pybiolib 1.2.1040__tar.gz → 1.2.1045__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.
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/PKG-INFO +1 -1
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/biolib_api_client/biolib_app_api.py +9 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/cli/init.py +37 -1
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/pyproject.toml +1 -1
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/LICENSE +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/PYPI_README.md +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/__init__.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_data_record/data_record.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/__init__.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/add_copilot_prompts.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/add_gui_files.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/data_record/__init__.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/data_record/data_record.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/data_record/push_data.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/data_record/remote_storage_endpoint.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/errors.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/file_utils.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/fuse_mount/__init__.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/fuse_mount/experiment_fuse_mount.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/http_client.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/lfs/__init__.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/lfs/cache.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/libs/__init__.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/libs/fusepy/__init__.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/push_application.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/runtime.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/string_utils.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/templates/__init__.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/templates/copilot_template/.github/instructions/general-app-knowledge.instructions.md +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/templates/copilot_template/.github/instructions/style-general.instructions.md +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/templates/copilot_template/.github/instructions/style-python.instructions.md +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/templates/copilot_template/.github/instructions/style-react-ts.instructions.md +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/templates/copilot_template/.github/prompts/biolib_app_inputs.prompt.md +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/templates/copilot_template/.github/prompts/biolib_onboard_repo.prompt.md +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/templates/copilot_template/.github/prompts/biolib_run_apps.prompt.md +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/templates/gui_template/.yarnrc.yml +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/templates/gui_template/App.tsx +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/templates/gui_template/Dockerfile +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/templates/gui_template/index.css +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/templates/gui_template/index.html +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/templates/gui_template/index.tsx +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/templates/gui_template/package.json +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/templates/gui_template/tsconfig.json +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/templates/gui_template/vite.config.mts +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/templates/init_template/.biolib/config.yml +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/templates/init_template/.github/workflows/biolib.yml +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/templates/init_template/.gitignore +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/templates/init_template/Dockerfile +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/templates/init_template/requirements.txt +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/templates/init_template/run.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/templates/init_template/run.sh +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/templates/templates.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/tree_utils.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/types/__init__.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/types/account.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/types/account_member.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/types/app.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/types/data_record.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/types/experiment.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/types/file_node.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/types/push.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/types/resource.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/types/resource_permission.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/types/resource_version.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/types/result.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/types/typing.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/types/user.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/utils/__init__.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/utils/multinode.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_runtime/runtime.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_session/session.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/api/__init__.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/api/client.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/app/__init__.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/app/app.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/app/search_apps.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/biolib_api_client/__init__.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/biolib_api_client/api_client.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/biolib_api_client/app_types.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/biolib_api_client/auth.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/biolib_api_client/biolib_job_api.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/biolib_api_client/common_types.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/biolib_api_client/job_types.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/biolib_api_client/lfs_types.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/biolib_api_client/user_state.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/biolib_binary_format/__init__.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/biolib_binary_format/base_bbf_package.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/biolib_binary_format/file_in_container.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/biolib_binary_format/module_input.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/biolib_binary_format/module_output_v2.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/biolib_binary_format/remote_endpoints.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/biolib_binary_format/remote_stream_seeker.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/biolib_binary_format/saved_job.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/biolib_binary_format/stdout_and_stderr.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/biolib_binary_format/system_exception.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/biolib_binary_format/system_status_update.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/biolib_binary_format/utils.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/biolib_docker_client/__init__.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/biolib_download_container.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/biolib_errors.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/biolib_logging.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/cli/__init__.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/cli/auth.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/cli/data_record.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/cli/download_container.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/cli/lfs.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/cli/push.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/cli/run.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/cli/runtime.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/cli/sdk.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/cli/start.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/compute_node/.gitignore +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/compute_node/__init__.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/compute_node/cloud_utils/__init__.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/compute_node/cloud_utils/cloud_utils.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/compute_node/job_worker/__init__.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/compute_node/job_worker/cache_state.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/compute_node/job_worker/cache_types.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/compute_node/job_worker/docker_image_cache.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/compute_node/job_worker/executors/__init__.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/compute_node/job_worker/executors/docker_executor.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/compute_node/job_worker/executors/docker_types.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/compute_node/job_worker/executors/tars/__init__.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/compute_node/job_worker/executors/types.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/compute_node/job_worker/job_legacy_input_wait_timeout_thread.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/compute_node/job_worker/job_max_runtime_timer_thread.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/compute_node/job_worker/job_storage.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/compute_node/job_worker/job_worker.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/compute_node/job_worker/large_file_system.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/compute_node/job_worker/mappings.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/compute_node/job_worker/utilization_reporter_thread.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/compute_node/job_worker/utils.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/compute_node/remote_host_proxy.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/compute_node/socker_listener_thread.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/compute_node/socket_sender_thread.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/compute_node/utils.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/compute_node/webserver/__init__.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/compute_node/webserver/gunicorn_flask_application.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/compute_node/webserver/webserver.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/compute_node/webserver/webserver_types.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/compute_node/webserver/webserver_utils.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/compute_node/webserver/worker_thread.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/experiments/__init__.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/experiments/experiment.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/jobs/__init__.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/jobs/job.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/jobs/job_result.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/jobs/types.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/py.typed +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/runtime/__init__.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/sdk/__init__.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/tables.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/typing_utils.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/user/__init__.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/user/sign_in.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/utils/__init__.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/utils/app_uri.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/utils/cache_state.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/utils/multipart_uploader.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/utils/seq_util.py +0 -0
- {pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/utils/zip/remote_zip.py +0 -0
@@ -99,6 +99,15 @@ class BiolibAppApi:
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def create_app(uri: str):
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uri = _get_app_uri_from_str(uri)
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response = biolib.api.client.post(path='/resources/apps/', data={'uri': uri})
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def push_app_version(
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from biolib import (
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utils, # Import like this to let BASE_URL_IS_PUBLIC_BIOLIB be set correctly
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from biolib._internal.add_copilot_prompts import add_copilot_prompts
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from biolib._internal.templates import templates
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from biolib.biolib_api_client.api_client import BiolibApiClient
|
16
|
+
from biolib.biolib_api_client.biolib_app_api import BiolibAppApi
|
17
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+
from biolib.user.sign_in import sign_in
|
12
18
|
from biolib.utils import BIOLIB_PACKAGE_VERSION
|
13
19
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|
14
20
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|
@@ -19,6 +25,36 @@ def init() -> None:
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19
25
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app_uri = input('What URI do you want to create the application under? (leave blank to skip): ')
|
20
26
|
app_name = app_uri.split('/')[-1] if app_uri else None
|
21
27
|
docker_tag = normalize_for_docker_tag(app_name) if app_name else None
|
28
|
+
|
29
|
+
if app_uri:
|
30
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+
try:
|
31
|
+
if BiolibApiClient.is_reauthentication_needed():
|
32
|
+
sign_in_input = input('You need to sign in to validate/create apps. Would you like to sign in? [y/N]: ')
|
33
|
+
if sign_in_input.lower() in ['y', 'yes']:
|
34
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+
sign_in()
|
35
|
+
else:
|
36
|
+
print('Skipping app validation and creation. You can set the URI in .biolib/config.yml later.')
|
37
|
+
return
|
38
|
+
|
39
|
+
BiolibAppApi.get_by_uri(app_uri)
|
40
|
+
print(f'App {app_uri} already exists.')
|
41
|
+
except biolib_errors.NotFound:
|
42
|
+
create_app_input = input(f'App {app_uri} does not exist. Would you like to create it? [y/N]: ')
|
43
|
+
if create_app_input.lower() in ['y', 'yes']:
|
44
|
+
try:
|
45
|
+
BiolibAppApi.create_app(app_uri)
|
46
|
+
print(f'Successfully created app {app_uri}')
|
47
|
+
except Exception as e:
|
48
|
+
print(f'Failed to create app {app_uri}: {str(e)}')
|
49
|
+
print('You can create the app manually later or set the URI in .biolib/config.yml')
|
50
|
+
else:
|
51
|
+
print(
|
52
|
+
'App creation skipped. You can create the app manually later or set the URI in .biolib/config.yml'
|
53
|
+
)
|
54
|
+
except Exception as e:
|
55
|
+
print(f'Failed to validate app {app_uri}: {str(e)}')
|
56
|
+
print('Continuing with initialization...')
|
57
|
+
|
22
58
|
if not app_uri:
|
23
59
|
print(
|
24
60
|
'Remember to set the app URI in the .biolib/config.yml file later, '
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{pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/data_record/remote_storage_endpoint.py
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{pybiolib-1.2.1040 → pybiolib-1.2.1045}/biolib/_internal/fuse_mount/experiment_fuse_mount.py
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