Switch to pydantic2-argparse

looper/cli_pydantic.py

@@ -21,10 +21,10 @@
 import sys
 
 import logmuse
-import pydantic_argparse
+import pydantic2_argparse
 import yaml
 from pephubclient import PEPHubClient
-from pydantic_argparse.argparse.parser import ArgumentParser
+from pydantic2_argparse.argparse.parser import ArgumentParser
 
 from divvy import select_divvy_config
 
@@ -241,7 +241,7 @@ def run_looper(args: TopLevelParser, parser: ArgumentParser, test_args=None):
 
 
 def main(test_args=None) -> None:
-    parser = pydantic_argparse.ArgumentParser(
+    parser = pydantic2_argparse.ArgumentParser(
         model=TopLevelParser,
         prog="looper",
         description="Looper Pydantic Argument Parser",

looper/command_models/arguments.py

@@ -7,7 +7,7 @@
 from copy import copy
 from typing import Any, List
 
-import pydantic
+import pydantic.v1 as pydantic
 
 
 class Argument(pydantic.fields.FieldInfo):

looper/command_models/commands.py

@@ -5,7 +5,7 @@
 from dataclasses import dataclass
 from typing import List, Optional, Type
 
-import pydantic
+import pydantic.v1 as pydantic
 
 from ..const import MESSAGE_BY_SUBCOMMAND
 from .arguments import Argument, ArgumentEnum

requirements/requirements-all.txt

@@ -11,4 +11,4 @@ pyyaml>=3.12
 rich>=9.10.0
 ubiquerg>=0.5.2
 yacman==0.9.3
-pydantic-argparse>=0.8.0
+pydantic2-argparse>=0.9.2

tests/smoketests/test_other.py

@@ -28,9 +28,9 @@ class TestLooperPipestat:
     @pytest.mark.parametrize("cmd", ["report", "table", "check"])
     def test_fail_no_pipestat_config(self, prep_temp_pep, cmd):
         "report, table, and check should fail if pipestat is NOT configured."
-        #tp = prep_temp_pep
+        # tp = prep_temp_pep
         dot_file_path = os.path.abspath(prepare_pep_with_dot_file)
-        #x = test_args_expansion(tp, cmd, dry=False)
+        # x = test_args_expansion(tp, cmd, dry=False)
         x = ["--looper-config", dot_file_path, cmd]
         with pytest.raises(PipestatConfigurationException):
             main(test_args=x)

tests/smoketests/test_run.py

@@ -10,6 +10,7 @@
 
 CMD_STRS = ["string", " --string", " --sjhsjd 212", "7867#$@#$cc@@"]
 
+
 @pytest.mark.skip(reason="prep_temp_pep needs to be rewritten")
 def test_cli(prep_temp_pep):
     tp = prep_temp_pep
@@ -98,6 +99,7 @@ def test_unrecognized_args_not_passing(self, prep_temp_pep, cmd):
         except Exception:
             raise pytest.fail("DID RAISE {0}".format(Exception))
 
+
 @pytest.mark.skip(reason="prep_temp_pep needs to be rewritten")
 class TestLooperRunBehavior:
     def test_looper_run_basic(self, prep_temp_pep):
@@ -315,6 +317,7 @@ def test_cmd_extra_override_sample(self, prep_temp_pep, arg):
         subs_list = [os.path.join(sd, f) for f in os.listdir(sd) if f.endswith(".sub")]
         assert_content_not_in_any_files(subs_list, arg)
 
+
 @pytest.mark.skip(reason="prep_temp_pep needs to be rewritten")
 class TestLooperRunpBehavior:
     def test_looper_runp_basic(self, prep_temp_pep):
@@ -364,6 +367,7 @@ def test_cmd_extra_project(self, prep_temp_pep, arg):
         subs_list = [os.path.join(sd, f) for f in os.listdir(sd) if f.endswith(".sub")]
         assert_content_in_all_files(subs_list, arg)
 
+
 @pytest.mark.skip(reason="prep_temp_pep needs to be rewritten")
 class TestLooperRunPreSubmissionHooks:
     def test_looper_basic_plugin(self, prep_temp_pep):
@@ -423,6 +427,7 @@ def test_looper_command_templates_hooks(self, prep_temp_pep, cmd):
         sd = os.path.join(get_outdir(tp), "submission")
         verify_filecount_in_dir(sd, "test.txt", 3)
 
+
 @pytest.mark.skip(reason="prep_temp_pep needs to be rewritten")
 class TestLooperRunSubmissionScript:
     def test_looper_run_produces_submission_scripts(self, prep_temp_pep):
@@ -475,6 +480,7 @@ def test_looper_limiting(self, prep_temp_pep):
         sd = os.path.join(get_outdir(tp), "submission")
         verify_filecount_in_dir(sd, ".sub", 4)
 
+
 @pytest.mark.skip(reason="prep_temp_pep needs to be rewritten")
 class TestLooperCompute:
     @pytest.mark.parametrize("cmd", ["run", "runp"])

tests/test_clean.py

@@ -23,6 +23,7 @@ def build_namespace(**kwargs):
     ]
 ]
 
+
 @pytest.mark.skip(reason="Test needs to be rewritten")
 @pytest.mark.parametrize(["args", "preview"], DRYRUN_OR_NOT_PREVIEW)
 def test_cleaner_does_not_crash(args, preview, prep_temp_pep):