Release 0.40.1

docs/changelog.md

@@ -2,6 +2,11 @@
 
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format.
 
+## [0.40.1] -- 2024-01-11
+### Fixed
+- Initializing Project with `NaN` value instead of `None` in `from_pandas` method
+
+
 ## [0.40.0] -- 2023-12-18
 
 **This version introduced backwards-incompatible changes.**

peppy/__init__.py

@@ -14,6 +14,6 @@
 from .sample import Sample
 
 __classes__ = ["Project", "Sample"]
-__all__ = __classes__ + ["PeppyError"]
+__all__ = __classes__ + ["PeppyError", "__version__"]
 
 LOGGING_LEVEL = "INFO"

peppy/_version.py

@@ -1 +1 @@
-__version__ = "0.40.0"
+__version__ = "0.40.1"

peppy/project.py

@@ -6,7 +6,7 @@
 from collections.abc import Mapping, MutableMapping
 from contextlib import suppress
 from logging import getLogger
-from typing import Iterable, List, Tuple, Union, Literal, NoReturn
+from typing import Iterable, List, Tuple, Union, Literal
 
 import numpy as np
 import pandas as pd
@@ -223,13 +223,15 @@ def _from_dict(self, pep_dictionary) -> "Project":
                                                                              _samples: list | dict,
                                                                              _subsamples: list[list | dict]}
         """
-        self[SAMPLE_DF_KEY] = pd.DataFrame(pep_dictionary[SAMPLE_RAW_DICT_KEY])
+        self[SAMPLE_DF_KEY] = pd.DataFrame(pep_dictionary[SAMPLE_RAW_DICT_KEY]).replace(
+            np.nan, ""
+        )
         self[CONFIG_KEY] = pep_dictionary[CONFIG_KEY]
 
         if SUBSAMPLE_RAW_LIST_KEY in pep_dictionary:
             if pep_dictionary[SUBSAMPLE_RAW_LIST_KEY]:
                 self[SUBSAMPLE_DF_KEY] = [
-                    pd.DataFrame(sub_a)
+                    pd.DataFrame(sub_a).replace(np.nan, "")
                     for sub_a in pep_dictionary[SUBSAMPLE_RAW_LIST_KEY]
                 ]
         if NAME_KEY in self[CONFIG_KEY]:
@@ -467,7 +469,7 @@ def parse_config_file(
         relative_vars = [CFG_SAMPLE_TABLE_KEY, CFG_SUBSAMPLE_TABLE_KEY]
         _make_sections_absolute(self[CONFIG_KEY], relative_vars, cfg_path)
 
-    def _set_indexes(self, config: Mapping) -> NoReturn:
+    def _set_indexes(self, config: Mapping) -> None:
         """
         Set sample and subsample indexes if they are different then Default
 
@@ -483,6 +485,7 @@ def _set_indexes(self, config: Mapping) -> NoReturn:
             if SUBSAMPLE_TABLE_INDEX_KEY in config
             else SUBSAMPLE_NAME_ATTR
         )
+        return None
 
     def load_samples(self):
         """
@@ -1333,7 +1336,7 @@ def _read_sample_data(self):
 
         if st is not None:
             parser_class = select_parser(path=st)
-            self[SAMPLE_DF_KEY] = parser_class(path=st).table
+            self[SAMPLE_DF_KEY] = parser_class(path=st).table.replace(np.nan, "")
             self[SAMPLE_DF_LARGE] = self[SAMPLE_DF_KEY].shape[0] > 1000
         else:
             _LOGGER.warning(no_metadata_msg.format(CFG_SAMPLE_TABLE_KEY))

tests/test_Project.py

@@ -10,7 +10,6 @@
 from yaml import dump, safe_load
 import pickle
 
-import peppy
 from peppy import Project
 from peppy.const import SAMPLE_NAME_ATTR, SAMPLE_TABLE_FILE_KEY
 from peppy.exceptions import (
@@ -350,10 +349,6 @@ def test_from_dict_instatiation(self, example_pep_cfg_path):
         representation.
         """
         p1 = Project(cfg=example_pep_cfg_path)
-        ff = p1.to_dict(extended=True)
-        import pprint
-
-        pprint.pprint(ff)
         p2 = Project.from_dict(p1.to_dict(extended=True))
         assert p1 == p2
 
@@ -694,7 +689,7 @@ def test_sample_getattr(self, example_pep_cfg_path):
             assert s2.organism == s2["organism"]
 
     @pytest.mark.parametrize("example_pep_cfg_path", ["append"], indirect=True)
-    def test_sample_getattr(self, example_pep_cfg_path):
+    def test_sample_settatr(self, example_pep_cfg_path):
         """
         Verify that the setattr works
         """