seqslab-cli 3.3.2__tar.gz → 3.3.2.post0__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 (108) hide show
  1. {seqslab-cli-3.3.2/python/seqslab_cli.egg-info → seqslab-cli-3.3.2.post0}/PKG-INFO +1 -1
  2. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/__init__.py +1 -1
  3. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/runsheet/runsheet.py +1 -1
  4. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/wes/internal/parameters.py +1 -0
  5. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/wes/resource/base.py +1 -1
  6. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0/python/seqslab_cli.egg-info}/PKG-INFO +1 -1
  7. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/LICENSE +0 -0
  8. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/MANIFEST.in +0 -0
  9. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/README.md +0 -0
  10. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/auth/__init__.py +0 -0
  11. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/auth/azuread.py +0 -0
  12. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/auth/commands.py +0 -0
  13. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/cli.py +0 -0
  14. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/context.py +0 -0
  15. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/drs/__init__.py +0 -0
  16. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/drs/api/__init__.py +0 -0
  17. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/drs/api/azure.py +0 -0
  18. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/drs/api/base.py +0 -0
  19. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/drs/api/common.py +0 -0
  20. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/drs/api/template.py +0 -0
  21. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/drs/commands.py +0 -0
  22. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/drs/internal/__init__.py +0 -0
  23. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/drs/internal/aiocopy.py +0 -0
  24. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/drs/internal/common.py +0 -0
  25. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/drs/internal/utils.py +0 -0
  26. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/drs/storage/__init__.py +0 -0
  27. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/drs/storage/azure.py +0 -0
  28. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/drs/storage/base.py +0 -0
  29. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/drs/utils/__init__.py +0 -0
  30. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/drs/utils/atgxmetadata.py +0 -0
  31. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/drs/utils/biomimetype.py +0 -0
  32. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/drs/utils/progressbar.py +0 -0
  33. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/exceptions.py +0 -0
  34. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/organization/__init__.py +0 -0
  35. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/organization/commands.py +0 -0
  36. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/organization/resource/__init__.py +0 -0
  37. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/organization/resource/base.py +0 -0
  38. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/plugin.py +0 -0
  39. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/role/__init__.py +0 -0
  40. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/role/commands.py +0 -0
  41. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/role/internal/__init__.py +0 -0
  42. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/role/internal/common.py +0 -0
  43. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/role/resource/__init__.py +0 -0
  44. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/role/resource/azure.py +0 -0
  45. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/role/resource/base.py +0 -0
  46. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/runsheet/__init__.py +0 -0
  47. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/sample_sheet/__init__.py +0 -0
  48. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/sample_sheet/_version.py +0 -0
  49. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/sample_sheet/util.py +0 -0
  50. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/scr/__init__.py +0 -0
  51. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/scr/commands.py +0 -0
  52. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/scr/internal/__init__.py +0 -0
  53. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/scr/internal/common.py +0 -0
  54. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/scr/resource/__init__.py +0 -0
  55. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/scr/resource/azure.py +0 -0
  56. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/scr/resource/base.py +0 -0
  57. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/session_logger.py +0 -0
  58. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/settings.py +0 -0
  59. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/statusbar.py +0 -0
  60. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/trs/__init__.py +0 -0
  61. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/trs/commands.py +0 -0
  62. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/trs/internal/__init__.py +0 -0
  63. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/trs/internal/utils.py +0 -0
  64. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/trs/register/__init__.py +0 -0
  65. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/trs/register/azure.py +0 -0
  66. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/trs/register/base.py +0 -0
  67. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/trs/register/common.py +0 -0
  68. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/trs/register/template.py +0 -0
  69. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/trs/resource/__init__.py +0 -0
  70. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/trs/resource/azure.py +0 -0
  71. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/trs/resource/base.py +0 -0
  72. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/trs/resource/common.py +0 -0
  73. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/trs/template/__init__.py +0 -0
  74. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/trs/template/base.py +0 -0
  75. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/trs/template/template.py +0 -0
  76. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/usage_logger.py +0 -0
  77. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/user/__init__.py +0 -0
  78. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/user/commands.py +0 -0
  79. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/user/internal/__init__.py +0 -0
  80. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/user/internal/common.py +0 -0
  81. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/user/resource/__init__.py +0 -0
  82. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/user/resource/azure.py +0 -0
  83. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/user/resource/base.py +0 -0
  84. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/wes/__init__.py +0 -0
  85. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/wes/commands.py +0 -0
  86. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/wes/internal/__init__.py +0 -0
  87. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/wes/internal/common.py +0 -0
  88. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/wes/resource/__init__.py +0 -0
  89. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/wes/resource/azure.py +0 -0
  90. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/wes/template/__init__.py +0 -0
  91. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/wes/template/base.py +0 -0
  92. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/wes/template/template.py +0 -0
  93. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/workspace/__init__.py +0 -0
  94. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/workspace/commands.py +0 -0
  95. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/workspace/internal/__init__.py +0 -0
  96. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/workspace/internal/common.py +0 -0
  97. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/workspace/resource/__init__.py +0 -0
  98. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/workspace/resource/azure.py +0 -0
  99. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/workspace/resource/base.py +0 -0
  100. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab_cli.egg-info/SOURCES.txt +0 -0
  101. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab_cli.egg-info/dependency_links.txt +0 -0
  102. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab_cli.egg-info/entry_points.txt +0 -0
  103. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab_cli.egg-info/requires.txt +0 -0
  104. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab_cli.egg-info/top_level.txt +0 -0
  105. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab_cli.egg-info/zip-safe +0 -0
  106. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/requirements.txt +0 -0
  107. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/setup.cfg +0 -0
  108. {seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/setup.py +0 -0
{seqslab-cli-3.3.2/python/seqslab_cli.egg-info → seqslab-cli-3.3.2.post0}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
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  Name: seqslab-cli
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- Version: 3.3.2
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+ Version: 3.3.2.post0
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  Summary: Atgenomix SeqsLab Command Line Tool
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  Home-page: https://github.com/AnomeGAP/seqslab-cli
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  Author: Allen Chang
{seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/__init__.py RENAMED
@@ -21,6 +21,6 @@ name = "seqslab"
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  __all__ = []
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- __version__ = "3.3.2"
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+ __version__ = "3.3.2.post0"
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  LOGGING = {"DIR_PATH": "/var/log/seqslab"}
{seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/runsheet/runsheet.py RENAMED
@@ -171,7 +171,7 @@ class RunSheet:
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  run_name_set.add(rn)
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  else:
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  raise RuntimeError(
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- f"Inconsistent run_name set {run_name_set} and run sig {runs.keys()}"
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+ f"Inconsistent run_name/run_name_set {rn}/{run_name_set} and run sig/runs {rsig}/{runs.keys()}"
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  )
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  for k, v in runs.items():
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  self._runs.append(Run(v, k[0], k[1], k[2]))
{seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/wes/internal/parameters.py RENAMED
@@ -92,6 +92,7 @@ def populate_fqn(labels: list, names: list):
92
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  for i in range(len(labels)):
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  indices = sample_indices[i]
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  ret[indices[0]][indices[1]] = f"{names[i]}.fastq.gz"
95
+ ret = [[item for item in inner_list if item != ""] for inner_list in ret]
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  else:
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  d1_size = max([ind[0] for ind in sample_indices]) + 1
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  ret = ["" for i in range(d1_size)]
{seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/python/seqslab/wes/resource/base.py RENAMED
@@ -215,7 +215,7 @@ class BaseResource(ABC):
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  else:
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  query = ""
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  else:
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- query = f"rerun_id={quote(rerun_id)}"
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+ query = f"smart_reuse_id={quote(rerun_id)}"
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  response = requests.post(
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  f"{self.WES_RUNS_URL.format(backend=backend)}&{query}",
{seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0/python/seqslab_cli.egg-info}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
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2
  Name: seqslab-cli
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- Version: 3.3.2
3
+ Version: 3.3.2.post0
4
4
  Summary: Atgenomix SeqsLab Command Line Tool
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  Home-page: https://github.com/AnomeGAP/seqslab-cli
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  Author: Allen Chang
{seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/LICENSE RENAMED
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{seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/README.md RENAMED
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{seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/setup.cfg RENAMED
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{seqslab-cli-3.3.2 → seqslab-cli-3.3.2.post0}/setup.py RENAMED
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