Fix test by extracting arg parsing to separate cli module that doesn'…

…t need to access seqrepo

clinvar_gk_pilot/cli.py

@@ -0,0 +1,21 @@
+import argparse
+from typing import List
+
+
+def parse_args(args: List[str]) -> dict:
+    """
+    Parse arguments and return as dict.
+    """
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--filename", required=True, help="Filename to read")
+    parser.add_argument(
+        "--parallelism",
+        type=int,
+        default=1,
+        help=(
+            "Number of worker threads. "
+            "Default 1, which still uses a separate process to run tasks. "
+            "Set to 0 to run in main thread."
+        ),
+    )
+    return vars(parser.parse_args(args))

clinvar_gk_pilot/main.py

@@ -13,6 +13,7 @@
 from ga4gh.vrs.dataproxy import create_dataproxy
 from ga4gh.vrs.extras.translator import AlleleTranslator, CnvTranslator
 
+from clinvar_gk_pilot.cli import parse_args
 from clinvar_gk_pilot.gcs import (
     _local_file_path_for,
     already_downloaded,
@@ -42,25 +43,6 @@
 }
 
 
-def parse_args(args: List[str]) -> dict:
-    """
-    Parse arguments and return as dict.
-    """
-    parser = argparse.ArgumentParser()
-    parser.add_argument("--filename", required=True, help="Filename to read")
-    parser.add_argument(
-        "--parallelism",
-        type=int,
-        default=1,
-        help=(
-            "Number of worker threads. "
-            "Default 1, which still uses a separate process to run tasks. "
-            "Set to 0 to run in main thread."
-        ),
-    )
-    return vars(parser.parse_args(args))
-
-
 def process_line(line: str) -> str:
     """
     Takes a line of JSON, processes it, and returns the result as a JSON string.

test/test_main.py → test/test_cli.py

@@ -1,8 +1,9 @@
-from clinvar_gk_pilot.main import parse_args
+from clinvar_gk_pilot.cli import parse_args
 
 
 def test_parse_args():
     argv = ["--filename", "test.txt"]
     opts = parse_args(argv)
     assert opts["filename"] == "test.txt"
-    assert len(opts) == 1
+    assert opts["parallelism"] == 1
+    assert len(opts) == 2