Read Zarr datasets + read multiple datasets + read CDL strings

.pre-commit-config.yaml

@@ -33,8 +33,9 @@ repos:
   # https://google.github.io/styleguide/pyguide.html#381-docstrings) as much
   # as possible (see https://github.com/myint/docformatter for docs, with
   # configuration as below)
-  - repo: https://github.com/myint/docformatter
-    rev: v1.4
+#  - repo: https://github.com/myint/docformatter
+  - repo: https://github.com/PyCQA/docformatter
+    rev: v1.7.6
     hooks:
       - id: docformatter
         # These arguments act as the configuration for docformatter. They:
@@ -48,7 +49,7 @@ repos:
   # be detected by the 'pydocstyle' checker
   # (see http://www.pydocstyle.org/en/stable/index.html for
   # docs and see the cfdm .pydocstyle.ini file for our custom configuration)
-  - repo: https://github.com/pycqa/pydocstyle
+  - repo: https://github.com/PyCQA/pydocstyle
     rev: 6.3.0
     hooks:
       - id: pydocstyle
@@ -67,7 +68,7 @@ repos:
   # (see https://pycqa.github.io/isort/ for documentation). It is fully
   # compatible with 'black' with the lines set to ensure so in the repo's
   # pyproject.toml. Other than that and the below, no extra config is required.
-  - repo: https://github.com/pycqa/isort
+  - repo: https://github.com/PyCQA/isort
     rev: 5.13.2
     hooks:
       - id: isort

Changelog.rst

@@ -3,10 +3,19 @@ Version NEXTVERSION
 
 **2025-??-??**
 
+* Read Zarr datasets with `cfdm.read`
+  (https://github.com/NCAS-CMS/cfdm/issues/335)
+* Read multiple datasets simultaneausly with `cfdm.read`
+  (https://github.com/NCAS-CMS/cfdm/issues/336)
+* New keyword parameters to `cfdm.read`: ``recursive``,
+  ``followlinks`` (https://github.com/NCAS-CMS/cfdm/issues/336)
+* New keyword parameters to `cfdm.read`: ``cdl_string``
+  (https://github.com/NCAS-CMS/cfdm/issues/337)
 * Update CF aggregation keywords
   (https://github.com/NCAS-CMS/cfdm/issues/341)
 * Set new minimum version of `dask`: ``2025.5.1``
   (https://github.com/NCAS-CMS/cfdm/issues/339)
+* New dependency: ``zarr>=3.0.8``
 * Changed dependency: ``dask>=2025.5.1``
 
 ----

README.md

@@ -79,8 +79,8 @@ inspecting it:
 
 The ``cfdm`` package can:
 
-* read field and domain constructs from netCDF and CDL datasets with a
-  choice of netCDF backends,and in  local, http, and s3 locations,
+* read field and domain constructs from netCDF, CDL, and Zarr datasets
+  with a choice of netCDF backends, and in  local, http, and s3 locations,
 * be fully flexible with respect to HDF5 chunking,
 * create new field and domain constructs in memory,
 * write and append field and domain constructs to netCDF datasets on disk,

cfdm/__init__.py

@@ -1,4 +1,4 @@
-"""cfdm is a reference implementation of the CF data model.
+"""Cfdm is a reference implementation of the CF data model.
 
 It identifies the fundamental elements of the CF conventions and
 shows how they relate to each other, independently of the netCDF
@@ -18,7 +18,7 @@
 
 The cfdm package can:
 
-    * read field constructs from netCDF and CDL datasets,
+    * read field constructs from netCDF, CDL, and Zarr datasets,
     * create new field constructs in memory,
     * write and append field constructs to netCDF datasets on disk,
     * read, write, and create datasets containing hierarchical groups,
@@ -54,6 +54,7 @@
     "dask",
     "scipy",
     "h5netcdf",
+    "zarr",
     "s3fs",
     "uritools",
     "cfunits",
@@ -113,6 +114,19 @@
             f"Got {h5py.__version__} at {h5py.__file__}"
         )
 
+# Check the version of zarr
+try:
+    import zarr
+except ImportError as error1:
+    raise ImportError(_error0 + str(error1))
+else:
+    _minimum_vn = "3.0.8"
+    if Version(zarr.__version__) < Version(_minimum_vn):
+        raise ValueError(
+            f"Bad zarr version: cfdm requires zarr>={_minimum_vn}. "
+            f"Got {zarr.__version__} at {zarr.__file__}"
+        )
+
 # Check the version of s3fs
 try:
     import s3fs
@@ -244,6 +258,7 @@
     RaggedIndexedContiguousArray,
     SparseArray,
     SubsampledArray,
+    ZarrArray,
 )
 
 from .data import (

cfdm/auxiliarycoordinate.py

@@ -40,7 +40,7 @@ class AuxiliaryCoordinate(
 
     {{netCDF UGRID node coordinate}}
 
-    {{netCDF HDF5 chunks}}
+    {{netCDF dataset chunks}}
 
     .. versionadded:: (cfdm) 1.7.0
 

cfdm/bounds.py

@@ -38,7 +38,7 @@ class Bounds(
 
     {{netCDF variable group}}
 
-    {{netCDF HDF5 chunks}}
+    {{netCDF dataset chunks}}
 
     .. versionadded:: (cfdm) 1.7.0
 

cfdm/cellconnectivity.py

@@ -60,6 +60,8 @@ class CellConnectivity(
 
     {{netCDF variable}}
 
+    {{netCDF dataset chunks}}
+
     .. versionadded:: (cfdm) 1.11.0.0
 
     """

cfdm/cellmeasure.py

@@ -39,7 +39,7 @@ class CellMeasure(
 
     {{netCDF global attributes}}
 
-    {{netCDF HDF5 chunks}}
+    {{netCDF dataset chunks}}
 
     .. versionadded:: (cfdm) 1.7.0