v2.0.1 release

docs/changelog.md

@@ -2,6 +2,14 @@
 
 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
+
+### 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

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!!!

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)

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.
 """

looper/conductor.py

@@ -1,4 +1,4 @@
-""" Pipeline job submission orchestration """
+"""Pipeline job submission orchestration"""
 
 import importlib
 import logging
@@ -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]}"
         )

looper/const.py

@@ -1,4 +1,4 @@
-""" Shared project constants """
+"""Shared project constants"""
 
 import os
 from enum import Enum

looper/divvy.py

@@ -1,4 +1,4 @@
-""" Computing configuration representation """
+"""Computing configuration representation"""
 
 import logging
 import os

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

looper/parser_types.py

@@ -1,4 +1,4 @@
-""" Definitions of the parser argument types """
+"""Definitions of the parser argument types"""
 
 from yacman import YAMLConfigManager
 

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

looper/project.py

@@ -1,4 +1,4 @@
-""" Looper version of NGS project model. """
+"""Looper version of NGS project model."""
 
 import itertools
 import os

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 = {}

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

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

tests/divvytests/helpers.py

@@ -1,4 +1,4 @@
-""" Test helpers """
+"""Test helpers"""
 
 import random
 import string

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