Miscellaneous-fixes

.gitignore

@@ -64,5 +64,8 @@ src/nexusformat/_version.py
 # miscellaneous system files
 .directoryhash
 
+# Claude settings
+.claude
+
 # uv
 uv.lock

src/nexusformat/nexus/tree.py

@@ -352,15 +352,15 @@ def natural_sort(key):
 
     Parameters
     ----------
-    key : str
+    key : str or Path
         String in the list to be sorted.
 
     Returns
     -------
     list
         List of components splitting embedded numbers as integers.
     """
-    return [int(t) if t.isdigit() else t for t in re.split(r'(\d+)', key)]
+    return [int(t) if t.isdigit() else t for t in re.split(r'(\d+)', str(key))]
 
 
 class NeXusError(Exception):
@@ -2345,10 +2345,7 @@ def save(self, filename=None, mode='w-', **kwargs):
                 f.writefile(root)
                 root = f._root
                 root._file = f
-            if mode == 'w' or mode == 'w-':
-                root._mode = 'rw'
-            else:
-                root._mode = mode
+            root._mode = 'rw'
             self.set_changed()
             return root
         else:
@@ -4383,17 +4380,9 @@ def plot_shape(self):
         """
         Shape of NXfield for plotting.
 
-        Size-1 axes are removed from the shape for multidimensional
-        data.
+        Size-1 axes are removed from the shape.
         """
-        try:
-            _shape = list(self.shape)
-            if len(_shape) > 1:
-                while 1 in _shape:
-                    _shape.remove(1)
-            return tuple(_shape)
-        except Exception:
-            return ()
+        return tuple(s for s in self.shape if s > 1)
 
     @property
     def plot_rank(self):
@@ -4614,7 +4603,10 @@ def __deepcopy__(self, memo={}):
         dpcpy._vidx = copy(obj._vidx)
         dpcpy._vpath = copy(obj._vpath)
         dpcpy._vfiles = copy(obj._vfiles)
-        shape = (len(obj._vfiles),) + slice_shape(obj._vidx, obj._vshape)
+        if obj._vidx:
+            shape = (len(obj._vfiles),) + slice_shape(obj._vidx, obj._vshape)
+        else:
+            shape = (len(obj._vfiles),) + obj._vshape
         dpcpy._create_virtual_data(shape=shape, idx=obj._vidx)
         dpcpy._h5opts = copy(obj._h5opts)
         dpcpy._changed = True
@@ -6364,12 +6356,15 @@ def __enter__(self):
             Current NXroot instance.
         """
         if self.nxfile:
+            self._current_mode = self._mode
+            self._mode = self._file.mode = 'rw'
             self.nxfile.__enter__()
         return self
 
     def __exit__(self, *args):
         """Close the NeXus file."""
         if self.nxfile:
+            self._mode = self._file.mode = self._current_mode
             self.nxfile.__exit__()
 
     def serialize(self):
@@ -7912,7 +7907,8 @@ def nxauxiliary_signals(self, signals):
             signals = list(signals)
             if all(isinstance(signal, str) for signal in signals):
                 self.attrs['auxiliary_signals'] = signals
-            elif all(isinstance(signal, NXfield) for signal in signals):
+            elif all(isinstance(signal, NXfield) or
+                     isinstance(signal, NXlink)for signal in signals):
                 self.attrs['auxiliary_signals'] = [signal.nxname for signal
                                                    in signals]
             else:
@@ -8002,6 +7998,12 @@ def __init__(self, *args, **kwargs):
             from datetime import datetime as dt
             self.date = dt.isoformat(dt.today())
 
+    def set_date(self, date=None):
+        """Set the date to a specific value."""
+        from datetime import datetime as dt
+        if date is None:
+            date = dt.today()
+        self.date = dt.isoformat(date)
 
 class NXnote(NXgroup):
 
@@ -8590,7 +8592,7 @@ def consolidate(files, data_path, scan_path=None, idx=None):
         Data slice to be used in the virtual field, by default None
     """
 
-    if isinstance(files[0], str):
+    if isinstance(files[0], str) or isinstance(files[0], Path):
         files = [nxload(f) for f in files]
     if isinstance(data_path, NXdata):
         data_path = data_path.nxpath
@@ -8602,6 +8604,8 @@ def consolidate(files, data_path, scan_path=None, idx=None):
     else:
         scan_files = [f for f in files if data_path in f
                       and f[data_path].nxsignal.exists()]
+    if len(scan_files) == 0:
+        raise NeXusError(f'{data_path} not found in files')
     scan_file = scan_files[0]
     if scan_path:
         scan_values = [f[scan_path] for f in scan_files]
@@ -8616,15 +8620,18 @@ def consolidate(files, data_path, scan_path=None, idx=None):
     else:
         scan_axis = NXfield(range(len(scan_files)), name='file_index',
                             long_name='File Index')
-    signal = scan_file[data_path].nxsignal
     axes = scan_file[data_path].nxaxes
-    if idx is not None:
-        axes = [axis[s] for axis, s in zip(axes, idx)]
-    sources = [f[signal.nxpath].nxfilename for f in scan_files]
-    scan_field = NXvirtualfield(signal, sources, shape=signal.shape, idx=idx,
-                                name=signal.nxname)
-    scan_data = NXdata(scan_field, [scan_axis] + axes,
-                       name=scan_file[data_path].nxname)
+    for signal in [s for s in scan_file[data_path].nxsignals if s.exists()]:
+        if idx is not None:
+            axes = [axis[s] for axis, s in zip(axes, idx)]
+        sources = [f[signal.nxpath].nxfilename for f in scan_files]
+        scan_field = NXvirtualfield(signal, sources, shape=signal.shape,
+                                    idx=idx, name=signal.nxname)
+        if signal.nxname == scan_file[data_path].nxsignal.nxname:
+            scan_data = NXdata(scan_field, [scan_axis] + axes,
+                               name=scan_file[data_path].nxname)
+        else:
+            scan_data[signal.nxname] = scan_field
     scan_data.title = data_path
     return scan_data
 

src/nexusformat/nexus/utils.py

@@ -22,7 +22,7 @@
 from dateutil.parser import parse
 
 
-name_pattern = re.compile(r'^[a-zA-Z0-9_]([a-zA-Z0-9_.]*[a-zA-Z0-9_])?$')
+name_pattern = re.compile(r'^[a-zA-Z_][a-zA-Z0-9_]*$')
 
 
 def get_logger():