Add virtual tiff as an optional dependency (#810)

Author: maxrjones

docs/api/parsers/tiff.md

@@ -0,0 +1,3 @@
+# TIFF
+
+The [virtual-tiff](https://github.com/virtual-zarr/virtual-tiff) library provides a TIFF parser. See [their API documentation for details](https://virtual-tiff.readthedocs.io/en/latest/api/parser/).

docs/faq.md

@@ -128,7 +128,7 @@ Users of Kerchunk may find the following comparison table useful, which shows wh
 | **Generation of references from archival files (1)**                     |                                                                                                                                     |                                                                                                                                                  |
 | From a netCDF4/HDF5 file                                                 | `kerchunk.hdf.SingleHdf5ToZarr`                                                                                                     | `open_virtual_dataset(..., parser=HDFParser())`                                                            |
 | From a netCDF3 file                                                      | `kerchunk.netCDF3.NetCDF3ToZarr`                                                                                                    | `open_virtual_dataset(..., parser=NetCDF3Parser())`, via `kerchunk.netCDF3.NetCDF3ToZarr`                                                                                     |
-| From a COG / tiff file                                                   | `kerchunk.tiff.tiff_to_zarr`                                                                                                        | `open_virtual_dataset(..., parser=TIFFParser())`, via `kerchunk.tiff.tiff_to_zarr` or potentially `tifffile` (❌ Not yet implemented - see [issue #291](https://github.com/zarr-developers/VirtualiZarr/issues/291))                                                               |
+| From a COG / tiff file                                                   | `kerchunk.tiff.tiff_to_zarr`                                                                                                        | `open_virtual_dataset(..., parser=VirtualTIFF())`, via [virtual_tiff](https://github.com/virtual-zarr/virtual-tiff)                                                              |
 | From a Zarr v2 store                                                     | `kerchunk.zarr.ZarrToZarr`                                                                                                          | `open_virtual_dataset(..., parser=ZarrParser())` (❌ Not yet implemented - see [issue #262](https://github.com/zarr-developers/VirtualiZarr/issues/262))                                                                                       |
 | From a Zarr v3 store                                                     |                                                                                                          | `open_virtual_dataset(..., parser=ZarrParser())`                                                                                        |
 | From a GRIB2 file                                                        | `kerchunk.grib2.scan_grib`                                                                                                          | `open_virtual_datatree(..., parser=GribParser())` (❌ Not yet implemented - see [issue #11](https://github.com/zarr-developers/VirtualiZarr/issues/11))                                                                                |

mkdocs.yml

@@ -35,6 +35,7 @@ nav:
       - api/parsers/netcdf3.md
       - api/parsers/zarr.md
       - api/parsers/dmrpp.md
+      - api/parsers/tiff.md
     - api/serialization.md
     - api/developer.md
   - "migration_guide.md"

pyproject.toml

@@ -60,6 +60,9 @@ fits = [
     "kerchunk>=0.2.8",
     "astropy",
 ]
+tiff = [
+    "virtual-tiff",
+]
 kerchunk_parquet = [
    "virtualizarr[remote]",
    "fastparquet",
@@ -71,6 +74,7 @@ all_parsers = [
     "virtualizarr[netcdf3]",
     "virtualizarr[fits]",
     "virtualizarr[kerchunk_parquet]",
+    "virtualizarr[tiff]",
 ]
 
 # writers
@@ -193,14 +197,14 @@ run-tests-html-cov = { cmd = "pytest -n auto --run-network-tests --verbose --cov
 [tool.pixi.environments]
 min-deps = ["dev", "test", "hdf", "hdf5-lib"] # VirtualiZarr/conftest.py using h5py, so the minimum set of dependencies for testing still includes hdf libs
 # Inherit from min-deps to get all the test commands, along with optional dependencies
-test = ["dev", "test", "remote", "hdf", "netcdf3", "fits", "icechunk", "kerchunk", "kerchunk_parquet", "hdf5-lib", "py313"]
-test-py311 = ["dev", "test", "remote", "hdf", "netcdf3", "fits", "icechunk", "kerchunk", "kerchunk_parquet", "hdf5-lib", "py311"] # test against python 3.11
-test-py312 = ["dev", "test", "remote", "hdf", "netcdf3", "fits", "icechunk", "kerchunk", "kerchunk_parquet", "hdf5-lib", "py312"] # test against python 3.12
-minio = ["dev", "remote", "hdf", "netcdf3", "fits", "icechunk", "kerchunk", "hdf5-lib", "py312", "minio"]
-minimum-versions = ["dev", "test", "remote", "hdf", "netcdf3", "fits", "icechunk", "kerchunk", "kerchunk_parquet", "hdf5-lib", "minimum-versions"]
+test = ["dev", "test", "remote", "hdf", "netcdf3", "fits", "icechunk", "kerchunk", "kerchunk_parquet", "hdf5-lib", "tiff", "py313"]
+test-py311 = ["dev", "test", "remote", "hdf", "netcdf3", "fits", "icechunk", "kerchunk", "kerchunk_parquet", "hdf5-lib", "tiff", "py311"] # test against python 3.11
+test-py312 = ["dev", "test", "remote", "hdf", "netcdf3", "fits", "icechunk", "kerchunk", "kerchunk_parquet", "hdf5-lib", "tiff", "py312"] # test against python 3.12
+minio = ["dev", "remote", "hdf", "netcdf3", "fits", "icechunk", "kerchunk", "hdf5-lib", "tiff", "py312", "minio"]
+minimum-versions = ["dev", "test", "remote", "hdf", "netcdf3", "fits", "icechunk", "kerchunk", "kerchunk_parquet", "tiff", "hdf5-lib", "minimum-versions"]
 upstream = ["dev", "test", "hdf", "hdf5-lib", "netcdf3", "upstream", "icechunk-dev", "py313"]
-all = ["dev", "test", "remote", "hdf", "netcdf3", "fits", "icechunk", "kerchunk", "kerchunk_parquet", "hdf5-lib", "all_parsers", "all_writers", "py313"]
-docs = ["docs", "dev", "remote", "hdf", "netcdf3", "fits", "icechunk", "kerchunk", "kerchunk_parquet", "hdf5-lib", "py313"]
+all = ["dev", "test", "remote", "hdf", "netcdf3", "fits", "icechunk", "kerchunk", "kerchunk_parquet", "hdf5-lib", "tiff", "all_parsers", "all_writers", "py313"]
+docs = ["docs", "dev", "remote", "hdf", "netcdf3", "fits", "icechunk", "kerchunk", "kerchunk_parquet", "hdf5-lib", "tiff", "py313"]
 
 # Define commands to run within the docs environment
 [tool.pixi.feature.docs.tasks]

virtualizarr/tests/__init__.py

@@ -41,3 +41,4 @@ def _importorskip(
 has_zarr_python, requires_zarr_python = _importorskip("zarr")
 has_dask, requires_dask = _importorskip("dask")
 has_obstore, requires_obstore = _importorskip("obstore")
+has_tiff, requires_tiff = _importorskip("virtual_tiff")

virtualizarr/tests/test_parsers/test_tiff.py

@@ -0,0 +1,24 @@
+import pytest
+from obstore.store import S3Store
+from xarray import Dataset
+
+from virtualizarr import open_virtual_dataset
+from virtualizarr.registry import ObjectStoreRegistry
+from virtualizarr.tests import requires_network, requires_tiff
+
+virtual_tiff = pytest.importorskip("virtual_tiff")
+
+
+@requires_tiff
+@requires_network
+def test_virtual_tiff() -> None:
+    store = S3Store("sentinel-cogs", region="us-west-2", skip_signature=True)
+    registry = ObjectStoreRegistry({"s3://sentinel-cogs/": store})
+    url = "s3://sentinel-cogs/sentinel-s2-l2a-cogs/12/S/UF/2022/6/S2B_12SUF_20220609_0_L2A/B04.tif"
+    parser = virtual_tiff.VirtualTIFF(ifd=0)
+    with open_virtual_dataset(url=url, parser=parser, registry=registry) as vds:
+        assert isinstance(vds, Dataset)
+        assert list(vds.variables) == ["0"]
+        var = vds["0"].variable
+        assert var.sizes == {"y": 10980, "x": 10980}
+        assert var.dtype == "<u2"