelFactory = (configSchema: ApolloInternetAccountConfigModel) => { socket.on( 'REQUEST_INFORMATION', (message: RequestUserInformationMessage) => { - const { channel, reqType, userSessionId } = message + const { channel, userSessionId } = message if (channel === 'REQUEST_INFORMATION' && userSessionId !== token) { - switch (reqType) { - case 'CURRENT_LOCATION': { - session.broadcastLocations() - break - } - } + session.broadcastLocations() } }, ) @@ -462,6 +457,6 @@ export type ApolloInternetAccountStateModel = ReturnType< > // eslint disable because of // https://mobx-state-tree.js.org/tips/typescript#using-a-mst-type-at-design-time -// eslint-disable-next-line @typescript-eslint/no-empty-interface +// eslint-disable-next-line @typescript-eslint/no-empty-object-type export interface ApolloInternetAccountModel extends Instance {} diff --git a/packages/jbrowse-plugin-apollo/src/ApolloRefNameAliasAdapter/ApolloRefNameAliasAdapter.ts b/packages/jbrowse-plugin-apollo/src/ApolloRefNameAliasAdapter/ApolloRefNameAliasAdapter.ts index 35ef95692..9d03e0231 100644 --- a/packages/jbrowse-plugin-apollo/src/ApolloRefNameAliasAdapter/ApolloRefNameAliasAdapter.ts +++ b/packages/jbrowse-plugin-apollo/src/ApolloRefNameAliasAdapter/ApolloRefNameAliasAdapter.ts @@ -88,7 +88,7 @@ export default class RefNameAliasAdapter return refNameAliases } - async freeResources() { + freeResources() { // no resources to free } } diff --git a/packages/jbrowse-plugin-apollo/src/BackendDrivers/DesktopFileDriver.ts b/packages/jbrowse-plugin-apollo/src/BackendDrivers/DesktopFileDriver.ts index 157e92a6a..a1b0092c4 100644 --- a/packages/jbrowse-plugin-apollo/src/BackendDrivers/DesktopFileDriver.ts +++ b/packages/jbrowse-plugin-apollo/src/BackendDrivers/DesktopFileDriver.ts @@ -31,7 +31,8 @@ export class DesktopFileDriver extends BackendDriver { const { file } = getConf(assembly, ['sequence', 'metadata']) as { file: string } - // eslint-disable-next-line @typescript-eslint/no-var-requires + + // eslint-disable-next-line @typescript-eslint/no-require-imports const fs = require('node:fs') as typeof import('fs') const fileContents = await fs.promises.readFile(file, 'utf8') return loadAssemblyIntoClient(assemblyName, fileContents, this.clientStore) @@ -165,7 +166,7 @@ export class DesktopFileDriver extends BackendDriver { const gff3Contents = gff.formatSync(gff3Items) - // eslint-disable-next-line @typescript-eslint/no-var-requires + // eslint-disable-next-line @typescript-eslint/no-require-imports const fs = require('node:fs') as typeof import('fs') await fs.promises.writeFile(file, gff3Contents, 'utf8') diff --git a/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/model.ts b/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/model.ts index a9ff3afc6..a39372b0d 100644 --- a/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/model.ts +++ b/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/model.ts @@ -65,10 +65,10 @@ export const ApolloFeatureDetailsWidgetModel = types // eslint disables because of // https://mobx-state-tree.js.org/tips/typescript#using-a-mst-type-at-design-time -// eslint-disable-next-line @typescript-eslint/no-empty-interface +// eslint-disable-next-line @typescript-eslint/no-empty-object-type export interface ApolloFeatureDetailsWidget extends Instance {} -// eslint-disable-next-line @typescript-eslint/no-empty-interface +// eslint-disable-next-line @typescript-eslint/no-empty-object-type export interface ApolloFeatureDetailsWidgetSnapshot extends SnapshotIn {} @@ -126,9 +126,9 @@ export const ApolloTranscriptDetailsModel = types // eslint disables because of // https://mobx-state-tree.js.org/tips/typescript#using-a-mst-type-at-design-time -// eslint-disable-next-line @typescript-eslint/no-empty-interface +// eslint-disable-next-line @typescript-eslint/no-empty-object-type export interface ApolloTranscriptDetailsWidget extends Instance {} -// eslint-disable-next-line @typescript-eslint/no-empty-interface +// eslint-disable-next-line @typescript-eslint/no-empty-object-type export interface ApolloTranscriptDetailsWidgetSnapshot extends SnapshotIn {} diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/components/LinearApolloDisplay.tsx b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/components/LinearApolloDisplay.tsx index 88b4100e4..2ab5d4378 100644 --- a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/components/LinearApolloDisplay.tsx +++ b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/components/LinearApolloDisplay.tsx @@ -1,3 +1,4 @@ +/* eslint-disable @typescript-eslint/no-unsafe-call */ /* eslint-disable @typescript-eslint/unbound-method */ /* eslint-disable @typescript-eslint/no-misused-promises */ /* eslint-disable @typescript-eslint/no-unnecessary-condition */ diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/index.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/index.ts index 7461d6c22..ecbf0d416 100644 --- a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/index.ts +++ b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/index.ts @@ -19,6 +19,6 @@ export function stateModelFactory( export type LinearApolloDisplayStateModel = ReturnType // eslint disable because of // https://mobx-state-tree.js.org/tips/typescript#using-a-mst-type-at-design-time -// eslint-disable-next-line @typescript-eslint/no-empty-interface +// eslint-disable-next-line @typescript-eslint/no-empty-object-type export interface LinearApolloDisplay extends Instance {} diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/mouseEvents.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/mouseEvents.ts index 34b649e0c..d8325640c 100644 --- a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/mouseEvents.ts +++ b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/mouseEvents.ts @@ -499,6 +499,6 @@ export type LinearApolloDisplayMouseEventsModel = ReturnType< > // eslint disable because of // https://mobx-state-tree.js.org/tips/typescript#using-a-mst-type-at-design-time -// eslint-disable-next-line @typescript-eslint/no-empty-interface +// eslint-disable-next-line @typescript-eslint/no-empty-object-type export interface LinearApolloDisplayMouseEvents extends Instance {} diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/rendering.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/rendering.ts index 35cb0b322..28656f3d6 100644 --- a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/rendering.ts +++ b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/rendering.ts @@ -445,6 +445,6 @@ export type LinearApolloDisplayRenderingModel = ReturnType< > // eslint disable because of // https://mobx-state-tree.js.org/tips/typescript#using-a-mst-type-at-design-time -// eslint-disable-next-line @typescript-eslint/no-empty-interface +// eslint-disable-next-line @typescript-eslint/no-empty-object-type export interface LinearApolloDisplayRendering extends Instance {} diff --git a/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/index.ts b/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/index.ts index 09763c1a2..26ae05219 100644 --- a/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/index.ts +++ b/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/index.ts @@ -5,6 +5,7 @@ import { BlobLocation, LocalPathLocation, UriLocation, + isLocalPathLocation, isUriLocation, } from '@jbrowse/core/util' import { @@ -43,15 +44,6 @@ export type Transaction< /** the format of the loading data source */ type SourceType = 'obo-graph-json' | 'obo' | 'owl' -/** - * @deprecated use the one from jbrowse core when it is published - **/ -function isLocalPathLocation(location: unknown): location is LocalPathLocation { - return ( - typeof location === 'object' && location !== null && 'localPath' in location - ) -} - async function arrayFromAsync(iter: AsyncIterable) { const a = [] for await (const i of iter) { @@ -508,7 +500,7 @@ export default class OntologyStore { // fetch the full nodes and filter out deprecated ones const terms: OntologyClass[] = [] - for await (const termId of termIds) { + for (const termId of termIds) { const node = await myTx.objectStore('nodes').get(termId) if (node && isOntologyClass(node) && !isDeprecated(node)) { terms.push(node) diff --git a/packages/jbrowse-plugin-apollo/src/OntologyManager/index.ts b/packages/jbrowse-plugin-apollo/src/OntologyManager/index.ts index d10f0edf6..6273f095c 100644 --- a/packages/jbrowse-plugin-apollo/src/OntologyManager/index.ts +++ b/packages/jbrowse-plugin-apollo/src/OntologyManager/index.ts @@ -180,9 +180,9 @@ export const OntologyRecordConfiguration = ConfigurationSchema( // eslint disables because of // https://mobx-state-tree.js.org/tips/typescript#using-a-mst-type-at-design-time -// eslint-disable-next-line @typescript-eslint/no-empty-interface +// eslint-disable-next-line @typescript-eslint/no-empty-object-type export interface OntologyManager extends Instance {} -// eslint-disable-next-line @typescript-eslint/no-empty-interface +// eslint-disable-next-line @typescript-eslint/no-empty-object-type export interface OntologyRecord extends Instance {} export type OntologyTerm = OntologyDBNode diff --git a/packages/jbrowse-plugin-apollo/src/SixFrameFeatureDisplay/stateModel.ts b/packages/jbrowse-plugin-apollo/src/SixFrameFeatureDisplay/stateModel.ts index 41c2dad84..e9a3930dc 100644 --- a/packages/jbrowse-plugin-apollo/src/SixFrameFeatureDisplay/stateModel.ts +++ b/packages/jbrowse-plugin-apollo/src/SixFrameFeatureDisplay/stateModel.ts @@ -425,6 +425,6 @@ export type SixFrameFeatureDisplayStateModel = ReturnType< > // eslint disable because of // https://mobx-state-tree.js.org/tips/typescript#using-a-mst-type-at-design-time -// eslint-disable-next-line @typescript-eslint/no-empty-interface +// eslint-disable-next-line @typescript-eslint/no-empty-object-type export interface SixFrameFeatureDisplay extends Instance {} diff --git a/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/HybridGrid.tsx b/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/HybridGrid.tsx index d33bd0d12..9672d47fe 100644 --- a/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/HybridGrid.tsx +++ b/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/HybridGrid.tsx @@ -1,3 +1,4 @@ +/* eslint-disable @typescript-eslint/no-unsafe-call */ import { Menu, MenuItem } from '@jbrowse/core/ui' import { useTheme } from '@mui/material' import { observer } from 'mobx-react' diff --git a/packages/jbrowse-plugin-apollo/src/TabularEditor/model.ts b/packages/jbrowse-plugin-apollo/src/TabularEditor/model.ts index 967d2529c..e541da824 100644 --- a/packages/jbrowse-plugin-apollo/src/TabularEditor/model.ts +++ b/packages/jbrowse-plugin-apollo/src/TabularEditor/model.ts @@ -41,6 +41,6 @@ export const TabularEditorStateModelType = types // eslint disable because of // https://mobx-state-tree.js.org/tips/typescript#using-a-mst-type-at-design-time -// eslint-disable-next-line @typescript-eslint/no-empty-interface +// eslint-disable-next-line @typescript-eslint/no-empty-object-type export interface TabularEditorStateModel extends Instance {} diff --git a/packages/jbrowse-plugin-apollo/src/components/OntologyTermAutocomplete.tsx b/packages/jbrowse-plugin-apollo/src/components/OntologyTermAutocomplete.tsx index 83cbde99b..21c515983 100644 --- a/packages/jbrowse-plugin-apollo/src/components/OntologyTermAutocomplete.tsx +++ b/packages/jbrowse-plugin-apollo/src/components/OntologyTermAutocomplete.tsx @@ -1,6 +1,5 @@ /* eslint-disable @typescript-eslint/no-unnecessary-condition */ -/* eslint-disable @typescript-eslint/no-unsafe-argument */ -/* eslint-disable @typescript-eslint/no-unsafe-member-access */ + import { AbstractSessionModel, isAbortException } from '@jbrowse/core/util' import { Autocomplete, @@ -93,7 +92,7 @@ export function OntologyTermAutocomplete({ setCurrentOntologyTerm(term) } }, - (error) => { + (error: unknown) => { if (!signal.aborted && !isAbortException(error)) { setCurrentOntologyTermInvalid(String(error)) } @@ -116,10 +115,10 @@ export function OntologyTermAutocomplete({ setTermChoices(soTerms) } }, - (error) => { + (error: unknown) => { if (!signal.aborted && !isAbortException(error)) { ;(session as unknown as AbstractSessionModel).notify( - error.message, + error instanceof Error ? error.message : String(error), 'error', ) } diff --git a/packages/jbrowse-plugin-apollo/src/components/OpenLocalFile.tsx b/packages/jbrowse-plugin-apollo/src/components/OpenLocalFile.tsx index 28ac3f24a..fe2f060da 100644 --- a/packages/jbrowse-plugin-apollo/src/components/OpenLocalFile.tsx +++ b/packages/jbrowse-plugin-apollo/src/components/OpenLocalFile.tsx @@ -1,3 +1,4 @@ +/* eslint-disable @typescript-eslint/no-unsafe-call */ /* eslint-disable @typescript-eslint/unbound-method */ /* eslint-disable @typescript-eslint/no-unnecessary-condition */ /* eslint-disable @typescript-eslint/no-misused-promises */ @@ -36,7 +37,7 @@ export function OpenLocalFile({ handleClose, session }: OpenLocalFileProps) { const { apolloDataStore } = session const { addAssembly, addSessionAssembly, assemblyManager, notify } = session as unknown as AbstractSessionModel & { - // eslint-disable-next-line @typescript-eslint/ban-types + // eslint-disable-next-line @typescript-eslint/no-unsafe-function-type addSessionAssembly: Function } diff --git a/packages/jbrowse-plugin-apollo/src/extensions/annotationFromPileup.ts b/packages/jbrowse-plugin-apollo/src/extensions/annotationFromPileup.ts index bc9b3671f..89c789a74 100644 --- a/packages/jbrowse-plugin-apollo/src/extensions/annotationFromPileup.ts +++ b/packages/jbrowse-plugin-apollo/src/extensions/annotationFromPileup.ts @@ -17,7 +17,7 @@ import { ApolloSessionModel } from '../session' function parseCigar(cigar: string): [string | undefined, number][] { return (cigar.toUpperCase().match(/\d+\D/g) ?? []).map((op) => { - return [(op.match(/\D/) ?? [])[0], Number.parseInt(op, 10)] + return [(/\D/.exec(op) ?? [])[0], Number.parseInt(op, 10)] }) } diff --git a/packages/jbrowse-plugin-apollo/src/session/session.ts b/packages/jbrowse-plugin-apollo/src/session/session.ts index 615ff0e47..85bb21e3f 100644 --- a/packages/jbrowse-plugin-apollo/src/session/session.ts +++ b/packages/jbrowse-plugin-apollo/src/session/session.ts @@ -434,5 +434,5 @@ export type ApolloSessionStateModel = ReturnType // @ts-expect-error Snapshots seem to mess up types here // eslint disable because of // https://mobx-state-tree.js.org/tips/typescript#using-a-mst-type-at-design-time -// eslint-disable-next-line @typescript-eslint/no-empty-interface +// eslint-disable-next-line @typescript-eslint/no-empty-object-type export interface ApolloSessionModel extends Instance {} diff --git a/packages/website/src/components/HomepageFeatures/index.tsx b/packages/website/src/components/HomepageFeatures/index.tsx index 6b9c9c9ad..b15099074 100755 --- a/packages/website/src/components/HomepageFeatures/index.tsx +++ b/packages/website/src/components/HomepageFeatures/index.tsx @@ -1,17 +1,19 @@ +/* eslint-disable @typescript-eslint/no-require-imports */ import { clsx } from 'clsx' import Heading from '@theme/Heading' +import React from 'react' import styles from './styles.module.css' interface FeatureItem { title: string Svg: React.ComponentType> - description: JSX.Element + description: React.JSX.Element } const FeatureList: FeatureItem[] = [ { title: 'Easy to Use', - // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment, @typescript-eslint/no-var-requires, @typescript-eslint/no-unsafe-member-access + // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment, @typescript-eslint/no-unsafe-member-access Svg: require('@site/static/img/undraw_docusaurus_mountain.svg').default, description: ( <> @@ -22,7 +24,7 @@ const FeatureList: FeatureItem[] = [ }, { title: 'Focus on What Matters', - // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment, @typescript-eslint/no-var-requires, @typescript-eslint/no-unsafe-member-access + // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment, @typescript-eslint/no-unsafe-member-access Svg: require('@site/static/img/undraw_docusaurus_tree.svg').default, description: ( <> @@ -33,7 +35,7 @@ const FeatureList: FeatureItem[] = [ }, { title: 'Powered by React', - // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment, @typescript-eslint/no-var-requires, @typescript-eslint/no-unsafe-member-access + // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment, @typescript-eslint/no-unsafe-member-access Svg: require('@site/static/img/undraw_docusaurus_react.svg').default, description: ( <> @@ -58,7 +60,7 @@ function Feature({ Svg, description, title }: FeatureItem) { ) } -export default function HomepageFeatures(): JSX.Element { +export default function HomepageFeatures(): React.JSX.Element { return (
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version: 7.18.0 - resolution: "@typescript-eslint/visitor-keys@npm:7.18.0" +"@typescript-eslint/visitor-keys@npm:8.14.0": + version: 8.14.0 + resolution: "@typescript-eslint/visitor-keys@npm:8.14.0" dependencies: - "@typescript-eslint/types": "npm:7.18.0" + "@typescript-eslint/types": "npm:8.14.0" eslint-visitor-keys: "npm:^3.4.3" - checksum: 10c0/538b645f8ff1d9debf264865c69a317074eaff0255e63d7407046176b0f6a6beba34a6c51d511f12444bae12a98c69891eb6f403c9f54c6c2e2849d1c1cb73c0 + checksum: 10c0/d0faf70ed9ecff5e36694bbb161a90bea6db59e0e79a7d4f264d67d565c12b13733d664b736b2730935f013c87ce3155cea954a533d28e99987681bc5f6259c3 languageName: node linkType: hard @@ -10996,7 +10994,7 @@ __metadata: languageName: node linkType: hard -"ajv@npm:8.12.0, ajv@npm:^8.0.0": +"ajv@npm:8.12.0, ajv@npm:^8.0.0, ajv@npm:~8.12.0": version: 8.12.0 resolution: "ajv@npm:8.12.0" dependencies: @@ -11008,7 +11006,7 @@ __metadata: languageName: node linkType: hard -"ajv@npm:^6.12.2, ajv@npm:^6.12.4, ajv@npm:^6.12.5, ajv@npm:~6.12.6": +"ajv@npm:^6.12.2, ajv@npm:^6.12.4, ajv@npm:^6.12.5": version: 6.12.6 resolution: "ajv@npm:6.12.6" dependencies: @@ -11197,19 +11195,19 @@ __metadata: "@types/node": "npm:^18.14.2" "@types/semver": "npm:^7" "@types/yargs": "npm:^17.0.32" - "@typescript-eslint/eslint-plugin": "npm:^7.18.0" - "@typescript-eslint/parser": "npm:^7.18.0" + "@typescript-eslint/eslint-plugin": "npm:^8.14.0" + "@typescript-eslint/parser": "npm:^8.14.0" "@yarnpkg/types": "npm:^4.0.0" cross-env: "npm:^7.0.3" cross-spawn: "npm:^7.0.3" eslint: "npm:^8.57.1" eslint-import-resolver-typescript: "npm:^3.6.3" - eslint-plugin-cypress: "npm:^2.15.2" + eslint-plugin-cypress: "npm:^4.1.0" eslint-plugin-import: "npm:^2.31.0" eslint-plugin-jsx-a11y: "npm:^6.10.2" eslint-plugin-react: "npm:^7.37.2" - eslint-plugin-react-hooks: "npm:^4.6.2" - eslint-plugin-tsdoc: "npm:^0.2.17" + eslint-plugin-react-hooks: "npm:^5.0.0" + eslint-plugin-tsdoc: "npm:^0.3.0" eslint-plugin-unicorn: "npm:^48.0.1" husky: "npm:^9.0.11" lint-staged: "npm:^15.2.2" @@ -16013,14 +16011,14 @@ __metadata: languageName: node linkType: hard -"eslint-plugin-cypress@npm:^2.15.2": - version: 2.15.2 - resolution: "eslint-plugin-cypress@npm:2.15.2" +"eslint-plugin-cypress@npm:^4.1.0": + version: 4.1.0 + resolution: "eslint-plugin-cypress@npm:4.1.0" dependencies: - globals: "npm:^13.20.0" + globals: "npm:^15.11.0" peerDependencies: - eslint: ">= 3.2.1" - checksum: 10c0/bcc521633251a852dc3c115455ddda931435bb61c0895e5ad1abe43acb3a15fc0b0e79bf73b7aa078794a2b1084232f1b74ffe39d631a3f312265f97941cd290 + eslint: ">=9" + checksum: 10c0/991d3cc48ed139a52bec4e48e3be2b97274c63f0dd1d14f5b2a1a86315c9adf8a85c91837d64a83b177f07b8c410634d6db44f2555b97aeb96549f4dfac04b10 languageName: node linkType: hard @@ -16104,12 +16102,12 @@ __metadata: languageName: node linkType: hard -"eslint-plugin-react-hooks@npm:^4.6.2": - version: 4.6.2 - resolution: "eslint-plugin-react-hooks@npm:4.6.2" +"eslint-plugin-react-hooks@npm:^5.0.0": + version: 5.0.0 + resolution: "eslint-plugin-react-hooks@npm:5.0.0" peerDependencies: - eslint: ^3.0.0 || ^4.0.0 || ^5.0.0 || ^6.0.0 || ^7.0.0 || ^8.0.0-0 - checksum: 10c0/4844e58c929bc05157fb70ba1e462e34f1f4abcbc8dd5bbe5b04513d33e2699effb8bca668297976ceea8e7ebee4e8fc29b9af9d131bcef52886feaa2308b2cc + eslint: ^3.0.0 || ^4.0.0 || ^5.0.0 || ^6.0.0 || ^7.0.0 || ^8.0.0-0 || ^9.0.0 + checksum: 10c0/bcb74b421f32e4203a7100405b57aab85526be4461e5a1da01bc537969a30012d2ee209a2c2a6cac543833a27188ce1e6ad71e4628d0bb4a2e5365cad86c5002 languageName: node linkType: hard @@ -16141,13 +16139,13 @@ __metadata: languageName: node linkType: hard -"eslint-plugin-tsdoc@npm:^0.2.17": - version: 0.2.17 - resolution: "eslint-plugin-tsdoc@npm:0.2.17" +"eslint-plugin-tsdoc@npm:^0.3.0": + version: 0.3.0 + resolution: "eslint-plugin-tsdoc@npm:0.3.0" dependencies: - "@microsoft/tsdoc": "npm:0.14.2" - "@microsoft/tsdoc-config": "npm:0.16.2" - checksum: 10c0/26cad40b22f3dc0adfb06b1ea12f7d3c9cb257ac8bb56ad6a023e3b3bdfc6144d95a8b01323563e75283cca90baaf4d68816f5cea6994c6cd660a642e820847a + "@microsoft/tsdoc": "npm:0.15.0" + "@microsoft/tsdoc-config": "npm:0.17.0" + checksum: 10c0/2ee35c661ad9cd3032ec40a4f7b02c04dddd3ecc40afcd8ea509b744c8bedafb408b0a0466e6f28ef771645fa55bf4600a4ad534723f36fc149ef92dc1f6719e languageName: node linkType: hard @@ -17890,7 +17888,7 @@ __metadata: languageName: node linkType: hard -"globals@npm:^13.19.0, globals@npm:^13.20.0": +"globals@npm:^13.19.0": version: 13.23.0 resolution: "globals@npm:13.23.0" dependencies: @@ -17899,6 +17897,13 @@ __metadata: languageName: node linkType: hard +"globals@npm:^15.11.0": + version: 15.12.0 + resolution: "globals@npm:15.12.0" + checksum: 10c0/f34e0a1845b694f45188331742af9f488b07ba7440a06e9d2039fce0386fbbfc24afdbb9846ebdccd4092d03644e43081c49eb27b30f4b88e43af156e1c1dc34 + languageName: node + linkType: hard + "globalthis@npm:^1.0.3": version: 1.0.3 resolution: "globalthis@npm:1.0.3" @@ -19213,7 +19218,7 @@ __metadata: languageName: node linkType: hard -"is-core-module@npm:^2.1.0, is-core-module@npm:^2.13.0": +"is-core-module@npm:^2.13.0": version: 2.13.0 resolution: "is-core-module@npm:2.13.0" dependencies: @@ -24796,7 +24801,7 @@ __metadata: languageName: node linkType: hard -"path-parse@npm:^1.0.6, path-parse@npm:^1.0.7": +"path-parse@npm:^1.0.7": version: 1.0.7 resolution: "path-parse@npm:1.0.7" checksum: 10c0/11ce261f9d294cc7a58d6a574b7f1b935842355ec66fba3c3fd79e0f036462eaf07d0aa95bb74ff432f9afef97ce1926c720988c6a7451d8a584930ae7de86e1 @@ -26899,7 +26904,7 @@ __metadata: languageName: node linkType: hard -"resolve@npm:^1.0.0, resolve@npm:^1.1.6, resolve@npm:^1.10.0, resolve@npm:^1.14.2, resolve@npm:^1.17.0, resolve@npm:^1.19.0, resolve@npm:^1.20.0, resolve@npm:^1.22.4": +"resolve@npm:^1.0.0, resolve@npm:^1.1.6, resolve@npm:^1.10.0, resolve@npm:^1.14.2, resolve@npm:^1.17.0, resolve@npm:^1.19.0, resolve@npm:^1.20.0, resolve@npm:^1.22.4, resolve@npm:~1.22.2": version: 1.22.8 resolution: "resolve@npm:1.22.8" dependencies: @@ -26925,17 +26930,7 @@ __metadata: languageName: node linkType: hard -"resolve@npm:~1.19.0": - version: 1.19.0 - resolution: "resolve@npm:1.19.0" - dependencies: - is-core-module: "npm:^2.1.0" - path-parse: "npm:^1.0.6" - checksum: 10c0/1c8afdfb88c9adab0a19b6f16756d47f5917f64047bf5a38c17aa543aae5ccca2a0631671b19ce8460a7a3e65ead98ee70e046d3056ec173d3377a27487848a8 - languageName: node - linkType: hard - -"resolve@patch:resolve@npm%3A^1.0.0#optional!builtin, resolve@patch:resolve@npm%3A^1.1.6#optional!builtin, resolve@patch:resolve@npm%3A^1.10.0#optional!builtin, resolve@patch:resolve@npm%3A^1.14.2#optional!builtin, resolve@patch:resolve@npm%3A^1.17.0#optional!builtin, resolve@patch:resolve@npm%3A^1.19.0#optional!builtin, resolve@patch:resolve@npm%3A^1.20.0#optional!builtin, resolve@patch:resolve@npm%3A^1.22.4#optional!builtin": +"resolve@patch:resolve@npm%3A^1.0.0#optional!builtin, resolve@patch:resolve@npm%3A^1.1.6#optional!builtin, resolve@patch:resolve@npm%3A^1.10.0#optional!builtin, resolve@patch:resolve@npm%3A^1.14.2#optional!builtin, resolve@patch:resolve@npm%3A^1.17.0#optional!builtin, resolve@patch:resolve@npm%3A^1.19.0#optional!builtin, resolve@patch:resolve@npm%3A^1.20.0#optional!builtin, resolve@patch:resolve@npm%3A^1.22.4#optional!builtin, resolve@patch:resolve@npm%3A~1.22.2#optional!builtin": version: 1.22.8 resolution: "resolve@patch:resolve@npm%3A1.22.8#optional!builtin::version=1.22.8&hash=c3c19d" dependencies: @@ -26961,16 +26956,6 @@ __metadata: languageName: node linkType: hard -"resolve@patch:resolve@npm%3A~1.19.0#optional!builtin": - version: 1.19.0 - resolution: "resolve@patch:resolve@npm%3A1.19.0#optional!builtin::version=1.19.0&hash=c3c19d" - dependencies: - is-core-module: "npm:^2.1.0" - path-parse: "npm:^1.0.6" - checksum: 10c0/254980f60dd9fdb28b34a511e70df6e3027d9627efce86a40757eea9b87252d172829c84517554560c4541ebfe207868270c19a0f086997b41209367aa8ef74f - languageName: node - linkType: hard - "responselike@npm:^2.0.0": version: 2.0.1 resolution: "responselike@npm:2.0.1" From 7bb9019e80aab512fed0453f3ea3f536e12bdaff Mon Sep 17 00:00:00 2001 From: Garrett Stevens Date: Fri, 15 Nov 2024 20:00:12 -0700 Subject: [PATCH 05/12] eslint-plugin-unicorn major version updates --- package.json | 2 +- .../src/commands/assembly/add-from-fasta.ts | 2 +- .../src/commands/assembly/add-from-gff.ts | 2 +- .../src/commands/assembly/get.test.ts | 8 +- .../src/commands/change/get.test.ts | 4 +- .../src/commands/feature/add-child.ts | 4 +- .../apollo-cli/src/commands/file/upload.ts | 4 +- .../apollo-cli/src/commands/user/get.test.ts | 4 +- packages/apollo-cli/src/fileCommand.ts | 2 +- packages/apollo-cli/src/utils.ts | 2 +- .../src/files/files.service.ts | 10 +- .../src/files/filesUtil.ts | 8 +- .../src/refSeqs/refSeqs.service.ts | 1 + .../src/Changes/AddFeatureChange.ts | 4 +- packages/apollo-shared/src/util.ts | 1 + .../cypress/e2e/editFeature.cy.ts | 4 +- .../src/ApolloInternetAccount/model.ts | 4 +- .../components/ApolloRendering.tsx | 9 +- .../LinearApolloDisplay/glyphs/GeneGlyph.ts | 2 +- .../OntologyManager/OntologyStore/fulltext.ts | 5 +- .../OntologyStore/index.test.ts | 3 +- .../src/components/AddFeature.tsx | 1 - .../src/components/LogOut.tsx | 2 +- .../src/components/ManageChecks.tsx | 2 +- .../src/components/ManageUsers.tsx | 2 +- .../components/OntologyTermAutocomplete.tsx | 4 +- .../src/makeDisplayComponent.tsx | 12 +- yarn.lock | 112 +++++++++++++++--- 28 files changed, 152 insertions(+), 68 deletions(-) diff --git a/package.json b/package.json index 5c6bcc247..ede125594 100644 --- a/package.json +++ b/package.json @@ -34,7 +34,7 @@ "eslint-plugin-react": "^7.37.2", "eslint-plugin-react-hooks": "^5.0.0", "eslint-plugin-tsdoc": "^0.3.0", - "eslint-plugin-unicorn": "^48.0.1", + "eslint-plugin-unicorn": "^56.0.0", "husky": "^9.0.11", "lint-staged": "^15.2.2", "npm-run-all": "^4.1.5", diff --git a/packages/apollo-cli/src/commands/assembly/add-from-fasta.ts b/packages/apollo-cli/src/commands/assembly/add-from-fasta.ts index 1b9b9b318..78ae3ebd1 100644 --- a/packages/apollo-cli/src/commands/assembly/add-from-fasta.ts +++ b/packages/apollo-cli/src/commands/assembly/add-from-fasta.ts @@ -1,6 +1,6 @@ /* eslint-disable @typescript-eslint/no-unnecessary-condition */ import * as fs from 'node:fs' -import * as path from 'node:path' +import path from 'node:path' import { Args, Flags } from '@oclif/core' import { ObjectId } from 'bson' diff --git a/packages/apollo-cli/src/commands/assembly/add-from-gff.ts b/packages/apollo-cli/src/commands/assembly/add-from-gff.ts index 1eede29bb..ae7dbad97 100644 --- a/packages/apollo-cli/src/commands/assembly/add-from-gff.ts +++ b/packages/apollo-cli/src/commands/assembly/add-from-gff.ts @@ -1,5 +1,5 @@ import * as fs from 'node:fs' -import * as path from 'node:path' +import path from 'node:path' import { Args, Flags } from '@oclif/core' import { ObjectId } from 'bson' diff --git a/packages/apollo-cli/src/commands/assembly/get.test.ts b/packages/apollo-cli/src/commands/assembly/get.test.ts index 2d203383e..d9aafbefe 100644 --- a/packages/apollo-cli/src/commands/assembly/get.test.ts +++ b/packages/apollo-cli/src/commands/assembly/get.test.ts @@ -1,5 +1,5 @@ import fs from 'node:fs' -import { dirname } from 'node:path' +import path from 'node:path' import { fileURLToPath } from 'node:url' import { expect, test } from '@oclif/test' @@ -26,7 +26,7 @@ describe.skip('apollo assembly get: Fail without token', () => { const cmd = ['assembly:get'] test .stderr() - .command(cmd, { root: dirname(dirname(__dirname)) }) + .command(cmd, { root: path.dirname(path.dirname(__dirname)) }) .exit(1) .do((output) => expect(output.stderr).to.contain('Profile "default" has no access token'), @@ -47,7 +47,7 @@ describe.skip('apollo assembly get: Get assemblies as YAML string', () => { const cmd = ['assembly:get'] test .stdout() - .command(cmd, { root: dirname(dirname(__dirname)) }) + .command(cmd, { root: path.dirname(path.dirname(__dirname)) }) .it(cmd.join(' '), (output) => { JSON.parse(output.stdout) }) @@ -60,7 +60,7 @@ describe.skip('apollo assembly get: Test nock', () => { .nock('http://127.0.0.1:3999', (api) => api.persist().get('/assemblies').reply(200, { stuff: 'foo' }), ) - .command(cmd, { root: dirname(dirname(__dirname)) }) + .command(cmd, { root: path.dirname(path.dirname(__dirname)) }) .it(cmd.join(' '), (output) => { console.error(output.stdout) // const out = JSON.parse(output.stdout) diff --git a/packages/apollo-cli/src/commands/change/get.test.ts b/packages/apollo-cli/src/commands/change/get.test.ts index 690800953..0ab56eccd 100644 --- a/packages/apollo-cli/src/commands/change/get.test.ts +++ b/packages/apollo-cli/src/commands/change/get.test.ts @@ -1,5 +1,5 @@ import fs from 'node:fs' -import { dirname } from 'node:path' +import path from 'node:path' import { fileURLToPath } from 'node:url' import { test } from '@oclif/test' @@ -25,7 +25,7 @@ describe.skip('apollo change get: Get changes as YAML string', () => { const cmd = ['change:get'] test .stdout() - .command(cmd, { root: dirname(dirname(__dirname)) }) + .command(cmd, { root: path.dirname(path.dirname(__dirname)) }) .it(cmd.join(' '), (output) => { JSON.parse(output.stdout) }) diff --git a/packages/apollo-cli/src/commands/feature/add-child.ts b/packages/apollo-cli/src/commands/feature/add-child.ts index e82cdfb82..0ce89018d 100644 --- a/packages/apollo-cli/src/commands/feature/add-child.ts +++ b/packages/apollo-cli/src/commands/feature/add-child.ts @@ -130,7 +130,7 @@ to retrive the parent ID of interest and to populate the child feature with attr } const change: SerializedAddFeatureChange = { typeName: 'AddFeatureChange', - // eslint-disable-next-line unicorn/consistent-destructuring + changedIds: [parentFeature._id], assembly, addedFeature: { @@ -140,7 +140,7 @@ to retrive the parent ID of interest and to populate the child feature with attr max, type, }, - // eslint-disable-next-line unicorn/consistent-destructuring + parentFeatureId: parentFeature._id, } const url = new URL(localhostToAddress(`${address}/changes`)) diff --git a/packages/apollo-cli/src/commands/file/upload.ts b/packages/apollo-cli/src/commands/file/upload.ts index 97076bf8f..ddbe15fd1 100644 --- a/packages/apollo-cli/src/commands/file/upload.ts +++ b/packages/apollo-cli/src/commands/file/upload.ts @@ -81,11 +81,11 @@ export default class Upload extends FileCommand { } let isGzip = args['input-file'].endsWith('.gz') - // eslint-disable-next-line unicorn/consistent-destructuring + if (flags.gzip) { isGzip = true } - // eslint-disable-next-line unicorn/consistent-destructuring + if (flags.decompressed) { isGzip = false } diff --git a/packages/apollo-cli/src/commands/user/get.test.ts b/packages/apollo-cli/src/commands/user/get.test.ts index 9f117d2a9..ebff4eeaa 100644 --- a/packages/apollo-cli/src/commands/user/get.test.ts +++ b/packages/apollo-cli/src/commands/user/get.test.ts @@ -1,5 +1,5 @@ import fs from 'node:fs' -import { dirname } from 'node:path' +import path from 'node:path' import { fileURLToPath } from 'node:url' import { expect, test } from '@oclif/test' @@ -25,7 +25,7 @@ describe.skip('apollo user get: Get users as YAML string', () => { const cmd = ['user:get'] test .stdout() - .command(cmd, { root: dirname(dirname(__dirname)) }) + .command(cmd, { root: path.dirname(path.dirname(__dirname)) }) .it(cmd.join(' '), (output) => { const str: string = JSON.stringify(JSON.parse(output.stdout)) expect(str).contain('username') diff --git a/packages/apollo-cli/src/fileCommand.ts b/packages/apollo-cli/src/fileCommand.ts index 88489c2ef..6ac2b632a 100644 --- a/packages/apollo-cli/src/fileCommand.ts +++ b/packages/apollo-cli/src/fileCommand.ts @@ -1,5 +1,5 @@ import * as fs from 'node:fs' -import * as path from 'node:path' +import path from 'node:path' import { Transform, TransformCallback, diff --git a/packages/apollo-cli/src/utils.ts b/packages/apollo-cli/src/utils.ts index ba494b34e..41a74815d 100644 --- a/packages/apollo-cli/src/utils.ts +++ b/packages/apollo-cli/src/utils.ts @@ -123,7 +123,7 @@ export async function getAssembly( const assemblies = (await res.json()) as ApolloAssemblySnapshot[] for (const x of assemblies) { if (x._id === assemblyId[0]) { - return JSON.parse(JSON.stringify(x)) as ApolloAssemblySnapshot + return structuredClone(x) } } throw new Error(`Assembly "${assemblyNameOrId}" not found`) diff --git a/packages/apollo-collaboration-server/src/files/files.service.ts b/packages/apollo-collaboration-server/src/files/files.service.ts index 571341c6e..63f81f00c 100644 --- a/packages/apollo-collaboration-server/src/files/files.service.ts +++ b/packages/apollo-collaboration-server/src/files/files.service.ts @@ -1,6 +1,6 @@ import { ReadStream, createReadStream } from 'node:fs' import { unlink } from 'node:fs/promises' -import { join } from 'node:path' +import path from 'node:path' import { Gunzip, createGunzip } from 'node:zlib' import { File, FileDocument } from '@apollo-annotation/schemas' @@ -76,7 +76,9 @@ export class FilesService { const fileUploadFolder = this.configService.get('FILE_UPLOAD_FOLDER', { infer: true, }) - const fileStream = createReadStream(join(fileUploadFolder, file.checksum)) + const fileStream = createReadStream( + path.join(fileUploadFolder, file.checksum), + ) if (compressed) { return fileStream } @@ -90,7 +92,7 @@ export class FilesService { const fileUploadFolder = this.configService.get('FILE_UPLOAD_FOLDER', { infer: true, }) - const fileName = join(fileUploadFolder, file.checksum) + const fileName = path.join(fileUploadFolder, file.checksum) switch (file.type) { case 'text/x-fai': case 'application/x-gzi': { @@ -142,7 +144,7 @@ export class FilesService { const fileUploadFolder = this.configService.get('FILE_UPLOAD_FOLDER', { infer: true, }) - const compressedFullFileName = join(fileUploadFolder, file.checksum) + const compressedFullFileName = path.join(fileUploadFolder, file.checksum) this.logger.debug( `Delete the file "${compressedFullFileName}" from server folder`, ) diff --git a/packages/apollo-collaboration-server/src/files/filesUtil.ts b/packages/apollo-collaboration-server/src/files/filesUtil.ts index 85ec3ef04..ce959c66e 100644 --- a/packages/apollo-collaboration-server/src/files/filesUtil.ts +++ b/packages/apollo-collaboration-server/src/files/filesUtil.ts @@ -8,7 +8,7 @@ import { rename, rmdir, } from 'node:fs/promises' -import { join } from 'node:path' +import path from 'node:path' import { Readable } from 'node:stream' import { pipeline } from 'node:stream/promises' import { promisify } from 'node:util' @@ -41,8 +41,8 @@ export async function writeFileAndCalculateHash( const { contentEncoding, originalname, size, stream } = file await mkdir(fileUploadFolder, { recursive: true }) logger.log(`Starting file upload: "${originalname}"`) - const tmpDir = await mkdtemp(join(fileUploadFolder, 'upload-tmp-')) - const tmpFileName = join(tmpDir, `${originalname}.gz`) + const tmpDir = await mkdtemp(path.join(fileUploadFolder, 'upload-tmp-')) + const tmpFileName = path.join(tmpDir, `${originalname}.gz`) logger.debug(`Uploading to temporary file "${tmpFileName}"`) // We calculate the md5 hash as the file is being uploaded @@ -81,7 +81,7 @@ export async function writeFileAndCalculateHash( const fileChecksum = hash.digest('hex') logger.debug(`Uploaded file checksum: "${fileChecksum}"`) - const uploadedFileName = join(fileUploadFolder, fileChecksum) + const uploadedFileName = path.join(fileUploadFolder, fileChecksum) logger.debug( `File uploaded successfully, moving temporary file to final location: "${uploadedFileName}"`, ) diff --git a/packages/apollo-collaboration-server/src/refSeqs/refSeqs.service.ts b/packages/apollo-collaboration-server/src/refSeqs/refSeqs.service.ts index 14dc25330..d5471e1be 100644 --- a/packages/apollo-collaboration-server/src/refSeqs/refSeqs.service.ts +++ b/packages/apollo-collaboration-server/src/refSeqs/refSeqs.service.ts @@ -21,6 +21,7 @@ export class RefSeqsService { } findAll(filter?: FindRefSeqDto) { + // eslint-disable-next-line unicorn/no-array-callback-reference return this.refSeqModel.find(filter ?? {}).exec() } diff --git a/packages/apollo-shared/src/Changes/AddFeatureChange.ts b/packages/apollo-shared/src/Changes/AddFeatureChange.ts index e250d909f..7f4dd2132 100644 --- a/packages/apollo-shared/src/Changes/AddFeatureChange.ts +++ b/packages/apollo-shared/src/Changes/AddFeatureChange.ts @@ -1,5 +1,5 @@ /* eslint-disable @typescript-eslint/restrict-template-expressions */ -/* eslint-disable @typescript-eslint/no-unsafe-assignment */ + /* eslint-disable @typescript-eslint/require-await */ /* eslint-disable @typescript-eslint/no-unnecessary-condition */ import { @@ -143,7 +143,7 @@ export class AddFeatureChange extends FeatureChange { } attributes = { _id: [parentFeature._id.toString()], - ...JSON.parse(JSON.stringify(attributes)), + ...structuredClone(attributes), } parentFeature.attributes = attributes } diff --git a/packages/apollo-shared/src/util.ts b/packages/apollo-shared/src/util.ts index 36dda6c67..cfedc71a9 100644 --- a/packages/apollo-shared/src/util.ts +++ b/packages/apollo-shared/src/util.ts @@ -12,6 +12,7 @@ export function makeGFF3Feature( // const locations = feature.discontinuousLocations?.length // ? feature.discontinuousLocations // : [{ start: feature.start, end: feature.end, phase: feature.phase }] + // eslint-disable-next-line unicorn/prefer-structured-clone const attributes: Record = JSON.parse( JSON.stringify(feature.attributes), ) diff --git a/packages/jbrowse-plugin-apollo/cypress/e2e/editFeature.cy.ts b/packages/jbrowse-plugin-apollo/cypress/e2e/editFeature.cy.ts index 5a25a3d66..5f1cc46a3 100644 --- a/packages/jbrowse-plugin-apollo/cypress/e2e/editFeature.cy.ts +++ b/packages/jbrowse-plugin-apollo/cypress/e2e/editFeature.cy.ts @@ -2,10 +2,10 @@ describe('Different ways of editing features', () => { before(() => { cy.deleteAssemblies() cy.wrap( - window.indexedDB.databases().then((dbs) => { + globalThis.indexedDB.databases().then((dbs) => { for (const db of dbs) { if (db.name) { - window.indexedDB.deleteDatabase(db.name) + globalThis.indexedDB.deleteDatabase(db.name) } } }), diff --git a/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/model.ts b/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/model.ts index 2b7d4fbe0..c0a728311 100644 --- a/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/model.ts +++ b/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/model.ts @@ -135,7 +135,7 @@ const stateModelFactory = (configSchema: ApolloInternetAccountConfigModel) => { ) { const redirectUri = isElectron ? 'http://localhost/auth' - : window.location.origin + window.location.pathname + : globalThis.location.origin + globalThis.location.pathname const url = new URL('auth/login', self.baseURL) const params = new URLSearchParams({ type, @@ -144,7 +144,7 @@ const stateModelFactory = (configSchema: ApolloInternetAccountConfigModel) => { url.search = params.toString() const eventName = `JBrowseAuthWindow-${self.internetAccountId}` if (isElectron) { - const { ipcRenderer } = window.require('electron') + const { ipcRenderer } = globalThis.require('electron') const redirectUriFromElectron = await ipcRenderer.invoke( 'openAuthWindow', { diff --git a/packages/jbrowse-plugin-apollo/src/ApolloSixFrameRenderer/components/ApolloRendering.tsx b/packages/jbrowse-plugin-apollo/src/ApolloSixFrameRenderer/components/ApolloRendering.tsx index cccef00e4..99551b21a 100644 --- a/packages/jbrowse-plugin-apollo/src/ApolloSixFrameRenderer/components/ApolloRendering.tsx +++ b/packages/jbrowse-plugin-apollo/src/ApolloSixFrameRenderer/components/ApolloRendering.tsx @@ -551,7 +551,7 @@ function ApolloRendering(props: ApolloRenderingProps) { } await changeManager.submit(change) } - // eslint-disable-next-line unicorn/no-useless-undefined + setDragging(undefined) setMovedDuringLastMouseDown(false) } @@ -575,7 +575,6 @@ function ApolloRendering(props: ApolloRenderingProps) { } data-testid="base_linear_display_context_menu" onClose={() => { - // eslint-disable-next-line unicorn/no-useless-undefined setContextMenuFeature(undefined) }} > @@ -595,7 +594,7 @@ function ApolloRendering(props: ApolloRenderingProps) { session, handleClose: () => { doneCallback() - // eslint-disable-next-line unicorn/no-useless-undefined + setContextMenuFeature(undefined) }, changeManager, @@ -625,7 +624,7 @@ function ApolloRendering(props: ApolloRenderingProps) { session, handleClose: () => { doneCallback() - // eslint-disable-next-line unicorn/no-useless-undefined + setContextMenuFeature(undefined) }, changeManager, @@ -654,7 +653,7 @@ function ApolloRendering(props: ApolloRenderingProps) { session, handleClose: () => { doneCallback() - // eslint-disable-next-line unicorn/no-useless-undefined + setContextMenuFeature(undefined) }, changeManager, diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/GeneGlyph.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/GeneGlyph.ts index f8e01be7c..5e2bf515d 100644 --- a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/GeneGlyph.ts +++ b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/GeneGlyph.ts @@ -17,7 +17,7 @@ let forwardFillLight: CanvasPattern | null = null let backwardFillLight: CanvasPattern | null = null let forwardFillDark: CanvasPattern | null = null let backwardFillDark: CanvasPattern | null = null -if ('document' in window) { +if ('document' in globalThis) { for (const direction of ['forward', 'backward']) { for (const themeMode of ['light', 'dark']) { const canvas = document.createElement('canvas') diff --git a/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/fulltext.ts b/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/fulltext.ts index 0f5500c58..2354fa6cb 100644 --- a/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/fulltext.ts +++ b/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/fulltext.ts @@ -170,7 +170,10 @@ export function elaborateMatch( const sortedWordIndexes = [...queryWordIndexes].sort() const matchedQueryWords = sortedWordIndexes.map((i) => queryWords[i]) const queryWordRegexps = matchedQueryWords.map((queryWord) => { - const escaped = queryWord.replaceAll(/[$()*+./?[\\\]^{|}-]/g, '\\$&') + const escaped = queryWord.replaceAll( + /[$()*+./?[\\\]^{|}-]/g, + String.raw`\$&`, + ) return new RegExp(`\\b${escaped}`, 'gi') }) // const needle = matchedQueryWords.join(' ') diff --git a/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/index.test.ts b/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/index.test.ts index d7a5e8a7c..57f7f2b81 100644 --- a/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/index.test.ts +++ b/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/index.test.ts @@ -24,8 +24,7 @@ jest.mock('jsonpath', () => { ...original, // eslint-disable-next-line @typescript-eslint/no-explicit-any query: jest.fn((obj: any, pathExpression: string, count?: number) => { - const newObj = - obj instanceof Object ? obj : JSON.parse(JSON.stringify(obj)) + const newObj = obj instanceof Object ? obj : structuredClone(obj) return original.query(newObj, pathExpression, count) }), } diff --git a/packages/jbrowse-plugin-apollo/src/components/AddFeature.tsx b/packages/jbrowse-plugin-apollo/src/components/AddFeature.tsx index 71d11fe5b..0c589e7a1 100644 --- a/packages/jbrowse-plugin-apollo/src/components/AddFeature.tsx +++ b/packages/jbrowse-plugin-apollo/src/components/AddFeature.tsx @@ -102,7 +102,6 @@ export function AddFeature({ break } default: { - // eslint-disable-next-line unicorn/no-useless-undefined setStrand(undefined) } } diff --git a/packages/jbrowse-plugin-apollo/src/components/LogOut.tsx b/packages/jbrowse-plugin-apollo/src/components/LogOut.tsx index c4d0a07d2..4f58cfe2d 100644 --- a/packages/jbrowse-plugin-apollo/src/components/LogOut.tsx +++ b/packages/jbrowse-plugin-apollo/src/components/LogOut.tsx @@ -50,7 +50,7 @@ export function LogOut({ handleClose, session }: DeleteAssemblyProps) { event.preventDefault() setErrorMessage('') selectedInternetAccount.removeToken() - window.location.reload() + globalThis.location.reload() } return ( diff --git a/packages/jbrowse-plugin-apollo/src/components/ManageChecks.tsx b/packages/jbrowse-plugin-apollo/src/components/ManageChecks.tsx index 86962a1c6..2e08f9aa1 100644 --- a/packages/jbrowse-plugin-apollo/src/components/ManageChecks.tsx +++ b/packages/jbrowse-plugin-apollo/src/components/ManageChecks.tsx @@ -182,7 +182,7 @@ export function ManageChecks({ handleClose, session }: ManageChecksProps) { } } else { const index = checks.indexOf(_id, 0) - if (index > -1) { + if (index !== -1) { checks.splice(index, 1) } setSelectedChecks(checks) diff --git a/packages/jbrowse-plugin-apollo/src/components/ManageUsers.tsx b/packages/jbrowse-plugin-apollo/src/components/ManageUsers.tsx index c3047d3ae..2a77ce77c 100644 --- a/packages/jbrowse-plugin-apollo/src/components/ManageUsers.tsx +++ b/packages/jbrowse-plugin-apollo/src/components/ManageUsers.tsx @@ -155,7 +155,7 @@ export function ManageUsers({ key={`delete-${params.id}`} icon={} onClick={async () => { - if (window.confirm('Delete this user?')) { + if (globalThis.confirm('Delete this user?')) { await deleteUser(params.id) } }} diff --git a/packages/jbrowse-plugin-apollo/src/components/OntologyTermAutocomplete.tsx b/packages/jbrowse-plugin-apollo/src/components/OntologyTermAutocomplete.tsx index 21c515983..3feaa47e3 100644 --- a/packages/jbrowse-plugin-apollo/src/components/OntologyTermAutocomplete.tsx +++ b/packages/jbrowse-plugin-apollo/src/components/OntologyTermAutocomplete.tsx @@ -75,7 +75,6 @@ export function OntologyTermAutocomplete({ // effect for clearing choices when not open useEffect(() => { if (!open) { - // eslint-disable-next-line unicorn/no-useless-undefined setTermChoices(undefined) } }, [open]) @@ -144,7 +143,6 @@ export function OntologyTermAutocomplete({ return } if (typeof newValue === 'string') { - // eslint-disable-next-line unicorn/no-useless-undefined setCurrentOntologyTerm(undefined) onChange(valueString, newValue) } else if (newValue.lbl !== valueString) { @@ -211,7 +209,7 @@ async function getCurrentTerm( currentTermLabel, { includeSubclasses: false }, ) - const term = terms.find(filterTerms ?? (() => true)) + const term = terms.find((term) => (filterTerms ?? (() => true))(term)) if (!term) { throw new Error(`not a valid ${ontologyStore.ontologyName} term`) } diff --git a/packages/jbrowse-plugin-apollo/src/makeDisplayComponent.tsx b/packages/jbrowse-plugin-apollo/src/makeDisplayComponent.tsx index 6cb76a645..9e2d69ce9 100644 --- a/packages/jbrowse-plugin-apollo/src/makeDisplayComponent.tsx +++ b/packages/jbrowse-plugin-apollo/src/makeDisplayComponent.tsx @@ -95,9 +95,9 @@ const ResizeHandle = ({ (event: MouseEvent) => { event.stopPropagation() event.preventDefault() - window.removeEventListener('mousemove', mouseMove) - window.removeEventListener('mouseup', cancelDrag) - window.removeEventListener('mouseleave', cancelDrag) + globalThis.removeEventListener('mousemove', mouseMove) + globalThis.removeEventListener('mouseup', cancelDrag) + globalThis.removeEventListener('mouseleave', cancelDrag) }, [mouseMove], ) @@ -107,9 +107,9 @@ const ResizeHandle = ({
{ event.stopPropagation() - window.addEventListener('mousemove', mouseMove) - window.addEventListener('mouseup', cancelDrag) - window.addEventListener('mouseleave', cancelDrag) + globalThis.addEventListener('mousemove', mouseMove) + globalThis.addEventListener('mouseup', cancelDrag) + globalThis.addEventListener('mouseleave', cancelDrag) }} onClick={(e) => { e.stopPropagation() diff --git a/yarn.lock b/yarn.lock index d17f0f726..f8d429015 100644 --- a/yarn.lock +++ b/yarn.lock @@ -2450,7 +2450,7 @@ __metadata: languageName: node linkType: hard -"@babel/helper-validator-identifier@npm:^7.22.20, @babel/helper-validator-identifier@npm:^7.22.5": +"@babel/helper-validator-identifier@npm:^7.22.20": version: 7.22.20 resolution: "@babel/helper-validator-identifier@npm:7.22.20" checksum: 10c0/dcad63db345fb110e032de46c3688384b0008a42a4845180ce7cd62b1a9c0507a1bed727c4d1060ed1a03ae57b4d918570259f81724aaac1a5b776056f37504e @@ -11208,7 +11208,7 @@ __metadata: eslint-plugin-react: "npm:^7.37.2" eslint-plugin-react-hooks: "npm:^5.0.0" eslint-plugin-tsdoc: "npm:^0.3.0" - eslint-plugin-unicorn: "npm:^48.0.1" + eslint-plugin-unicorn: "npm:^56.0.0" husky: "npm:^9.0.11" lint-staged: "npm:^15.2.2" npm-run-all: "npm:^4.1.5" @@ -12410,6 +12410,20 @@ __metadata: languageName: node linkType: hard +"browserslist@npm:^4.24.2": + version: 4.24.2 + resolution: "browserslist@npm:4.24.2" + dependencies: + caniuse-lite: "npm:^1.0.30001669" + electron-to-chromium: "npm:^1.5.41" + node-releases: "npm:^2.0.18" + update-browserslist-db: "npm:^1.1.1" + bin: + browserslist: cli.js + checksum: 10c0/d747c9fb65ed7b4f1abcae4959405707ed9a7b835639f8a9ba0da2911995a6ab9b0648fd05baf2a4d4e3cf7f9fdbad56d3753f91881e365992c1d49c8d88ff7a + languageName: node + linkType: hard + "bs-logger@npm:0.x": version: 0.2.6 resolution: "bs-logger@npm:0.2.6" @@ -12821,6 +12835,13 @@ __metadata: languageName: node linkType: hard +"caniuse-lite@npm:^1.0.30001669": + version: 1.0.30001680 + resolution: "caniuse-lite@npm:1.0.30001680" + checksum: 10c0/11a4e7f6f5d5f965cfd4b7dc4aef34e12a26e99647f02b5ac9fd7f7670845473b95ada416a785473237e4b1b67281f7b043c8736c85b77097f6b697e8950b15f + languageName: node + linkType: hard + "canvas-sequencer@npm:^3.1.0": version: 3.1.0 resolution: "canvas-sequencer@npm:3.1.0" @@ -13138,13 +13159,20 @@ __metadata: languageName: node linkType: hard -"ci-info@npm:^3.2.0, ci-info@npm:^3.8.0": +"ci-info@npm:^3.2.0": version: 3.9.0 resolution: "ci-info@npm:3.9.0" checksum: 10c0/6f0109e36e111684291d46123d491bc4e7b7a1934c3a20dea28cba89f1d4a03acd892f5f6a81ed3855c38647e285a150e3c9ba062e38943bef57fee6c1554c3a languageName: node linkType: hard +"ci-info@npm:^4.0.0": + version: 4.1.0 + resolution: "ci-info@npm:4.1.0" + checksum: 10c0/0f969ce32a974c542bc8abe4454b220d9d9323bb9415054c92a900faa5fdda0bb222eda68c490127c1d78503510d46b6aca614ecaba5a60515b8ac7e170119e6 + languageName: node + linkType: hard + "cipher-base@npm:^1.0.0, cipher-base@npm:^1.0.1, cipher-base@npm:^1.0.3": version: 1.0.4 resolution: "cipher-base@npm:1.0.4" @@ -13958,6 +13986,15 @@ __metadata: languageName: node linkType: hard +"core-js-compat@npm:^3.38.1": + version: 3.39.0 + resolution: "core-js-compat@npm:3.39.0" + dependencies: + browserslist: "npm:^4.24.2" + checksum: 10c0/880579a3dab235e3b6350f1e324269c600753b48e891ea859331618d5051e68b7a95db6a03ad2f3cc7df4397318c25a5bc7740562ad39e94f56568638d09d414 + languageName: node + linkType: hard + "core-js-pure@npm:^3.30.2": version: 3.38.1 resolution: "core-js-pure@npm:3.38.1" @@ -15346,6 +15383,13 @@ __metadata: languageName: node linkType: hard +"electron-to-chromium@npm:^1.5.41": + version: 1.5.62 + resolution: "electron-to-chromium@npm:1.5.62" + checksum: 10c0/93dc628f0359df0cae475cf5e91fa0cf357611f14da7cf15c28fe92f89dede7def20c04b24787e6166181ae582b060d02b252e906d7ec84020485579a95bc8e9 + languageName: node + linkType: hard + "elliptic@npm:^6.5.3": version: 6.5.4 resolution: "elliptic@npm:6.5.4" @@ -15884,6 +15928,13 @@ __metadata: languageName: node linkType: hard +"escalade@npm:^3.2.0": + version: 3.2.0 + resolution: "escalade@npm:3.2.0" + checksum: 10c0/ced4dd3a78e15897ed3be74e635110bbf3b08877b0a41be50dcb325ee0e0b5f65fc2d50e9845194d7c4633f327e2e1c6cce00a71b617c5673df0374201d67f65 + languageName: node + linkType: hard + "escape-goat@npm:^4.0.0": version: 4.0.0 resolution: "escape-goat@npm:4.0.0" @@ -16149,28 +16200,29 @@ __metadata: languageName: node linkType: hard -"eslint-plugin-unicorn@npm:^48.0.1": - version: 48.0.1 - resolution: "eslint-plugin-unicorn@npm:48.0.1" +"eslint-plugin-unicorn@npm:^56.0.0": + version: 56.0.0 + resolution: "eslint-plugin-unicorn@npm:56.0.0" dependencies: - "@babel/helper-validator-identifier": "npm:^7.22.5" + "@babel/helper-validator-identifier": "npm:^7.24.7" "@eslint-community/eslint-utils": "npm:^4.4.0" - ci-info: "npm:^3.8.0" + ci-info: "npm:^4.0.0" clean-regexp: "npm:^1.0.0" - esquery: "npm:^1.5.0" + core-js-compat: "npm:^3.38.1" + esquery: "npm:^1.6.0" + globals: "npm:^15.9.0" indent-string: "npm:^4.0.0" is-builtin-module: "npm:^3.2.1" jsesc: "npm:^3.0.2" - lodash: "npm:^4.17.21" pluralize: "npm:^8.0.0" read-pkg-up: "npm:^7.0.1" regexp-tree: "npm:^0.1.27" regjsparser: "npm:^0.10.0" - semver: "npm:^7.5.4" + semver: "npm:^7.6.3" strip-indent: "npm:^3.0.0" peerDependencies: - eslint: ">=8.44.0" - checksum: 10c0/158a9fc41c213a2d4a4d7ed9c866c86f9f1901d7f7371c60f3e18d05be73cb6982b72c33a679955142116032127835f8550b466484885c0cedb2e7ed951136ac + eslint: ">=8.56.0" + checksum: 10c0/514b8da5423041e88723e9a46e1d9b77b8713b4bb3cd9beb58949907f2f4ce6533a9e1d7508bd0583d2f48c191f8134f27cd229dfb05f97431ecec49f24fcbf6 languageName: node linkType: hard @@ -16280,7 +16332,7 @@ __metadata: languageName: node linkType: hard -"esquery@npm:^1.4.2, esquery@npm:^1.5.0": +"esquery@npm:^1.4.2": version: 1.5.0 resolution: "esquery@npm:1.5.0" dependencies: @@ -16289,6 +16341,15 @@ __metadata: languageName: node linkType: hard +"esquery@npm:^1.6.0": + version: 1.6.0 + resolution: "esquery@npm:1.6.0" + dependencies: + estraverse: "npm:^5.1.0" + checksum: 10c0/cb9065ec605f9da7a76ca6dadb0619dfb611e37a81e318732977d90fab50a256b95fee2d925fba7c2f3f0523aa16f91587246693bc09bc34d5a59575fe6e93d2 + languageName: node + linkType: hard + "esrecurse@npm:^4.3.0": version: 4.3.0 resolution: "esrecurse@npm:4.3.0" @@ -17897,7 +17958,7 @@ __metadata: languageName: node linkType: hard -"globals@npm:^15.11.0": +"globals@npm:^15.11.0, globals@npm:^15.9.0": version: 15.12.0 resolution: "globals@npm:15.12.0" checksum: 10c0/f34e0a1845b694f45188331742af9f488b07ba7440a06e9d2039fce0386fbbfc24afdbb9846ebdccd4092d03644e43081c49eb27b30f4b88e43af156e1c1dc34 @@ -24956,6 +25017,13 @@ __metadata: languageName: node linkType: hard +"picocolors@npm:^1.1.0": + version: 1.1.1 + resolution: "picocolors@npm:1.1.1" + checksum: 10c0/e2e3e8170ab9d7c7421969adaa7e1b31434f789afb9b3f115f6b96d91945041ac3ceb02e9ec6fe6510ff036bcc0bf91e69a1772edc0b707e12b19c0f2d6bcf58 + languageName: node + linkType: hard + "picomatch@npm:2.3.1, picomatch@npm:^2.0.4, picomatch@npm:^2.2.1, picomatch@npm:^2.2.2, picomatch@npm:^2.2.3, picomatch@npm:^2.3.1": version: 2.3.1 resolution: "picomatch@npm:2.3.1" @@ -30197,6 +30265,20 @@ __metadata: languageName: node linkType: hard +"update-browserslist-db@npm:^1.1.1": + version: 1.1.1 + resolution: "update-browserslist-db@npm:1.1.1" + dependencies: + escalade: "npm:^3.2.0" + picocolors: "npm:^1.1.0" + peerDependencies: + browserslist: ">= 4.21.0" + bin: + update-browserslist-db: cli.js + checksum: 10c0/536a2979adda2b4be81b07e311bd2f3ad5e978690987956bc5f514130ad50cac87cd22c710b686d79731e00fbee8ef43efe5fcd72baa241045209195d43dcc80 + languageName: node + linkType: hard + "update-check@npm:1.5.4": version: 1.5.4 resolution: "update-check@npm:1.5.4" From a8b5b15b4eded06296369e0c0f5a8cd09c341d79 Mon Sep 17 00:00:00 2001 From: Garrett Stevens Date: Mon, 18 Nov 2024 12:40:38 -0700 Subject: [PATCH 06/12] Fix js file lint --- .eslintrc.js | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/.eslintrc.js b/.eslintrc.js index 1ac1038c5..62d5f04c0 100644 --- a/.eslintrc.js +++ b/.eslintrc.js @@ -123,12 +123,14 @@ module.exports = { }, // Specify Node env and tsconfig for cypress testing and config files { - files: [ - './packages/jbrowse-plugin-apollo/cypress.config.js', - './packages/jbrowse-plugin-apollo/cypress/**/*.{j,t}s', - ], + files: ['packages/jbrowse-plugin-apollo/cypress.config.js'], parserOptions: { - project: 'packages/jbrowse-plugin-apollo/cypress/tsconfig.json', + projectService: { + allowDefaultProject: [ + 'packages/jbrowse-plugin-apollo/cypress.config.js', + ], + }, + defaultProject: 'packages/jbrowse-plugin-apollo/cypress/tsconfig.json', }, env: { node: true }, }, From 99da59fd64c412acd6d012361b4e6b9a78f4cfc8 Mon Sep 17 00:00:00 2001 From: Garrett Stevens Date: Mon, 18 Nov 2024 16:07:24 -0700 Subject: [PATCH 07/12] Update base tslint structure --- .eslintrc.js | 18 +---- packages/apollo-cli/tsconfig.eslint.json | 5 -- .../apollo-collaboration-server/tsconfig.json | 2 +- packages/apollo-common/tsconfig.json | 2 +- packages/apollo-mst/tsconfig.json | 2 +- packages/apollo-schemas/tsconfig.json | 2 +- packages/apollo-shared/tsconfig.json | 2 +- .../tsconfig.eslint.json | 5 -- packages/jbrowse-plugin-apollo/tsconfig.json | 2 +- tsconfig-base.json | 73 +++++++++++++++++++ tsconfig.json | 73 ++----------------- 11 files changed, 89 insertions(+), 97 deletions(-) create mode 100644 tsconfig-base.json diff --git a/.eslintrc.js b/.eslintrc.js index 62d5f04c0..c9c253ce4 100644 --- a/.eslintrc.js +++ b/.eslintrc.js @@ -12,7 +12,10 @@ module.exports = { plugins: ['import', 'tsdoc'], parser: '@typescript-eslint/parser', parserOptions: { - project: true, + projectService: { + allowDefaultProject: ['packages/jbrowse-plugin-apollo/*.js'], + }, + defaultProject: 'tsconfig.json', }, env: { 'shared-node-browser': true }, settings: { @@ -121,19 +124,6 @@ module.exports = { }, env: { node: true }, }, - // Specify Node env and tsconfig for cypress testing and config files - { - files: ['packages/jbrowse-plugin-apollo/cypress.config.js'], - parserOptions: { - projectService: { - allowDefaultProject: [ - 'packages/jbrowse-plugin-apollo/cypress.config.js', - ], - }, - defaultProject: 'packages/jbrowse-plugin-apollo/cypress/tsconfig.json', - }, - env: { node: true }, - }, // Specify Node env for apollo-collaboration-server/ { files: ['./packages/apollo-collaboration-server/**/*.ts'], diff --git a/packages/apollo-cli/tsconfig.eslint.json b/packages/apollo-cli/tsconfig.eslint.json index 455d2080c..d22466d83 100644 --- a/packages/apollo-cli/tsconfig.eslint.json +++ b/packages/apollo-cli/tsconfig.eslint.json @@ -1,9 +1,4 @@ { "extends": "../../tsconfig.json", - "compilerOptions": { - "types": ["@types/node"], - "noEmit": true, - "allowJs": true, - }, "include": ["jest.config.cjs, babel.config.js"], } diff --git a/packages/apollo-collaboration-server/tsconfig.json b/packages/apollo-collaboration-server/tsconfig.json index f3c7d5490..40aef39a5 100644 --- a/packages/apollo-collaboration-server/tsconfig.json +++ b/packages/apollo-collaboration-server/tsconfig.json @@ -1,5 +1,5 @@ { - "extends": "../../tsconfig.json", + "extends": "../../tsconfig-base.json", "compilerOptions": { "module": "commonjs", "removeComments": true, diff --git a/packages/apollo-common/tsconfig.json b/packages/apollo-common/tsconfig.json index 321ecb228..9ea29de08 100644 --- a/packages/apollo-common/tsconfig.json +++ b/packages/apollo-common/tsconfig.json @@ -1,5 +1,5 @@ { - "extends": "../../tsconfig.json", + "extends": "../../tsconfig-base.json", "compilerOptions": { "composite": true, "incremental": true, diff --git a/packages/apollo-mst/tsconfig.json b/packages/apollo-mst/tsconfig.json index b78a94f9f..ae9e5b6c4 100644 --- a/packages/apollo-mst/tsconfig.json +++ b/packages/apollo-mst/tsconfig.json @@ -1,5 +1,5 @@ { - "extends": "../../tsconfig.json", + "extends": "../../tsconfig-base.json", "compilerOptions": { "composite": true, "incremental": true, diff --git a/packages/apollo-schemas/tsconfig.json b/packages/apollo-schemas/tsconfig.json index b78a94f9f..ae9e5b6c4 100644 --- a/packages/apollo-schemas/tsconfig.json +++ b/packages/apollo-schemas/tsconfig.json @@ -1,5 +1,5 @@ { - "extends": "../../tsconfig.json", + "extends": "../../tsconfig-base.json", "compilerOptions": { "composite": true, "incremental": true, diff --git a/packages/apollo-shared/tsconfig.json b/packages/apollo-shared/tsconfig.json index aaed27558..d786167aa 100644 --- a/packages/apollo-shared/tsconfig.json +++ b/packages/apollo-shared/tsconfig.json @@ -1,5 +1,5 @@ { - "extends": "../../tsconfig.json", + "extends": "../../tsconfig-base.json", "compilerOptions": { "composite": true, "incremental": true, diff --git a/packages/jbrowse-plugin-apollo/tsconfig.eslint.json b/packages/jbrowse-plugin-apollo/tsconfig.eslint.json index 51ddddecc..49e941452 100644 --- a/packages/jbrowse-plugin-apollo/tsconfig.eslint.json +++ b/packages/jbrowse-plugin-apollo/tsconfig.eslint.json @@ -1,9 +1,4 @@ { "extends": "../../tsconfig.json", - "compilerOptions": { - "types": ["@types/node"], - "noEmit": true, - "allowJs": true, - }, "include": ["jest.config.js", "jestSetup.js", "rollup.config.js"], } diff --git a/packages/jbrowse-plugin-apollo/tsconfig.json b/packages/jbrowse-plugin-apollo/tsconfig.json index 0a1b8f905..9c1819ee1 100644 --- a/packages/jbrowse-plugin-apollo/tsconfig.json +++ b/packages/jbrowse-plugin-apollo/tsconfig.json @@ -1,5 +1,5 @@ { - "extends": "../../tsconfig.json", + "extends": "../../tsconfig-base.json", "compilerOptions": { "declaration": false, "target": "ES6", diff --git a/tsconfig-base.json b/tsconfig-base.json new file mode 100644 index 000000000..fff121c6f --- /dev/null +++ b/tsconfig-base.json @@ -0,0 +1,73 @@ +{ + "compilerOptions": { + /* Visit https://aka.ms/tsconfig.json to read more about this file */ + + /* Basic Options */ + // "incremental": true, /* Enable incremental compilation */ + "target": "es5" /* Specify ECMAScript target version: 'ES3' (default), 'ES5', 'ES2015', 'ES2016', 'ES2017', 'ES2018', 'ES2019', 'ES2020', or 'ESNEXT'. */, + "module": "esnext" /* Specify module code generation: 'none', 'commonjs', 'amd', 'system', 'umd', 'es2015', 'es2020', or 'ESNext'. */, + "lib": [ + "dom", + "esnext", + ] /* Specify library files to be included in the compilation. */, + // "allowJs": true, /* Allow javascript files to be compiled. */ + // "checkJs": true, /* Report errors in .js files. */ + "jsx": "react" /* Specify JSX code generation: 'preserve', 'react-native', or 'react'. */, + "declaration": true /* Generates corresponding '.d.ts' file. */, + // "declarationMap": true, /* Generates a sourcemap for each corresponding '.d.ts' file. */ + "sourceMap": true /* Generates corresponding '.map' file. */, + // "outFile": "./", /* Concatenate and emit output to single file. */ + // "outDir": "./", /* Redirect output structure to the directory. */ + // "rootDir": "./", /* Specify the root directory of input files. Use to control the output directory structure with --outDir. */ + // "composite": true, /* Enable project compilation */ + // "tsBuildInfoFile": "./", /* Specify file to store incremental compilation information */ + // "removeComments": true, /* Do not emit comments to output. */ + // "noEmit": true, /* Do not emit outputs. */ + "importHelpers": true /* Import emit helpers from 'tslib'. */, + "downlevelIteration": true /* Provide full support for iterables in 'for-of', spread, and destructuring when targeting 'ES5' or 'ES3'. */, + // "isolatedModules": true, /* Transpile each file as a separate module (similar to 'ts.transpileModule'). */ + + /* Strict Type-Checking Options */ + "strict": true /* Enable all strict type-checking options. */, + // "noImplicitAny": true, /* Raise error on expressions and declarations with an implied 'any' type. */ + // "strictNullChecks": true, /* Enable strict null checks. */ + // "strictFunctionTypes": true, /* Enable strict checking of function types. */ + // "strictBindCallApply": true, /* Enable strict 'bind', 'call', and 'apply' methods on functions. */ + // "strictPropertyInitialization": true, /* Enable strict checking of property initialization in classes. */ + // "noImplicitThis": true, /* Raise error on 'this' expressions with an implied 'any' type. */ + // "alwaysStrict": true, /* Parse in strict mode and emit "use strict" for each source file. */ + + /* Additional Checks */ + // "noUnusedLocals": true, /* Report errors on unused locals. */ + // "noUnusedParameters": true, /* Report errors on unused parameters. */ + "noImplicitReturns": true /* Report error when not all code paths in function return a value. */, + "noFallthroughCasesInSwitch": true /* Report errors for fallthrough cases in switch statement. */, + // "noUncheckedIndexedAccess": true, /* Include 'undefined' in index signature results */ + + /* Module Resolution Options */ + "moduleResolution": "node" /* Specify module resolution strategy: 'node' (Node.js) or 'classic' (TypeScript pre-1.6). */, + // "baseUrl": "./", /* Base directory to resolve non-absolute module names. */ + // "paths": {}, /* A series of entries which re-map imports to lookup locations relative to the 'baseUrl'. */ + // "rootDirs": [], /* List of root folders whose combined content represents the structure of the project at runtime. */ + // "typeRoots": [], /* List of folders to include type definitions from. */ + // "types": [], /* Type declaration files to be included in compilation. */ + // "allowSyntheticDefaultImports": true, /* Allow default imports from modules with no default export. This does not affect code emit, just typechecking. */ + "esModuleInterop": true /* Enables emit interoperability between CommonJS and ES Modules via creation of namespace objects for all imports. Implies 'allowSyntheticDefaultImports'. */, + // "preserveSymlinks": true, /* Do not resolve the real path of symlinks. */ + // "allowUmdGlobalAccess": true, /* Allow accessing UMD globals from modules. */ + + /* Source Map Options */ + // "sourceRoot": "", /* Specify the location where debugger should locate TypeScript files instead of source locations. */ + // "mapRoot": "", /* Specify the location where debugger should locate map files instead of generated locations. */ + // "inlineSourceMap": true, /* Emit a single file with source maps instead of having a separate file. */ + // "inlineSources": true, /* Emit the source alongside the sourcemaps within a single file; requires '--inlineSourceMap' or '--sourceMap' to be set. */ + + /* Experimental Options */ + // "experimentalDecorators": true, /* Enables experimental support for ES7 decorators. */ + // "emitDecoratorMetadata": true, /* Enables experimental support for emitting type metadata for decorators. */ + + /* Advanced Options */ + "skipLibCheck": true /* Skip type checking of declaration files. */, + "forceConsistentCasingInFileNames": true /* Disallow inconsistently-cased references to the same file. */, + }, +} diff --git a/tsconfig.json b/tsconfig.json index 7340b5b89..52ceabfc3 100644 --- a/tsconfig.json +++ b/tsconfig.json @@ -1,70 +1,9 @@ { + "extends": "./tsconfig-base.json", "compilerOptions": { - /* Visit https://aka.ms/tsconfig.json to read more about this file */ - - /* Basic Options */ - // "incremental": true, /* Enable incremental compilation */ - "target": "es5", /* Specify ECMAScript target version: 'ES3' (default), 'ES5', 'ES2015', 'ES2016', 'ES2017', 'ES2018', 'ES2019', 'ES2020', or 'ESNEXT'. */ - "module": "esnext", /* Specify module code generation: 'none', 'commonjs', 'amd', 'system', 'umd', 'es2015', 'es2020', or 'ESNext'. */ - "lib": ["dom", "esnext"], /* Specify library files to be included in the compilation. */ - // "allowJs": true, /* Allow javascript files to be compiled. */ - // "checkJs": true, /* Report errors in .js files. */ - "jsx": "react", /* Specify JSX code generation: 'preserve', 'react-native', or 'react'. */ - "declaration": true, /* Generates corresponding '.d.ts' file. */ - // "declarationMap": true, /* Generates a sourcemap for each corresponding '.d.ts' file. */ - "sourceMap": true, /* Generates corresponding '.map' file. */ - // "outFile": "./", /* Concatenate and emit output to single file. */ - // "outDir": "./", /* Redirect output structure to the directory. */ - // "rootDir": "./", /* Specify the root directory of input files. Use to control the output directory structure with --outDir. */ - // "composite": true, /* Enable project compilation */ - // "tsBuildInfoFile": "./", /* Specify file to store incremental compilation information */ - // "removeComments": true, /* Do not emit comments to output. */ - // "noEmit": true, /* Do not emit outputs. */ - "importHelpers": true, /* Import emit helpers from 'tslib'. */ - "downlevelIteration": true, /* Provide full support for iterables in 'for-of', spread, and destructuring when targeting 'ES5' or 'ES3'. */ - // "isolatedModules": true, /* Transpile each file as a separate module (similar to 'ts.transpileModule'). */ - - /* Strict Type-Checking Options */ - "strict": true, /* Enable all strict type-checking options. */ - // "noImplicitAny": true, /* Raise error on expressions and declarations with an implied 'any' type. */ - // "strictNullChecks": true, /* Enable strict null checks. */ - // "strictFunctionTypes": true, /* Enable strict checking of function types. */ - // "strictBindCallApply": true, /* Enable strict 'bind', 'call', and 'apply' methods on functions. */ - // "strictPropertyInitialization": true, /* Enable strict checking of property initialization in classes. */ - // "noImplicitThis": true, /* Raise error on 'this' expressions with an implied 'any' type. */ - // "alwaysStrict": true, /* Parse in strict mode and emit "use strict" for each source file. */ - - /* Additional Checks */ - // "noUnusedLocals": true, /* Report errors on unused locals. */ - // "noUnusedParameters": true, /* Report errors on unused parameters. */ - "noImplicitReturns": true, /* Report error when not all code paths in function return a value. */ - "noFallthroughCasesInSwitch": true, /* Report errors for fallthrough cases in switch statement. */ - // "noUncheckedIndexedAccess": true, /* Include 'undefined' in index signature results */ - - /* Module Resolution Options */ - "moduleResolution": "node", /* Specify module resolution strategy: 'node' (Node.js) or 'classic' (TypeScript pre-1.6). */ - // "baseUrl": "./", /* Base directory to resolve non-absolute module names. */ - // "paths": {}, /* A series of entries which re-map imports to lookup locations relative to the 'baseUrl'. */ - // "rootDirs": [], /* List of root folders whose combined content represents the structure of the project at runtime. */ - // "typeRoots": [], /* List of folders to include type definitions from. */ - // "types": [], /* Type declaration files to be included in compilation. */ - // "allowSyntheticDefaultImports": true, /* Allow default imports from modules with no default export. This does not affect code emit, just typechecking. */ - "esModuleInterop": true, /* Enables emit interoperability between CommonJS and ES Modules via creation of namespace objects for all imports. Implies 'allowSyntheticDefaultImports'. */ - // "preserveSymlinks": true, /* Do not resolve the real path of symlinks. */ - // "allowUmdGlobalAccess": true, /* Allow accessing UMD globals from modules. */ - - /* Source Map Options */ - // "sourceRoot": "", /* Specify the location where debugger should locate TypeScript files instead of source locations. */ - // "mapRoot": "", /* Specify the location where debugger should locate map files instead of generated locations. */ - // "inlineSourceMap": true, /* Emit a single file with source maps instead of having a separate file. */ - // "inlineSources": true, /* Emit the source alongside the sourcemaps within a single file; requires '--inlineSourceMap' or '--sourceMap' to be set. */ - - /* Experimental Options */ - // "experimentalDecorators": true, /* Enables experimental support for ES7 decorators. */ - // "emitDecoratorMetadata": true, /* Enables experimental support for emitting type metadata for decorators. */ - - /* Advanced Options */ - "skipLibCheck": true, /* Skip type checking of declaration files. */ - "forceConsistentCasingInFileNames": true /* Disallow inconsistently-cased references to the same file. */ - } + "types": ["@types/node"], + "noEmit": true, + "allowJs": true, + }, + "include": ["./*.js", "./*.mjs", "./*.cjs", "scripts/*.ts"], } From b9c9babd5944f916af377576a4dc17921d68ec03 Mon Sep 17 00:00:00 2001 From: Garrett Stevens Date: Mon, 18 Nov 2024 16:37:30 -0700 Subject: [PATCH 08/12] Update to latest eslint major version --- .eslintignore | 5 - .eslintrc.js | 147 -------- .github/workflows/pull_request.yml | 4 +- .github/workflows/push.yml | 2 +- .husky/pre-commit.js | 2 +- eslint.config.mjs | 127 +++++++ package.json | 12 +- .../src/commands/feature/add-child.ts | 6 +- .../apollo-cli/src/commands/file/upload.ts | 5 +- .../src/refSeqs/refSeqs.service.ts | 1 - packages/apollo-shared/src/util.ts | 1 - packages/website/babel.config.js | 1 - packages/website/src/pages/index.tsx | 1 + tsconfig.json | 11 +- yarn.config.cjs | 12 +- yarn.lock | 344 ++++++++++++------ 16 files changed, 396 insertions(+), 285 deletions(-) delete mode 100644 .eslintignore delete mode 100644 .eslintrc.js create mode 100644 eslint.config.mjs diff --git a/.eslintignore b/.eslintignore deleted file mode 100644 index bf23340d3..000000000 --- a/.eslintignore +++ /dev/null @@ -1,5 +0,0 @@ -dist/ -.eslintrc.js -esm/ -coverage/ -bin/ diff --git a/.eslintrc.js b/.eslintrc.js deleted file mode 100644 index c9c253ce4..000000000 --- a/.eslintrc.js +++ /dev/null @@ -1,147 +0,0 @@ -/** @type {import('eslint').Linter.Config} */ - -module.exports = { - extends: [ - 'eslint:recommended', - 'plugin:unicorn/recommended', - 'plugin:cypress/recommended', - 'plugin:import/typescript', - 'plugin:@typescript-eslint/strict-type-checked', - 'plugin:@typescript-eslint/stylistic-type-checked', - ], - plugins: ['import', 'tsdoc'], - parser: '@typescript-eslint/parser', - parserOptions: { - projectService: { - allowDefaultProject: ['packages/jbrowse-plugin-apollo/*.js'], - }, - defaultProject: 'tsconfig.json', - }, - env: { 'shared-node-browser': true }, - settings: { - 'import/resolver': { - typescript: true, - node: true, - }, - }, - rules: { - // eslint built-in rules (override recommended) - curly: 'warn', - 'new-cap': [ - 'error', - { - newIsCap: true, - newIsCapExceptions: [], - capIsNew: false, - capIsNewExceptions: [ - 'Immutable.Map', - 'Immutable.Set', - 'Immutable.List', - ], - }, - ], - 'no-console': ['warn', { allow: ['error', 'warn', 'debug'] }], - 'no-else-return': ['error', { allowElseIf: false }], - 'no-extra-semi': 'off', - 'object-shorthand': 'warn', - 'prefer-destructuring': 'warn', - 'prefer-template': 'warn', - quotes: ['error', 'single', { avoidEscape: true }], - radix: 'error', - 'spaced-comment': [ - 'warn', - 'always', - // allow TS /// directives - { line: { markers: ['/'] } }, - ], - // @typescript-eslint/eslint-plugin rules (override recommended) - '@typescript-eslint/no-extraneous-class': [ - 'error', - { allowWithDecorator: true }, - ], - '@typescript-eslint/no-unused-vars': [ - 'warn', - { argsIgnorePattern: '^_', ignoreRestSiblings: true }, - ], - '@typescript-eslint/restrict-template-expressions': [ - 'warn', - { allowNumber: true }, - ], - '@typescript-eslint/return-await': 'error', - // eslint-plugin-import rules - 'import/export': 'error', - 'import/no-duplicates': 'warn', - 'import/no-extraneous-dependencies': 'error', - 'import/no-named-as-default': 'warn', - // eslint-plugin-tsdoc rules - 'tsdoc/syntax': 'warn', - // eslint-plugin-unicorn rules (override recommended) - 'unicorn/filename-case': 'off', // Doesn't match our file naming, maybe can be configured later - 'unicorn/no-empty-file': 'off', // False positives - 'unicorn/no-null': 'off', // A lot of null in React and other libraries - 'unicorn/prefer-module': 'off', // Cypress and apollo-collaboration-server need this - 'unicorn/prevent-abbreviations': 'off', // Doesn't guess a lot of abbreviations correctly - }, - overrides: [ - // Only use React-specific lint rules in jbrowse-plugin-apollo - { - files: ['./packages/jbrowse-plugin-apollo/**/*.{ts,tsx}'], - env: { browser: true }, - extends: [ - 'plugin:react/recommended', - 'plugin:react-hooks/recommended', - 'plugin:jsx-a11y/recommended', - ], - settings: { - // These settings are from eslint-plugin-react - react: { - // React version. "detect" automatically picks the version you have installed. - // You can also use `16.0`, `16.3`, etc, if you want to override the detected value. - // It will default to "latest" and warn if missing, and to "detect" in the future - version: 'detect', - }, - componentWrapperFunctions: [ - // The name of any function used to wrap components, e.g. Mobx `observer` function. If this isn't set, components wrapped by these functions will be skipped. - 'observer', // `property` - { property: 'styled' }, // `object` is optional - { property: 'observer', object: 'Mobx' }, - { property: 'observer', object: '' }, // sets `object` to whatever value `settings.react.pragma` is set to - ], - }, - }, - // Lint non-src JS files (e.g. jest.config.js) using a separate tsconfig - { - files: ['./packages/jbrowse-plugin-apollo/*.js'], - parserOptions: { - project: 'packages/jbrowse-plugin-apollo/tsconfig.eslint.json', - }, - env: { node: true }, - }, - { - files: ['./packages/apollo-cli/*.{c,}js'], - parserOptions: { - project: 'packages/apollo-cli/tsconfig.eslint.json', - }, - env: { node: true }, - }, - // Specify Node env for apollo-collaboration-server/ - { - files: ['./packages/apollo-collaboration-server/**/*.ts'], - env: { node: true }, - }, - // Don't enforce tsdoc syntax in JS files - { - files: ['**/*.js'], - rules: { - 'tsdoc/syntax': 'off', - }, - }, - // Temporary override - { - files: ['packages/apollo-cli/src/**/*.ts'], - rules: { - '@typescript-eslint/no-deprecated': 'off', - }, - }, - ], -} diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml index d823790f7..d671caa82 100644 --- a/.github/workflows/pull_request.yml +++ b/.github/workflows/pull_request.yml @@ -22,9 +22,7 @@ jobs: run: yarn build working-directory: packages/apollo-shared - name: Lint codebase - run: - yarn eslint --report-unused-disable-directives --max-warnings 0 --ext - .js,.ts,.jsx,.tsx . + run: yarn eslint --max-warnings 0 - name: Run Jest tests run: yarn test - name: Get latest JBrowse diff --git a/.github/workflows/push.yml b/.github/workflows/push.yml index b97234bec..a4f29eea0 100644 --- a/.github/workflows/push.yml +++ b/.github/workflows/push.yml @@ -46,7 +46,7 @@ jobs: run: yarn build working-directory: packages/apollo-shared - name: Lint codebase - run: yarn eslint --ext .js,.ts,.jsx,.tsx . + run: yarn eslint docker: if: ${{ github.ref == 'refs/heads/main' }} uses: ./.github/workflows/docker.yml diff --git a/.husky/pre-commit.js b/.husky/pre-commit.js index 06ed20e05..b453b5d4f 100644 --- a/.husky/pre-commit.js +++ b/.husky/pre-commit.js @@ -3,7 +3,7 @@ * JS/TS files ignored since ESLint provides formatting feedback for those */ -// eslint-disable-next-line @typescript-eslint/no-var-requires, no-undef +// eslint-disable-next-line @typescript-eslint/no-require-imports const spawn = require('cross-spawn') function main() { diff --git a/eslint.config.mjs b/eslint.config.mjs new file mode 100644 index 000000000..365098edd --- /dev/null +++ b/eslint.config.mjs @@ -0,0 +1,127 @@ +import js from '@eslint/js' +import pluginCypress from 'eslint-plugin-cypress/flat' +import pluginImport from 'eslint-plugin-import' +import pluginJSXA11y from 'eslint-plugin-jsx-a11y' +import pluginReact from 'eslint-plugin-react' +import pluginReactHooks from 'eslint-plugin-react-hooks' +import pluginTSDoc from 'eslint-plugin-tsdoc' +import pluginUnicorn from 'eslint-plugin-unicorn' +import globals from 'globals' +import tseslint from 'typescript-eslint' + +/** @type {import('eslint').Linter.Config[]} */ +export default [ + { + ignores: [ + '.pnp.*', + '.yarn/', + '**/bin/', + '**/build/', + '**/coverage/', + '**/dist/', + 'packages/website/.docusaurus/', + 'packages/jbrowse-plugin-apollo/.jbrowse/', + ], + }, + js.configs.recommended, + // eslint-disable-next-line @typescript-eslint/no-unsafe-member-access + pluginUnicorn.configs['flat/recommended'], + // eslint-disable-next-line @typescript-eslint/no-unsafe-member-access + pluginImport.flatConfigs.typescript, + ...tseslint.configs.strictTypeChecked, + ...tseslint.configs.stylisticTypeChecked, + pluginReact.configs.flat.recommended, + // eslint-disable-next-line @typescript-eslint/no-unsafe-member-access + pluginJSXA11y.flatConfigs.recommended, + // eslint-disable-next-line @typescript-eslint/no-unsafe-member-access + pluginCypress.configs.recommended, + { + languageOptions: { + globals: { ...globals.browser, ...globals.node }, + parserOptions: { + projectService: { + allowDefaultProject: ['packages/jbrowse-plugin-apollo/*.js'], + }, + defaultProject: 'tsconfig.json', + // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment + tsconfigRootDir: import.meta.dirname, + }, + }, + settings: { react: { version: '18.2.0' } }, + // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment + plugins: { tsdoc: pluginTSDoc, import: pluginImport }, + rules: { + // eslint built-in rules (override recommended) + curly: 'warn', + 'new-cap': [ + 'error', + { + newIsCap: true, + newIsCapExceptions: [], + capIsNew: false, + capIsNewExceptions: [ + 'Immutable.Map', + 'Immutable.Set', + 'Immutable.List', + ], + }, + ], + 'no-console': ['warn', { allow: ['error', 'warn', 'debug'] }], + 'no-else-return': ['error', { allowElseIf: false }], + 'no-extra-semi': 'off', + 'object-shorthand': 'warn', + 'prefer-destructuring': 'warn', + 'prefer-template': 'warn', + radix: 'error', + // @typescript-eslint/eslint-plugin rules (override recommended) + '@typescript-eslint/no-extraneous-class': [ + 'error', + { allowWithDecorator: true }, + ], + '@typescript-eslint/no-unused-vars': [ + 'warn', + { argsIgnorePattern: '^_', ignoreRestSiblings: true }, + ], + '@typescript-eslint/restrict-template-expressions': [ + 'warn', + { allowNumber: true }, + ], + '@typescript-eslint/return-await': 'error', + // eslint-plugin-import rules + 'import/export': 'error', + 'import/no-duplicates': 'warn', + 'import/no-extraneous-dependencies': 'error', + 'import/no-named-as-default': 'warn', + // eslint-plugin-tsdoc rules + 'tsdoc/syntax': 'warn', + // eslint-plugin-unicorn rules (override recommended) + 'unicorn/filename-case': 'off', // Doesn't match our file naming, maybe can be configured later + 'unicorn/no-empty-file': 'off', // False positives + 'unicorn/no-null': 'off', // A lot of null in React and other libraries + 'unicorn/prefer-module': 'off', // Cypress and apollo-collaboration-server need this + 'unicorn/prevent-abbreviations': 'off', // Doesn't guess a lot of abbreviations correctly + }, + }, + { + name: 'eslint-plugin-react-hooks/recommended', + files: [ + 'packages/jbrowse-plugin-apollo/src/**/*.{jsx,tsx}', + 'packages/website/src/**/*.{jsx,tsx}', + ], + // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment + plugins: { 'react-hooks': pluginReactHooks }, + // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment, @typescript-eslint/no-unsafe-member-access + rules: { ...pluginReactHooks.configs.recommended.rules }, + }, + // Don't enforce tsdoc syntax in JS files + { + files: ['*.{c,m,}js', '**/*.{c,m,}js'], + rules: { + 'tsdoc/syntax': 'off', + }, + }, + { + files: ['packages/apollo-cli/src/**/*.ts'], + rules: { '@typescript-eslint/no-deprecated': 'off' }, + }, +] diff --git a/package.json b/package.json index ede125594..8159c2d7c 100644 --- a/package.json +++ b/package.json @@ -6,7 +6,7 @@ "packages/*" ], "scripts": { - "lint": "cross-env NODE_OPTIONS='--max-old-space-size=4096' yarn eslint --report-unused-disable-directives --max-warnings 0 --ext .js,.ts,.jsx,.tsx .", + "lint": "cross-env NODE_OPTIONS='--max-old-space-size=4096' yarn eslint --max-warnings 0", "build:shared": "yarn workspace @apollo-annotation/shared run build", "release": "tsx scripts/makeGitTag.ts", "start:shared": "yarn workspace @apollo-annotation/shared run start", @@ -17,24 +17,25 @@ "postinstall": "husky" }, "devDependencies": { + "@eslint/js": "^9.14.0", "@types/cross-spawn": "^6.0.6", "@types/node": "^18.14.2", "@types/semver": "^7", "@types/yargs": "^17.0.32", - "@typescript-eslint/eslint-plugin": "^8.14.0", "@typescript-eslint/parser": "^8.14.0", "@yarnpkg/types": "^4.0.0", "cross-env": "^7.0.3", "cross-spawn": "^7.0.3", - "eslint": "^8.57.1", + "eslint": "9.14.0", "eslint-import-resolver-typescript": "^3.6.3", "eslint-plugin-cypress": "^4.1.0", "eslint-plugin-import": "^2.31.0", "eslint-plugin-jsx-a11y": "^6.10.2", "eslint-plugin-react": "^7.37.2", - "eslint-plugin-react-hooks": "^5.0.0", + "eslint-plugin-react-hooks": "5.1.0-rc-4beb1fd8-20241118", "eslint-plugin-tsdoc": "^0.3.0", - "eslint-plugin-unicorn": "^56.0.0", + "eslint-plugin-unicorn": "^50.0.0", + "globals": "^15.12.0", "husky": "^9.0.11", "lint-staged": "^15.2.2", "npm-run-all": "^4.1.5", @@ -44,6 +45,7 @@ "tslib": "^2.3.1", "tsx": "^4.6.2", "typescript": "^5.5.3", + "typescript-eslint": "^8.14.0", "yargs": "^17.7.2" }, "packageManager": "yarn@4.3.1" diff --git a/packages/apollo-cli/src/commands/feature/add-child.ts b/packages/apollo-cli/src/commands/feature/add-child.ts index 0ce89018d..63ec77940 100644 --- a/packages/apollo-cli/src/commands/feature/add-child.ts +++ b/packages/apollo-cli/src/commands/feature/add-child.ts @@ -120,7 +120,7 @@ to retrive the parent ID of interest and to populate the child feature with attr } const res = await queryApollo(address, accessToken, 'refSeqs') const refSeqs = (await res.json()) as object[] - const { refSeq } = parentFeature + const { refSeq, _id } = parentFeature let assembly = '' for (const x of refSeqs) { if (x['_id' as keyof typeof x] === refSeq) { @@ -131,7 +131,7 @@ to retrive the parent ID of interest and to populate the child feature with attr const change: SerializedAddFeatureChange = { typeName: 'AddFeatureChange', - changedIds: [parentFeature._id], + changedIds: [_id], assembly, addedFeature: { _id: new ObjectId().toHexString(), @@ -141,7 +141,7 @@ to retrive the parent ID of interest and to populate the child feature with attr type, }, - parentFeatureId: parentFeature._id, + parentFeatureId: _id, } const url = new URL(localhostToAddress(`${address}/changes`)) const auth = { diff --git a/packages/apollo-cli/src/commands/file/upload.ts b/packages/apollo-cli/src/commands/file/upload.ts index ddbe15fd1..50de557e7 100644 --- a/packages/apollo-cli/src/commands/file/upload.ts +++ b/packages/apollo-cli/src/commands/file/upload.ts @@ -57,6 +57,7 @@ export default class Upload extends FileCommand { const access = await this.getAccess() let { type } = flags + const { gzip, decompressed } = flags if (type === undefined) { const hasGzipExt = args['input-file'].endsWith('.gz') const infile = args['input-file'].replace(/\.gz$/, '') @@ -82,11 +83,11 @@ export default class Upload extends FileCommand { let isGzip = args['input-file'].endsWith('.gz') - if (flags.gzip) { + if (gzip) { isGzip = true } - if (flags.decompressed) { + if (decompressed) { isGzip = false } diff --git a/packages/apollo-collaboration-server/src/refSeqs/refSeqs.service.ts b/packages/apollo-collaboration-server/src/refSeqs/refSeqs.service.ts index d5471e1be..14dc25330 100644 --- a/packages/apollo-collaboration-server/src/refSeqs/refSeqs.service.ts +++ b/packages/apollo-collaboration-server/src/refSeqs/refSeqs.service.ts @@ -21,7 +21,6 @@ export class RefSeqsService { } findAll(filter?: FindRefSeqDto) { - // eslint-disable-next-line unicorn/no-array-callback-reference return this.refSeqModel.find(filter ?? {}).exec() } diff --git a/packages/apollo-shared/src/util.ts b/packages/apollo-shared/src/util.ts index cfedc71a9..36dda6c67 100644 --- a/packages/apollo-shared/src/util.ts +++ b/packages/apollo-shared/src/util.ts @@ -12,7 +12,6 @@ export function makeGFF3Feature( // const locations = feature.discontinuousLocations?.length // ? feature.discontinuousLocations // : [{ start: feature.start, end: feature.end, phase: feature.phase }] - // eslint-disable-next-line unicorn/prefer-structured-clone const attributes: Record = JSON.parse( JSON.stringify(feature.attributes), ) diff --git a/packages/website/babel.config.js b/packages/website/babel.config.js index bbfa5de3c..675264818 100755 --- a/packages/website/babel.config.js +++ b/packages/website/babel.config.js @@ -1,4 +1,3 @@ -/* eslint-disable no-undef */ module.exports = { presets: [require.resolve('@docusaurus/core/lib/babel/preset')], } diff --git a/packages/website/src/pages/index.tsx b/packages/website/src/pages/index.tsx index eee2f35b1..cf64f6f6b 100755 --- a/packages/website/src/pages/index.tsx +++ b/packages/website/src/pages/index.tsx @@ -4,6 +4,7 @@ import useDocusaurusContext from '@docusaurus/useDocusaurusContext' import Heading from '@theme/Heading' import Layout from '@theme/Layout' import { clsx } from 'clsx' +import React from 'react' import styles from './index.module.css' diff --git a/tsconfig.json b/tsconfig.json index 52ceabfc3..d6a0d0570 100644 --- a/tsconfig.json +++ b/tsconfig.json @@ -5,5 +5,14 @@ "noEmit": true, "allowJs": true, }, - "include": ["./*.js", "./*.mjs", "./*.cjs", "scripts/*.ts"], + "include": [ + "./*.js", + "./.*.js", + "./*.mjs", + "./.*.mjs", + "./*.cjs", + "./.*.cjs", + "scripts/*.ts", + ".husky/*.js", + ], } diff --git a/yarn.config.cjs b/yarn.config.cjs index ef7976d1a..4269fbbed 100644 --- a/yarn.config.cjs +++ b/yarn.config.cjs @@ -1,6 +1,7 @@ // @ts-check /** @type {import('@yarnpkg/types')} */ +// eslint-disable-next-line @typescript-eslint/no-require-imports const { defineConfig } = require('@yarnpkg/types') /** @@ -13,12 +14,16 @@ const { defineConfig } = require('@yarnpkg/types') */ function enforceConsistentDependenciesAcrossTheProject({ Yarn }) { for (const dependency of Yarn.dependencies()) { - if (dependency.type === 'peerDependencies') continue + if (dependency.type === 'peerDependencies') { + continue + } for (const otherDependency of Yarn.dependencies({ ident: dependency.ident, })) { - if (otherDependency.type === 'peerDependencies') continue + if (otherDependency.type === 'peerDependencies') { + continue + } dependency.update(otherDependency.range) } @@ -26,7 +31,8 @@ function enforceConsistentDependenciesAcrossTheProject({ Yarn }) { } module.exports = defineConfig({ - constraints: async (ctx) => { + constraints: (ctx) => { enforceConsistentDependenciesAcrossTheProject(ctx) + return Promise.resolve() }, }) diff --git a/yarn.lock b/yarn.lock index f8d429015..519f969b5 100644 --- a/yarn.lock +++ b/yarn.lock @@ -5564,10 +5564,28 @@ __metadata: languageName: node linkType: hard -"@eslint-community/regexpp@npm:^4.6.1": - version: 4.9.1 - resolution: "@eslint-community/regexpp@npm:4.9.1" - checksum: 10c0/d0e1bd1a37cb2cb6bbac88dfe97b62b412d4b6ea3a4bb1c4e1e503be03125063db5d80999cef9728f57b19b49979aa902ac68182bcf5f80dfce6fa9a9d34eee1 +"@eslint-community/regexpp@npm:^4.12.1": + version: 4.12.1 + resolution: "@eslint-community/regexpp@npm:4.12.1" + checksum: 10c0/a03d98c246bcb9109aec2c08e4d10c8d010256538dcb3f56610191607214523d4fb1b00aa81df830b6dffb74c5fa0be03642513a289c567949d3e550ca11cdf6 + languageName: node + linkType: hard + +"@eslint/config-array@npm:^0.18.0": + version: 0.18.0 + resolution: "@eslint/config-array@npm:0.18.0" + dependencies: + "@eslint/object-schema": "npm:^2.1.4" + debug: "npm:^4.3.1" + minimatch: "npm:^3.1.2" + checksum: 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file-entry-cache: "npm:^8.0.0" find-up: "npm:^5.0.0" glob-parent: "npm:^6.0.2" - globals: "npm:^13.19.0" - graphemer: "npm:^1.4.0" ignore: "npm:^5.2.0" imurmurhash: "npm:^0.1.4" is-glob: "npm:^4.0.0" - is-path-inside: "npm:^3.0.3" - js-yaml: "npm:^4.1.0" json-stable-stringify-without-jsonify: "npm:^1.0.1" - levn: "npm:^0.4.1" lodash.merge: "npm:^4.6.2" minimatch: "npm:^3.1.2" natural-compare: "npm:^1.4.0" optionator: "npm:^0.9.3" - strip-ansi: "npm:^6.0.1" text-table: "npm:^0.2.0" + peerDependencies: + jiti: "*" + peerDependenciesMeta: + jiti: + optional: true bin: eslint: bin/eslint.js - checksum: 10c0/1fd31533086c1b72f86770a4d9d7058ee8b4643fd1cfd10c7aac1ecb8725698e88352a87805cf4b2ce890aa35947df4b4da9655fb7fdfa60dbb448a43f6ebcf1 + checksum: 10c0/e1cbf571b75519ad0b24c27e66a6575e57cab2671ef5296e7b345d9ac3adc1a549118dcc74a05b651a7a13a5e61ebb680be6a3e04a80e1f22eba1931921b5187 languageName: node linkType: hard -"espree@npm:^9.6.0, espree@npm:^9.6.1": +"espree@npm:^10.0.1, espree@npm:^10.3.0": + version: 10.3.0 + resolution: "espree@npm:10.3.0" + dependencies: + acorn: "npm:^8.14.0" + acorn-jsx: "npm:^5.3.2" + eslint-visitor-keys: "npm:^4.2.0" + checksum: 10c0/272beeaca70d0a1a047d61baff64db04664a33d7cfb5d144f84bc8a5c6194c6c8ebe9cc594093ca53add88baa23e59b01e69e8a0160ab32eac570482e165c462 + languageName: node + linkType: hard + +"espree@npm:^9.6.0": version: 9.6.1 resolution: "espree@npm:9.6.1" dependencies: @@ -16332,16 +16443,7 @@ __metadata: languageName: node linkType: hard -"esquery@npm:^1.4.2": - version: 1.5.0 - resolution: "esquery@npm:1.5.0" - dependencies: - estraverse: "npm:^5.1.0" - checksum: 10c0/a084bd049d954cc88ac69df30534043fb2aee5555b56246493f42f27d1e168f00d9e5d4192e46f10290d312dc30dc7d58994d61a609c579c1219d636996f9213 - languageName: node - linkType: hard - -"esquery@npm:^1.6.0": +"esquery@npm:^1.5.0": version: 1.6.0 resolution: "esquery@npm:1.6.0" dependencies: @@ -17008,12 +17110,12 @@ __metadata: languageName: node linkType: hard -"file-entry-cache@npm:^6.0.1": - version: 6.0.1 - resolution: "file-entry-cache@npm:6.0.1" +"file-entry-cache@npm:^8.0.0": + version: 8.0.0 + resolution: "file-entry-cache@npm:8.0.0" dependencies: - flat-cache: "npm:^3.0.4" - checksum: 10c0/58473e8a82794d01b38e5e435f6feaf648e3f36fdb3a56e98f417f4efae71ad1c0d4ebd8a9a7c50c3ad085820a93fc7494ad721e0e4ebc1da3573f4e1c3c7cdd + flat-cache: "npm:^4.0.0" + checksum: 10c0/9e2b5938b1cd9b6d7e3612bdc533afd4ac17b2fc646569e9a8abbf2eb48e5eb8e316bc38815a3ef6a1b456f4107f0d0f055a614ca613e75db6bf9ff4d72c1638 languageName: node linkType: hard @@ -17201,14 +17303,13 @@ __metadata: languageName: node linkType: hard -"flat-cache@npm:^3.0.4": - version: 3.1.1 - resolution: "flat-cache@npm:3.1.1" +"flat-cache@npm:^4.0.0": + version: 4.0.1 + resolution: "flat-cache@npm:4.0.1" dependencies: flatted: "npm:^3.2.9" - keyv: "npm:^4.5.3" - rimraf: "npm:^3.0.2" - checksum: 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languageName: node linkType: hard -"is-path-inside@npm:^3.0.2, is-path-inside@npm:^3.0.3": +"is-path-inside@npm:^3.0.2": version: 3.0.3 resolution: "is-path-inside@npm:3.0.3" checksum: 10c0/cf7d4ac35fb96bab6a1d2c3598fe5ebb29aafb52c0aaa482b5a3ed9d8ba3edc11631e3ec2637660c44b3ce0e61a08d54946e8af30dec0b60a7c27296c68ffd05 @@ -20943,7 +21051,7 @@ __metadata: languageName: node linkType: hard -"keyv@npm:^4.0.0, keyv@npm:^4.5.3": +"keyv@npm:^4.0.0, keyv@npm:^4.5.3, keyv@npm:^4.5.4": version: 4.5.4 resolution: "keyv@npm:4.5.4" dependencies: @@ -29882,6 +29990,20 @@ __metadata: languageName: node linkType: hard +"typescript-eslint@npm:^8.14.0": + version: 8.14.0 + resolution: "typescript-eslint@npm:8.14.0" + dependencies: + "@typescript-eslint/eslint-plugin": "npm:8.14.0" + "@typescript-eslint/parser": "npm:8.14.0" + "@typescript-eslint/utils": "npm:8.14.0" + peerDependenciesMeta: + typescript: + optional: true + checksum: 10c0/b9c2f32139d3df52057bfb80d4663fd5e440ccd0da75d92fe91582fe5216213e7012ef691e7d91c75e402e373b9aded6b128b005aaeeae32d7b9d7b39732bcc7 + languageName: node + linkType: hard + "typescript@npm:5.2.2": version: 5.2.2 resolution: "typescript@npm:5.2.2" From 5e6f7825ad7f729271ae5029fdaeb4aa32dadde4 Mon Sep 17 00:00:00 2001 From: Garrett Stevens Date: Mon, 18 Nov 2024 17:23:16 -0700 Subject: [PATCH 09/12] Revert usage of structuredClone --- .../src/OntologyManager/OntologyStore/index.test.ts | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/index.test.ts b/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/index.test.ts index 57f7f2b81..d7a5e8a7c 100644 --- a/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/index.test.ts +++ b/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/index.test.ts @@ -24,7 +24,8 @@ jest.mock('jsonpath', () => { ...original, // eslint-disable-next-line @typescript-eslint/no-explicit-any query: jest.fn((obj: any, pathExpression: string, count?: number) => { - const newObj = obj instanceof Object ? obj : structuredClone(obj) + const newObj = + obj instanceof Object ? obj : JSON.parse(JSON.stringify(obj)) return original.query(newObj, pathExpression, count) }), } From b92ec086b49fab4845d90f20600d39c3ee12c724 Mon Sep 17 00:00:00 2001 From: Garrett Stevens Date: Mon, 18 Nov 2024 17:35:40 -0700 Subject: [PATCH 10/12] Restore missing react import --- eslint.config.mjs | 2 +- package.json | 1 + yarn.lock | 1 + 3 files changed, 3 insertions(+), 1 deletion(-) diff --git a/eslint.config.mjs b/eslint.config.mjs index 365098edd..0035ea0c9 100644 --- a/eslint.config.mjs +++ b/eslint.config.mjs @@ -47,7 +47,7 @@ export default [ tsconfigRootDir: import.meta.dirname, }, }, - settings: { react: { version: '18.2.0' } }, + settings: { react: { version: 'detect' } }, // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment plugins: { tsdoc: pluginTSDoc, import: pluginImport }, rules: { diff --git a/package.json b/package.json index 8159c2d7c..3c86f58a8 100644 --- a/package.json +++ b/package.json @@ -41,6 +41,7 @@ "npm-run-all": "^4.1.5", "prettier": "^3.3.2", "prettier-plugin-packagejson": "^2.5.2", + "react": "^18.2.0", "semver": "^7.6.3", "tslib": "^2.3.1", "tsx": "^4.6.2", diff --git a/yarn.lock b/yarn.lock index 519f969b5..62a52aa27 100644 --- a/yarn.lock +++ b/yarn.lock @@ -11302,6 +11302,7 @@ __metadata: npm-run-all: "npm:^4.1.5" prettier: "npm:^3.3.2" prettier-plugin-packagejson: "npm:^2.5.2" + react: "npm:^18.2.0" semver: "npm:^7.6.3" tslib: "npm:^2.3.1" tsx: "npm:^4.6.2" From 033fcd00f13ce8c4745585f69bf386c3803a135b Mon Sep 17 00:00:00 2001 From: Garrett Stevens Date: Tue, 19 Nov 2024 18:06:03 +0000 Subject: [PATCH 11/12] Remove all instances of structureClone --- packages/apollo-cli/src/utils.ts | 2 +- packages/apollo-shared/src/Changes/AddFeatureChange.ts | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/packages/apollo-cli/src/utils.ts b/packages/apollo-cli/src/utils.ts index 41a74815d..ba494b34e 100644 --- a/packages/apollo-cli/src/utils.ts +++ b/packages/apollo-cli/src/utils.ts @@ -123,7 +123,7 @@ export async function getAssembly( const assemblies = (await res.json()) as ApolloAssemblySnapshot[] for (const x of assemblies) { if (x._id === assemblyId[0]) { - return structuredClone(x) + return JSON.parse(JSON.stringify(x)) as ApolloAssemblySnapshot } } throw new Error(`Assembly "${assemblyNameOrId}" not found`) diff --git a/packages/apollo-shared/src/Changes/AddFeatureChange.ts b/packages/apollo-shared/src/Changes/AddFeatureChange.ts index 7f4dd2132..e250d909f 100644 --- a/packages/apollo-shared/src/Changes/AddFeatureChange.ts +++ b/packages/apollo-shared/src/Changes/AddFeatureChange.ts @@ -1,5 +1,5 @@ /* eslint-disable @typescript-eslint/restrict-template-expressions */ - +/* eslint-disable @typescript-eslint/no-unsafe-assignment */ /* eslint-disable @typescript-eslint/require-await */ /* eslint-disable @typescript-eslint/no-unnecessary-condition */ import { @@ -143,7 +143,7 @@ export class AddFeatureChange extends FeatureChange { } attributes = { _id: [parentFeature._id.toString()], - ...structuredClone(attributes), + ...JSON.parse(JSON.stringify(attributes)), } parentFeature.attributes = attributes } From 962c313595ee2cbea71bd1e889af3ed2c7f7654d Mon Sep 17 00:00:00 2001 From: Garrett Stevens Date: Tue, 19 Nov 2024 19:27:44 +0000 Subject: [PATCH 12/12] Update for compatibility with latest JBrowse --- .../src/ApolloInternetAccount/components/AuthTypeSelector.tsx | 2 +- .../src/OntologyManager/OntologyStore/fulltext.ts | 2 +- .../src/components/OntologyTermAutocomplete.tsx | 3 ++- .../src/components/OntologyTermMultiSelect.tsx | 2 +- 4 files changed, 5 insertions(+), 4 deletions(-) diff --git a/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/components/AuthTypeSelector.tsx b/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/components/AuthTypeSelector.tsx index 2361f003c..26cd4da0f 100644 --- a/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/components/AuthTypeSelector.tsx +++ b/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/components/AuthTypeSelector.tsx @@ -1,5 +1,5 @@ /* eslint-disable @typescript-eslint/use-unknown-in-catch-callback-variable */ -import { isAbortException } from '@jbrowse/core/util' +import { isAbortException } from '@jbrowse/core/util/aborting' import { Button, DialogActions, diff --git a/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/fulltext.ts b/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/fulltext.ts index 2354fa6cb..2be5d8c6c 100644 --- a/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/fulltext.ts +++ b/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/fulltext.ts @@ -2,7 +2,7 @@ /* eslint-disable @typescript-eslint/no-unsafe-return */ // jsonpath triggers this rule for some reason. import { query } from 'jsonpath' does not work -import { checkAbortSignal } from '@jbrowse/core/util' +import { checkAbortSignal } from '@jbrowse/core/util/aborting' import jsonpath from 'jsonpath' import { stopwords } from './fulltext-stopwords' diff --git a/packages/jbrowse-plugin-apollo/src/components/OntologyTermAutocomplete.tsx b/packages/jbrowse-plugin-apollo/src/components/OntologyTermAutocomplete.tsx index 3feaa47e3..9c7031551 100644 --- a/packages/jbrowse-plugin-apollo/src/components/OntologyTermAutocomplete.tsx +++ b/packages/jbrowse-plugin-apollo/src/components/OntologyTermAutocomplete.tsx @@ -1,6 +1,7 @@ /* eslint-disable @typescript-eslint/no-unnecessary-condition */ -import { AbstractSessionModel, isAbortException } from '@jbrowse/core/util' +import { AbstractSessionModel } from '@jbrowse/core/util' +import { isAbortException } from '@jbrowse/core/util/aborting' import { Autocomplete, AutocompleteRenderInputParams, diff --git a/packages/jbrowse-plugin-apollo/src/components/OntologyTermMultiSelect.tsx b/packages/jbrowse-plugin-apollo/src/components/OntologyTermMultiSelect.tsx index 01700490e..258f5ee5c 100644 --- a/packages/jbrowse-plugin-apollo/src/components/OntologyTermMultiSelect.tsx +++ b/packages/jbrowse-plugin-apollo/src/components/OntologyTermMultiSelect.tsx @@ -1,7 +1,7 @@ /* eslint-disable @typescript-eslint/unbound-method */ /* eslint-disable @typescript-eslint/use-unknown-in-catch-callback-variable */ /* eslint-disable @typescript-eslint/no-unnecessary-condition */ -import { isAbortException } from '@jbrowse/core/util' +import { isAbortException } from '@jbrowse/core/util/aborting' import { Autocomplete, AutocompleteRenderGetTagProps,