Update API schema

docs/_static/api.yaml

@@ -270,50 +270,51 @@ components:
         mixed:
           description: Gets data[5, 0:10:2]
           value: [5, '0:10:2']
+
   schemas:
     # Metadata schemas
     attrMetadata:
       type: object
       description: Attribute metadata. Does not include the value.
       properties:
-        dtype:
-          $ref: '#/components/schemas/dtype'
         name:
           type: string
           example: 'attr1_name'
         shape:
           $ref: '#/components/schemas/shape'
+        type:
+          $ref: '#/components/schemas/type'
     entityMetadata:
       type: object
       properties:
+        kind:
+          enum: ['other']
+          type: string
         name:
           type: string
           example: 'entity_name'
-        type:
-          enum: ['other']
-          type: string
     softLinkMetadata:
       allOf:
         - $ref: '#/components/schemas/entityMetadata'
         - type: object
           properties:
+            kind:
+              enum: ['soft_link']
+              type: string
             target_path:
               type: string
               example: '/path/to/linked/entity'
-            type:
-              enum: ['soft_link']
-              type: string
     externalLinkMetadata:
       allOf:
         - $ref: '#/components/schemas/softLinkMetadata'
         - type: object
           properties:
-            target_file:
-              type: string
-            type:
+            kind:
               enum: ['external_link']
               type: string
               example: 'path/to/another/file.h5'
+            target_file:
+              type: string
     resolvedEntityMetadata:
       allOf:
         - $ref: '#/components/schemas/entityMetadata'
@@ -328,25 +329,28 @@ components:
         - $ref: '#/components/schemas/resolvedEntityMetadata'
         - type: object
           properties:
+            kind:
+              enum: ['dataset']
+              type: string
+            shape:
+              $ref: '#/components/schemas/shape'
+            type:
+              $ref: '#/components/schemas/type'
             chunks:
               $ref: '#/components/schemas/shape'
-            dtype:
-              $ref: '#/components/schemas/dtype'
             filters:
               type: array
               items:
                 $ref: '#/components/schemas/filterInfo'
               nullable: true
-            shape:
-              $ref: '#/components/schemas/shape'
-            type:
-              enum: ['dataset']
-              type: string
     groupMetadata:
       allOf:
         - $ref: '#/components/schemas/resolvedEntityMetadata'
         - type: object
           properties:
+            kind:
+              enum: ['group']
+              type: string
             children:
               type: array
               items:
@@ -356,18 +360,49 @@ components:
                   - $ref: '#/components/schemas/externalLinkMetadata'
                   - $ref: '#/components/schemas/resolvedEntityMetadata'
                   - $ref: '#/components/schemas/softLinkMetadata'
-            type:
-              enum: ['group']
-              type: string
     childGroupMetadata:
       allOf:
         - $ref: '#/components/schemas/resolvedEntityMetadata'
         - type: object
           properties:
-            type:
+            kind:
               enum: ['group']
               type: string
+
     # Other schemas
+    type:
+      type: object
+      properties:
+        class:
+          type: integer
+        dtype:
+          $ref: '#/components/schemas/dtype'
+        size:
+          type: integer
+        order:
+          type: integer
+        sign:
+          type: integer
+        cset:
+          type: integer
+        vlen:
+          type: boolean
+        tag:
+          type: string
+        dims:
+          $ref: '#/components/schemas/shape'
+        dims:
+          $ref: '#/components/schemas/shape'
+        members:
+          oneOf:
+            - type: object
+              additionalProperties:
+                $ref: '#/components/schemas/type'
+            - type: object
+              additionalProperties:
+                type: integer
+        base:
+          $ref: '#/components/schemas/type'
     dtype:
       oneOf:
         - type: 'string'

docs/conf.py

@@ -22,7 +22,7 @@
 # -- Project information -----------------------------------------------------
 
 project = "h5grove"
-copyright = "2021, ESRF"
+copyright = "2024, ESRF"
 author = "ESRF"
 
 # The full version, including alpha/beta/rc tags

h5grove/fastapi_utils.py

@@ -1,4 +1,5 @@
 """Helpers for usage with `FastAPI <https://fastapi.tiangolo.com/>`_"""
+
 from fastapi import APIRouter, Depends, Response, Query, Request
 from fastapi.routing import APIRoute
 from pydantic_settings import BaseSettings

h5grove/flask_utils.py

@@ -1,4 +1,5 @@
 """Helpers for usage with `Flask <https://flask.palletsprojects.com/>`_"""
+
 from werkzeug.exceptions import HTTPException
 from flask import Blueprint, current_app, request, Response, Request
 import os

h5grove/tornado_utils.py

@@ -1,4 +1,5 @@
 """Helpers for usage with `Tornado <https://www.tornadoweb.org>`_"""
+
 import os
 from typing import Any, Optional
 

h5grove/utils.py

@@ -170,9 +170,9 @@ def get_type_metadata(type_id: h5py.h5t.TypeID) -> TypeMetadata:
 
     if isinstance(type_id, h5py.h5t.TypeEnumID):
         for i in range(0, type_id.get_nmembers()):
-            members[
-                type_id.get_member_name(i).decode("utf-8")
-            ] = type_id.get_member_value(i)
+            members[type_id.get_member_name(i).decode("utf-8")] = (
+                type_id.get_member_value(i)
+            )
 
         return {
             **base_metadata,
@@ -267,12 +267,14 @@ def get_array_stats(data: np.ndarray) -> Dict[str, Union[float, int, None]]:
     strict_positive_data = data[data > 0]
     positive_data = data[data >= 0]
     return {
-        "strict_positive_min": cast(np.min(strict_positive_data))
-        if strict_positive_data.size != 0
-        else None,
-        "positive_min": cast(np.min(positive_data))
-        if positive_data.size != 0
-        else None,
+        "strict_positive_min": (
+            cast(np.min(strict_positive_data))
+            if strict_positive_data.size != 0
+            else None
+        ),
+        "positive_min": (
+            cast(np.min(positive_data)) if positive_data.size != 0 else None
+        ),
         "min": cast(np.min(data)),
         "max": cast(np.max(data)),
         "mean": cast(np.mean(data)),

setup.cfg

@@ -49,7 +49,6 @@ dev =
 	myst-parser
 	# Needed for fastapi tests. Could be removed by setting fastapi[all] as dep in the future.
 	httpx >= 0.23
-	pydantic_settings
 	pytest
 	pytest-benchmark
 	pytest-cov

tasks.py

@@ -37,7 +37,7 @@ def test(c, verbose=False, keyword="", cov_lines=False):
     c.run(
         "pytest --benchmark-skip"
         + (" -vv" if verbose else "")
-        + ((" -k" + keyword) if keyword else "")
+        + (f" -k{keyword}" if keyword else "")
         + (" --cov-report term-missing" if cov_lines else "")
     )
 

test/base_test.py

@@ -1,4 +1,5 @@
 """Base class for testing with different servers"""
+
 import os
 import stat
 from typing import Generator

test/test_benchmark_data.py

@@ -1,4 +1,5 @@
 """Benchmark data requests with server apps in example/ folder"""
+
 import pathlib
 from typing import Generator
 from urllib.parse import urlencode

test/test_fastapi.py

@@ -1,4 +1,5 @@
 """Test fastapi_utils with fastapi testing"""
+
 import pathlib
 from typing import Callable
 from fastapi import FastAPI

test/test_flask.py

@@ -1,4 +1,5 @@
 """Test flask_utils blueprint with Flask testing"""
+
 import pathlib
 from typing import Callable
 from flask import Flask

test/test_tornado.py

@@ -1,4 +1,5 @@
 """Test tornado_utils using pytest-tornado"""
+
 import pathlib
 from typing import Callable
 import pytest