Add Python symmetry tests for ingested DAQ sessions

src/ndi/__init__.py

@@ -65,6 +65,12 @@
 from .neuron import ndi_neuron
 from .probe import ndi_probe
 from .query import ndi_query
+
+# Expose ndi_query as ``ndi.query`` so that MATLAB-style calling
+# conventions (``ndi.query('','isa','base')``) work directly.
+# The underlying ``ndi.query`` *module* remains importable via
+# ``from ndi.query import ...``.
+query = ndi_query
 from .session import empty_id, ndi_session, ndi_session_dir
 
 # Import Phase 8 classes

src/ndi/daq/metadatareader/__init__.py

@@ -62,7 +62,7 @@ def __init__(
         if document is not None:
             doc_props = getattr(document, "document_properties", document)
             if hasattr(doc_props, "base") and hasattr(doc_props.base, "id"):
-                self.identifier = doc_props.base.id
+                self._id = doc_props.base.id
             if hasattr(doc_props, "daqmetadatareader"):
                 self._tab_separated_file_parameter = getattr(
                     doc_props.daqmetadatareader, "tab_separated_file_parameter", ""

src/ndi/daq/reader_base.py

@@ -58,7 +58,7 @@ def __init__(
         if document is not None:
             doc_props = getattr(document, "document_properties", document)
             if hasattr(doc_props, "base") and hasattr(doc_props.base, "id"):
-                self.identifier = doc_props.base.id
+                self._id = doc_props.base.id
 
     def epochclock(
         self,

src/ndi/file/navigator/__init__.py

@@ -214,7 +214,7 @@ def _prop(obj: Any, key: str, default: Any = None) -> Any:
         if base is not None:
             base_id = _prop(base, "id")
             if base_id is not None:
-                self.identifier = base_id
+                self._id = base_id
             self._name = _prop(base, "name", "") or "unknown"
 
         filenavigator = _prop(doc_props, "filenavigator")

src/ndi/subject.py

@@ -106,7 +106,7 @@ def _load_from_session(self, session: Any, doc_or_id: Any) -> None:
         # Use document ID as our identifier
         base_id = props.get("base", {}).get("id", "")
         if base_id:
-            self.identifier = base_id
+            self._id = base_id
 
     @property
     def local_identifier(self) -> str:

tests/symmetry/make_artifacts/session/_ingestion_helpers.py

@@ -0,0 +1,197 @@
+"""Shared helpers for ingestion-based symmetry makeArtifacts tests.
+
+Provides functions to locate example data files and set up sessions
+with DAQ systems for ingestion testing.
+"""
+
+from __future__ import annotations
+
+import os
+import shutil
+from pathlib import Path
+
+
+def _find_intan_rhd() -> Path | None:
+    """Locate an Intan .rhd example data file.
+
+    Searches several well-known locations used by CI and local development.
+
+    Returns:
+        Path to the directory containing .rhd + epochprobemap files,
+        or None if no example data can be found.
+    """
+    candidates = [
+        # Explicit env var
+        Path(os.environ.get("NDI_EXAMPLE_DATA", "")) / "exp1_eg_saved",
+        # CI layout: NDI-matlab checked out beside NDI-python
+        Path(__file__).resolve().parents[4]
+        / ".."
+        / "NDI-matlab"
+        / "example_data"
+        / "exp1_eg_saved",
+        # Home directory
+        Path.home() / "ndi_example_data" / "exp1_eg_saved",
+        # ndi_common within the package
+        Path(__file__).resolve().parents[4]
+        / "src"
+        / "ndi"
+        / "ndi_common"
+        / "example_sessions"
+        / "exp1_eg_saved",
+    ]
+    for d in candidates:
+        d = d.resolve()
+        if d.is_dir() and list(d.glob("*.rhd")):
+            return d
+    return None
+
+
+def _find_axon_abf() -> Path | None:
+    """Locate an Axon .abf example data file.
+
+    Searches several well-known locations used by CI and local development.
+
+    Returns:
+        Path to the directory containing .abf file(s),
+        or None if no example data can be found.
+    """
+    candidates = [
+        # Explicit env var
+        Path(os.environ.get("NDI_EXAMPLE_DATA", "")) / "axon",
+        # CI layout: NDR library example data
+        Path(__file__).resolve().parents[4]
+        / ".."
+        / "NDI-matlab"
+        / "tools"
+        / "NDR"
+        / "example_data",
+        # Home directory
+        Path.home() / "ndi_example_data" / "axon",
+    ]
+
+    # Also try to find NDR's example_data via the installed ndr package
+    try:
+        import ndr.fun
+
+        ndr_path = Path(ndr.fun.ndrpath()) / "example_data"
+        candidates.insert(0, ndr_path)
+    except Exception:
+        pass
+
+    for d in candidates:
+        d = d.resolve()
+        if d.is_dir() and list(d.glob("*.abf")):
+            return d
+    return None
+
+
+def setup_intan_session(session_dir: Path, reader_class: str = "intan") -> dict:
+    """Set up a session directory with Intan data for ingestion testing.
+
+    Copies example .rhd file and creates required epochprobemap file.
+
+    Args:
+        session_dir: Directory to create the session in.
+        reader_class: Either ``"intan"`` for the native reader or
+            ``"ndr"`` for the NDR wrapper reader.
+
+    Returns:
+        Dict with keys: ``data_dir`` (source dir), ``rhd_file`` (copied file name),
+        ``reader_class_str``, ``daqreader_class_str``.
+
+    Raises:
+        FileNotFoundError: If no example data could be found.
+    """
+    data_dir = _find_intan_rhd()
+    if data_dir is None:
+        raise FileNotFoundError("Intan example data (.rhd) not found")
+
+    # Find the first .rhd file
+    rhd_files = sorted(data_dir.glob("*.rhd"))
+    rhd_file = rhd_files[0]
+
+    # Copy .rhd to session dir
+    shutil.copy2(str(rhd_file), str(session_dir / rhd_file.name))
+
+    # Create epochprobemap file
+    stem = rhd_file.stem
+    probemap_path = session_dir / f"{stem}.epochprobemap.ndi"
+    if not probemap_path.exists():
+        probemap_path.write_text(
+            "name\treference\ttype\tdevicestring\tsubjectstring\n"
+            "ctx\t1\tn-trode\tintan1:ai1\tanteater27@nosuchlab.org\n"
+        )
+
+    if reader_class == "intan":
+        return {
+            "data_dir": data_dir,
+            "rhd_file": rhd_file.name,
+            "daqreader_class_str": "ndi.daq.reader.mfdaq.intan",
+            "reader_class_str": "ndi_daq_reader_mfdaq_intan",
+        }
+    else:
+        return {
+            "data_dir": data_dir,
+            "rhd_file": rhd_file.name,
+            "daqreader_class_str": "ndi.daq.reader.mfdaq.ndr",
+            "reader_class_str": "ndi_daq_reader_mfdaq_ndr",
+        }
+
+
+def setup_axon_session(session_dir: Path) -> dict:
+    """Set up a session directory with Axon ABF data for ingestion testing.
+
+    Copies example .abf file and creates required epochprobemap file.
+
+    Args:
+        session_dir: Directory to create the session in.
+
+    Returns:
+        Dict with keys: ``data_dir``, ``abf_file``, ``daqreader_class_str``.
+
+    Raises:
+        FileNotFoundError: If no example data could be found.
+    """
+    data_dir = _find_axon_abf()
+    if data_dir is None:
+        raise FileNotFoundError("Axon example data (.abf) not found")
+
+    # Find the first .abf file
+    abf_files = sorted(data_dir.glob("*.abf"))
+    abf_file = abf_files[0]
+
+    # Copy .abf to session dir
+    shutil.copy2(str(abf_file), str(session_dir / abf_file.name))
+
+    # Create epochprobemap file
+    stem = abf_file.stem
+    probemap_path = session_dir / f"{stem}.epochprobemap.ndi"
+    if not probemap_path.exists():
+        probemap_path.write_text(
+            "name\treference\ttype\tdevicestring\tsubjectstring\n"
+            "ctx\t1\tn-trode\taxon1:ai1\tanteateri27@nosuchlab.org\n"
+        )
+
+    return {
+        "data_dir": data_dir,
+        "abf_file": abf_file.name,
+        "daqreader_class_str": "ndi.daq.reader.mfdaq.ndr",
+    }
+
+
+def delete_raw_files(session_path: Path) -> None:
+    """Delete all files in a session directory except the ``.ndi`` database.
+
+    This mirrors the MATLAB ingestion test behavior of removing raw data
+    after ingestion so that only the ingested database remains.
+
+    Args:
+        session_path: Root directory of the NDI session.
+    """
+    for item in session_path.iterdir():
+        if item.name == ".ndi":
+            continue
+        if item.is_dir():
+            shutil.rmtree(item)
+        else:
+            item.unlink()