Merge branch 'main' into felipenarv/refactored_unchained_labs_to_use_datacube

Author: felipenarv

CHANGELOG.md

@@ -5,6 +5,13 @@ All notable changes to this packages will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.1.104] - 2025-08-29
+
+### Added
+
+- Luminex xPONENT - get unread data (#1059)
+- Unchained Labs Lunatic & Stunner - Add support for Stunner files (#1054)
+
 ## [0.1.103] - 2025-08-18
 
 ### Added

src/allotropy/__about__.py

@@ -1 +1 @@
-__version__ = "0.1.103"
+__version__ = "0.1.104"

src/allotropy/allotrope/allotrope.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import copy
 from typing import Any
 
 import jsonschema
@@ -11,6 +12,12 @@
     AllotropeValidationError,
 )
 
+# Override format checker to remove "uri-reference" check, which ASM schemas fail against.
+FORMAT_CHECKER = copy.deepcopy(
+    jsonschema.validators.Draft202012Validator.FORMAT_CHECKER
+)
+FORMAT_CHECKER.checkers.pop("uri-reference", None)
+
 
 def serialize_and_validate_allotrope(model: Any) -> dict[str, Any]:
     try:
@@ -26,11 +33,11 @@ def serialize_and_validate_allotrope(model: Any) -> dict[str, Any]:
         raise AllotropeSerializationError(msg) from e
 
     try:
-        jsonschema.validate(
-            allotrope_dict,
-            allotrope_schema,
-            cls=jsonschema.validators.Draft202012Validator,
+        jsonschema.validators.Draft202012Validator.check_schema(
+            allotrope_schema, format_checker=FORMAT_CHECKER
         )
+        validator = jsonschema.validators.Draft202012Validator(allotrope_schema)
+        validator.validate(allotrope_dict)
     except Exception as e:
         msg = f"Failed to validate allotrope model against schema: {e}"
         raise AllotropeValidationError(msg) from e

src/allotropy/allotrope/converter.py

@@ -106,6 +106,7 @@
     "^": "_CARET_",
     "=": "_EQUALS_",
     "@": "_AT_",
+    "'": "_QUOTE_",
     # NOTE: this MUST be at the end, or it will break other key replacements.
     " ": "_",
 }

src/allotropy/testing/utils.py

@@ -45,6 +45,7 @@ def _replace_asm_converter_version(allotrope_dict: DictType) -> DictType:
     "batch identifier",
     "data source identifier",
     "device identifier",
+    "device method identifier",
     "experimental data identifier",
     "flow cell identifier",
     "group identifier",

tests/allotrope/converter_test.py

@@ -135,11 +135,11 @@ def test_custom_information_document() -> None:
                 cycle_threshold_value_setting=TQuantityValueUnitless(value=1.0),
             ),
         ),
-        {"extra key": "Value", "weird-key/(value)°": "Other value"},
+        {"extra key": "Value", "$w.e\\ir:[d]-k'e~y/(v^a=l@ue)°#": "Other value"},
     )
 
     assert item.custom_information_document.extra_key == "Value"  # type: ignore
-    assert item.custom_information_document.weird_DASH_key_SLASH__OPAREN_value_CPAREN__DEG_ == "Other value"  # type: ignore
+    assert item.custom_information_document._DOLLAR_w_POINT_e_BSLASH_ir_COLON__OBRACKET_d_CBRACKET__DASH_k_QUOTE_e_TILDE_y_SLASH__OPAREN_v_CARET_a_EQUALS_l_AT_ue_CPAREN__DEG__NUMBER_ == "Other value"  # type: ignore
     asm_dict = unstructure(item)
     assert asm_dict == {
         "cycle threshold result": {"value": None, "unit": "(unitless)"},
@@ -148,7 +148,7 @@ def test_custom_information_document() -> None:
         },
         "custom information document": {
             "extra key": "Value",
-            "weird-key/(value)°": "Other value",
+            "$w.e\\ir:[d]-k'e~y/(v^a=l@ue)°#": "Other value",
         },
     }
     assert structure(asm_dict, ProcessedDataDocumentItem) == item