CHANGELOG.md

Changelog

1.5.2 (2024-11-05)

Misc

• deps: bump werkzeug from 3.0.4 to 3.0.6 in /server (#1141) (a6aca42)

Code Refactoring

• AnnoDialog (SCE-34) (#1138) (d494730)
• DiffExpButtons (SCE-34) (#1140) (186fea8)

1.5.1 (2024-10-10)

Misc

• add codecov github action to unit tests (#1134) (a6c8564)
• deps: bump body-parser and express in /client (#1131) (358b0a0)
• deps: bump dset from 3.1.3 to 3.1.4 in /client (#1102) (33a88a3)
• update scale bar position (#1136) (6b0933d)

1.5.0 (2024-10-09)

Misc

• Add newsletter signup to bottom banner (SCE-29) (#1116) (1f0048f)
• update playwright to pause animation (#1128) (284eb4f)

Features

• scale bar for zoom (SCE-26, SCE-25, SCE-27) (#1125) (49e8d14)

1.4.2 (2024-09-26)

Misc

• Add aliases and shared folders for renaming (#1107) (e15a2a4)
• Add new readme section and dev_doc file (#1101) (7218253)
• bump chart version for prod (#1118) (5ddf710)
• bump chart versions (#1117) (e442d6c)
• default dot opacity 50% (SCE-27) (#1124) (c2552bf)
• Fractal renaming - Graph (#1111) (5cfc851)
• Move src/components/utils into src/utils (#1109) (1dfdbf7)
• Python 3.12 (SCE-16) (#1100) (f767f66)
• Rename - Right Sidebar (#1112) (52ec34a)
• Rename Left Sidebar (#1113) (487de2f)
• Rename NavBar, MenuBar, Hotkeys (#1114) (ba2087a)
• Update Dev Docs (#1104) (a891910)
• Upgrade BE deps (SCE-18) (#1092) (284dd6c)
• Upgrade codecov (#1119) (920c0fb)
• Upgrade React 18 (SCE-1) (#1079) (5607bf3)
• Use staging env deep zoom assets for localhost (#1103) (c951f21)

Bug Fixes

• SCE-20 Navbar use font Inter (#1115) (2ffd87b)

Tests

• Chromatic auto accept main (78427b4)
• SCE-6 e2e tests tabilize snapshots (#1086) (901355a)

1.4.1 (2024-08-27)

Bug Fixes

• og:title/image and fontFamily (#1082) (b17d22d)

1.4.0 (2024-08-23)

Misc

• Upgrade MUI and SDS - SCE-3 SCE-2 (#1075) (270653c)

Features

• Add og:image and og:title (#1078) (261ff81)

1.3.0 (2024-08-16)

Misc

• Upgrade to BlueprintJS 5 - SCE-4 (#1068) (f3a4184)

Features

• SCE-9 NavBar Update (#1072) (deb9ec1)

Bug Fixes

• Check for slide-seq (#1071) (0bf3040)
• Spatial mode dot size on highlight (#1074) (2190482)

Tests

• Fix e2e test cellCount diff by 1 (#1069) (4ce2809)

1.2.0 (2024-08-07)

Misc

• bump argus builder version (#1065) (cf3608f)
• Changes to analytics names and timing (#1051) (ec42d18)
• DP#7155 Update analytics Part 1 (#1041) (d155d63)
• DP#7155 Update analytics part 2 (#1045) (6eda411)
• remove .happy directory and happy-related GH Actions (#1052) (0b5eee9)
• Turn off logging comments (#1055) (0ae463c)
• Update conventional commit GHA (2125709)

Features

• Add survey banner to Explorer (#1063) (a875df6)
• cell type info and info panel refactor (#1043) (f4ddb1a)
• info panel search for gene and cell type (#1061) (22e4f44)
• Remove spatial feature flag (#1015) (f95a8c1)

Bug Fixes

• 1053 Truncate histogram and dataset info panel (#1054) (88bf816)
• Add mix blend mode to canvas (#1042) (f3210d0)
• add spatial to default layout list (#1067) (6f3f122)
• Add tissue_type to standard categories (#1060) (2d9a721)
• Conditionally apply opacity to the dots (#1047) (2cd5fd3)
• Make menu bar responsive (#1059) (2856e60)

Tests

• Make test more robust (#1049) (c977612)

1.1.1 (2024-07-15)

Misc

• invoke smoke tests against every prod deploy (#1037) (b425a52)

Bug Fixes

• Prod analytics (#1039) (86fc4a7)

1.1.0 (2024-07-15)

Misc

• Add test for bug #1022 color by category (#1024) (791e93d)
• Update conventional commit GHA (#1025) (405b087)
• use cloudfront domains in Argus config (#1036) (20dabf9)

Features

• 6867 6868 image and dot opacity (#1029) (97f57e6)
• accurate and dynamic dot size for spatial (#1021) (c6c195e)
• add docker login line for core platform (#1018) (a6b5196)
• de: add diffex notice (#1028) (2c4d9b0)
• limit zoom level for hires (#1026) (e92be7c)

Bug Fixes

• 1022 Fix color by category bug (#1023) (ba46be0)
• diffexp notif (#1031) (c4dbb37)
• hide side panel toggle for single embedding (#1027) (867311d)
• info panel tabs (#1030) (68c42d5)
• local console errors (#1033) (f062d10)
• padding of info panel content (#1032) (5319564)
• Remove the wrong lasso in the other panel (#1035) (9dffc9e)

1.0.1 (2024-07-02)

Bug Fixes

• GE scroll and overflow (#1011) (8879f03)

Misc

• allow smoke tests to be a required check (#1016) (b6bf390)
• bump staging memory (#1014) (4ecebd1)
• configure e2e tests to run against staging before prod can deploy (#1012) (3995a74)
• tune smoke test invocation (#1017) (231ad56)

1.0.0 (2024-06-27)

Features

• 70 add portal collection homepage to /config (#83) (8e0dd91)
• 88 add dataset_id to the metadata endpoint (#93) (ae60d1b)
• Add a Github Action that automatically closes stale PRs. (#647) (f15b4db)
• add back navbar to all instances regardless of dataset metadata (#883) (4ca479d)
• add cellxgene schema 3.0.0 fields to Standard Categories (#412) (b265fcf)
• add cellxgene schema 3.0.0 fields to Standard Categories (#412) (#486) (6d25ccc)
• Add correlation ids to logs to improve debugging (#606) (2540fd9)
• add deployed_version endpoint (#588) (64b4979)
• add DOCUMENTATION_CLICK_NAV for Documentation click (#546) (4d456b5)
• add feature flags to explorer (#769) (b50116e)
• add geneset initialization (#803) (0d204de)
• add hotkeys for undo redo and remove buttons (#467) (fafc539)
• add mypy to the server/common/utils directory (#672) (39b088d)
• add new api rule for cellguide cxgs (#777) (790682b)
• add publisher_metadata to the dataset metadata endpoint (#224) (24ba6e5)
• add quick gene lookup functionality (#2250) (82de417)
• add some structured support for mocking the dataset-metadata endpoint (#691) (d95b90d)
• added add-gene-and-* analytics for issue 275 (#283) (21f0739)
• analytics: 1631 Add analytics (#249) (8af586a)
• Bump max zoom from 12 to 80 (#961) (1859de5)
• census-spotlight: update navbar to new layout (#677) (9027420)
• dataset metadata endpoint (#64) (6536f05)
• Deep zoom (#929) (164aa76)
• differential expression performance improvements (#234) (1e9965a)
• diffexp returns two genesets (#2230) (28b526b)
• download: include a continuous legend in image downloads (#878) (c44d9d9)
• drop int64 fields from cxg_schema in the obs array (#653) (7a96def)
• enable image capture and download of graph (#817) (c00d3ab)
• Enable permissions to support happy shell (#349) (acd8932)
• exclude observation join id from standard and author categories (#674) (8661a4e)
• fix explorer API for handling subpaths in S3 (#792) (4ba67ac)
• frontend geneset validation (#2258) (b714c18)
• gene info cards (#298) (8cf1341)
• geneset: save diff exp result as geneset (#2216) (a4050f1)
• img: capture graph as a image for testing and user download (#796) (bb2735f)
• include a legend image for categorical colorby (#884) (332644f)
• include localhost and canary env as allowed origins for staging backend (#71) (8758ce5)
• increase zoom limits by a factor of 4 (#577) (db5051d)
• move continuous fields to the dataset drawer if there is a single value for all cells (#918) (055b24d)
• Newsletter Banner (#601) (d99f066)
• remove author and standard categories for cellguide cxgs and add singletons back (#795) (67502f6)
• setup explorer on argus (#886) (a6ecee7)
• side by side (#977) (bf2babc)
• Spatial Mode User Story 1 (#805) (df7d42d)
• spatial refactor (#852) (ffd7281)
• spatial: analytics (#974) (9986a37)
• split new cellguide cxg regex into another constant (#786) (b0e2793)
• wmg: 3701 Remove beta tag (#545) (4028070)

Bug Fixes

• 1001 No download image for minimized panel (#1004) (db0944e)
• 104 dataframe histogram memoization (#116) (b0360b8)
• 156 obsolete browsers (#159) (656b63e)
• 270 analytics expand events (#271) (6a75d87)
• 73 - add 2.0.0 to the recognized FE versions (#74) (a16acc9)
• 84 Do not cache index.html (#86) (8bc3e06)
• 858 jason bug 2 (#948) (6beebe8)
• 936 embedding cell count (#942) (65d1281)
• add census link in explorer (#625) (202a90f)
• add max_age to immutable caches (#205) (52579c5)
• add missing ECS folder (#526) (7d91243)
• add placeholder test so suite doesn't fail (#2233) (7ed53c0)
• add screenCap to cached props for diffing during render check (#835) (056704f)
• Add services to happy config (#409) (90f976e)
• Allow Connection to Hubspot (#633) (b8f9f5e)
• analytics: #262 adds event payloads (#264) (be75ba1)
• Assume NavBar is present when calculating height of explorer initially. (#502) (92cbcf0)
• Assume navbar present by default and only remove padding if dataset metadata errors (#517) (fde15ae)
• change path for static font files (#370) (c93f3b3)
• collection_url prefix in dataset-metadata (#140) (9558db3)
• Continuous legend properly disappears after coloring by continuous metadata and subsequently coloring by anything else (#513) (fa59fa5)
• convert sparse numpy matrix to ndarray (#2271) (5f976cc)
• Correctly load image underlay when initial layout is spatial (#859) (2cace76)
• dataset metadata response parsing (#43) (084dc5c)
• dataset-metadata private collections call (#127) (79e4424)
• decrease the topN count explicitly on hosted (#2320) (bbf1950)
• disable FE auth testing on compatibility tests (#2377) (925b785)
• disable portion of noisy env screenshots (#75) (47b206a)
• Docker-compose specify platform to get around arm vs amd arch mismatches (#241) (5c2a4b3)
• docker: explicitly install node (#307) (c3d4fd8)
• docker: fix script url (#308) (a05db9d)
• don't run lint with --fix on push tests (#2273) (1998c0a)
• dont cache dataset metadata (#177) (b4c4471)
• e2e base url (#179) (3d240c8)
• eb dir -> ecs dir (#524) (847141d)
• empty object triggers spatial normalization (#973) (b50ccbf)
• enable deployment on rdev (#299) (10fe915)
• envfile in deploy-happy-stack (#612) (1e2e1b2)
• exclude specific ontology term id keys (#953) (5e9bfec)
• explicitly depend on favicons (#2143) (f36d889)
• explorer: bundle images (#707) (2c60abf)
• explorer: enable Safari and fix bundled image path (#708) (80fc7c6)
• explorer: filter out where feature_is_filtered is true (#684) (cd045db)
• fail happy deploy if service does not start successfully (#663) (7796ef7)
• fix lasso canceling by removing definition checking (#848) (188c4de)
• Fix menubar overflow by removing undo redo, some letters, and umap icon (#466) (20251bb)
• fix regex API prefix substitution for dataset selection (#807) (bd4f07a)
• Fix squished side panel after download (#1006) (ead9c8a)
• Fixed bug where continuous legend is appearing for categorical color-bys (#440) (fc35d0c)
• Fixed issue where config was not generating properly due to CXG version upgrade (#492) (e0500d7)
• Fixes missing breadcrumbs introduced in unified navbar update. (#465) (20227b1)
• fixing a bug that occurs when there are more than 1000 categories (#462) (f35d88b)
• Full fix QuickGene (#151) (7eb97f7)
• gene info QA changes (#351) (24009c5)
• hide navbar when seamless not enabled (#482) (5901e1e)
• implemented temporary workaround suggested by TileDB. (#2251) (#58) (4d94a26)
• invalidate metadata cache when dataset fails to load (#87) (db9f875)
• linting (#559) (79b42e0)
• make integration secret non-sensitive (ebb7d07)
• make push rdev use happy go client (#336) (1b10f5e)
• missing uns array returns error instead of None (#832) (f157e0c)
• missing uns array returns error instead on None (f0d7c62)
• Modify CSP to Allow Hubspot (#634) (c466aff)
• navbar: WMG link (#449) (050e1f3)
• no floating promises (#946) (f3d49fd)
• override default so that issues are not marked as stale (#650) (af78145)
• pin Wekzeug to 2.2.3 (#595) (7a9385d)
• point to local server (#2274) (873b3a2)
• reactivate strict slashes (#789) (5027bf2)
• regen package-lock.json file to solve dependency issue in dev (#301) (4d58c23)
• remove empty attribute from config (#821) (9a68bdb)
• remove implicit state toggling for spatial underlay in favor of explicit state setting (#876) (a0a3322)
• remove spaces in param setup (#2380) (3fdf5ca)
• remove trailing slash from s3_uri (#198) (fdda2f4)
• reset gene set colorScale on gene set deletion (#2264) (b8b1d0d)
• return response caching (#199) (844c61f)
• Revert quickGene partially (#149) (2414fd0)
• same category and gene name coloring issues (#276) (e96a705)
• server/requirements-dev.txt to reduce vulnerabilities (#2055) (09466a5)
• set count to 15 for testing (#2324) (1ebde22)
• spatial test and dataset (#881) (e1ef4a5)
• spatial: use global api prefix for /spatial/meta calls (#822) (2e286ba)
• thuang-fix-tsconfig-path (#2372) (fc60b2a)
• treat boolean types as categoricals (#656) (4b43040)
• unit tests and slight refactor (#877) (2a3b298)
• update colorTable code so linear scan only happens once (#328) (c238e99)
• update CSP to allow for image fetching from backend (#819) (d3ddc40)
• update server version to 0.16.7 (#2276) (90da04b)
• update spatial url condition (#967) (02db419)
• upgrade github actions (#598) (4e30db8)
• upgraded tiledb (#2251) (#44) (8d21a55)
• upgraded tiledb and reverted workaround (#61) (#66) (6841c72)
• use AppConfig to configure logging for server (#720) (1104f80)
• use env specific secret (#2204) (265ccf3)
• verify caching headers for dataset-metadata (#204) (a188c9e)
• wrong integration secret in the rdev environment (#655) (89e0acb)
• wrong path in start.sh (#522) (ea9f3e4)

Misc

• 1210 Add Plausible (#91) (70b0439)
• 717 Add Chromatic and Storybook (#723) (3977efd)
• 991 Add pan and zoom analytics events (#992) (34824b9)
• add analytics to cg marker gene sets (#814) (49f8bc9)
• add cellguide to navbar in explorer (#645) (2a8496f)
• add e2e tests for cellguide cxgs and related features (#902) (be168f7)
• Add global type file (#2363) (95ce39f)
• add happy locking (#318) (9d73ec7)
• add missing config.yaml file (#312) (b94d32b)
• add schema types (#2369) (26de334)
• add script to patch explorer to find portal rdev stack (#671) (1766d30)
• add SECURITY.md file at top level (#531) (0b11f8e)
• Add server timings to gene expression API routes (#451) (ded3e0f)
• Add timeout to unit test (#908) (427c695)
• add to software catalog (#649) (93101f4)
• Add types for rrecognized version commit (#81) (e807dca)
• Added tech issue template (#560) (65b3890)
• Analytics - embedding mode selection event only tracks open event (#1000) (7dcee26)
• back merge hotfix (#157) (2922f4a)
• beanstalk cleanup (#268) (dbbbb5e)
• bump chart to 1.3.0 (#1009) (e0407fe)
• Clean up development guidelines. (#253) (baeb431)
• clean up documentation and fix broken links. (#252) (f6c32b4)
• clean up e2eAnnotations.test.ts #213 (#281) (85b215b)
• decrease memory usage in staging explorer (#661) (7157144)
• deps-dev: bump express from 4.18.1 to 4.19.2 in /client (#857) (8507436)
• deps-dev: bump follow-redirects from 1.15.2 to 1.15.4 in /client (#702) (c6aa2a7)
• deps-dev: bump ip from 2.0.0 to 2.0.1 in /client (#771) (b7d377b)
• deps: bump axios from 0.21.1 to 0.21.4 in /client (#239) (981cb3e)
• deps: bump cross-fetch from 3.1.4 to 3.1.5 in /client (#248) (65a525d)
• deps: bump decode-uri-component from 0.2.0 to 0.2.2 in /client (#543) (bbf51b0)
• deps: bump follow-redirects from 1.14.1 to 1.14.8 in /client (#225) (0961cc9)
• deps: bump jinja2 from 2.11.2 to 2.11.3 in /hosted (#185) (4e2472c)
• deps: bump json5 from 2.2.1 to 2.2.3 in /client (#552) (19870eb)
• deps: bump loader-utils from 2.0.2 to 2.0.4 in /client (#536) (23477dd)
• deps: bump minimist and jimp in /client (#468) (901aaa6)
• deps: bump nanoid from 3.1.23 to 3.3.1 in /client (#238) (561ba71)
• deps: bump semver-regex from 3.1.2 to 3.1.3 in /client (#254) (615ce76)
• deps: bump simple-get from 3.1.0 to 3.1.1 in /client (#221) (1838c68)
• deps: bump terser from 5.14.1 to 5.14.2 in /client (#329) (da05256)
• deps: bump urllib3 from 1.25.9 to 1.26.5 in /hosted (#186) (ad883ca)
• disable e2e debugging code (#77) (0624e07)
• downsize dev explorer to 14G (#620) (90e6673)
• ECS ci/cd (#251) (25070e1)
• enforce conventional commits (#996) (d0d9643)
• explorer: enable safari fix browser page (#704) (8ebd1a1)
• extract schema types (#2375) (59c475b)
• Fix double image download analytics event (#999) (dc7be25)
• fix GHA upload syntax (#767) (fb15cf0)
• fix latent lint errors (#851) (fe6683e)
• fix local development (#584) (f52be5a)
• gene info e2e testing (#365) (5d73e6f)
• happy terraform staging (#256) (f5993b9)
• increase rdev memory (#372) (18f364e)
• increase staging container count to 2 (#313) (aa4beab)
• migrate sds theme to explorer (#305) (d247926)
• migrate sds to explorer (#300) (8720b99)
• misc typing (#849) (92e478f)
• nest common yaml values (#1008) (ddaa9bb)
• node: Upgrade to 16 in Dockerfile (#448) (208ddb7)
• pin black version to avoid breaking compatibility with click 8 (#220) (00a6934)
• PR runs npm run lint (14d4035)
• prevent subset when 0 cells are selected (#921) (1de020b)
• purge autosave from codebase (#425) (3a3feba)
• remove debug code (#768) (dc02367)
• Remove python happy and references to it (#315) (7d60bd0)
• remove terms deprecated in schema 3.0.0 from standard categories (#533) (fe66b71)
• rename codecov to coverage (#589) (fd966b9)
• replaced deprecated method to open TileDB array (#56) (#236) (4e7bf79)
• restore logs (#359) (3146f19)
• restore path (#781) (782d4d1)
• revert font to roboto condensed (#394) (025beb1)
• runtime config (#310) (5311344)
• set DEPLOYMENT_STAGE in Dockerfile (#260) (78f36b5)
• set explorer instance count to 3 (#259) (eec0310)
• side by side analytics (#998) (565e9db)
• stage -> staging in the config generation file (#266) (b7d16b8)
• staging->prod (#722) (9b4210f)
• test artifact upload again (#766) (49f89f0)
• ts: Type the graph, lasso, and some rendering code (#788) (91ef413)
• tune Argus configuration (#1003) (a5f014f)
• type centroid util (#36) (0721964)
• type general utils (#2381) (08b03ac)
• typed cascade reducer (#426) (e6967da)
• typed config reducer (#424) (d11f8c6)
• typed controls reducer (#418) (2269ec0)
• typed genesetsUI reducer (#423) (51086b4)
• update Argus values (#997) (c53322c)
• update BE dependencies (3d07afd)
• update BE dependencies (#571) (3d07afd)
• update chromatic project dir (#782) (49fb0df)
• Update clipping smoke test to ensure categorical data appears properly when clipping (#456) (77cf3d8)
• update CXG docs (#882) (c5f2ccf)
• Update deploy GHA artifact upload paths (#765) (c24c451)
• update Docker base image to ubuntu 22 (#586) (260354e)
• update documentation links (#353) (799f002)
• Update e2e test timeout to prevent flaky tests (#770) (441cd4c)
• update env vars and set up additional ingress rules (#1007) (7e31718)
• update env vars to use cloudfront domains (#1005) (10d1638)
• update happy actions to latest (#573) (072ec6b)
• update happy config task launch type (#651) (65e5da0)
• Update license copyright year (#557) (f904ef6)
• Update spaital analytics (#990) (339f7c9)
• update spatial test dataset (#862) (2d76056)
• update super-cool-spatial (#962) (ab1f6f7)
• updating logo (#389) (9670366)
• upgrade aws provider (#364) (f632e82)
• upgrade tiledb to 0.16.5 (#404) (f495d09)
• upgrade tiledb to 0.16.5 part 2 (eeab220)
• upgrade tiledb to 0.21.4 (#617) (99211b2)
• use correct roles for staging & prod (#1002) (2a1219e)
• use gunicorn for ecs (#250) (8544eb5)