Update dependencies

.ci/aiida-version.json

@@ -1,6 +1,6 @@
 {
   "schemaVersion": 1,
   "label": "AiiDA",
-  "message": "v2.0.4",
+  "message": "v2.1.2",
   "color": "brightgreen"
 }

.github/aiida/setup_aiida.sh

@@ -4,10 +4,10 @@ set -ev
 # Replace the placeholders in configuration files with actual values
 CONFIG="${GITHUB_WORKSPACE}/.github/aiida"
 sed -i "s|PLACEHOLDER_BACKEND|${AIIDA_TEST_BACKEND}|" "${CONFIG}/profile.yaml"
-sed -i "s|PLACEHOLDER_PROFILE|test_${AIIDA_TEST_BACKEND}|" "${CONFIG}/profile.yaml"
-sed -i "s|PLACEHOLDER_DATABASE_NAME|test_${AIIDA_TEST_BACKEND}|" "${CONFIG}/profile.yaml"
-sed -i "s|PLACEHOLDER_REPOSITORY|/tmp/test_repository_test_${AIIDA_TEST_BACKEND}/|" "${CONFIG}/profile.yaml"
+sed -i "s|PLACEHOLDER_PROFILE|test_${AIIDA_TEST_BACKEND#core.}|" "${CONFIG}/profile.yaml"
+sed -i "s|PLACEHOLDER_DATABASE_NAME|test_${AIIDA_TEST_BACKEND#core.}|" "${CONFIG}/profile.yaml"
+sed -i "s|PLACEHOLDER_REPOSITORY|/tmp/test_repository_test_${AIIDA_TEST_BACKEND#core.}/|" "${CONFIG}/profile.yaml"
 
 verdi setup --config "${CONFIG}/profile.yaml"
 
-verdi profile setdefault test_${AIIDA_TEST_BACKEND}
+verdi profile setdefault test_${AIIDA_TEST_BACKEND#core.}

.github/workflows/ci_tests.yml

@@ -46,7 +46,6 @@ jobs:
             fail-fast: false
             matrix:
                 python-version: ['3.8', '3.9', '3.10']
-                backend: [psql_dos]
 
         services:
             mongo:
@@ -56,7 +55,7 @@ jobs:
             postgres:
                 image: postgres:12
                 env:
-                    POSTGRES_DB: test_${{ matrix.backend }}
+                    POSTGRES_DB: test_psql_dos
                     POSTGRES_PASSWORD: test
                 options: >-
                     --health-cmd pg_isready
@@ -66,6 +65,11 @@ jobs:
                 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@v3
               with:
@@ -83,30 +87,18 @@ jobs:
                   pip install -e .[testing]
 
             - name: Setup up environment for AiiDA
-              env:
-                  AIIDA_TEST_BACKEND: ${{ matrix.backend }}
               run: .github/aiida/setup_aiida.sh
 
             - name: Test with pytest (AiiDA)
-              env:
-                  AIIDA_TEST_BACKEND: ${{ matrix.backend }}
-                  AIIDA_TEST_PROFILE: test_${{ matrix.backend }}
-                  AIIDA_PROFILE: test_${{ matrix.backend }}
               run: pytest -v --cov=./aiida_optimade/ --cov-report=xml --durations=20
 
             - name: Test with pytest (Data Curation)
               env:
-                  AIIDA_TEST_BACKEND: ${{ matrix.backend }}
-                  AIIDA_TEST_PROFILE: test_${{ matrix.backend }}
-                  AIIDA_PROFILE: test_${{ matrix.backend }}
                   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:
-                  AIIDA_TEST_BACKEND: ${{ matrix.backend }}
-                  AIIDA_TEST_PROFILE: test_${{ matrix.backend }}
-                  AIIDA_PROFILE: test_${{ matrix.backend }}
                   PYTEST_OPTIMADE_CONFIG_FILE: ./tests/static/test_mongo_config.json
                   OPTIMADE_MONGO_URI: mongodb://localhost:27017
                   OPTIMADE_DATABASE_BACKEND: mongodb
@@ -178,7 +170,7 @@ jobs:
 
             - name: Setup up environment for AiiDA
               env:
-                  AIIDA_TEST_BACKEND: psql_dos
+                  AIIDA_TEST_BACKEND: core.psql_dos
               run: .github/aiida/setup_aiida.sh
 
             - name: Load test data
@@ -251,7 +243,7 @@ jobs:
 
             - name: Setup up environment for AiiDA
               env:
-                  AIIDA_TEST_BACKEND: psql_dos
+                  AIIDA_TEST_BACKEND: core.psql_dos
               run: .github/aiida/setup_aiida.sh
 
             - name: Load test data (AiiDA)
@@ -320,7 +312,7 @@ jobs:
 
             - name: Setup up environment for AiiDA
               env:
-                  AIIDA_TEST_BACKEND: psql_dos
+                  AIIDA_TEST_BACKEND: core.psql_dos
               run: .github/aiida/setup_aiida.sh
 
             - name: Build docker image

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 ---
 repos:
     - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.3.0
+      rev: v4.4.0
       hooks:
           - id: trailing-whitespace
             args: [--markdown-linebreak-ext=md]
@@ -33,7 +33,7 @@ repos:
             language: system
 
     - repo: https://github.com/pycqa/flake8
-      rev: 5.0.4
+      rev: 6.0.0
       hooks:
           - id: flake8
 

Dockerfile

@@ -4,7 +4,7 @@ WORKDIR /app
 
 # Install specific optimade and aiida-core versions
 ARG OPTIMADE_TOOLS_VERSION=0.19.4
-ARG AIIDA_VERSION=2.0.4
+ARG AIIDA_VERSION=2.1.2
 
 # Copy repo contents
 COPY setup.py setup.json README.md requirements*.txt ./

aiida_optimade/cli/cmd_aiida_optimade.py

@@ -1,20 +1,27 @@
 import os
 from pathlib import Path
+from typing import TYPE_CHECKING
 
 import click
-from aiida.cmdline.params.options import PROFILE as VERDI_PROFILE
+from aiida.cmdline.groups import VerdiCommandGroup
+from aiida.cmdline.params.options import PROFILE as AIIDA_PROFILE
 from aiida.cmdline.params.types import ProfileParamType as VerdiProfileParamType
-from aiida.manage.configuration import Profile, get_config
 
 from aiida_optimade.cli.options import AIIDA_PROFILES
 from aiida_optimade.cli.utils import AIIDA_OPTIMADE_TEST_PROFILE
 
+if TYPE_CHECKING:  # pragma: no cover
+    from aiida.cmdline.groups.verdi import VerdiContext
+    from aiida.manage.configuration import Profile
 
-@click.group(context_settings={"help_option_names": ["-h", "--help"]})
+
+@click.command(
+    cls=VerdiCommandGroup, context_settings={"help_option_names": ["-h", "--help"]}
+)
 @click.version_option(
     None, "-v", "--version", message="AiiDA-OPTIMADE version %(version)s"
 )
-@VERDI_PROFILE(
+@AIIDA_PROFILE(
     type=VerdiProfileParamType(),
     default="optimade",
     show_default=True,
@@ -30,17 +37,14 @@
     "profile and `--debug` options).",
 )
 @click.pass_context
-def cli(ctx, profile: Profile, dev: bool):  # pragma: no cover
+def cli(ctx: "VerdiContext", profile: "Profile", dev: bool):  # pragma: no cover
     """AiiDA-OPTIMADE command line interface (CLI)."""
 
-    if ctx.obj is None:
-        ctx.obj = {}
-
     if dev:
-        profile = get_config(create=True).get_profile(AIIDA_OPTIMADE_TEST_PROFILE)
+        profile = ctx.obj.config.get_profile(AIIDA_OPTIMADE_TEST_PROFILE)
 
-    ctx.obj["profile"] = profile
-    ctx.obj["dev"] = dev
+    ctx.obj.profile = profile
+    ctx.obj.dev = dev
 
     # Set config
     if (

aiida_optimade/cli/cmd_calc.py

@@ -1,12 +1,17 @@
 # pylint: disable=protected-access,too-many-locals,too-many-branches
-from typing import Tuple
+from typing import TYPE_CHECKING
 
 import click
 from tqdm import tqdm
 
 from aiida_optimade.cli.cmd_aiida_optimade import cli
 from aiida_optimade.common.logger import LOGGER, disable_logging
 
+if TYPE_CHECKING:  # pragma: no cover
+    from typing import Tuple
+
+    from aiida.common.extendeddicts import AttributeDict
+
 
 @cli.command()
 @click.argument(
@@ -35,7 +40,7 @@
     help="Suppress informational output.",
 )
 @click.pass_obj
-def calc(obj: dict, fields: Tuple[str], force_yes: bool, silent: bool):
+def calc(obj: "AttributeDict", fields: "Tuple[str]", force_yes: bool, silent: bool):
     """Calculate OPTIMADE fields in the AiiDA database."""
     from aiida import load_profile
     from aiida.cmdline.utils import echo
@@ -45,7 +50,7 @@ def calc(obj: dict, fields: Tuple[str], force_yes: bool, silent: bool):
     echo.CMDLINE_LOGGER.setLevel("INFO")
 
     try:
-        profile: str = obj.get("profile").name
+        profile: str = obj.profile.name
     except AttributeError:
         profile = None
     profile = load_profile(profile).name

aiida_optimade/cli/cmd_init.py

@@ -1,13 +1,18 @@
 # pylint: disable=protected-access,too-many-statements
 from pathlib import Path
-from typing import IO, Generator, Iterator, List, Union
+from typing import TYPE_CHECKING
 
 import click
 from tqdm import tqdm
 
 from aiida_optimade.cli.cmd_aiida_optimade import cli
 from aiida_optimade.common.logger import LOGGER, disable_logging
 
+if TYPE_CHECKING:  # pragma: no cover
+    from typing import IO, Generator, Iterator, List, Union
+
+    from aiida.common.extendeddicts import AttributeDict
+
 
 @cli.command()
 @click.option(
@@ -43,7 +48,7 @@
     help="Filename to load as database (currently only usable for MongoDB).",
 )
 @click.pass_obj
-def init(obj: dict, force: bool, silent: bool, mongo: bool, filename: str):
+def init(obj: "AttributeDict", force: bool, silent: bool, mongo: bool, filename: str):
     """Initialize an AiiDA database to be served with AiiDA-OPTIMADE."""
     from aiida import load_profile
     from aiida.cmdline.utils import echo
@@ -58,7 +63,7 @@ def init(obj: dict, force: bool, silent: bool, mongo: bool, filename: str):
         profile = f"MongoDB JSON file {filename.name}"
     else:
         try:
-            profile: str = obj.get("profile").name
+            profile: str = obj.profile.name
         except AttributeError:
             profile = None
         profile = load_profile(profile).name
@@ -221,8 +226,8 @@ def init(obj: dict, force: bool, silent: bool, mongo: bool, filename: str):
 
 
 def read_chunks(
-    file_object: IO, chunk_size: int = None
-) -> Generator[Union[str, bytes], None, None]:
+    file_object: "IO", chunk_size: int = None
+) -> "Generator[Union[str, bytes], None, None]":
     """Generator to read a file piece by piece
 
     Parameters:
@@ -243,8 +248,8 @@ def read_chunks(
 
 
 def get_documents(
-    chunk_iterator: Union[Generator[str, None, None], Iterator[str]]
-) -> Generator[List[dict], None, None]:
+    chunk_iterator: "Union[Generator[str, None, None], Iterator[str]]",
+) -> "Generator[List[dict], None, None]":
     """Generator to return MongoDB documents from file"""
     rest_chunk = ""
 

aiida_optimade/cli/cmd_run.py

@@ -1,9 +1,14 @@
 # pylint: disable=too-many-arguments
+from typing import TYPE_CHECKING
+
 import click
 
 from aiida_optimade.cli.cmd_aiida_optimade import cli
 from aiida_optimade.cli.options import LOGGING_LEVELS
 
+if TYPE_CHECKING:  # pragma: no cover
+    from aiida.common.extendeddicts import AttributeDict
+
 
 @cli.command()
 @click.option(
@@ -43,13 +48,20 @@
     help="Enable auto-reload. Note, if --debug is set, this will also be set to True.",
 )
 @click.pass_obj
-def run(obj: dict, log_level: str, debug: bool, host: str, port: int, reload: bool):
+def run(
+    obj: "AttributeDict",
+    log_level: str,
+    debug: bool,
+    host: str,
+    port: int,
+    reload: bool,
+):
     """Run AiiDA-OPTIMADE server."""
     import os
 
     import uvicorn
 
-    if obj.get("dev", False):
+    if getattr(obj, "dev", False):
         debug = True
 
     log_level = log_level.lower()
@@ -70,7 +82,7 @@ def run(obj: dict, log_level: str, debug: bool, host: str, port: int, reload: bo
         from aiida import load_profile
 
         try:
-            profile: str = obj.get("profile").name
+            profile: str = obj.profile.name
         except AttributeError:
             profile = None
         profile_name: str = load_profile(profile).name
@@ -82,5 +94,4 @@ def run(obj: dict, log_level: str, debug: bool, host: str, port: int, reload: bo
         host=host,
         port=port,
         log_level=log_level,
-        debug=debug,
     )

aiida_optimade/cli/utils.py

@@ -1,12 +1,15 @@
-from typing import List
+from typing import TYPE_CHECKING
 
 from aiida.common.exceptions import ConfigurationError, MissingConfigurationError
 from aiida.manage.configuration import get_config
 
+if TYPE_CHECKING:  # pragma: no cover
+    from typing import List
+
 AIIDA_OPTIMADE_TEST_PROFILE = "aiida-optimade_test"
 
 
-def get_aiida_profiles() -> List[str]:
+def get_aiida_profiles() -> "List[str]":
     """Retrieve list of configured AiiDA profiles"""
 
     try:

profiles/docker-compose-mongo.j2

@@ -11,7 +11,7 @@ services:
       dockerfile: Dockerfile
       args:
         OPTIMADE_TOOLS_VERSION: 0.19.4
-        AIIDA_VERSION: 2.0.4
+        AIIDA_VERSION: 2.1.2
         CONFIG_FILE: aiida_optimade/config.json
     environment:
       AIIDA_PATH: /app

profiles/docker-compose-mongo.yml

@@ -12,7 +12,7 @@ services:
             dockerfile: Dockerfile
             args:
                 OPTIMADE_TOOLS_VERSION: 0.19.4
-                AIIDA_VERSION: 2.0.4
+                AIIDA_VERSION: 2.1.2
                 CONFIG_FILE: aiida_optimade/config.json
         environment:
             AIIDA_PATH: /app

profiles/docker-compose.j2

@@ -9,7 +9,7 @@ services:
       dockerfile: Dockerfile
       args:
         OPTIMADE_TOOLS_VERSION: 0.19.4
-        AIIDA_VERSION: 2.0.4
+        AIIDA_VERSION: 2.1.2
         CONFIG_FILE: aiida_optimade/config.json
     environment:
       AIIDA_PATH: /app

profiles/docker-compose.yml

@@ -10,7 +10,7 @@ services:
             dockerfile: Dockerfile
             args:
                 OPTIMADE_TOOLS_VERSION: 0.19.4
-                AIIDA_VERSION: 2.0.4
+                AIIDA_VERSION: 2.1.2
                 CONFIG_FILE: aiida_optimade/config.json
         environment:
             AIIDA_PATH: /app