Merge branch 'main' into cfg-to-app-state

ml-evs · web-flow · commit 36327b21adb8 · 2025-11-20T17:53:32.000Z
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -14,7 +14,7 @@ default_language_version:
 # pre-commit hooks
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
     - id: check-symlinks
     - id: check-yaml
@@ -35,7 +35,7 @@ repos:
       args: [--py310-plus]
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: 'v0.12.7'
+    rev: 'v0.13.3'
 
     hooks:
     - id: ruff
@@ -59,7 +59,7 @@ repos:
       description: Update the API Reference documentation whenever a Python file is touched in the code base.
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.17.1
+    rev: v1.18.2
     hooks:
       - id: mypy
         name: "MyPy"
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,36 @@
 # Changelog
 
+## [Unreleased](https://github.com/Materials-Consortia/optimade-python-tools/tree/HEAD)
+
+[Full Changelog](https://github.com/Materials-Consortia/optimade-python-tools/compare/v1.3.1...HEAD)
+
+**Merged pull requests:**
+
+- Bump providers from `a479de9` to `c0a4a05` [\#2324](https://github.com/Materials-Consortia/optimade-python-tools/pull/2324) ([dependabot[bot]](https://github.com/apps/dependabot))
+
+## [v1.3.1](https://github.com/Materials-Consortia/optimade-python-tools/tree/v1.3.1) (2025-10-11)
+
+[Full Changelog](https://github.com/Materials-Consortia/optimade-python-tools/compare/v1.3.0...v1.3.1)
+
+**Implemented enhancements:**
+
+- Add a gzip compression middleware [\#2095](https://github.com/Materials-Consortia/optimade-python-tools/issues/2095)
+
+**Fixed bugs:**
+
+- `insert_from_jsonl` fails when number of entries is exactly divisible by `batch_size` [\#2320](https://github.com/Materials-Consortia/optimade-python-tools/issues/2320)
+
+**Merged pull requests:**
+
+- Fix issue when inserting from JSONL when batch size matches number of entries [\#2321](https://github.com/Materials-Consortia/optimade-python-tools/pull/2321) ([ml-evs](https://github.com/ml-evs))
+- Bump providers from `a479de9` to `c0a4a05` [\#2319](https://github.com/Materials-Consortia/optimade-python-tools/pull/2319) ([dependabot[bot]](https://github.com/apps/dependabot))
+- Allow Mongo DBs that share 12 first ID characters [\#2317](https://github.com/Materials-Consortia/optimade-python-tools/pull/2317) ([eimrek](https://github.com/eimrek))
+- Fix docs builds with latest griffe [\#2309](https://github.com/Materials-Consortia/optimade-python-tools/pull/2309) ([ml-evs](https://github.com/ml-evs))
+- Add `GZipMiddleware` to compress JSON responses on-the-fly [\#2308](https://github.com/Materials-Consortia/optimade-python-tools/pull/2308) ([Bud-Macaulay](https://github.com/Bud-Macaulay))
+- Bump actions/setup-python from 5 to 6 in the github-actions group and pin griffe [\#2301](https://github.com/Materials-Consortia/optimade-python-tools/pull/2301) ([dependabot[bot]](https://github.com/apps/dependabot))
+- \[pre-commit.ci\] pre-commit autoupdate [\#2300](https://github.com/Materials-Consortia/optimade-python-tools/pull/2300) ([pre-commit-ci[bot]](https://github.com/apps/pre-commit-ci))
+- Bump actions/checkout from 4 to 5 in the github-actions group [\#2294](https://github.com/Materials-Consortia/optimade-python-tools/pull/2294) ([dependabot[bot]](https://github.com/apps/dependabot))
+
 ## [v1.3.0](https://github.com/Materials-Consortia/optimade-python-tools/tree/v1.3.0) (2025-08-11)
 
 [Full Changelog](https://github.com/Materials-Consortia/optimade-python-tools/compare/v1.2.4...v1.3.0)
diff --git a/docs/static/default_config.json b/docs/static/default_config.json
@@ -12,7 +12,7 @@
     "base_url": null,
     "implementation": {
         "name": "OPTIMADE Python Tools",
-        "version": "1.3.0",
+        "version": "1.3.1",
         "source_url": "https://github.com/Materials-Consortia/optimade-python-tools",
         "maintainer": {"email": "dev@optimade.org"}
     },
diff --git a/openapi/index_openapi.json b/openapi/index_openapi.json
@@ -2,7 +2,7 @@
   "openapi": "3.1.0",
   "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/v1.3.0) v1.3.0.",
+    "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/v1.3.1) v1.3.1.",
     "version": "1.2.0"
   },
   "paths": {
diff --git a/openapi/openapi.json b/openapi/openapi.json
@@ -2,7 +2,7 @@
   "openapi": "3.1.0",
   "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/v1.3.0) v1.3.0.",
+    "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/v1.3.1) v1.3.1.",
     "version": "1.2.0"
   },
   "paths": {
diff --git a/optimade/__init__.py b/optimade/__init__.py
@@ -1,2 +1,2 @@
-__version__ = "1.3.0"
+__version__ = "1.3.1"
 __api_version__ = "1.2.0"
diff --git a/optimade/utils.py b/optimade/utils.py
@@ -111,8 +111,9 @@ def insert_from_jsonl(
 
         # Insert any remaining data
         for entry_type in batch:
-            entry_collections[entry_type].insert(batch[entry_type])
-            batch[entry_type] = []
+            if batch[entry_type]:
+                ENTRY_COLLECTIONS[entry_type].insert(batch[entry_type])
+                batch[entry_type] = []
 
         if bad_rows:
             LOGGER.warning("Could not read %d rows from the JSONL file", bad_rows)
diff --git a/providers b/providers
@@ -1 +1 @@
-Subproject commit a479de9acfbeee2e6d3d7398fddf965b37e2312b
+Subproject commit c0a4a05d71b55dfb3bed80563a9242e116c78f05
diff --git a/pyproject.toml b/pyproject.toml
@@ -103,7 +103,7 @@ testing = [
     "jsondiff~=2.0",
     "pytest~=8.3",
     "pytest-asyncio>=0.25,<2.0",
-    "pytest-cov~=6.0",
+    "pytest-cov>=6,<8",
     "optimade[server]",
 ]
 
diff --git a/requirements-client.txt b/requirements-client.txt
@@ -2,4 +2,4 @@ aiida-core==2.7.1
 ase==3.26.0
 jarvis-tools==2025.5.30; python_version < '3.13'
 numpy>=1.20
-pymatgen==2025.6.14; python_version < '3.13'
+pymatgen==2025.10.7; python_version < '3.13'
diff --git a/requirements-dev.txt b/requirements-dev.txt
@@ -1,11 +1,11 @@
 build==1.3.0
-invoke==2.2.0
+invoke==2.2.1
 jsondiff==2.2.1
-mypy==1.17.1
+mypy==1.18.2
 pre-commit==4.3.0
-pytest==8.4.1
-pytest-asyncio==1.1.0
-pytest-cov==6.2.1
-ruff==0.12.9
+pytest==8.4.2
+pytest-asyncio==1.2.0
+pytest-cov==7.0.0
+ruff==0.14.0
 types-pyyaml
 types-requests
diff --git a/requirements-docs.txt b/requirements-docs.txt
@@ -3,5 +3,5 @@ mike==2.1.3
 mkdocs==1.6.1
 mkdocs-autorefs==1.4.3
 mkdocs-awesome-pages-plugin==2.10.1
-mkdocs-material==9.6.19
+mkdocs-material==9.6.22
 mkdocstrings[python]==0.30.1
diff --git a/requirements-http-client.txt b/requirements-http-client.txt
@@ -1,3 +1,3 @@
 click==8.1.8
 httpx==0.28.1
-rich==14.1.0
+rich==14.2.0
diff --git a/requirements-server.txt b/requirements-server.txt
@@ -1,6 +1,6 @@
 elasticsearch==7.17.12
 elasticsearch-dsl==7.4.1
-fastapi==0.116.1
+fastapi==0.120.1
 mongomock==4.3.0
-pymongo==4.14.0
-starlette==0.47.2
+pymongo==4.15.3
+starlette==0.49.1
diff --git a/requirements.txt b/requirements.txt
@@ -1,6 +1,6 @@
-lark==1.2.2
-pydantic[email]==2.11.7
-pydantic_settings==2.10.1
-pyyaml==6.0.2
-requests==2.32.4
-uvicorn==0.35.0
+lark==1.3.1
+pydantic[email]==2.12.3
+pydantic_settings==2.11.0
+pyyaml==6.0.3
+requests==2.32.5
+uvicorn==0.38.0

Original file line number	Diff line number	Diff line change
`@@ -1,2 +1,2 @@`
`1`		`-__version__ = "1.3.0"`
	`1`	`+__version__ = "1.3.1"`
`2`	`2`	`__api_version__ = "1.2.0"`
Original file line number	Diff line number	Diff line change
`@@ -103,7 +103,7 @@ testing = [`
`103`	`103`	`"jsondiff~=2.0",`
`104`	`104`	`"pytest~=8.3",`
`105`	`105`	`"pytest-asyncio>=0.25,<2.0",`
`106`		`- "pytest-cov~=6.0",`
	`106`	`+ "pytest-cov>=6,<8",`
`107`	`107`	`"optimade[server]",`
`108`	`108`	`]`
`109`	`109`