looper 1.7.0__py3-none-any.whl → 2.0.0__py3-none-any.whl

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Files changed (25) hide show
  1. looper/__main__.py +1 -1
  2. looper/_version.py +2 -1
  3. looper/cli_divvy.py +10 -6
  4. looper/cli_pydantic.py +413 -0
  5. looper/command_models/DEVELOPER.md +85 -0
  6. looper/command_models/README.md +4 -0
  7. looper/command_models/__init__.py +6 -0
  8. looper/command_models/arguments.py +293 -0
  9. looper/command_models/commands.py +335 -0
  10. looper/conductor.py +147 -28
  11. looper/const.py +9 -0
  12. looper/divvy.py +56 -47
  13. looper/exceptions.py +9 -1
  14. looper/looper.py +196 -169
  15. looper/pipeline_interface.py +2 -12
  16. looper/project.py +154 -176
  17. looper/schemas/pipeline_interface_schema_generic.yaml +14 -6
  18. looper/utils.py +450 -78
  19. {looper-1.7.0.dist-info → looper-2.0.0.dist-info}/METADATA +24 -14
  20. {looper-1.7.0.dist-info → looper-2.0.0.dist-info}/RECORD +24 -19
  21. {looper-1.7.0.dist-info → looper-2.0.0.dist-info}/WHEEL +1 -1
  22. {looper-1.7.0.dist-info → looper-2.0.0.dist-info}/entry_points.txt +1 -1
  23. looper/cli_looper.py +0 -796
  24. {looper-1.7.0.dist-info → looper-2.0.0.dist-info}/LICENSE.txt +0 -0
  25. {looper-1.7.0.dist-info → looper-2.0.0.dist-info}/top_level.txt +0 -0
{looper-1.7.0.dist-info → looper-2.0.0.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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- Metadata-Version: 2.1
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+ Metadata-Version: 2.2
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  Name: looper
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- Version: 1.7.0
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+ Version: 2.0.0
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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
@@ -15,19 +15,29 @@ Classifier: Programming Language :: Python :: 3.11
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  Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
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  Description-Content-Type: text/markdown
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  License-File: LICENSE.txt
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- Requires-Dist: colorama >=0.3.9
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- Requires-Dist: divvy >=0.5.0
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- Requires-Dist: eido >=0.2.1
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+ Requires-Dist: colorama>=0.3.9
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+ Requires-Dist: eido>=0.2.4
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  Requires-Dist: jinja2
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- Requires-Dist: logmuse >=0.2.0
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- Requires-Dist: pandas >=2.0.2
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- Requires-Dist: pephubclient >=0.1.2
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- Requires-Dist: peppy >=0.40.0
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- Requires-Dist: pipestat >=0.8.0
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- Requires-Dist: pyyaml >=3.12
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- Requires-Dist: rich >=9.10.0
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- Requires-Dist: ubiquerg >=0.5.2
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- Requires-Dist: yacman >=0.9.2
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+ Requires-Dist: logmuse>=0.2.0
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+ Requires-Dist: pandas>=2.0.2
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+ Requires-Dist: pephubclient>=0.4.0
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+ Requires-Dist: pipestat>=0.12.0a1
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+ Requires-Dist: peppy>=0.40.6
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+ Requires-Dist: pyyaml>=3.12
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+ Requires-Dist: rich>=9.10.0
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+ Requires-Dist: ubiquerg>=0.8.1a1
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+ Requires-Dist: yacman==0.9.3
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+ Requires-Dist: pydantic-argparse>=0.9.0
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+ Requires-Dist: psutil
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+ Dynamic: author
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+ Dynamic: classifier
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+ Dynamic: description
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+ Dynamic: description-content-type
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+ Dynamic: home-page
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+ Dynamic: keywords
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+ Dynamic: license
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+ Dynamic: requires-dist
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+ Dynamic: summary
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  # <img src="docs/img/looper_logo.svg" alt="looper logo" height="70">
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{looper-1.7.0.dist-info → looper-2.0.0.dist-info}/RECORD RENAMED
@@ -1,19 +1,24 @@
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  looper/__init__.py,sha256=f_z9YY4ibOk7eyWoaViH_VaCXMlPQeiftbnibSFj-3E,1333
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- looper/__main__.py,sha256=8CX2ae8mUQNI_Z8pdBT4i5UFqROFX1awyFnuYCKuYXg,238
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- looper/_version.py,sha256=lEEx5lwinUby-YNl7w-VFGUcjcibsJ9EuzgJ2W7ocrU,22
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- looper/cli_divvy.py,sha256=J07x83sqC4jJeu3_yS6KOARPWmwKGAV7JvN33T5zDac,5907
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- looper/cli_looper.py,sha256=se-EbQ4nucWxMiU0VLnmV0Kss-JMjSmWih6vHaOiLi0,26367
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- looper/conductor.py,sha256=9k0r_vsHCP25MrDjz7GR16_EEdqP9JZELYZJVm6ny1g,30777
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- looper/const.py,sha256=bPj4lTuj2l6gwHROWqj16iHfJFo9ghZAz8THNREWW4U,8558
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- looper/divvy.py,sha256=qa1ebbQTfNupAyDfhfEJ6mbZ_V3zk-D_E-Tck7miJ38,15688
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- looper/exceptions.py,sha256=r6SKKt-m8CXQnXGDnuiwoA6zBJhIZflygBKjX4RCloI,3419
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- looper/looper.py,sha256=U3mNqXRDZRzmFXV26TcPQYKPdY1plPvMraNHTnps4mQ,30448
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+ looper/__main__.py,sha256=OOCmI-dPUvInnJHkHNMf54cblNJ3Yl9ELOwZcfOXmD8,240
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+ looper/_version.py,sha256=s89pfV00vM-j--kn4pBzMBBFQJtP1tuSRanGar6qHKE,119
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+ looper/cli_divvy.py,sha256=_VGbOFLkXtKdkZA6omlzgXbXkuUM5aLQ50aTTtbTrVI,5975
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+ looper/cli_pydantic.py,sha256=Yw5-Jt_stStTe5dQrQNJjsEfVlN8wkpFlBios074q9w,14423
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+ looper/conductor.py,sha256=lzY6Gzsb8oX-KLzLkRa0XrYWSxLeiy6jRmmD15WNAkw,35116
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+ looper/const.py,sha256=OscEELQsyLKlSrmwuXfyLRwpAUJUEpGD2UxBeLJDXgw,8703
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+ looper/divvy.py,sha256=yokD0--xN0kaxPuPRZrRPgKinl0Sqt0cvkmNMvwe94A,15860
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+ looper/exceptions.py,sha256=weSXsPadikAHVJvUUOT1uE56C_nKqgC3iBOvDebPDVE,3572
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+ looper/looper.py,sha256=zNszsV50ZkC5ioaLHgMg9H3hSTEHAAV-jBpLra3OIKw,31624
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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/pipeline_interface.py,sha256=mN4-XICyZzuVLTOq3b0ijppYe6ib_Ljlyf6KxZCJh2A,14537
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  looper/plugins.py,sha256=MaMdPmK9U_4FkNJE5kccohBbY1i2qj1NTEucubFOJek,5747
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  looper/processed_project.py,sha256=jZxoMYafvr-OHFxylc5ivGty1VwXBZhl0kgoFkY-174,9837
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- looper/project.py,sha256=nkNP7ftVs82Tnk2Yn6FUp60_D6bjE9sSvySE0SHqsmg,36171
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- looper/utils.py,sha256=i7srIXPEnQjtNaoP0ziRpdYfB7HNY5_3rW5LoKIM15I,27257
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+ looper/project.py,sha256=SFHdi58eRBWtye5lUFhwzBcG7ejrMurmDzmkrC3XAic,34339
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+ looper/utils.py,sha256=-4QlScIB7eewIbmEJdAv2d0ZE0qr_q9acm2XUOiMEek,39769
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+ looper/command_models/DEVELOPER.md,sha256=eRxnrO-vqNJjExzamXKEq5wr_-Zw6PQEwkS9RPinYrk,2775
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+ looper/command_models/README.md,sha256=3RGegeZlTZYnhcHXRu6bdI_81WZom2q7QYMV-KGYY7U,588
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+ looper/command_models/__init__.py,sha256=6QWC2TewowEL7dATli5YpMmFWuXaLEPktofJCXkYUBI,187
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+ looper/command_models/arguments.py,sha256=I9IUdDcklfctA9gdYvxyy29WawSCYPO5FwozgisCO94,9025
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+ looper/command_models/commands.py,sha256=nBD8uOxpjby2G0n-PuMKvRBM6m5tra_Mz_nlZALwmRE,9813
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  looper/default_config/divvy_config.yaml,sha256=wK5kLDGBV2wwoyqg2rl3X8SXjds4x0mwBUjUzF1Ln7g,1705
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  looper/default_config/divvy_templates/localhost_bulker_template.sub,sha256=yn5VB9Brt7Hck9LT17hD2o8Kn-76gYJQk_A-8C1Gr4k,164
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  looper/default_config/divvy_templates/localhost_docker_template.sub,sha256=XRr7AlR7-TP1L3hyBMfka_RgWRL9vzOlS5Kd1xSNwT0,183
@@ -52,12 +57,12 @@ looper/jinja_templates_old/status.html,sha256=FBH2hqw3tVJgmR1kY3Cz5SQRHmnH6JqaDL
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  looper/jinja_templates_old/status_table.html,sha256=VbHax7cGENIfVnU-O9p2ELSAJIONJ41m-mHJBy4r4dQ,3271
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  looper/jinja_templates_old/status_table_no_links.html,sha256=vrPNCKen-yrkM_dg13f0yCVyeJHCQVNNY_bchUW_sVY,2396
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  looper/schemas/divvy_config_schema.yaml,sha256=7GJfKLc3VX4RGjHnOE1zxwsHXhj_ur9za6dKdfJTFkc,450
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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_generic.yaml,sha256=3YfKFyRUIwxG41FEidR1dXe9IU6ye51LSUBfSpmMuss,1773
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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-1.7.0.dist-info/LICENSE.txt,sha256=oB6ZGDa4kcznznJKJsLLFFcOZyi8Y6e2Jv0rJozgp-I,1269
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- looper-1.7.0.dist-info/METADATA,sha256=pGYwFxwYKiFtzUuYx4t0q-cMKmCF_fhsKwAFlbwBfP0,1733
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- looper-1.7.0.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
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- looper-1.7.0.dist-info/entry_points.txt,sha256=AEL1eb0gPLYvAEUewM35Ng4scXGZIWJK4Mxdj3Hm8Fw,83
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- looper-1.7.0.dist-info/top_level.txt,sha256=I0Yf7djsoQAMzwHBbDiQi9hGtq4Z41_Ma5CX8qXG8Y8,7
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- looper-1.7.0.dist-info/RECORD,,
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+ looper-2.0.0.dist-info/LICENSE.txt,sha256=oB6ZGDa4kcznznJKJsLLFFcOZyi8Y6e2Jv0rJozgp-I,1269
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+ looper-2.0.0.dist-info/METADATA,sha256=qH7xYrLFK7532qLOi0RZeCxuipdsT5nKcDdAq_41avo,1945
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+ looper-2.0.0.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
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+ looper-2.0.0.dist-info/entry_points.txt,sha256=iHltI2_Jdved27vccmWhvmcHWUZ7Mf6CfDV6QkY1Lc8,91
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+ looper-2.0.0.dist-info/top_level.txt,sha256=I0Yf7djsoQAMzwHBbDiQi9hGtq4Z41_Ma5CX8qXG8Y8,7
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+ looper-2.0.0.dist-info/RECORD,,
{looper-1.7.0.dist-info → looper-2.0.0.dist-info}/WHEEL RENAMED
@@ -1,5 +1,5 @@
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  Wheel-Version: 1.0
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- Generator: bdist_wheel (0.42.0)
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+ Generator: setuptools (75.8.0)
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  Root-Is-Purelib: true
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  Tag: py3-none-any
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{looper-1.7.0.dist-info → looper-2.0.0.dist-info}/entry_points.txt RENAMED
@@ -1,3 +1,3 @@
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  [console_scripts]
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  divvy = looper.__main__:divvy_main
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- looper = looper.__main__:main
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+ looper = looper.cli_pydantic:main_cli