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prDatams.json
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"additions": 36540,
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"author": {
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"body": "This branch begins a large-scale move of the app to redux and redux sagas for state management. It also restructures the app in a way I think is easier to navigate and think about.\r\n\r\n### Cleanup\r\n* Webpack config based on [this](https://github.com/taniarascia/webpack-boilerplate).\r\n* Remove unnecessary/unused build machinery and unused files.\r\n* Remove Google Analytics integration\r\n* Dynamically generate artifact and use default WebPack output directory\r\n* Update most dependencies, removed unused or unnecessary dependincies\r\n* Add a script to visualise the size of the compiled build artifact (bundle-size-analyse)\r\n* Use ts-loader rather than babel to compile ts/tsx (type-checking)\r\n* Upgrade to webpack 5\r\n* Remove reliance on polyfilled Node APIs (path and zip)\r\n* Add linting for use of abstract equality and block delimiters with braces\r\n* Add tests for the front-end using Jest and react-testing-library. Including tests for `fetch()` And GProfiler previously introduced.\r\n* Use `jest-css-modules-transform` to handle imports for CSS. Version is intentionally pinned as \"4.0.2\" breaks tests.\r\n* Wrap the old API in a scary `LegacyAPI` name\r\n* Extract some of the complexity in the `App` component in new `Main` and `FullPageNotify` components.\r\n* Turn on strict TypeScript type checking and fix all type errors.\r\n* Remove as much CSS as possible and simplify DOM structure\r\n* Introduce a TEST_ONLY flag to avoid hard-to-test side-effects from the legacy API while testing.\r\n* Add local CSS imported only by the component that uses it.\r\n* Remove as many uses of Lodash as possible\r\n* Add a utility function `zipLists` to `zip()` a list of lists.\r\n* Refactor the UploadModal to be responsive.\r\n* Reduce use of `default exports`\r\n\r\n### Code structure and redesign\r\n* Document code style and design decisions in CONTRIBUTING.md\r\n* Change the structure of `getFeature()` requests and responses\r\n* Add a \"filter by type/category\" argument to `getFeature()` requests\r\n* Redisign of FeatureSearchBox components following the guidelines outlines in CONTRIBUTING.md\r\n* LegacyAPI no longer tracks UUID, sessionMode, sidebar visibility, and cookie consent. These have been moved to Redux.\r\n* Wire in Redux to existing components where useful.\r\n* Use `immer` to update Redux state.\r\n* Add a `Result` type similar to the backend `Result` type.\r\n\r\n### UI\r\n* Viewer component is now responsive and does less work to render data\r\n* Redisign of UI, the whole UI is a little more responsive and more traditionally \"single-page\".\r\n* Centre the Welcome page and make it scrollable.\r\n\r\n### Breaking changes and known issues\r\n* Does not keep (removes) the functionality for \"locking\" related search entries on searches like \"batch\" and \"All clusters\" (#447)\r\n* ~~This PR breaks ViewerSidebar \"Clustering Controls\". Fixing this is out of scope for the PR, this should instead be fixed after @dweemx cleanup of the ViewerSidebar is merged.~~\r\n* Lasso selections are not \"remembered\" when switching between tabs.\r\n* The Babel config file is necessary for Jest. It duplicates the webpack config. If you have a solution to remove the duplication please let me know.\r\n* [VISUAL/STYLING] Annotation voting popup does not persist on mouseover (#427)\r\n* ~~Compare tab break when performing a DnD of one of the annotation onto a viewer.~~\r\n* [VISUAL/STYLING] Styling changes cause text to overlap in many locations (i.e. Loom selection in sidebar) (#428)\r\n* [BREAKING] Getting metadata from a cell section fails (#429)\r\n* [MINOR] Settings in sidebar do not display when selecting a loom, only after selecting a gene or changing loom (#430) \r\n* [BREAKING] Selecting a cluster in the results, always selects the first result by name (#431)\r\n* [BREAKING] Adding annotations fails with python error (#432)\r\n* [MINOR] Annotation labels remain after clearing feature (#433)\r\n* [VISUAL/STYLING] Regulon tab plots done fill screen (#434)\r\n* [MAJOR] Selecting a regulon causes an infinite loop in the backend (#435)\r\n* [BREAKING] Regulon histogram never displays data (#436)\r\n* [MAJOR] Unable to search for clusters by annotation name (#437)\r\n* [MINOR] Permalink button does nothing (#438)\r\n* [MAJOR] Compare tab does not work with more that one annotation per viewer (#439)",
"changedFiles": 109,
"closed": true,
"closedAt": "2021-05-28T08:23:55Z",
"comments": [
{
"id": "MDEyOklzc3VlQ29tbWVudDcxNTA5MDAyNg==",
"author": {
"login": "MaybeJustJames"
},
"authorAssociation": "COLLABORATOR",
"body": "Add PR summary points to documentation (conribution manual??)",
"createdAt": "2020-10-23T07:42:19Z",
"includesCreatedEdit": false,
"isMinimized": false,
"minimizedReason": "",
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"url": "https://github.com/aertslab/SCope/pull/381#issuecomment-715090026",
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"author": {
"login": "dweemx"
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"authorAssociation": "CONTRIBUTOR",
"body": "/!\\ I noticed that `<- Pevious` and `Next ->` buttons of the cluster controls (right side bar) don't work anymore. They work in the `master` branch",
"createdAt": "2020-10-26T14:05:36Z",
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"url": "https://github.com/aertslab/SCope/pull/381#issuecomment-716568413",
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"body": "> /!\\ I noticed that `<- Pevious` and `Next ->` buttons of the cluster controls (right side bar) don't work anymore. They work in the `master` branch\r\n\r\nReproductions steps:\r\n1. Query \"Unannotated Cluster 0\"\r\n1. Click on \"Next ->\" button in the right side bar should take you to the next cluster i.e.: \"Unannotated Cluster 1\"\r\n1. Click on \"<- Previous\" button in the right side bar should take you to the previous cluster i.e.: \"Unannotated Cluster 0\"",
"createdAt": "2020-12-08T10:09:53Z",
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"author": {
"login": "MaybeJustJames"
},
"authorAssociation": "COLLABORATOR",
"body": "@dweemx wrt an `.nvmrc` Node 10 is EOL end of this month. I'm fine leaving this out. What about you?",
"createdAt": "2021-04-02T10:31:14Z",
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"url": "https://github.com/aertslab/SCope/pull/381#issuecomment-812473688",
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"author": {
"login": "MaybeJustJames"
},
"authorAssociation": "COLLABORATOR",
"body": "@dweemx Can you elaborate on what \"switch from loom\" means?",
"createdAt": "2021-04-02T10:34:27Z",
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"id": "MDEyOklzc3VlQ29tbWVudDgxMjQ4NTAzOQ==",
"author": {
"login": "dweemx"
},
"authorAssociation": "CONTRIBUTOR",
"body": "> @dweemx wrt an `.nvmrc` Node 10 is EOL end of this month. I'm fine leaving this out. What about you?\r\n\r\nYou mean not having a `.nvmrc` file or just upgrade to use higher Node version ?",
"createdAt": "2021-04-02T11:09:36Z",
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"url": "https://github.com/aertslab/SCope/pull/381#issuecomment-812485039",
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"author": {
"login": "MaybeJustJames"
},
"authorAssociation": "COLLABORATOR",
"body": "> > @dweemx wrt an `.nvmrc` Node 10 is EOL end of this month. I'm fine leaving this out. What about you?\r\n> \r\n> You mean not having a `.nvmrc` file or just upgrade to use higher Node version ?\r\n\r\nNo I mean it's a users fault if they use an EOL node version. So why have an `.nvmrc`?",
"createdAt": "2021-04-02T12:34:39Z",
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"url": "https://github.com/aertslab/SCope/pull/381#issuecomment-812511020",
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"id": "MDEyOklzc3VlQ29tbWVudDgxNTA1MzQzOA==",
"author": {
"login": "dweemx"
},
"authorAssociation": "CONTRIBUTOR",
"body": "> > > @dweemx wrt an `.nvmrc` Node 10 is EOL end of this month. I'm fine leaving this out. What about you?\r\n> > \r\n> > \r\n> > You mean not having a `.nvmrc` file or just upgrade to use higher Node version ?\r\n> \r\n> No I mean it's a users fault if they use an EOL node version. So why have an `.nvmrc`?\r\n\r\nBecause the user will be sure that the software will work with that version of Node. ",
"createdAt": "2021-04-07T16:30:26Z",
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"commits": [
{
"authoredDate": "2020-08-13T14:49:05Z",
"authors": [
{
"email": "james.collier@vib.be",
"id": "MDQ6VXNlcjI2NDQ0MzEy",
"login": "MaybeJustJames",
"name": "James Collier"
}
],
"committedDate": "2021-05-28T08:11:20Z",
"messageBody": "* Move to typescript\n* Remove unnecessary and unused code\n* Upgrade semantic-ui-react to a more recent version\n* Re-organise some dependant code\n* Update packages and install immer",
"messageHeadline": "Simplify and organise the FeatureSearchBox component",
"oid": "1b9216d8b9d228c727c3e5736c5daaab2fe0c78f"
},
{
"authoredDate": "2020-08-14T12:10:02Z",
"authors": [
{
"email": "james.collier@vib.be",
"id": "MDQ6VXNlcjI2NDQ0MzEy",
"login": "MaybeJustJames",
"name": "James Collier"
}
],
"committedDate": "2021-05-28T08:11:29Z",
"messageBody": "",
"messageHeadline": "Us ESLint to replace use of `let` with `const` where possible",
"oid": "53d6870ec4fd54c89c83dd478fe11825f22a6c37"
},
{
"authoredDate": "2020-08-25T07:00:03Z",
"authors": [
{
"email": "james.collier@vib.be",
"id": "MDQ6VXNlcjI2NDQ0MzEy",
"login": "MaybeJustJames",
"name": "James Collier"
}
],
"committedDate": "2021-05-28T08:11:29Z",
"messageBody": "This can be used to only search for genes or regulons, etc. that match\nthe search query rather than everything that matches the search query.\n\n* Add \"MENU\" text to the header menu button\n* Default session mode should be \"read\"\n* Remove dropdown on the FeatureSearchBox. Filter is imposed by the\n page and is not user selectable.\n* Adjust getFeatures gRPC/protocol buffers interface\n* Modify the gRPC definition of getFeatures to be more convenient\n* Fix a react warning\n The warning triggered when trying to update the old state management\n system using onResultSelect() while rendering. This is a no-no\n so now it just calls the old state management update API.\n This also moves remaining logic out of the component\n* Do some error handling\n* Some documentation",
"messageHeadline": "Implement filtering in the FeatureSearchBox",
"oid": "8c6c87ba4bbf3d46d52dcb7bbada7e6bcf19e3a0"
},
{
"authoredDate": "2020-09-14T09:03:34Z",
"authors": [
{
"email": "james.collier@vib.be",
"id": "MDQ6VXNlcjI2NDQ0MzEy",
"login": "MaybeJustJames",
"name": "James Collier"
}
],
"committedDate": "2021-05-28T08:11:30Z",
"messageBody": "* Add basic Saga side-effect generation testing\n* Add Reducer type annotation (thanks @dweemx)\n* Use a clearer variable name for search results\n* Prefer `type` over `interface`\n* Use constants in App\n* The name \"handleUpdateScatterPlot\" is a more accurate than \"handleUpdateTSNE\"\n* Do not open the bundle analyzer by default\n* Bump semantic-ui-react version\n* use Sagas debounce() rather than throttle()\n* Remove unused import of lodash\n* Fix bug: Cannot model category as strict type, revert to string\n* Fix bug: Correct ordering in displayed search results",
"messageHeadline": "Add some testing for the Search related components",
"oid": "74f7dad14a74ca6b866d857406bf23584ebbbd2d"
},
{
"authoredDate": "2020-11-02T16:13:44Z",
"authors": [
{
"email": "james.collier@vib.be",
"id": "MDQ6VXNlcjI2NDQ0MzEy",
"login": "MaybeJustJames",
"name": "James Collier"
}
],
"committedDate": "2021-05-28T08:11:50Z",
"messageBody": "* Add some tests\n* Wire up redux hooks and fix tests\n* Fix \"cancel\" button in search box\n* Track cookie consent in redux",
"messageHeadline": "Turn on strict type checking and start fixing errors",
"oid": "f4df49b536783683828696f4e4500165f87ab307"
},
{
"authoredDate": "2020-11-04T10:03:53Z",
"authors": [
{
"email": "james.collier@vib.be",
"id": "MDQ6VXNlcjI2NDQ0MzEy",
"login": "MaybeJustJames",
"name": "James Collier"
}
],
"committedDate": "2021-05-28T08:11:50Z",
"messageBody": "",
"messageHeadline": "Wrap filenames in the AppSidebar",
"oid": "b4842a01f6c29fc143dc75a89fc01c07beb04d4b"
},
{
"authoredDate": "2020-11-04T10:33:38Z",
"authors": [
{
"email": "james.collier@vib.be",
"id": "MDQ6VXNlcjI2NDQ0MzEy",
"login": "MaybeJustJames",
"name": "James Collier"
}
],
"committedDate": "2021-05-28T08:11:51Z",
"messageBody": "So that users immediately see where to load their data.\nAlso centres content in the Welcome screen so still\nvisible with the sidebar open.",
"messageHeadline": "Display the sidebar by default",
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"body": "Minor things that I picked up.\r\nOtherwise nice stuff in there: cleanup & testing :+1: \r\n\r\nExperienced a problem when trying to run SCope:\r\n```\r\n> SCope@1.8.2 dev ~/SCope/master\r\n> cross-env NODE_ENV=development NODE_TYPE=local webpack-dev-server --hot\r\n\r\n~/SCope/master/node_modules/terser-webpack-plugin/node_modules/p-limit/index.js:30\r\n\t\t} catch {}\r\n\t\t ^\r\n\r\nSyntaxError: Unexpected token {\r\n at new Script (vm.js:51:7)\r\n at createScript (vm.js:136:10)\r\n at Object.runInThisContext (vm.js:197:10)\r\n at Module._compile (internal/modules/cjs/loader.js:618:28)\r\n at Object.Module._extensions..js (internal/modules/cjs/loader.js:665:10)\r\n at Module.load (internal/modules/cjs/loader.js:566:32)\r\n at tryModuleLoad (internal/modules/cjs/loader.js:506:12)\r\n at Function.Module._load (internal/modules/cjs/loader.js:498:3)\r\n at Module.require (internal/modules/cjs/loader.js:598:17)\r\n at require (internal/modules/cjs/helpers.js:11:18)\r\nnpm ERR! code ELIFECYCLE\r\nnpm ERR! errno 1\r\nnpm ERR! SCope@1.8.2 dev: `cross-env NODE_ENV=development NODE_TYPE=local webpack-dev-server --hot`\r\nnpm ERR! Exit status 1\r\nnpm ERR! \r\nnpm ERR! Failed at the SCope@1.8.2 dev script.\r\nnpm ERR! This is probably not a problem with npm. There is likely additional logging output above.\r\n\r\nnpm ERR! A complete log of this run can be found in:\r\nnpm ERR! ~/.npm/_logs/2020-09-18T12_47_32_043Z-debug.lo\r\n```\r\neven after removing `node_modules` and `package-lock.json`",
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