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gosling-lang / gos

A declarative interactive genomics visualization library for Python.
https://gosling-lang.github.io/gos
MIT License
218 stars 14 forks source link

feat: v0.9.28 #122

Closed manzt closed 1 year ago

manzt commented 1 year ago

~- chore: migrate build system to hatch~ ~- run tools/generate_schema_wrappers.py~ ~- chore: update GH Actions~ ~- chore: bump higlass to v1.12~

Things seem to be working ... but some behavior is deprecated? @sehilyi the brushes in this example not longer link with the brushes on the right:

https://user-images.githubusercontent.com/24403730/223539685-f52538d2-b0c0-422c-99ef-2cc14f1dc898.mov

Note: the project now uses hatchling instead of setuptools for a build system. This is the new modern standard for python, and integrates well with the hatch CLI. hatch is like npm/yarn/pnpm but for python projects. You can install it globally on your system with pipx.

pipx install hatch
cd gos
# commands defined in pyproject.toml
hatch run test
hatch run docs
hatch shell # enter a virtual environment with gosling installed and all development deps (like conda activate)
jupyter lab # open examples
sehilyi commented 1 year ago

I don't think we deprecated something related to brushes – Let me take a look.

manzt commented 1 year ago

@sehilyi any thoughts on how to move forward with this?

sehilyi commented 1 year ago

@manzt I am working on upgrading a HiGlass dependency in Gosling.js (https://github.com/gosling-lang/gosling.js/pull/866). There are some breaking changes introduced in HiGlass that I have to address in Gosling.js (e.g., d3 APIs). I will be able to work on it this Friday afternoon but feel free to chime in with the PR.

manzt commented 1 year ago

I moved the hatchling/hatch stuff to #123

manzt commented 1 year ago

I reverted to the old rendering pipeline in #124, at least until we clean up Gosling/HiGlass packaging further. This means that things are working with the latest gosling.js v0.9.28. We should strive to improve the JS loading, but I don't want to be blocked from making a release.