Updates to align with OTE v1 changes (#295)

* Add markdownlint-cli2 pre-commit hook

Update pyupgrade args to drop Python 3.9.
Update code base accordingly.

* New workflow to add 'skip_changelog' label to Bot PRs

Remove safety ignore statements.

Use OTEAPI_PLUGIN_PACKAGES instead of overriding entrypoint in CI job.

Try running pytest for Python 3.13.

* Don't get stuck trying to run oteapi service

* Update Docker Compose file

* Change extra name to testing

* Explicitly support Python 3.13

Author: CasperWA

.github/workflows/ci_bot_pr_change.yml

@@ -0,0 +1,45 @@
+name: CI - Update [bot] PR
+
+on:
+  pull_request:
+    types: [opened, reopened]
+    branches:
+      - 'main'
+
+jobs:
+  add_skip_changelog_label:
+    name: Add 'skip_changelog' label
+    runs-on: ubuntu-latest
+
+    if: github.event.pull_request.user.type == 'Bot'
+
+    permissions:
+      contents: read
+      issues: write
+      pull-requests: write
+
+    steps:
+    - name: Add 'skip_changelog' label
+      uses: actions/github-script@v7
+      with:
+        script: |
+          const labels = await github.rest.issues.listLabelsOnIssue({
+            owner: context.repo.owner,
+            repo: context.repo.repo,
+            issue_number: context.issue.number
+          })
+
+          for (const label of labels.data) {
+            if (label.name === 'skip_changelog') {
+              console.log("Label 'skip_changelog' already exists 👌")
+              return  // Skip adding the label if it already exists
+            }
+          }
+
+          await github.rest.issues.addLabels({
+            owner: context.repo.owner,
+            repo: context.repo.repo,
+            issue_number: context.issue.number,
+            labels: ['skip_changelog']
+          })
+          console.log("Label 'skip_changelog' added 🎉")

.github/workflows/ci_tests.yml

@@ -23,12 +23,6 @@ jobs:
       run_pylint: false
 
       run_safety: true
-      # ID: 70612
-      #   Package: Jinja2
-      #   Has been disputed by the maintainer and multiple third parties.
-      #   For more information see: https://github.com/advisories/GHSA-f6pv-j8mr-w6rr
-      safety_options: |
-        --ignore=70612
 
       # Build dist
       python_version_package: "3.10"
@@ -47,7 +41,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
         os:
         - ["ubuntu-latest", "linux"]
         - ["windows-latest", "windows"]
@@ -67,7 +61,7 @@ jobs:
       run: |
         python -m pip install -U pip
         pip install -U setuptools wheel flit
-        pip install -e .[test]
+        pip install -e .[testing]
 
     - name: Test with pytest
       run: pytest -vvv --cov-report=xml
@@ -129,12 +123,11 @@ jobs:
           --env "OTEAPI_REDIS_TYPE=redis" \
           --env "OTEAPI_REDIS_HOST=localhost" \
           --env "OTEAPI_REDIS_PORT=6379" \
-          --env "OTEAPI_PREFIX=${OTEAPI_PREFIX}" \
+          --env OTEAPI_PREFIX \
+          --env "OTEAPI_PLUGIN_PACKAGES=-v -e /oteapi-optimade" \
           --network "host" \
           --volume "${PWD}:/oteapi-optimade" \
-          --entrypoint "" \
-          ghcr.io/emmc-asbl/oteapi:${DOCKER_OTEAPI_VERSION} \
-          /bin/bash -c "pip install -v -e /oteapi-optimade && ./entrypoint.sh" &
+          ghcr.io/emmc-asbl/oteapi:${DOCKER_OTEAPI_VERSION} &
 
         .github/utils/wait_for_it.sh localhost:${OTEAPI_PORT} -t 240
         sleep 5

.markdownlint.yaml

@@ -0,0 +1,12 @@
+# Default state for all rules
+default: true
+
+# MD013/line-length - Line length
+MD013:
+  # Number of characters
+  # Set very long to support 1-sentence-per-line style.
+  line_length: 999
+  # Number of characters for headings (match that of black's default)
+  heading_line_length: 88
+  # Number of characters for code blocks (match that of black's default)
+  code_block_line_length: 88

.pre-commit-config.yaml

@@ -16,6 +16,8 @@ repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v5.0.0
     hooks:
+    - id: check-json
+      name: Check JSON
     - id: check-toml
       name: Check TOML
     - id: check-yaml
@@ -29,11 +31,21 @@ repos:
     - id: trailing-whitespace
       args: [--markdown-linebreak-ext=md]
 
+  - repo: https://github.com/DavidAnson/markdownlint-cli2
+    rev: v0.17.2
+    hooks:
+    - id: markdownlint-cli2
+      name: markdownlint
+      exclude: ^(docs/)?(index|LICENSE|CHANGELOG).md$
+      args:
+      - --fix
+      - --config=.markdownlint.yaml
+
   - repo: https://github.com/asottile/pyupgrade
     rev: v3.19.1
     hooks:
     - id: pyupgrade
-      args: [--py39-plus, --keep-runtime-typing]
+      args: [--py310-plus]
 
   - repo: https://github.com/psf/black
     rev: 25.1.0

compose.yaml

@@ -1,25 +1,20 @@
 services:
   oteapi:
-    image: ghcr.io/emmc-asbl/oteapi:${DOCKER_OTEAPI_VERSION:-latest}
+    image: ghcr.io/emmc-asbl/oteapi:${DOCKER_OTEAPI_VERSION:-latest-dev}
     ports:
       - "${OTEAPI_PORT:-8080}:8080"
     environment:
       OTEAPI_REDIS_TYPE: redis
       OTEAPI_REDIS_HOST: redis
       OTEAPI_REDIS_PORT: 6379
       OTEAPI_PREFIX: "${OTEAPI_PREFIX:-/api/v1}"
-      PATH_TO_OTEAPI_CORE:
       OTEAPI_PLUGIN_PACKAGES: "-v -e /oteapi-optimade"
     depends_on:
       - redis
     networks:
       - otenet
     volumes:
-      - "${PATH_TO_OTEAPI_CORE:-/dev/null}:/oteapi-core"
       - "${PWD}:/oteapi-optimade"
-    entrypoint: |
-      /bin/bash -c "if [ \"${PATH_TO_OTEAPI_CORE}\" != \"/dev/null\" ] && [ -n \"${PATH_TO_OTEAPI_CORE}\" ]; then \
-      pip install -U --force-reinstall -e /oteapi-core; fi && ./entrypoint.sh --reload --debug --log-level debug"
     stop_grace_period: 1s
 
   redis:

oteapi_optimade/_utils.py

@@ -9,13 +9,7 @@
 import dlite
 
 if TYPE_CHECKING:  # pragma: no cover
-    import sys
-    from typing import Any
-
-    if sys.version_info >= (3, 9, 1):
-        from typing import Literal
-    else:
-        from typing_extensions import Literal  # type: ignore[assignment]
+    from typing import Any, Literal
 
 LOGGER = logging.getLogger(__name__)
 

oteapi_optimade/models/config.py

@@ -2,7 +2,7 @@
 
 from __future__ import annotations
 
-from typing import Annotated, Literal, Optional
+from typing import Annotated, Literal
 
 from oteapi.models import AttrDict, DataCacheConfig
 from pydantic import BeforeValidator, Field, field_validator
@@ -22,12 +22,12 @@ class OPTIMADEConfig(AttrDict):
 
     # OTEAPI-specific attributes
     downloadUrl: Annotated[
-        Optional[OPTIMADEUrl],
+        OPTIMADEUrl | None,
         Field(description="Either a base OPTIMADE URL or a full OPTIMADE URL."),
     ] = None
 
     mediaType: Annotated[
-        Optional[Literal["application/vnd.optimade+json", "application/vnd.optimade"]],
+        Literal["application/vnd.optimade+json", "application/vnd.optimade"] | None,
         BeforeValidator(lambda x: x.lower() if isinstance(x, str) else x),
         Field(
             description="The registered strategy name for OPTIMADEParseStrategy.",
@@ -36,7 +36,7 @@ class OPTIMADEConfig(AttrDict):
 
     # OPTIMADE parse result attributes
     optimade_config: Annotated[
-        Optional[OPTIMADEConfig],
+        OPTIMADEConfig | None,
         Field(description="A pre-existing instance of this OPTIMADE configuration."),
     ] = None
 
@@ -57,7 +57,7 @@ class OPTIMADEConfig(AttrDict):
     ] = "structures"
 
     query_parameters: Annotated[
-        Optional[OPTIMADEQueryParameters],
+        OPTIMADEQueryParameters | None,
         Field(
             description="URL query parameters to be used in the OPTIMADE query.",
         ),
@@ -108,7 +108,7 @@ class OPTIMADEDLiteConfig(OPTIMADEConfig):
 
     # OTEAPI-specific attributes
     mediaType: Annotated[
-        Optional[Literal["application/vnd.optimade+dlite"]],
+        Literal["application/vnd.optimade+dlite"] | None,
         BeforeValidator(lambda x: x.lower() if isinstance(x, str) else x),
         Field(
             description="The registered strategy name for OPTIMADEDLiteParseStrategy.",
@@ -117,6 +117,6 @@ class OPTIMADEDLiteConfig(OPTIMADEConfig):
 
     # Dlite specific attributes
     collection_id: Annotated[
-        Optional[str],
+        str | None,
         Field(description="A reference to a DLite Collection."),
     ] = None

oteapi_optimade/models/custom_types.py

@@ -22,7 +22,7 @@
 from pydantic_core import Url, core_schema
 
 if TYPE_CHECKING:  # pragma: no cover
-    from typing import Any, Optional, TypedDict, Union
+    from typing import Any, TypedDict
 
     from pydantic import GetCoreSchemaHandler, GetJsonSchemaHandler
     from pydantic.json_schema import JsonSchemaValue
@@ -91,10 +91,10 @@ def __init__(
         self,
         url: str,
         *,
-        base_url: Optional[str] = None,
-        version: Optional[str] = None,
-        endpoint: Optional[str] = None,
-        query: Optional[str] = None,
+        base_url: str | None = None,
+        version: str | None = None,
+        endpoint: str | None = None,
+        query: str | None = None,
     ) -> None:
         str.__init__(url)
 
@@ -115,7 +115,7 @@ def __init__(
                 pydantic_url = None
 
         # Build OPTIMADE URL parts
-        optimade_parts: Union[OPTIMADEParts, dict[str, Any]] = {}
+        optimade_parts: OPTIMADEParts | dict[str, Any] = {}
         if pydantic_url:
             optimade_parts = self._build_optimade_parts(pydantic_url)
 
@@ -145,9 +145,9 @@ def __repr__(self) -> str:
     def _build(
         *,
         base_url: str,
-        version: Optional[str] = None,
-        endpoint: Optional[str] = None,
-        query: Optional[str] = None,
+        version: str | None = None,
+        endpoint: str | None = None,
+        query: str | None = None,
     ) -> str:
         """Build complete OPTIMADE URL from URL parts."""
         url = base_url.rstrip("/")
@@ -176,21 +176,21 @@ def base_url(self) -> str:
         return self._base_url
 
     @property
-    def version(self) -> Optional[str]:
+    def version(self) -> str | None:
         """The version part of the OPTIMADE URL."""
         return self._version
 
     @property
-    def endpoint(self) -> Optional[str]:
+    def endpoint(self) -> str | None:
         """The endpoint part of the OPTIMADE URL."""
         return self._endpoint
 
     @property
-    def query(self) -> Optional[str]:
+    def query(self) -> str | None:
         """The query part of the OPTIMADE URL."""
         return self._query
 
-    def response_model(self) -> Union[tuple[Success, Success], Success, None]:
+    def response_model(self) -> tuple[Success, Success] | Success | None:
         """Return the endpoint's corresponding response model(s) (from OPT)."""
         if not self.endpoint or self.endpoint == "versions":
             return None
@@ -265,7 +265,7 @@ def __get_pydantic_json_schema__(
         )
 
     @classmethod
-    def _validate_from_str_or_url(cls, value: Union[Url, str]) -> OPTIMADEUrl:
+    def _validate_from_str_or_url(cls, value: Url | str) -> OPTIMADEUrl:
         """Pydantic validation of an OPTIMADE URL."""
         # Parse as URL
         url = AnyHttpUrl(str(value))