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]>

CHANGELOG.md

@@ -2,6 +2,59 @@
 
 ## Unreleased
 
+### NetCDF-4: variables' dimensions come from the file (2026-09-28)
+- `clawhdf5-netcdf4` gave each variable the first unused dimension of
+  equal size (else an anonymous `dim_<n>`), so a variable on an unlimited
+  dimension it had written fewer records of got `dim_<n>`, and dimensions
+  of one size could be swapped. It now resolves them as netCDF-C does
+  (`libhdf5/hdf5open.c`): the ids in the variable's `_Netcdf4Coordinates`
+  (each scale's `_Netcdf4Dimid`), else the scales its `DIMENSION_LIST`
+  references (object references, also the revised `H5T_STD_REF`; of
+  several scales attached to one axis, the last, as netCDF-C's
+  `dimscale_visitor` keeps), looked up in its group and then each parent
+  group; a coordinate variable is on
+  its own scale. Only an axis with neither (a file not written by a netCDF
+  library) is still matched by size. A variable may use one dimension
+  twice (`(p, p)`).
+- `variables()` and `variable_names()` leave out the dimension scales that
+  are only dimensions (`NAME` "This is a netCDF dimension but not a netCDF
+  variable."), as netCDF-C does, and `variable()` refuses them
+  (`VariableNotFound`). A variable stored as `_nc4_non_coord_<name>`
+  (netCDF-C's name for a variable sharing a dimension's name without being
+  its coordinate variable) is listed and found as `<name>`.
+  `NetCDF4File::variable_names` is new; `NetCDF4Group::variable_names` used
+  to list every dataset.
+- A variable along an unlimited dimension has the dimension's length, as in
+  netCDF: `Variable::shape` is that length and the reads return that many
+  values, the records it has not written as the fill value (`_FillValue`,
+  else netCDF's `NC_FILL_*` for the type; `""` for strings; NaN from
+  `read_f64`). It was the HDF5 extent. `Variable::stored_shape` (new) is the
+  HDF5 extent. Where the unlimited dimension is not a variable's first,
+  unwritten values are placed per row, as netCDF-C's element and row reads
+  return them; a whole-variable read through netCDF-C 4.9.3
+  (netCDF4-python 1.7.4) instead returns the written values first, then the
+  fill.
+- A variable's attributes are read when it is opened (they were read on
+  first use).
+- Tests, compared with netCDF4-python 1.7.4 (netCDF-C 4.9.3) variable by
+  variable (dimensions, shape, every value): the known-issues reproducer;
+  two dimensions of one size in either order, one dimension used twice, a
+  scalar, a non-coordinate variable named like a dimension, a subgroup and
+  a sub-subgroup on their ancestors' dimensions; unwritten records of
+  `i1`/`i4`/`u8`/`f4`/`f8`/string variables, with and without
+  `_FillValue`; a file of h5py dimension scales (no netCDF attributes);
+  h5netcdf 1.8.1 and xarray 2026.7.0 files (engines netcdf4 and h5netcdf).
+  The h5netcdf cases skip when h5netcdf is not installed; CI now installs
+  it. A one-off comparison over the 78 conformance-corpus files
+  netCDF4-python opens (tank, 2026-09-28; a throwaway test, not committed)
+  found 52 files with the same variables, dimensions and shapes, and the
+  same values in every numeric variable of up to 5000 elements (enum
+  variables were not compared). The other 26 have no dimension scales
+  (netCDF-C names their axes `phony_dim_<n>`; this crate still matches by
+  size or names them `dim_<size>`) or hold datasets of types netCDF-C
+  skips (opaque, references). Affected v2.1.0 to v2.7.0.
+  `docs/known-issues.md`.
+
 ### A dropped `FileEditor` releases its lock at once (2026-09-28)
 - `FileEditor`'s `flock` could outlive the editor for a moment when
   another thread forked to spawn a process: the child shared the locked