geoseeq 0.7.3.dev2__tar.gz → 0.7.3.dev3__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 (138) hide show
  1. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/PKG-INFO +1 -1
  2. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/project.py +6 -6
  3. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/sample.py +6 -6
  4. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/pyproject.toml +1 -1
  5. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/.devcontainer/devcontainer.json +0 -0
  6. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/.github/workflows/python-publish.yml +0 -0
  7. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/.github/workflows/run_unit_tests.yml +0 -0
  8. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/.gitignore +0 -0
  9. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/.pre-commit-config.yaml +0 -0
  10. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/AGENTS.md +0 -0
  11. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/LICENSE +0 -0
  12. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/Makefile +0 -0
  13. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/README.md +0 -0
  14. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/commit_pylintrc +0 -0
  15. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/docs/about_geoseeq.md +0 -0
  16. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/docs/contributing.md +0 -0
  17. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/docs/downloading_data_examples.md +0 -0
  18. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/docs/examples/simple_python_example/README.md +0 -0
  19. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/docs/examples/simple_python_example/project_dashboard_example.py +0 -0
  20. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/docs/examples/simple_python_example/sample_dashboard_example.py +0 -0
  21. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/docs/examples/simple_python_example/simple_python_example.py +0 -0
  22. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/docs/examples/simple_python_example/smart_table_example.py +0 -0
  23. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/docs/examples/simple_snakemake_example/README.md +0 -0
  24. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/docs/examples/simple_snakemake_example/Snakefile +0 -0
  25. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/docs/examples/simple_snakemake_example/config.yaml +0 -0
  26. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/docs/uploading_data_examples.md +0 -0
  27. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/__init__.py +0 -0
  28. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/app.py +0 -0
  29. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/blob_constructors.py +0 -0
  30. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/bulk_creators.py +0 -0
  31. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/cli/__init__.py +0 -0
  32. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/cli/constants.py +0 -0
  33. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/cli/copy.py +0 -0
  34. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/cli/detail.py +0 -0
  35. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/cli/download.py +0 -0
  36. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/cli/fastq_utils.py +0 -0
  37. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/cli/find_grn.py +0 -0
  38. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/cli/get_eula.py +0 -0
  39. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/cli/main.py +0 -0
  40. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/cli/manage.py +0 -0
  41. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/cli/progress_bar.py +0 -0
  42. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/cli/project.py +0 -0
  43. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/cli/raw.py +0 -0
  44. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/cli/run.py +0 -0
  45. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/cli/search.py +0 -0
  46. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/cli/shared_params/__init__.py +0 -0
  47. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/cli/shared_params/common_state.py +0 -0
  48. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/cli/shared_params/config.py +0 -0
  49. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/cli/shared_params/id_handlers.py +0 -0
  50. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/cli/shared_params/obj_getters.py +0 -0
  51. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/cli/shared_params/opts_and_args.py +0 -0
  52. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/cli/upload/__init__.py +0 -0
  53. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/cli/upload/upload.py +0 -0
  54. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/cli/upload/upload_advanced.py +0 -0
  55. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/cli/upload/upload_reads.py +0 -0
  56. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/cli/user.py +0 -0
  57. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/cli/utils.py +0 -0
  58. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/cli/view.py +0 -0
  59. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/constants.py +0 -0
  60. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/contrib/__init__.py +0 -0
  61. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/contrib/ncbi/README.md +0 -0
  62. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/contrib/ncbi/__init__.py +0 -0
  63. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/contrib/ncbi/api.py +0 -0
  64. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/contrib/ncbi/bioproject.py +0 -0
  65. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/contrib/ncbi/cli.py +0 -0
  66. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/contrib/ncbi/setup_logging.py +0 -0
  67. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/dashboard/dashboard.py +0 -0
  68. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/file_system/filesystem_download.py +0 -0
  69. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/file_system/main.py +0 -0
  70. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/file_system_cache.py +0 -0
  71. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/id_constructors/__init__.py +0 -0
  72. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/id_constructors/from_blobs.py +0 -0
  73. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/id_constructors/from_ids.py +0 -0
  74. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/id_constructors/from_names.py +0 -0
  75. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/id_constructors/from_uuids.py +0 -0
  76. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/id_constructors/resolvers.py +0 -0
  77. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/id_constructors/utils.py +0 -0
  78. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/knex.py +0 -0
  79. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/organization.py +0 -0
  80. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/pipeline.py +0 -0
  81. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/plotting/README.md +0 -0
  82. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/plotting/__init__.py +0 -0
  83. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/plotting/constants.py +0 -0
  84. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/plotting/highcharts.py +0 -0
  85. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/plotting/map/__init__.py +0 -0
  86. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/plotting/map/base_layer.py +0 -0
  87. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/plotting/map/map.py +0 -0
  88. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/plotting/map/overlay.py +0 -0
  89. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/plotting/selectable.py +0 -0
  90. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/remote_object.py +0 -0
  91. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/result/__init__.py +0 -0
  92. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/result/bioinfo.py +0 -0
  93. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/result/file_chunker.py +0 -0
  94. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/result/file_download.py +0 -0
  95. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/result/file_upload.py +0 -0
  96. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/result/result_file.py +0 -0
  97. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/result/result_folder.py +0 -0
  98. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/result/resumable_download_tracker.py +0 -0
  99. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/result/resumable_upload_tracker.py +0 -0
  100. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/result/smart_objects.py +0 -0
  101. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/result/utils.py +0 -0
  102. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/search.py +0 -0
  103. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/smart_table.py +0 -0
  104. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/smart_tree.py +0 -0
  105. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/upload_download_manager.py +0 -0
  106. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/user.py +0 -0
  107. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/utils.py +0 -0
  108. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/vc/README.md +0 -0
  109. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/vc/__init__.py +0 -0
  110. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/vc/checksum.py +0 -0
  111. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/vc/cli.py +0 -0
  112. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/vc/clone.py +0 -0
  113. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/vc/constants.py +0 -0
  114. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/vc/vc_cache.py +0 -0
  115. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/vc/vc_dir.py +0 -0
  116. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/vc/vc_sample.py +0 -0
  117. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/vc/vc_stub.py +0 -0
  118. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/geoseeq/work_orders.py +0 -0
  119. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/setup.py +0 -0
  120. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/tests/__init__.py +0 -0
  121. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/tests/conftest.py +0 -0
  122. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/tests/test_api_client.py +0 -0
  123. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/tests/test_download.py +0 -0
  124. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/tests/test_download_cli.py +0 -0
  125. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/tests/test_file_chunker.py +0 -0
  126. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/tests/test_file_system_cache.py +0 -0
  127. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/tests/test_files/files_path.txt +0 -0
  128. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/tests/test_files/sampleclit.R1.fastq.gz +0 -0
  129. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/tests/test_files/sampleclit.R2.fastq.gz +0 -0
  130. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/tests/test_files/single-end.fastq.gz +0 -0
  131. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/tests/test_files/test_metadata.csv +0 -0
  132. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/tests/test_files/test_small.R1.fastq.gz +0 -0
  133. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/tests/test_files/test_small.R2.fastq.gz +0 -0
  134. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/tests/test_plotting.py +0 -0
  135. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/tests/test_remote_object.py +0 -0
  136. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/tests/test_upload.py +0 -0
  137. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/tests/test_upload_cli.py +0 -0
  138. {geoseeq-0.7.3.dev2 → geoseeq-0.7.3.dev3}/tests/test_utils.py +0 -0
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: geoseeq
3
- Version: 0.7.3.dev2
3
+ Version: 0.7.3.dev3
4
4
  Summary: GeoSeeq command line tools and python API
5
5
  Project-URL: Homepage, https://github.com/biotia/geoseeq_api_client
6
6
  Project-URL: Issues, https://github.com/biotia/geoseeq_api_client/issues
@@ -390,7 +390,7 @@ class Project(RemoteObject):
390
390
 
391
391
  return Dashboard(knex=self.knex, project=self, title=title, default=default)
392
392
 
393
- def get_default_dashbaord(self):
393
+ def get_default_dashboard(self):
394
394
  """Get the default dashboard for this project."""
395
395
  from geoseeq.dashboard.dashboard import Dashboard, DashboardTile
396
396
 
@@ -419,15 +419,15 @@ class Project(RemoteObject):
419
419
  pass
420
420
  return None
421
421
 
422
- def get_or_create_default_dashbaord(self):
422
+ def get_or_create_default_dashboard(self):
423
423
  """Get the default dashboard for this project or create it if does not exist."""
424
- default_dashboard = self.get_default_dashbaord()
424
+ default_dashboard = self.get_default_dashboard()
425
425
  if default_dashboard:
426
426
  return default_dashboard
427
427
  else:
428
428
  return self.create_dashboard(default=True)
429
429
 
430
- def get_dashbaord_by_title(self, title):
430
+ def get_dashboard_by_title(self, title):
431
431
  """Get dashboard for this project by the title of the dashboard."""
432
432
  from geoseeq.dashboard.dashboard import Dashboard, DashboardTile
433
433
 
@@ -454,9 +454,9 @@ class Project(RemoteObject):
454
454
  pass
455
455
  return None
456
456
 
457
- def get_or_create_dashbaord_by_title(self, title: str):
457
+ def get_or_create_dashboard_by_title(self, title: str):
458
458
  """Get dashboard by title for this project or create it if does not exist."""
459
- default_dashboard = self.get_dashbaord_by_title(title)
459
+ default_dashboard = self.get_dashboard_by_title(title)
460
460
  if default_dashboard:
461
461
  return default_dashboard
462
462
  else:
@@ -249,7 +249,7 @@ class Sample(RemoteObject):
249
249
  dashboard._already_fetched = True
250
250
  return dashboard
251
251
 
252
- def get_default_dashbaord(self):
252
+ def get_default_dashboard(self):
253
253
  """Get the default dashboard for this sample."""
254
254
  from geoseeq.dashboard.dashboard import SampleDashboard
255
255
 
@@ -267,15 +267,15 @@ class Sample(RemoteObject):
267
267
  pass
268
268
  return None
269
269
 
270
- def get_or_create_default_dashbaord(self):
270
+ def get_or_create_default_dashboard(self):
271
271
  """Get the default dashboard for this sample or create it if does not exist."""
272
- default_dashboard = self.get_default_dashbaord()
272
+ default_dashboard = self.get_default_dashboard()
273
273
  if default_dashboard:
274
274
  return default_dashboard
275
275
  else:
276
276
  return self.create_dashboard(default=True)
277
277
 
278
- def get_dashbaord_by_title(self, title):
278
+ def get_dashboard_by_title(self, title):
279
279
  """Get dashboard by title for this sample."""
280
280
  from geoseeq.dashboard.dashboard import SampleDashboard
281
281
 
@@ -293,9 +293,9 @@ class Sample(RemoteObject):
293
293
  pass
294
294
  return None
295
295
 
296
- def get_or_create_dashbaord_by_title(self, title):
296
+ def get_or_create_dashboard_by_title(self, title):
297
297
  """Get dashboard by title for this sample or create it if does not exist."""
298
- default_dashboard = self.get_dashbaord_by_title(title)
298
+ default_dashboard = self.get_dashboard_by_title(title)
299
299
  if default_dashboard:
300
300
  return default_dashboard
301
301
  else:
@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
4
4
 
5
5
  [project]
6
6
  name = "geoseeq"
7
- version = "0.7.3dev2"
7
+ version = "0.7.3dev3"
8
8
  authors = [
9
9
  { name="David C. Danko", email="dcdanko@biotia.io" },
10
10
  ]
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File without changes
File without changes
File without changes
File without changes
File without changes