Temp: Use pylint

.github/mongo/load_data.py

@@ -8,8 +8,11 @@
 client = MongoClient("mongodb://localhost:27017")
 collection = client["aiida_optimade"]["structures"]
 
-with open(Path(__file__).parent.joinpath("test_structures_mongo.json")) as handle:
-    data = bson.json_util.loads(handle.read())
+data = bson.json_util.loads(
+    Path(__file__)
+    .parent.joinpath("test_structures_mongo.json")
+    .read_text(encoding="utf8")
+)
 
 try:
     print(f"Inserting {len(data)} structures into {collection.full_name}")

.pre-commit-config.yaml

@@ -29,7 +29,6 @@ repos:
   rev: 22.10.0
   hooks:
   - id: black
-    name: Blacken
 
 - repo: local
   hooks:
@@ -42,3 +41,25 @@ repos:
         .codecov.yml
       )$
     language: system
+  - id: pylint
+    name: pylint
+    entry: pylint
+    args:
+    - --rcfile=pyproject.toml
+    - --extension-pkg-whitelist='pydantic'
+    language: python
+    types: [python]
+    require_serial: true
+    files: ^.*$
+    exclude: ^tests/.*$
+  - id: pylint-tests
+    name: pylint - tests
+    entry: pylint
+    args:
+    - --rcfile=pyproject.toml
+    - --extension-pkg-whitelist='pydantic'
+    - --disable=import-outside-toplevel,redefined-outer-name
+    language: python
+    types: [python]
+    require_serial: true
+    files: ^tests/.*$

aiida_optimade/cli/cmd_calc.py

@@ -1,7 +1,10 @@
 # pylint: disable=protected-access,too-many-locals,too-many-branches
+import traceback
 from typing import Tuple
 
 import click
+from aiida import load_profile
+from aiida.cmdline.utils import echo
 from tqdm import tqdm
 
 from aiida_optimade.cli.cmd_aiida_optimade import cli
@@ -35,11 +38,10 @@
     help="Suppress informational output.",
 )
 @click.pass_obj
-def calc(obj: dict, fields: Tuple[str], force_yes: bool, silent: bool):
+def calc(
+    obj: dict, fields: Tuple[str], force_yes: bool, silent: bool
+):  # pylint: disable=too-many-statements
     """Calculate OPTIMADE fields in the AiiDA database."""
-    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")
@@ -52,6 +54,7 @@ def calc(obj: dict, fields: Tuple[str], force_yes: bool, silent: bool):
 
     try:
         with disable_logging():
+            # pylint: disable=import-outside-toplevel
             from aiida_optimade.routers.structures import STRUCTURES
 
         extras_key = STRUCTURES.resource_mapper.PROJECT_PREFIX.split(".")[1]
@@ -139,8 +142,6 @@ def calc(obj: dict, fields: Tuple[str], force_yes: bool, silent: bool):
         echo.echo_warning("Aborted!")
         return
     except Exception as exc:  # pylint: disable=broad-except
-        import traceback
-
         exception = traceback.format_exc()
 
         LOGGER.error("Full exception from 'aiida-optimade calc' CLI:\n%s", exception)

aiida_optimade/cli/cmd_init.py

@@ -1,8 +1,12 @@
 # pylint: disable=protected-access,too-many-statements
+import traceback
 from pathlib import Path
 from typing import IO, Generator, Iterator, List, Union
 
+import bson.json_util
 import click
+from aiida import load_profile
+from aiida.cmdline.utils import echo
 from tqdm import tqdm
 
 from aiida_optimade.cli.cmd_aiida_optimade import cli
@@ -43,11 +47,10 @@
     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: dict, force: bool, silent: bool, mongo: bool, filename: str
+):  # pylint: disable=too-many-locals,too-many-branches
     """Initialize an AiiDA database to be served with AiiDA-OPTIMADE."""
-    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")
@@ -65,6 +68,7 @@ def init(obj: dict, force: bool, silent: bool, mongo: bool, filename: str):
 
     try:
         with disable_logging():
+            # pylint: disable=import-outside-toplevel
             from aiida_optimade.routers.structures import STRUCTURES
 
             if mongo:
@@ -136,8 +140,6 @@ def init(obj: dict, force: bool, silent: bool, mongo: bool, filename: str):
                     "Passing a filename currently only works for a MongoDB backend"
                 )
 
-            import bson.json_util
-
             updated_pks = range(len(STRUCTURES_MONGO))
             chunk_size = 2**24  # 16 MB
 
@@ -148,7 +150,7 @@ def init(obj: dict, force: bool, silent: bool, mongo: bool, filename: str):
                     "consider using --force to first drop the collection, if possible."
                 )
 
-            with open(filename, "r") as handle:
+            with open(filename, "r", encoding="utf8") as handle:
                 if silent:
                     all_chunks = read_chunks(handle, chunk_size=chunk_size)
                 else:
@@ -196,8 +198,6 @@ def init(obj: dict, force: bool, silent: bool, mongo: bool, filename: str):
                 entries=entries if mongo else None,
             )
     except Exception as exc:  # pylint: disable=broad-except
-        import traceback
-
         exception = traceback.format_exc()
 
         LOGGER.error("Full exception from 'aiida-optimade init' CLI:\n%s", exception)

aiida_optimade/cli/cmd_run.py

@@ -1,5 +1,9 @@
 # pylint: disable=too-many-arguments
+import os
+
 import click
+import uvicorn
+from aiida import load_profile
 
 from aiida_optimade.cli.cmd_aiida_optimade import cli
 from aiida_optimade.cli.options import LOGGING_LEVELS
@@ -45,10 +49,6 @@
 @click.pass_obj
 def run(obj: dict, log_level: str, debug: bool, host: str, port: int, reload: bool):
     """Run AiiDA-OPTIMADE server."""
-    import os
-
-    import uvicorn
-
     if obj.get("dev", False):
         debug = True
 
@@ -67,8 +67,6 @@ def run(obj: dict, log_level: str, debug: bool, host: str, port: int, reload: bo
     os.environ["AIIDA_OPTIMADE_LOG_LEVEL"] = log_level.upper()
 
     if os.getenv("AIIDA_PROFILE") is None:
-        from aiida import load_profile
-
         try:
             profile: str = obj.get("profile").name
         except AttributeError:

aiida_optimade/config.py

@@ -5,10 +5,17 @@
 
 
 class CustomServerConfig(ServerConfig):
+    """Custom AiiDA-OPTIMADE server config.
+
+    This extends the server config class from the OPTIMADE Python server.
+    """
 
     query_group: Optional[str] = Field(
         None,
-        description="The AiiDA Group containing the data that will be served, allowing one to serve a curated set of data from a given database.",
+        description=(
+            "The AiiDA Group containing the data that will be served, allowing one to "
+            "serve a curated set of data from a given database."
+        ),
     )
 
 

aiida_optimade/entry_collections.py

@@ -1,4 +1,5 @@
 import warnings
+from copy import deepcopy
 from typing import Any, Dict, List, Optional, Set, Tuple, Union
 
 from aiida.orm import Group
@@ -96,7 +97,7 @@ def set_data_returned(self, **criteria):
             and criteria.get("filters", {}) != self._latest_filter
         ):
             for key in ["limit", "offset"]:
-                if key in list(criteria.keys()):
+                if key in list(criteria):
                     del criteria[key]
             self._latest_filter = criteria.get("filters", {}).copy()
             LOGGER.debug("Setting data_returned using filter: %s", self._latest_filter)
@@ -130,7 +131,7 @@ def count(self, **kwargs) -> int:
                 "offset": kwargs.get("offset", None),
             }
         else:
-            for limiting_param in {"filters", "limit", "offset"}:
+            for limiting_param in ["filters", "limit", "offset"]:
                 if kwargs.get(limiting_param, None) != self._count.get(
                     limiting_param, None
                 ):
@@ -438,7 +439,6 @@ def _find_extras_fields(self, filters: Union[dict, list]) -> None:
                 parameter.
 
         """
-        from copy import deepcopy
 
         def __filter_fields_util(  # pylint: disable=unused-private-member
             _filters: Union[dict, list]

aiida_optimade/main.py

@@ -1,3 +1,4 @@
+# pylint: disable=ungrouped-imports
 import json
 import os
 import warnings
@@ -117,46 +118,47 @@ async def startup():
     LOGGER.info("AiiDA Profile: %s", profile_name)
 
     # Load links
-    with open(Path(__file__).parent.joinpath("data/links.json").resolve()) as handle:
-        data = json.load(handle)
-
-        if CONFIG.debug:
-            data.append(
-                {
-                    "id": "local",
-                    "type": "links",
-                    "name": "Local server",
-                    "description": (
-                        "Locally running instance of the AiiDA-OPTIMADE server using "
-                        f"AiiDA profile {profile_name!r}."
-                    ),
-                    "base_url": "http://localhost:5000",
-                    "homepage": "https://github.com/aiidateam/aiida-optimade",
-                    "link_type": "child",
-                }
-            )
+    data = json.loads(
+        Path(__file__).parent.joinpath("data/links.json").resolve().read_bytes()
+    )
 
-        processed = []
-        for link in data:
-            link["_id"] = {"$oid": mongo_id_for_database(link["id"], link["type"])}
-            processed.append(link)
-
-        LOGGER.info("Loading links")
-        if CONFIG.database_backend == SupportedBackend.MONGODB:
-            LOGGER.info("  Using real MongoDB.")
-            if links.LINKS.count(
-                filter={"id": {"$in": [_["id"] for _ in processed]}}
-            ) != len(links.LINKS):
-                LOGGER.info(
-                    "  Will drop and reinsert links data in %s",
-                    links.LINKS.collection.full_name,
-                )
-                links.LINKS.collection.drop()
-                links.LINKS.collection.insert_many(
-                    bson.json_util.loads(bson.json_util.dumps(processed)),
-                )
-        else:
-            LOGGER.info("  Using mock MongoDB.")
+    if CONFIG.debug:
+        data.append(
+            {
+                "id": "local",
+                "type": "links",
+                "name": "Local server",
+                "description": (
+                    "Locally running instance of the AiiDA-OPTIMADE server using "
+                    f"AiiDA profile {profile_name!r}."
+                ),
+                "base_url": "http://localhost:5000",
+                "homepage": "https://github.com/aiidateam/aiida-optimade",
+                "link_type": "child",
+            }
+        )
+
+    processed = []
+    for link in data:
+        link["_id"] = {"$oid": mongo_id_for_database(link["id"], link["type"])}
+        processed.append(link)
+
+    LOGGER.info("Loading links")
+    if CONFIG.database_backend == SupportedBackend.MONGODB:
+        LOGGER.info("  Using real MongoDB.")
+        if links.LINKS.count(
+            filter={"id": {"$in": [_["id"] for _ in processed]}}
+        ) != len(links.LINKS):
+            LOGGER.info(
+                "  Will drop and reinsert links data in %s",
+                links.LINKS.collection.full_name,
+            )
+            links.LINKS.collection.drop()
             links.LINKS.collection.insert_many(
                 bson.json_util.loads(bson.json_util.dumps(processed)),
             )
+    else:
+        LOGGER.info("  Using mock MongoDB.")
+        links.LINKS.collection.insert_many(
+            bson.json_util.loads(bson.json_util.dumps(processed)),
+        )

aiida_optimade/mappers/entries.py

@@ -37,7 +37,9 @@ def all_aliases(cls) -> Tuple[Tuple[str, str]]:
         )
 
     @classmethod
-    def map_back(cls, entity_properties: Dict[str, Any]) -> dict:
+    def map_back(  # pylint: disable=arguments-renamed
+        cls, entity_properties: Dict[str, Any]
+    ) -> dict:
         """Map properties from AiiDA to OPTIMADE
 
         Parameters:

aiida_optimade/middleware.py

@@ -1,3 +1,4 @@
+# pylint: disable=too-few-public-methods
 import urllib.parse
 
 from optimade.server.routers.utils import BASE_URL_PREFIXES

aiida_optimade/models/structures.py

@@ -7,11 +7,11 @@
 )
 from pydantic import Field
 
+from aiida_optimade.config import CONFIG
+
 
 def prefix_provider(string: str) -> str:
     """Prefix string with `_{provider}_`"""
-    from optimade.server.config import CONFIG
-
     if string in CONFIG.provider_fields.get("structures", []):
         return f"_{CONFIG.provider.prefix}_{string}"
     return string