Add plink2zarr script and add tests in CI

Closes #401

Systematicaly use _main suffix for entry points

Author: jeromekelleher

.github/workflows/ci.yml

@@ -69,6 +69,12 @@ jobs:
           python -m bio2zarr vcf2zarr dencode-partition sample.vcz 1
           python -m bio2zarr vcf2zarr dencode-partition sample.vcz 2
           python -m bio2zarr vcf2zarr dencode-finalise sample.vcz
+      - name: Run tskit2zarr example
+        run: |
+          python -m bio2zarr tskit2zarr convert tests/data/tskit/example.trees sample.vcz -f
+      - name: Run plink2zarr example
+        run: |
+          python -m bio2zarr plink2zarr convert tests/data/plink/example sample.vcz -f
       - name: Run tests
         run: |
           pytest --cov=bio2zarr
@@ -137,6 +143,14 @@ jobs:
         run: |
           vcfpartition --help
           python -m bio2zarr vcfpartition --help
+      - name: Check tskit2zarr CLI
+        run: |
+          tskit2zarr --help
+          python -m bio2zarr tskit2zarr --help
+      - name: Check plink2zarr CLI
+        run: |
+          plink2zarr --help
+          python -m bio2zarr plink2zarr --help
 
   test-numpy-version:
     name: Test numpy versions

bio2zarr/__main__.py

@@ -15,9 +15,9 @@ def bio2zarr():
 # is handy for development and for those whose PATHs aren't set
 # up in the right way.
 bio2zarr.add_command(cli.vcf2zarr_main)
-bio2zarr.add_command(cli.plink2zarr)
+bio2zarr.add_command(cli.plink2zarr_main)
+bio2zarr.add_command(cli.tskit2zarr_main)
 bio2zarr.add_command(cli.vcfpartition)
-bio2zarr.add_command(cli.tskit2zarr)
 
 if __name__ == "__main__":
     bio2zarr()

bio2zarr/cli.py

@@ -583,14 +583,14 @@ def convert_plink(
 
 @version
 @click.group()
-def plink2zarr():
+def plink2zarr_main(name="plink2zarr"):
     """
     Convert plink fileset(s) to VCF Zarr format
     """
     pass
 
 
-plink2zarr.add_command(convert_plink)
+plink2zarr_main.add_command(convert_plink)
 
 
 @click.command
@@ -684,12 +684,12 @@ def convert_tskit(
 
 
 @version
-@click.group()
-def tskit2zarr():
+@click.group(name="tskit2zarr")
+def tskit2zarr_main():
     """
     Convert tskit tree sequence(s) to VCF Zarr format
     """
     pass
 
 
-tskit2zarr.add_command(convert_tskit)
+tskit2zarr_main.add_command(convert_tskit)

pyproject.toml

@@ -52,6 +52,7 @@ documentation = "https://sgkit-dev.github.io/bio2zarr/"
 vcf2zarr = "bio2zarr.cli:vcf2zarr_main"
 vcfpartition = "bio2zarr.cli:vcfpartition"
 tskit2zarr = "bio2zarr.cli:tskit2zarr_main"
+plink2zarr = "bio2zarr.cli:plink2zarr_main"
 
 [project.optional-dependencies]
 dev = [

tests/test_cli.py

@@ -616,7 +616,7 @@ def test_vcf_convert_overwrite_zarr_confirm_no(self, mocked, tmp_path, response)
     def test_convert_plink(self, mocked, progress, flag):
         runner = ct.CliRunner()
         result = runner.invoke(
-            cli.plink2zarr, ["convert", "in", "out", flag], catch_exceptions=False
+            cli.plink2zarr_main, ["convert", "in", "out", flag], catch_exceptions=False
         )
         assert result.exit_code == 0
         assert len(result.stdout) == 0
@@ -651,7 +651,7 @@ def test_convert_tskit(self, mocked, tmp_path, progress, flag):
         zarr_path = tmp_path / "zarr"
         runner = ct.CliRunner()
         result = runner.invoke(
-            cli.tskit2zarr,
+            cli.tskit2zarr_main,
             f"convert {ts_path} {zarr_path} {flag}",
             catch_exceptions=False,
         )
@@ -674,7 +674,7 @@ def test_tskit_convert_overwrite_zarr_confirm_yes(self, mocked, tmp_path, respon
         zarr_path.mkdir()
         runner = ct.CliRunner()
         result = runner.invoke(
-            cli.tskit2zarr,
+            cli.tskit2zarr_main,
             f"convert {ts_path} {zarr_path}",
             catch_exceptions=False,
             input=response,
@@ -696,7 +696,7 @@ def test_tskit_convert_overwrite_zarr_confirm_no(self, mocked, tmp_path, respons
         zarr_path.mkdir()
         runner = ct.CliRunner()
         result = runner.invoke(
-            cli.tskit2zarr,
+            cli.tskit2zarr_main,
             f"convert {ts_path} {zarr_path}",
             catch_exceptions=False,
             input=response,
@@ -713,7 +713,7 @@ def test_tskit_convert_overwrite_zarr_force(self, mocked, tmp_path, force_arg):
         zarr_path.mkdir()
         runner = ct.CliRunner()
         result = runner.invoke(
-            cli.tskit2zarr,
+            cli.tskit2zarr_main,
             f"convert {ts_path} {zarr_path} {force_arg}",
             catch_exceptions=False,
         )
@@ -732,7 +732,7 @@ def test_tskit_convert_with_options(self, mocked, tmp_path):
         zarr_path = tmp_path / "zarr"
         runner = ct.CliRunner()
         result = runner.invoke(
-            cli.tskit2zarr,
+            cli.tskit2zarr_main,
             f"convert {ts_path} {zarr_path} --contig-id chr1 "
             "--isolated-as-missing -l 100 -w 50 -p 4",
             catch_exceptions=False,
@@ -1032,7 +1032,7 @@ def test_convert(self, tmp_path):
         zarr_path = tmp_path / "zarr"
         runner = ct.CliRunner()
         result = runner.invoke(
-            cli.tskit2zarr,
+            cli.tskit2zarr_main,
             f"convert {ts_path} {zarr_path}",
             catch_exceptions=False,
         )
@@ -1051,7 +1051,7 @@ def test_convert(self, tmp_path):
         zarr_path = tmp_path / "zarr"
         runner = ct.CliRunner()
         result = runner.invoke(
-            cli.plink2zarr,
+            cli.plink2zarr_main,
             f"convert {ts_path} {zarr_path}",
             catch_exceptions=False,
         )
@@ -1069,9 +1069,9 @@ def test_convert(self, tmp_path):
     [
         main.bio2zarr,
         cli.vcf2zarr_main,
-        cli.plink2zarr,
+        cli.plink2zarr_main,
         cli.vcfpartition,
-        cli.tskit2zarr,
+        cli.tskit2zarr_main,
     ],
 )
 def test_version(cmd):