diff --git a/.ci/aiida-version.json b/.ci/aiida-version.json index 9fa9976a..35a8585a 100644 --- a/.ci/aiida-version.json +++ b/.ci/aiida-version.json @@ -1,6 +1,6 @@ { "schemaVersion": 1, "label": "AiiDA", - "message": "v1.6.8", + "message": "v2.0.1", "color": "brightgreen" } diff --git a/.github/aiida/profile.yaml b/.github/aiida/profile.yaml index 0313a75d..ffbe7c57 100644 --- a/.github/aiida/profile.yaml +++ b/.github/aiida/profile.yaml @@ -18,3 +18,4 @@ broker_password: guest broker_host: 127.0.0.1 broker_port: 5672 broker_virtual_host: '' +test_profile: true diff --git a/.github/mongo/test_structures_mongo.json b/.github/mongo/test_structures_mongo.json index e4aaec0f..9851563e 100644 --- a/.github/mongo/test_structures_mongo.json +++ b/.github/mongo/test_structures_mongo.json @@ -1 +1 @@ -[{"nsites": 24, "species": [{"mass": [22.98977], "name": "Na", "concentration": [1.0], "original_name": "Na", "chemical_symbols": ["Na"]}, {"mass": [35.453], "name": "Cl", "concentration": 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"eb432995-3132-4c65-a9a1-9d581844e88a"}] diff --git a/.github/workflows/ci_dependabot.yml b/.github/workflows/ci_dependabot.yml index ba1cfd67..23e0fecb 100644 --- a/.github/workflows/ci_dependabot.yml +++ b/.github/workflows/ci_dependabot.yml @@ -98,4 +98,3 @@ jobs: - name: Information run: 'echo "${{ steps.cpr.outputs.pull-request-operation }} PR #${{ steps.cpr.outputs.pull-request-number }}: ${{ steps.cpr.outputs.pull-request-url }}"' - diff --git a/.github/workflows/ci_tests.yml b/.github/workflows/ci_tests.yml index 18df4286..dd3dd326 100644 --- a/.github/workflows/ci_tests.yml +++ b/.github/workflows/ci_tests.yml @@ -44,8 +44,8 @@ jobs: strategy: fail-fast: false matrix: - python-version: [3.7, 3.8, 3.9] - backend: ['django', 'sqlalchemy'] + python-version: ['3.8', '3.9', '3.10'] + backend: ['psql_dos'] services: mongo: @@ -53,7 +53,7 @@ jobs: ports: - 27017:27017 postgres: - image: postgres:10 + image: postgres:12 env: POSTGRES_DB: test_${{ matrix.backend }} POSTGRES_PASSWORD: test @@ -80,7 +80,6 @@ jobs: python -m pip install -U pip pip install -U setuptools pip install -e .[testing] - reentry scan - name: Setup up environment for AiiDA env: @@ -133,9 +132,9 @@ jobs: ports: - 27017:27017 postgres: - image: postgres:10 + image: postgres:12 env: - POSTGRES_DB: test_django + POSTGRES_DB: test_psql_dos POSTGRES_PASSWORD: test options: >- --health-cmd pg_isready @@ -165,19 +164,18 @@ jobs: done < requirements.txt pip install ${aiida_core} - reentry scan pip install pymongo - name: Setup up environment for AiiDA env: - AIIDA_TEST_BACKEND: django + AIIDA_TEST_BACKEND: psql_dos run: .github/aiida/setup_aiida.sh - name: Load test data run: | if [ "${{ matrix.database }}" == "aiida" ]; then - verdi import --migration --non-interactive .github/aiida/optimade.aiida + verdi archive import --migration .github/aiida/optimade.aiida else .github/mongo/load_data.py fi @@ -209,9 +207,9 @@ jobs: services: postgres: - image: postgres:10 + image: postgres:12 env: - POSTGRES_DB: test_django + POSTGRES_DB: test_psql_dos POSTGRES_PASSWORD: test options: >- --health-cmd pg_isready @@ -241,15 +239,14 @@ jobs: done < requirements.txt pip install ${aiida_core} - reentry scan - name: Setup up environment for AiiDA env: - AIIDA_TEST_BACKEND: django + AIIDA_TEST_BACKEND: psql_dos run: .github/aiida/setup_aiida.sh - name: Load test data (AiiDA) - run: verdi import --migration --non-interactive .github/aiida/optimade.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" @@ -279,9 +276,9 @@ jobs: services: postgres: - image: postgres:10 + image: postgres:12 env: - POSTGRES_DB: test_django + POSTGRES_DB: test_psql_dos POSTGRES_PASSWORD: test options: >- --health-cmd pg_isready @@ -311,11 +308,10 @@ jobs: done < requirements.txt pip install ${aiida_core} - reentry scan - name: Setup up environment for AiiDA env: - AIIDA_TEST_BACKEND: django + AIIDA_TEST_BACKEND: psql_dos run: .github/aiida/setup_aiida.sh - name: Build docker image diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 409a1aa8..9030fe5c 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -6,6 +6,7 @@ repos: exclude: README.md - id: check-yaml - id: check-json + - id: end-of-file-fixer - repo: https://github.com/ambv/black rev: 22.6.0 diff --git a/Dockerfile b/Dockerfile index 16bf4eb2..c71ce415 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,10 +1,10 @@ -FROM python:3.8 +FROM python:3.9 WORKDIR /app # Install specific optimade and aiida-core versions ARG OPTIMADE_TOOLS_VERSION=0.18.0 -ARG AIIDA_VERSION=1.6.8 +ARG AIIDA_VERSION=2.0.1 # Copy repo contents COPY setup.py setup.json README.md requirements*.txt ./ @@ -13,7 +13,6 @@ COPY aiida_optimade ./aiida_optimade RUN pip install -U pip setuptools wheel \ && pip install optimade==${OPTIMADE_TOOLS_VERSION} \ && pip install aiida-core==${AIIDA_VERSION} \ - && reentry scan \ && pip install -e . COPY .docker/run.sh ./ diff --git a/README.md b/README.md index 95a95f3d..eba8d899 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,12 @@ # OPTIMADE API implementation for AiiDA +The compatibility matrix below assumes the user always install the latest patch release of the specified minor version, which is recommended. + +| Plugin | AiiDA | Python | Specification | +|-|-|-|-| +| `v1.0 < v2.0` | ![Compatibility for v1.0][AiiDA v2 range] | [![PyPI pyversions](https://img.shields.io/pypi/pyversions/aiida-optimade)](https://pypi.org/project/aiida-optimade) | ![OPTIMADE API compatibility][OPTIMADE from OPT] | +| `v0.18 <= v0.20` | ![Compatibility for v0][AiiDA v1 range] | [![PyPI pyversions][Python v3.7-v3.9]](https://pypi.org/project/aiida-optimade/0.20.0/) | ![OPTIMADE API compatibility][OPTIMADE from OPT] | + | Latest release | Build status | Activity | |:--------------:|:------------:|:--------:| | [![AiiDA](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/aiidateam/aiida-optimade/develop/.ci/aiida-version.json)](https://github.com/aiidateam/aiida-core/)
[![PyPI](https://img.shields.io/pypi/v/aiida-optimade)](https://pypi.org/project/aiida-optimade/)
[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/aiida-optimade)](https://pypi.org/project/aiida-optimade/)
[![OPTIMADE](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/Materials-Consortia/optimade-python-tools/v0.18.0/optimade-version.json)](https://github.com/Materials-Consortia/OPTIMADE/) | [![GitHub Workflow Status](https://img.shields.io/github/workflow/status/aiidateam/aiida-optimade/aiida-optimade)](https://github.com/aiidateam/aiida-optimade/actions/)
[![Codecov](https://img.shields.io/codecov/c/gh/aiidateam/aiida-optimade)](https://codecov.io/gh/aiidateam/aiida-optimade) | [![GitHub last commit](https://img.shields.io/github/last-commit/aiidateam/aiida-optimade)](https://github.com/aiidateam/aiida-optimade) | @@ -122,7 +129,7 @@ Navigate to `http://localhost:5000/v1/info` ### With Docker -Adapt `profiles/test_django.json` and `profiles/docker-compose.yml` appropriately. +Adapt `profiles/test_psql_dos.json` and `profiles/docker-compose.yml` appropriately. ```shell $ docker-compose -f profiles/docker-compose.yml up --build @@ -157,3 +164,11 @@ To release the new version, go to GitHub release API of the repo create a new re The release action will be triggered by newly created release. Note, the tag should start with a `v` and be followed by a full semantic version (see [SemVer](https://semver.org)). For example: `v2.3.12`. + +[AiiDA v2 range]: https://img.shields.io/badge/AiiDA->=2.0.0,<3.0.0-007ec6.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAACMAAAAhCAYAAABTERJSAAAABHNCSVQICAgIfAhkiAAAAAlwSFlzAAAFhgAABYYBG6Yz4AAAABl0RVh0U29mdHdhcmUAd3d3Lmlua3NjYXBlLm9yZ5vuPBoAAAUbSURBVFiFzZhrbFRVEMd%2Fc%2B5uu6UUbIFC%2FUAUVEQCLbQJBIiBDyiImJiIhmohYNCkqJAQxASLF8tDgYRHBLXRhIcKNtFEhVDgAxBJqgmVh4JEKg3EIn2QYqBlt917xg%2BFss%2ByaDHOtzsz5z%2B%2FuZl7ztmF%2F5HJvxVQN6cPYX8%2FPLnOmsvNAvqfwuib%2FbNIk9cQeQnLcKRL5xLIV%2Fic9eJeunjPYbRs4FjQSpTB3aS1IpRKeeOOewajy%2FKKEO8Q0DuVdKy8IqsbPulxGHUfCBBu%2BwUYGuFuBTK7wQnht6PEbf4tlRomVRjCbXNjQEB0AyrFQOL5ENIJm7dTLZE6DPJCnEtFZVXDLny%2B4Sjv0PmmYu1ZdUek9RiMgoDmJ8V0L7XJqsZ3UW8YsBOwEeHeeFce7jEYXBy0m9m4BbXqSj2%2Bxnkg26MCVrN6DEZcwggtd8pTFx%2Fh3B9B50YLaFOPwXQKUt0tBLegtSomfBlfY13PwijbEnhztGzgJsK5h9W9qeWwBqjvyhB2iBs1Qz0AU974DciRGO8CVN8AJhAeMAdA3KbrKEtvxhsI%2B9emWiJlGBEU680Cfk%2BSsVqXZvcFYGXjF8ABVJ%2BTNfVXehyms1zzn1gmIOxLEB6E31%2FWBe5rnCarmo7elf7dJEeaLh80GasliI5F6Q9cAz1GY1OJVNDxTzQTw7iY%2FHEZRQY7xqJ9RU2LFe%2FYqakdP911ha0XhjjiTVAkDwgatWfCGeYocx8M3glG8g8EXhSrLrHnEFJ5Ymow%2FkhIYv6ttYUW1iFmEqqxdVoUs9FmsDYSqmtmJh3Cl1%2BVtl2s7owDUdocR5bceiyoSivGTT5vzpbzL1uoBpmcAAQgW7ArnKD9ng9rc%2BNgrobSNwpSkkhcRN%2BvmXLjIsDovYHHEfmsYFygPAnIDEQrQPzJYCOaLHLUfIt7Oq0LJn9fxkSgNCb1qEIQ5UKgT%2Fs6gJmVOOroJhQBXVqw118QtWLdyUxEP45sUpSzqP7RDdFYMyB9UReMiF1MzPwoUqHt8hjGFFeP5wZAbZ%2F0%2BcAtAAcji6LeSq%2FMYiAvSsdw3GtrfVSVFUBbIhwRWYR7yOcr%2FBi%2FB1MSJZ16JlgH1AGM3EO2QnmMyrSbTSiACgFBv4yCUapZkt9qwWVL7aeOyHvArJjm8%2Fz9BhdI4XcZgz2%2FvRALosjsk1ODOyMcJn9%2FYI6IrkS5vxMGdUwou2YKfyVqJpn5t9aNs3gbQMbdbkxnGdsr4bTHm2AxWo9yNZK4PXR3uzhAh%2BM0AZejnCrGdy0UvJxl0oMKgWSLR%2B1LH2aE9ViejiFs%2BXn6bTjng3MlIhJ1I1TkuLdg6OcAbD7Xx%2Bc3y9TrWAiSHqVkbZ2v9ilCo6s4AjwZCzFyD9mOL305nV9aonvsQeT2L0gVk4OwOJqXXVRW7naaxswDKVdlYLyMXAnntteYmws2xcVVZzq%2BtHPAooQggmJkc6TLSusOiL4RKgwzzYU1iFQgiUBA1H7E8yPau%2BZl9P7AblVNebtHqTgxLfRqrNvZWjsHZFuqMqKcDWdlFjF7UGvX8Jn24DyEAykJwNcdg0OvJ4p5pQ9tV6SMlP4A0PNh8aYze1ArROyUNTNouy8tNF3Rt0CSXb6bRFl4%2FIfQzNMjaE9WwpYOWQnOdEF%2BTdJNO0iFh7%2BI0kfORzQZb6P2kymS9oTxzBiM9rUqLWr1WE5G6ODhycQd%2FUnNVeMbcH68hYkGycNoUNWc8fxaxfwhDbHpfwM5oeTY7rUX8QAAAABJRU5ErkJggg%3D%3D + +[AiiDA v1 range]: https://img.shields.io/badge/AiiDA->=1.6.0,<2.0.0-007ec6.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAACMAAAAhCAYAAABTERJSAAAABHNCSVQICAgIfAhkiAAAAAlwSFlzAAAFhgAABYYBG6Yz4AAAABl0RVh0U29mdHdhcmUAd3d3Lmlua3NjYXBlLm9yZ5vuPBoAAAUbSURBVFiFzZhrbFRVEMd%2Fc%2B5uu6UUbIFC%2FUAUVEQCLbQJBIiBDyiImJiIhmohYNCkqJAQxASLF8tDgYRHBLXRhIcKNtFEhVDgAxBJqgmVh4JEKg3EIn2QYqBlt917xg%2BFss%2ByaDHOtzsz5z%2B%2FuZl7ztmF%2F5HJvxVQN6cPYX8%2FPLnOmsvNAvqfwuib%2FbNIk9cQeQnLcKRL5xLIV%2Fic9eJeunjPYbRs4FjQSpTB3aS1IpRKeeOOewajy%2FKKEO8Q0DuVdKy8IqsbPulxGHUfCBBu%2BwUYGuFuBTK7wQnht6PEbf4tlRomVRjCbXNjQEB0AyrFQOL5ENIJm7dTLZE6DPJCnEtFZVXDLny%2B4Sjv0PmmYu1ZdUek9RiMgoDmJ8V0L7XJqsZ3UW8YsBOwEeHeeFce7jEYXBy0m9m4BbXqSj2%2Bxnkg26MCVrN6DEZcwggtd8pTFx%2Fh3B9B50YLaFOPwXQKUt0tBLegtSomfBlfY13PwijbEnhztGzgJsK5h9W9qeWwBqjvyhB2iBs1Qz0AU974DciRGO8CVN8AJhAeMAdA3KbrKEtvxhsI%2B9emWiJlGBEU680Cfk%2BSsVqXZvcFYGXjF8ABVJ%2BTNfVXehyms1zzn1gmIOxLEB6E31%2FWBe5rnCarmo7elf7dJEeaLh80GasliI5F6Q9cAz1GY1OJVNDxTzQTw7iY%2FHEZRQY7xqJ9RU2LFe%2FYqakdP911ha0XhjjiTVAkDwgatWfCGeYocx8M3glG8g8EXhSrLrHnEFJ5Ymow%2FkhIYv6ttYUW1iFmEqqxdVoUs9FmsDYSqmtmJh3Cl1%2BVtl2s7owDUdocR5bceiyoSivGTT5vzpbzL1uoBpmcAAQgW7ArnKD9ng9rc%2BNgrobSNwpSkkhcRN%2BvmXLjIsDovYHHEfmsYFygPAnIDEQrQPzJYCOaLHLUfIt7Oq0LJn9fxkSgNCb1qEIQ5UKgT%2Fs6gJmVOOroJhQBXVqw118QtWLdyUxEP45sUpSzqP7RDdFYMyB9UReMiF1MzPwoUqHt8hjGFFeP5wZAbZ%2F0%2BcAtAAcji6LeSq%2FMYiAvSsdw3GtrfVSVFUBbIhwRWYR7yOcr%2FBi%2FB1MSJZ16JlgH1AGM3EO2QnmMyrSbTSiACgFBv4yCUapZkt9qwWVL7aeOyHvArJjm8%2Fz9BhdI4XcZgz2%2FvRALosjsk1ODOyMcJn9%2FYI6IrkS5vxMGdUwou2YKfyVqJpn5t9aNs3gbQMbdbkxnGdsr4bTHm2AxWo9yNZK4PXR3uzhAh%2BM0AZejnCrGdy0UvJxl0oMKgWSLR%2B1LH2aE9ViejiFs%2BXn6bTjng3MlIhJ1I1TkuLdg6OcAbD7Xx%2Bc3y9TrWAiSHqVkbZ2v9ilCo6s4AjwZCzFyD9mOL305nV9aonvsQeT2L0gVk4OwOJqXXVRW7naaxswDKVdlYLyMXAnntteYmws2xcVVZzq%2BtHPAooQggmJkc6TLSusOiL4RKgwzzYU1iFQgiUBA1H7E8yPau%2BZl9P7AblVNebtHqTgxLfRqrNvZWjsHZFuqMqKcDWdlFjF7UGvX8Jn24DyEAykJwNcdg0OvJ4p5pQ9tV6SMlP4A0PNh8aYze1ArROyUNTNouy8tNF3Rt0CSXb6bRFl4%2FIfQzNMjaE9WwpYOWQnOdEF%2BTdJNO0iFh7%2BI0kfORzQZb6P2kymS9oTxzBiM9rUqLWr1WE5G6ODhycQd%2FUnNVeMbcH68hYkGycNoUNWc8fxaxfwhDbHpfwM5oeTY7rUX8QAAAABJRU5ErkJggg%3D%3D + +[Python v3.7-v3.9]: https://img.shields.io/badge/python-3.7%20%7C%203.8%20%7C%203.9-blue + +[OPTIMADE from OPT]: https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/Materials-Consortia/optimade-python-tools/v0.18.0/optimade-version.json diff --git a/aiida_optimade/cli/__init__.py b/aiida_optimade/cli/__init__.py index 4c95e0ba..110e881f 100644 --- a/aiida_optimade/cli/__init__.py +++ b/aiida_optimade/cli/__init__.py @@ -1,8 +1,2 @@ -# pylint: disable=wrong-import-position -import click_completion - -# Activate the completion of parameter types provided by the click_completion package -click_completion.init() - # Import to populate sub commands from aiida_optimade.cli import cmd_calc, cmd_init, cmd_run # noqa: E402,F401 diff --git a/aiida_optimade/cli/cmd_calc.py b/aiida_optimade/cli/cmd_calc.py index 88008e7b..345b3432 100644 --- a/aiida_optimade/cli/cmd_calc.py +++ b/aiida_optimade/cli/cmd_calc.py @@ -40,6 +40,10 @@ def calc(obj: dict, fields: Tuple[str], force_yes: bool, silent: bool): from aiida import load_profile from aiida.cmdline.utils import echo + # The default aiida.cmdline loglevel inherit from aiida loglevel is REPORT + # Here we use INFO loglevel for the operations + echo.CMDLINE_LOGGER.setLevel("INFO") + try: profile: str = obj.get("profile").name except AttributeError: diff --git a/aiida_optimade/cli/cmd_init.py b/aiida_optimade/cli/cmd_init.py index 43d7b1d8..06180932 100644 --- a/aiida_optimade/cli/cmd_init.py +++ b/aiida_optimade/cli/cmd_init.py @@ -48,6 +48,10 @@ def init(obj: dict, force: bool, silent: bool, mongo: bool, filename: str): from aiida import load_profile from aiida.cmdline.utils import echo + # The default aiida.cmdline loglevel inherit from aiida loglevel is REPORT + # Here we use INFO loglevel for the operations + echo.CMDLINE_LOGGER.setLevel("INFO") + filename: Path = Path(filename) if filename else filename if mongo and filename: diff --git a/aiida_optimade/mappers/structures.py b/aiida_optimade/mappers/structures.py index 4684dec9..303c25de 100644 --- a/aiida_optimade/mappers/structures.py +++ b/aiida_optimade/mappers/structures.py @@ -22,8 +22,8 @@ class StructureMapper(ResourceMapper): """Map 'structure' resources from OPTIMADE to AiiDA""" TRANSLATORS: Dict[str, AiidaEntityTranslator] = { - "data.cif.CifData.": CifDataTranslator, - "data.structure.StructureData.": StructureDataTranslator, + "data.core.cif.CifData.": CifDataTranslator, + "data.core.structure.StructureData.": StructureDataTranslator, } REQUIRED_ATTRIBUTES = set(StructureResourceAttributes.schema().get("required")) # This should be REQUIRED_FIELDS, but should be set as such in `optimade` diff --git a/aiida_optimade/routers/structures.py b/aiida_optimade/routers/structures.py index a9c0f195..2d22585c 100644 --- a/aiida_optimade/routers/structures.py +++ b/aiida_optimade/routers/structures.py @@ -24,7 +24,7 @@ ROUTER = APIRouter(redirect_slashes=True) STRUCTURES = AiidaCollection( - entities=["data.cif.CifData.", "data.structure.StructureData."], + entities=["data.core.cif.CifData.", "data.core.structure.StructureData."], resource_cls=StructureResource, resource_mapper=StructureMapper, ) diff --git a/aiida_optimade/translators/entities.py b/aiida_optimade/translators/entities.py index 266c81d3..ee417bcc 100644 --- a/aiida_optimade/translators/entities.py +++ b/aiida_optimade/translators/entities.py @@ -1,8 +1,9 @@ from typing import Any, List, Union +from aiida import orm from aiida.orm.nodes import Node from aiida.orm.querybuilder import QueryBuilder -from aiida_optimade.common import AiidaEntityNotFound, AiidaError, LOGGER +from aiida_optimade.common import AiidaEntityNotFound, LOGGER __all__ = ("AiidaEntityTranslator",) @@ -138,41 +139,12 @@ def _store_attributes_mongo(self) -> None: def _store_attributes_node_extra(self) -> None: """Store new attributes in Node extras""" - from aiida.manage.manager import get_manager - optimade = self._get_optimade_extras() if optimade: optimade.update(self.new_attributes) else: optimade = self.new_attributes - extras = ( - self._get_unique_node_property("extras") - if self._get_unique_node_property("extras") - else {} - ) - extras[self.EXTRAS_KEY] = optimade - - profile = get_manager().get_profile() - LOGGER.debug( - "(%s) Updating Node %s in AiiDA DB!", profile.database_backend, self._pk - ) - if profile.database_backend == "django": - from aiida.backends.djsite.db.models import DbNode - - with get_manager().get_backend().transaction(): - DbNode.objects.filter(pk=self._pk).update(extras=extras) - elif profile.database_backend == "sqlalchemy": - from aiida.backends.sqlalchemy.models.node import DbNode - - with get_manager().get_backend().transaction() as session: - session.query(DbNode).filter(DbNode.id == self._pk).update( - values={"extras": extras} - ) - else: - raise AiidaError( - f'Unknown AiiDA backend "{profile.database_backend}" for profile' - f"{profile}" - ) - # For posterity, this is how to do the same, going through AiiDA's API: - # self._node.set_extra(self.EXTRAS_KEY, optimade) + LOGGER.debug("Updating Node %s in AiiDA DB!", self._pk) + node = orm.load_node(self._pk) + node.set_extra(self.EXTRAS_KEY, optimade) diff --git a/profiles/config.j2 b/profiles/config.j2 index 111d4262..77cafc64 100644 --- a/profiles/config.j2 +++ b/profiles/config.j2 @@ -1,26 +1,34 @@ { "CONFIG_VERSION": { - "CURRENT": 4, - "OLDEST_COMPATIBLE": 3 + "CURRENT": 8, + "OLDEST_COMPATIBLE": 8 }, "default_profile": "{{ aiida_profile }}", "profiles": { "{{ aiida_profile }}": { - "AIIDADB_ENGINE": "postgresql_psycopg2", - "AIIDADB_PASS": "{{ aiida_db_pass }}", - "AIIDADB_NAME": "{{ aiida_db_name }}", - "AIIDADB_HOST": "{{ aiida_db_host }}", - "AIIDADB_USER": "{{ aiida_db_user }}", - "AIIDADB_PORT": {{ aiida_db_port }}, - "AIIDADB_BACKEND": "{{ aiida_db_backend }}", - "default_user_email": "aiida@localhost", - "AIIDADB_REPOSITORY_URI": "file:///app/.aiida/repository-quicksetup", - "broker_protocol": "amqp", - "broker_username": "guest", - "broker_password": "guest", - "broker_host": "127.0.0.1", - "broker_port": 5672, - "broker_virtual_host": "", + "storage": { + "backend": "psql_dos", + "config": { + "database_engine": "postgresql_psycopg2", + "database_hostname": "{{ aiida_db_host }}", + "database_port": {{ aiida_db_port }}, + "database_name": "{{ aiida_db_name }}", + "database_username": "{{ aiida_db_user }}", + "database_password": "{{ aiida_db_pass }}", + "repository_uri": "file:///app/.aiida/repository-quicksetup" + } + }, + "process_control": { + "backend": "rabbitmq", + "config": { + "broker_protocol": "amqp", + "broker_username": "guest", + "broker_password": "guest", + "broker_host": "127.0.0.1", + "broker_port": 5672, + "broker_virtual_host": "" + } + }, "options": {} } } diff --git a/profiles/docker-compose-mongo.j2 b/profiles/docker-compose-mongo.j2 index 2f6fef20..1f2dad5f 100644 --- a/profiles/docker-compose-mongo.j2 +++ b/profiles/docker-compose-mongo.j2 @@ -11,7 +11,7 @@ services: dockerfile: Dockerfile args: OPTIMADE_TOOLS_VERSION: 0.18.0 - AIIDA_VERSION: 1.6.8 + AIIDA_VERSION: 2.0.1 CONFIG_FILE: aiida_optimade/config.json environment: AIIDA_PATH: /app diff --git a/profiles/docker-compose-mongo.yml b/profiles/docker-compose-mongo.yml index 5b15b374..80f1cf8d 100644 --- a/profiles/docker-compose-mongo.yml +++ b/profiles/docker-compose-mongo.yml @@ -11,18 +11,18 @@ services: dockerfile: Dockerfile args: OPTIMADE_TOOLS_VERSION: 0.18.0 - AIIDA_VERSION: 1.6.8 + AIIDA_VERSION: 2.0.1 CONFIG_FILE: aiida_optimade/config.json environment: AIIDA_PATH: /app - AIIDA_PROFILE: test_django + AIIDA_PROFILE: test_psql_dos FORCE_INIT: USE_MONGO: MONGO_FILENAME: AIIDA_OPTIMADE_LOG_LEVEL: OPTIMADE_MONGO_URI: 'mongodb://mongo:27017' volumes: - - '/tmp/test_repository_test_django:/app/.aiida/repository-quicksetup' + - '/tmp/test_repository_test_psql_dos:/app/.aiida/repository-quicksetup' - '.:/profiles' - '../.github/mongo:/app/.mongo' ports: diff --git a/profiles/docker-compose.j2 b/profiles/docker-compose.j2 index 5a4d6d6c..053c980a 100644 --- a/profiles/docker-compose.j2 +++ b/profiles/docker-compose.j2 @@ -9,7 +9,7 @@ services: dockerfile: Dockerfile args: OPTIMADE_TOOLS_VERSION: 0.18.0 - AIIDA_VERSION: 1.6.8 + AIIDA_VERSION: 2.0.1 CONFIG_FILE: aiida_optimade/config.json environment: AIIDA_PATH: /app diff --git a/profiles/docker-compose.yml b/profiles/docker-compose.yml index ca3cee82..35fa8cea 100644 --- a/profiles/docker-compose.yml +++ b/profiles/docker-compose.yml @@ -9,17 +9,17 @@ services: dockerfile: Dockerfile args: OPTIMADE_TOOLS_VERSION: 0.18.0 - AIIDA_VERSION: 1.6.8 + AIIDA_VERSION: 2.0.1 CONFIG_FILE: aiida_optimade/config.json environment: AIIDA_PATH: /app - AIIDA_PROFILE: test_django + AIIDA_PROFILE: test_psql_dos FORCE_INIT: USE_MONGO: MONGO_FILENAME: AIIDA_OPTIMADE_LOG_LEVEL: volumes: - - '/tmp/test_repository_test_django:/app/.aiida/repository-quicksetup' + - '/tmp/test_repository_test_psql_dos:/app/.aiida/repository-quicksetup' - '.:/profiles' - '../.github/mongo:/app/.mongo' ports: diff --git a/profiles/test_django.json b/profiles/test_django.json deleted file mode 100644 index 1920b370..00000000 --- a/profiles/test_django.json +++ /dev/null @@ -1,27 +0,0 @@ -{ - "CONFIG_VERSION": { - "CURRENT": 4, - "OLDEST_COMPATIBLE": 3 - }, - "default_profile": "test_django", - "profiles": { - "test_django": { - "AIIDADB_ENGINE": "postgresql_psycopg2", - "AIIDADB_PASS": "test", - "AIIDADB_NAME": "test_django", - "AIIDADB_HOST": "docker.host.internal", - "AIIDADB_USER": "postgres", - "AIIDADB_PORT": 5432, - "AIIDADB_BACKEND": "django", - "default_user_email": "aiida@localhost", - "AIIDADB_REPOSITORY_URI": "file:///app/.aiida/repository-quicksetup", - "broker_protocol": "amqp", - "broker_username": "guest", - "broker_password": "guest", - "broker_host": "127.0.0.1", - "broker_port": 5672, - "broker_virtual_host": "", - "options": {} - } - } -} diff --git a/profiles/test_psql_dos.json b/profiles/test_psql_dos.json new file mode 100644 index 00000000..3493c415 --- /dev/null +++ b/profiles/test_psql_dos.json @@ -0,0 +1,37 @@ +{ + "CONFIG_VERSION": { + "CURRENT": 8, + "OLDEST_COMPATIBLE": 8 + }, + "default_profile": "test_psql_dos", + "profiles": { + "test_psql_dos": { + "storage": { + "backend": "psql_dos", + "config": { + "database_engine": "postgresql_psycopg2", + "database_hostname": "docker.host.internal", + "database_port": 5432, + "database_name": "test_psql_dos", + "database_username": "postgres", + "database_password": "test", + "repository_uri": "file:///app/.aiida/repository-quicksetup" + } + }, + "process_control": { + "backend": "rabbitmq", + "config": { + "broker_protocol": "amqp", + "broker_username": "guest", + "broker_password": "guest", + "broker_host": "127.0.0.1", + "broker_port": 5672, + "broker_virtual_host": "" + } + }, + "options": {}, + "test_profile": true, + "default_user_email": "aiida@localhost" + } + } +} diff --git a/requirements.txt b/requirements.txt index 048c4da8..8de6c538 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,6 +1,6 @@ -aiida-core~=1.6.8 +aiida-core~=2.0.1 optimade[mongo]~=0.18.0 -pymatgen~=2021.3 +pymatgen>=2019.7.2,<=2022.1.9,!=2019.9.7 uvicorn~=0.18.2 # Dependencies used directly in this package, but included through other dependencies: diff --git a/setup.json b/setup.json index e76c87ec..53ecfd0b 100644 --- a/setup.json +++ b/setup.json @@ -16,9 +16,9 @@ "Operating System :: MacOS :: MacOS X", "Operating System :: POSIX :: Linux", "Programming Language :: Python :: 3 :: Only", - "Programming Language :: Python :: 3.7", "Programming Language :: Python :: 3.8", "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", "Intended Audience :: Developers", "Topic :: Database", "Topic :: Database :: Database Engines/Servers", diff --git a/setup.py b/setup.py index 67807915..b1cdd5c4 100644 --- a/setup.py +++ b/setup.py @@ -20,7 +20,7 @@ long_description=open(MODULE_DIR.joinpath("README.md")).read(), long_description_content_type="text/markdown", packages=find_packages(exclude=["tests", "profiles"]), - python_requires=">=3.7", + python_requires=">=3.8", install_requires=REQUIREMENTS, extras_require={"dev": DEV, "testing": TESTING}, entry_points={ diff --git a/tests/cli/static/cif_data_nodes.aiida b/tests/cli/static/cif_data_nodes.aiida index bf531841..e570cce7 100644 Binary files a/tests/cli/static/cif_data_nodes.aiida and b/tests/cli/static/cif_data_nodes.aiida differ diff --git a/tests/cli/static/initialized_structure_nodes.aiida b/tests/cli/static/initialized_structure_nodes.aiida index e9e64545..8bc105d8 100644 Binary files a/tests/cli/static/initialized_structure_nodes.aiida and b/tests/cli/static/initialized_structure_nodes.aiida differ diff --git a/tests/cli/static/structure_data_nodes.aiida b/tests/cli/static/structure_data_nodes.aiida index ad808312..fb244dbc 100644 Binary files a/tests/cli/static/structure_data_nodes.aiida and b/tests/cli/static/structure_data_nodes.aiida differ diff --git a/tests/cli/test_calc.py b/tests/cli/test_calc.py index 16214166..ac89a691 100644 --- a/tests/cli/test_calc.py +++ b/tests/cli/test_calc.py @@ -17,7 +17,7 @@ def test_calc_all_new(run_cli_command, aiida_profile, top_dir, caplog): any Nodes. """ from aiida import orm - from aiida.tools.importexport import import_data + from aiida.tools.archive.imports import import_archive from aiida_optimade.cli import cmd_calc from aiida_optimade.translators.entities import AiidaEntityTranslator @@ -25,7 +25,7 @@ def test_calc_all_new(run_cli_command, aiida_profile, top_dir, caplog): # Clear database and get initialized_structure_nodes.aiida aiida_profile.reset_db() archive = top_dir.joinpath("tests/cli/static/initialized_structure_nodes.aiida") - import_data(archive) + import_archive(archive) fields = ["elements", "chemical_formula_hill"] @@ -98,7 +98,7 @@ def test_calc_all_new(run_cli_command, aiida_profile, top_dir, caplog): # Repopulate database with the "proper" test data aiida_profile.reset_db() original_data = top_dir.joinpath("tests/static/test_structures.aiida") - import_data(original_data) + import_archive(original_data) @pytest.mark.skipif( @@ -108,7 +108,7 @@ def test_calc_all_new(run_cli_command, aiida_profile, top_dir, caplog): def test_calc(run_cli_command, aiida_profile, top_dir): """Test `aiida-optimade -p profile_name calc` works.""" from aiida import orm - from aiida.tools.importexport import import_data + from aiida.tools.archive.imports import import_archive from aiida_optimade.cli import cmd_calc from aiida_optimade.translators.entities import AiidaEntityTranslator @@ -116,7 +116,7 @@ def test_calc(run_cli_command, aiida_profile, top_dir): # Clear database and get initialized_structure_nodes.aiida aiida_profile.reset_db() archive = top_dir.joinpath("tests/cli/static/initialized_structure_nodes.aiida") - import_data(archive) + import_archive(archive) fields = ["elements", "chemical_formula_hill"] @@ -160,7 +160,7 @@ def test_calc(run_cli_command, aiida_profile, top_dir): # Repopulate database with the "proper" test data aiida_profile.reset_db() original_data = top_dir.joinpath("tests/static/test_structures.aiida") - import_data(original_data) + import_archive(original_data) @pytest.mark.skipif( @@ -170,7 +170,7 @@ def test_calc(run_cli_command, aiida_profile, top_dir): def test_calc_partially_init(run_cli_command, aiida_profile, top_dir, caplog): """Test `aiida-optimade -p profile_name calc` works for a partially initalized DB""" from aiida import orm - from aiida.tools.importexport import import_data + from aiida.tools.archive.imports import import_archive from aiida_optimade.cli import cmd_calc from aiida_optimade.translators.entities import AiidaEntityTranslator @@ -178,7 +178,7 @@ def test_calc_partially_init(run_cli_command, aiida_profile, top_dir, caplog): # Clear database and get initialized_structure_nodes.aiida aiida_profile.reset_db() archive = top_dir.joinpath("tests/cli/static/initialized_structure_nodes.aiida") - import_data(archive) + import_archive(archive) extras_key = AiidaEntityTranslator.EXTRAS_KEY original_data = orm.QueryBuilder().append( @@ -257,4 +257,4 @@ def test_calc_partially_init(run_cli_command, aiida_profile, top_dir, caplog): # Repopulate database with the "proper" test data aiida_profile.reset_db() original_data = top_dir.joinpath("tests/static/test_structures.aiida") - import_data(original_data) + import_archive(original_data) diff --git a/tests/cli/test_init.py b/tests/cli/test_init.py index 9798a407..c9b27b67 100644 --- a/tests/cli/test_init.py +++ b/tests/cli/test_init.py @@ -16,7 +16,7 @@ def test_init_structuredata(run_cli_command, aiida_profile, top_dir, caplog): Also, check the `-f/--force` option. """ from aiida import orm - from aiida.tools.importexport import import_data + from aiida.tools.archive.imports import import_archive from aiida_optimade.cli import cmd_init from aiida_optimade.translators.entities import AiidaEntityTranslator @@ -25,7 +25,7 @@ def test_init_structuredata(run_cli_command, aiida_profile, top_dir, caplog): aiida_profile.reset_db() archive = top_dir.joinpath("tests/cli/static/structure_data_nodes.aiida") - import_data(archive) + import_archive(archive) n_structure_data = orm.QueryBuilder().append(orm.StructureData).count() @@ -84,7 +84,7 @@ def test_init_structuredata(run_cli_command, aiida_profile, top_dir, caplog): # Repopulate database with the "proper" test data aiida_profile.reset_db() original_data = top_dir.joinpath("tests/static/test_structures.aiida") - import_data(original_data) + import_archive(original_data) @pytest.mark.skipif( @@ -94,7 +94,7 @@ def test_init_structuredata(run_cli_command, aiida_profile, top_dir, caplog): def test_init_cifdata(run_cli_command, aiida_profile, top_dir, caplog): """Test `aiida-optimade -p profile_name init` works for CifData Nodes.""" from aiida import orm - from aiida.tools.importexport import import_data + from aiida.tools.archive.imports import import_archive from aiida_optimade.cli import cmd_init from aiida_optimade.translators.entities import AiidaEntityTranslator @@ -103,7 +103,7 @@ def test_init_cifdata(run_cli_command, aiida_profile, top_dir, caplog): aiida_profile.reset_db() archive = top_dir.joinpath("tests/cli/static/cif_data_nodes.aiida") - import_data(archive) + import_archive(archive) n_cif_data = orm.QueryBuilder().append(orm.CifData).count() @@ -138,7 +138,7 @@ def test_init_cifdata(run_cli_command, aiida_profile, top_dir, caplog): # Repopulate database with the "proper" test data aiida_profile.reset_db() original_data = top_dir.joinpath("tests/static/test_structures.aiida") - import_data(original_data) + import_archive(original_data) @pytest.mark.skipif( @@ -151,7 +151,7 @@ def test_init_structuredata_mongo(run_cli_command, aiida_profile, top_dir, caplo """ import bson.json_util from aiida import orm - from aiida.tools.importexport import import_data + from aiida.tools.archive.imports import import_archive from aiida_optimade.cli import cmd_init from aiida_optimade.routers.structures import STRUCTURES_MONGO @@ -162,7 +162,7 @@ def test_init_structuredata_mongo(run_cli_command, aiida_profile, top_dir, caplo STRUCTURES_MONGO.collection.drop() archive = top_dir.joinpath("tests/cli/static/structure_data_nodes.aiida") - import_data(archive) + import_archive(archive) n_structure_data = orm.QueryBuilder().append(orm.StructureData).count() @@ -223,7 +223,7 @@ def test_init_structuredata_mongo(run_cli_command, aiida_profile, top_dir, caplo # Repopulate databases with the "proper" test data aiida_profile.reset_db() - import_data(top_dir.joinpath("tests/static/test_structures.aiida")) + import_archive(top_dir.joinpath("tests/static/test_structures.aiida")) STRUCTURES_MONGO.collection.drop() with open(top_dir.joinpath("tests/static/test_structures_mongo.json")) as handle: data = bson.json_util.loads(handle.read()) @@ -237,7 +237,7 @@ def test_init_cifdata_mongo(run_cli_command, aiida_profile, top_dir, caplog): """Test `aiida-optimade -p profile_name init` works for CifData Nodes.""" import bson.json_util from aiida import orm - from aiida.tools.importexport import import_data + from aiida.tools.archive.imports import import_archive from aiida_optimade.cli import cmd_init from aiida_optimade.routers.structures import STRUCTURES_MONGO @@ -248,7 +248,7 @@ def test_init_cifdata_mongo(run_cli_command, aiida_profile, top_dir, caplog): STRUCTURES_MONGO.collection.drop() archive = top_dir.joinpath("tests/cli/static/cif_data_nodes.aiida") - import_data(archive) + import_archive(archive) n_cif_data = orm.QueryBuilder().append(orm.CifData).count() @@ -284,7 +284,7 @@ def test_init_cifdata_mongo(run_cli_command, aiida_profile, top_dir, caplog): # Repopulate database with the "proper" test data aiida_profile.reset_db() - import_data(top_dir.joinpath("tests/static/test_structures.aiida")) + import_archive(top_dir.joinpath("tests/static/test_structures.aiida")) STRUCTURES_MONGO.collection.drop() with open(top_dir.joinpath("tests/static/test_structures_mongo.json")) as handle: data = bson.json_util.loads(handle.read()) diff --git a/tests/cli/test_run.py b/tests/cli/test_run.py index e5f3526c..225f6cc0 100644 --- a/tests/cli/test_run.py +++ b/tests/cli/test_run.py @@ -83,10 +83,12 @@ def test_log_level_warning(run_and_terminate_server): def test_non_valid_log_level(run_and_terminate_server): """Test passing a non-valid log level to `aiida-optimade run`""" - options = ["--log-level", "test"] + options = ["--log-level", "novalidloglevel"] output, errors = run_and_terminate_server(command="run", options=options) assert not output, f"output: {output!r}, errors: {errors!r}" - assert "invalid choice: test" in errors, f"output: {output!r}, errors: {errors!r}" + assert ( + "Invalid value for '--log-level': 'novalidloglevel' is not one of" in errors + ), f"output: {output!r}, errors: {errors!r}" @pytest.mark.skip( diff --git a/tests/conftest.py b/tests/conftest.py index 4b87998f..5c796dc5 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -44,7 +44,7 @@ def aiida_profile(top_dir, setup_config) -> TestManager: get_test_profile_name, test_manager, ) - from aiida.tools.importexport import import_data + from aiida.tools.archive.imports import import_archive org_env_var = os.getenv("AIIDA_PROFILE") test_env_var = os.getenv("PYTEST_OPTIMADE_CONFIG_FILE") @@ -56,12 +56,13 @@ def aiida_profile(top_dir, setup_config) -> TestManager: ) as manager: manager.reset_db() - profile = load_profile().name - assert profile in ["test_profile", "test_django", "test_sqlalchemy"] - os.environ["AIIDA_PROFILE"] = profile + profile = load_profile() + # If test locally `AIIDA_TEST_PROFILE` may not set and `test_profile` will be used + assert profile.name in ["test_profile", "test_psql_dos"] + os.environ["AIIDA_PROFILE"] = profile.name # Use AiiDA DB - import_data(top_dir.joinpath("tests/static/test_structures.aiida")) + import_archive(top_dir.joinpath("tests/static/test_structures.aiida")) if test_env_var: # Use MongoDB diff --git a/tests/server/query_params/test_filter.py b/tests/server/query_params/test_filter.py index 9b2dfc3c..036754c4 100644 --- a/tests/server/query_params/test_filter.py +++ b/tests/server/query_params/test_filter.py @@ -417,7 +417,7 @@ def test_count_filter(caplog): } # Changing filters' "node_type" shouldn't result in a new QueryBuilder call - filters["node_type"] = {"==": "data.structure.StructureData."} + filters["node_type"] = {"==": "data.core.structure.StructureData."} count_two = STRUCTURES.count(filters=filters) assert "self._count is None" not in caplog.text assert "was not the same as was found in self._count" not in caplog.text @@ -425,7 +425,7 @@ def test_count_filter(caplog): caplog.clear() # _find method is not called, so the updated node_type shouldn't change after # count() - assert filters["node_type"] == {"==": "data.structure.StructureData."} + assert filters["node_type"] == {"==": "data.core.structure.StructureData."} assert count_one == count_two assert STRUCTURES._count == { "count": count_two, diff --git a/tests/static/test_structures.aiida b/tests/static/test_structures.aiida index 796a7a7c..044f920b 100644 Binary files a/tests/static/test_structures.aiida and b/tests/static/test_structures.aiida differ