fix pydantic issues

zavolanlab · Nov 1, 2023 · c79d9d6 · c79d9d6
1 parent 5fde74a
commit c79d9d6
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Showing 2 changed files with 4 additions and 5 deletions.
diff --git a/htsinfer/htsinfer.py b/htsinfer/htsinfer.py
@@ -315,8 +315,7 @@ def clean_up(self):
     def print(self):
         """Print results to STDOUT."""
         sys.stdout.write(
-            self.config.results.json(
+            self.config.results.model_dump_json(
                 indent=3,
-                sort_keys=False,
             ) + linesep
         )
diff --git a/tests/test_htsinfer.py b/tests/test_htsinfer.py
@@ -305,7 +305,7 @@ def test_clean_up_keep_none(self, tmpdir):
     def test_clean_up_keep_results(self, tmpdir):
         """Remove temporary data."""
         arguments = Args(path_1=FILE_MATE_1,
-                         out_dir=tmpdir,
+                         out_dir=tmpdir.strpath,
                          tmpdir=tmpdir,
                          )
         results = Results()
@@ -323,8 +323,8 @@ def test_clean_up_keep_results(self, tmpdir):
     def test_clean_up_keep_all(self, tmpdir):
         """Remove no data."""
         arguments = Args(path_1=FILE_MATE_1,
-                         out_dir=tmpdir,
-                         tmpdir=tmpdir,
+                         out_dir=tmpdir.strpath,
+                         tmpdir=tmpdir.strpath,
                          )
         results = Results()
         configs = Config(