From 10ffbac4ba3cce7d24b9a05c61dd4cda4a64198b Mon Sep 17 00:00:00 2001 From: Colin Diesh Date: Wed, 18 Dec 2024 23:08:10 -0500 Subject: [PATCH] Update cram-js to avoid requesting file size for more CORS compatibility (#4729) --- .../app-core/src/ui/App/ViewsContainer.tsx | 9 +- packages/core/ui/index.ts | 2 - .../LinearGenomeView/components/Highlight.tsx | 23 +-- .../components/TracksContainer.tsx | 48 ++++-- .../sv-inspector/src/SvInspectorView/index.ts | 5 +- .../jbrowse-web/src/components/Loader.tsx | 10 +- yarn.lock | 140 +++++++++--------- 7 files changed, 125 insertions(+), 112 deletions(-) diff --git a/packages/app-core/src/ui/App/ViewsContainer.tsx b/packages/app-core/src/ui/App/ViewsContainer.tsx index 2d5073d2ce..8130c37f11 100644 --- a/packages/app-core/src/ui/App/ViewsContainer.tsx +++ b/packages/app-core/src/ui/App/ViewsContainer.tsx @@ -1,12 +1,15 @@ +import { Suspense, lazy } from 'react' + import { observer } from 'mobx-react' import { makeStyles } from 'tss-react/mui' -import ViewLauncher from './ViewLauncher' import ViewPanel from './ViewPanel' import type { SnackbarMessage } from '@jbrowse/core/ui/SnackbarModel' import type { SessionWithFocusedViewAndDrawerWidgets } from '@jbrowse/core/util' +const ViewLauncher = lazy(() => import('./ViewLauncher')) + const useStyles = makeStyles()({ viewsContainer: { overflowY: 'auto', @@ -34,7 +37,9 @@ const ViewsContainer = observer(function ViewsContainer(props: Props) { )) ) : ( - + + + )} {/* blank space at the bottom of screen allows scroll */} diff --git a/packages/core/ui/index.ts b/packages/core/ui/index.ts index 164aec86ab..83a00cb2c1 100644 --- a/packages/core/ui/index.ts +++ b/packages/core/ui/index.ts @@ -5,13 +5,11 @@ export { default as CascadingMenu } from './CascadingMenu' export { default as Dialog } from './Dialog' export { default as EditableTypography } from './EditableTypography' export { default as ErrorMessage } from './ErrorMessage' -export { default as FactoryResetDialog } from './FactoryResetDialog' export { default as FatalErrorDialog } from './FatalErrorDialog' export { default as FileSelector } from './FileSelector' export { default as LoadingEllipses } from './LoadingEllipses' export { default as Menu } from './Menu' export { default as PrerenderedCanvas } from './PrerenderedCanvas' -export { default as ReturnToImportFormDialog } from './ReturnToImportFormDialog' export { default as ResizeHandle } from './ResizeHandle' export { default as SanitizedHTML } from './SanitizedHTML' export * from './Menu' diff --git a/plugins/linear-genome-view/src/LinearGenomeView/components/Highlight.tsx b/plugins/linear-genome-view/src/LinearGenomeView/components/Highlight.tsx index 47e22e7867..9614a001e3 100644 --- a/plugins/linear-genome-view/src/LinearGenomeView/components/Highlight.tsx +++ b/plugins/linear-genome-view/src/LinearGenomeView/components/Highlight.tsx @@ -25,9 +25,12 @@ const useStyles = makeStyles()(theme => ({ linkIcon: { color: colord(theme.palette.highlight.main).darken(0.2).toRgbString(), }, + z3: { + zIndex: 3, + }, })) -const Highlight = observer(function Highlight({ +const Highlight = observer(function ({ model, highlight, }: { @@ -94,10 +97,10 @@ const Highlight = observer(function Highlight({ { setOpen(true) }} - style={{ zIndex: 3 }} > @@ -140,18 +143,4 @@ const Highlight = observer(function Highlight({ ) : null }) -const HighlightGroup = observer(function HighlightGroup({ - model, -}: { - model: LGV -}) { - return model.highlight.map((highlight, idx) => ( - - )) -}) - -export default HighlightGroup +export default Highlight diff --git a/plugins/linear-genome-view/src/LinearGenomeView/components/TracksContainer.tsx b/plugins/linear-genome-view/src/LinearGenomeView/components/TracksContainer.tsx index 681007ae8d..3f2b6d0c18 100644 --- a/plugins/linear-genome-view/src/LinearGenomeView/components/TracksContainer.tsx +++ b/plugins/linear-genome-view/src/LinearGenomeView/components/TracksContainer.tsx @@ -1,15 +1,12 @@ -import { useRef } from 'react' +import { Suspense, lazy, useRef } from 'react' import { Menu } from '@jbrowse/core/ui' import { getEnv } from '@jbrowse/core/util' import { observer } from 'mobx-react' import { makeStyles } from 'tss-react/mui' -import CenterLine from './CenterLine' import Gridlines from './Gridlines' -import HighlightGroup from './Highlight' import Rubberband from './Rubberband' -import RubberbandSpan from './RubberbandSpan' import Scalebar from './Scalebar' import VerticalGuide from './VerticalGuide' import { SCALE_BAR_HEIGHT } from '../consts' @@ -19,6 +16,10 @@ import { useWheelScroll } from './useWheelScroll' import type { LinearGenomeViewModel } from '..' +const CenterLine = lazy(() => import('./CenterLine')) +const Highlight = lazy(() => import('./Highlight')) +const RubberbandSpan = lazy(() => import('./RubberbandSpan')) + const useStyles = makeStyles()({ tracksContainer: { position: 'relative', @@ -62,7 +63,6 @@ const TracksContainer = observer(function TracksContainer({ undefined, { model }, ) as React.ReactNode - return (
{showGridlines ? : null} - {showCenterLine ? : null} + + {showCenterLine ? : null} + {guideX !== undefined ? ( ) : rubberbandOn ? ( - + + + ) : null} {anchorPosition ? ( + {model.highlight.map((highlight, idx) => ( + + ))} + + ) : null +}) + export default TracksContainer diff --git a/plugins/sv-inspector/src/SvInspectorView/index.ts b/plugins/sv-inspector/src/SvInspectorView/index.ts index 2951335104..f9c68d89b3 100644 --- a/plugins/sv-inspector/src/SvInspectorView/index.ts +++ b/plugins/sv-inspector/src/SvInspectorView/index.ts @@ -1,9 +1,10 @@ +import { lazy } from 'react' + import ViewType from '@jbrowse/core/pluggableElementTypes/ViewType' import { getContainingView, getSession } from '@jbrowse/core/util' import { navToMultiLevelBreak } from '@jbrowse/sv-core' import { type IAnyStateTreeNode, getParent } from 'mobx-state-tree' -import ReactComponent from './components/SvInspectorView' import stateModelFactory from './model' import type { SvInspectorViewModel } from './model' @@ -42,7 +43,7 @@ export default function SvInspectorViewF(pluginManager: PluginManager) { name: 'SvInspectorView', displayName: 'SV inspector', stateModel, - ReactComponent, + ReactComponent: lazy(() => import('./components/SvInspectorView')), }) }) } diff --git a/products/jbrowse-web/src/components/Loader.tsx b/products/jbrowse-web/src/components/Loader.tsx index 337b2defe2..68641df363 100644 --- a/products/jbrowse-web/src/components/Loader.tsx +++ b/products/jbrowse-web/src/components/Loader.tsx @@ -15,9 +15,8 @@ import '@fontsource/roboto' import JBrowse from './JBrowse' import Loading from './Loading' import SessionLoader from '../SessionLoader' -import factoryReset from '../factoryReset' -import StartScreenErrorMessage from './StartScreenErrorMessage' import { createPluginManager } from '../createPluginManager' +import factoryReset from '../factoryReset' import type { SessionLoaderModel, SessionTriagedInfo } from '../SessionLoader' import type { WebRootModel } from '../rootModel/rootModel' @@ -26,6 +25,7 @@ import type PluginManager from '@jbrowse/core/PluginManager' const ConfigWarningDialog = lazy(() => import('./ConfigWarningDialog')) const SessionWarningDialog = lazy(() => import('./SessionWarningDialog')) const StartScreen = lazy(() => import('./StartScreen')) +const StartScreenErrorMessage = lazy(() => import('./StartScreenErrorMessage')) function normalize(param: T | null | undefined) { return param === null ? undefined : param @@ -162,7 +162,11 @@ const Renderer = observer(function ({ const err = configError || error if (err) { - return + return ( + + + + ) } else if (sessionTriaged) { return } else if (pluginManager) { diff --git a/yarn.lock b/yarn.lock index a5dfd84362..ebae1ef8b7 100644 --- a/yarn.lock +++ b/yarn.lock @@ -139,9 +139,9 @@ tslib "^2.6.2" "@aws-sdk/client-s3@^3.712.0": - version "3.714.0" - resolved "https://registry.yarnpkg.com/@aws-sdk/client-s3/-/client-s3-3.714.0.tgz#74d056a57525a1289c7934015f2ce3f3714e7464" - integrity sha512-DqzfbecKrhUEpsYTsYRIm4cKKlIvAl4I/A2NpzDPDSiA2EmCWLy0T5fK1ivUA4XL+09+4pHJGNVTpMyDs7n6vg== + version "3.715.0" + resolved "https://registry.yarnpkg.com/@aws-sdk/client-s3/-/client-s3-3.715.0.tgz#31534aba9abff83e9b5444f425e129edf723c70e" + integrity sha512-7Qq8nW+/Yf+1Prjbwt2I6BsxhY28V6mbi8WF0n8m4qbC+y9wvreNuGv0PgzuLpfcP1bacB1ItW/Wkwuw2mau0w== dependencies: "@aws-crypto/sha1-browser" "5.2.0" "@aws-crypto/sha256-browser" "5.2.0" @@ -152,7 +152,7 @@ "@aws-sdk/credential-provider-node" "3.714.0" "@aws-sdk/middleware-bucket-endpoint" "3.714.0" "@aws-sdk/middleware-expect-continue" "3.714.0" - 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longfn "^1.3.1" md5 "^2.2.1" pako "^1.0.4" quick-lru "^4.0.1" @@ -2296,14 +2293,13 @@ quick-lru "^4.0.0" "@gmod/tabix@^2.0.0": - version "2.0.3" - resolved "https://registry.yarnpkg.com/@gmod/tabix/-/tabix-2.0.3.tgz#d8e1145d932a55a053f2fb0c53d18df08d291ee7" - integrity sha512-YdLEkjVFKJ/aQqwlCDmbt1EnAqTIupsyZTIt6Kucqq2w5Xyg1fedSRY/1eO75q4bXGsxpe384EEmyhP9PoC1AQ== + version "2.0.4" + resolved "https://registry.yarnpkg.com/@gmod/tabix/-/tabix-2.0.4.tgz#02ebf78ed1dc7b891aa315358ea746c967155951" + integrity sha512-7ibuWMDmbtljiWAA1NfjhtZyv6ctONct2qvuNoIOOW/fZS6qg4+eREF4sOWwS0ZnH+/vBCSaojXMPyZepLHXlQ== dependencies: "@gmod/abortable-promise-cache" "^2.0.0" "@gmod/bgzf-filehandle" "^2.0.1" generic-filehandle2 "^1.0.0" - longfn "^1.3.1" quick-lru "^4.0.0" "@gmod/trix@^3.0.0": @@ -5117,9 +5113,9 @@ "@types/react" "*" "@types/react@*", "@types/react@^19.0.1": - version "19.0.1" - resolved "https://registry.yarnpkg.com/@types/react/-/react-19.0.1.tgz#a000d5b78f473732a08cecbead0f3751e550b3df" - integrity sha512-YW6614BDhqbpR5KtUYzTA+zlA7nayzJRA9ljz9CQoxthR0sDisYZLuvSMsil36t4EH/uAt8T52Xb4sVw17G+SQ== + version "19.0.2" + resolved "https://registry.yarnpkg.com/@types/react/-/react-19.0.2.tgz#9363e6b3ef898c471cb182dd269decc4afc1b4f6" + integrity sha512-USU8ZI/xyKJwFTpjSVIrSeHBVAGagkHQKPNbxeWwql/vDmnTIBgx+TJnhFnj1NXgz8XfprU0egV2dROLGpsBEg== dependencies: csstype "^3.0.2" @@ -8037,7 +8033,7 @@ dotenv@^16.3.1, dotenv@^16.4.5, dotenv@~16.4.5: resolved "https://registry.yarnpkg.com/dotenv/-/dotenv-16.4.7.tgz#0e20c5b82950140aa99be360a8a5f52335f53c26" integrity sha512-47qPchRCykZC03FhkYAhrvwU4xDBFIj1QPqaarj6mdM/hgUzfPHcpkHJOn3mJAufFeeAxAzeGsr5X0M4k6fLZQ== -dunder-proto@^1.0.0: +dunder-proto@^1.0.0, dunder-proto@^1.0.1: version "1.0.1" resolved "https://registry.yarnpkg.com/dunder-proto/-/dunder-proto-1.0.1.tgz#d7ae667e1dc83482f8b70fd0f6eefc50da30f58a" integrity sha512-KIN/nDJBQRcXw0MLVhZE9iQHmG68qAVIBg9CqmUYjmQIhgij9U5MFvrqkUL5FbtyyzZuOeOt0zdeRe4UY7ct+A== @@ -8278,7 +8274,7 @@ error-stack-parser@^2.0.6: dependencies: stackframe "^1.3.4" -es-abstract@^1.17.5, es-abstract@^1.23.2, es-abstract@^1.23.3, es-abstract@^1.23.5: +es-abstract@^1.17.5, es-abstract@^1.23.2, es-abstract@^1.23.3, es-abstract@^1.23.5, es-abstract@^1.23.6: version "1.23.6" resolved "https://registry.yarnpkg.com/es-abstract/-/es-abstract-1.23.6.tgz#55f0e1ce7128995cc04ace0a57d7dca348345108" integrity sha512-Ifco6n3yj2tMZDWNLyloZrytt9lqqlwvS83P3HtaETR0NUOYnIULGGHpktqYGObGy+8wc1okO25p8TjemhImvA== @@ -9611,9 +9607,9 @@ globals@^14.0.0: integrity sha512-oahGvuMGQlPw/ivIYBjVSrWAfWLBeku5tpPE2fOPLi+WHffIWbuh2tCjhyQhTBPMf5E9jDEH4FOmTYgYwbKwtQ== globals@^15.9.0: - 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version "1.0.3" - resolved "https://registry.yarnpkg.com/is-shared-array-buffer/-/is-shared-array-buffer-1.0.3.tgz#1237f1cba059cdb62431d378dcc37d9680181688" - integrity sha512-nA2hv5XIhLR3uVzDDfCIknerhx8XUKnstuOERPNNIinXG7v9u+ohXF67vxm4TPTEPU6lm61ZkwP3c9PCB97rhg== + version "1.0.4" + resolved "https://registry.yarnpkg.com/is-shared-array-buffer/-/is-shared-array-buffer-1.0.4.tgz#9b67844bd9b7f246ba0708c3a93e34269c774f6f" + integrity sha512-ISWac8drv4ZGfwKl5slpHG9OwPNty4jOWPRIhBpxOoD+hqITiwuipOQ2bNthAzwA3B4fIjO4Nln74N0S9byq8A== dependencies: - call-bind "^1.0.7" + call-bound "^1.0.3" is-ssh@^1.4.0: version "1.4.0" @@ -10566,9 +10562,9 @@ is-text-path@^1.0.1: text-extensions "^1.0.0" is-typed-array@^1.1.13, is-typed-array@^1.1.14, is-typed-array@^1.1.3: - version "1.1.14" - resolved "https://registry.yarnpkg.com/is-typed-array/-/is-typed-array-1.1.14.tgz#205d51d499d5e336f4a3aa480c8ead5ff9e2e3e8" - integrity sha512-lQUsHzcTb7rH57dajbOuZEuMDXjs9f04ZloER4QOpjpKcaw4f98BRUrs8aiO9Z4G7i7B0Xhgarg6SCgYcYi8Nw== + version "1.1.15" + resolved "https://registry.yarnpkg.com/is-typed-array/-/is-typed-array-1.1.15.tgz#4bfb4a45b61cee83a5a46fba778e4e8d59c0ce0b" + integrity sha512-p3EcsicXjit7SaskXHs1hA91QxgTw46Fv6EFKKGS5DRFLD8yKnohjF3hxoju94b/OcMZoQukzpPpBE9uLVKzgQ== dependencies: which-typed-array "^1.1.16" @@ -11689,11 +11685,6 @@ log-symbols@^4.0.0, log-symbols@^4.1.0: chalk "^4.1.0" is-unicode-supported "^0.1.0" -longfn@^1.3.1: - version "1.3.1" - resolved "https://registry.yarnpkg.com/longfn/-/longfn-1.3.1.tgz#1655fef1034bcb9f7b7911a4afb493d4acc8751d" - integrity sha512-sFNpfHBvO+mK6bSMr//CGeeXCJX4nKaBJ9M7QsJkzZT8ez+z12lkzRlyZibjdtjLHlfYPv9rmwHGGuwJOglFFQ== - loose-envify@^1.1.0, loose-envify@^1.4.0: version "1.4.0" resolved "https://registry.yarnpkg.com/loose-envify/-/loose-envify-1.4.0.tgz#71ee51fa7be4caec1a63839f7e682d8132d30caf" @@ -12725,13 +12716,15 @@ object-keys@^1.1.1: integrity sha512-NuAESUOUMrlIXOfHKzD6bpPu3tYt3xvjNdRIQ+FeT0lNb4K8WR70CaDxhuNguS2XG+GjkyMwOzsN5ZktImfhLA== object.assign@^4.1.4, object.assign@^4.1.5: - version "4.1.5" - resolved "https://registry.yarnpkg.com/object.assign/-/object.assign-4.1.5.tgz#3a833f9ab7fdb80fc9e8d2300c803d216d8fdbb0" - integrity sha512-byy+U7gp+FVwmyzKPYhW2h5l3crpmGsxl7X2s8y43IgxvG4g3QZ6CffDtsNQy1WsmZpQbO+ybo0AlW7TY6DcBQ== + version "4.1.7" + resolved "https://registry.yarnpkg.com/object.assign/-/object.assign-4.1.7.tgz#8c14ca1a424c6a561b0bb2a22f66f5049a945d3d" + integrity sha512-nK28WOo+QIjBkDduTINE4JkF/UJJKyf2EJxvJKfblDpyg0Q+pkOHNTL0Qwy6NP6FhE/EnzV73BxxqcJaXY9anw== dependencies: - call-bind "^1.0.5" + call-bind "^1.0.8" + call-bound "^1.0.3" define-properties "^1.2.1" - has-symbols "^1.0.3" + es-object-atoms "^1.0.0" + has-symbols "^1.1.0" object-keys "^1.1.1" object.entries@^1.1.8: @@ -14170,18 +14163,18 @@ redent@^3.0.0: strip-indent "^3.0.0" reflect.getprototypeof@^1.0.6, reflect.getprototypeof@^1.0.8: - version "1.0.8" - resolved "https://registry.yarnpkg.com/reflect.getprototypeof/-/reflect.getprototypeof-1.0.8.tgz#c58afb17a4007b4d1118c07b92c23fca422c5d82" - integrity sha512-B5dj6usc5dkk8uFliwjwDHM8To5/QwdKz9JcBZ8Ic4G1f0YmeeJTtE/ZTdgRFPAfxZFiUaPhZ1Jcs4qeagItGQ== + version "1.0.9" + resolved "https://registry.yarnpkg.com/reflect.getprototypeof/-/reflect.getprototypeof-1.0.9.tgz#c905f3386008de95a62315f3ea8630404be19e2f" + integrity sha512-r0Ay04Snci87djAsI4U+WNRcSw5S4pOH7qFjd/veA5gC7TbqESR3tcj28ia95L/fYUDw11JKP7uqUKUAfVvV5Q== dependencies: call-bind "^1.0.8" define-properties "^1.2.1" - dunder-proto "^1.0.0" - es-abstract "^1.23.5" + dunder-proto "^1.0.1" + es-abstract "^1.23.6" es-errors "^1.3.0" - get-intrinsic "^1.2.4" + get-intrinsic "^1.2.6" gopd "^1.2.0" - which-builtin-type "^1.2.0" + which-builtin-type "^1.2.1" regenerate-unicode-properties@^10.2.0: version "10.2.0" @@ -15820,13 +15813,13 @@ type-is@1.6.18, type-is@~1.6.18: mime-types "~2.1.24" typed-array-buffer@^1.0.2: - version "1.0.2" - resolved "https://registry.yarnpkg.com/typed-array-buffer/-/typed-array-buffer-1.0.2.tgz#1867c5d83b20fcb5ccf32649e5e2fc7424474ff3" - integrity sha512-gEymJYKZtKXzzBzM4jqa9w6Q1Jjm7x2d+sh19AdsD4wqnMPDYyvwpsIc2Q/835kHuo3BEQ7CjelGhfTsoBb2MQ== + version "1.0.3" + resolved "https://registry.yarnpkg.com/typed-array-buffer/-/typed-array-buffer-1.0.3.tgz#a72395450a4869ec033fd549371b47af3a2ee536" + integrity sha512-nAYYwfY3qnzX30IkA6AQZjVbtK6duGontcQm1WSG1MD94YLqK0515GNApXkoxKOWMusVssAHWLh9SeaoefYFGw== dependencies: - call-bind "^1.0.7" + call-bound "^1.0.3" es-errors "^1.3.0" - is-typed-array "^1.1.13" + is-typed-array "^1.1.14" typed-array-byte-length@^1.0.1: version "1.0.3" @@ -15884,9 +15877,9 @@ typescript-eslint@^8.0.1: integrity sha512-i5t66RHxDvVN40HfDd1PsEThGNnlMCMT3jMUuoh9/0TaqWevNontacunWyN02LA9/fIbEWlcHZcgTKb9QoaLfg== typescript@^5.8.0-dev.20241213: - version "5.8.0-dev.20241217" - resolved "https://registry.yarnpkg.com/typescript/-/typescript-5.8.0-dev.20241217.tgz#07d7e46c927572f7e8a5095a16090477aaff2496" - integrity sha512-Q/I+eHfiwN0aWhitenThTT2FcA1lTlUZR1z+6d2WaD/8/wHfdjQjdHynCpYXjAwDkfG8Apf9LdzZ3rLRD3O9iQ== + version "5.8.0-dev.20241218" + resolved "https://registry.yarnpkg.com/typescript/-/typescript-5.8.0-dev.20241218.tgz#64a079b5a8d30e1c6d6e21f23279d5a45f3efd6a" + integrity sha512-MIBYE1oO/aI9B3oluGzDOqTYMmPhGK1Xwvjk4LOCu+1CeKQMtPF3pLC9n/VcznkI0n6k7MQ4S8a8VJdbOEE96A== uglify-js@^3.1.4: version "3.19.3" @@ -16447,7 +16440,7 @@ which-boxed-primitive@^1.1.0, which-boxed-primitive@^1.1.1: is-string "^1.1.1" is-symbol "^1.1.1" -which-builtin-type@^1.2.0: +which-builtin-type@^1.2.1: version "1.2.1" resolved "https://registry.yarnpkg.com/which-builtin-type/-/which-builtin-type-1.2.1.tgz#89183da1b4907ab089a6b02029cc5d8d6574270e" integrity sha512-6iBczoX+kDQ7a3+YJBnh3T+KZRxM/iYNPXicqk66/Qfm1b93iu+yOImkg0zHbj5LNOcNv1TEADiZ0xa34B4q6Q== @@ -16477,14 +16470,15 @@ which-collection@^1.0.2: is-weakset "^2.0.3" which-typed-array@^1.1.16, which-typed-array@^1.1.2: - version "1.1.16" - resolved "https://registry.yarnpkg.com/which-typed-array/-/which-typed-array-1.1.16.tgz#db4db429c4706feca2f01677a144278e4a8c216b" - integrity sha512-g+N+GAWiRj66DngFwHvISJd+ITsyphZvD1vChfVg6cEdnzy53GzB3oy0fUNlvhz7H7+MiqhYr26qxQShCpKTTQ== + version "1.1.18" + resolved "https://registry.yarnpkg.com/which-typed-array/-/which-typed-array-1.1.18.tgz#df2389ebf3fbb246a71390e90730a9edb6ce17ad" + integrity sha512-qEcY+KJYlWyLH9vNbsr6/5j59AXk5ni5aakf8ldzBvGde6Iz4sxZGkJyWSAueTG7QhOvNRYb1lDdFmL5Td0QKA== dependencies: available-typed-arrays "^1.0.7" - call-bind "^1.0.7" + call-bind "^1.0.8" + call-bound "^1.0.3" for-each "^0.3.3" - gopd "^1.0.1" + gopd "^1.2.0" has-tostringtag "^1.0.2" which@^1.2.9, which@^1.3.1: