Update pymatgen requirement from !=2019.9.7,<2024.7.19,>=2019.7.2 to >=2019.7.2,!=2019.9.7,<2024.10.4 #786

Workflow file for this run

.github/workflows/ci_tests.yml at a281456

	---
	name: CI - Tests

	on:
	pull_request:
	push:
	branches:
	- develop
	- push-action/**

	jobs:

	pre-commit:
	runs-on: ubuntu-latest
	timeout-minutes: 2

	steps:
	- uses: actions/checkout@v4

	- name: Set up Python 3.9
	uses: actions/setup-python@v5
	with:
	python-version: 3.9

	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install -U setuptools

	while IFS="" read -r line \|\| [ -n "${line}" ]; do
	if [[ "${line}" =~ ^pre-commit.*$ ]]; then
	pre_commit="${line}"
	fi
	done < requirements_dev.txt

	pip install ${pre_commit}

	- name: Test with pre-commit
	run: SKIP=codecov-validator pre-commit run --all-files --show-diff-on-failure

	pytest:
	runs-on: ubuntu-latest
	timeout-minutes: 20

	strategy:
	fail-fast: false
	matrix:
	python-version: ['3.9', '3.10', '3.11']

	services:
	mongo:
	image: mongo:4
	ports:
	- 27017:27017
	postgres:
	image: postgres:12
	env:
	POSTGRES_DB: test_psql_dos
	POSTGRES_PASSWORD: test
	options: >-
	--health-cmd pg_isready
	--health-interval 10s
	--health-timeout 5s
	--health-retries 5
	ports:
	- 5432:5432

	env:
	AIIDA_TEST_BACKEND: core.psql_dos
	AIIDA_TEST_PROFILE: test_psql_dos
	AIIDA_PROFILE: test_psql_dos

	steps:
	- uses: actions/checkout@v4
	with:
	fetch-depth: 2

	- name: Set up Python ${{ matrix.python-version}}
	uses: actions/setup-python@v5
	with:
	python-version: ${{ matrix.python-version}}

	- name: Install python dependencies
	run: \|
	python -m pip install -U pip
	pip install -U setuptools
	pip install -e .[testing]

	- name: Setup up environment for AiiDA
	run: .github/aiida/setup_aiida.sh

	- name: Test with pytest (AiiDA)
	run: pytest -v --cov=./aiida_optimade/ --cov-report=xml --durations=20

	- name: Test with pytest (Data Curation)
	env:
	PYTEST_OPTIMADE_CONFIG_FILE: ./tests/static/test_data_curation_config.json
	run: pytest -v --cov=./aiida_optimade/ --cov-report=xml --cov-append --durations=20 tests/server/routers/test_structures.py::test_structures_endpoint_data

	- name: Test with pytest (MongoDB)
	env:
	PYTEST_OPTIMADE_CONFIG_FILE: ./tests/static/test_mongo_config.json
	OPTIMADE_MONGO_URI: mongodb://localhost:27017
	OPTIMADE_DATABASE_BACKEND: mongodb
	run: pytest -v --cov=./aiida_optimade/ --cov-report=xml:mongo_cov.xml --durations=20

	- name: Upload coverage to Codecov
	if: matrix.python-version == 3.9
	uses: codecov/codecov-action@v4
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	flags: aiida
	file: ./coverage.xml

	- name: Upload coverage to Codecov
	if: matrix.python-version == 3.9
	uses: codecov/codecov-action@v4
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	flags: mongo
	file: ./mongo_cov.xml

	docker:
	runs-on: ubuntu-latest
	timeout-minutes: 14

	strategy:
	fail-fast: false
	matrix:
	database: [aiida, mongo]

	services:
	mongo:
	image: mongo:4
	ports:
	- 27017:27017
	postgres:
	image: postgres:12
	env:
	POSTGRES_DB: test_psql_dos
	POSTGRES_PASSWORD: test
	options: >-
	--health-cmd pg_isready
	--health-interval 10s
	--health-timeout 5s
	--health-retries 5
	ports:
	- 5432:5432

	steps:
	- uses: actions/checkout@v4

	- name: Set up Python 3.9
	uses: actions/setup-python@v5
	with:
	python-version: 3.9

	- name: Install python dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install -U setuptools

	while IFS="" read -r line \|\| [ -n "${line}" ]; do
	if [[ "${line}" =~ ^aiida-core.*$ ]]; then
	aiida_core="${line}"
	fi
	done < requirements.txt

	pip install ${aiida_core}

	pip install pymongo

	- name: Setup up environment for AiiDA
	env:
	AIIDA_TEST_BACKEND: core.psql_dos
	run: .github/aiida/setup_aiida.sh

	- name: Load test data
	run: \|
	if [ "${{ matrix.database }}" == "aiida" ]; then
	verdi archive import --migration .github/aiida/optimade.aiida
	else
	.github/mongo/load_data.py
	fi

	- name: Build docker image
	if: matrix.database == 'mongo'
	run: docker-compose -f profiles/docker-compose.yml build --build-arg CONFIG_FILE=".github/mongo/ci_config.json"

	- name: Start the Docker image
	env:
	AIIDA_OPTIMADE_LOG_LEVEL: DEBUG
	run: \|
	export DOCKER_HOST_IP=$(ip route \| grep docker0 \| awk '{print $9}')
	docker-compose -f profiles/docker-compose.yml up &
	.github/utils/wait_for_it.sh localhost:3253 -t 360
	sleep 15

	- name: Test server with OPTIMADE Validator
	uses: Materials-Consortia/optimade-validator-action@v2
	with:
	port: 3253
	all versioned paths: yes
	validate unversioned path: yes
	validator version: latest

	docker-mongo:
	runs-on: ubuntu-latest
	timeout-minutes: 14

	services:
	postgres:
	image: postgres:12
	env:
	POSTGRES_DB: test_psql_dos
	POSTGRES_PASSWORD: test
	options: >-
	--health-cmd pg_isready
	--health-interval 10s
	--health-timeout 5s
	--health-retries 5
	ports:
	- 5432:5432

	steps:
	- uses: actions/checkout@v4

	- name: Set up Python 3.9
	uses: actions/setup-python@v5
	with:
	python-version: 3.9

	- name: Install python dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install -U setuptools

	while IFS="" read -r line \|\| [ -n "${line}" ]; do
	if [[ "${line}" =~ ^aiida-core.*$ ]]; then
	aiida_core="${line}"
	fi
	done < requirements.txt

	pip install ${aiida_core}

	- name: Setup up environment for AiiDA
	env:
	AIIDA_TEST_BACKEND: core.psql_dos
	run: .github/aiida/setup_aiida.sh

	- name: Load test data (AiiDA)
	run: verdi archive import --migration .github/aiida/optimade.aiida

	- name: Build docker image
	run: docker-compose -f profiles/docker-compose-mongo.yml build --build-arg CONFIG_FILE=".github/mongo/ci_config.json"

	- name: Start the Docker image
	env:
	AIIDA_OPTIMADE_LOG_LEVEL: INFO
	USE_MONGO: --mongo
	run: \|
	export DOCKER_HOST_IP=$(ip route \| grep docker0 \| awk '{print $9}')
	docker-compose -f profiles/docker-compose-mongo.yml up &
	.github/utils/wait_for_it.sh localhost:3253 -t 360
	# Long sleep, because the initialization is needed
	sleep 150

	- name: Test server with OPTIMADE Validator
	uses: Materials-Consortia/optimade-validator-action@v2
	with:
	port: 3253
	all versioned paths: yes
	validate unversioned path: yes
	validator version: latest

	docker-mongo-filename:
	runs-on: ubuntu-latest
	timeout-minutes: 14

	services:
	postgres:
	image: postgres:12
	env:
	POSTGRES_DB: test_psql_dos
	POSTGRES_PASSWORD: test
	options: >-
	--health-cmd pg_isready
	--health-interval 10s
	--health-timeout 5s
	--health-retries 5
	ports:
	- 5432:5432

	steps:
	- uses: actions/checkout@v4

	- name: Set up Python 3.9
	uses: actions/setup-python@v5
	with:
	python-version: 3.9

	- name: Install python dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install -U setuptools

	while IFS="" read -r line \|\| [ -n "${line}" ]; do
	if [[ "${line}" =~ ^aiida-core.*$ ]]; then
	aiida_core="${line}"
	fi
	done < requirements.txt

	pip install ${aiida_core}

	- name: Setup up environment for AiiDA
	env:
	AIIDA_TEST_BACKEND: core.psql_dos
	run: .github/aiida/setup_aiida.sh

	- name: Build docker image
	run: docker-compose -f profiles/docker-compose-mongo.yml build --build-arg CONFIG_FILE=".github/mongo/ci_config.json"

	- name: Start the Docker image
	env:
	AIIDA_OPTIMADE_LOG_LEVEL: INFO
	USE_MONGO: --mongo
	MONGO_FILENAME: test_structures_mongo.json
	run: \|
	export DOCKER_HOST_IP=$(ip route \| grep docker0 \| awk '{print $9}')
	docker-compose -f profiles/docker-compose-mongo.yml up &
	.github/utils/wait_for_it.sh localhost:3253 -t 360
	# Longer sleep, because the initialization is needed
	sleep 30

	- name: Test server with OPTIMADE Validator
	uses: Materials-Consortia/optimade-validator-action@v2
	with:
	port: 3253
	all versioned paths: yes
	validate unversioned path: yes
	validator version: latest

	build-package:
	runs-on: ubuntu-latest
	timeout-minutes: 5

	steps:
	- uses: actions/checkout@v4

	- name: Check build and install source distribution
	uses: CasperWA/check-sdist-action@v1

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Update pymatgen requirement from !=2019.9.7,<2024.7.19,>=2019.7.2 to >=2019.7.2,!=2019.9.7,<2024.10.4 #786

Workflow file

Update pymatgen requirement from !=2019.9.7,<2024.7.19,>=2019.7.2 to >=2019.7.2,!=2019.9.7,<2024.10.4 #786

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Workflow file for this run