Merge branch 'master' into ml-evs/demote_fastapi

.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

@@ -20,10 +20,10 @@ jobs:
     steps:
     - uses: actions/checkout@v3
 
-    - name: Set up Python 3.8
-      uses: actions/setup-python@v3
+    - 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
-      uses: actions/setup-python@v3
+    - 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
-      uses: actions/setup-python@v3
+    - 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:
@@ -162,12 +162,13 @@ jobs:
         ports:
         - 5432:5432
       elasticsearch:
-        image: elasticsearch:6.8.23
+        image: elasticsearch:7.17.1
         ports:
           - 9200:9200
           - 9300:9300
         env:
           discovery.type: single-node
+          xpack.security.enabled: 'false'
 
 
     steps:
@@ -177,7 +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 }}
 
@@ -210,16 +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: |
@@ -229,20 +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'
@@ -277,15 +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
@@ -300,9 +292,9 @@ jobs:
       with:
         submodules: true
 
-    - uses: actions/setup-python@v3
+    - uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: '3.10'
 
     - name: Install dependencies
       run: |
@@ -328,10 +320,10 @@ jobs:
     - name: Checkout repository
       uses: actions/checkout@v3
 
-    - name: Set up Python 3.8
-      uses: actions/setup-python@v3
+    - 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: |

.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
 
@@ -73,7 +73,7 @@ jobs:
 
     - name: Fetch PR body
       id: pr_body
-      uses: chuhlomin/render-template@v1.4
+      uses: chuhlomin/render-template@v1.5
       with:
         template: .github/utils/single_dependency_pr_body.txt
 

.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

CHANGELOG.md

@@ -1,9 +1,89 @@
 # Changelog
 
+## [v0.19.1](https://github.com/Materials-Consortia/optimade-python-tools/tree/v0.19.1) (2022-08-08)
+
+[Full Changelog](https://github.com/Materials-Consortia/optimade-python-tools/compare/v0.19.0...v0.19.1)
+
+**Implemented enhancements:**
+
+- Add `from_pymatgen` structure adapter method and concept of ingesters [\#1296](https://github.com/Materials-Consortia/optimade-python-tools/pull/1296) ([ml-evs](https://github.com/ml-evs))
+- Add `lru_cache` to many mapper properties [\#1245](https://github.com/Materials-Consortia/optimade-python-tools/pull/1245) ([ml-evs](https://github.com/ml-evs))
+
+**Merged pull requests:**
+
+- Use animated SVG logo for optimade-python-tools landing page [\#1297](https://github.com/Materials-Consortia/optimade-python-tools/pull/1297) ([ml-evs](https://github.com/ml-evs))
+
+## [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)
+
+This is a feature release that includes the new `optimade.client.OptimadeClient` class, a client capable asynchronously querying multiple OPTIMADE APIs simultaneously.
+It also contains a patch for the OPTIMADE models that allows them to be used with more recent FastAPI versions without breaking OpenAPI 3.0 compatibility.
+Other changes can be found below.
+This release includes improvements to the validator to catch more cases where OPTIMADE APIs are only partially implemented.
+Previously, APIs that did not support filtering, pagination or limiting response fields at all (i.e., the query parameter is simply ignored) would pass most validation tests erroneously in some unlucky situations (#1180).
+
+**Implemented enhancements:**
+
+- The validator should use a custom `User-Agent` header [\#1187](https://github.com/Materials-Consortia/optimade-python-tools/issues/1187)
+- Suggestion to include an OPTIMADE python API client [\#932](https://github.com/Materials-Consortia/optimade-python-tools/issues/932)
+- Implementation of an OPTIMADE client [\#1154](https://github.com/Materials-Consortia/optimade-python-tools/pull/1154) ([ml-evs](https://github.com/ml-evs))
+
+**Fixed bugs:**
+
+- `OptimadeClient` crashes if an index meta-database is down [\#1196](https://github.com/Materials-Consortia/optimade-python-tools/issues/1196)
+- Catch connection errors when populating client database list [\#1197](https://github.com/Materials-Consortia/optimade-python-tools/pull/1197) ([ml-evs](https://github.com/ml-evs))
+
+**Merged pull requests:**
+
+- Add a clearer error message on when trying to use client with missing deps [\#1200](https://github.com/Materials-Consortia/optimade-python-tools/pull/1200) ([ml-evs](https://github.com/ml-evs))
+- Use a custom `User-Agent` with validator [\#1189](https://github.com/Materials-Consortia/optimade-python-tools/pull/1189) ([ml-evs](https://github.com/ml-evs))
+- Syntactic tweaks to models and schemas for compatibility with `fastapi>0.66` [\#1131](https://github.com/Materials-Consortia/optimade-python-tools/pull/1131) ([ml-evs](https://github.com/ml-evs))
+
 ## [v0.17.2](https://github.com/Materials-Consortia/optimade-python-tools/tree/v0.17.2) (2022-05-21)
 
 [Full Changelog](https://github.com/Materials-Consortia/optimade-python-tools/compare/v0.17.1...v0.17.2)
 
+This release includes improvements to the validator to catch more cases where OPTIMADE APIs are only partially implemented.
+Previously, APIs that did not support filtering, pagination or limiting response fields at all (i.e., the query parameter is simply ignored) would pass most validation tests erroneously in some unlucky situations (#1180).
+
 **Fixed bugs:**
 
 - Server validation incorrectly passes with various unimplemented features [\#1180](https://github.com/Materials-Consortia/optimade-python-tools/issues/1180)

INSTALL.md

@@ -41,8 +41,8 @@ All contributed Python code, must use the [black](https://github.com/ambv/black)
 git clone --recursive git@github.com:Materials-Consortia/optimade-python-tools.git
 cd optimade-python-tools
 
-# Ensure a Python>=3.7 (virtual) environment (example below using Anaconda/Miniconda)
-conda create -n optimade python=3.7
+# Ensure a Python>=3.8 (virtual) environment (example below using Anaconda/Miniconda)
+conda create -n optimade python=3.10
 conda activate optimade
 
 # Install package and dependencies in editable mode (including "dev" requirements).
@@ -101,7 +101,7 @@ These commands should be run from a local optimade-python-tools directory.
 The following command starts a local Elasticsearch v6 instance, runs the test suite, then stops and deletes the containers (required as the tests insert some data):
 
 ```shell
-docker run -d --name elasticsearch_test -p 9200:9200 -p 9300:9300 -e "discovery.type=single-node" elasticsearch:6.8.23 \
+docker run -d --name elasticsearch_test -p 9200:9200 -p 9300:9300 -e "discovery.type=single-node" -e "xpack.security.enabled=false" elasticsearch:7.17.1 \
 && sleep 10 \
 && OPTIMADE_DATABASE_BACKEND="elastic" py.test; \
 docker container stop elasticsearch_test; docker container rm elasticsearch_test

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