From 0dc785ebdf038dad98f8b8b4dcc5792c99f71f4e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?M=C3=A1t=C3=A9=20Balajti?= <mate.balajti@unibas.ch>
Date: Thu, 9 Nov 2023 12:24:53 +0100
Subject: [PATCH] fix: update pydantic version

---
 environment-dev.yml    | 2 +-
 environment.yml        | 2 +-
 htsinfer/htsinfer.py   | 3 +--
 tests/test_htsinfer.py | 6 +++---
 4 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/environment-dev.yml b/environment-dev.yml
index 40f4f5f4..f8bcf898 100644
--- a/environment-dev.yml
+++ b/environment-dev.yml
@@ -13,7 +13,7 @@ dependencies:
   - pandas >=1.3.5, <1.4.0
   - pip >=20.2.3
   - pyahocorasick >=1.4.0
-  - pydantic >=1.8.1, <2
+  - pydantic >=2, <3
   - pylint >=2.4.4
   - pysam >=0.16.0
   - pytest >=6.1.0
diff --git a/environment.yml b/environment.yml
index 08e4fd28..273edbed 100644
--- a/environment.yml
+++ b/environment.yml
@@ -10,7 +10,7 @@ dependencies:
   - pandas >=1.3.5, <1.4.0
   - pip >=20.2.3
   - pyahocorasick >=1.4.0
-  - pydantic >=1.8.1, <2
+  - pydantic >=2, <3
   - pysam >=0.16.0
   - python >=3.8, <=3.10
   - star >=2.7.6
diff --git a/htsinfer/htsinfer.py b/htsinfer/htsinfer.py
index 9f2f6602..4967a4d9 100755
--- 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
index 0489023b..ea6e65f7 100644
--- 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(