From 534319a48337cb8e3cd824238b20e477a934a06c Mon Sep 17 00:00:00 2001
From: Michael Franklin <illusional@users.noreply.github.com>
Date: Thu, 14 Sep 2023 16:35:43 +1000
Subject: [PATCH] Slight linting updates

---
 .github/workflows/lint.yaml  | 2 ++
 scripts/parse_ped.py         | 4 ++--
 test/test_generic_auditor.py | 7 +++++--
 3 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
index d4863658a..01424f2df 100644
--- a/.github/workflows/lint.yaml
+++ b/.github/workflows/lint.yaml
@@ -20,6 +20,8 @@ jobs:
         run: |
           pip install -r requirements-dev.txt
           pip install .
+          # test to see if this is happier
+          mkdir .mypy_cache
 
       - name: pre-commit
         run: pre-commit run --all-files
diff --git a/scripts/parse_ped.py b/scripts/parse_ped.py
index 894d0c241..d77b46fc0 100644
--- a/scripts/parse_ped.py
+++ b/scripts/parse_ped.py
@@ -1,7 +1,6 @@
 """ A really simple script to import a pedigree file """
 
 import click
-
 from cloudpathlib import CloudPath
 
 from metamist.apis import (
@@ -17,7 +16,8 @@ def main(ped_file_path: str, project: str):
 
     fapi = FamilyApi()
 
-    with CloudPath(ped_file_path).open() as ped_file:
+    # pylint: disable=no-member
+    with CloudPath(ped_file_path).open() as ped_file:  # type: ignore
         fapi.import_pedigree(
             file=ped_file,
             has_header=True,
diff --git a/test/test_generic_auditor.py b/test/test_generic_auditor.py
index 4fb526dc9..f9aa1c2e8 100644
--- a/test/test_generic_auditor.py
+++ b/test/test_generic_auditor.py
@@ -1,6 +1,7 @@
-from collections import namedtuple
 import unittest
+from collections import namedtuple
 from unittest.mock import MagicMock, patch
+
 from metamist.audit.generic_auditor import GenericAuditor
 
 # pylint: disable=dangerous-default-value
@@ -569,7 +570,9 @@ def test_analyses_for_sgs_without_crams(self, mock_query):
         }
 
         with self.assertLogs(level='WARNING') as log:
-            _ = auditor.analyses_for_sgs_without_crams(sgs_without_crams)
+            # catch the warning logs from here and check below
+            auditor.analyses_for_sgs_without_crams(sgs_without_crams)
+
             self.assertEqual(len(log.output), 8)  # 8 analysis types checked
             self.assertEqual(len(log.records), 8)
             self.assertIn(