looper 2.0.0a3__tar.gz → 2.0.1__tar.gz

{looper-2.0.0a3/looper.egg-info → looper-2.0.1}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: looper
-Version: 2.0.0a3
+Version: 2.0.1
 Summary: A pipeline submission engine that parses sample inputs and submits pipelines for each sample.
 Home-page: https://github.com/pepkit/looper
 Author: Nathan Sheffield, Vince Reuter, Michal Stolarczyk, Johanna Klughammer, Andre Rendeiro
@@ -16,7 +16,7 @@ Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Description-Content-Type: text/markdown
 License-File: LICENSE.txt
 Requires-Dist: colorama>=0.3.9
-Requires-Dist: eido>=0.2.3
+Requires-Dist: eido>=0.2.4
 Requires-Dist: jinja2
 Requires-Dist: logmuse>=0.2.0
 Requires-Dist: pandas>=2.0.2
@@ -25,10 +25,19 @@ Requires-Dist: pipestat>=0.12.0a1
 Requires-Dist: peppy>=0.40.6
 Requires-Dist: pyyaml>=3.12
 Requires-Dist: rich>=9.10.0
-Requires-Dist: ubiquerg>=0.8.1a1
+Requires-Dist: ubiquerg>=0.8.1
 Requires-Dist: yacman==0.9.3
 Requires-Dist: pydantic-argparse>=0.9.0
 Requires-Dist: psutil
+Dynamic: author
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: requires-dist
+Dynamic: summary
 
 # <img src="docs/img/looper_logo.svg" alt="looper logo" height="70">
 

{looper-2.0.0a3 → looper-2.0.1}/looper/_version.py

@@ -1,2 +1,2 @@
-__version__ = "2.0.0a3"
+__version__ = "2.0.1"
 # You must change the version in parser = pydantic_argparse.ArgumentParser in cli_pydantic.py!!!

{looper-2.0.0a3 → looper-2.0.1}/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="2.0.0a3",
+        version="2.0.1",
     )
 
     parser = add_short_arguments(parser, ArgumentEnum)

{looper-2.0.0a3 → looper-2.0.1}/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-2.0.0a3 → looper-2.0.1}/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 import read_schema, get_input_files_size
 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-2.0.0a3 → looper-2.0.1}/looper/const.py

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

{looper-2.0.0a3 → looper-2.0.1}/looper/divvy.py

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

{looper-2.0.0a3 → looper-2.0.1}/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-2.0.0a3 → looper-2.0.1}/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-2.0.0a3 → looper-2.0.1}/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-2.0.0a3 → looper-2.0.1}/looper/project.py

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

{looper-2.0.0a3 → looper-2.0.1}/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 = {}

{looper-2.0.0a3 → looper-2.0.1/looper.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: looper
-Version: 2.0.0a3
+Version: 2.0.1
 Summary: A pipeline submission engine that parses sample inputs and submits pipelines for each sample.
 Home-page: https://github.com/pepkit/looper
 Author: Nathan Sheffield, Vince Reuter, Michal Stolarczyk, Johanna Klughammer, Andre Rendeiro
@@ -16,7 +16,7 @@ Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Description-Content-Type: text/markdown
 License-File: LICENSE.txt
 Requires-Dist: colorama>=0.3.9
-Requires-Dist: eido>=0.2.3
+Requires-Dist: eido>=0.2.4
 Requires-Dist: jinja2
 Requires-Dist: logmuse>=0.2.0
 Requires-Dist: pandas>=2.0.2
@@ -25,10 +25,19 @@ Requires-Dist: pipestat>=0.12.0a1
 Requires-Dist: peppy>=0.40.6
 Requires-Dist: pyyaml>=3.12
 Requires-Dist: rich>=9.10.0
-Requires-Dist: ubiquerg>=0.8.1a1
+Requires-Dist: ubiquerg>=0.8.1
 Requires-Dist: yacman==0.9.3
 Requires-Dist: pydantic-argparse>=0.9.0
 Requires-Dist: psutil
+Dynamic: author
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: requires-dist
+Dynamic: summary
 
 # <img src="docs/img/looper_logo.svg" alt="looper logo" height="70">
 

{looper-2.0.0a3 → looper-2.0.1}/looper.egg-info/requires.txt

@@ -1,5 +1,5 @@
 colorama>=0.3.9
-eido>=0.2.3
+eido>=0.2.4
 jinja2
 logmuse>=0.2.0
 pandas>=2.0.2
@@ -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

{looper-2.0.0a3 → looper-2.0.1}/requirements/requirements-all.txt

@@ -1,5 +1,5 @@
 colorama>=0.3.9
-eido>=0.2.3
+eido>=0.2.4
 jinja2
 logmuse>=0.2.0
 pandas>=2.0.2
@@ -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