Merge branch 'master' into ml-evs/validate_meta_schema_field

.github/workflows/cd_release.yml

@@ -25,7 +25,7 @@ jobs:
         fetch-depth: 0
 
     - name: Set up Python 3.8
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v4
       with:
         python-version: 3.8
 
@@ -98,7 +98,7 @@ jobs:
         ref: ${{ env.PUBLISH_UPDATE_BRANCH }}
 
     - name: Set up Python 3.8
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v4
       with:
         python-version: 3.8
 

.github/workflows/ci.yml

@@ -21,7 +21,7 @@ jobs:
     - uses: actions/checkout@v3
 
     - name: Set up Python 3.8
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v4
       with:
         python-version: 3.8
 
@@ -47,7 +47,7 @@ jobs:
         submodules: true
 
     - name: Set up Python 3.8
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v4
       with:
         python-version: 3.8
 
@@ -72,7 +72,7 @@ jobs:
         submodules: true
 
     - name: Set up Python 3.8
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v4
       with:
         python-version: 3.8
 
@@ -178,7 +178,7 @@ jobs:
         fetch-depth: 2
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
@@ -301,7 +301,7 @@ jobs:
       with:
         submodules: true
 
-    - uses: actions/setup-python@v3
+    - uses: actions/setup-python@v4
       with:
         python-version: 3.8
 
@@ -330,7 +330,7 @@ jobs:
       uses: actions/checkout@v3
 
     - name: Set up Python 3.8
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v4
       with:
         python-version: 3.8
 

.github/workflows/ci_cd_updated_master.yml

@@ -45,7 +45,7 @@ jobs:
 
     - name: Set up Python 3.8
       if: env.RELEASE_RUN == 'false'
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v4
       with:
         python-version: 3.8
 

.github/workflows/ci_dependabot.yml

@@ -25,7 +25,7 @@ jobs:
         ref: ${{ env.DEFAULT_REPO_BRANCH }}
 
     - name: Set up Python 3.8
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v4
       with:
         python-version: 3.8
 

.pre-commit-config.yaml

@@ -3,13 +3,13 @@ default_language_version:
 
 repos:
   - repo: https://github.com/ambv/black
-    rev: 22.3.0
+    rev: 22.6.0
     hooks:
     - id: black
       name: Blacken
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.2.0
+    rev: v4.3.0
     hooks:
     - id: check-symlinks
     - id: check-yaml

docs/api_reference/models/baseinfo.md

@@ -1,5 +1,5 @@
 # baseinfo
 
 ::: optimade.models.baseinfo
-    rendering:
+    options:
       show_if_no_docstring: true

docs/api_reference/models/entries.md

@@ -1,5 +1,5 @@
 # entries
 
 ::: optimade.models.entries
-    rendering:
+    options:
       show_if_no_docstring: true

docs/api_reference/models/index_metadb.md

@@ -1,5 +1,5 @@
 # index_metadb
 
 ::: optimade.models.index_metadb
-    rendering:
+    options:
       show_if_no_docstring: true

docs/api_reference/models/jsonapi.md

@@ -1,5 +1,5 @@
 # jsonapi
 
 ::: optimade.models.jsonapi
-    rendering:
+    options:
       show_if_no_docstring: true

docs/api_reference/models/links.md

@@ -1,5 +1,5 @@
 # links
 
 ::: optimade.models.links
-    rendering:
+    options:
       show_if_no_docstring: true

docs/api_reference/models/optimade_json.md

@@ -1,5 +1,5 @@
 # optimade_json
 
 ::: optimade.models.optimade_json
-    rendering:
+    options:
       show_if_no_docstring: true

docs/api_reference/models/references.md

@@ -1,5 +1,5 @@
 # references
 
 ::: optimade.models.references
-    rendering:
+    options:
       show_if_no_docstring: true

docs/api_reference/models/responses.md

@@ -1,5 +1,5 @@
 # responses
 
 ::: optimade.models.responses
-    rendering:
+    options:
       show_if_no_docstring: true

docs/api_reference/models/structures.md

@@ -1,5 +1,5 @@
 # structures
 
 ::: optimade.models.structures
-    rendering:
+    options:
       show_if_no_docstring: true

docs/api_reference/models/utils.md

@@ -1,5 +1,5 @@
 # utils
 
 ::: optimade.models.utils
-    rendering:
+    options:
       show_if_no_docstring: true

docs/api_reference/server/config.md

@@ -1,3 +1,5 @@
 # config
 
 ::: optimade.server.config
+    options:
+      show_if_no_docstring: true

mkdocs.yml

@@ -51,7 +51,7 @@ plugins:
       default_handler: python
       handlers:
         python:
-          rendering:
+          options:
             show_root_heading: false
             show_root_toc_entry: true
             show_root_full_path: true
@@ -62,18 +62,18 @@ plugins:
             show_bases: false
             group_by_category: true
             heading_level: 2
-          selection:
             filters:
               - "!^_[^_]"
               - "!__json_encoder__$"
               - "!__all__$"
               - "!__config__$"
               - "!ValidatorResults$"
-            members: true
-            inherited_members: false
+            members: null
+            # inherited_members: false  # not yet supported
             docstring_style: google
-            docstring_options:
-              replace_admonitions: true
-      watch:
-        - optimade
+            enable_inventory: true
   - awesome-pages
+  - autorefs
+
+watch:
+  - optimade

optimade/adapters/base.py

@@ -115,7 +115,7 @@ def convert(self, format: str) -> Any:
 
     @staticmethod
     def _get_model_attributes(
-        starting_instances: Union[Tuple[BaseModel], List[BaseModel]], name: str
+        starting_instances: Union[Tuple[BaseModel, ...], List[BaseModel]], name: str
     ) -> Any:
         """Helper method for retrieving the OPTIMADE model's attribute, supporting "."-nested attributes"""
         for res in starting_instances:

optimade/adapters/structures/utils.py

@@ -295,7 +295,7 @@ def _pad_iter_of_iters(
 def pad_cell(
     lattice_vectors: Tuple[Vector3D, Vector3D, Vector3D],
     padding: Optional[float] = None,
-) -> Tuple[Tuple[Vector3D, Vector3D, Vector3D], bool]:
+) -> tuple:  # Setting this properly makes MkDocs fail.
     """Turn any `null`/`None` values into a `float` in given `tuple` of
     [`lattice_vectors`][optimade.models.structures.StructureResourceAttributes.lattice_vectors].
 

optimade/models/utils.py

@@ -3,11 +3,15 @@
 import re
 import itertools
 from enum import Enum
-from typing import Optional
+from typing import Optional, TYPE_CHECKING
 
 from pydantic import Field
 from pydantic.fields import FieldInfo
 
+if TYPE_CHECKING:  # pragma: no cover
+    from typing import Any
+
+
 _PYDANTIC_FIELD_KWARGS = list(inspect.signature(Field).parameters.keys())
 
 __all__ = (
@@ -55,9 +59,9 @@ def StrictPydanticField(*args, **kwargs):
 
 
 def StrictField(
-    *args,
+    *args: "Any",
     description: str = None,
-    **kwargs,
+    **kwargs: "Any",
 ) -> StrictFieldInfo:
     """A wrapper around `pydantic.Field` that does the following:
 

optimade/server/entry_collections/entry_collections.py

@@ -108,12 +108,12 @@ def insert(self, data: List[EntryResource]) -> None:
         """
 
     @abstractmethod
-    def count(self, **kwargs) -> int:
+    def count(self, **kwargs: Any) -> int:
         """Returns the number of entries matching the query specified
         by the keyword arguments.
 
         Parameters:
-            kwargs (dict): Query parameters as keyword arguments.
+            **kwargs: Query parameters as keyword arguments.
 
         """
 
@@ -160,12 +160,13 @@ def find(
 
         bad_optimade_fields = set()
         bad_provider_fields = set()
+        supported_prefixes = self.resource_mapper.SUPPORTED_PREFIXES
+        all_attributes = self.resource_mapper.ALL_ATTRIBUTES
         for field in include_fields:
-            if field not in self.resource_mapper.ALL_ATTRIBUTES:
+            if field not in all_attributes:
                 if field.startswith("_"):
                     if any(
-                        field.startswith(f"_{prefix}_")
-                        for prefix in self.resource_mapper.SUPPORTED_PREFIXES
+                        field.startswith(f"_{prefix}_") for prefix in supported_prefixes
                     ):
                         bad_provider_fields.add(field)
                 else:

optimade/server/entry_collections/mongo.py

@@ -70,12 +70,12 @@ def __len__(self) -> int:
         """Returns the total number of entries in the collection."""
         return self.collection.estimated_document_count()
 
-    def count(self, **kwargs) -> int:
+    def count(self, **kwargs: Any) -> int:
         """Returns the number of entries matching the query specified
         by the keyword arguments.
 
         Parameters:
-            kwargs (dict): Query parameters as keyword arguments. The keys
+            **kwargs: Query parameters as keyword arguments. The keys
                 'filter', 'skip', 'limit', 'hint' and 'maxTimeMS' will be passed
                 to the `pymongo.collection.Collection.count_documents` method.
 

optimade/server/routers/landing.py

@@ -26,7 +26,7 @@ def render_landing_page(url: str) -> HTMLResponse:
         web safe before inclusion in the template.
 
     """
-    meta = meta_values(url, 1, 1, more_data_available=False)
+    meta = meta_values(url, 1, 1, more_data_available=False, schema=CONFIG.schema_url)
     major_version = __api_version__.split(".")[0]
     versioned_url = f"{get_base_url(url)}/v{major_version}/"
 

optimade/utils.py

@@ -3,8 +3,10 @@
 
 """
 
+import json
 from typing import List, Iterable
 
+from pydantic import ValidationError
 from optimade.models.links import LinksResource
 
 PROVIDER_LIST_URLS = (
@@ -37,7 +39,8 @@ def get_providers(add_mongo_id: bool = False) -> list:
        `/links`-endpoint.
 
     Arguments:
-        Whether to populate the `_id` field of the provider with MongoDB ObjectID.
+        add_mongo_id: Whether to populate the `_id` field of the provider with MongoDB
+            ObjectID.
 
     Returns:
         List of raw JSON-decoded providers including MongoDB object IDs.
@@ -127,15 +130,21 @@ def get_child_database_links(
     links_endp = base_url + "/v1/links"
     try:
         links = requests.get(links_endp, timeout=10)
-    except requests.ConnectionError as exc:
+    except (requests.ConnectionError, requests.Timeout) as exc:
         raise RuntimeError(f"Unable to connect to provider {provider['id']}") from exc
 
     if links.status_code != 200:
         raise RuntimeError(
             f"Invalid response from {links_endp} for provider {provider['id']}: {links.content}."
         )
 
-    links = LinksResponse(**links.json())
+    try:
+        links = LinksResponse(**links.json())
+    except (ValidationError, json.JSONDecodeError) as exc:
+        raise RuntimeError(
+            f"Did not understand response from {provider['id']}: {links.content}"
+        ) from exc
+
     return [
         link
         for link in links.data

requirements-client.txt

@@ -3,5 +3,5 @@ aiida-core==2.0.1;python_version>='3.8'
 ase==3.22.1
 jarvis-tools==2022.5.20
 numpy==1.21.5;python_version<'3.8'
-numpy==1.22.4;python_version>='3.8'
+numpy==1.23.0;python_version>='3.8'
 pymatgen==2022.0.16

requirements-dev.txt

@@ -3,7 +3,7 @@ codecov==2.1.12
 invoke==1.7.1
 jsondiff==2.0.0
 pre-commit==2.19.0
-pylint==2.13.9
+pylint==2.14.3
 pytest==7.1.2
 pytest-cov==3.0.0
 pytest-httpx==0.21.0

requirements-docs.txt

@@ -1,6 +1,7 @@
+griffe==0.21 # Currently mkdocstrings-python does not pin a griffe version, but it is quite flaky...
 markupsafe==2.0.1 # Can be removed once aiida supports Jinja2>=3, see pallets/markupsafe#284
 mike==1.1.2
 mkdocs==1.3.0
 mkdocs-awesome-pages-plugin==2.7.0
-mkdocs-material==8.2.16
-mkdocstrings==0.18.1
+mkdocs-material==8.3.8
+mkdocstrings[python]==0.19.0

requirements.txt

@@ -6,6 +6,6 @@ mongomock==4.0.0
 pydantic==1.9.1
 pymongo==4.1.1
 pyyaml==5.4
-requests==2.27.1
+requests==2.28.0
 typing-extensions==4.0.0;python_version<'3.8'
-uvicorn==0.17.6
+uvicorn==0.18.1