Merge branch 'dev' into add_org_param

.readthedocs.yaml

@@ -13,4 +13,4 @@ formats:
    - pdf
    - epub
 conda:
-  environment: environment.yml
+  environment: environment-dev.yml

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 .

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

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
         )

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(