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

looper/_version.py

@@ -1 +1,2 @@
-__version__ = "1.8.0"
+__version__ = "1.8.1"
+# You must change the version in parser = pydantic2_argparse.ArgumentParser in cli_pydantic.py!!!

looper/cli_pydantic.py

@@ -246,11 +246,15 @@ def run_looper(args: TopLevelParser, parser: ArgumentParser, test_args=None):
         # Check at the beginning if user wants to use pipestat and pipestat is configurable
         is_pipestat_configured = (
             prj._check_if_pipestat_configured(pipeline_type=PipelineLevel.PROJECT.value)
-            if getattr(args, "project", None)
+            if getattr(subcommand_args, "project", None)
             else prj._check_if_pipestat_configured()
         )
 
         if subcommand_name in ["run", "rerun"]:
+            if getattr(subcommand_args, "project", None):
+                _LOGGER.warning(
+                    "Project flag set but 'run' command was used. Please use 'runp' to run at project-level."
+                )
             rerun = subcommand_name == "rerun"
             run = Runner(prj)
             try:
@@ -324,8 +328,9 @@ def main(test_args=None) -> None:
     parser = pydantic2_argparse.ArgumentParser(
         model=TopLevelParser,
         prog="looper",
-        description="Looper Pydantic Argument Parser",
+        description="Looper: A job submitter for Portable Encapsulated Projects",
         add_help=True,
+        version="1.8.1",
     )
 
     parser = add_short_arguments(parser, ArgumentEnum)

looper/looper.py

@@ -94,7 +94,7 @@ class Checker(Executor):
         psms = {}
         if getattr(args, "project", None):
 
-            for piface in self.prj.pipeline_interfaces:
+            for piface in self.prj.project_pipeline_interfaces:
                 if piface.psm.pipeline_type == PipelineLevel.PROJECT.value:
                     psms[piface.psm.pipeline_name] = piface.psm
                     s = piface.psm.get_status() or "unknown"
@@ -565,7 +565,7 @@ class Reporter(Executor):
 
         if project_level:
 
-            for piface in self.prj.pipeline_interfaces:
+            for piface in self.prj.project_pipeline_interfaces:
                 if piface.psm.pipeline_type == PipelineLevel.PROJECT.value:
                     psms[piface.psm.pipeline_name] = piface.psm
                     report_directory = piface.psm.summarize(
@@ -598,7 +598,7 @@ class Linker(Executor):
         psms = {}
 
         if project_level:
-            for piface in self.prj.pipeline_interfaces:
+            for piface in self.prj.project_pipeline_interfaces:
                 if piface.psm.pipeline_type == PipelineLevel.PROJECT.value:
                     psms[piface.psm.pipeline_name] = piface.psm
                     linked_results_path = piface.psm.link(link_dir=link_dir)
@@ -623,7 +623,7 @@ class Tabulator(Executor):
         results = []
         psms = {}
         if project_level:
-            for piface in self.prj.pipeline_interfaces:
+            for piface in self.prj.project_pipeline_interfaces:
                 if piface.psm.pipeline_type == PipelineLevel.PROJECT.value:
                     psms[piface.psm.pipeline_name] = piface.psm
                     results = piface.psm.table()

{looper-1.8.0.dist-info → looper-1.8.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: looper
-Version: 1.8.0
+Version: 1.8.1
 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

{looper-1.8.0.dist-info → looper-1.8.1.dist-info}/RECORD

@@ -1,13 +1,13 @@
 looper/__init__.py,sha256=f_z9YY4ibOk7eyWoaViH_VaCXMlPQeiftbnibSFj-3E,1333
 looper/__main__.py,sha256=OOCmI-dPUvInnJHkHNMf54cblNJ3Yl9ELOwZcfOXmD8,240
-looper/_version.py,sha256=Oc_xF94AMAHKZkZlB5rBt1iO0TXWFalg65MP4T2qt-A,22
+looper/_version.py,sha256=4PW0MsS2hyMf0_fTJkhk2ShkZAu_CHYqiO9slLwCFjI,120
 looper/cli_divvy.py,sha256=J07x83sqC4jJeu3_yS6KOARPWmwKGAV7JvN33T5zDac,5907
-looper/cli_pydantic.py,sha256=QKG-rvy7ORkTivDIkrk4tWpVAcuxmUSZePV35hvag0k,13541
+looper/cli_pydantic.py,sha256=_qGlgRoQFf4lU6BOao9cwBXybO7gIe-gJUY2q9kRH8U,13823
 looper/conductor.py,sha256=WAEtzZFElCK_mvsnaiGKnu5x6quYKsDMno6j6TuNG-g,31448
 looper/const.py,sha256=KbQD-Q62g61pUroEF4ogQerYhJE-xbt4cX9m15oYHTo,8682
 looper/divvy.py,sha256=SPoC7fpWHjC82NEKkpnObV1Koamt3M2tCmfAXpjdGRM,15399
 looper/exceptions.py,sha256=r6SKKt-m8CXQnXGDnuiwoA6zBJhIZflygBKjX4RCloI,3419
-looper/looper.py,sha256=XomJIis4sFHOO5qEwzmyKT85X-lKNURX8yhOftTFmbY,30099
+looper/looper.py,sha256=3ixmeIiTdXm80xJHrmt4trbSMa8883xSr6nXXN2NGn4,30131
 looper/parser_types.py,sha256=d3FHt54f9jo9VZMr5SQkbghcAdABqiYZW2JBGO5EBnw,2327
 looper/pipeline_interface.py,sha256=y46tB1_73d1FX8N1w4-GGvRBJ7rqhenuUYVtUfIhK5s,14974
 looper/plugins.py,sha256=MaMdPmK9U_4FkNJE5kccohBbY1i2qj1NTEucubFOJek,5747
@@ -60,9 +60,9 @@ looper/schemas/divvy_config_schema.yaml,sha256=7GJfKLc3VX4RGjHnOE1zxwsHXhj_ur9za
 looper/schemas/pipeline_interface_schema_generic.yaml,sha256=D16Rkpj03H9WnvA_N18iNU-hH_HwOuyESJ8Hk5hZSXc,1518
 looper/schemas/pipeline_interface_schema_project.yaml,sha256=-ZWyA0lKXWik3obuLNVk3IsAZYfbLVbCDvJnD-Fcluo,1567
 looper/schemas/pipeline_interface_schema_sample.yaml,sha256=x0OwVnijJpvm50DscvvJujdK4UAI7d71pqVemQS-D-0,1564
-looper-1.8.0.dist-info/LICENSE.txt,sha256=oB6ZGDa4kcznznJKJsLLFFcOZyi8Y6e2Jv0rJozgp-I,1269
-looper-1.8.0.dist-info/METADATA,sha256=JNbHNlDh1i0dMn7wee_Mix6Hagjqq1iNRfvK6fe5lH8,1775
-looper-1.8.0.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-looper-1.8.0.dist-info/entry_points.txt,sha256=ejZpghZG3OoTK69u9rTW-yLyI6SC63bBTUb-Vw26HG4,87
-looper-1.8.0.dist-info/top_level.txt,sha256=I0Yf7djsoQAMzwHBbDiQi9hGtq4Z41_Ma5CX8qXG8Y8,7
-looper-1.8.0.dist-info/RECORD,,
+looper-1.8.1.dist-info/LICENSE.txt,sha256=oB6ZGDa4kcznznJKJsLLFFcOZyi8Y6e2Jv0rJozgp-I,1269
+looper-1.8.1.dist-info/METADATA,sha256=hngy4pa5zn5D2jvQQoQ-JLDrpkRHZsJT3Zit_kgMjvI,1775
+looper-1.8.1.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+looper-1.8.1.dist-info/entry_points.txt,sha256=ejZpghZG3OoTK69u9rTW-yLyI6SC63bBTUb-Vw26HG4,87
+looper-1.8.1.dist-info/top_level.txt,sha256=I0Yf7djsoQAMzwHBbDiQi9hGtq4Z41_Ma5CX8qXG8Y8,7
+looper-1.8.1.dist-info/RECORD,,