clawhdf5-netcdf4: phony dimensions, skipped types and order as netCDF-C
Read a file's metadata the way netCDF-C 4.9.3 does (libhdf5/hdf5open.c), for the whole file on first use (src/model.rs, replacing src/scope.rs): - links in creation order when the group tracks it, else name order; a group's datasets before its subgroups; dimension ids file-wide; - variables' dimensions from _Netcdf4Coordinates (file-wide ids), else the scales DIMENSION_LIST attaches when the first axis has one, else netCDF-C's phony dimensions phony_dim_<id> (create_phony_dims: shared by length and unlimitedness within a group, not between two axes of one variable, numbered subgroups first, a zero length unlimited); - datasets of types netCDF-C cannot represent are not variables (references, bit fields, time, arrays, compounds/enums/VLENs over them), replaying netCDF-C's file-wide type list, failed types included; - unlimited lengths as nc4_find_dim_len (its group and below). NcType gains Enum, Compound, VLen, Opaque and is #[non_exhaustive]; Variable::nc_type is netCDF-C's type (1-byte strings NC_CHAR). New clawhdf5_format::group_v2::links_in_creation_order_in. Tests compare with netCDF-C itself (tests/netcdf_c_view.py calls the libnetcdf netCDF4-python bundles through ctypes): new interop cases for h5py files without dimension scales, every type class, link order; and the gated corpus_vs_netcdf_c (CLAWHDF5_NETCDF_CORPUS): 420 of the 429 conformance-corpus files netCDF-C opens match (main: 68); the other 9 are explained in tests/corpus_known_differences.txt and known-issues. Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
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osobh
@@ -36,23 +36,46 @@ let values: Vec<f64> = temp.read_f64()?;
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| Item | What |
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|---|---|
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| `NetCDF4File` | `open`, `from_bytes`, `dimensions`, `variables`, `variable_names`, `variable`, `global_attrs`, `group`, `group_names`, `nc_properties`, and `hdf5_file` for the underlying `clawhdf5::File` |
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| `NetCDF4File` | `open`, `from_bytes`, `dimensions`, `variables`, `variable_names`, `variable` (a name or a path into a subgroup), `global_attrs`, `group` (a name or a path), `group_names`, `nc_properties`, and `hdf5_file` for the underlying `clawhdf5::File` |
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| `NetCDF4Group` | the same for a sub-group (`dimensions`, `variables`, `variable_names`, `attrs`, nested `group`) |
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| `Variable` | `name`, `shape`, `stored_shape`, `dimensions`, `nc_type`, `is_coordinate`, `attrs`, `cf_attributes`; `read_f64` (CF scale/offset and fill applied), `read_raw_f32`/`_f64`/`_i32`/`_i64`/`_u64`, `read_string`, `read_raw` |
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| `Dimension` | `name`, `size`, `is_unlimited` (an unlimited dimension's `size` is its current length as netCDF-C reports it: the largest extent of the variables using it) |
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| `CfAttributes` | CF convention attributes: `units`, `long_name`, `standard_name`, `fill_value` (`_FillValue`), `missing_value`, `scale_factor`, `add_offset`, `valid_range`, `calendar`, `axis` |
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| `NcType` | the NetCDF type of a variable |
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| `NcType` | the NetCDF type of a variable: an atomic type (`Byte` ... `UInt64`, `Float`, `Double`, `Char`, `String`) or the class of a user-defined one (`Enum`, `Compound`, `VLen`, `Opaque`); `#[non_exhaustive]` |
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Variables and dimensions follow netCDF-C:
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Groups, dimensions and variables are what netCDF-C 4.9.3 reports
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(`libhdf5/hdf5open.c`), names, order and types included. The first call
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that needs them reads the metadata of the whole file, as `nc_open` does:
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- A variable's dimensions are the ones the file names: the ids in its
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`_Netcdf4Coordinates` attribute, else the dimension scales its
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`DIMENSION_LIST` references, found in its group or a parent group. Only
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an axis the file names no dimension for (an HDF5 file not written by a
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netCDF library) gets the first dimension of the group of the same size,
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else an anonymous `dim_<size>`.
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- Dimension scales that are only dimensions are not variables; a dataset
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- Order: a group's links in creation order when it tracks it (netCDF-4
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files do), else in name order (h5py's default); groups and variables in
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that order, dimensions by id.
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- A dimension scale defines a dimension (its `_Netcdf4Dimid`, else the
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next free id; unlimited when its first axis is or its length is 0);
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scales that are only dimensions are not variables, and a dataset
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`_nc4_non_coord_<name>` is the variable `<name>`.
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- A variable's dimensions are the ones the file names: the ids in its
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`_Netcdf4Coordinates` attribute (any group), else — when its first axis
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has one — the dimension scales its `DIMENSION_LIST` attaches, found in
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its group or a parent group.
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- Otherwise (an HDF5 file not written by a netCDF library) its axes get
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netCDF-C's **phony dimensions** `phony_dim_<n>`: per axis, the first
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dimension of the variable's group with the same length and
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unlimitedness that an earlier axis of the variable does not use, else a
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new one. The numbers run file-wide, a group's subgroups before its own
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variables.
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- Datasets of types netCDF-C cannot represent are not variables:
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references, bit fields, time and array types, and compounds, enums and
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VLENs over members or base types that are not netCDF atomic types (4-
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and 8-byte floats only) or types netCDF-C has read before in the file.
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Enum, compound, VLEN and opaque datasets are variables of those classes
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(netCDF4-python itself leaves out opaque ones).
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- Two deliberate differences: floats of other than 4 or 8 bytes (half,
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bfloat16, 4/6/8-bit floats, `long double`) are `Float`/`Double` and
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read as numbers, where netCDF-C 4.9.3 on libhdf5 1.14.6 labels them
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`NC_STRING`; and an axis netCDF-C leaves without a dimension (an id or
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scale it cannot find, or no scale on an axis after a first one that has
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one, where it reads uninitialised memory) gets one by the phony rule.
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- A variable along an unlimited dimension has the dimension's length:
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`shape` is that length, and the reads return that many values, the
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records the variable has not written as its fill value (`_FillValue`,
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@@ -60,11 +83,23 @@ Variables and dimensions follow netCDF-C:
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`stored_shape` is the HDF5 dataset's extent.
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No cargo features. Tests compare against files written by netCDF4-python,
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h5py dimension scales, h5netcdf and xarray, variable by variable with what
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netCDF4-python reads (`tests/interop_tests.rs`; the CI job requires them
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with `CLAWHDF5_REQUIRE_INTEROP=1`; the h5netcdf cases skip when h5netcdf is
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not installed). What the HDF5 reader underneath cannot read is listed in
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[`docs/known-issues.md`](../../docs/known-issues.md).
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h5py (with and without dimension scales, every HDF5 type class), h5netcdf
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and xarray, with what netCDF4-python reads and with what netCDF-C itself
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reports (`tests/interop_tests.rs`; `tests/netcdf_c_view.py` calls the
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libnetcdf netCDF4-python bundles; the CI job requires them with
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`CLAWHDF5_REQUIRE_INTEROP=1`; the h5netcdf cases skip when h5netcdf is not
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installed). `tests/corpus_vs_netcdf_c.rs` compares every file of a corpus
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netCDF-C opens, when `CLAWHDF5_NETCDF_CORPUS` names one: over the
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conformance corpus, 420 of 429 files match (tank, 2026-09-29), and the
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other 9 are explained in `tests/corpus_known_differences.txt`:
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```sh
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CLAWHDF5_NETCDF_CORPUS=conformance/.cache/corpus CLAWHDF5_PYTHON=$PWD/.venv/bin/python \
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cargo test -p clawhdf5-netcdf4 --test corpus_vs_netcdf_c -- --nocapture
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```
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The differences from netCDF-C, and what the HDF5 reader underneath cannot
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read, are listed in [`docs/known-issues.md`](../../docs/known-issues.md).
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## License
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