Merge branch 'master' into JPBergsma/return_2d_lattice

.github/workflows/ci.yml

@@ -20,10 +20,10 @@ jobs:
     steps:
     - uses: actions/checkout@v3
 
-    - name: Set up Python 3.8
+    - name: Set up Python 3.10
       uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: '3.10'
 
     - name: Install dependencies
       run: |
@@ -46,10 +46,10 @@ jobs:
       with:
         submodules: true
 
-    - name: Set up Python 3.8
+    - name: Set up Python 3.10
       uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: '3.10'
 
     - name: Install dependencies
       run: |
@@ -71,10 +71,10 @@ jobs:
       with:
         submodules: true
 
-    - name: Set up Python 3.8
+    - name: Set up Python 3.10
       uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: '3.10'
 
     - name: Install tools
       run: |
@@ -142,7 +142,7 @@ jobs:
       fail-fast: false
       max-parallel: 4
       matrix:
-        python-version: ['3.7', '3.8', '3.9', '3.10']
+        python-version: ['3.8', '3.9', '3.10']
 
     services:
       mongo:
@@ -211,16 +211,7 @@ jobs:
       run: |
         pip install -r requirements-client.txt
 
-    - name: Setup environment for AiiDA v1 (Python 3.7)
-      if: matrix.python-version == 3.7
-      env:
-        AIIDA_TEST_BACKEND: django
-      run: |
-        reentry scan
-        .github/aiida/setup_aiida.sh
-
-    - name: Setup environment for AiiDA v2 (Python 3.8+)
-      if: matrix.python-version != 3.7
+    - name: Setup environment for AiiDA
       env:
         AIIDA_TEST_BACKEND: psql_dos
       run: |
@@ -230,20 +221,20 @@ jobs:
       run: pytest -rs -vvv --cov=./optimade/ --cov-report=xml --cov-append tests/adapters/
 
     - name: Run tests for validator only to assess coverage (mongomock)
-      if: matrix.python-version == 3.8
+      if: matrix.python-version == 3.10
       run: pytest -rs --cov=./optimade/ --cov-report=xml:validator_cov.xml --cov-append tests/server/test_server_validation.py
       env:
         OPTIMADE_DATABASE_BACKEND: 'mongomock'
 
     - name: Run tests for validator only to assess coverage (Elasticsearch)
-      if: matrix.python-version == 3.8
+      if: matrix.python-version == 3.10
       run: pytest -rs --cov=./optimade/ --cov-report=xml:validator_cov.xml --cov-append tests/server/test_server_validation.py
       env:
         OPTIMADE_DATABASE_BACKEND: 'elastic'
         OPTIMADE_INSERT_TEST_DATA: false # Must be specified as previous steps will have already inserted the test data
 
     - name: Run tests for validator only to assess coverage (MongoDB)
-      if: matrix.python-version == 3.8
+      if: matrix.python-version == 3.10
       run: pytest -rs --cov=./optimade/ --cov-report=xml:validator_cov.xml --cov-append tests/server/test_server_validation.py
       env:
         OPTIMADE_DATABASE_BACKEND: 'mongodb'
@@ -278,15 +269,15 @@ jobs:
         coverage xml
 
     - name: Upload coverage to Codecov
-      if: matrix.python-version == 3.8 && github.repository == 'Materials-Consortia/optimade-python-tools'
+      if: matrix.python-version == '3.10' && github.repository == 'Materials-Consortia/optimade-python-tools'
       uses: codecov/codecov-action@v3
       with:
         name: project
         file: ./coverage.xml
         flags: project
 
     - name: Upload validator coverage to Codecov
-      if: matrix.python-version == 3.8 && github.repository == 'Materials-Consortia/optimade-python-tools'
+      if: matrix.python-version == '3.10' && github.repository == 'Materials-Consortia/optimade-python-tools'
       uses: codecov/codecov-action@v3
       with:
         name: validator
@@ -303,7 +294,7 @@ jobs:
 
     - uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: '3.10'
 
     - name: Install dependencies
       run: |
@@ -329,10 +320,10 @@ jobs:
     - name: Checkout repository
       uses: actions/checkout@v3
 
-    - name: Set up Python 3.8
+    - name: Set up Python 3.10
       uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: '3.10'
 
     - name: Install Python dependencies
       run: |

CHANGELOG.md

@@ -1,5 +1,49 @@
 # Changelog
 
+## [Unreleased](https://github.com/Materials-Consortia/optimade-python-tools/tree/HEAD)
+
+[Full Changelog](https://github.com/Materials-Consortia/optimade-python-tools/compare/v0.19.0...HEAD)
+
+This minor release includes several usability improvements for the server and client arising from the OPTIMADE workshop.
+This release also drops support for Python 3.7, which should allow us to streamline our dependencies going forward.
+
+## [v0.19.0](https://github.com/Materials-Consortia/optimade-python-tools/tree/v0.19.0) (2022-07-18)
+
+[Full Changelog](https://github.com/Materials-Consortia/optimade-python-tools/compare/v0.18.0...v0.19.0)
+
+This minor release includes several usability improvements for the server and client arising from the OPTIMADE workshop.
+This release also drops support for Python 3.7, which should allow us to streamline our dependencies going forward.
+
+**Implemented enhancements:**
+
+- Support for Elasticsearch v7 [\#1216](https://github.com/Materials-Consortia/optimade-python-tools/pull/1216) ([markus1978](https://github.com/markus1978))
+
+**Fixed bugs:**
+
+- Landing page not loading  [\#1256](https://github.com/Materials-Consortia/optimade-python-tools/issues/1256)
+- Config values are not cached by `@classproperty` [\#1219](https://github.com/Materials-Consortia/optimade-python-tools/issues/1219)
+- Prevent internal validator errors when entries are missing ID/type  [\#1273](https://github.com/Materials-Consortia/optimade-python-tools/pull/1273) ([ml-evs](https://github.com/ml-evs))
+- Improve error handling for client when updating provider list [\#1222](https://github.com/Materials-Consortia/optimade-python-tools/pull/1222) ([ml-evs](https://github.com/ml-evs))
+
+**Closed issues:**
+
+- Internal validator failures [\#1272](https://github.com/Materials-Consortia/optimade-python-tools/issues/1272)
+- Use versioned Dockerfiles for CI services to allow dependabot to update them [\#1241](https://github.com/Materials-Consortia/optimade-python-tools/issues/1241)
+- Wrong links to available endpoints [\#1214](https://github.com/Materials-Consortia/optimade-python-tools/issues/1214)
+- The validator should check for `meta->schema` [\#1209](https://github.com/Materials-Consortia/optimade-python-tools/issues/1209)
+- Add configurable `meta->schemas` field to reference server [\#1208](https://github.com/Materials-Consortia/optimade-python-tools/issues/1208)
+
+**Merged pull requests:**
+
+- Bump providers from `fb05359` to `a92e5bc` [\#1267](https://github.com/Materials-Consortia/optimade-python-tools/pull/1267) ([dependabot[bot]](https://github.com/apps/dependabot))
+- Add schema parameter when calling meta\_values in landing.py [\#1257](https://github.com/Materials-Consortia/optimade-python-tools/pull/1257) ([JPBergsma](https://github.com/JPBergsma))
+- Update `lark` dependency to new name [\#1231](https://github.com/Materials-Consortia/optimade-python-tools/pull/1231) ([ml-evs](https://github.com/ml-evs))
+- Use Python 3.10 instead of 3.7 in installation instructions [\#1229](https://github.com/Materials-Consortia/optimade-python-tools/pull/1229) ([JPBergsma](https://github.com/JPBergsma))
+- Optimisation: do not re-access mapper properties inside the request loop [\#1223](https://github.com/Materials-Consortia/optimade-python-tools/pull/1223) ([ml-evs](https://github.com/ml-evs))
+- Add meta-\>schema validation warning [\#1211](https://github.com/Materials-Consortia/optimade-python-tools/pull/1211) ([ml-evs](https://github.com/ml-evs))
+- Add configurable `schema_url` and `index_schema_url` options [\#1210](https://github.com/Materials-Consortia/optimade-python-tools/pull/1210) ([ml-evs](https://github.com/ml-evs))
+- Drop support for Python 3.7 [\#1179](https://github.com/Materials-Consortia/optimade-python-tools/pull/1179) ([ml-evs](https://github.com/ml-evs))
+
 ## [v0.18.0](https://github.com/Materials-Consortia/optimade-python-tools/tree/v0.18.0) (2022-05-29)
 
 [Full Changelog](https://github.com/Materials-Consortia/optimade-python-tools/compare/v0.17.2...v0.18.0)

docs/getting_started/client.md

@@ -101,7 +101,7 @@ optimade-get --filter 'nsites = 1' --output-file results.json https://optimade.h
 cat results.json
 ```
 
-has the followng (truncated) output:
+has the following (truncated) output:
 
 ```json
 {  

docs/static/default_config.json

@@ -13,7 +13,7 @@
     "base_url": null,
     "implementation": {
         "name": "OPTIMADE Python Tools",
-        "version": "0.18.0",
+        "version": "0.19.0",
         "source_url": "https://github.com/Materials-Consortia/optimade-python-tools",
         "maintainer": {"email": "dev@optimade.org"}
     },

openapi/index_openapi.json

@@ -2,7 +2,7 @@
   "openapi": "3.0.2",
   "info": {
     "title": "OPTIMADE API - Index meta-database",
-    "description": "The [Open Databases Integration for Materials Design (OPTIMADE) consortium](https://www.optimade.org/) aims to make materials databases interoperational by developing a common REST API.\nThis is the \"special\" index meta-database.\n\nThis specification is generated using [`optimade-python-tools`](https://github.com/Materials-Consortia/optimade-python-tools/tree/v0.18.0) v0.18.0.",
+    "description": "The [Open Databases Integration for Materials Design (OPTIMADE) consortium](https://www.optimade.org/) aims to make materials databases interoperational by developing a common REST API.\nThis is the \"special\" index meta-database.\n\nThis specification is generated using [`optimade-python-tools`](https://github.com/Materials-Consortia/optimade-python-tools/tree/v0.19.0) v0.19.0.",
     "version": "1.1.0"
   },
   "paths": {

openapi/openapi.json

@@ -2,7 +2,7 @@
   "openapi": "3.0.2",
   "info": {
     "title": "OPTIMADE API",
-    "description": "The [Open Databases Integration for Materials Design (OPTIMADE) consortium](https://www.optimade.org/) aims to make materials databases interoperational by developing a common REST API.\n\nThis specification is generated using [`optimade-python-tools`](https://github.com/Materials-Consortia/optimade-python-tools/tree/v0.18.0) v0.18.0.",
+    "description": "The [Open Databases Integration for Materials Design (OPTIMADE) consortium](https://www.optimade.org/) aims to make materials databases interoperational by developing a common REST API.\n\nThis specification is generated using [`optimade-python-tools`](https://github.com/Materials-Consortia/optimade-python-tools/tree/v0.19.0) v0.19.0.",
     "version": "1.1.0"
   },
   "paths": {
@@ -3365,9 +3365,9 @@
               "type": "number"
             },
             "description": "If present MUST be a list of floats expressed in a.m.u.\nElements denoting vacancies MUST have masses equal to 0.",
-            "x-optimade-unit": "a.m.u.",
             "x-optimade-support": "optional",
-            "x-optimade-queryable": "optional"
+            "x-optimade-queryable": "optional",
+            "x-optimade-unit": "a.m.u."
           },
           "original_name": {
             "title": "Original Name",
@@ -3645,9 +3645,9 @@
             },
             "description": "The three lattice vectors in Cartesian coordinates, in \u00e5ngstr\u00f6m (\u00c5).\n\n- **Type**: list of list of floats or unknown values.\n\n- **Requirements/Conventions**:\n    - **Support**: SHOULD be supported by all implementations, i.e., SHOULD NOT be `null`.\n    - **Query**: Support for queries on this property is OPTIONAL.\n      If supported, filters MAY support only a subset of comparison operators.\n    - MUST be a list of three vectors *a*, *b*, and *c*, where each of the vectors MUST BE a list of the vector's coordinates along the x, y, and z Cartesian coordinates.\n      (Therefore, the first index runs over the three lattice vectors and the second index runs over the x, y, z Cartesian coordinates).\n    - For databases that do not define an absolute Cartesian system (e.g., only defining the length and angles between vectors), the first lattice vector SHOULD be set along *x* and the second on the *xy*-plane.\n    - MUST always contain three vectors of three coordinates each, independently of the elements of property `dimension_types`.\n      The vectors SHOULD by convention be chosen so the determinant of the `lattice_vectors` matrix is different from zero.\n      The vectors in the non-periodic directions have no significance beyond fulfilling these requirements.\n    - The coordinates of the lattice vectors of non-periodic dimensions (i.e., those dimensions for which `dimension_types` is `0`) MAY be given as a list of all `null` values.\n        If a lattice vector contains the value `null`, all coordinates of that lattice vector MUST be `null`.\n\n- **Examples**:\n    - `[[4.0,0.0,0.0],[0.0,4.0,0.0],[0.0,1.0,4.0]]` represents a cell, where the first vector is `(4, 0, 0)`, i.e., a vector aligned along the `x` axis of length 4 \u00c5; the second vector is `(0, 4, 0)`; and the third vector is `(0, 1, 4)`.",
             "nullable": true,
-            "x-optimade-unit": "\u00c5",
             "x-optimade-support": "should",
-            "x-optimade-queryable": "optional"
+            "x-optimade-queryable": "optional",
+            "x-optimade-unit": "\u00c5"
           },
           "cartesian_site_positions": {
             "title": "Cartesian Site Positions",
@@ -3662,9 +3662,9 @@
             },
             "description": "Cartesian positions of each site in the structure.\nA site is usually used to describe positions of atoms; what atoms can be encountered at a given site is conveyed by the `species_at_sites` property, and the species themselves are described in the `species` property.\n\n- **Type**: list of list of floats\n\n- **Requirements/Conventions**:\n    - **Support**: SHOULD be supported by all implementations, i.e., SHOULD NOT be `null`.\n    - **Query**: Support for queries on this property is OPTIONAL.\n      If supported, filters MAY support only a subset of comparison operators.\n    - It MUST be a list of length equal to the number of sites in the structure, where every element is a list of the three Cartesian coordinates of a site expressed as float values in the unit angstrom (\u00c5).\n    - An entry MAY have multiple sites at the same Cartesian position (for a relevant use of this, see e.g., the property `assemblies`).\n\n- **Examples**:\n    - `[[0,0,0],[0,0,2]]` indicates a structure with two sites, one sitting at the origin and one along the (positive) *z*-axis, 2 \u00c5 away from the origin.",
             "nullable": true,
-            "x-optimade-unit": "\u00c5",
             "x-optimade-support": "should",
-            "x-optimade-queryable": "optional"
+            "x-optimade-queryable": "optional",
+            "x-optimade-unit": "\u00c5"
           },
           "nsites": {
             "title": "Nsites",

optimade/__init__.py

@@ -1,19 +1,2 @@
-__version__ = "0.18.0"
+__version__ = "0.19.0"
 __api_version__ = "1.1.0"
-
-import sys
-
-if sys.version_info.minor == 7:
-    import warnings
-
-    warnings.filterwarnings(
-        action="once",
-        message=r"v0\.17 of the `optimade` package.*",
-        category=DeprecationWarning,
-        append=True,
-    )
-    warnings.warn(
-        "v0.17 of the `optimade` package will be the last to support Python 3.7. "
-        "Please upgrade to Python 3.8+ to use v0.18 and later versions of `optimade`.",
-        DeprecationWarning,
-    )

optimade/adapters/base.py

@@ -19,7 +19,7 @@
 and [`StructureResource`][optimade.models.structures.StructureResource]s, respectively.
 """
 import re
-from typing import Union, Dict, Callable, Any, Tuple, List
+from typing import Union, Dict, Callable, Any, Tuple, List, Type
 
 from pydantic import BaseModel  # pylint: disable=no-name-in-module
 
@@ -33,14 +33,16 @@ class EntryAdapter:
     Base class for lazy resource entry adapters.
 
     Attributes:
-        ENTRY_RESOURCE (EntryResource): Entry resource to store entry as.
-        _type_converters (Dict[str, Callable]): Dictionary of valid conversion types for entry.
+        ENTRY_RESOURCE: Entry resource to store entry as.
+        _type_converters: Dictionary of valid conversion types for entry.
         as_<_type_converters>: Convert entry to a type listed in `_type_converters`.
+        from_<_type_converters>: Convert an external type to the corresponding OPTIMADE model.
 
     """
 
-    ENTRY_RESOURCE: EntryResource = EntryResource
+    ENTRY_RESOURCE: Type[EntryResource] = EntryResource
     _type_converters: Dict[str, Callable] = {}
+    _type_ingesters: Dict[str, Callable] = {}
 
     def __init__(self, entry: dict) -> None:
         """

optimade/adapters/structures/adapter.py

@@ -1,11 +1,12 @@
+from typing import Callable, Dict, Type
 from optimade.models import StructureResource
 from optimade.adapters.base import EntryAdapter
 
 from .aiida import get_aiida_structure_data
 from .ase import get_ase_atoms
 from .cif import get_cif
 from .proteindatabank import get_pdb, get_pdbx_mmcif
-from .pymatgen import get_pymatgen
+from .pymatgen import get_pymatgen, from_pymatgen
 from .jarvis import get_jarvis_atoms
 
 
@@ -17,9 +18,9 @@ class Structure(EntryAdapter):
     and properties.
 
     Attributes:
-        ENTRY_RESOURCE (StructureResource): This adapter stores entry resources as
+        ENTRY_RESOURCE: This adapter stores entry resources as
             [`StructureResource`][optimade.models.structures.StructureResource]s.
-        _type_converters (Dict[str, Callable]): Dictionary of valid conversion types for entry.
+        _type_converters: Dictionary of valid conversion types for entry.
 
             Currently available types:
 
@@ -31,12 +32,17 @@ class Structure(EntryAdapter):
             - `pymatgen`
             - `jarvis`
 
+        _type_ingesters: Dictionary of valid ingesters.
+
         as_<_type_converters>: Convert entry to a type listed in `_type_converters`.
+        from_<_type_converters>: Convert an external type to an OPTIMADE
+            [`StructureResourceAttributes`][optimade.models.structures.StructureResourceAttributes]
+            model.
 
     """
 
-    ENTRY_RESOURCE: StructureResource = StructureResource
-    _type_converters = {
+    ENTRY_RESOURCE: Type[StructureResource] = StructureResource
+    _type_converters: Dict[str, Callable] = {
         "aiida_structuredata": get_aiida_structure_data,
         "ase": get_ase_atoms,
         "cif": get_cif,
@@ -45,3 +51,7 @@ class Structure(EntryAdapter):
         "pymatgen": get_pymatgen,
         "jarvis": get_jarvis_atoms,
     }
+
+    _type_ingesters: Dict[str, Callable] = {
+        "pymatgen": from_pymatgen,
+    }