feat(cli): add --version flag and show version in help

docs/reference/cli.md

@@ -4,6 +4,19 @@ All AFQuery commands follow the pattern `afquery <command> [OPTIONS]`.
 
 ---
 
+## Global options
+
+| Option | Description |
+|--------|-------------|
+| `--version` | Print the AFQuery version and exit |
+| `--help` | Show help for the command and exit |
+
+`afquery --version` prints the installed package version (e.g. `afquery 0.4.2`),
+taken from the Git release tag at build time. In an editable install
+(`pip install -e .`) it reflects the last build, not later local commits.
+
+---
+
 ## create-db
 
 Build a new AFQuery database from a manifest of single-sample VCFs.

src/afquery/cli.py

@@ -4,6 +4,8 @@
 
 import click
 
+from afquery import __version__
+
 from .database import Database
 
 
@@ -168,15 +170,18 @@ def _print_carriers(carriers, variant_key, fmt: str) -> None:
             click.echo(fmt_row.format(*row))
 
 
-@click.group()
-def cli():
-    """AFQuery: bitmap-indexed allele frequency engine for local genomic cohorts.
+_CLI_HELP = f"""\
+AFQuery v{__version__} — bitmap-indexed allele frequency engine for local genomic cohorts.
 
-    Enables fast AC/AN/AF queries on user-defined subcohorts (phenotype, sex,
-    technology) without rescanning VCFs.
+Enables fast AC/AN/AF queries on user-defined subcohorts (phenotype, sex,
+technology) without rescanning VCFs.
+"""
 
-    Commands: query, variant-info, annotate, dump, info, version, create-db, update-db, check, benchmark
-    """
+
+@click.group(help=_CLI_HELP)
+@click.version_option(version=__version__, prog_name="afquery", message="%(prog)s %(version)s")
+def cli():
+    pass
 
 
 @cli.command()

tests/test_cli.py

@@ -375,6 +375,29 @@ def test_version_set_then_show(runner, db_copy):
     assert "MYVER" in result.output
 
 
+# --- afquery --version / --help ---
+
+def test_version_flag(runner):
+    from afquery import __version__
+    result = runner.invoke(cli, ["--version"])
+    assert result.exit_code == 0
+    assert __version__ in result.output
+
+
+def test_help_shows_program_name_and_version(runner):
+    from afquery import __version__
+    result = runner.invoke(cli, ["--help"])
+    assert result.exit_code == 0
+    assert f"AFQuery v{__version__}" in result.output
+
+
+def test_help_lists_all_commands(runner):
+    result = runner.invoke(cli, ["--help"])
+    for cmd in ("query", "variant-info", "annotate", "dump", "info",
+                "version", "create-db", "update-db", "check", "benchmark"):
+        assert cmd in result.output
+
+
 # --- afquery check ---
 
 def test_check_ok(runner, test_db):