Add --version option to the cli

Author: tomwhite

.gitignore

@@ -1,3 +1,6 @@
+# auto generated by setuptools_scm and configured in pyproject.toml
+vcztools/_version.py
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

tests/test_cli.py

@@ -7,6 +7,7 @@
 import vcztools.cli as cli
 from tests.test_bcftools_validation import run_vcztools
 from tests.utils import vcz_path_cache
+from vcztools import provenance
 
 
 @pytest.fixture()
@@ -184,3 +185,10 @@ def test_top_level():
     assert result.exit_code == 0
     assert len(result.stdout) > 0
     assert len(result.stderr) == 0
+
+
+def test_version():
+    runner = ct.CliRunner(mix_stderr=False)
+    result = runner.invoke(cli.vcztools_main, ["--version"], catch_exceptions=False)
+    s = f"version {provenance.__version__}\n"
+    assert result.stdout.endswith(s)

vcztools/__init__.py

@@ -0,0 +1 @@
+from .provenance import __version__  # noqa F401

vcztools/cli.py

@@ -6,7 +6,7 @@
 
 import click
 
-from . import plink, vcf_writer
+from . import plink, provenance, vcf_writer
 from . import query as query_module
 from . import stats as stats_module
 
@@ -60,6 +60,7 @@ def wrapper(*args, **kwargs):
     default="-",
     help="File path to write output to (defaults to stdout '-').",
 )
+version = click.version_option(version=f"{provenance.__version__}")
 
 
 class NaturalOrderGroup(click.Group):
@@ -278,6 +279,7 @@ def view_plink1(path, include, exclude, out):
     writer.run()
 
 
+@version
 @click.group(cls=NaturalOrderGroup, name="vcztools")
 def vcztools_main():
     pass

vcztools/provenance.py

@@ -0,0 +1,7 @@
+__version__ = "undefined"
+try:
+    from . import _version
+
+    __version__ = _version.version
+except ImportError:  # pragma: nocover
+    pass