Prepare 0.10.0 release (#251)

* Fix badges

* Remove references to region refs in docs

* Update pyproject.toml python range and dev status

* Update changelog date

* Fix asset typo and change caps on dandiset

* Remove invalid sphinx_rtd_theme option

* Update conda workflows to address warning

* Incorporate fix from #238

.github/workflows/run_all_tests.yml

@@ -155,12 +155,13 @@ jobs:
           auto-update-conda: true
           python-version: ${{ matrix.python-ver }}
           channels: conda-forge
+          conda-remove-defaults: "true"
 
       - name: Install build dependencies
         run: |
           conda config --set always_yes yes --set changeps1 no
           conda info
-          conda install -c conda-forge tox
+          conda install tox
 
       - name: Conda reporting
         run: |

.github/workflows/run_tests.yml

@@ -139,12 +139,13 @@ jobs:
           auto-update-conda: true
           python-version: ${{ matrix.python-ver }}
           channels: conda-forge
+          conda-remove-defaults: "true"
 
       - name: Install build dependencies
         run: |
           conda config --set always_yes yes --set changeps1 no
           conda info
-          conda install -c conda-forge tox
+          conda install tox
 
       - name: Conda reporting
         run: |

CHANGELOG.md

@@ -1,6 +1,6 @@
 # HDMF-ZARR Changelog
 
-## 0.10.0 (Upcoming)
+## 0.10.0 (December 18, 2024)
 
 ### Enhancements
 * Added initial refactor of export, supporting references and internal/external links from Zarr to Zarr. This will introduce breaking changes that could lead to existing exported files to be invalid. This update removes '.' as the object default file source. @mavaylon1 [#194](https://github.com/hdmf-dev/hdmf-zarr/pull/194)

README.rst

@@ -22,30 +22,30 @@ CI / Health Status
 .. image:: https://codecov.io/gh/hdmf-dev/hdmf-zarr/branch/dev/graph/badge.svg
     :target: https://codecov.io/gh/hdmf-dev/hdmf-zarr
 
-.. image:: https://github.com/hdmf-dev/hdmf-zarr/workflows/Run%20code%20coverage/badge.svg
+.. image:: https://github.com/hdmf-dev/hdmf-zarr/actions/workflows/run_coverage.yml/badge.svg
     :target: https://github.com/hdmf-dev/hdmf-zarr/actions/workflows/run_coverage.yml
 
-.. image:: https://github.com/hdmf-dev/hdmf-zarr/workflows/Run%20tests/badge.svg
+.. image:: https://github.com/hdmf-dev/hdmf-zarr/actions/workflows/run_tests.yml/badge.svg
     :target: https://github.com/hdmf-dev/hdmf-zarr/actions/workflows/run_tests.yml
 
-.. image:: https://github.com/hdmf-dev/hdmf-zarr/workflows/Run%20all%20tests/badge.svg
+.. image:: https://github.com/hdmf-dev/hdmf-zarr/actions/workflows/run_all_tests.yml/badge.svg
     :target: https://github.com/hdmf-dev/hdmf-zarr/actions/workflows/run_all_tests.yml
 
-.. image:: https://github.com/hdmf-dev/hdmf-zarr/workflows/Check%20Sphinx%20external%20links/badge.svg
+.. image:: https://github.com/hdmf-dev/hdmf-zarr/actions/workflows/check_external_links.yml/badge.svg
     :target: https://github.com/hdmf-dev/hdmf-zarr/actions/workflows/check_external_links.yml
 
-.. image:: https://github.com/hdmf-dev/hdmf-zarr/workflows/Deploy%20release/badge.svg
+.. image:: https://github.com/hdmf-dev/hdmf-zarr/actions/workflows/deploy_release.yml/badge.svg
     :target: https://github.com/hdmf-dev/hdmf-zarr/actions/workflows/deploy_release.yml
 
-.. image:: https://github.com/hdmf-dev/hdmf-zarr/workflows/black/badge.svg
-    :target: https://github.com/hdmf-dev/hdmf-zarr/actions/workflows/black.yml
+.. image:: https://github.com/hdmf-dev/hdmf-zarr/actions/workflows/ruff.yml/badge.svg
+    :target: https://github.com/hdmf-dev/hdmf-zarr/actions/workflows/ruff.yml
 
-.. image:: https://github.com/hdmf-dev/hdmf-zarr/workflows/Run%20style%20check/badge.svg
-    :target: https://github.com/hdmf-dev/hdmf-zarr/actions/workflows/run_flake8.yml
+.. image:: https://github.com/hdmf-dev/hdmf-zarr/actions/workflows/codespell.yml/badge.svg
+    :target: https://github.com/hdmf-dev/hdmf-zarr/actions/workflows/codespell.yml
 
+.. image:: https://github.com/hdmf-dev/hdmf-zarr/actions/workflows/HDMF_dev.yaml/badge.svg
+    :target: https://github.com/hdmf-dev/hdmf-zarr/actions/workflows/HDMF_dev.yaml
 
-
-Citing hdmf-zarr
 ----------------
 
 If you use HDMF or hdmf_zarr in your research, please use the following citation:

docs/gallery/plot_convert_nwb_hdf5.py

@@ -14,7 +14,7 @@
 # -----
 #
 # Here we use a small NWB file from the DANDI neurophysiology data archive from
-# `DANDIset 000009 <https://dandiarchive.org/dandiset/000009/0.220126.1903>`_ as an example.
+# `Dandiset 000009 <https://dandiarchive.org/dandiset/000009/0.220126.1903>`_ as an example.
 # To download the file directly from DANDI we can use:
 #
 # .. code-block:: python
@@ -29,7 +29,7 @@
 #        filename = os.path.basename(asset.path)
 #    asset.download(filename)
 #
-# We here use a local copy of a small file from this DANDIset as an example:
+# We here use a local copy of a small file from this Dandiset as an example:
 
 
 # sphinx_gallery_thumbnail_path = 'figures/gallery_thumbnail_plot_convert_nwb.png'

docs/gallery/resources/README.rst

@@ -4,11 +4,11 @@ Resources
 sub_anm00239123_ses_20170627T093549_ecephys_and_ogen.nwb
 --------------------------------------------------------
 
-This NWB file was downloaded from `DANDIset 000009 <https://dandiarchive.org/dandiset/000009/0.220126.1903>`_
+This NWB file was downloaded from `Dandiset 000009 <https://dandiarchive.org/dandiset/000009/0.220126.1903>`_
 The file was modified to replace ``:`` characters used in the name of the ``ElectrodeGroup`` called ``ADunit: 32`` in
 ``'general/extracellular_ephys/`` to ``'ADunit_32'``. The dataset ``general/extracellular_ephys/electrodes/group_name``
 as part of the electrodes table was updated accordingly to list the appropriate group name. This is to avoid issues
-on Windows file systems that do not support ``:`` as part of folder names. The asses can be downloaded from DANDI via:
+on Windows file systems that do not support ``:`` as part of folder names. The asset can be downloaded from DANDI via:
 
 .. code-block:: python
     :linenos:

docs/source/conf.py

@@ -119,7 +119,6 @@
 
 html_theme_options = {
     'logo_only': False,  # Only show the hdmf-zarr logo without the documentation title
-    'display_version': True,
     'prev_next_buttons_location': 'bottom',  # Show previous/next button at the bottom
     'style_external_links': True,  # Add marker to indicate external links
     'vcs_pageview_mode': '',

docs/source/overview.rst

@@ -29,7 +29,6 @@ Supported features
 Known Limitations
 -----------------
 
-- Support for region references is not yet implemented. See also :ref:`sec-zarr-storage-references-region` for details.
 - The Zarr backend is currently experimental and may still change.
 - Attributes are stored as JSON documents in Zarr (using the DirectoryStore). As such, all attributes must be JSON serializable. The :py:class:`~hdmf_zarr.backend.ZarrIO` backend attempts to cast types to JSON serializable types as much as possible.
 - Currently the :py:class:`~hdmf_zarr.backend.ZarrIO` backend supports Zarr's directory-based stores :py:class:`~zarr.storage.DirectoryStore`, :py:class:`~zarr.storage.NestedDirectoryStore`, and :py:class:`~zarr.storage.TempStore`. Other `Zarr stores <https://zarr.readthedocs.io/en/stable/api/storage.html>`_ could be added but will require proper treatment of links and references for those backends as links are not supported in Zarr (see `zarr-python issues #389 <https://github.com/zarr-developers/zarr-python/issues/389>`_.

docs/source/storage.rst

@@ -260,7 +260,7 @@ Storing object references in Attributes
 Object references are stored in a attributes as dicts with the following keys:
 
 * ``zarr_dtype`` : Indicating the data type for the attribute. For object references
-  ``zarr_dtype`` is set to ``"object"`` (or ``"region"`` for :ref:`sec-zarr-storage-references-region`)
+  ``zarr_dtype`` is set to ``"object"``
 * ``value``: The value of the object references, i.e., here the py:class:`~hdmf_zarr.utils.ZarrReference`
   dictionary with the ``source``, ``path``, ``object_id``, and ``source_object_id`` keys defining
   the object reference, with the definition of the keys being the same as
@@ -280,36 +280,6 @@ For example in NWB, the attribute ``ElectricalSeries.electrodes.table`` would be
         "zarr_dtype": "object"
     }
 
-.. _sec-zarr-storage-references-region:
-
-Region references
------------------
-
-Region references are similar to object references, but instead of references other Datasets or Groups,
-region references link to subsets of another Dataset. To identify region references, the reserved attribute
-``zarr_dtype`` is set to ``'region'`` (see also :ref:`sec-zarr-storage-attributes-reserved`). In addition
-to the ``source`` and ``path``, the  py:class:`~hdmf_zarr.utils.ZarrReference` object will also need to
-store the definition of the ``region`` that is being referenced, e.g., a slice or list on point indices.
-
-.. warning::
-
-    Region references are not yet fully implemented in :py:class:`~hdmf_zarr.backend.ZarrIO`.
-    To implement region references will require updating:
-    1)  py:class:`~hdmf_zarr.utils.ZarrReference` to add a ``region`` key to support storing
-    the selection for the region,
-    2) :py:meth:`~hdmf_zarr.backend.ZarrIO._create_ref` to support passing in the region definition to
-    be added to the py:class:`~hdmf_zarr.utils.ZarrReference`,
-    3) :py:meth:`~hdmf_zarr.backend.ZarrIO.write_dataset` already partially implements the required
-    logic for creating region references by checking for :py:class:`hdmf.build.RegionBuilder` inputs
-    but will likely need updates as well
-    4) :py:meth:`~hdmf_zarr.backend.ZarrIO.__read_dataset` to support reading region references,
-    which may also require updates to :py:meth:`~hdmf_zarr.backend.ZarrIO.__parse_ref` and
-    :py:meth:`~hdmf_zarr.backend.ZarrIO.__resolve_ref`, and
-    5) and possibly other parts of :py:class:`~hdmf_zarr.backend.ZarrIO`.
-    6) The py:class:`~hdmf_zarr.zarr_utils.ContainerZarrRegionDataset` and
-    py:class:`~hdmf_zarr.zarr_utils.ContainerZarrRegionDataset` classes will also need to be finalized
-    to support region references.
-
 
 .. _sec-zarr-storage-dtypes:
 
@@ -357,10 +327,6 @@ The mappings of data types is as follows
     |  * "reference"           | dataset. See                       |                |
     |  * "object"              | :ref:`sec-zarr-storage-references` |                |
     +--------------------------+------------------------------------+----------------+
-    |  * region                | Reference to a region              |                |
-    |                          | of another dataset. See            |                |
-    |                          | :ref:sec-zarr-storage-references`  |                |
-    +--------------------------+------------------------------------+----------------+
     |  * compound dtype        | Compound data type                 |                |
     +--------------------------+------------------------------------+----------------+
     |  * "isodatetime"         | ASCII ISO8061 datetime string.     | variable       |

pyproject.toml

@@ -7,6 +7,7 @@ name = "hdmf_zarr"
 authors = [
   { name="Oliver Ruebel", email="[email protected]" },
   { name="Matthew Avaylon", email="[email protected]" },
+  { name="Ryan Ly", email="[email protected]" },
 ]
 description = "A package defining a Zarr I/O backend for HDMF"
 readme = "README.rst"
@@ -18,8 +19,9 @@ classifiers = [
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "License :: OSI Approved :: BSD License",
-    "Development Status :: 5 - Production/Stable",
+    "Development Status :: 4 - Beta",
     "Intended Audience :: Developers",
     "Intended Audience :: Science/Research",
     "Operating System :: Microsoft :: Windows",
@@ -130,7 +132,6 @@ line-length = 120
 
 [tool.ruff.lint.per-file-ignores]
 "docs/gallery/*" = ["E402", "T201"]
-"src/*/__init__.py" = ["F401"]
 "test_gallery.py" = ["T201"]
 
 [tool.ruff.lint.mccabe]

src/hdmf_zarr/backend.py

@@ -803,7 +803,10 @@ def resolve_ref(self, zarr_ref):
             source_file = str(zarr_ref["source"])
         # Resolve the path relative to the current file
         if not self.is_remote():
-            source_file = os.path.abspath(source_file)
+            if isinstance(self.source, str) and self.source.startswith(("s3://")):
+                source_file = self.source
+            else:
+                source_file = os.path.abspath(source_file)
         else:
             # get rid of extra "/" and "./" in the path root and source_file
             root_path = str(self.path).rstrip("/")