Merge branch 'main' into hdf5_reader

.pre-commit-config.yaml

@@ -11,7 +11,7 @@ repos:
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: "v0.6.9"
+    rev: "v0.7.2"
     hooks:
       # Run the linter.
       - id: ruff

.readthedocs.yml

@@ -13,6 +13,7 @@ build:
 # Build documentation in the doc/ directory with Sphinx
 sphinx:
   configuration: docs/conf.py
+  fail_on_warning: true
 
 # Optionally declare the Python requirements required to build your docs
 conda:

README.md

@@ -2,7 +2,7 @@
 
 **VirtualiZarr creates virtual Zarr stores for cloud-friendly access to archival data, using familiar xarray syntax.**
 
-VirtualiZarr (pronounced like "virtualize" but more piratey) grew out of [discussions](https://github.com/fsspec/kerchunk/issues/377) on the [kerchunk repository](https://github.com/fsspec/kerchunk), and is an attempt to provide the game-changing power of kerchunk in a zarr-native way, and with a familiar array-like API.
+VirtualiZarr (pronounced like "virtualizer" but more piratey) grew out of [discussions](https://github.com/fsspec/kerchunk/issues/377) on the [kerchunk repository](https://github.com/fsspec/kerchunk), and is an attempt to provide the game-changing power of kerchunk in a zarr-native way, and with a familiar array-like API.
 
 You now have a choice between using VirtualiZarr and Kerchunk: VirtualiZarr provides [almost all the same features](https://virtualizarr.readthedocs.io/en/latest/faq.html#how-do-virtualizarr-and-kerchunk-compare) as Kerchunk.
 

ci/environment.yml

@@ -7,7 +7,7 @@ dependencies:
   - h5py
   - hdf5
   - netcdf4
-  - xarray>=2024.6.0
+  - xarray>=2024.10.0
   - kerchunk>=0.2.5
   - numpy>=2.0.0
   - ujson

ci/min-deps.yml

@@ -6,7 +6,7 @@ dependencies:
   - h5py
   - hdf5
   - netcdf4
-  - xarray>=2024.6.0
+  - xarray>=2024.10.0
   - numpy>=2.0.0
   - numcodecs
   - packaging

ci/upstream.yml

@@ -3,6 +3,7 @@ channels:
   - conda-forge
   - nodefaults
 dependencies:
+  - xarray>=2024.10.0
   - h5netcdf
   - h5py
   - hdf5
@@ -28,7 +29,5 @@ dependencies:
   - pip
   - pip:
     - icechunk # Installs zarr v3 as dependency
-    - git+https://github.com/pydata/xarray@zarr-v3  # zarr-v3 compatibility branch
-    - git+https://github.com/zarr-developers/numcodecs@zarr3-codecs  # zarr-v3 compatibility branch
     # - git+https://github.com/fsspec/kerchunk@main  # kerchunk is currently incompatible with zarr-python v3 (https://github.com/fsspec/kerchunk/pull/516)
     - imagecodecs-numcodecs==2024.6.1

conftest.py

@@ -35,6 +35,15 @@ def netcdf4_file(tmpdir):
     return filepath
 
 
+@pytest.fixture
+def netcdf4_file_with_2d_coords(tmpdir):
+    ds = xr.tutorial.open_dataset("ROMS_example")
+    filepath = f"{tmpdir}/ROMS_example.nc"
+    ds.to_netcdf(filepath, format="NETCDF4")
+    ds.close()
+    return filepath
+
+
 @pytest.fixture
 def netcdf4_virtual_dataset(netcdf4_file):
     from virtualizarr import open_virtual_dataset

docs/conf.py

@@ -18,12 +18,18 @@
     "myst_nb",
     "sphinx.ext.autodoc",
     "sphinx.ext.autosummary",
+    "sphinx.ext.extlinks",
     "sphinx_copybutton",
     "sphinx_togglebutton",
     "sphinx_design",
     "sphinx.ext.napoleon",
 ]
 
+extlinks = {
+    "issue": ("https://github.com/zarr-developers/virtualizarr/issues/%s", "GH%s"),
+    "pull": ("https://github.com/zarr-developers/virtualizarr/pull/%s", "PR%s"),
+    "discussion": ("https://github.com/zarr-developers/virtualizarr/discussions/%s", "D%s"),
+}
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
@@ -49,6 +55,9 @@
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = False
 
+# -- Myst Options -------------------------------------------------
+
+myst_heading_anchors = 3
 
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
@@ -78,7 +87,7 @@
     'custom.css',
 ]
 
-html_logo = "_static/_future_logo.png"
+# html_logo = "_static/_future_logo.png"
 
 html_static_path = ["_static"]
 

docs/contributing.md

@@ -1,7 +1,11 @@
 # Contributing
 
+Contributions are welcome and encouraged! We ask only that all contributors follow the [Zarr Developers Code of Conduct](https://github.com/zarr-developers/.github/blob/main/CODE_OF_CONDUCT.md).
+
 ## Contributing code
 
+Before opening a PR to contribute code you should check that your changes work by running the test suite locally.
+
 ```bash
 mamba env create -f ci/environment.yml
 mamba activate virtualizarr-tests
@@ -11,13 +15,18 @@ python -m pip install -e . --no-deps
 python -m pytest ./virtualizarr --run-network-tests --cov=./ --cov-report=xml --verbose
 ```
 
+The `--run-network-tests` argument is optional - it will run additional tests that require downloading files over the network. Skip this if you want the tests to run faster or you have no internet access.
+
 ## Contributing documentation
 
+Whilst the CI will build the updated documentation for each PR, it can also be useful to check that the documentation has rendered as expected by building it locally.
+
 ### Build the documentation locally
 
 ```bash
 mamba env create -f ci/doc.yml
-mamba activate docs
+mamba activate virtualizarr-docs
+python -m pip install -e .  # From project's root - needed to generate API docs
 cd docs # From project's root
 rm -rf generated
 make clean
@@ -26,14 +35,17 @@ make html
 
 ### Access the documentation locally
 
-Open `docs/_build/html/index.html` in a web browser
+Open `docs/_build/html/index.html` in a web browser (on MacOS you can do this from the terminal using `open docs/_build/html/index.html`).
 
 ## Making a release
 
-1. Navigate to the [https://github.com/zarr-developers/virtualizarr/releases](https://github.com/zarr-developers/virtualizarr/releases) release page.
+Anyone with commit privileges to the repository can issue a release.
+
+1. Navigate to the [https://github.com/zarr-developers/virtualizarr/releases](https://github.com/zarr-developers/virtualizarr/releases) releases page.
 2. Select draft a new release.
 3. Select 'Choose a tag', then 'create a new tag'
-4. Enter the name for the new tag following the [EffVer](https://jacobtomlinson.dev/effver/) versioning scheme (e.g., releasing v0.2.0 as the next release denotes that “some small effort may be required to make sure this version works for you”).
+4. Enter the name for the new tag following the [EffVer](https://jacobtomlinson.dev/effver/) versioning scheme (e.g., releasing v0.2.0 as the next release after v0.1.0 denotes that “some small effort may be required to make sure this version works for you”).
 4. Click 'Generate Release Notes' to draft notes based on merged pull requests.
 5. Edit the draft release notes for consistency.
-6. Publish the release.
+6. Select 'Publish' to publish the release. This should automatically upload the new release to PyPI and Conda-Forge.
+7. Create and merge a PR to add a new empty section to the `docs/releases.rst` for the next release in the future.