Merge remote-tracking branch 'origin/minor_fixes' into minor_fixes

# Conflicts:
#	peppy/_version.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/sample.py

@@ -4,6 +4,7 @@
 from copy import copy as cp
 from logging import getLogger
 from string import Formatter
+from typing import Optional, Union
 
 import pandas as pd
 import yaml
@@ -134,31 +135,39 @@ def _obj2dict(obj, name=None):
  serial.update({"prj": grab_project_data(self[PRJ_REF])})
  return serial
 
- def to_yaml(self, path, add_prj_ref=False):
+ def to_yaml(
+ self, path: Optional[str] = None, add_prj_ref=False
+ ) -> Union[str, None]:
  """
- Serializes itself in YAML format.
+ Serializes itself in YAML format. Writes to file if path is provided, else returns string representation.
 
  :param str path: A file path to write yaml to; provide this or
- the subs_folder_path
+ the subs_folder_path, defaults to None
  :param bool add_prj_ref: whether the project reference bound do the
  Sample object should be included in the YAML representation
+ :return str | None: returns string representation of sample yaml or None
  """
  serial = self.to_dict(add_prj_ref=add_prj_ref)
- path = os.path.expandvars(path)
- if not os.path.exists(os.path.dirname(path)):
- _LOGGER.warning(
- "Could not write sample data to: {}. "
- "Directory does not exist".format(path)
- )
- return
- with open(path, "w") as outfile:
- try:
- yaml_data = yaml.safe_dump(serial, default_flow_style=False)
- except yaml.representer.RepresenterError:
- _LOGGER.error("Serialized sample data: {}".format(serial))
- raise
- outfile.write(yaml_data)
- _LOGGER.debug("Sample data written to: {}".format(path))
+ if path:
+ path = os.path.expandvars(path)
+ if os.path.exists(os.path.dirname(path)):
+ with open(path, "w") as outfile:
+ try:
+ yaml_data = yaml.safe_dump(serial, default_flow_style=False)
+ except yaml.representer.RepresenterError:
+ _LOGGER.error("Serialized sample data: {}".format(serial))
+ raise
+ outfile.write(yaml_data)
+ _LOGGER.debug("Sample data written to: {}".format(path))
+ else:
+ _LOGGER.warning(
+ "Could not write sample data to: {}. "
+ "Directory does not exist".format(path)
+ )
+ return
+ else:
+ yaml_data = yaml.safe_dump(serial, stream=None, default_flow_style=False)
+ return yaml_data
 
  def derive_attribute(self, data_sources, attr_name):
  """
@@ -302,6 +311,16 @@ 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):

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/smoketests/test_Sample.py

@@ -58,6 +58,16 @@ def test_str_repr_correctness(self, example_pep_cfg_path):
  assert example_pep_cfg_path in str_repr
  assert "Sample '{}'".format(sample["sample_name"]) in str_repr
 
+ @pytest.mark.parametrize("example_pep_cfg_path", EXAMPLE_TYPES, indirect=True)
+ def test_sample_to_yaml_no_path(self, example_pep_cfg_path):
+ """
+ Verify that to_yaml returns representation without requiring a path.
+ """
+ p = Project(cfg=example_pep_cfg_path)
+ for sample in p.samples:
+ yaml_repr = sample.to_yaml()
+ assert "sample_name" in yaml_repr
+
  @pytest.mark.parametrize("example_pep_cfg_path", ["basic"], indirect=True)
  def test_sheet_dict_excludes_private_attrs(self, example_pep_cfg_path):
  """

tests/test_Project.py

@@ -330,6 +330,15 @@ 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_path", ["custom_index"], indirect=True)
+ def test_sample_name_custom_index(self, example_pep_cfg_path):
+ """
+ Verify that sample_name attribute becomes st_index from cfg
+ """
+ p = Project(cfg=example_pep_cfg_path)
+ assert p.sample_name_colname == "NOT_SAMPLE_NAME"
+ assert p.samples[0].sample_name == "frog_1"
+
  @pytest.mark.parametrize(
  "example_pep_cfg_path",
  ["basic"],