add json validation to tests

pyproject.toml

@@ -40,6 +40,7 @@ package-dir = {"probeinterface" = "src/probeinterface"}
 [project.optional-dependencies]
 
 test = [
+    "jsonschema",
     "pytest",
     "pytest-cov",
     "matplotlib",

resources/probe.json.schema

@@ -26,10 +26,10 @@
           "annotations": {
             "type": "object",
             "properties": {
-              "name": { "type": "string" },
+              "model_name": { "type": "string" },
               "manufacturer": { "type": "string" }
             },
-            "required": ["name", "manufacturer"],
+            "required": ["model_name", "manufacturer"],
             "additionalProperties": true
           },
           "contact_annotations": {
@@ -101,6 +101,10 @@
           "shank_ids": {
             "type": "array",
             "items": { "type": "string" }
+          },
+          "device_channel_indices": {
+            "type": "array",
+            "items": { "type": "integer" }
           }
         },
         "required": [

src/probeinterface/probe.py

@@ -2,7 +2,6 @@
 import numpy as np
 from typing import Optional
 from pathlib import Path
-import json
 
 from .shank import Shank
 

src/probeinterface/testing.py

@@ -0,0 +1,13 @@
+import json
+from pathlib import Path
+
+from probeinterface import __version__ as version
+import jsonschema
+
+json_schema_file = Path(__file__).absolute().parent.parent.parent / "resources" / "probe.json.schema"
+schema = json.load(open(json_schema_file, "r"))
+
+
+def validate_probe_dict(probe_dict):
+    instance = dict(specification="probeinterface", version=version, probes=[probe_dict])
+    jsonschema.validate(instance=instance, schema=schema)

tests/test_io/test_3brain.py

@@ -1,11 +1,24 @@
+import glob
 from pathlib import Path
 import numpy as np
 
 import pytest
 
 from probeinterface import read_3brain
 
+from probeinterface.testing import validate_probe_dict
+
+
 data_path = Path(__file__).absolute().parent.parent / "data" / "3brain"
+brw_files = glob.glob(str(data_path / "*.brw"))
+
+
+@pytest.mark.parametrize("file_", brw_files)
+def test_valid_probe_dict(file_: str):
+    probe = read_3brain(data_path / file_)
+    probe_dict = probe.to_dict(array_as_list=True)
+    probe_dict["annotations"].update(model_name="placeholder")
+    validate_probe_dict(probe_dict)
 
 
 def test_3brain():

tests/test_io/test_imro.py

@@ -1,11 +1,22 @@
+import glob
 from pathlib import Path
 
 import pytest
 import numpy as np
 
 from probeinterface import read_imro, write_imro
+from probeinterface.testing import validate_probe_dict
 
 data_path = Path(__file__).absolute().parent.parent / "data" / "imro"
+imro_files = glob.glob(str(data_path / "*.imro"))
+
+imro_files.pop(imro_files.index(str(data_path / "test_non_standard.imro")))
+
+
+@pytest.mark.parametrize("file_", imro_files)
+def test_valid_probe_dict(file_: str):
+    probe = read_imro(data_path / file_)
+    validate_probe_dict(probe.to_dict(array_as_list=True))
 
 
 def test_reading_multishank_imro(tmp_path):

tests/test_io/test_maxwell.py

@@ -4,10 +4,19 @@
 import pytest
 
 from probeinterface import read_maxwell
+from probeinterface.testing import validate_probe_dict
 
 data_path = Path(__file__).absolute().parent.parent / "data" / "maxwell"
 
 
+def test_valid_probe_dict():
+    file_ = "data.raw.h5"
+    probe = read_maxwell(data_path / file_)
+    probe_dict = probe.to_dict(array_as_list=True)
+    probe_dict["annotations"].update(model_name="placeholder")
+    validate_probe_dict(probe_dict)
+
+
 def test_maxwell():
     """Basic file taken from the ephys data repository and provided by Alessio Buccino"""
 

tests/test_io/test_spikeglx.py

@@ -1,3 +1,4 @@
+import glob
 from pathlib import Path
 import numpy as np
 
@@ -8,8 +9,16 @@
     parse_spikeglx_meta,
     get_saved_channel_indices_from_spikeglx_meta,
 )
+from probeinterface.testing import validate_probe_dict
 
 data_path = Path(__file__).absolute().parent.parent / "data" / "spikeglx"
+meta_files = glob.glob(str(data_path / "*.meta"))
+
+
+@pytest.mark.parametrize("meta_file", meta_files)
+def test_valid_probe_dict(meta_file: str):
+    probe = read_spikeglx(data_path / meta_file)
+    validate_probe_dict(probe.to_dict(array_as_list=True))
 
 
 def test_parse_meta():