looper 2.0.2__tar.gz → 2.0.3__tar.gz

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.
Files changed (82) hide show
  1. {looper-2.0.2/looper.egg-info → looper-2.0.3}/PKG-INFO +1 -1
  2. {looper-2.0.2 → looper-2.0.3}/looper/_version.py +1 -1
  3. {looper-2.0.2 → looper-2.0.3}/looper/cli_pydantic.py +1 -1
  4. {looper-2.0.2 → looper-2.0.3}/looper/conductor.py +1 -0
  5. {looper-2.0.2 → looper-2.0.3}/looper/project.py +17 -7
  6. {looper-2.0.2 → looper-2.0.3/looper.egg-info}/PKG-INFO +1 -1
  7. {looper-2.0.2 → looper-2.0.3}/LICENSE.txt +0 -0
  8. {looper-2.0.2 → looper-2.0.3}/MANIFEST.in +0 -0
  9. {looper-2.0.2 → looper-2.0.3}/README.md +0 -0
  10. {looper-2.0.2 → looper-2.0.3}/logo_looper.svg +0 -0
  11. {looper-2.0.2 → looper-2.0.3}/looper/__init__.py +0 -0
  12. {looper-2.0.2 → looper-2.0.3}/looper/__main__.py +0 -0
  13. {looper-2.0.2 → looper-2.0.3}/looper/cli_divvy.py +0 -0
  14. {looper-2.0.2 → looper-2.0.3}/looper/command_models/DEVELOPER.md +0 -0
  15. {looper-2.0.2 → looper-2.0.3}/looper/command_models/README.md +0 -0
  16. {looper-2.0.2 → looper-2.0.3}/looper/command_models/__init__.py +0 -0
  17. {looper-2.0.2 → looper-2.0.3}/looper/command_models/arguments.py +0 -0
  18. {looper-2.0.2 → looper-2.0.3}/looper/command_models/commands.py +0 -0
  19. {looper-2.0.2 → looper-2.0.3}/looper/const.py +0 -0
  20. {looper-2.0.2 → looper-2.0.3}/looper/default_config/divvy_config.yaml +0 -0
  21. {looper-2.0.2 → looper-2.0.3}/looper/default_config/divvy_templates/localhost_bulker_template.sub +0 -0
  22. {looper-2.0.2 → looper-2.0.3}/looper/default_config/divvy_templates/localhost_docker_template.sub +0 -0
  23. {looper-2.0.2 → looper-2.0.3}/looper/default_config/divvy_templates/localhost_singularity_template.sub +0 -0
  24. {looper-2.0.2 → looper-2.0.3}/looper/default_config/divvy_templates/localhost_template.sub +0 -0
  25. {looper-2.0.2 → looper-2.0.3}/looper/default_config/divvy_templates/lsf_template.sub +0 -0
  26. {looper-2.0.2 → looper-2.0.3}/looper/default_config/divvy_templates/sge_template.sub +0 -0
  27. {looper-2.0.2 → looper-2.0.3}/looper/default_config/divvy_templates/slurm_singularity_template.sub +0 -0
  28. {looper-2.0.2 → looper-2.0.3}/looper/default_config/divvy_templates/slurm_template.sub +0 -0
  29. {looper-2.0.2 → looper-2.0.3}/looper/divvy.py +0 -0
  30. {looper-2.0.2 → looper-2.0.3}/looper/exceptions.py +0 -0
  31. {looper-2.0.2 → looper-2.0.3}/looper/jinja_templates/footer.html +0 -0
  32. {looper-2.0.2 → looper-2.0.3}/looper/jinja_templates/footer_index.html +0 -0
  33. {looper-2.0.2 → looper-2.0.3}/looper/jinja_templates/head.html +0 -0
  34. {looper-2.0.2 → looper-2.0.3}/looper/jinja_templates/index.html +0 -0
  35. {looper-2.0.2 → looper-2.0.3}/looper/jinja_templates/logo.html +0 -0
  36. {looper-2.0.2 → looper-2.0.3}/looper/jinja_templates/navbar.html +0 -0
  37. {looper-2.0.2 → looper-2.0.3}/looper/jinja_templates/navbar_links.html +0 -0
  38. {looper-2.0.2 → looper-2.0.3}/looper/jinja_templates/navbar_list_parent.html +0 -0
  39. {looper-2.0.2 → looper-2.0.3}/looper/jinja_templates/object.html +0 -0
  40. {looper-2.0.2 → looper-2.0.3}/looper/jinja_templates/project_object.html +0 -0
  41. {looper-2.0.2 → looper-2.0.3}/looper/jinja_templates/sample.html +0 -0
  42. {looper-2.0.2 → looper-2.0.3}/looper/jinja_templates/status.html +0 -0
  43. {looper-2.0.2 → looper-2.0.3}/looper/jinja_templates/status_table.html +0 -0
  44. {looper-2.0.2 → looper-2.0.3}/looper/jinja_templates/status_table_no_links.html +0 -0
  45. {looper-2.0.2 → looper-2.0.3}/looper/jinja_templates_old/footer.html +0 -0
  46. {looper-2.0.2 → looper-2.0.3}/looper/jinja_templates_old/footer_index.html +0 -0
  47. {looper-2.0.2 → looper-2.0.3}/looper/jinja_templates_old/head.html +0 -0
  48. {looper-2.0.2 → looper-2.0.3}/looper/jinja_templates_old/index.html +0 -0
  49. {looper-2.0.2 → looper-2.0.3}/looper/jinja_templates_old/logo.html +0 -0
  50. {looper-2.0.2 → looper-2.0.3}/looper/jinja_templates_old/navbar.html +0 -0
  51. {looper-2.0.2 → looper-2.0.3}/looper/jinja_templates_old/navbar_links.html +0 -0
  52. {looper-2.0.2 → looper-2.0.3}/looper/jinja_templates_old/navbar_list_parent.html +0 -0
  53. {looper-2.0.2 → looper-2.0.3}/looper/jinja_templates_old/object.html +0 -0
  54. {looper-2.0.2 → looper-2.0.3}/looper/jinja_templates_old/project_object.html +0 -0
  55. {looper-2.0.2 → looper-2.0.3}/looper/jinja_templates_old/sample.html +0 -0
  56. {looper-2.0.2 → looper-2.0.3}/looper/jinja_templates_old/status.html +0 -0
  57. {looper-2.0.2 → looper-2.0.3}/looper/jinja_templates_old/status_table.html +0 -0
  58. {looper-2.0.2 → looper-2.0.3}/looper/jinja_templates_old/status_table_no_links.html +0 -0
  59. {looper-2.0.2 → looper-2.0.3}/looper/looper.py +0 -0
  60. {looper-2.0.2 → looper-2.0.3}/looper/parser_types.py +0 -0
  61. {looper-2.0.2 → looper-2.0.3}/looper/pipeline_interface.py +0 -0
  62. {looper-2.0.2 → looper-2.0.3}/looper/plugins.py +0 -0
  63. {looper-2.0.2 → looper-2.0.3}/looper/processed_project.py +0 -0
  64. {looper-2.0.2 → looper-2.0.3}/looper/schemas/divvy_config_schema.yaml +0 -0
  65. {looper-2.0.2 → looper-2.0.3}/looper/schemas/pipeline_interface_schema_generic.yaml +0 -0
  66. {looper-2.0.2 → looper-2.0.3}/looper/schemas/pipeline_interface_schema_project.yaml +0 -0
  67. {looper-2.0.2 → looper-2.0.3}/looper/schemas/pipeline_interface_schema_sample.yaml +0 -0
  68. {looper-2.0.2 → looper-2.0.3}/looper/utils.py +0 -0
  69. {looper-2.0.2 → looper-2.0.3}/looper.egg-info/SOURCES.txt +0 -0
  70. {looper-2.0.2 → looper-2.0.3}/looper.egg-info/dependency_links.txt +0 -0
  71. {looper-2.0.2 → looper-2.0.3}/looper.egg-info/entry_points.txt +0 -0
  72. {looper-2.0.2 → looper-2.0.3}/looper.egg-info/requires.txt +0 -0
  73. {looper-2.0.2 → looper-2.0.3}/looper.egg-info/top_level.txt +0 -0
  74. {looper-2.0.2 → looper-2.0.3}/requirements/requirements-all.txt +0 -0
  75. {looper-2.0.2 → looper-2.0.3}/requirements/requirements-doc.txt +0 -0
  76. {looper-2.0.2 → looper-2.0.3}/requirements/requirements-test.txt +0 -0
  77. {looper-2.0.2 → looper-2.0.3}/setup.cfg +0 -0
  78. {looper-2.0.2 → looper-2.0.3}/setup.py +0 -0
  79. {looper-2.0.2 → looper-2.0.3}/tests/test_clean.py +0 -0
  80. {looper-2.0.2 → looper-2.0.3}/tests/test_comprehensive.py +0 -0
  81. {looper-2.0.2 → looper-2.0.3}/tests/test_desired_sample_range.py +0 -0
  82. {looper-2.0.2 → looper-2.0.3}/tests/test_natural_range.py +0 -0
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: looper
3
- Version: 2.0.2
3
+ Version: 2.0.3
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
@@ -1,2 +1,2 @@
1
- __version__ = "2.0.2"
1
+ __version__ = "2.0.3"
2
2
  # You must change the version in parser = pydantic_argparse.ArgumentParser in cli_pydantic.py!!!
@@ -340,7 +340,7 @@ def main(test_args=None) -> dict:
340
340
  prog="looper",
341
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  description="Looper: A job submitter for Portable Encapsulated Projects",
342
342
  add_help=True,
343
- version="2.0.2",
343
+ version="2.0.3",
344
344
  )
345
345
 
346
346
  parser = add_short_arguments(parser, ArgumentEnum)
@@ -662,6 +662,7 @@ class SubmissionConductor(object):
662
662
  "config_file": psm.config_path,
663
663
  "output_schema": psm.cfg["_schema_path"],
664
664
  "pephub_path": psm.cfg["pephub_path"],
665
+ "flag_file_dir": psm.cfg["_config"].data.get("flag_file_dir"),
665
666
  }
666
667
  filtered_namespace = {k: v for k, v in full_namespace.items() if v}
667
668
  return YAMLConfigManager(filtered_namespace)
@@ -553,6 +553,17 @@ class Project(peppyProject):
553
553
  except KeyError:
554
554
  flag_file_dir = None
555
555
 
556
+ try:
557
+ pephub_path = expandpath(pipestat_config_dict["pephub_path"])
558
+ if is_pephub_registry_path(pephub_path):
559
+ pipestat_config_dict.update({"pephub_path": pephub_path})
560
+ else:
561
+ _LOGGER.warning(
562
+ msg=f"Warning: PEPhub path provided is NOT a PEPhub registry {pephub_path}"
563
+ )
564
+ except KeyError:
565
+ pephub_path = None
566
+
556
567
  # Pipestat_dict_ is now updated from all sources and can be written to a yaml.
557
568
  pipestat_config_path = os.path.join(
558
569
  output_dir,
@@ -889,11 +900,10 @@ def fetch_samples(
889
900
 
890
901
 
891
902
  def make_set(items):
892
- try:
893
- # Check if user input single integer value for inclusion/exclusion criteria
894
- if len(items) == 1:
895
- items = list(map(str, items)) # list(int(items[0]))
896
- except:
897
- if isinstance(items, str):
898
- items = [items]
903
+ if isinstance(items, str):
904
+ items = [items]
905
+ elif len(items) == 1:
906
+ items = list(map(str, items)) # list(int(items[0]))
907
+ else:
908
+ pass
899
909
  return items
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: looper
3
- Version: 2.0.2
3
+ Version: 2.0.3
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
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