Remove VCF support

.github/workflows/build-numpy-2.yml

@@ -23,7 +23,8 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install -r requirements.txt -r requirements-dev.txt
-        pip install -U 'numpy<2.1'
+        # update bio2zarr for NumPy 2, see https://github.com/sgkit-dev/bio2zarr/issues/256
+        pip install -U 'numpy<2.1' -U git+https://github.com/sgkit-dev/bio2zarr.git
     - name: Run pre-commit
       uses: pre-commit/[email protected]
     - name: Test with pytest (numba jit disabled)
@@ -32,7 +33,6 @@ jobs:
       run: |
         # avoid guvectorized functions #1194
         pytest -v sgkit/tests/test_pedigree.py
-        pytest -v sgkit/tests/io/vcf/test_vcf_writer_utils.py
     - name: Test with pytest and coverage
       run: |
         pytest -v --cov=sgkit --cov-report=term-missing

.github/workflows/build.yml

@@ -34,7 +34,6 @@ jobs:
       run: |
         # avoid guvectorized functions #1194
         pytest -v sgkit/tests/test_pedigree.py
-        pytest -v sgkit/tests/io/vcf/test_vcf_writer_utils.py
     - name: Test with pytest and coverage
       run: |
         pytest -v --cov=sgkit --cov-report=term-missing

.github/workflows/wheels.yml

@@ -38,14 +38,14 @@ jobs:
       with:
         path: dist
 
-  unix-test:
+  test:
     # This workflow only runs on the origin org
     if: github.repository_owner == 'sgkit-dev'
     needs: ['build']
     strategy:
       matrix:
         # don't use macos-latest as it uses M1 which doesn't work
-        os: [ubuntu-latest, macos-12]
+        os: [ubuntu-latest, macos-12, windows-latest]
         python-version: ["3.9", "3.10", "3.11"]
     runs-on: ${{ matrix.os }}
     steps:
@@ -64,46 +64,16 @@ jobs:
           python -VV
           # Install the local wheel
           wheel=$(ls artifact/sgkit-*.whl)
-          pip install ${wheel} ${wheel}[bgen] ${wheel}[plink] ${wheel}[vcf]
+          pip install ${wheel} ${wheel}[bgen] ${wheel}[plink]
           python sgkit-copy/.github/scripts/test_sgkit.py
           python sgkit-copy/.github/scripts/test_sgkit_bgen.py
           python sgkit-copy/.github/scripts/test_sgkit_plink.py
-          python sgkit-copy/.github/scripts/test_sgkit_vcf.py
 
-  # Windows doesn't support vcf
-  windows-test:
-    # This workflow only runs on the origin org
-    if: github.repository_owner == 'sgkit-dev'
-    runs-on: windows-latest
-    needs: ['build']
-    strategy:
-      matrix:
-        python-version: ["3.9"]
-    steps:
-      # checkout repo to subdirectory to get access to scripts
-      - uses: actions/checkout@v2
-        with:
-          path: sgkit-copy
-      - name: Download artifacts
-        uses: actions/[email protected]
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
-        with:
-          python-version: ${{ matrix.python-version }}
-      - name: Install wheel and test
-        run: |
-          python -VV
-          # Install the local wheel
-          $env:wheel = $(ls artifact/sgkit-*.whl)
-          pip install $env:wheel "$env:wheel[bgen]" "$env:wheel[plink]"
-          python sgkit-copy/.github/scripts/test_sgkit.py
-          python sgkit-copy/.github/scripts/test_sgkit_bgen.py
-          python sgkit-copy/.github/scripts/test_sgkit_plink.py
 
   pypi-upload:
     if: github.repository_owner == 'sgkit-dev'
     runs-on: ubuntu-latest
-    needs: ['unix-test', 'windows-test']
+    needs: ['test']
     steps:
       - name: Download all
         uses: actions/[email protected]

conftest.py

@@ -1,5 +1,4 @@
-# Ignore VCF files during pytest collection, so it doesn't fail if cyvcf2 isn't installed.
-collect_ignore_glob = ["benchmarks/**", "sgkit/io/vcf/*.py", ".github/scripts/*.py"]
+collect_ignore_glob = ["benchmarks/**", ".github/scripts/*.py"]
 
 
 def pytest_addoption(parser):

docs/api.rst

@@ -32,47 +32,11 @@ PLINK
    write_plink
    zarr_to_plink
 
-VCF (reading)
+VCF
 -------------
 
-.. deprecated:: 0.9.0
-   Functions for reading VCF are deprecated, please use the `bio2zarr <https://github.com/sgkit-dev/bio2zarr>`_ package.
-
-.. currentmodule:: sgkit.io.vcf
-.. autosummary::
-   :toctree: generated/
-
-   read_vcf
-   vcf_to_zarr
-
-For more low-level control:
-
-.. currentmodule:: sgkit.io.vcf
-.. autosummary::
-   :toctree: generated/
-
-   partition_into_regions
-   vcf_to_zarrs
-   concat_zarrs
-   zarr_array_sizes
-
-For converting from `scikit-allel's VCF Zarr representation <https://scikit-allel.readthedocs.io/en/stable/io.html#allel.vcf_to_zarr>`_ to sgkit's Zarr representation:
-
-.. currentmodule:: sgkit
-.. autosummary::
-   :toctree: generated/
-
-   read_scikit_allel_vcfzarr
-
-VCF (writing)
--------------
-
-.. currentmodule:: sgkit.io.vcf
-.. autosummary::
-   :toctree: generated/
-
-   write_vcf
-   zarr_to_vcf
+Functions for reading and writing VCF were removed from sgkit, please use the `bio2zarr <https://github.com/sgkit-dev/bio2zarr>`_
+and `vcztools <https://github.com/sgkit-dev/vcztools>`_ packages.
 
 Dataset
 -------

docs/changelog.rst

@@ -14,8 +14,12 @@ New Features
 - Add 'matching' method to :func:`identity_by_state` function.
   (:user:`timothymillar`, :pr:`1229`, :issue:`1227`)
 
-.. Breaking changes
-.. ~~~~~~~~~~~~~~~~
+Breaking changes
+~~~~~~~~~~~~~~~~
+
+- Functions for reading and writing VCF were removed from sgkit, please use the `bio2zarr <https://github.com/sgkit-dev/bio2zarr>`_
+  and `vcztools <https://github.com/sgkit-dev/vcztools>`_ packages instead.
+  (:user:`tomwhite`, :pr:`1264`)
 
 .. Deprecations
 .. ~~~~~~~~~~~~
@@ -147,22 +151,22 @@ New Features
 - Add :func:`sgkit.convert_call_to_index` method.
   (:user:`timothymillar`, :pr:`1050`, :issue:`1048`)
 
-- Add ``read_chunk_length`` option to :func:`sgkit.io.vcf.vcf_to_zarr` and
-  :func:`sgkit.io.vcf.vcf_to_zarrs` functions. These are useful to reduce memory usage
+- Add ``read_chunk_length`` option to ``sgkit.io.vcf.vcf_to_zarr`` and
+  ``sgkit.io.vcf.vcf_to_zarrs`` functions. These are useful to reduce memory usage
   with large sample counts or a large ``chunk_length``.
   (:user:`benjeffery`, :pr:`1044`, :issue:`1042`)
 
-- Add ``retain_temp_files`` to :func:`sgkit.io.vcf.vcf_to_zarr` function.
+- Add ``retain_temp_files`` to ``sgkit.io.vcf.vcf_to_zarr`` function.
   (:user:`benjeffery`, :pr:`1046`, :issue:`1036`)
 
-- Add :func:`sgkit.io.vcf.read_vcf` convenience function.
+- Add ``sgkit.io.vcf.read_vcf`` convenience function.
   (:user:`tomwhite`, :pr:`1052`, :issue:`1004`)
 
 - Add :func:`sgkit.hybrid_relationship`, :func:`sgkit.hybrid_inverse_relationship`
   and :func:`invert_relationship_matrix` methods.
   (:user:`timothymillar`, :pr:`1053`, :issue:`993`)
 
-- Add :func:`sgkit.io.vcf.zarr_array_sizes` for determining array sizes for storage in Zarr.
+- Add ``sgkit.io.vcf.zarr_array_sizes`` for determining array sizes for storage in Zarr.
   (:user:`tomwhite`, :pr:`1073`, :issue:`734`)
 
 - Add ``skipna`` option to :func:`genomic_relationship` function.
@@ -174,7 +178,7 @@ New Features
 Breaking changes
 ~~~~~~~~~~~~~~~~
 
-- Generate VCF header by default when writing VCF using :func:`sgkit.io.vcf.write_vcf` or :func:`sgkit.io.vcf.zarr_to_vcf`.
+- Generate VCF header by default when writing VCF using ``sgkit.io.vcf.write_vcf`` or ``sgkit.io.vcf.zarr_to_vcf``.
   Previously, the dataset had to contain a ``vcf_header`` attribute.
   (:user:`tomwhite`, :pr:`1021`, :issue:`1020`)
 

docs/index.rst

@@ -19,7 +19,6 @@ both popular Python genetics toolkits with a respective focus on population and
 
     getting_started
     user_guide
-    vcf
     examples/index
     api
     how_do_i