Support OPTIMADE v1.2.0 & drop Python 3.9 support (#294)

Support OPTIMADE v1.2.0
At least concerning the updated Structure resource model.

Drop Python 3.9 support.

Remove python version requirement in pre-commit config.

Upgrade to v1 for all OTEAPI dependencies.

Author: CasperWA

.github/workflows/cd_release.yml

@@ -20,7 +20,7 @@ jobs:
       package_dirs: oteapi_optimade
       release_branch: main
       install_extras: "[dev]"
-      python_version_build: "3.9"
+      python_version_build: "3.10"
       build_libs: flit
       build_cmd: "flit build"
       build_dir: "dist"
@@ -29,8 +29,8 @@ jobs:
 
       # Documentation
       update_docs: true
-      python_version_docs: "3.9"
-      doc_extras: "[doc]"
+      python_version_docs: "3.10"
+      doc_extras: "[docs]"
       changelog_exclude_labels: "skip_changelog,duplicate,question,invalid,wontfix"
 
     secrets:

.github/workflows/ci_cd_updated_main.yml

@@ -22,8 +22,8 @@ jobs:
       update_python_api_ref: true
       update_docs_landing_page: true
       package_dirs: oteapi_optimade
-      python_version: "3.9"
-      doc_extras: "[doc]"
+      python_version: "3.10"
+      doc_extras: "[docs]"
       full_docs_dirs: models
       changelog_exclude_labels: "skip_changelog,duplicate,question,invalid,wontfix"
 

.github/workflows/ci_tests.yml

@@ -19,7 +19,7 @@ jobs:
       run_pre-commit: false
 
       # pylint & safety
-      python_version_pylint_safety: "3.9"
+      python_version_pylint_safety: "3.10"
       run_pylint: false
 
       run_safety: true
@@ -31,12 +31,12 @@ jobs:
         --ignore=70612
 
       # Build dist
-      python_version_package: "3.9"
+      python_version_package: "3.10"
       build_libs: flit
       build_cmd: flit build
 
       # Build documentation
-      python_version_docs: "3.9"
+      python_version_docs: "3.10"
       package_dirs: oteapi_optimade
       full_docs_dirs: "models"
 
@@ -47,7 +47,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12"]
         os:
         - ["ubuntu-latest", "linux"]
         - ["windows-latest", "windows"]
@@ -111,10 +111,10 @@ jobs:
       with:
         fetch-depth: 2
 
-    - name: Set up Python 3.9
+    - name: Set up Python 3.10
       uses: actions/setup-python@v5
       with:
-        python-version: "3.9"
+        python-version: "3.10"
 
     - name: Install python dependencies
       run: |

.pre-commit-config.yaml

@@ -12,9 +12,6 @@ ci:
   submodules: false
 
 # hooks
-default_language_version:
-  python: python3.9
-
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v5.0.0

docs/examples/dlite.ipynb

@@ -184,7 +184,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 42,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {

docs/examples/index.md

@@ -18,7 +18,7 @@ Using OTElib should be done as a backend task in a web application, and the resu
 
 ### Prerequisites
 
-To run the examples locally, you need to have the following tools available (in addition to a working Python 3.9+ installation):
+To run the examples locally, you need to have the following tools available (in addition to a working Python 3.10+ installation):
 
 - [Jupyter](https://jupyter.org/)
 - [Docker](https://www.docker.com/) (or similar containerization tool)

entities/OPTIMADEStructure.yaml

@@ -1,4 +1,4 @@
-uri: http://onto-ns.com/meta/1.0.1/OPTIMADEStructure
+uri: http://onto-ns.com/meta/1.2.0/OPTIMADEStructure
 meta: http://onto-ns.com/meta/0.3/EntitySchema
 description: An OPTIMADE structure.
 dimensions: {}
@@ -8,7 +8,7 @@ properties:
     description: The name of the type of an entry. Must always be 'structures'.
   attributes:
     type: ref
-    $ref: http://onto-ns.com/meta/1.0.1/OPTIMADEStructureAttributes
+    $ref: http://onto-ns.com/meta/1.2.0/OPTIMADEStructureAttributes
     description: The attributes used to represent a structure, e.g. unit cell, atoms, positions.
   id:
     type: str

entities/OPTIMADEStructureAttributes.yaml

@@ -1,10 +1,11 @@
-uri: http://onto-ns.com/meta/1.0.1/OPTIMADEStructureAttributes
+uri: http://onto-ns.com/meta/1.2.0/OPTIMADEStructureAttributes
 meta: http://onto-ns.com/meta/0.3/EntitySchema
 description: The attributes used to represent a structure, e.g. unit cell, atoms, positions.
 dimensions:
   nelements: Number of different elements in the structure as an integer.
   dimensionality: Number of spatial dimensions. Must always be 3.
   nsites: An integer specifying the length of the `cartesian_site_positions` property.
+  nspace_group_symmetry_operations: Number of space group symmetry operations.
   nspecies: Number of species.
   nstructure_features: Number of structure features.
 properties:
@@ -40,6 +41,22 @@ properties:
     shape: [dimensionality, dimensionality]
     unit: Å
     description: The three lattice vectors in Cartesian coordinates, in ångström (Å).
+  space_group_symmetry_operations_xyz:
+    type: string
+    shape: [nspace_group_symmetry_operations]
+    description: List of symmetry operations given as general position x, y and z coordinates in algebraic form.
+  space_group_symbol_hall:
+    type: string
+    description: A Hall space group symbol representing the symmetry of the structure as defined in (Hall, 1981, 1981a).
+  space_group_symbol_hermann_mauguin:
+    type: string
+    description: A human- and machine-readable string containing the short Hermann-Mauguin (H-M) symbol which specifies the space group of the structure in the response.
+  space_group_symbol_hermann_mauguin_extended:
+    type: string
+    description: A human- and machine-readable string containing the extended Hermann-Mauguin (H-M) symbol which specifies the space group of the structure in the response.
+  space_group_it_number:
+    type: int
+    description: Space group number which specifies the space group of the structure as defined in the International Tables for Crystallography Vol. A. (IUCr, 2005).
   cartesian_site_positions:
     type: float
     shape: [nsites, dimensionality]

entities/OPTIMADEStructureResource.yaml

@@ -1,12 +1,11 @@
-uri: http://onto-ns.com/meta/1.0.1/OPTIMADEStructureResource
+uri: http://onto-ns.com/meta/1.2.0/OPTIMADEStructureResource
 description: An OPTIMADE structure resource.
 dimensions:
   nelements: Number of different elements in the structure as an integer.
   dimensionality: Number of spatial dimensions. Must always be 3.
   nsites: An integer specifying the length of the `cartesian_site_positions` property.
   nstructure_features: Number of structure features.
-  ## Uncomment when space_group attributes are implemented in OPT.
-  # nspace_group_symmetry_operations: Number of space group symmetry operations.
+  nspace_group_symmetry_operations: Number of space group symmetry operations.
   nspecies: Number of species.
   nassemblies: Number of assemblies.
 properties:
@@ -59,23 +58,22 @@ properties:
     shape: [dimensionality, dimensionality]
     unit: Å
     description: The three lattice vectors in Cartesian coordinates, in ångström (Å).
-  ## Uncomment when space_group attributes are implemented in OPT.
-  # space_group_symmetry_operations_xyz:
-  #   type: string
-  #   shape: [nspace_group_symmetry_operations]
-  #   description: List of symmetry operations given as general position x, y and z coordinates in algebraic form.
-  # space_group_symbol_hall:
-  #   type: string
-  #   description: A Hall space group symbol representing the symmetry of the structure as defined in (Hall, 1981, 1981a).
-  # space_group_symbol_hermann_mauguin:
-  #   type: string
-  #   description: A human- and machine-readable string containing the short Hermann-Mauguin (H-M) symbol which specifies the space group of the structure in the response.
-  # space_group_symbol_hermann_mauguin_extended:
-  #   type: string
-  #   description: A human- and machine-readable string containing the extended Hermann-Mauguin (H-M) symbol which specifies the space group of the structure in the response.
-  # space_group_it_number:
-  #   type: int
-  #   description: Space group number which specifies the space group of the structure as defined in the International Tables for Crystallography Vol. A. (IUCr, 2005).
+  space_group_symmetry_operations_xyz:
+    type: string
+    shape: [nspace_group_symmetry_operations]
+    description: List of symmetry operations given as general position x, y and z coordinates in algebraic form.
+  space_group_symbol_hall:
+    type: string
+    description: A Hall space group symbol representing the symmetry of the structure as defined in (Hall, 1981, 1981a).
+  space_group_symbol_hermann_mauguin:
+    type: string
+    description: A human- and machine-readable string containing the short Hermann-Mauguin (H-M) symbol which specifies the space group of the structure in the response.
+  space_group_symbol_hermann_mauguin_extended:
+    type: string
+    description: A human- and machine-readable string containing the extended Hermann-Mauguin (H-M) symbol which specifies the space group of the structure in the response.
+  space_group_it_number:
+    type: int
+    description: Space group number which specifies the space group of the structure as defined in the International Tables for Crystallography Vol. A. (IUCr, 2005).
   cartesian_site_positions:
     type: float
     shape: [nsites, dimensionality]

oteapi_optimade/dlite/parse.py

@@ -14,7 +14,7 @@
     StructureResponseOne,
     Success,
 )
-from oteapi_dlite.models import DLiteSessionUpdate
+from oteapi_dlite.models import DLiteResult
 from oteapi_dlite.utils import get_collection, update_collection
 from pydantic import BaseModel, ValidationError
 from pydantic.dataclasses import dataclass
@@ -42,7 +42,7 @@ class OPTIMADEDLiteParseStrategy:
 
     parse_config: OPTIMADEDLiteParseConfig
 
-    def initialize(self) -> DLiteSessionUpdate:
+    def initialize(self) -> DLiteResult:
         """Initialize strategy.
 
         This method will be called through the `/initialize` endpoint of the OTE-API
@@ -53,7 +53,7 @@ def initialize(self) -> DLiteSessionUpdate:
             context from services.
 
         """
-        return DLiteSessionUpdate(
+        return DLiteResult(
             collection_id=get_collection(
                 collection_id=self.parse_config.configuration.collection_id
             ).uuid
@@ -386,6 +386,13 @@ def get(self) -> OPTIMADEParseResult:
                         "nstructure_features": len(
                             structure.attributes.structure_features
                         ),
+                        "nspace_group_symmetry_operations": (
+                            len(
+                                structure.attributes.space_group_symmetry_operations_xyz
+                            )
+                            if structure.attributes.space_group_symmetry_operations_xyz
+                            else 0
+                        ),
                         **single_entity_dimensions,
                     },
                     properties=new_structure_attributes,
@@ -414,6 +421,13 @@ def get(self) -> OPTIMADEParseResult:
                                 "nstructure_features": len(
                                     structure.attributes.structure_features
                                 ),
+                                "nspace_group_symmetry_operations": (
+                                    len(
+                                        structure.attributes.space_group_symmetry_operations_xyz
+                                    )
+                                    if structure.attributes.space_group_symmetry_operations_xyz
+                                    else 0
+                                ),
                             },
                             properties=new_structure_attributes,
                         ),
@@ -423,6 +437,7 @@ def get(self) -> OPTIMADEParseResult:
                 )
 
             dlite_collection.add(label=structure.id, inst=new_structure)
+            new_structure._incref()
 
         update_collection(collection=dlite_collection)