allow jcvi-cli to launch modules (#833)

Author: tanghaibao

src/jcvi/cli.py

@@ -1,15 +1,47 @@
-# cli.py
 import argparse
+import runpy
+import sys
 
 from . import __version__
 
 
-def main():
-    parser = argparse.ArgumentParser()
+def _normalize_module_name(module: str) -> str:
+    if module.startswith("jcvi."):
+        return module
+    return f"jcvi.{module}"
+
+
+def main(argv=None):
+    parser = argparse.ArgumentParser(
+        prog="jcvi",
+        description="Run jcvi modules, e.g. `jcvi formats.fasta extract`.",
+    )
     parser.add_argument(
         "--version", action="version", version=f"%(prog)s {__version__}"
     )
-    args = parser.parse_args()
+    parser.add_argument(
+        "module",
+        nargs="?",
+        help="Module path without the `jcvi.` prefix (for example: formats.fasta).",
+    )
+    parser.add_argument("module_args", nargs=argparse.REMAINDER)
+    args = parser.parse_args(argv)
+
+    if not args.module:
+        parser.print_help()
+        return 0
+
+    module_name = _normalize_module_name(args.module)
+
+    original_argv = sys.argv[:]
+    try:
+        # Match `python -m jcvi.<module> ...` behavior for argument parsing.
+        sys.argv = [module_name, *args.module_args]
+        runpy.run_module(module_name, run_name="__main__", alter_sys=True)
+    finally:
+        sys.argv = original_argv
+
+    return 0
 
 
 if __name__ == "__main__":

tests/test_cli.py

@@ -0,0 +1,51 @@
+from jcvi import cli
+
+
+def test_normalize_module_name():
+    assert cli._normalize_module_name("formats.fasta") == "jcvi.formats.fasta"
+    assert cli._normalize_module_name("jcvi.formats.fasta") == "jcvi.formats.fasta"
+
+
+def test_main_dispatches_module(monkeypatch):
+    called = {}
+
+    def fake_run_module(module_name, run_name=None, alter_sys=False):
+        called["module_name"] = module_name
+        called["run_name"] = run_name
+        called["alter_sys"] = alter_sys
+        called["argv"] = cli.sys.argv[:]
+        return {}
+
+    monkeypatch.setattr(cli.runpy, "run_module", fake_run_module)
+    rc = cli.main(["formats.fasta", "extract", "in.fa"])
+
+    assert rc == 0
+    assert called["module_name"] == "jcvi.formats.fasta"
+    assert called["run_name"] == "__main__"
+    assert called["alter_sys"] is True
+    assert called["argv"] == ["jcvi.formats.fasta", "extract", "in.fa"]
+
+
+def test_main_version_exits():
+    try:
+        cli.main(["--version"])
+    except SystemExit as exc:
+        assert exc.code == 0
+    else:
+        raise AssertionError("Expected --version to exit")
+
+
+def test_main_no_module_prints_help(capsys):
+    rc = cli.main([])
+    assert rc == 0
+    captured = capsys.readouterr()
+    assert "Run jcvi modules" in captured.out
+
+
+def test_main_missing_module_raises_import_error():
+    try:
+        cli.main(["does.not.exist"])
+    except ImportError:
+        pass
+    else:
+        raise AssertionError("Expected ImportError for missing module")