Merge pull request #173 from jeromekelleher/more-platforms

Platform and distribution CI

Author: jeromekelleher

.github/workflows/ci.yml

@@ -17,10 +17,19 @@ jobs:
       - uses: pre-commit/[email protected]
   test:
     name: Test
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
     strategy:
       matrix:
+        # Use macos-13 because pip binary packages for ARM aren't
+        # available for many dependencies
+        os: [macos-13, ubuntu-latest]
         python-version: ["3.9", "3.10", "3.11"]
+        exclude:
+          # Just run macos tests on one Python version
+          - os: macos-13
+            python-version: "3.9"
+          - os: macos-13
+            python-version: "3.10"
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
@@ -32,3 +41,30 @@ jobs:
           python -m pip install --upgrade pip
           python -m pip install '.[dev]'
       - run: pytest
+
+  packaging:
+    name: Packaging
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install build twine validate-pyproject[all]
+      - name: Check and install package
+        run: |
+          validate-pyproject pyproject.toml
+          python -m build
+          python -m twine check --strict dist/*
+          python -m pip install dist/*.whl
+      - name: Check vcf2zarr CLI
+        run: |
+          vcf2zarr --help
+          python -m bio2zarr vcf2zarr --help
+      - name: Check vcfpartition CLI
+        run: |
+          vcfpartition --help
+          python -m bio2zarr vcfpartition --help

bio2zarr/__main__.py

@@ -16,7 +16,7 @@ def bio2zarr():
 # up in the right way.
 bio2zarr.add_command(cli.vcf2zarr)
 bio2zarr.add_command(cli.plink2zarr)
-bio2zarr.add_command(cli.vcf_partition)
+bio2zarr.add_command(cli.vcfpartition)
 
 if __name__ == "__main__":
     bio2zarr()

bio2zarr/cli.py

@@ -529,7 +529,7 @@ def plink2zarr():
 @click.option("-i", "--index", type=click.Path(), default=None)
 @click.option("-n", "--num-parts", type=int, default=None)
 # @click.option("-s", "--part-size", type=int, default=None)
-def vcf_partition(vcf_path, index, num_parts):
+def vcfpartition(vcf_path, index, num_parts):
     indexed_vcf = vcf_utils.IndexedVcf(vcf_path, index)
     regions = indexed_vcf.partition_into_regions(num_parts=num_parts)
     click.echo("\n".join(map(str, regions)))

pyproject.toml

@@ -26,7 +26,10 @@ requires-python = ">=3.9"
 classifiers = [
   "Development Status :: 3 - Alpha",
   "License :: OSI Approved :: Apache Software License",
-  "Operating System :: OS Independent",
+  "Operating System :: POSIX",
+  "Operating System :: POSIX :: Linux",
+  "Operating System :: MacOS",
+  "Operating System :: MacOS :: MacOS X",
   "Intended Audience :: Science/Research",
   "Programming Language :: Python",
   "Programming Language :: Python :: 3",
@@ -43,8 +46,7 @@ documentation = "https://sgkit-dev.github.io/bio2zarr/intro.html"
 
 [project.scripts]
 vcf2zarr = "bio2zarr.cli:vcf2zarr"
-plink2zarr = "bio2zarr.cli:plink2zarr"
-vcf_partition = "bio2zarr.cli:vcf_partition"
+vcfpartition = "bio2zarr.cli:vcfpartition"
 
 [project.optional-dependencies]
 dev = [

tests/test_cli.py

@@ -611,7 +611,7 @@ def test_num_parts(self):
 
         runner = ct.CliRunner(mix_stderr=False)
         result = runner.invoke(
-            cli.vcf_partition, [path, "-n", "5"], catch_exceptions=False
+            cli.vcfpartition, [path, "-n", "5"], catch_exceptions=False
         )
         assert list(result.stdout.splitlines()) == [
             "20:60001-278528",
@@ -623,7 +623,7 @@ def test_num_parts(self):
 
 
 @pytest.mark.parametrize(
-    "cmd", [main.bio2zarr, cli.vcf2zarr, cli.plink2zarr, cli.vcf_partition]
+    "cmd", [main.bio2zarr, cli.vcf2zarr, cli.plink2zarr, cli.vcfpartition]
 )
 def test_version(cmd):
     runner = ct.CliRunner(mix_stderr=False)

tests/test_core.py

@@ -1,3 +1,5 @@
+import sys
+
 import numpy as np
 import pytest
 import zarr
@@ -54,6 +56,7 @@ def test_bad_min_max(self, min_value, max_value):
             core.min_int_dtype(min_value, max_value)
 
 
+@pytest.mark.skipif(sys.platform == "darwin", reason="Issue #75")
 class TestParallelWorkManager:
     @pytest.mark.parametrize("total", [1, 10, 2**63])
     @pytest.mark.parametrize("workers", [0, 1])
@@ -181,6 +184,7 @@ def test_5_chunk_1(self, n, expected):
         assert result == expected
 
 
+@pytest.mark.skipif(sys.platform != "linux", reason="Only valid on Linux")
 @pytest.mark.parametrize(
     ("path", "expected"),
     [