angelolab / ark-analysis / 5226602002

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GitHub Actions, Python 3.9+ Support, Jupyterlab Extensions (#991)

* GitHub Actions updates, Conda environment file

* readme package info table

* readme fix

* unpinned ipywidgets

* testing windows path fix

* set cell_cluster_col type to np.int64

* set cell_cluster_col type to np.int64 v2

* dtype for pandas merge_asof explictly converted

* dtype for pandas merge_asof convert to int

* convert to int

* huggingface cache

* shutil fix

* change type to int

* changed a type to int

* example dataset cache download script

* moved getting the dataset from test to ci workflow file

* pycodestyle

* cache in ci fix

* python-version fix

* correct data path

* caching logic updates

* save / restore cache

* set cache dir to ./data/cache

* removed exampled dataset download in `fiber_segmentation_test`

* windows caching test

* remove misc notebook metadata

* import json fix

* test dtype change

* example dataset optimizations

* type hinting

* type hinting 2

* type hinting 3

* pycodestyle

* dimensionality_reduction_test speed up

* parallel tests

* removed parallel tests, unfortunatly it hangs indefinity on windows

* removed xdist decorators

* removed xdist decorators 2

* proper path for cache_dir on windows

* windows paths

* no posix() path

* pytest-xdist test 2

* added docker badge

* added jupyterlab extensions as a set of optional dependencies

* remove unused imports

* remove unused imports

* sort imports

* environment.yml updates

* dockerfile updates

* removed duplicate markdown section

* updated cibuildwheel

* type def updates

* fixed pandas dtype for `calculate_mean_distance_to_all_cell_types`

* type fix

* make sure args of watershed are np.int32

* set pixie types to int for som cluster

* removed xdist, when the notebooks test in parallel, it copies data for each -> no more space on the runner

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