Merge branch 'master' of github.com:wfondrie/ppx

ppx/ppx.py

@@ -12,11 +12,9 @@
 
 def get_parser():
     """Parse the command line arguments"""
-    desc = f"""
-        ppx version {__version__}. Use this command line utility to download
-        files from the PRIDE and MassIVE proteomics repositories. The paths
-        to the downloaded files are written to stdout.
-    """
+    desc = f"""Use this command line utility to download files from the PRIDE and MassIVE
+    proteomics repositories. The paths to the downloaded files are written to
+    stdout."""
 
     epilog = "More documentation and examples at: https://ppx.readthedocs.io"
     parser = ArgumentParser(description=desc, epilog=epilog)
@@ -55,6 +53,13 @@ def get_parser():
         ),
     )
 
+    parser.add_argument(
+        "-t",
+        "--timeout",
+        type=float,
+        help="The maximum amount of time to wait for a server response.",
+    )
+
     parser.add_argument(
         "-f",
         "--force",
@@ -66,6 +71,13 @@ def get_parser():
         ),
     )
 
+    parser.add_argument(
+        "--version",
+        action="version",
+        help="Get the version of ppx.",
+        version="%(prog)s " + __version__,
+    )
+
     return parser
 
 
@@ -77,7 +89,7 @@ def main():
 
     parser = get_parser()
     args = parser.parse_args()
-    proj = find_project(args.identifier, args.local)
+    proj = find_project(args.identifier, args.local, timeout=args.timeout)
     remote_files = proj.remote_files()
 
     if len(args.files) > 0:

tests/system_tests/test_cli.py

@@ -12,7 +12,7 @@
 def test_pride(tmp_path):
     """Test the CLI for pride"""
     out_dir = tmp_path / PXID
-    cmd = ["ppx", "-l", str(out_dir), PXID, "*.txt"]
+    cmd = ["ppx", "-l", str(out_dir), "-t", "10", PXID, "*.txt"]
     subprocess.run(cmd, check=True)
     print(list(out_dir.iterdir()))
 
@@ -23,3 +23,8 @@ def test_massive(tmp_path):
     cmd = ["ppx", "-l", str(out_dir), MSVID, "*/statistics.tsv"]
     subprocess.run(cmd, check=True)
     assert (out_dir / "ccms_statistics" / "statistics.tsv").exists()
+
+
+def test_version(tmp_path):
+    """Test ppx version"""
+    subprocess.run(["ppx", "--version"], check=True)