From e1c69aac834b3183e859340768a8929e36207737 Mon Sep 17 00:00:00 2001 From: Guillaume Fraux Date: Tue, 8 Oct 2024 18:40:42 +0200 Subject: [PATCH] Update depdencies --- .eslintrc.yml | 25 - .github/workflows/tests.yml | 6 +- .github/workflows/website.yml | 2 +- package-lock.json | 4175 ++++++++++++++++++++++++--------- package.json | 23 +- pyproject.toml | 4 +- src/structure/viewer.ts | 3 +- 7 files changed, 3033 insertions(+), 1205 deletions(-) diff --git a/.eslintrc.yml b/.eslintrc.yml index 6e74aa024..b78975fe7 100644 --- a/.eslintrc.yml +++ b/.eslintrc.yml @@ -23,28 +23,3 @@ extends: - plugin:@typescript-eslint/recommended - plugin:@typescript-eslint/recommended-requiring-type-checking - prettier - -rules: - # Extra rules - arrow-parens: error - eqeqeq: error - grouped-accessor-pairs: error - no-console: error - no-extra-parens: off - no-loss-of-precision: error - no-sequences: error - no-template-curly-in-string: error - no-throw-literal: error - no-unused-expressions: error - no-useless-concat: error - no-var: error - radix: error - semi: error - # only sort inside groups, not between separate import lines - sort-imports: [error, { ignoreDeclarationSort: true }] - # sort-keys: [error, asc, {minKeys: 4}] - # disabled until https://github.com/eslint/eslint/issues/12759 is implemented - sort-keys: off - # disabled rules - '@typescript-eslint/no-inferrable-types': off - '@typescript-eslint/no-empty-function': off diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 3a986ca5a..c8e758585 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -17,7 +17,7 @@ jobs: fetch-depth: 0 - uses: actions/setup-node@v3 with: - node-version: '21.x' + node-version: '22.x' cache: 'npm' - name: configure access to git repositories in package-lock.json @@ -43,6 +43,10 @@ jobs: uses: actions/setup-python@v4 with: python-version: ${{ matrix.python-version }} + - uses: actions/setup-node@v3 + with: + node-version: '22.x' + cache: 'npm' - name: configure access to git repositories in package-lock.json run: git config --global url."https://github.com/".insteadOf ssh://git@github.com - name: Install dependencies diff --git a/.github/workflows/website.yml b/.github/workflows/website.yml index 7f9f6023b..1c65cc66a 100644 --- a/.github/workflows/website.yml +++ b/.github/workflows/website.yml @@ -17,7 +17,7 @@ jobs: fetch-depth: 0 - uses: actions/setup-node@v3 with: - node-version: '18.x' + node-version: '22.x' cache: 'npm' - uses: actions/setup-python@v4 with: diff --git a/package-lock.json b/package-lock.json index 429da91f1..2a570b4cb 100644 --- a/package-lock.json +++ b/package-lock.json @@ -14,19 +14,18 @@ "@popperjs/core": "^2.11.2", "@types/jquery": "^3.5", "@types/markdown-it": "^14", - "@types/node": "^20", + "@types/node": "^22", "@types/pako": "^2", "@types/plotly.js": "^2.12", "@types/tmp": "^0.2.1", "@typescript-eslint/eslint-plugin": "^7.2", "@typescript-eslint/parser": "^7.2", - "3dmol": "^2", + "3dmol": "2.2.1", "assert": "^2", - "bootstrap": "5.2", - "bubleify": "^2.0.0", + "bootstrap": "5.2.3", + "bubleify": "^2.0", "buffer": "^6", - "color-parse": "^1", - "construct-style-sheets-polyfill": "^3.1.0", + "construct-style-sheets-polyfill": "^3.1", "css-loader": "^7", "dts-bundle-generator": "^9", "eslint": "^8.7", @@ -39,17 +38,17 @@ "markdown-it": "^14", "node-loader": "^2", "pako": "^2", - "plausible-tracker": "^0.3.8", - "plotly.js": "2.32.0", - "prettier": "3.2.5", + "plausible-tracker": "^0.3", + "plotly.js": "2.35.2", + "prettier": "3.3.3", "raw-loader": "^4", - "rimraf": "^5", + "rimraf": "^6", "style-loader": "^4", "tmp": "^0.2", "ts-loader": "^9", "ts-node": "^10", - "typedoc": "^0.25", - "typescript": "^5.4", + "typedoc": "^0.26", + "typescript": "^5.6", "webpack": "^5.76", "webpack-cli": "^5", "webpack-dev-server": "^5" @@ -59,20 +58,12 @@ "npm": ">=9" } }, - "node_modules/@aashutoshrathi/word-wrap": { - "version": "1.2.6", - "resolved": "https://registry.npmjs.org/@aashutoshrathi/word-wrap/-/word-wrap-1.2.6.tgz", - "integrity": "sha512-1Yjs2SvM8TflER/OD3cOjhWWOZb58A2t7wpE2S9XfBYTiIl+XFhQG2bjy4Pu1I+EAlCNUzRDYDdFwFYUKvXcIA==", - "dev": true, - "engines": { - "node": ">=0.10.0" - } - }, "node_modules/@choojs/findup": { "version": "0.2.1", "resolved": "https://registry.npmjs.org/@choojs/findup/-/findup-0.2.1.tgz", "integrity": "sha512-YstAqNb0MCN8PjdLCDfRsBcGVRN41f3vgLvaI0IrIcBp4AqILRSS0DeWNGkicC+f/zRIPJLc+9RURVSepwvfBw==", "dev": true, + "license": "MIT", "dependencies": { "commander": "^2.15.1" }, @@ -84,13 +75,15 @@ "version": "2.20.3", "resolved": "https://registry.npmjs.org/commander/-/commander-2.20.3.tgz", "integrity": "sha512-GpVkmM8vF2vQUkj2LvZmD35JxeJOLCwJ9cUkugyk2nuhbv3+mJvpLYYt+0+USMxE+oj+ey/lJEnhZw75x/OMcQ==", - "dev": true + "dev": true, + "license": "MIT" }, "node_modules/@cspotcode/source-map-support": { "version": "0.8.1", "resolved": "https://registry.npmjs.org/@cspotcode/source-map-support/-/source-map-support-0.8.1.tgz", "integrity": "sha512-IchNf6dN4tHoMFIn/7OE8LWZ19Y6q/67Bmf6vnGREv8RSbBVb9LPJxEcnwrcwX6ixSvaiGoomAUvu4YSxXrVgw==", "dev": true, + "license": "MIT", "dependencies": { "@jridgewell/trace-mapping": "0.3.9" }, @@ -103,6 +96,7 @@ "resolved": "https://registry.npmjs.org/@jridgewell/trace-mapping/-/trace-mapping-0.3.9.tgz", "integrity": "sha512-3Belt6tdc8bPgAtbcmdtNJlirVoTmEb5e2gC94PnkwEW9jI6CAHUeoG85tjWP5WquqfavoMtMwiG4P926ZKKuQ==", "dev": true, + "license": "MIT", "dependencies": { "@jridgewell/resolve-uri": "^3.0.3", "@jridgewell/sourcemap-codec": "^1.4.10" @@ -113,6 +107,7 @@ "resolved": "https://registry.npmjs.org/@discoveryjs/json-ext/-/json-ext-0.5.7.tgz", "integrity": "sha512-dBVuXR082gk3jsFp7Rd/JI4kytwGHecnCoTtXFb7DB6CNHp4rg5k1bhg0nWdLGLnOV71lmDzGQaLMy8iPLY0pw==", "dev": true, + "license": "MIT", "engines": { "node": ">=10.0.0" } @@ -122,6 +117,7 @@ "resolved": "https://registry.npmjs.org/@eslint-community/eslint-utils/-/eslint-utils-4.4.0.tgz", "integrity": "sha512-1/sA4dwrzBAyeUoQ6oxahHKmrZvsnLCg4RfxW3ZFGGmQkSNQPFNLV9CUEFQP1x9EYXHTo5p6xdhZM1Ne9p/AfA==", "dev": true, + "license": "MIT", "dependencies": { "eslint-visitor-keys": "^3.3.0" }, @@ -133,10 +129,11 @@ } }, "node_modules/@eslint-community/regexpp": { - "version": "4.10.0", - "resolved": "https://registry.npmjs.org/@eslint-community/regexpp/-/regexpp-4.10.0.tgz", - "integrity": "sha512-Cu96Sd2By9mCNTx2iyKOmq10v22jUVQv0lQnlGNy16oE9589yE+QADPbrMGCkA51cKZSg3Pu/aTJVTGfL/qjUA==", + "version": "4.11.1", + "resolved": "https://registry.npmjs.org/@eslint-community/regexpp/-/regexpp-4.11.1.tgz", + "integrity": "sha512-m4DVN9ZqskZoLU5GlWZadwDnYo3vAEydiUayB9widCl9ffWx2IvPnp6n3on5rJmziJSw9Bv+Z3ChDVdMwXCY8Q==", "dev": true, + "license": "MIT", "engines": { "node": "^12.0.0 || ^14.0.0 || >=16.0.0" } @@ -146,6 +143,7 @@ "resolved": "https://registry.npmjs.org/@eslint/eslintrc/-/eslintrc-2.1.4.tgz", "integrity": "sha512-269Z39MS6wVJtsoUl10L60WdkhJVdPG24Q4eZTH3nnF6lpvSShEK3wQjDX9JRWAUPvPh7COouPpU9IrqaZFvtQ==", "dev": true, + "license": "MIT", "dependencies": { "ajv": "^6.12.4", "debug": "^4.3.2", @@ -169,6 +167,7 @@ "resolved": "https://registry.npmjs.org/ajv/-/ajv-6.12.6.tgz", "integrity": "sha512-j3fVLgvTo527anyYyJOGTYJbG+vnnQYvE0m5mmkc1TK+nxAppkCLMIL0aZ4dblVCNoGShhm+kzE4ZUykBoMg4g==", "dev": true, + "license": "MIT", "dependencies": { "fast-deep-equal": "^3.1.1", "fast-json-stable-stringify": "^2.0.0", @@ -185,6 +184,7 @@ "resolved": "https://registry.npmjs.org/brace-expansion/-/brace-expansion-1.1.11.tgz", "integrity": "sha512-iCuPHDFgrHX7H2vEI/5xpz07zSHB00TpugqhmYtVmMO6518mCuRMoOYFldEBl0g187ufozdaHgWKcYFb61qGiA==", "dev": true, + "license": "MIT", "dependencies": { "balanced-match": "^1.0.0", "concat-map": "0.0.1" @@ -194,13 +194,15 @@ "version": "0.4.1", "resolved": "https://registry.npmjs.org/json-schema-traverse/-/json-schema-traverse-0.4.1.tgz", "integrity": "sha512-xbbCH5dCYU5T8LcEhhuh7HJ88HXuW3qsI3Y0zOZFKfZEHcpWiHU/Jxzk629Brsab/mMiHQti9wMP+845RPe3Vg==", - "dev": true + "dev": true, + "license": "MIT" }, "node_modules/@eslint/eslintrc/node_modules/minimatch": { "version": "3.1.2", "resolved": "https://registry.npmjs.org/minimatch/-/minimatch-3.1.2.tgz", "integrity": "sha512-J7p63hRiAjw1NDEww1W7i37+ByIrOWO5XQQAzZ3VOcL0PNybwpfmV/N05zFAzwQ9USyEcX6t3UO+K5aqBQOIHw==", "dev": true, + "license": "ISC", "dependencies": { "brace-expansion": "^1.1.7" }, @@ -209,21 +211,24 @@ } }, "node_modules/@eslint/js": { - "version": "8.57.0", - "resolved": "https://registry.npmjs.org/@eslint/js/-/js-8.57.0.tgz", - "integrity": "sha512-Ys+3g2TaW7gADOJzPt83SJtCDhMjndcDMFVQ/Tj9iA1BfJzFKD9mAUXT3OenpuPHbI6P/myECxRJrofUsDx/5g==", + "version": "8.57.1", + "resolved": "https://registry.npmjs.org/@eslint/js/-/js-8.57.1.tgz", + "integrity": "sha512-d9zaMRSTIKDLhctzH12MtXvJKSSUhaHcjV+2Z+GK+EEY7XKpP5yR4x+N3TAcHTcu963nIr+TMcCb4DBCYX1z6Q==", "dev": true, + "license": "MIT", "engines": { "node": "^12.22.0 || ^14.17.0 || >=16.0.0" } }, "node_modules/@humanwhocodes/config-array": { - "version": "0.11.14", - "resolved": "https://registry.npmjs.org/@humanwhocodes/config-array/-/config-array-0.11.14.tgz", - "integrity": "sha512-3T8LkOmg45BV5FICb15QQMsyUSWrQ8AygVfC7ZG32zOalnqrilm018ZVCw0eapXux8FtA33q8PSRSstjee3jSg==", + "version": "0.13.0", + "resolved": "https://registry.npmjs.org/@humanwhocodes/config-array/-/config-array-0.13.0.tgz", + "integrity": "sha512-DZLEEqFWQFiyK6h5YIeynKx7JlvCYWL0cImfSRXZ9l4Sg2efkFGTuFf6vzXjK1cq6IYkU+Eg/JizXw+TD2vRNw==", + "deprecated": "Use @eslint/config-array instead", "dev": true, + "license": "Apache-2.0", "dependencies": { - "@humanwhocodes/object-schema": "^2.0.2", + "@humanwhocodes/object-schema": "^2.0.3", "debug": "^4.3.1", "minimatch": "^3.0.5" }, @@ -236,6 +241,7 @@ "resolved": "https://registry.npmjs.org/brace-expansion/-/brace-expansion-1.1.11.tgz", "integrity": "sha512-iCuPHDFgrHX7H2vEI/5xpz07zSHB00TpugqhmYtVmMO6518mCuRMoOYFldEBl0g187ufozdaHgWKcYFb61qGiA==", "dev": true, + "license": "MIT", "dependencies": { "balanced-match": "^1.0.0", "concat-map": "0.0.1" @@ -246,6 +252,7 @@ "resolved": "https://registry.npmjs.org/minimatch/-/minimatch-3.1.2.tgz", "integrity": "sha512-J7p63hRiAjw1NDEww1W7i37+ByIrOWO5XQQAzZ3VOcL0PNybwpfmV/N05zFAzwQ9USyEcX6t3UO+K5aqBQOIHw==", "dev": true, + "license": "ISC", "dependencies": { "brace-expansion": "^1.1.7" }, @@ -258,6 +265,7 @@ "resolved": "https://registry.npmjs.org/@humanwhocodes/module-importer/-/module-importer-1.0.1.tgz", "integrity": "sha512-bxveV4V8v5Yb4ncFTT3rPSgZBOpCkjfK0y4oVVVJwIuDVBRMDXrPyXRL988i5ap9m9bnyEEjWfm5WkBmtffLfA==", "dev": true, + "license": "Apache-2.0", "engines": { "node": ">=12.22" }, @@ -270,13 +278,16 @@ "version": "2.0.3", "resolved": "https://registry.npmjs.org/@humanwhocodes/object-schema/-/object-schema-2.0.3.tgz", "integrity": "sha512-93zYdMES/c1D69yZiKDBj0V24vqNzB/koF26KPaagAfd3P/4gUlh3Dys5ogAK+Exi9QyzlD8x/08Zt7wIKcDcA==", - "dev": true + "deprecated": "Use @eslint/object-schema instead", + "dev": true, + "license": "BSD-3-Clause" }, "node_modules/@isaacs/cliui": { "version": "8.0.2", "resolved": "https://registry.npmjs.org/@isaacs/cliui/-/cliui-8.0.2.tgz", "integrity": "sha512-O8jcjabXaleOG9DQ0+ARXWZBTfnP4WNAqzuiJK7ll44AmxGKv/J2M4TPjxjY3znBCfvBXFzucm1twdyFybFqEA==", "dev": true, + "license": "ISC", "dependencies": { "string-width": "^5.1.2", "string-width-cjs": "npm:string-width@^4.2.0", @@ -290,10 +301,11 @@ } }, "node_modules/@isaacs/cliui/node_modules/ansi-regex": { - "version": "6.0.1", - "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-6.0.1.tgz", - "integrity": "sha512-n5M855fKb2SsfMIiFFoVrABHJC8QtHwVx+mHWP3QcEqBHYienj5dHSgjbxtC0WEZXYt4wcD6zrQElDPhFuZgfA==", + "version": "6.1.0", + "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-6.1.0.tgz", + "integrity": "sha512-7HSX4QQb4CspciLpVFwyRe79O3xsIZDDLER21kERQ71oaPodF8jL725AgJMFAYbooIqolJoRLuM81SpeUkpkvA==", "dev": true, + "license": "MIT", "engines": { "node": ">=12" }, @@ -306,6 +318,7 @@ "resolved": "https://registry.npmjs.org/ansi-styles/-/ansi-styles-6.2.1.tgz", "integrity": "sha512-bN798gFfQX+viw3R7yrGWRqnrN2oRkEkUjjl4JNn4E8GxxbjtG3FbrEIIY3l8/hrwUwIeCZvi4QuOTP4MErVug==", "dev": true, + "license": "MIT", "engines": { "node": ">=12" }, @@ -317,13 +330,15 @@ "version": "9.2.2", "resolved": "https://registry.npmjs.org/emoji-regex/-/emoji-regex-9.2.2.tgz", "integrity": "sha512-L18DaJsXSUk2+42pv8mLs5jJT2hqFkFE4j21wOmgbUqsZ2hL72NsUU785g9RXgo3s0ZNgVl42TiHp3ZtOv/Vyg==", - 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"integrity": "sha512-tVpsJW7DdjecAiFpbIB1e3qxIQsE6NoPc5/eTdrbbIC4h0LVsWhnoa3g+m2HclBIujHzsxZ4VJVA+GUuc2/LBw==", "dev": true, + "license": "ISC", "engines": { "node": ">=12" } }, "node_modules/yjs": { - "version": "13.6.14", - "resolved": "https://registry.npmjs.org/yjs/-/yjs-13.6.14.tgz", - "integrity": "sha512-D+7KcUr0j+vBCUSKXXEWfA+bG4UQBviAwP3gYBhkstkgwy5+8diOPMx0iqLIOxNo/HxaREUimZRxqHGAHCL2BQ==", + "version": "13.6.19", + "resolved": "https://registry.npmjs.org/yjs/-/yjs-13.6.19.tgz", + "integrity": "sha512-GNKw4mEUn5yWU2QPHRx8jppxmCm9KzbBhB4qJLUJFiiYD0g/tDVgXQ7aPkyh01YO28kbs2J/BEbWBagjuWyejw==", "dev": true, + "license": "MIT", "dependencies": { "lib0": "^0.2.86" }, @@ -10453,6 +12291,7 @@ "resolved": "https://registry.npmjs.org/yn/-/yn-3.1.1.tgz", "integrity": "sha512-Ux4ygGWsu2c7isFWe8Yu1YluJmqVhxqK2cLXNQA5AcC3QfbGNpM7fu0Y8b/z16pXLnFxZYvWhd3fhBY9DLmC6Q==", "dev": true, + "license": "MIT", "engines": { "node": ">=6" } @@ -10462,12 +12301,24 @@ "resolved": 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"^0.2.1", "@typescript-eslint/eslint-plugin": "^7.2", "@typescript-eslint/parser": "^7.2", - "3dmol": "^2", + "3dmol": "2.2.1", "assert": "^2", - "bootstrap": "5.2", - "bubleify": "^2.0.0", + "bootstrap": "5.2.3", + "bubleify": "^2.0", "buffer": "^6", - "construct-style-sheets-polyfill": "^3.1.0", - "color-parse": "^1", + "construct-style-sheets-polyfill": "^3.1", "css-loader": "^7", "dts-bundle-generator": "^9", "eslint": "^8.7", @@ -70,17 +69,17 @@ "markdown-it": "^14", "node-loader": "^2", "pako": "^2", - "plausible-tracker": "^0.3.8", - "plotly.js": "2.32.0", - "prettier": "3.2.5", + "plausible-tracker": "^0.3", + "plotly.js": "2.35.2", + "prettier": "3.3.3", "raw-loader": "^4", - "rimraf": "^5", + "rimraf": "^6", "style-loader": "^4", "tmp": "^0.2", "ts-loader": "^9", "ts-node": "^10", - "typedoc": "^0.25", - "typescript": "^5.4", + "typedoc": "^0.26", + "typescript": "^5.6", "webpack": "^5.76", "webpack-cli": "^5", "webpack-dev-server": "^5" diff --git a/pyproject.toml b/pyproject.toml index ad3633332..ee9298a22 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -77,6 +77,6 @@ explore = [ ] metatensor = [ - "metatensor", - "metatensor[torch]" + "metatensor-operations >=0.2,<0.3", + "metatensor-torch >=0.5,<0.6" ] diff --git a/src/structure/viewer.ts b/src/structure/viewer.ts index cd75f5526..fd98cbf75 100644 --- a/src/structure/viewer.ts +++ b/src/structure/viewer.ts @@ -587,8 +587,7 @@ export class MoleculeViewer { return; } - // eslint-disable-next-line @typescript-eslint/no-non-null-assertion - const active = this._environments.filter((e) => e !== undefined).map((e) => e!.center); + const active = this._environments.filter((e) => e !== undefined).map((e) => e.center); // resets clickable and hoverable state interactions for (const atom of this._viewer.selectedAtoms({})) {