clawhdf5-netcdf4: variables' dimensions come from the file

Variables got the first unused dimension of equal size, so a variable on
an unlimited dimension with fewer records got an anonymous dim_<n>, and
dimensions of one size could be swapped. Resolve them as netCDF-C does
(libhdf5/hdf5open.c): _Netcdf4Coordinates ids, else the scales
DIMENSION_LIST references (the last one attached to an axis), searched in
the variable's group and its parents; a coordinate variable is on its own
scale. Size matching remains only for axes the file names nothing for.

variables()/variable_names() leave out dimension scales that are only
dimensions, and _nc4_non_coord_<name> is the variable <name>.
Variable::shape is the netCDF shape (an unlimited dimension's length) and
the reads pad unwritten records with the fill value (_FillValue, else
NC_FILL_*; NaN from read_f64); Variable::stored_shape is the HDF5 extent.
New NetCDF4File::variable_names.

Tests compare with netCDF4-python variable by variable: the known-issues
reproducer, equal sizes, (p, p), scalars, inherited dimensions, unwritten
records, h5py dimension scales, h5netcdf and xarray files. CI installs
h5netcdf. known-issues entry moved to Fixed (history); stale open-table
row for the unlimited-size fix removed.

Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>

crates/clawhdf5-netcdf4/src/lib.rs

@@ -27,6 +27,7 @@ pub mod cf;
 pub mod dimension;
 pub mod error;
 pub mod group;
+mod scope;
 pub mod types;
 pub mod variable;
 
@@ -75,25 +76,25 @@ impl NetCDF4File {
 
     /// List dimensions defined in the root group.
     pub fn dimensions(&self) -> Result<Vec<Dimension>, Error> {
-        dimension::extract_dimensions_from_datasets(&self.hdf5.root(), &self.hdf5)
+        Ok(dimension::group_dims(&self.hdf5, &self.hdf5.root())?.dims)
     }
 
-    /// List all variables in the root group.
+    /// List all variables in the root group: its datasets, except the
+    /// dimension scales that are only dimensions (netCDF-C does not list
+    /// them either).
     pub fn variables(&self) -> Result<Vec<Variable<'_>>, Error> {
-        let dims = self.dimensions()?;
-        variable::build_variables(&self.hdf5.root(), &dims)
+        scope::Scope::new(&self.hdf5, "/")?.variables()
+    }
+
+    /// The names of the root group's variables (see
+    /// [`variables`](Self::variables)).
+    pub fn variable_names(&self) -> Result<Vec<String>, Error> {
+        scope::Scope::new(&self.hdf5, "/")?.variable_names()
     }
 
     /// Get a specific variable by name from the root group.
     pub fn variable(&self, name: &str) -> Result<Variable<'_>, Error> {
-        let dims = self.dimensions()?;
-        let ds = self
-            .hdf5
-            .dataset(name)
-            .map_err(|_| Error::VariableNotFound(name.to_string()))?;
-        let shape = ds.shape()?;
-        let var_dims = variable::match_dimensions_to_variable(&shape, &dims);
-        Ok(Variable::new(name.to_string(), ds, var_dims))
+        scope::variable_at(&self.hdf5, "", name)
     }
 
     /// Read all global (root group) attributes.
@@ -112,7 +113,12 @@ impl NetCDF4File {
             .hdf5
             .group(name)
             .map_err(|_| Error::GroupNotFound(name.to_string()))?;
-        Ok(NetCDF4Group::new(name.to_string(), &self.hdf5, hdf5_group))
+        Ok(NetCDF4Group::new(
+            name.to_string(),
+            name.to_string(),
+            &self.hdf5,
+            hdf5_group,
+        ))
     }
 
     /// Access the underlying HDF5 file for advanced operations.