PR: Finish xtb-YARP for pytest/Github workflow + add back organometal… #7

	name: Python application test

	on: [push, pull_request]

	jobs:
	build:

	runs-on: ubuntu-latest

	steps:
	- uses: actions/checkout@v2
	- name: Set up Python
	uses: actions/setup-python@v2
	with:
	python-version: '3.9' # Specify the Python version

	- name: Install dependencies
	run: \|
	if [ -f pytest_requirements.txt ]; then
	pip install -r pytest_requirements.txt;
	fi
	export CONDA_ALWAYS_YES="true"
	pip install 'rdkit==2024.3.5'
	pip install 'scipy==1.11.1'
	pip install xtb
	pip install 'joblib==1.3.1'
	pip install 'PyYAML==6.0.1'
	pip install openbabel-wheel
	pip install 'pandas==2.0.3'
	pip install 'ase==3.22.1'
	conda install -y conda-forge::xtb
	pip install 'xgboost==1.7.6'
	pip install 'h5py==3.9.0'
	pip install pysisyphus
	conda install -y conda-forge::crest
	unset CONDA_ALWAYS_YES
	pip install --force-reinstall 'scikit-learn==1.3.0'
	pip install --force-reinstall 'numpy==1.24.4'
	pip install .

	# CHECK
	pip freeze

	# Prepare pysis env
	cp .pysisyphusrc /home/runner/.pysisyphusrc
	cond=asd
	sed -i "s\|CONDA_ENV\|${CONDA}\|g" /home/runner/.pysisyphusrc

	- name: Run pytest
	run: \|
	home=$(pwd)
	cd /opt/hostedtoolcache/Python/3.9.20/x64/bin/
	ls
	echo $CONDA
	cd $CONDA/bin

	#ls
	#echo $(pwd)
	#$CONDA/bin/xtb --version
	#$CONDA/bin/crest --version
	#pysis --version
	# test Organometallics
	#obabel --version
	#
	# run Organometallic YARP Example #
	cd $home/examples/
	pytest -s
	cd $home/pyTEST_Example/
	# xtb and crest are in conda bin, others in pip bin
	sed -i "s\|CONDA_PATH\|${CONDA}\|g" test_rxn.py
	pytest -s
	shell: bash

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