looper 1.8.0__py3-none-any.whl → 1.8.1__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
looper/_version.py CHANGED
@@ -1 +1,2 @@
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- __version__ = "1.8.0"
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+ __version__ = "1.8.1"
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+ # You must change the version in parser = pydantic2_argparse.ArgumentParser in cli_pydantic.py!!!
looper/cli_pydantic.py CHANGED
@@ -246,11 +246,15 @@ def run_looper(args: TopLevelParser, parser: ArgumentParser, test_args=None):
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  # Check at the beginning if user wants to use pipestat and pipestat is configurable
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  is_pipestat_configured = (
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  prj._check_if_pipestat_configured(pipeline_type=PipelineLevel.PROJECT.value)
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- if getattr(args, "project", None)
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+ if getattr(subcommand_args, "project", None)
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  else prj._check_if_pipestat_configured()
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  )
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  if subcommand_name in ["run", "rerun"]:
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+ if getattr(subcommand_args, "project", None):
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+ _LOGGER.warning(
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+ "Project flag set but 'run' command was used. Please use 'runp' to run at project-level."
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+ )
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  rerun = subcommand_name == "rerun"
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  run = Runner(prj)
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  try:
@@ -324,8 +328,9 @@ def main(test_args=None) -> None:
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  parser = pydantic2_argparse.ArgumentParser(
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  model=TopLevelParser,
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  prog="looper",
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- description="Looper Pydantic Argument Parser",
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+ description="Looper: A job submitter for Portable Encapsulated Projects",
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  add_help=True,
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+ version="1.8.1",
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  )
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  parser = add_short_arguments(parser, ArgumentEnum)
looper/looper.py CHANGED
@@ -94,7 +94,7 @@ class Checker(Executor):
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  psms = {}
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  if getattr(args, "project", None):
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- for piface in self.prj.pipeline_interfaces:
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+ for piface in self.prj.project_pipeline_interfaces:
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  if piface.psm.pipeline_type == PipelineLevel.PROJECT.value:
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  psms[piface.psm.pipeline_name] = piface.psm
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  s = piface.psm.get_status() or "unknown"
@@ -565,7 +565,7 @@ class Reporter(Executor):
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  if project_level:
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- for piface in self.prj.pipeline_interfaces:
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+ for piface in self.prj.project_pipeline_interfaces:
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  if piface.psm.pipeline_type == PipelineLevel.PROJECT.value:
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  psms[piface.psm.pipeline_name] = piface.psm
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  report_directory = piface.psm.summarize(
@@ -598,7 +598,7 @@ class Linker(Executor):
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  psms = {}
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  if project_level:
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- for piface in self.prj.pipeline_interfaces:
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+ for piface in self.prj.project_pipeline_interfaces:
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  if piface.psm.pipeline_type == PipelineLevel.PROJECT.value:
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  psms[piface.psm.pipeline_name] = piface.psm
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  linked_results_path = piface.psm.link(link_dir=link_dir)
@@ -623,7 +623,7 @@ class Tabulator(Executor):
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  results = []
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  psms = {}
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  if project_level:
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- for piface in self.prj.pipeline_interfaces:
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+ for piface in self.prj.project_pipeline_interfaces:
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  if piface.psm.pipeline_type == PipelineLevel.PROJECT.value:
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  psms[piface.psm.pipeline_name] = piface.psm
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  results = piface.psm.table()
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: looper
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- Version: 1.8.0
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+ Version: 1.8.1
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  Summary: A pipeline submission engine that parses sample inputs and submits pipelines for each sample.
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  Home-page: https://github.com/pepkit/looper
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  Author: Nathan Sheffield, Vince Reuter, Michal Stolarczyk, Johanna Klughammer, Andre Rendeiro
@@ -1,13 +1,13 @@
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  looper/__init__.py,sha256=f_z9YY4ibOk7eyWoaViH_VaCXMlPQeiftbnibSFj-3E,1333
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  looper/__main__.py,sha256=OOCmI-dPUvInnJHkHNMf54cblNJ3Yl9ELOwZcfOXmD8,240
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- looper/_version.py,sha256=Oc_xF94AMAHKZkZlB5rBt1iO0TXWFalg65MP4T2qt-A,22
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+ looper/_version.py,sha256=4PW0MsS2hyMf0_fTJkhk2ShkZAu_CHYqiO9slLwCFjI,120
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  looper/cli_divvy.py,sha256=J07x83sqC4jJeu3_yS6KOARPWmwKGAV7JvN33T5zDac,5907
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- looper/cli_pydantic.py,sha256=QKG-rvy7ORkTivDIkrk4tWpVAcuxmUSZePV35hvag0k,13541
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+ looper/cli_pydantic.py,sha256=_qGlgRoQFf4lU6BOao9cwBXybO7gIe-gJUY2q9kRH8U,13823
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  looper/conductor.py,sha256=WAEtzZFElCK_mvsnaiGKnu5x6quYKsDMno6j6TuNG-g,31448
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  looper/const.py,sha256=KbQD-Q62g61pUroEF4ogQerYhJE-xbt4cX9m15oYHTo,8682
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  looper/divvy.py,sha256=SPoC7fpWHjC82NEKkpnObV1Koamt3M2tCmfAXpjdGRM,15399
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  looper/exceptions.py,sha256=r6SKKt-m8CXQnXGDnuiwoA6zBJhIZflygBKjX4RCloI,3419
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- looper/looper.py,sha256=XomJIis4sFHOO5qEwzmyKT85X-lKNURX8yhOftTFmbY,30099
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+ looper/looper.py,sha256=3ixmeIiTdXm80xJHrmt4trbSMa8883xSr6nXXN2NGn4,30131
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  looper/parser_types.py,sha256=d3FHt54f9jo9VZMr5SQkbghcAdABqiYZW2JBGO5EBnw,2327
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  looper/pipeline_interface.py,sha256=y46tB1_73d1FX8N1w4-GGvRBJ7rqhenuUYVtUfIhK5s,14974
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  looper/plugins.py,sha256=MaMdPmK9U_4FkNJE5kccohBbY1i2qj1NTEucubFOJek,5747
@@ -60,9 +60,9 @@ looper/schemas/divvy_config_schema.yaml,sha256=7GJfKLc3VX4RGjHnOE1zxwsHXhj_ur9za
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  looper/schemas/pipeline_interface_schema_generic.yaml,sha256=D16Rkpj03H9WnvA_N18iNU-hH_HwOuyESJ8Hk5hZSXc,1518
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  looper/schemas/pipeline_interface_schema_project.yaml,sha256=-ZWyA0lKXWik3obuLNVk3IsAZYfbLVbCDvJnD-Fcluo,1567
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  looper/schemas/pipeline_interface_schema_sample.yaml,sha256=x0OwVnijJpvm50DscvvJujdK4UAI7d71pqVemQS-D-0,1564
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- looper-1.8.0.dist-info/LICENSE.txt,sha256=oB6ZGDa4kcznznJKJsLLFFcOZyi8Y6e2Jv0rJozgp-I,1269
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- looper-1.8.0.dist-info/METADATA,sha256=JNbHNlDh1i0dMn7wee_Mix6Hagjqq1iNRfvK6fe5lH8,1775
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- looper-1.8.0.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
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- looper-1.8.0.dist-info/entry_points.txt,sha256=ejZpghZG3OoTK69u9rTW-yLyI6SC63bBTUb-Vw26HG4,87
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- looper-1.8.0.dist-info/top_level.txt,sha256=I0Yf7djsoQAMzwHBbDiQi9hGtq4Z41_Ma5CX8qXG8Y8,7
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- looper-1.8.0.dist-info/RECORD,,
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+ looper-1.8.1.dist-info/LICENSE.txt,sha256=oB6ZGDa4kcznznJKJsLLFFcOZyi8Y6e2Jv0rJozgp-I,1269
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+ looper-1.8.1.dist-info/METADATA,sha256=hngy4pa5zn5D2jvQQoQ-JLDrpkRHZsJT3Zit_kgMjvI,1775
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+ looper-1.8.1.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
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+ looper-1.8.1.dist-info/entry_points.txt,sha256=ejZpghZG3OoTK69u9rTW-yLyI6SC63bBTUb-Vw26HG4,87
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+ looper-1.8.1.dist-info/top_level.txt,sha256=I0Yf7djsoQAMzwHBbDiQi9hGtq4Z41_Ma5CX8qXG8Y8,7
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+ looper-1.8.1.dist-info/RECORD,,
File without changes