diff --git a/.github/workflows/benchmark.yml b/.github/workflows/benchmark.yml index 9b7ded7b0..091b2a1dd 100644 --- a/.github/workflows/benchmark.yml +++ b/.github/workflows/benchmark.yml @@ -17,11 +17,11 @@ jobs: if: github.repository_owner == 'sgkit-dev' runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 with: fetch-depth: 0 # To fetch all commits to be able to generate benchmarks html - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 + uses: actions/setup-python@v5 with: python-version: "3.10" - name: Install dependencies diff --git a/.github/workflows/build-gpu.yml b/.github/workflows/build-gpu.yml index 2a8e4ce9f..3292de308 100644 --- a/.github/workflows/build-gpu.yml +++ b/.github/workflows/build-gpu.yml @@ -20,7 +20,7 @@ jobs: python-version: ["3.10"] steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Run Nvidia-smi run: | diff --git a/.github/workflows/build-numpy-1.yml b/.github/workflows/build-numpy-1.yml index ea2e77b67..329a10c40 100644 --- a/.github/workflows/build-numpy-1.yml +++ b/.github/workflows/build-numpy-1.yml @@ -14,9 +14,9 @@ jobs: python-version: ["3.10", "3.11"] steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - name: Install dependencies @@ -24,7 +24,7 @@ jobs: python -m pip install --upgrade pip pip install -r requirements-numpy1.txt -r requirements-numpy1-dev.txt # - name: Run pre-commit - # uses: pre-commit/action@v2.0.0 + # uses: pre-commit/action@v3.0.1 - name: Test with pytest and coverage run: | pytest -v --cov=sgkit --cov-report=term-missing diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index ba0c91ed2..1a02613df 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -17,9 +17,9 @@ jobs: python-version: ["3.10", "3.11", "3.12"] steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - name: Install dependencies @@ -27,7 +27,7 @@ jobs: python -m pip install --upgrade pip pip install -r requirements.txt -r requirements-dev.txt - name: Run pre-commit - uses: pre-commit/action@v2.0.0 + uses: pre-commit/action@v3.0.1 - name: Test with pytest and coverage run: | pytest -v --cov=sgkit --cov-report=term-missing diff --git a/.github/workflows/check-docs.yml b/.github/workflows/check-docs.yml index dad7e1764..ccef828d5 100644 --- a/.github/workflows/check-docs.yml +++ b/.github/workflows/check-docs.yml @@ -17,9 +17,9 @@ jobs: python-version: ["3.11"] steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - name: Install dependencies @@ -30,7 +30,7 @@ jobs: pip install -r requirements.txt -r requirements-dev.txt -r requirements-doc.txt pip install -U dask distributed # need latest versions to successully build docs - name: Run pre-commit - uses: pre-commit/action@v2.0.0 + uses: pre-commit/action@v3.0.1 - name: Check for Sphinx doc warnings run: | cd docs diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 874af615d..5f80cf659 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -11,9 +11,9 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 + uses: actions/setup-python@v5 with: python-version: "3.11" - name: Install dependencies diff --git a/.github/workflows/upstream.yml b/.github/workflows/upstream.yml index c4a663137..a57d0f92a 100644 --- a/.github/workflows/upstream.yml +++ b/.github/workflows/upstream.yml @@ -17,9 +17,9 @@ jobs: python-version: ["3.10", "3.11"] steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml index 58e7c3bc6..70875fa70 100644 --- a/.github/workflows/validation.yml +++ b/.github/workflows/validation.yml @@ -15,7 +15,7 @@ jobs: if: github.repository_owner == 'sgkit-dev' runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - uses: google-github-actions/setup-gcloud@v0 with: project_id: ${{ secrets.GCP_PROJECT_ID }} diff --git a/.github/workflows/wheels.yml b/.github/workflows/wheels.yml index 71cd4be39..e94e4e451 100644 --- a/.github/workflows/wheels.yml +++ b/.github/workflows/wheels.yml @@ -21,9 +21,9 @@ jobs: python-version: ["3.10"] steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - name: Install dependencies @@ -50,13 +50,13 @@ jobs: runs-on: ${{ matrix.os }} steps: # checkout repo to subdirectory to get access to scripts - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 with: path: sgkit-copy - name: Download artifacts uses: actions/download-artifact@v4.1.7 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - name: Install wheel and test @@ -79,13 +79,13 @@ jobs: python-version: ["3.10"] steps: # checkout repo to subdirectory to get access to scripts - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 with: path: sgkit-copy - name: Download artifacts uses: actions/download-artifact@v4.1.7 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - name: Install wheel and test diff --git a/.github/workflows/windows.yml b/.github/workflows/windows.yml index 5b2ca3313..b9c9cdd90 100644 --- a/.github/workflows/windows.yml +++ b/.github/workflows/windows.yml @@ -17,7 +17,7 @@ jobs: python-version: ["3.10"] steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Set up Miniconda with Python version ${{ matrix.python-version }} uses: conda-incubator/setup-miniconda@v2 with: diff --git a/docs/examples/1kg.schema.json b/docs/examples/1kg.schema.json index 108e0f9e7..808185f2f 100644 --- a/docs/examples/1kg.schema.json +++ b/docs/examples/1kg.schema.json @@ -1,7 +1,1205 @@ { - "format_version": "0.5", - "samples_chunk_size": 10000, - "variants_chunk_size": 1000, + "format_version": "0.4", + "samples_chunk_size": 1000, + 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"chunks": [ - 1000, + 10000, 1 ], "dimensions": [ @@ -60,7 +1258,7 @@ 2 ], "chunks": [ - 1000, + 10000, 2 ], "dimensions": [ @@ -85,7 +1283,7 @@ 10879 ], "chunks": [ - 1000 + 10000 ], "dimensions": [ "variants" @@ -108,7 +1306,7 @@ 10879 ], "chunks": [ - 1000 + 10000 ], "dimensions": [ "variants" @@ -131,7 +1329,7 @@ 10879 ], "chunks": [ - 1000 + 10000 ], "dimensions": [ "variants" @@ -154,7 +1352,7 @@ 10879 ], "chunks": [ - 1000 + 10000 ], "dimensions": [ "variants" @@ -177,7 +1375,7 @@ 10879 ], "chunks": [ - 1000 + 10000 ], "dimensions": [ "variants" @@ -202,8 +1400,8 @@ 2 ], "chunks": [ - 1000, 10000, + 1000, 2 ], "dimensions": [ @@ -230,8 +1428,8 @@ 284 ], "chunks": [ - 1000, - 10000 + 10000, + 1000 ], "dimensions": [ "variants", @@ -256,8 +1454,8 @@ 284 ], "chunks": [ - 1000, - 10000 + 10000, + 1000 ], "dimensions": [ "variants", @@ -282,8 +1480,8 @@ 284 ], "chunks": [ - 1000, - 10000 + 10000, + 1000 ], "dimensions": [ "variants", @@ -309,8 +1507,8 @@ 2 ], "chunks": [ - 1000, 10000, + 1000, 2 ], "dimensions": [ @@ -338,8 +1536,8 @@ 2 ], "chunks": [ - 1000, 10000, + 1000, 2 ], "dimensions": [ diff --git a/requirements-dev.txt b/requirements-dev.txt index 70a4c44a1..e338c94be 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -13,7 +13,7 @@ partd bed-reader rechunker cbgen > 1.0.5 -bio2zarr @ git+https://github.com/sgkit-dev/bio2zarr.git; platform_system != "Windows" +bio2zarr; platform_system != "Windows" yarl matplotlib asv diff --git a/requirements-numpy1-dev.txt b/requirements-numpy1-dev.txt index 9cbbf449a..d1df99192 100644 --- a/requirements-numpy1-dev.txt +++ b/requirements-numpy1-dev.txt @@ -13,7 +13,7 @@ partd bed-reader rechunker cbgen < 1.0.5 -bio2zarr @ git+https://github.com/sgkit-dev/bio2zarr.git; platform_system != "Windows" +bio2zarr; platform_system != "Windows" yarl matplotlib asv diff --git a/sgkit/tests/io/test_vcf2zarr_compat.py b/sgkit/tests/io/test_vcf2zarr_compat.py index ab7c8eb4a..696180fed 100644 --- a/sgkit/tests/io/test_vcf2zarr_compat.py +++ b/sgkit/tests/io/test_vcf2zarr_compat.py @@ -2,7 +2,7 @@ import pytest pytest.importorskip("bio2zarr") -from bio2zarr import icf +from bio2zarr import vcf2zarr from bio2zarr.constants import ( FLOAT32_FILL, FLOAT32_MISSING, @@ -23,7 +23,7 @@ def test_vcf2zarr_compat(shared_datadir, tmp_path): vcf_path = shared_datadir / "sample.vcf.gz" vcz_path = tmp_path.joinpath("sample.vcz").as_posix() - icf.convert( + vcf2zarr.convert( [vcf_path], vcz_path, variants_chunk_size=5,