looper 2.0.0a3__py3-none-any.whl → 2.0.1__py3-none-any.whl

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/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/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 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/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 = {}

{looper-2.0.0a3.dist-info → looper-2.0.1.dist-info}/METADATA

@@ -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.dist-info → looper-2.0.1.dist-info}/RECORD

@@ -1,22 +1,22 @@
 looper/__init__.py,sha256=f_z9YY4ibOk7eyWoaViH_VaCXMlPQeiftbnibSFj-3E,1333
 looper/__main__.py,sha256=OOCmI-dPUvInnJHkHNMf54cblNJ3Yl9ELOwZcfOXmD8,240
-looper/_version.py,sha256=MwJwmoXPcF0oLwdO3af_PLuTBNXWHfGxew5Q7p37mTQ,121
+looper/_version.py,sha256=DW9L8zOJPcNY9ZbgS_iQmVE_rIc1YpAHFt8cZRRXFZU,119
 looper/cli_divvy.py,sha256=_VGbOFLkXtKdkZA6omlzgXbXkuUM5aLQ50aTTtbTrVI,5975
-looper/cli_pydantic.py,sha256=BA-jq6lyFnGoNNLCKAFrfqMQ7qRR3qxYK62PfMEoKA4,14425
-looper/conductor.py,sha256=lzY6Gzsb8oX-KLzLkRa0XrYWSxLeiy6jRmmD15WNAkw,35116
-looper/const.py,sha256=OscEELQsyLKlSrmwuXfyLRwpAUJUEpGD2UxBeLJDXgw,8703
-looper/divvy.py,sha256=yokD0--xN0kaxPuPRZrRPgKinl0Sqt0cvkmNMvwe94A,15860
-looper/exceptions.py,sha256=weSXsPadikAHVJvUUOT1uE56C_nKqgC3iBOvDebPDVE,3572
+looper/cli_pydantic.py,sha256=KS26gh_vF9fxjVpuBbI1K4sgokT1PWme4klwwcphLWQ,14423
+looper/conductor.py,sha256=EvVSZ9czG8-cRDLl2aXHZPeQ02J4xM0T_Y6mYO_2jTQ,35131
+looper/const.py,sha256=eClmwc0c1r7zjQKrqBPa_OUOnoCqNNe0e64xElvLQHA,8701
+looper/divvy.py,sha256=KQSIxgeiFJf73c7xpAV8CoxUIuXjcfMphNWKSZXmuP0,15858
+looper/exceptions.py,sha256=-VEExHqjAtOSacBx45DA_9c-2i4EqxqGRLttTKxXXgg,3570
 looper/looper.py,sha256=zNszsV50ZkC5ioaLHgMg9H3hSTEHAAV-jBpLra3OIKw,31624
-looper/parser_types.py,sha256=d3FHt54f9jo9VZMr5SQkbghcAdABqiYZW2JBGO5EBnw,2327
-looper/pipeline_interface.py,sha256=mN4-XICyZzuVLTOq3b0ijppYe6ib_Ljlyf6KxZCJh2A,14537
+looper/parser_types.py,sha256=PgAdrtCGvXhXcX7UbW8E3oC414uv1mKV4sTnXVHtIzE,2325
+looper/pipeline_interface.py,sha256=NSAHx1ITmODy--Eh_b2oO4hP4mSHvs_7lkwuFLXbjsE,14535
 looper/plugins.py,sha256=MaMdPmK9U_4FkNJE5kccohBbY1i2qj1NTEucubFOJek,5747
 looper/processed_project.py,sha256=jZxoMYafvr-OHFxylc5ivGty1VwXBZhl0kgoFkY-174,9837
-looper/project.py,sha256=SFHdi58eRBWtye5lUFhwzBcG7ejrMurmDzmkrC3XAic,34339
-looper/utils.py,sha256=-4QlScIB7eewIbmEJdAv2d0ZE0qr_q9acm2XUOiMEek,39769
+looper/project.py,sha256=uoh8zGP4pdo630pcxLW5hdB5a2cP-YK8-CFd6F26Yus,34337
+looper/utils.py,sha256=42YP5Qz41TDUW45ptDio_2w8f3iEi2judeBo9d5yJh0,39765
 looper/command_models/DEVELOPER.md,sha256=eRxnrO-vqNJjExzamXKEq5wr_-Zw6PQEwkS9RPinYrk,2775
 looper/command_models/README.md,sha256=3RGegeZlTZYnhcHXRu6bdI_81WZom2q7QYMV-KGYY7U,588
-looper/command_models/__init__.py,sha256=6QWC2TewowEL7dATli5YpMmFWuXaLEPktofJCXkYUBI,187
+looper/command_models/__init__.py,sha256=suzlc6tiNFQlv9b--aZdE9uyklTcKQ_z4YGyLfO0Ru0,186
 looper/command_models/arguments.py,sha256=I9IUdDcklfctA9gdYvxyy29WawSCYPO5FwozgisCO94,9025
 looper/command_models/commands.py,sha256=nBD8uOxpjby2G0n-PuMKvRBM6m5tra_Mz_nlZALwmRE,9813
 looper/default_config/divvy_config.yaml,sha256=wK5kLDGBV2wwoyqg2rl3X8SXjds4x0mwBUjUzF1Ln7g,1705
@@ -60,9 +60,9 @@ looper/schemas/divvy_config_schema.yaml,sha256=7GJfKLc3VX4RGjHnOE1zxwsHXhj_ur9za
 looper/schemas/pipeline_interface_schema_generic.yaml,sha256=3YfKFyRUIwxG41FEidR1dXe9IU6ye51LSUBfSpmMuss,1773
 looper/schemas/pipeline_interface_schema_project.yaml,sha256=-ZWyA0lKXWik3obuLNVk3IsAZYfbLVbCDvJnD-Fcluo,1567
 looper/schemas/pipeline_interface_schema_sample.yaml,sha256=x0OwVnijJpvm50DscvvJujdK4UAI7d71pqVemQS-D-0,1564
-looper-2.0.0a3.dist-info/LICENSE.txt,sha256=oB6ZGDa4kcznznJKJsLLFFcOZyi8Y6e2Jv0rJozgp-I,1269
-looper-2.0.0a3.dist-info/METADATA,sha256=tP0InSt3Xn7098v19ZDWawfATd2Ez2zoMsecZKv6SCM,1762
-looper-2.0.0a3.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
-looper-2.0.0a3.dist-info/entry_points.txt,sha256=iHltI2_Jdved27vccmWhvmcHWUZ7Mf6CfDV6QkY1Lc8,91
-looper-2.0.0a3.dist-info/top_level.txt,sha256=I0Yf7djsoQAMzwHBbDiQi9hGtq4Z41_Ma5CX8qXG8Y8,7
-looper-2.0.0a3.dist-info/RECORD,,
+looper-2.0.1.dist-info/LICENSE.txt,sha256=oB6ZGDa4kcznznJKJsLLFFcOZyi8Y6e2Jv0rJozgp-I,1269
+looper-2.0.1.dist-info/METADATA,sha256=GPVKXrQreBCtmdWPvAiXb1Hci6InnMu3OgawD_IDcF0,1943
+looper-2.0.1.dist-info/WHEEL,sha256=jB7zZ3N9hIM9adW7qlTAyycLYW9npaWKLRzaoVcLKcM,91
+looper-2.0.1.dist-info/entry_points.txt,sha256=iHltI2_Jdved27vccmWhvmcHWUZ7Mf6CfDV6QkY1Lc8,91
+looper-2.0.1.dist-info/top_level.txt,sha256=I0Yf7djsoQAMzwHBbDiQi9hGtq4Z41_Ma5CX8qXG8Y8,7
+looper-2.0.1.dist-info/RECORD,,

{looper-2.0.0a3.dist-info → looper-2.0.1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.6.0)
+Generator: setuptools (75.8.2)
 Root-Is-Purelib: true
 Tag: py3-none-any