change directories on the fly #24

	name: Download dataset

	on:
	push:
	branches:
	- nk/add-post-training-script-to-compute-csa
	# release:
	# types: [published]

	jobs:
	run_dataset_download:
	runs-on: ubuntu-latest

	steps:
	- name: Checkout repository
	uses: actions/checkout@v4

	- name: Set up Python
	uses: actions/setup-python@v4
	with:
	python-version: '3.10'

	- name: Set up Conda
	uses: conda-incubator/setup-miniconda@v2
	with:
	auto-update-conda: true
	channels: conda-forge

	- name: Install dependencies
	run: \|
	conda install -y git-annex

	- name: Ensure git-annex is accessible via git
	run: \|
	echo "$(conda info --base)/bin" >> $GITHUB_PATH
	export PATH="$(conda info --base)/bin:$PATH"
	which git-annex
	git-annex version

	- name: Configure Git identity
	run: \|
	git config --global user.email "[email protected]"
	git config --global user.name "GitHub Actions"

	- name: Run dataset setup script
	shell: bash -l {0} # Ensures the Conda environment is properly loaded
	run: \|
	chmod +x scripts/compute_morphometrics_spine_generic.sh
	source scripts/compute_morphometrics_spine_generic.sh

	# - name: Run model script
	# run: ./scripts/run_model.sh

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