diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 2b58856ca..3cbe6a248 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -43,7 +43,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - zarr: ["==3.0.0b1"] + zarr: [">=3"] steps: - uses: actions/checkout@v4 - uses: actions/setup-python@v5 diff --git a/docs/examples/1kg.schema.json b/docs/examples/1kg.schema.json index 2142d9e07..808185f2f 100644 --- a/docs/examples/1kg.schema.json +++ b/docs/examples/1kg.schema.json @@ -1368,6 +1368,29 @@ }, "filters": [] }, + { + "name": "variant_length", + "dtype": "i1", + "shape": [ + 10879 + ], + "chunks": [ + 10000 + ], + "dimensions": [ + "variants" + ], + "description": "The length of the variant measured in bases", + "vcf_field": "rlen", + "compressor": { + "id": "blosc", + "cname": "zstd", + "clevel": 7, + "shuffle": 0, + "blocksize": 0 + }, + "filters": [] + }, { "name": "call_AD", "dtype": "i1", diff --git a/requirements-dev.txt b/requirements-dev.txt index d1df99192..9cbbf449a 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -13,7 +13,7 @@ partd bed-reader rechunker cbgen < 1.0.5 -bio2zarr; platform_system != "Windows" +bio2zarr @ git+https://github.com/sgkit-dev/bio2zarr.git; platform_system != "Windows" yarl matplotlib asv diff --git a/sgkit/tests/io/test_dataset.py b/sgkit/tests/io/test_dataset.py index 3151464fc..cb1a26405 100644 --- a/sgkit/tests/io/test_dataset.py +++ b/sgkit/tests/io/test_dataset.py @@ -58,7 +58,7 @@ def test_save_unequal_chunks_error(): # Normal zarr errors shouldn't be caught with pytest.raises( (FileExistsError, ValueError), - match="(path '' contains an array|Store already exists)", + match="(path '' contains an array|is not empty)", ): save_dataset(ds, {".zarray": ""}) diff --git a/sgkit/tests/test_testing.py b/sgkit/tests/test_testing.py index 7c107971a..20de6d662 100644 --- a/sgkit/tests/test_testing.py +++ b/sgkit/tests/test_testing.py @@ -7,6 +7,9 @@ from sgkit.testing import simulate_genotype_call_dataset +@pytest.mark.filterwarnings( + "ignore::UserWarning" +) # codec `vlen-utf8` not in Zarr v3 spec` def test_simulate_genotype_call_dataset__zarr(tmp_path): path = str(tmp_path / "ds.zarr") ds = simulate_genotype_call_dataset(n_variant=10, n_sample=10)