Merge pull request #485 from pepkit/dev

v0.40.2

MANIFEST.in

@@ -1,5 +1,3 @@
 include LICENSE.txt
 include requirements/*
 include README.md
-recursive-include docs *.md
-recursive-include tests *.py

docs/changelog.md

@@ -2,6 +2,10 @@
 
 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.
 
+## [0.40.2] -- 2024-05-28
+### Added
+- added `sample_name` property to samples object.
+
 ## [0.40.1] -- 2024-01-11
 ### Fixed
 - Initializing Project with `NaN` value instead of `None` in `from_pandas` method

peppy/_version.py

@@ -1 +1 @@
-__version__ = "0.40.1"
+__version__ = "0.40.2"

peppy/project.py

@@ -1,6 +1,7 @@
 """
 Build a Project object.
 """
+
 import os
 import sys
 from collections.abc import Mapping, MutableMapping
@@ -644,21 +645,7 @@ def _assert_samples_have_names(self):
                     f"{CFG_SAMPLE_TABLE_KEY} is missing '{self.st_index}' column; "
                     f"you must specify {CFG_SAMPLE_TABLE_KEY}s in {self.st_index} or derive them"
                 )
-                if self.st_index != SAMPLE_NAME_ATTR:
-                    try:
-                        custom_sample_name = sample[self.st_index]
-                    except KeyError:
-                        raise InvalidSampleTableFileException(
-                            f"Specified {CFG_SAMPLE_TABLE_KEY} index ({self.st_index}) does not exist"
-                        )
-                    sample[SAMPLE_NAME_ATTR] = custom_sample_name
-                    _LOGGER.warning(
-                        message
-                        + f"using specified {CFG_SAMPLE_TABLE_KEY} index ({self.st_index}) instead. "
-                        + f"Setting name: {custom_sample_name}"
-                    )
-                else:
-                    raise InvalidSampleTableFileException(message)
+                raise InvalidSampleTableFileException(message)
 
     def _auto_merge_duplicated_names(self):
         """

peppy/sample.py

@@ -302,6 +302,16 @@ def project(self):
         """
         return self[PRJ_REF]
 
+    @property
+    def sample_name(self):
+        """
+        Get the sample's name
+
+        :return str: current sample name derived from project's st_index
+        """
+
+        return self[self[PRJ_REF].st_index]
+
     # The __reduce__ function provides an interface for
     # correct object serialization with the pickle module.
     def __reduce__(self):

setup.py

@@ -40,7 +40,7 @@ def get_static(name, condition=None):
 
 setup(
     name=PACKAGE_NAME,
-    packages=find_packages(),
+    packages=[PACKAGE_NAME],
     version=version,
     description="A python-based project metadata manager for portable encapsulated projects",
     long_description=long_description,

tests/conftest.py

@@ -51,6 +51,11 @@ def example_pep_cfg_noname_path(request):
     return get_path_to_example_file(EPB, "noname", request.param)
 
 
+@pytest.fixture
+def example_pep_cfg_custom_index(request):
+    return get_path_to_example_file(EPB, "custom_index", request.param)
+
+
 @pytest.fixture
 def example_peps_cfg_paths(request):
     """

tests/data/example_peps-master/example_custom_index/project_config.yaml

@@ -1,3 +1,3 @@
 pep_version: "2.0.0"
 sample_table: sample_table.csv
-sample_table_index: sample_id
+sample_table_index: NOT_SAMPLE_NAME

tests/data/example_peps-master/example_custom_index/sample_table.csv

@@ -1,3 +1,3 @@
-sample_id,protocol,file
+NOT_SAMPLE_NAME,protocol,file
 frog_1,anySampleType,data/frog1_data.txt
 frog_2,anySampleType,data/frog2_data.txt

tests/data/example_peps-master/example_incorrect_index/project_config.yaml

@@ -0,0 +1,3 @@
+pep_version: "2.0.0"
+sample_table: sample_table.csv
+sample_table_index: sample_id

tests/data/example_peps-master/example_incorrect_index/sample_table.csv

@@ -0,0 +1,3 @@
+sample_name,protocol,file
+frog_1,anySampleType,data/frog1_data.txt
+frog_2,anySampleType,data/frog2_data.txt

tests/test_Project.py

@@ -233,6 +233,14 @@ def test_cutsom_sample_table_index_config(self, example_pep_cfg_path):
         """
         Project(cfg=example_pep_cfg_path)
 
+    @pytest.mark.parametrize("example_pep_cfg_path", ["incorrect_index"], indirect=True)
+    def test_cutsom_sample_table_index_config_exception(self, example_pep_cfg_path):
+        """
+        Verify that custom sample table index is sourced from the config
+        """
+        with pytest.raises(InvalidSampleTableFileException):
+            Project(cfg=example_pep_cfg_path)
+
     @pytest.mark.parametrize("example_pep_cfg_path", ["custom_index"], indirect=True)
     def test_cutsom_sample_table_index_constructor(self, example_pep_cfg_path):
         """
@@ -322,6 +330,17 @@ def test_missing_sample_name_custom_index(self, example_pep_cfg_noname_path):
         p = Project(cfg=example_pep_cfg_noname_path, sample_table_index="id")
         assert p.sample_name_colname == "id"
 
+    @pytest.mark.parametrize(
+        "example_pep_cfg_custom_index", ["project_config.yaml"], indirect=True
+    )
+    def test_sample_name_custom_index(self, example_pep_cfg_custom_index):
+        """
+        Verify that sample_name attribute becomes st_index from cfg
+        """
+        p = Project(cfg=example_pep_cfg_custom_index)
+        assert p.sample_name_colname == "NOT_SAMPLE_NAME"
+        assert p.samples[0].sample_name == "frog_1"
+
     @pytest.mark.parametrize(
         "example_pep_cfg_path",
         ["basic"],