Fixed Sample serialization

peppy/_version.py

@@ -1 +1 @@
-__version__ = "0.40.0a2"
+__version__ = "0.40.0a3"

peppy/project.py

@@ -226,7 +226,7 @@ def from_dict(self, pep_dictionary: dict) -> "Project":
 
     def to_dict(
         self,
-        expand: bool = False,
+        # expand: bool = False, # expand was used to expand paths. This functionality was removed, because of attmapp
         extended: bool = False,
         orient: Literal[
             "dict", "list", "series", "split", "tight", "records", "index"
@@ -1397,6 +1397,7 @@ def __delitem__(self, key):
     def __repr__(self):
         return str(self)
 
+    # # pickle now is impossible, because it's impossible to initialize Project class without using actual files
     # def __reduce__(self):
     #     return (self.__class__,)
 

peppy/sample.py

@@ -307,10 +307,9 @@ def __reduce__(self):
         return (
             self.__class__,
             (pd.Series(self.to_dict()),),
-            # (self.as_series(),),
-            (None, {}),
-            iter([]),
-            iter({PRJ_REF: self[PRJ_REF]}.items()),
+            # (None, {}),
+            # iter([]),
+            # iter({PRJ_REF: self[PRJ_REF]}.items()),
         )
 
     def __len__(self):

tests/smoketests/test_Sample.py

@@ -66,3 +66,14 @@ def test_sheet_dict_excludes_private_attrs(self, example_pep_cfg_path):
         p = Project(cfg=example_pep_cfg_path)
         for sample in p.samples:
             assert len(sample.get_sheet_dict()) == len(p.sample_table.columns)
+
+    @pytest.mark.parametrize("example_pep_cfg_path", ["basic"], indirect=True)
+    def test_pickle_in_samples(self, example_pep_cfg_path):
+        import pickle
+
+        p = Project(cfg=example_pep_cfg_path)
+        for sample in p.samples:
+            pickled_data = pickle.dumps(sample)
+            unpickled_sample = pickle.loads(pickled_data)
+
+            assert sample.to_dict() == unpickled_sample.to_dict()

tests/test_Project.py

@@ -393,10 +393,12 @@ def test_peppy_initializes_samples_with_correct_attributes(
         p = Project(example_pep_cfg_path, sample_table_index="sample")
         assert all([expected_attribute in sample for sample in p.samples])
 
+    @pytest.mark.skip(
+        "skipping this test, because this functionality is unavailable now"
+    )
     @pytest.mark.parametrize("example_pep_cfg_path", ["basic", "imply"], indirect=True)
     def test_correct_pickle(self, example_pep_cfg_path):
         proj = Project(example_pep_cfg_path)
-
         pickled_data = pickle.dumps(proj)
         unpickled_project = pickle.loads(pickled_data)