add SofaStream.verify

HISTORY.rst

@@ -2,6 +2,10 @@
 History
 =======
 
+1.2.3 (2026-02-03)
+------------------
+* Fix: Restrict netCDF4 version to not equal 1.7.4 due to a bug related to strings and string variables (#133)
+
 1.2.2 (2025-05-09)
 ------------------
 * Docs: Improve layout of header (#125)

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "sofar"
-version = "1.2.2"
+version = "1.2.3"
 description = "Maybe the most complete python package for SOFA files so far."
 readme = "README.md"
 license = {file = "LICENSE"}
@@ -26,7 +26,7 @@ classifiers = [
     "Programming Language :: Python :: 3.13",
 ]
 dependencies = [
-    'netCDF4',
+    'netCDF4!=1.7.4',
     'numpy>=1.14.0',
     'beautifulsoup4',
     'requests',
@@ -126,7 +126,7 @@ convention = "numpy"
 
 
 [tool.bumpversion]
-current_version = "1.2.2"
+current_version = "1.2.3"
 parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
 serialize = ["{major}.{minor}.{patch}"]
 search = "{current_version}"

sofar/__init__.py

@@ -2,7 +2,7 @@
 # -*- coding: utf-8 -*-
 __author__ = """The pyfar developers"""
 __email__ = 'info@pyfar.org'
-__version__ = '1.2.2'
+__version__ = '1.2.3'
 
 from .sofa import Sofa
 

sofar/sofa.py

@@ -76,8 +76,9 @@ class Sofa():
        will be a scalar inside SOFA objects after reading from disk.
 
 
-    For more examples refer to the `Quick tour of SOFA and sofar` at
-    https://sofar.readthedocs.io/en/stable/
+    For more examples refer to the
+    `sofar and SOFA <https://pyfar-gallery.readthedocs.io/en/latest/gallery/interactive/sofar_introduction.html>`__
+    notebook in the pyfar example gallery.
     """
 
     # these have to be set here, because they are used in __setattr__ and

sofar/sofastream.py

@@ -5,14 +5,34 @@
 from netCDF4 import Dataset
 import numpy as np
 
+import sofar as sf
+
+from .io import _format_value_from_netcdf
+
+
+class _LazyArray(np.ndarray):
+    """Represent a NetCDF numeric variable without reading its data."""
+
+    def __new__(cls, shape, dtype):
+        data = np.array(0, dtype=dtype)
+        strides = (0, ) * len(shape)
+        return np.lib.stride_tricks.as_strided(
+            data, shape=shape, strides=strides).view(cls)
+
+    def copy(self, order='C'):
+        """Return a view instead of materializing the full array."""
+        _ = order
+        return self
+
 
 class SofaStream():
     """
     Read desired data from SOFA-file directly from disk without loading entire
     file into memory.
 
     :class:`SofaStream` opens a SOFA-file and retrieves only the requested
-    data.
+    data. It can also verify the file against the SOFA convention using the
+    same checks as :py:func:`~sofar.Sofa.verify`.
 
     If you want to use all the data from a SOFA-file use :class:`Sofa`
     class and :func:`read_sofa` function instead.
@@ -83,6 +103,134 @@ def __exit__(self, *args):
         """
         self._file.close()
 
+    def verify(self, issue_handling="raise", mode="write"):
+        """
+        Verify a SOFA file against the SOFA standard.
+
+        See :py:func:`~sofar.Sofa.verify` for details.
+
+        This method checks whether mandatory data are present, names, data
+        types, and dimensions follow the SOFA standard, and attribute values
+        are consistent with the SOFA standard. Missing mandatory data raise an
+        error when ``issue_handling='raise'``; otherwise, they are added with
+        their default value and a warning is given.
+
+        Numeric variables are represented by lazy placeholders, so only their
+        type and dimensions are checked without loading their contents into
+        memory. String variables are loaded because their values and lengths
+        can be relevant for convention verification.
+
+        A detailed set of validation rules can be found at
+        https://github.com/pyfar/sofar/tree/main/sofar/verification_rules
+
+        Parameters
+        ----------
+        issue_handling : str, optional
+            Defines how detected issues are handled.
+
+            ``'raise'``
+                Warnings and errors are raised if issues are detected.
+            ``'print'``
+                Issues are printed without raising warnings and errors.
+            ``'return'``
+                Issues are returned as a string but neither raised nor printed.
+
+            The default is ``'raise'``.
+        mode : str, optional
+            The SOFA standard is more strict for writing data than for reading
+            data.
+
+            ``'write'``
+                All units (e.g., ``'meter'``) must be lower case.
+            ``'read'``
+                Units can contain upper case letters (e.g., ``'Meter'``).
+
+            The default is ``'write'``.
+
+        Returns
+        -------
+        issues : str, None
+            Detected issues as a string. None if no issues were detected. Note
+            that this is only returned if ``issue_handling='return'``.
+        """
+        return self._verify_open_file(issue_handling, mode)
+
+    def _verify_open_file(self, issue_handling, mode):
+        """Verify the currently opened NetCDF file."""
+        return self._read_open_file_for_verification().verify(
+            issue_handling=issue_handling, mode=mode)
+
+    def _read_open_file_for_verification(self):
+        """Read the currently opened file using lazy numeric variables."""
+        # get SOFA object with default values and convention metadata
+        sofa = sf.Sofa(
+            self._file.SOFAConventions,
+            version=self._file.SOFAConventionsVersion,
+            verify=False)
+        sofa.protected = False
+
+        # NetCDF attribute _Encoding is skipped when reading SOFA files
+        skip = ["_Encoding"]
+        all_attr = []
+
+        # load global attributes
+        for attr in self._file.ncattrs():
+            value = getattr(self._file, attr)
+            key = f"GLOBAL_{attr}"
+            all_attr.append(key)
+
+            if not hasattr(sofa, key):
+                sofa._add_custom_api_entry(key, value, None, None, "attribute")
+                sofa.protected = False
+            else:
+                setattr(sofa, key, value)
+
+        # load variable metadata and string values
+        for var in self._file.variables.keys():
+            netcdf_variable = self._file[var]
+            key = var.replace(".", "_")
+            all_attr.append(key)
+
+            if netcdf_variable.datatype == "S1":
+                value = _format_value_from_netcdf(netcdf_variable[:], var)
+                dtype = "string"
+            else:
+                value = _LazyArray(
+                    netcdf_variable.shape, netcdf_variable.dtype)
+                dtype = "double"
+
+            if hasattr(sofa, key):
+                setattr(sofa, key, value)
+            else:
+                dimensions = "".join(list(netcdf_variable.dimensions))
+                sofa._add_custom_api_entry(
+                    key, value, None, dimensions, dtype)
+                sofa.protected = False
+
+            # load variable attributes
+            for attr in [a for a in netcdf_variable.ncattrs()
+                         if a not in skip]:
+                value = getattr(netcdf_variable, attr)
+                attr_key = key + "_" + attr
+                all_attr.append(attr_key)
+
+                if not hasattr(sofa, attr_key):
+                    sofa._add_custom_api_entry(
+                        attr_key, value, None, None, "attribute")
+                    sofa.protected = False
+                else:
+                    setattr(sofa, attr_key, value)
+
+        # remove default entries that were not contained in the file
+        attrs = [attr for attr in sofa.__dict__.keys()
+                 if not attr.startswith("_")]
+        for attr in attrs:
+            if attr not in all_attr:
+                delattr(sofa, attr)
+
+        sofa.protected = True
+        return sofa
+
     def __getattr__(self, name):
         """
         Executed when accessing data within a with statement

sofar/utils.py

@@ -262,7 +262,7 @@ def _atleast_nd(array, ndim):
 
 def _nd_newaxis(array, ndim):
     """Append dimensions to the end of an array until array.ndim == ndim."""
-    array = np.array(array)
+    array = np.asarray(array)
 
     for _ in range(ndim - array.ndim):
         array = array[..., np.newaxis]

tests/test_sofastream.py

@@ -39,6 +39,45 @@ def test_sofastream_attribute_error(temp_sofa_file):
             _ = file.Wrong_Attribute
 
 
+def test_sofastream_verify_does_not_call_read_sofa(
+        temp_sofa_file, monkeypatch):
+    """Verify SofaStream does not load the full SOFA file."""
+
+    def fail_read_sofa(*_args, **_kwargs):
+        raise AssertionError("SofaStream.verify must not call read_sofa")
+
+    monkeypatch.setattr(sf, "read_sofa", fail_read_sofa)
+
+    with SofaStream(temp_sofa_file) as file:
+        file.verify()
+
+
+def test_sofastream_read_open_file_for_verification(temp_sofa_file):
+    """Verify the lazy SOFA object retains file metadata."""
+    expected = sf.read_sofa(temp_sofa_file, verify=False)
+
+    with SofaStream(temp_sofa_file) as file:
+        actual = file._read_open_file_for_verification()
+
+    expected_keys = {key for key in expected.__dict__
+                     if not key.startswith("_")}
+    actual_keys = {key for key in actual.__dict__
+                   if not key.startswith("_")}
+    assert actual_keys == expected_keys
+
+    for key in expected_keys:
+        expected_value = getattr(expected, key)
+        actual_value = getattr(actual, key)
+        if isinstance(actual_value, np.ndarray):
+            expected_array = np.atleast_1d(expected_value)
+            assert actual_value.shape == expected_array.shape
+            assert actual_value.dtype == expected_array.dtype
+            if np.issubdtype(expected_array.dtype, np.str_):
+                np.testing.assert_array_equal(actual_value, expected_array)
+        else:
+            assert actual_value == expected_value
+
+
 def test_sofastream_inspect(capfd, temp_sofa_file):
 
     tempdir = TemporaryDirectory()