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 +2 -1
- looper/cli_pydantic.py +7 -2
- looper/looper.py +4 -4
- {looper-1.8.0.dist-info → looper-1.8.1.dist-info}/METADATA +1 -1
- {looper-1.8.0.dist-info → looper-1.8.1.dist-info}/RECORD +9 -9
- {looper-1.8.0.dist-info → looper-1.8.1.dist-info}/LICENSE.txt +0 -0
- {looper-1.8.0.dist-info → looper-1.8.1.dist-info}/WHEEL +0 -0
- {looper-1.8.0.dist-info → looper-1.8.1.dist-info}/entry_points.txt +0 -0
- {looper-1.8.0.dist-info → looper-1.8.1.dist-info}/top_level.txt +0 -0
looper/_version.py
CHANGED
@@ -1 +1,2 @@
|
|
1
|
-
__version__ = "1.8.
|
1
|
+
__version__ = "1.8.1"
|
2
|
+
# 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):
|
|
246
246
|
# Check at the beginning if user wants to use pipestat and pipestat is configurable
|
247
247
|
is_pipestat_configured = (
|
248
248
|
prj._check_if_pipestat_configured(pipeline_type=PipelineLevel.PROJECT.value)
|
249
|
-
if getattr(
|
249
|
+
if getattr(subcommand_args, "project", None)
|
250
250
|
else prj._check_if_pipestat_configured()
|
251
251
|
)
|
252
252
|
|
253
253
|
if subcommand_name in ["run", "rerun"]:
|
254
|
+
if getattr(subcommand_args, "project", None):
|
255
|
+
_LOGGER.warning(
|
256
|
+
"Project flag set but 'run' command was used. Please use 'runp' to run at project-level."
|
257
|
+
)
|
254
258
|
rerun = subcommand_name == "rerun"
|
255
259
|
run = Runner(prj)
|
256
260
|
try:
|
@@ -324,8 +328,9 @@ def main(test_args=None) -> None:
|
|
324
328
|
parser = pydantic2_argparse.ArgumentParser(
|
325
329
|
model=TopLevelParser,
|
326
330
|
prog="looper",
|
327
|
-
description="Looper
|
331
|
+
description="Looper: A job submitter for Portable Encapsulated Projects",
|
328
332
|
add_help=True,
|
333
|
+
version="1.8.1",
|
329
334
|
)
|
330
335
|
|
331
336
|
parser = add_short_arguments(parser, ArgumentEnum)
|
looper/looper.py
CHANGED
@@ -94,7 +94,7 @@ class Checker(Executor):
|
|
94
94
|
psms = {}
|
95
95
|
if getattr(args, "project", None):
|
96
96
|
|
97
|
-
for piface in self.prj.
|
97
|
+
for piface in self.prj.project_pipeline_interfaces:
|
98
98
|
if piface.psm.pipeline_type == PipelineLevel.PROJECT.value:
|
99
99
|
psms[piface.psm.pipeline_name] = piface.psm
|
100
100
|
s = piface.psm.get_status() or "unknown"
|
@@ -565,7 +565,7 @@ class Reporter(Executor):
|
|
565
565
|
|
566
566
|
if project_level:
|
567
567
|
|
568
|
-
for piface in self.prj.
|
568
|
+
for piface in self.prj.project_pipeline_interfaces:
|
569
569
|
if piface.psm.pipeline_type == PipelineLevel.PROJECT.value:
|
570
570
|
psms[piface.psm.pipeline_name] = piface.psm
|
571
571
|
report_directory = piface.psm.summarize(
|
@@ -598,7 +598,7 @@ class Linker(Executor):
|
|
598
598
|
psms = {}
|
599
599
|
|
600
600
|
if project_level:
|
601
|
-
for piface in self.prj.
|
601
|
+
for piface in self.prj.project_pipeline_interfaces:
|
602
602
|
if piface.psm.pipeline_type == PipelineLevel.PROJECT.value:
|
603
603
|
psms[piface.psm.pipeline_name] = piface.psm
|
604
604
|
linked_results_path = piface.psm.link(link_dir=link_dir)
|
@@ -623,7 +623,7 @@ class Tabulator(Executor):
|
|
623
623
|
results = []
|
624
624
|
psms = {}
|
625
625
|
if project_level:
|
626
|
-
for piface in self.prj.
|
626
|
+
for piface in self.prj.project_pipeline_interfaces:
|
627
627
|
if piface.psm.pipeline_type == PipelineLevel.PROJECT.value:
|
628
628
|
psms[piface.psm.pipeline_name] = piface.psm
|
629
629
|
results = piface.psm.table()
|
@@ -1,6 +1,6 @@
|
|
1
1
|
Metadata-Version: 2.1
|
2
2
|
Name: looper
|
3
|
-
Version: 1.8.
|
3
|
+
Version: 1.8.1
|
4
4
|
Summary: A pipeline submission engine that parses sample inputs and submits pipelines for each sample.
|
5
5
|
Home-page: https://github.com/pepkit/looper
|
6
6
|
Author: Nathan Sheffield, Vince Reuter, Michal Stolarczyk, Johanna Klughammer, Andre Rendeiro
|
@@ -1,13 +1,13 @@
|
|
1
1
|
looper/__init__.py,sha256=f_z9YY4ibOk7eyWoaViH_VaCXMlPQeiftbnibSFj-3E,1333
|
2
2
|
looper/__main__.py,sha256=OOCmI-dPUvInnJHkHNMf54cblNJ3Yl9ELOwZcfOXmD8,240
|
3
|
-
looper/_version.py,sha256=
|
3
|
+
looper/_version.py,sha256=4PW0MsS2hyMf0_fTJkhk2ShkZAu_CHYqiO9slLwCFjI,120
|
4
4
|
looper/cli_divvy.py,sha256=J07x83sqC4jJeu3_yS6KOARPWmwKGAV7JvN33T5zDac,5907
|
5
|
-
looper/cli_pydantic.py,sha256=
|
5
|
+
looper/cli_pydantic.py,sha256=_qGlgRoQFf4lU6BOao9cwBXybO7gIe-gJUY2q9kRH8U,13823
|
6
6
|
looper/conductor.py,sha256=WAEtzZFElCK_mvsnaiGKnu5x6quYKsDMno6j6TuNG-g,31448
|
7
7
|
looper/const.py,sha256=KbQD-Q62g61pUroEF4ogQerYhJE-xbt4cX9m15oYHTo,8682
|
8
8
|
looper/divvy.py,sha256=SPoC7fpWHjC82NEKkpnObV1Koamt3M2tCmfAXpjdGRM,15399
|
9
9
|
looper/exceptions.py,sha256=r6SKKt-m8CXQnXGDnuiwoA6zBJhIZflygBKjX4RCloI,3419
|
10
|
-
looper/looper.py,sha256=
|
10
|
+
looper/looper.py,sha256=3ixmeIiTdXm80xJHrmt4trbSMa8883xSr6nXXN2NGn4,30131
|
11
11
|
looper/parser_types.py,sha256=d3FHt54f9jo9VZMr5SQkbghcAdABqiYZW2JBGO5EBnw,2327
|
12
12
|
looper/pipeline_interface.py,sha256=y46tB1_73d1FX8N1w4-GGvRBJ7rqhenuUYVtUfIhK5s,14974
|
13
13
|
looper/plugins.py,sha256=MaMdPmK9U_4FkNJE5kccohBbY1i2qj1NTEucubFOJek,5747
|
@@ -60,9 +60,9 @@ looper/schemas/divvy_config_schema.yaml,sha256=7GJfKLc3VX4RGjHnOE1zxwsHXhj_ur9za
|
|
60
60
|
looper/schemas/pipeline_interface_schema_generic.yaml,sha256=D16Rkpj03H9WnvA_N18iNU-hH_HwOuyESJ8Hk5hZSXc,1518
|
61
61
|
looper/schemas/pipeline_interface_schema_project.yaml,sha256=-ZWyA0lKXWik3obuLNVk3IsAZYfbLVbCDvJnD-Fcluo,1567
|
62
62
|
looper/schemas/pipeline_interface_schema_sample.yaml,sha256=x0OwVnijJpvm50DscvvJujdK4UAI7d71pqVemQS-D-0,1564
|
63
|
-
looper-1.8.
|
64
|
-
looper-1.8.
|
65
|
-
looper-1.8.
|
66
|
-
looper-1.8.
|
67
|
-
looper-1.8.
|
68
|
-
looper-1.8.
|
63
|
+
looper-1.8.1.dist-info/LICENSE.txt,sha256=oB6ZGDa4kcznznJKJsLLFFcOZyi8Y6e2Jv0rJozgp-I,1269
|
64
|
+
looper-1.8.1.dist-info/METADATA,sha256=hngy4pa5zn5D2jvQQoQ-JLDrpkRHZsJT3Zit_kgMjvI,1775
|
65
|
+
looper-1.8.1.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
|
66
|
+
looper-1.8.1.dist-info/entry_points.txt,sha256=ejZpghZG3OoTK69u9rTW-yLyI6SC63bBTUb-Vw26HG4,87
|
67
|
+
looper-1.8.1.dist-info/top_level.txt,sha256=I0Yf7djsoQAMzwHBbDiQi9hGtq4Z41_Ma5CX8qXG8Y8,7
|
68
|
+
looper-1.8.1.dist-info/RECORD,,
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|