From f063c3d8ec40c167dbaed0dd1e1b62ff4efb79a5 Mon Sep 17 00:00:00 2001
From: Donald Campbell <125581724+donaldcampbelljr@users.noreply.github.com>
Date: Tue, 28 Jan 2025 15:44:53 -0500
Subject: [PATCH 1/4] Solution for #541

---
 looper/conductor.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/looper/conductor.py b/looper/conductor.py
index 231a2366..952e48b2 100644
--- a/looper/conductor.py
+++ b/looper/conductor.py
@@ -18,7 +18,7 @@
 from eido.const import INPUT_FILE_SIZE_KEY, MISSING_KEY
 from jinja2.exceptions import UndefinedError
 
-from peppy.const import CONFIG_KEY, SAMPLE_NAME_ATTR, SAMPLE_YAML_EXT
+from peppy.const import CONFIG_KEY, SAMPLE_YAML_EXT
 from peppy.exceptions import RemoteYAMLError
 from pipestat import PipestatError
 from ubiquerg import expandpath
@@ -77,7 +77,7 @@ def _get_yaml_path(namespaces, template_key, default_name_appendix="", filename=
         # default YAML location
         f = (
             filename
-            or f"{namespaces['sample'][SAMPLE_NAME_ATTR]}"
+            or f"{namespaces['sample'][namespaces['sample']['_project'].sample_table_index]}"
             f"{default_name_appendix}"
             f"{SAMPLE_YAML_EXT[0]}"
         )

From ffed13f2b50465600aa8b744618b961b741b0d66 Mon Sep 17 00:00:00 2001
From: Donald Campbell <125581724+donaldcampbelljr@users.noreply.github.com>
Date: Wed, 5 Mar 2025 14:41:46 -0500
Subject: [PATCH 2/4] update ubiquerg req and update looper to v2.0.1

---
 docs/changelog.md                 | 5 +++++
 looper/_version.py                | 2 +-
 looper/cli_pydantic.py            | 2 +-
 requirements/requirements-all.txt | 2 +-
 4 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/docs/changelog.md b/docs/changelog.md
index 986d8550..6b11b8c9 100644
--- a/docs/changelog.md
+++ b/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.
 
+## [2.0.1] -- 2025-03-05
+
+### Changed
+- update ubiquerg>=0.8.1
+
 ## [2.0.0] -- 2025-01-16
 
 This release breaks backwards compatibility for Looper versions < 2.0.0
diff --git a/looper/_version.py b/looper/_version.py
index 0ac2c675..ad44a781 100644
--- a/looper/_version.py
+++ b/looper/_version.py
@@ -1,2 +1,2 @@
-__version__ = "2.0.0"
+__version__ = "2.0.1"
 # You must change the version in parser = pydantic_argparse.ArgumentParser in cli_pydantic.py!!!
diff --git a/looper/cli_pydantic.py b/looper/cli_pydantic.py
index 1bef39f3..0ede9dfa 100644
--- a/looper/cli_pydantic.py
+++ b/looper/cli_pydantic.py
@@ -340,7 +340,7 @@ def main(test_args=None) -> dict:
         prog="looper",
         description="Looper: A job submitter for Portable Encapsulated Projects",
         add_help=True,
-        version="2.0.0",
+        version="2.0.1",
     )
 
     parser = add_short_arguments(parser, ArgumentEnum)
diff --git a/requirements/requirements-all.txt b/requirements/requirements-all.txt
index 6533040a..88af67d8 100644
--- a/requirements/requirements-all.txt
+++ b/requirements/requirements-all.txt
@@ -8,7 +8,7 @@ pipestat>=0.12.0a1
 peppy>=0.40.6
 pyyaml>=3.12
 rich>=9.10.0
-ubiquerg>=0.8.1a1
+ubiquerg>=0.8.1
 yacman==0.9.3
 pydantic-argparse>=0.9.0
 psutil
\ No newline at end of file

From 2bdf2b8cdccf74978b6d9c5eebcd76efd0f80b1d Mon Sep 17 00:00:00 2001
From: Donald Campbell <125581724+donaldcampbelljr@users.noreply.github.com>
Date: Wed, 5 Mar 2025 14:46:08 -0500
Subject: [PATCH 3/4] lint with newer version

---
 looper/command_models/__init__.py                | 2 +-
 looper/conductor.py                              | 2 +-
 looper/const.py                                  | 2 +-
 looper/divvy.py                                  | 2 +-
 looper/exceptions.py                             | 2 +-
 looper/parser_types.py                           | 2 +-
 looper/pipeline_interface.py                     | 2 +-
 looper/project.py                                | 2 +-
 looper/utils.py                                  | 4 +---
 tests/divvytests/divvy_tests/test_divvy.py       | 2 +-
 tests/divvytests/helpers.py                      | 2 +-
 tests/divvytests/regression/test_write_script.py | 2 +-
 12 files changed, 12 insertions(+), 14 deletions(-)

diff --git a/looper/command_models/__init__.py b/looper/command_models/__init__.py
index 4258506b..46d1c396 100644
--- a/looper/command_models/__init__.py
+++ b/looper/command_models/__init__.py
@@ -1,6 +1,6 @@
 """
 This package holds `pydantic` models that describe commands and their arguments.
 
-These can be used either by an HTTP API or with the `pydantic-argparse` 
+These can be used either by an HTTP API or with the `pydantic-argparse`
 library to build a CLI.
 """
diff --git a/looper/conductor.py b/looper/conductor.py
index 952e48b2..5f24ebfb 100644
--- a/looper/conductor.py
+++ b/looper/conductor.py
@@ -1,4 +1,4 @@
-""" Pipeline job submission orchestration """
+"""Pipeline job submission orchestration"""
 
 import importlib
 import logging
diff --git a/looper/const.py b/looper/const.py
index de080260..bfa51309 100644
--- a/looper/const.py
+++ b/looper/const.py
@@ -1,4 +1,4 @@
-""" Shared project constants """
+"""Shared project constants"""
 
 import os
 from enum import Enum
diff --git a/looper/divvy.py b/looper/divvy.py
index e458bad6..84e66ed7 100644
--- a/looper/divvy.py
+++ b/looper/divvy.py
@@ -1,4 +1,4 @@
-""" Computing configuration representation """
+"""Computing configuration representation"""
 
 import logging
 import os
diff --git a/looper/exceptions.py b/looper/exceptions.py
index 7d478feb..62b9e041 100644
--- a/looper/exceptions.py
+++ b/looper/exceptions.py
@@ -1,4 +1,4 @@
-""" Exceptions for specific looper issues. """
+"""Exceptions for specific looper issues."""
 
 from abc import ABCMeta
 from collections.abc import Iterable
diff --git a/looper/parser_types.py b/looper/parser_types.py
index 2afc2c4a..98404965 100644
--- a/looper/parser_types.py
+++ b/looper/parser_types.py
@@ -1,4 +1,4 @@
-""" Definitions of the parser argument types """
+"""Definitions of the parser argument types"""
 
 from yacman import YAMLConfigManager
 
diff --git a/looper/pipeline_interface.py b/looper/pipeline_interface.py
index 387c6d49..f7f0793e 100644
--- a/looper/pipeline_interface.py
+++ b/looper/pipeline_interface.py
@@ -1,4 +1,4 @@
-""" Model the connection between a pipeline and a project or executor. """
+"""Model the connection between a pipeline and a project or executor."""
 
 import os
 from collections.abc import Mapping
diff --git a/looper/project.py b/looper/project.py
index d77dc368..df69ac5a 100644
--- a/looper/project.py
+++ b/looper/project.py
@@ -1,4 +1,4 @@
-""" Looper version of NGS project model. """
+"""Looper version of NGS project model."""
 
 import itertools
 import os
diff --git a/looper/utils.py b/looper/utils.py
index 5a8279bd..b5d904c5 100644
--- a/looper/utils.py
+++ b/looper/utils.py
@@ -1,4 +1,4 @@
-""" Helpers without an obvious logical home. """
+"""Helpers without an obvious logical home."""
 
 import argparse
 from collections import defaultdict
@@ -1112,7 +1112,6 @@ def inspect_looper_config_file(looper_config_dict) -> None:
 
 
 def expand_nested_var_templates(var_templates_dict, namespaces):
-
     "Takes all var_templates as a dict and recursively expands any paths."
 
     result = {}
@@ -1127,7 +1126,6 @@ def expand_nested_var_templates(var_templates_dict, namespaces):
 
 
 def render_nested_var_templates(var_templates_dict, namespaces):
-
     "Takes all var_templates as a dict and recursively renders the jinja templates."
 
     result = {}
diff --git a/tests/divvytests/divvy_tests/test_divvy.py b/tests/divvytests/divvy_tests/test_divvy.py
index da9ce7c8..a67e489d 100644
--- a/tests/divvytests/divvy_tests/test_divvy.py
+++ b/tests/divvytests/divvy_tests/test_divvy.py
@@ -1,4 +1,4 @@
-""" Assorted divvy tests """
+"""Assorted divvy tests"""
 
 import pytest
 from yacman import YacAttMap, load_yaml
diff --git a/tests/divvytests/helpers.py b/tests/divvytests/helpers.py
index e2e9d35c..be4b1104 100644
--- a/tests/divvytests/helpers.py
+++ b/tests/divvytests/helpers.py
@@ -1,4 +1,4 @@
-""" Test helpers """
+"""Test helpers"""
 
 import random
 import string
diff --git a/tests/divvytests/regression/test_write_script.py b/tests/divvytests/regression/test_write_script.py
index 1159ee46..0a82753c 100644
--- a/tests/divvytests/regression/test_write_script.py
+++ b/tests/divvytests/regression/test_write_script.py
@@ -1,4 +1,4 @@
-""" Specific case tests for writing submission script """
+"""Specific case tests for writing submission script"""
 
 from copy import deepcopy
 import random

From 5b78e4b4a178d2349e1109da8d9c701d9c7de850 Mon Sep 17 00:00:00 2001
From: Donald Campbell <125581724+donaldcampbelljr@users.noreply.github.com>
Date: Wed, 5 Mar 2025 14:52:50 -0500
Subject: [PATCH 4/4] update changelog with fixed issues

---
 docs/changelog.md | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/docs/changelog.md b/docs/changelog.md
index 6b11b8c9..9f5680d0 100644
--- a/docs/changelog.md
+++ b/docs/changelog.md
@@ -7,6 +7,9 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 ### Changed
 - update ubiquerg>=0.8.1
 
+### Fixed
+- [#541](https://github.com/pepkit/looper/issues/541)
+
 ## [2.0.0] -- 2025-01-16
 
 This release breaks backwards compatibility for Looper versions < 2.0.0