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Release 16.3.0 #828

Merged
merged 169 commits into from
Feb 7, 2023
Merged

Release 16.3.0 #828

merged 169 commits into from
Feb 7, 2023

Commits on May 6, 2022

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Commits on May 11, 2022

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  2. more bug fixes

    dvzacharycutler committed May 11, 2022
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Commits on May 13, 2022

  1. Refactor multi selection adapter

    - Add optional `diffSubtypes` to `IMultiSelectionAdapter`
    - Remove `ReprovisynMultiSelectionAdapter`
    - Add generics to `MultiSelectionAdapter`
    - Comment functions of `MultiSelectionAdapter`
    thinkh committed May 13, 2022
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  3. Replace () => IContext with IContext

    Unecessary convoluted call
    thinkh committed May 13, 2022
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  4. Remove waitForIt promise from selection adapter

    - Add and refactor return types `Promise<any>` to `Promise<void>`
    - Switch to async/await where possible
    - await `removeDynamicColumns` before `addDynamicColumns` -> previously it was not waited for the removal
    thinkh committed May 13, 2022
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Commits on May 19, 2022

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Commits on May 23, 2022

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Commits on May 24, 2022

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Commits on May 30, 2022

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  3. builds

    dvzacharycutler committed May 30, 2022
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  4. fixing bar selection

    dvzacharycutler committed May 30, 2022
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Commits on May 31, 2022

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  2. code improvements

    dvzacharycutler committed May 31, 2022
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Commits on Jun 10, 2022

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Commits on Jun 15, 2022

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Commits on Jun 17, 2022

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  4. Added build-storybook to build script (#733)

    * Added build-storybook to build script
    
    * Add tdp_core/dist alias to the storybook webpack config
    
    * updated version of storybook (#736)
    
    Co-authored-by: Moritz Heckmann <[email protected]>
    
    Co-authored-by: dvmoritzschoefl <[email protected]>
    Co-authored-by: Moritz Heckmann <[email protected]>
    3 people authored Jun 17, 2022
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  5. Fix eslint for AggregateTypeSelected

    Probably a missing type cast in PR #729
    thinkh committed Jun 17, 2022
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  6. Remove await this.built in withoutTracking()

    Waiting for `this.built` will never resolve/terminate and show an infite loading icon.
    
    Reason: `this.built` is created with `build()` in line 355 and it is only resolved after the `build()` call is complete.
    
    With the changes to the selection adapter the `this.selectionAdapter.selectionChanged` now returns a valid promise. Previously, `context.add()` did not return it's promise (see 919cfb2#diff-f0f07e4a6ac30a813315b152545245d4cf26830e01b701f3e82ff7b5c22363a7R18). Now, we are waiting until all dynamic columns are added. The circle closes when we add the columns which calls `withoutTracking()` which in-turn is waiting for the resolved `this.built` promise.
    
    As far as I can see, we always call `withoutTracking` on a built/resolved ranking view. In the other places (line 377 and 400) we have a dedicated `await this.built;` before triggering changes to dynamic columns.
    
    In my tests adding and removing columns via score and selection adapter worked as before. I also tested reloading the page and checked the result of the session. In all cases it looks the same as before.
    thinkh committed Jun 17, 2022
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Commits on Jun 21, 2022

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  2. Add Storybook stories for custom buttons (#708)

    * create first storybook for button styles
    
    * add story for single button
    
    * change background
    
    * linting
    
    * fix background
    
    * add additional kind of buttons
    
    * typing
    
    * add functions for buttons into stories
    
    * started chaning source of button
    
    * finish Button storybook docu
    
    * linting problems
    
    * linting
    
    * styling of code
    
    * change style to UI
    
    * add comments
    
    * Added build-storybook to build script
    
    * Add tdp_core/dist alias to the storybook webpack config
    
    * added outline buttons, adjusted layout to not contain margin inside a story, added link to styleguide
    
    Co-authored-by: Michael Puehringer <[email protected]>
    Co-authored-by: Moritz Heckmann <[email protected]>
    3 people authored Jun 21, 2022
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  3. added cypress run script to package json (#738)

    Co-authored-by: Moritz Heckmann <[email protected]>
    dvmoritzschoefl and dvmoritzschoefl authored Jun 21, 2022
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  4. Add exception handler middleware (#723)

    * Add exception handler middleware
    
    * Extract default logging config and set it on server startup
    
    Co-authored-by: dvtschachinger <[email protected]>
    puehringer and dvtschachinger authored Jun 21, 2022
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Commits on Jun 22, 2022

  1. address PR comments

    dvchristianbors committed Jun 22, 2022
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Commits on Jun 24, 2022

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Commits on Jun 27, 2022

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Commits on Jun 28, 2022

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Commits on Jun 30, 2022

  1. Add NODE_OPTIONS=--max_old_space_size=4096 to storybook scripts (#746)

    * Add NODE_OPTIONS=--max_old_space_size=4096  to storybook scripts
    
    * Update build script to include storybook:build
    
    * Update cache key
    puehringer authored Jun 30, 2022
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Commits on Jul 1, 2022

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Commits on Jul 6, 2022

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Commits on Jul 8, 2022

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Commits on Jul 13, 2022

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Commits on Jul 14, 2022

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Commits on Jul 15, 2022

  1. Updated npm scripts

    puehringer committed Jul 15, 2022
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Commits on Jul 29, 2022

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  2. Fix SCSS warning for divide numbers using / (#758)

    Fix SCSS warning for divide numbers using /
    thinkh authored Jul 29, 2022
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  3. Show selection indicator next to scroll bar in rankings (#756)

    Show LineUp selection indicator next to scroll bar
    thinkh authored Jul 29, 2022
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Commits on Aug 2, 2022

  1. Prepare github changes

    anita-steiner committed Aug 2, 2022
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  2. Update CODEOWNERS

    Anita Steiner authored Aug 2, 2022
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  3. Prepare github changes

    anita-steiner committed Aug 2, 2022
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  4. Prepare github changes

    anita-steiner committed Aug 2, 2022
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  5. Prepare github changes

    anita-steiner committed Aug 2, 2022
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  6. Prepare github changes

    anita-steiner committed Aug 2, 2022
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Commits on Aug 4, 2022

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  2. Remove circleci

    anita-steiner committed Aug 4, 2022
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Commits on Aug 8, 2022

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  2. Set modal focus based on tour visiblity and replace Bootstrap jQuery …

    …modal with plain JS modal (#754)
    
    * Replace BS jQuery modal with plain JS modal
    
    Caleydo/tdp_bi_bioinfodb#1371
    
    * Refactor modal options
    
    * Replace deprecated `evt.keyCode` with `evt.key`
    
    * Set modal focus flag based on tour's visibility
    
    Also revert dialog constructor parameter to `backdrop` only again.
    
    * Resolve some dependency cycles
    thinkh authored Aug 8, 2022
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Commits on Aug 9, 2022

  1. Upgrade to Font Awesome v6 (#732)

    * update to fontawesome v6
    
    * added fontawesome scss file
    
    * add dist files
    
    * Fix icon position in sidepanel tab
    
    * Update dependency [email protected]
    
    Co-authored-by: Moritz Heckmann <[email protected]>
    Co-authored-by: Holger Stitz <[email protected]>
    3 people authored Aug 9, 2022
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Commits on Aug 10, 2022

  1. Add package-lock.json

    puehringer committed Aug 10, 2022
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  2. Update build.yml

    Anita Steiner authored Aug 10, 2022
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Commits on Aug 11, 2022

  1. Fix Error Where FormDialog Fails to Be Instantiated (#766)

    check if `.tdp-tour-step-count` exists
    dvchristianbors authored Aug 11, 2022
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  2. refactor: Avoid general aside styles caused by CLUE (#763)

    Refactor CLUE aside styles
    
    * Avoid general `<aside>` styles
    * Copy general aside styles into nested panels
    thinkh authored Aug 11, 2022
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  4. feat: CLUE support for URL query parameter + rewrite hash parameters (#…

    …762)
    
    * Replace deprecated `substr` with `substring`
    
    * Move PropertyHandler and HashProperties
    
    * Add CommonPropertyHandler + QueryPropertyHandler
    
    - Move some static functions back to the CLUEGraphManager
    
    * Add property handler options to ATDPApplication
    
    * Add destroy hook to remove event listener
    
    * Add URL property rewrite to CLUEGraphManager
    
    * Extract rewrite URL function to unit test
    
    * Add unit test for rewrite URL function
    
    * Refactor graph URL after persisting session
    
    * Fix typings in interface
    
    * Avoid property symbol only in URL string
    
    * Amend last commit to avoid empty hash only
    
    Co-authored-by: Michael Pühringer <[email protected]>
    thinkh and puehringer authored Aug 11, 2022
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  5. Update package.json

    Anita Steiner authored Aug 11, 2022
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  6. Update package.json

    Anita Steiner authored Aug 11, 2022
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  7. Update package.json

    Anita Steiner authored Aug 11, 2022
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Commits on Aug 12, 2022

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  6. Delete dist directory

    Anita Steiner authored Aug 12, 2022
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  7. Update package.json

    Anita Steiner authored Aug 12, 2022
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Commits on Aug 15, 2022

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  5. Add yarn-3.2.2

    puehringer committed Aug 15, 2022
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  6. Change prepare to prepack

    puehringer committed Aug 15, 2022
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  7. Remove yarn again

    puehringer committed Aug 15, 2022
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  9. Add .yarnrc.yml

    puehringer committed Aug 15, 2022
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Commits on Aug 16, 2022

  1. Add yarn-3.2.2

    puehringer committed Aug 16, 2022
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  2. Add yarn-3.2.2

    puehringer committed Aug 16, 2022
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  3. Add webpack to overides

    puehringer committed Aug 16, 2022
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  7. Pin core-js to 2.6.5

    puehringer committed Aug 16, 2022
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  8. Add dist/

    puehringer committed Aug 16, 2022
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Commits on Aug 17, 2022

  1. Added d3v3 alias for d3

    puehringer committed Aug 17, 2022
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Commits on Aug 18, 2022

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Commits on Aug 19, 2022

  1. Added d3v7 alias (#769)

    puehringer authored Aug 19, 2022
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Commits on Aug 22, 2022

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Commits on Aug 23, 2022

  1. Update README.md

    puehringer authored Aug 23, 2022
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Commits on Aug 26, 2022

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  2. Bump pyjwt from 2.1.0 to 2.4.0 (#728)

    Bumps [pyjwt](https://github.com/jpadilla/pyjwt) from 2.1.0 to 2.4.0.
    - [Release notes](https://github.com/jpadilla/pyjwt/releases)
    - [Changelog](https://github.com/jpadilla/pyjwt/blob/master/CHANGELOG.rst)
    - [Commits](jpadilla/pyjwt@2.1.0...2.4.0)
    
    ---
    updated-dependencies:
    - dependency-name: pyjwt
      dependency-type: direct:production
    ...
    
    Signed-off-by: dependabot[bot] <[email protected]>
    
    Signed-off-by: dependabot[bot] <[email protected]>
    Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
    Co-authored-by: Michael Pühringer <[email protected]>
    dependabot[bot] and puehringer authored Aug 26, 2022
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  3. Rdkit images API (#748)

    * Add rdkit image to router (not working? ignoring prefix/namespace?)
    Add api to make rdkit produce SVGs
    Add optional extra flavor for rdkit in setup.py
    Add tests (working in a standalone project)
    Add models for molecule parsing
    Add utils for rdkit-stuff
    
    * Reformat + fix imports (via make format)
    Add prefix/namespace-functionality to visyn_server in the same way, flask has it
    Cleanup tests
    
    * Make tests not run if you don't have rdkit
    
    * Fix linter errors
    
    * Change tag from default (none) to images and change docstring (from "todo move" to actual)
    
    * Make rdkit mandatory
    
    * Remove router namespace support for fastapi and add warning if it's used
    Remove murcko wrapper
    Remove unneccesary fastapi object creation
    Remove create_api in img_api
    Add app via init_app instead of via registry
    
    * Changed path form /image/ to /rdkit/
    Changed kind of parameters from url params to query params, i.e. /rdkit/C -> /rdkit/?structure=C due to slashes
    Adapted tests
    Better / more correct type hints
    
    * Change to return no content (+ proper no content response code)
    
    * Fix imports
    
    * Add structured image column, renderer, and filter dialog for SMILES strings to ranking (#755)
    
    * Add molecule column + renderer for LineUp
    
    #741
    
    * Implement fetch structured image
    
    #741
    
    * Add SMILES renderer and column to Ranking.tsx
    
    #741
    
    * Adapt to latest rdkit API changes
    
    * Add custom structure image filter dialog (wip)
    
    * Add loading icon + error msg to filter dialog
    
    * Remove orphan import
    
    * Fix linter warnings and improve code
    
    * Deny to set string filter
    
    * Fix lint
    
    * Fix `filter = null` case
    
    * Rename folder to `structureImage` and add index.ts
    
    * Update dist files
    
    * Add empty summary renderer
    
    Otherwise an error is thrown when switching visualizations for the smiles column
    
    * Fix lint
    
    * Nest structured image i18n strings
    
    * Set default column width for smiles column
    
    * Set row height based on smiles column width
    
    * Set min/max domain for number col domain
    
    Related to #718
    
    The parameter default, i.e. `min = Number.NaN`, is only used if the parameter is `undefined`. However, when the parameter is `null` it does not assign `Number.NaN`.
    
    With this commit `null` and `undefined` result in `Number.NaN`.
    
    * Set default summary renderer for smiles col
    
    * StructuredImageColumn extends ValueColumn
    
    - Removes all string related dialogs and functionality (e.g., group, sort, ...)
    - Add rename dialog
    - Remove `order` to default -> in menu: rename then filter
    
    Co-authored-by: Michael Puehringer <[email protected]>
    Co-authored-by: Michael Pühringer <[email protected]>
    
    * Minor improvements and feedback incorporation
    
    Co-authored-by: Holger Stitz <[email protected]>
    Co-authored-by: Michael Puehringer <[email protected]>
    Co-authored-by: Michael Pühringer <[email protected]>
    4 people authored Aug 26, 2022
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Commits on Aug 29, 2022

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Commits on Aug 30, 2022

  1. Add test db setup fixture (#771)

    * Add test_db fixture
    
    * Reformatting
    
    * Simplify + fail better + test fixture
    
    * Fix weird import corner case
    
    * Fixed import order
    
    * Move test dev dependencies from requirements_dev to main, so things depending on core also have it.
    Also, mark both db-tests as xfail.
    
    Co-authored-by: Michael Puehringer <[email protected]>
    Co-authored-by: Michael Pühringer <[email protected]>
    3 people authored Aug 30, 2022
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Commits on Aug 31, 2022

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Commits on Sep 1, 2022

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Commits on Sep 8, 2022

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  3. Update publish.yml

    Anita Steiner authored Sep 8, 2022
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Commits on Sep 15, 2022

  1. Fixing Ranking.tsx bug (#777)

    * adding wrapper div around ranking.tsx
    
    * moving around styles from RankingViewComponent -> Ranking
    
    * adding back tdp-busy
    dvzacharycutler authored Sep 15, 2022
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  2. Fixed filtering of structure image column (#784)

    Co-authored-by: Holger Stitz <[email protected]>
    puehringer and thinkh authored Sep 15, 2022
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  3. Remove modal element when hiding a dialog (#783)

    Co-authored-by: Holger Stitz <[email protected]>
    oltionchampari and thinkh authored Sep 15, 2022
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  4. Improve typings for CLUE and refactor async functions (#785)

    * Improve typings for CLUE `graph.persist()`
    
    datavisyn/ordino_eins#525
    
    * Fix typing of MemoryGraph.restore()
    thinkh authored Sep 15, 2022
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Commits on Sep 19, 2022

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Commits on Sep 28, 2022

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Commits on Sep 29, 2022

  1. Add missing dist files

    thinkh committed Sep 29, 2022
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  2. fix: don't initialize general vis in ARankingView when disabled (#796)

    Previously the general vis was intialized and running the background, even though it was disabled; only the button was hidden. Now the general vis not even initialized.
    oltionchampari authored Sep 29, 2022
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Commits on Sep 30, 2022

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Commits on Oct 4, 2022

  1. feat: adding Mantine VisynApp (#787)

    Co-authored-by: Holger Stitz <[email protected]>
    dvzacharycutler and thinkh authored Oct 4, 2022
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Commits on Oct 5, 2022

  1. Add missing dist files.

    thinkh committed Oct 5, 2022
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Commits on Oct 11, 2022

  1. deps: Update dependency [email protected] (#793)

    chore: Update dependency [email protected]
    
    Co-authored-by: Michael Pühringer <[email protected]>
    thinkh and puehringer authored Oct 11, 2022
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  3. feat: Add removePlugins method to plugin registry (#799)

    Co-authored-by: Holger Stitz <[email protected]>
    oltionchampari and thinkh authored Oct 11, 2022
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Commits on Oct 14, 2022

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Commits on Oct 19, 2022

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Commits on Oct 24, 2022

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Commits on Nov 22, 2022

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Commits on Nov 23, 2022

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Commits on Nov 24, 2022

  1. add: missing dist files

    thinkh committed Nov 24, 2022
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Commits on Dec 7, 2022

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  2. fix: remove range id mapping in rangeOf in DB view filter (#813)

    * fix: remove range id mapping in DB view filter
    
    Closes Caleydo/tdp_bi_bioinfodb#1416
    
    * fix lint
    thinkh authored Dec 7, 2022
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Commits on Dec 13, 2022

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Commits on Dec 21, 2022

  1. Fix missing lineup color mappings by adjusting styles (#802)

    Adjusted color mapping styles
    puehringer authored Dec 21, 2022
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Commits on Jan 11, 2023

  1. Cypress and CI integration (#811)

    * Cypress 11 and CI integration
    
    * Enable cypress in build.yml
    
    * Delete build_nightly.yml
    puehringer authored Jan 11, 2023
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  2. Add make start

    puehringer committed Jan 11, 2023
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Commits on Jan 12, 2023

  1. Improve performance, upgrade deps and logging, remove numpy, numba, p…

    …andas (#816)
    
    * Upgrade deps and remove numpy, numba, pandas
    
    * Replace BaseHTTPMiddleware with much faster ASGI equalivalent
    
    * Increase anyio threads to 100
    
    * Remove broken etag support
    
    * Improved logging
    
    * Switch to a2wsgi
    
    * Remove a2wsgi again
    
    * Remove greenifier extension
    
    * Bump FastAPI to 0.89.0
    
    * Add pytest in settings.json
    
    * Set SQLAlchemy version to >= 1.4.40 and <= 1.4.46 to allow SQLModel > 0.0.6 (#819)
    
    * Loosen Flask and marshmallow-sqlalchemy versions for superset
    
    * Removed flake8, isort, pep8 in favor of ruff
    puehringer authored Jan 12, 2023
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Commits on Jan 13, 2023

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Commits on Jan 17, 2023

  1. fix(storybook): upgrade to webpack5 (#810)

    * upgrade webpack for storybook
    
    * use webpack.config from storybook and override rules
    
    * add HtmlWebpackPlugin
    
    * Fix storybook path aliases
    
    * use latest version of storybook
    
    Co-authored-by: Michael Puehringer <[email protected]>
    Co-authored-by: Michael Pühringer <[email protected]>
    3 people authored Jan 17, 2023
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Commits on Jan 24, 2023

  1. Enable Custom Vis in LineUp (#820)

    * enabled custom vis in lineup
    
    * Made idField optional
    
    Co-authored-by: Moritz Heckmann <[email protected]>
    Co-authored-by: Michael Puehringer <[email protected]>
    3 people authored Jan 24, 2023
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Commits on Jan 26, 2023

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Commits on Feb 3, 2023

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  2. feat: converting general vis to Mantine and add hexbin visualization (#…

    …786)
    
    Co-authored-by: Holger Stitz <[email protected]>
    Co-authored-by: Michael Pühringer <[email protected]>
    Co-authored-by: Michael Puehringer <[email protected]>
    4 people authored Feb 3, 2023
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Commits on Feb 6, 2023

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Commits on Feb 7, 2023

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  2. fix(cypress): health check component test (#829)

    fix(cypress): health check
    thinkh authored Feb 7, 2023
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