update argcomplete dependency & test

requirements.txt

@@ -6,7 +6,7 @@ regex>=2020.4.4
 xdg>=2.0.0
 docker>=3.4.0
 PyYAML>=5.4.1,<7
-argcomplete~=1.12
+argcomplete>=3,<4
 pygtail~=0.14
 coloredlogs>=15,<16
 python-json-logger>=2,<3

tests/test_cli_argcomplete.py

@@ -1,51 +1,54 @@
 import sys
 import unittest
-import subprocess
+import pytest
 import os
 from tempfile import NamedTemporaryFile
 import argcomplete
-import contextlib
 from .context import WDL
 
 IFS = "\013"
 COMP_WORDBREAKS = " \t\n\"'><=;|&(:"
 
+
 class TestArgcomplete(unittest.TestCase):
     def setUp(self):
         self._os_environ = os.environ
         os.environ = os.environ.copy()
         os.environ["_ARGCOMPLETE"] = "1"
         os.environ["IFS"] = IFS
         os.environ["_ARGCOMPLETE_COMP_WORDBREAKS"] = COMP_WORDBREAKS
-        #os.environ["_ARC_DEBUG"] = "yes"
+        # os.environ["_ARC_DEBUG"] = "yes"
         argcomplete.debug_stream = sys.stderr
 
     def tearDown(self):
         os.environ = self._os_environ
 
-    def run_completer(self, parser, command, point=None, completer=argcomplete.autocomplete, **kwargs):
+    def run_completer(
+        self, parser, command, point=None, completer=argcomplete.autocomplete, **kwargs
+    ):
         if point is None:
             point = str(len(command))
-        with NamedTemporaryFile() as t:
+        with NamedTemporaryFile(mode="w") as t:
             os.environ["COMP_LINE"] = command
             os.environ["COMP_POINT"] = point
             with self.assertRaises(SystemExit) as cm:
                 completer(parser, output_stream=t, exit_method=sys.exit, **kwargs)
             if cm.exception.code != 0:
                 raise Exception("Unexpected exit code %d" % cm.exception.code)
-            t.seek(0)
-            return t.read().decode().split(IFS)
+            with open(t.name, "r") as tr:
+                return tr.read().split(IFS)
 
+    @pytest.mark.skip(reason="must run with unittest, not pytest, due to fd capture conflict")
     def test_completion(self):
-        if "PYTEST_CURRENT_TEST" in os.environ:
-            # due to conflict with pytest fd capture, this case has to run under unittest only
-            return
         p = WDL.CLI.create_arg_parser()
 
         completions = self.run_completer(p, "miniwdl r")
         self.assertEqual(set(completions), {"run", "run_self_test", "run-self-test"})
 
-        completions = self.run_completer(p, "miniwdl run --path test_corpi/broadinstitute/viral-ngs/pipes/WDL/workflows/tasks test_corpi/broadinstitute/viral-ngs/pipes/WDL/workflows/assemble_refbased.wdl ")
+        completions = self.run_completer(
+            p,
+            "miniwdl run --path test_corpi/broadinstitute/viral-ngs/pipes/WDL/workflows/tasks test_corpi/broadinstitute/viral-ngs/pipes/WDL/workflows/assemble_refbased.wdl ",
+        )
         completions = set(completions)
         self.assertTrue("--json" in completions)
         self.assertTrue("refine_2x_and_plot.assembly_fasta=" in completions)
@@ -54,7 +57,10 @@ def test_completion(self):
         self.assertTrue("refine_2x_and_plot.refine2_min_coverage=" not in completions)
 
         # suggest optional inputs only when specifically prefixed
-        completions = self.run_completer(p, "miniwdl run --path test_corpi/broadinstitute/viral-ngs/pipes/WDL/workflows/tasks test_corpi/broadinstitute/viral-ngs/pipes/WDL/workflows/assemble_refbased.wdl refine_2x_and_plot.refine2_min_")
+        completions = self.run_completer(
+            p,
+            "miniwdl run --path test_corpi/broadinstitute/viral-ngs/pipes/WDL/workflows/tasks test_corpi/broadinstitute/viral-ngs/pipes/WDL/workflows/assemble_refbased.wdl refine_2x_and_plot.refine2_min_",
+        )
         completions = set(completions)
         self.assertTrue("refine_2x_and_plot.assembly_fasta=" not in completions)
         self.assertTrue("refine_2x_and_plot.refine2_min_coverage=" in completions)