Fixed #464

peppy/project.py

@@ -7,7 +7,6 @@
 from contextlib import suppress
 from logging import getLogger
 from typing import Iterable, List, Tuple, Union, Literal, NoReturn
-import yacman
 
 import numpy as np
 import pandas as pd

peppy/utils.py

@@ -5,6 +5,7 @@
 from typing import Dict
 from urllib.request import urlopen
 
+import yacman
 import yaml
 from ubiquerg import expandpath, is_url
 
@@ -123,11 +124,11 @@ def load_yaml(filepath):
             )
         else:
             data = response.read().decode("utf-8")
-            return yaml.safe_load(data)
+            return yacman.YAMLConfigManager(yamldata=data).exp
     else:
         with open(os.path.abspath(filepath), "r") as f:
             data = yaml.safe_load(f)
-        return data
+        return yacman.YAMLConfigManager(data).exp
 
 
 def is_cfg_or_anno(file_path, formats=None):

requirements/requirements-all.txt

@@ -2,4 +2,4 @@ pandas>=0.24.2
 pyyaml
 rich>=10.3.0
 ubiquerg>=0.6.2
-yacman>=0.9.0
+yacman>=0.9.2

tests/test_Project.py

@@ -93,6 +93,19 @@ def test_instantiaion(self, example_pep_cfg_path, defer):
         p = Project(cfg=example_pep_cfg_path, defer_samples_creation=defer)
         assert isinstance(p, Project)
 
+    @pytest.mark.parametrize("defer", [False, True])
+    @pytest.mark.parametrize("example_pep_cfg_path", ["amendments1"], indirect=True)
+    def test_expand_path(self, example_pep_cfg_path, defer):
+        """
+        Verify output_path is expanded
+        """
+        p = Project(
+            cfg=example_pep_cfg_path,
+            amendments="newLib",
+            defer_samples_creation=defer,
+        )
+        assert not p.config["output_dir"].startswith("$")
+
     @pytest.mark.parametrize(
         "config_path",
         [