github action for integration pipeline #1

	name: Tutorials 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: Download Conda YAML file
	run: curl -o pipeline_env.yaml https://raw.githubusercontent.com/DendrouLab/panpipes/main/pipeline_env.yaml

	- 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 # consider moving to etc/pipeline_env.yaml

	# Note: the pinned versions in pipeline_env.yaml are not respected during the miniconda step above
	- name: Pin version of pip dependencies
	shell: bash -el {0}
	run: pip install --force-reinstall -v \
	boto3==1.34.34 \
	botocore==1.34.34 \
	flax==0.8.0 \
	fonttools==4.47.2 \
	jax==0.4.23 \
	jaxlib==0.4.23 \
	numpy==1.22.4 \
	orbax-checkpoint==0.5.2 \
	pytorch-lightning==2.1.4

	- 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/integration && cd teaseq/integration
	curl -L -o teaseq.h5mu https://figshare.com/ndownloader/files/44471927

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

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