From 172eb99f404dda69b5648f492ac4ea02ecb824d0 Mon Sep 17 00:00:00 2001
From: balajtimate <51365402+balajtimate@users.noreply.github.com>
Date: Thu, 9 Nov 2023 15:12:15 +0100
Subject: [PATCH] fix: update Pydantic version (#146)

* fix pydantic issues

* fix: update pydantic version in envs

* fix: pin sphinx-rtd-theme into env

* fix: update readthedocs config
---
 .readthedocs.yaml      | 2 +-
 environment-dev.yml    | 5 +++--
 environment.yml        | 2 +-
 htsinfer/htsinfer.py   | 3 +--
 tests/test_htsinfer.py | 6 +++---
 5 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index 14c41f2e..0922ec04 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -13,4 +13,4 @@ formats:
    - pdf
    - epub
 conda:
-  environment: environment.yml
+  environment: environment-dev.yml
diff --git a/environment-dev.yml b/environment-dev.yml
index 40f4f5f4..c97c611a 100644
--- a/environment-dev.yml
+++ b/environment-dev.yml
@@ -13,12 +13,13 @@ 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
   - python >=3.8, <=3.10
+  - python-semantic-release >=8
+  - sphinx-rtd-theme
   - star >=2.7.6
   - pip:
-    - python-semantic-release>=7.15.0
     - -e .
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(