test jax dependecies #1

	name: Spatial CI

	on:
	push:
	branches:
	- main
	pull_request:
	branches:
	- main

	env:
	debug: 'true'

	jobs:
	ingestion:
	runs-on: ubuntu-latest
	strategy:
	fail-fast: false
	matrix:
	os: ["ubuntu-latest"] # , "macos-latest", "windows-latest"
	python-version: ["3.9"]

	steps:
	- uses: actions/checkout@v4

	- name: File tree
	if: env.debug == 'true'
	run: tree

	- uses: conda-incubator/setup-miniconda@v3
	with:
	miniforge-version: latest
	auto-activate-base: true
	auto-update-conda: true
	channels: conda-forge
	channel-priority: strict
	activate-environment: pipeline_env
	environment-file: pipeline_env.yaml

	- name: Install Panpipes
	shell: bash -el {0}
	run: \|
	pip install -e `.[spatial]`
	conda list

	- name: Conda info
	if: env.debug == 'true'
	shell: bash -el {0}
	run: conda info

	- name: Conda list
	if: env.debug == 'true'
	shell: pwsh
	run: conda list

	# Note: all three files are renamed during the download to trim the "subsample_" prefix
	- name: Preparing the data
	run: \|
	mkdir -p teaseq/ingest/data.dir
	cd teaseq/ingest/data.dir
	curl -L -o adt.h5ad https://figshare.com/ndownloader/files/41671551
	curl -L -o atac.h5ad https://figshare.com/ndownloader/files/41671554
	curl -L -o rna.h5ad https://figshare.com/ndownloader/files/41671557

	# Note: we run the following to test that the commands works
	# However, the following task will replacing the file anyway
	- name: Preparing the configuration file
	shell: bash -el {0}
	run: \|
	cd teaseq/ingest
	panpipes ingest config

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