Add config option `mongo_count_timeout` to skip the global count per request #2050

Workflow file for this run

	name: CI tests

	on:
	pull_request:
	push:
	branches:
	- master
	- 'push-action/**'

	env:
	PYTEST_ADDOPTS: "--color=yes"

	# Cancel running workflows when additional changes are pushed
	# https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#example-using-a-fallback-value
	concurrency:
	group: ${{ github.head_ref \|\| github.run_id }}
	cancel-in-progress: true

	jobs:

	pre-commit:
	runs-on: ubuntu-latest

	steps:
	- uses: actions/checkout@v3
	with:
	submodules: true

	- name: Set up Python 3.10
	uses: actions/setup-python@v4
	with:
	python-version: '3.10'
	cache: 'pip'
	cache-dependency-path: \|
	requirements*.txt


	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install -U setuptools wheel
	pip install -e .
	pip install -r requirements.txt
	pip install -r requirements-server.txt
	pip install -r requirements-dev.txt

	- name: Run pre-commit
	run: \|
	pre-commit run --all-files \|\| ( git status --short ; git diff ; exit 1 )

	openapi:
	runs-on: ubuntu-latest

	steps:
	- uses: actions/checkout@v3
	with:
	submodules: true

	- name: Set up Python 3.10
	uses: actions/setup-python@v4
	with:
	python-version: '3.10'
	cache: 'pip'
	cache-dependency-path: \|
	requirements*.txt

	- name: Install tools
	run: \|
	python -m pip install --upgrade pip
	pip install -U setuptools wheel
	pip install -e .
	pip install -r requirements.txt
	pip install -r requirements-server.txt
	pip install -r requirements-dev.txt

	- name: Pass generated OpenAPI schemas through validator.swagger.io
	run: \|
	invoke swagger-validator openapi/openapi.json
	invoke swagger-validator openapi/index_openapi.json

	- name: Check OpenAPI Schemas have not changed
	run: invoke check-openapi-diff

	docker-image:
	runs-on: ubuntu-latest

	steps:
	- uses: actions/checkout@v3
	with:
	submodules: true

	- name: Build the container image
	run: docker build -f Dockerfile --build-arg CONFIG_FILE=.docker/docker_config.json --tag optimade .

	- name: Start Docker image - server
	run: \|
	docker run --rm -d -p 3213:5000 --name optimade optimade
	.github/utils/wait_for_it.sh localhost:3213 -t 120
	sleep 15

	- name: Test server, including OPTIONAL base URLs
	uses: Materials-Consortia/optimade-validator-action@v2
	with:
	port: 3213
	path: /
	all versioned paths: yes
	validator version: ${{ github.sha }} # This ensures the head of a PR or latest push commit is tested

	- name: Start Docker image - index server
	run: \|
	docker run --rm -d -p 3214:5000 --name optimade-index -e MAIN=main_index optimade
	.github/utils/wait_for_it.sh localhost:3214 -t 120
	sleep 15

	- name: Test index server, including OPTIONAL base URLs
	uses: Materials-Consortia/optimade-validator-action@v2
	with:
	port: 3214
	path: /
	all versioned paths: yes
	index: yes
	validator version: ${{ github.sha }} # This ensures the head of a PR or latest push commit is tested

	pytest:
	runs-on: ubuntu-latest

	env:
	OPTIMADE_CONFIG_FILE: ${{ github.workspace }}/optimade_config.json

	strategy:
	fail-fast: false
	max-parallel: 4
	matrix:
	python-version: ['3.9', '3.10', '3.11']

	services:
	mongo:
	image: mongo:7
	ports:
	- 27017:27017
	postgres:
	image: postgres:10
	env:
	POSTGRES_DB: test_aiida
	POSTGRES_PASSWORD: test
	options: >-
	--health-cmd pg_isready
	--health-interval 10s
	--health-timeout 5s
	--health-retries 5
	ports:
	- 5432:5432
	elasticsearch:
	image: elasticsearch:7.17.7
	ports:
	- 9200:9200
	- 9300:9300
	env:
	discovery.type: single-node
	xpack.security.enabled: 'false'


	steps:
	- uses: actions/checkout@v3
	with:
	submodules: true
	fetch-depth: 2

	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v4
	with:
	python-version: ${{ matrix.python-version }}
	cache: 'pip'
	cache-dependency-path: \|
	requirements*.txt

	- name: Install latest compatible versions of immediate dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install -U setuptools wheel
	pip install -e .
	pip install -r requirements.txt
	pip install -r requirements-dev.txt
	pip install -r requirements-http-client.txt

	- name: Run non-server tests
	run: pytest -rs -vvv --cov=./optimade/ --cov-report=xml tests/ --ignore tests/server

	- name: Install latest server dependencies
	run: pip install -r requirements-server.txt

	- name: Run server tests (using `mongomock`)
	run: pytest -rs -vvv --cov=./optimade/ --cov-report=xml --cov-append tests/server tests/filtertransformers
	env:
	OPTIMADE_DATABASE_BACKEND: 'mongomock'

	- name: Run server tests with no API validation (using `mongomock`)
	run:
	pytest -rs -vvv --cov=./optimade/ --cov-report=xml --cov-append tests/server tests/filtertransformers
	env:
	OPTIMADE_DATABASE_BACKEND: 'mongomock'
	OPTIMADE_VALIDATE_API_RESPONSE: false

	- name: Run server tests (using a real MongoDB)
	run: pytest -rs -vvv --cov=./optimade/ --cov-report=xml --cov-append tests/server tests/filtertransformers
	env:
	OPTIMADE_DATABASE_BACKEND: 'mongodb'

	- name: Run server tests (using Elasticsearch)
	run: \|
	.github/utils/wait_for_it.sh localhost:9200 -t 120
	.github/utils/wait_for_it.sh localhost:9300 -t 120
	pytest -rs -vvv --cov=./optimade/ --cov-report=xml --cov-append tests/server tests/filtertransformers
	env:
	OPTIMADE_DATABASE_BACKEND: 'elastic'

	- name: Install adapter conversion dependencies
	run: pip install -r requirements-client.txt

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

	- name: Run previously skipped tests for adapter conversion
	run: pytest -rs -vvv --cov=./optimade/ --cov-report=xml --cov-append tests/adapters/

	- name: Run tests for validator only to assess coverage (mongomock)
	if: matrix.python-version == 3.10
	run: pytest -rs --cov=./optimade/ --cov-report=xml:validator_cov.xml --cov-append tests/server/test_server_validation.py
	env:
	OPTIMADE_DATABASE_BACKEND: 'mongomock'

	- name: Run tests for validator only to assess coverage (Elasticsearch)
	if: matrix.python-version == 3.10
	run: pytest -rs --cov=./optimade/ --cov-report=xml:validator_cov.xml --cov-append tests/server/test_server_validation.py
	env:
	OPTIMADE_DATABASE_BACKEND: 'elastic'
	OPTIMADE_INSERT_TEST_DATA: false # Must be specified as previous steps will have already inserted the test data

	- name: Run tests for validator only to assess coverage (MongoDB)
	if: matrix.python-version == 3.10
	run: pytest -rs --cov=./optimade/ --cov-report=xml:validator_cov.xml --cov-append tests/server/test_server_validation.py
	env:
	OPTIMADE_DATABASE_BACKEND: 'mongodb'
	OPTIMADE_INSERT_TEST_DATA: false # Must be specified as previous steps will have already inserted the test data

	- name: Run the OPTIMADE Client CLI
	if: matrix.python-version == 3.10
	run: \|
	coverage run --append --source optimade optimade/client/cli.py \
	--filter 'nsites = 1' \
	--output-file test_get_async.json \
	https://optimade.fly.dev
	test test_get_async.json

	coverage run --append --source optimade optimade/client/cli.py \
	--filter 'nsites = 1' \
	--count \
	--output-file test_count.json \
	https://optimade.fly.dev
	test test_count.json

	coverage run --append --source optimade optimade/client/cli.py \
	--no-async \
	--filter 'nsites = 1' \
	--count \
	--output-file test_count_no_async.json \
	https://optimade.fly.dev
	test test_count_no_async.json

	diff test_count_no_async.json test_count.json

	coverage xml

	- name: Upload coverage to Codecov
	if: matrix.python-version == '3.10' && github.repository == 'Materials-Consortia/optimade-python-tools'
	uses: codecov/codecov-action@v3
	with:
	name: project
	file: ./coverage.xml
	flags: project

	- name: Upload validator coverage to Codecov
	if: matrix.python-version == '3.10' && github.repository == 'Materials-Consortia/optimade-python-tools'
	uses: codecov/codecov-action@v3
	with:
	name: validator
	file: ./validator_cov.xml
	flags: validator

	docs:
	runs-on: ubuntu-latest

	steps:
	- uses: actions/checkout@v3
	with:
	submodules: true

	- uses: actions/setup-python@v4
	with:
	python-version: '3.10'
	cache: 'pip'
	cache-dependency-path: \|
	requirements*.txt

	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install -U setuptools wheel
	pip install -e .
	pip install -r requirements.txt
	pip install -r requirements-server.txt
	pip install -r requirements-dev.txt
	pip install -r requirements-http-client.txt
	pip install -r requirements-docs.txt

	# NOTE: While we're now using `mike`, this is still useful
	# to test the integrity of the documentation build.
	- name: Build
	run: \|
	invoke create-api-reference-docs --pre-clean
	mkdocs build --strict

	test_build:
	runs-on: ubuntu-latest

	steps:
	- name: Checkout repository
	uses: actions/checkout@v3

	- name: Set up Python 3.10
	uses: actions/setup-python@v4
	with:
	python-version: '3.10'
	cache: 'pip'
	cache-dependency-path: \|
	requirements*.txt

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

	- name: Install package
	run: \|
	pip install -r requirements.txt -r requirements-dev.txt -r requirements-client.txt -r requirements-http-client.txt -r requirements-docs.txt
	pip install -e .[all]

	- name: Build source distribution
	run: python -m build

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Add config option `mongo_count_timeout` to skip the global count per request #2050

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Add config option `mongo_count_timeout` to skip the global count per request #2050

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Workflow file for this run

Add config option mongo_count_timeout to skip the global count per request #2050

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Workflow file for this run

Add config option `mongo_count_timeout` to skip the global count per request #2050