feat: pixi-manager

feat: alias

feat: add to demo

feat(core): remove specProcessed event (#1076)

* feat: remove specProcessed event

* feat: update schema

feat(core): Make reactive default in component  (#1073)

* feat: default reactive

* fix: make component in editor use default

refactor(core): make header mark use underscore  (#1075)

* feat: update schema with _header

* fix: update uses of header mark

* refactor: update comment

refactor: add react import

feat: remove higlass dependencies, add vendored dependencies

feat: vendored higlass imports

feat(core): mouseEvent out of the experimental property (#1072)

* feat: move mouseEvents out of experimental

* fix: remove experimental from mouseEvents in goslingTrack

* fix: change mouseEvent in spec

* feat: updated schema

feat: higlass alias, fix pixi manager

feat: dummy track

feat: dummy track example

feat: higlass types

feat: export PixiTrack

feat: text track

feat: text track alias

feat: text track

feat: higlass utils

feat: text track example

feat: add signals

feat: circular brush

fix: alias name

feat: circular brush example

feat(core): remove DataTrack from schema and compiler (#1074)

* feat: remove DataTrack from schema

* feat: remove data track from compiler

* feat: update schema

* feat: remove overrideTemplate

* feat: remove tests

* fix(core): remove `"template"` key from template track after processing (#1079)

fix(core): remove 'template' key from a trample track after spec processing

---------

Co-authored-by: SEHI L'YI <sehilyi@gmail.com>

refactor(core): change _processedSpec to experimental_processedSpec (#1077)

* refactor: change to experimental_specProcessed

* Update src/core/gosling-component.tsx

Co-authored-by: SEHI L'YI <sehilyi@gmail.com>

* fix: change name

---------

Co-authored-by: SEHI L'YI <sehilyi@gmail.com>

feat: tile proxy

feat: basic gosling track

feat: make GoslingTrackClass standalone

feat: remove HGC from mark drawing

feat: export TiledPixiTrack

feat: add interactors

feat: export hg datafetcher

fix: linear brush model

feat: GoslingTrack plot

feat: gosling track example

feat: axis track

feat: axis track example

feat: brush linear

fix: add missing type package

refactor: remove types

feat: add example

feat: rename to brush-circular

feat: rename genomic axis

feat: bigwig datafetcher

fix: update datafetchers

feat: compile

feat: add basic layout

Co-authored-by: SEHI L'YI <sehilyi@gmail.com>

feat: new examples

feat: new render function

refactor: split into files

feat: beddb data

feat: don't show labels on overlay tracks

refactor: rendering

feat: corces example

feat: brush linear

feat: simple linked views

feat: linked brush

feat: refactored linking

fix: linkedEncoding

refactor: clean up circular brush

feat: dual circular brush plot

feat: linked circle

fix: brushing

feat: identify broken track

fix: give correct bounding box for circular

fix: cancer spec

feat: mocked worker

make vitest run on demo

test: linkedEncoding

feat: heatmap plot

feat: alias for heatmap

feat: heatmap example

refactor: heatmap plot inputs

refactor heatmap internals

feat: introduce signals

copy over zoomPan interactor

feat: zoomPanXY interactor

feat: full working zoomXY

refactor: rename to panZoomHeatmap

feat: heatmap options

feat: refactor connectivity

feat: working heatmap

feat: working heatmap

feat: add basic heatmap axis

feat: basic reverse orientation

feat: reverse example

feat: panZoom for axis track

feat: vertical Gosling track

feat: make brushes use new interactor

feat: working example

feat: basic fix to heatmap scaling

feat: working heatmap x and y

feat: refine heatmap axis

feat: static brushes

fix: unused imports

refine matrix linking

feat: basic gosling component

feat: basic editor

fix: x domain

feat: fix linking bugs

remove old test

fix: csv datafetcher options

feat: add csv example

fix: give spec

fix: json data fetcher

fix: single overlay

fix: no show heatmap label

fix: move effect to tracks

only put interactor if not overlaid on previous

fix: bounding box calculation

feat: add basic y domain

feat: add test

fix panZoom yDomain

feat: yDomain for gosling plot

update matrix example

fix: multiple same linkingId

update matrix

reorganize files

feat: basic resizing

refactor no more callback

resize pixi canvas after rendering

feat: rescale height

fixes for responsive height

pixi manager property comment

feat: basic pixi manager persistance

remove console warns

fix: brushes and types

comment about types

add documentation

feat: use color

feat: dummy track

make csv data fetcher take assembly

feat: gff data fetcher

feat: bam

feat: bed data fetcher

feat: vcf data fetcher

feat: basic tooltip

feat: working tooltip on static

no zoom pan with alt key

clear brush when click

clarify linked encoding

add explanation

chore: revert back the zoom speed

chore: remove dev dep of d3-drag

fix: typescript error about RenderTexture

PIXI API changed

fix: tsc error for an arrow function

fix(typing): typescript in jsdoc works in .js files, not .ts

chore: update typescript to latest

Seems to be needed to solve an type error coming from PIXI (see: pixijs/pixijs#9729).

fix: missing arrow function types

fix types in linear brush

fix(test): fix all test fails (#1097)

* fixed test fails related to compiled callback functions

* fix all tests except one

* remove comment statements

chore: upgrade lint/prettier for new TS version (#1099)

* chore: upgrade lint and prettier for new TS version

* fix: all lint/prettier errors

* chore: update the gosling schema

fix(core): typescript errors when building (#1102)

* fix: address all typescript errors

* last error

* format, fix tests more, fix build

fix: uncaught error on axis track

refactor(core): remove unused code related to HiGlass (#1105)

* working on removing unused higlass code

* further remove

* remove console log

* remove higlass specs from the editor

* fix test

* rename a file and a function that are no longer related to HiGlass

feat: pixi-manager

feat: alias

feat: add to demo

feat(core): remove specProcessed event (#1076)

* feat: remove specProcessed event

* feat: update schema

feat(core): Make reactive default in component  (#1073)

* feat: default reactive

* fix: make component in editor use default

refactor(core): make header mark use underscore  (#1075)

* feat: update schema with _header

* fix: update uses of header mark

* refactor: update comment

refactor: add react import

feat: remove higlass dependencies, add vendored dependencies

feat: vendored higlass imports

feat(core): mouseEvent out of the experimental property (#1072)

* feat: move mouseEvents out of experimental

* fix: remove experimental from mouseEvents in goslingTrack

* fix: change mouseEvent in spec

* feat: updated schema

feat: higlass alias, fix pixi manager

feat: dummy track

feat: dummy track example

feat: higlass types

feat: export PixiTrack

feat: text track

feat: text track alias

feat: text track

feat: higlass utils

feat: text track example

feat: add signals

feat: circular brush

fix: alias name

feat: circular brush example

feat(core): remove DataTrack from schema and compiler (#1074)

* feat: remove DataTrack from schema

* feat: remove data track from compiler

* feat: update schema

* feat: remove overrideTemplate

* feat: remove tests

* fix(core): remove `"template"` key from template track after processing (#1079)

fix(core): remove 'template' key from a trample track after spec processing

---------

Co-authored-by: SEHI L'YI <sehilyi@gmail.com>

refactor(core): change _processedSpec to experimental_processedSpec (#1077)

* refactor: change to experimental_specProcessed

* Update src/core/gosling-component.tsx

Co-authored-by: SEHI L'YI <sehilyi@gmail.com>

* fix: change name

---------

Co-authored-by: SEHI L'YI <sehilyi@gmail.com>

feat: tile proxy

feat: basic gosling track

feat: make GoslingTrackClass standalone

feat: remove HGC from mark drawing

feat: export TiledPixiTrack

feat: add interactors

feat: export hg datafetcher

fix: linear brush model

feat: GoslingTrack plot

feat: gosling track example

feat: axis track

feat: axis track example

feat: brush linear

fix: add missing type package

refactor: remove types

feat: add example

feat: rename to brush-circular

feat: rename genomic axis

feat: bigwig datafetcher

fix: update datafetchers

feat: compile

feat: add basic layout

Co-authored-by: SEHI L'YI <sehilyi@gmail.com>

feat: new examples

feat: new render function

refactor: split into files

feat: beddb data

feat: don't show labels on overlay tracks

refactor: rendering

feat: corces example

feat: brush linear

feat: simple linked views

feat: linked brush

feat: refactored linking

fix: linkedEncoding

refactor: clean up circular brush

feat: dual circular brush plot

feat: linked circle

fix: brushing

feat: identify broken track

fix: give correct bounding box for circular

fix: cancer spec

feat: mocked worker

make vitest run on demo

test: linkedEncoding

feat: heatmap plot

feat: alias for heatmap

feat: heatmap example

refactor: heatmap plot inputs

refactor heatmap internals

feat: introduce signals

copy over zoomPan interactor

feat: zoomPanXY interactor

feat: full working zoomXY

refactor: rename to panZoomHeatmap

feat: heatmap options

feat: refactor connectivity

feat: working heatmap

feat: working heatmap

feat: add basic heatmap axis

feat: basic reverse orientation

feat: reverse example

feat: panZoom for axis track

feat: vertical Gosling track

feat: make brushes use new interactor

feat: working example

feat: basic fix to heatmap scaling

feat: working heatmap x and y

feat: refine heatmap axis

feat: static brushes

fix: unused imports

refine matrix linking

feat: basic gosling component

feat: basic editor

fix: x domain

feat: fix linking bugs

remove old test

fix: csv datafetcher options

feat: add csv example

fix: give spec

fix: json data fetcher

fix: single overlay

fix: no show heatmap label

fix: move effect to tracks

only put interactor if not overlaid on previous

fix: bounding box calculation

feat: add basic y domain

feat: add test

fix panZoom yDomain

feat: yDomain for gosling plot

update matrix example

fix: multiple same linkingId

update matrix

reorganize files

feat: basic resizing

refactor no more callback

resize pixi canvas after rendering

feat: rescale height

fixes for responsive height

pixi manager property comment

feat: basic pixi manager persistance

remove console warns

fix: brushes and types

comment about types

add documentation

feat: use color

feat: dummy track

make csv data fetcher take assembly

feat: gff data fetcher

feat: bam

feat: bed data fetcher

feat: vcf data fetcher

feat: basic tooltip

feat: working tooltip on static

no zoom pan with alt key

clear brush when click

clarify linked encoding

add explanation

chore: revert back the zoom speed

chore: remove dev dep of d3-drag

fix: typescript error about RenderTexture

PIXI API changed

fix: tsc error for an arrow function

fix(typing): typescript in jsdoc works in .js files, not .ts

chore: update typescript to latest

Seems to be needed to solve an type error coming from PIXI (see: pixijs/pixijs#9729).

fix: missing arrow function types

fix types in linear brush

fix(test): fix all test fails (#1097)

* fixed test fails related to compiled callback functions

* fix all tests except one

* remove comment statements

chore: upgrade lint/prettier for new TS version (#1099)

* chore: upgrade lint and prettier for new TS version

* fix: all lint/prettier errors

* chore: update the gosling schema

fix(core): typescript errors when building (#1102)

* fix: address all typescript errors

* last error

* format, fix tests more, fix build

fix: uncaught error on axis track

refactor(core): remove unused code related to HiGlass (#1105)

* working on removing unused higlass code

* further remove

* remove console log

* remove higlass specs from the editor

* fix test

* rename a file and a function that are no longer related to HiGlass