geoseeq 0.7.3.dev3__tar.gz → 0.7.3.dev4__tar.gz

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Files changed (138) hide show
  1. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/PKG-INFO +1 -1
  2. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/docs/examples/simple_python_example/project_dashboard_example.py +2 -2
  3. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/project.py +6 -5
  4. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/pyproject.toml +1 -1
  5. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/.devcontainer/devcontainer.json +0 -0
  6. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/.github/workflows/python-publish.yml +0 -0
  7. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/.github/workflows/run_unit_tests.yml +0 -0
  8. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/.gitignore +0 -0
  9. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/.pre-commit-config.yaml +0 -0
  10. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/AGENTS.md +0 -0
  11. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/LICENSE +0 -0
  12. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/Makefile +0 -0
  13. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/README.md +0 -0
  14. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/commit_pylintrc +0 -0
  15. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/docs/about_geoseeq.md +0 -0
  16. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/docs/contributing.md +0 -0
  17. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/docs/downloading_data_examples.md +0 -0
  18. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/docs/examples/simple_python_example/README.md +0 -0
  19. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/docs/examples/simple_python_example/sample_dashboard_example.py +0 -0
  20. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/docs/examples/simple_python_example/simple_python_example.py +0 -0
  21. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/docs/examples/simple_python_example/smart_table_example.py +0 -0
  22. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/docs/examples/simple_snakemake_example/README.md +0 -0
  23. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/docs/examples/simple_snakemake_example/Snakefile +0 -0
  24. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/docs/examples/simple_snakemake_example/config.yaml +0 -0
  25. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/docs/uploading_data_examples.md +0 -0
  26. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/__init__.py +0 -0
  27. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/app.py +0 -0
  28. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/blob_constructors.py +0 -0
  29. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/bulk_creators.py +0 -0
  30. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/cli/__init__.py +0 -0
  31. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/cli/constants.py +0 -0
  32. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/cli/copy.py +0 -0
  33. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/cli/detail.py +0 -0
  34. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/cli/download.py +0 -0
  35. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/cli/fastq_utils.py +0 -0
  36. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/cli/find_grn.py +0 -0
  37. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/cli/get_eula.py +0 -0
  38. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/cli/main.py +0 -0
  39. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/cli/manage.py +0 -0
  40. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/cli/progress_bar.py +0 -0
  41. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/cli/project.py +0 -0
  42. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/cli/raw.py +0 -0
  43. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/cli/run.py +0 -0
  44. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/cli/search.py +0 -0
  45. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/cli/shared_params/__init__.py +0 -0
  46. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/cli/shared_params/common_state.py +0 -0
  47. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/cli/shared_params/config.py +0 -0
  48. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/cli/shared_params/id_handlers.py +0 -0
  49. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/cli/shared_params/obj_getters.py +0 -0
  50. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/cli/shared_params/opts_and_args.py +0 -0
  51. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/cli/upload/__init__.py +0 -0
  52. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/cli/upload/upload.py +0 -0
  53. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/cli/upload/upload_advanced.py +0 -0
  54. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/cli/upload/upload_reads.py +0 -0
  55. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/cli/user.py +0 -0
  56. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/cli/utils.py +0 -0
  57. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/cli/view.py +0 -0
  58. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/constants.py +0 -0
  59. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/contrib/__init__.py +0 -0
  60. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/contrib/ncbi/README.md +0 -0
  61. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/contrib/ncbi/__init__.py +0 -0
  62. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/contrib/ncbi/api.py +0 -0
  63. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/contrib/ncbi/bioproject.py +0 -0
  64. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/contrib/ncbi/cli.py +0 -0
  65. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/contrib/ncbi/setup_logging.py +0 -0
  66. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/dashboard/dashboard.py +0 -0
  67. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/file_system/filesystem_download.py +0 -0
  68. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/file_system/main.py +0 -0
  69. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/file_system_cache.py +0 -0
  70. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/id_constructors/__init__.py +0 -0
  71. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/id_constructors/from_blobs.py +0 -0
  72. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/id_constructors/from_ids.py +0 -0
  73. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/id_constructors/from_names.py +0 -0
  74. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/id_constructors/from_uuids.py +0 -0
  75. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/id_constructors/resolvers.py +0 -0
  76. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/id_constructors/utils.py +0 -0
  77. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/knex.py +0 -0
  78. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/organization.py +0 -0
  79. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/pipeline.py +0 -0
  80. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/plotting/README.md +0 -0
  81. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/plotting/__init__.py +0 -0
  82. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/plotting/constants.py +0 -0
  83. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/plotting/highcharts.py +0 -0
  84. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/plotting/map/__init__.py +0 -0
  85. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/plotting/map/base_layer.py +0 -0
  86. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/plotting/map/map.py +0 -0
  87. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/plotting/map/overlay.py +0 -0
  88. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/plotting/selectable.py +0 -0
  89. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/remote_object.py +0 -0
  90. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/result/__init__.py +0 -0
  91. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/result/bioinfo.py +0 -0
  92. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/result/file_chunker.py +0 -0
  93. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/result/file_download.py +0 -0
  94. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/result/file_upload.py +0 -0
  95. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/result/result_file.py +0 -0
  96. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/result/result_folder.py +0 -0
  97. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/result/resumable_download_tracker.py +0 -0
  98. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/result/resumable_upload_tracker.py +0 -0
  99. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/result/smart_objects.py +0 -0
  100. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/result/utils.py +0 -0
  101. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/sample.py +0 -0
  102. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/search.py +0 -0
  103. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/smart_table.py +0 -0
  104. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/smart_tree.py +0 -0
  105. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/upload_download_manager.py +0 -0
  106. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/user.py +0 -0
  107. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/utils.py +0 -0
  108. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/vc/README.md +0 -0
  109. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/vc/__init__.py +0 -0
  110. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/vc/checksum.py +0 -0
  111. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/vc/cli.py +0 -0
  112. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/vc/clone.py +0 -0
  113. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/vc/constants.py +0 -0
  114. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/vc/vc_cache.py +0 -0
  115. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/vc/vc_dir.py +0 -0
  116. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/vc/vc_sample.py +0 -0
  117. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/vc/vc_stub.py +0 -0
  118. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/work_orders.py +0 -0
  119. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/setup.py +0 -0
  120. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/tests/__init__.py +0 -0
  121. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/tests/conftest.py +0 -0
  122. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/tests/test_api_client.py +0 -0
  123. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/tests/test_download.py +0 -0
  124. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/tests/test_download_cli.py +0 -0
  125. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/tests/test_file_chunker.py +0 -0
  126. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/tests/test_file_system_cache.py +0 -0
  127. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/tests/test_files/files_path.txt +0 -0
  128. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/tests/test_files/sampleclit.R1.fastq.gz +0 -0
  129. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/tests/test_files/sampleclit.R2.fastq.gz +0 -0
  130. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/tests/test_files/single-end.fastq.gz +0 -0
  131. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/tests/test_files/test_metadata.csv +0 -0
  132. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/tests/test_files/test_small.R1.fastq.gz +0 -0
  133. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/tests/test_files/test_small.R2.fastq.gz +0 -0
  134. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/tests/test_plotting.py +0 -0
  135. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/tests/test_remote_object.py +0 -0
  136. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/tests/test_upload.py +0 -0
  137. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/tests/test_upload_cli.py +0 -0
  138. {geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/tests/test_utils.py +0 -0
{geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
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  Name: geoseeq
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- Version: 0.7.3.dev3
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+ Version: 0.7.3.dev4
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  Summary: GeoSeeq command line tools and python API
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  Project-URL: Homepage, https://github.com/biotia/geoseeq_api_client
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  Project-URL: Issues, https://github.com/biotia/geoseeq_api_client/issues
{geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/docs/examples/simple_python_example/project_dashboard_example.py RENAMED
@@ -19,7 +19,7 @@ knex.add_api_token(token)
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  project = project_from_uuid(knex, project_id)
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- dashboard = project.get_or_create_default_dashbaord()
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+ dashboard = project.get_or_create_default_dashboard()
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  # Rename dashboard
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  dashboard.title = "My default dashboard"
@@ -41,7 +41,7 @@ dashboard.add_tile(file2, title="Tile title 2", width="half")
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  dashboard.save()
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- dashboard2 = project.get_or_create_dashbaord_by_title(title="Dashboard Dix")
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+ dashboard2 = project.get_or_create_dashboard_by_title(title="Dashboard 2")
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  dashboard2.title = "Renamed dashboard"
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  # Set dashboard to default
{geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/geoseeq/project.py RENAMED
@@ -387,8 +387,9 @@ class Project(RemoteObject):
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  post_data = {"name": title, "is_default": default}
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  self.knex.post(f"sample_groups/{self.uuid}/dashboard-list", json=post_data)
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-
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- return Dashboard(knex=self.knex, project=self, title=title, default=default)
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+ return Dashboard(
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+ knex=self.knex, project=self, title=title, default=default, tiles=[]
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+ )
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393
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  def get_default_dashboard(self):
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  """Get the default dashboard for this project."""
@@ -456,9 +457,9 @@ class Project(RemoteObject):
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457
 
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  def get_or_create_dashboard_by_title(self, title: str):
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  """Get dashboard by title for this project or create it if does not exist."""
459
- default_dashboard = self.get_dashboard_by_title(title)
460
- if default_dashboard:
461
- return default_dashboard
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+ dashboard = self.get_dashboard_by_title(title)
461
+ if dashboard:
462
+ return dashboard
462
463
  else:
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  return self.create_dashboard(title=title, default=False)
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{geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/pyproject.toml RENAMED
@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
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  [project]
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  name = "geoseeq"
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- version = "0.7.3dev3"
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+ version = "0.7.3dev4"
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  authors = [
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  { name="David C. Danko", email="dcdanko@biotia.io" },
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  ]
{geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/.gitignore RENAMED
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{geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/AGENTS.md RENAMED
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{geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/LICENSE RENAMED
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{geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/Makefile RENAMED
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{geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/README.md RENAMED
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{geoseeq-0.7.3.dev3 → geoseeq-0.7.3.dev4}/setup.py RENAMED
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