Rename vcf_partition to vcfpartition

Closes #172

Author: jeromekelleher

.github/workflows/ci.yml

@@ -60,6 +60,11 @@ jobs:
           python -m build
           python -m twine check --strict dist/*
           python -m pip install dist/*.whl
-      - name: Check CLIs
+      - 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

@@ -47,7 +47,7 @@ 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)