pybiolib 0.2.951__py3-none-any.whl → 1.2.1890__py3-none-any.whl
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.
- biolib/__init__.py +357 -11
- biolib/_data_record/data_record.py +380 -0
- biolib/_index/__init__.py +0 -0
- biolib/_index/index.py +55 -0
- biolib/_index/query_result.py +103 -0
- biolib/_internal/__init__.py +0 -0
- biolib/_internal/add_copilot_prompts.py +58 -0
- biolib/_internal/add_gui_files.py +81 -0
- biolib/_internal/data_record/__init__.py +1 -0
- biolib/_internal/data_record/data_record.py +85 -0
- biolib/_internal/data_record/push_data.py +116 -0
- biolib/_internal/data_record/remote_storage_endpoint.py +43 -0
- biolib/_internal/errors.py +5 -0
- biolib/_internal/file_utils.py +125 -0
- biolib/_internal/fuse_mount/__init__.py +1 -0
- biolib/_internal/fuse_mount/experiment_fuse_mount.py +209 -0
- biolib/_internal/http_client.py +159 -0
- biolib/_internal/lfs/__init__.py +1 -0
- biolib/_internal/lfs/cache.py +51 -0
- biolib/_internal/libs/__init__.py +1 -0
- biolib/_internal/libs/fusepy/__init__.py +1257 -0
- biolib/_internal/push_application.py +488 -0
- biolib/_internal/runtime.py +22 -0
- biolib/_internal/string_utils.py +13 -0
- biolib/_internal/templates/__init__.py +1 -0
- biolib/_internal/templates/copilot_template/.github/instructions/general-app-knowledge.instructions.md +10 -0
- biolib/_internal/templates/copilot_template/.github/instructions/style-general.instructions.md +20 -0
- biolib/_internal/templates/copilot_template/.github/instructions/style-python.instructions.md +16 -0
- biolib/_internal/templates/copilot_template/.github/instructions/style-react-ts.instructions.md +47 -0
- biolib/_internal/templates/copilot_template/.github/prompts/biolib_app_inputs.prompt.md +11 -0
- biolib/_internal/templates/copilot_template/.github/prompts/biolib_onboard_repo.prompt.md +19 -0
- biolib/_internal/templates/copilot_template/.github/prompts/biolib_run_apps.prompt.md +12 -0
- biolib/_internal/templates/dashboard_template/.biolib/config.yml +5 -0
- biolib/_internal/templates/github_workflow_template/.github/workflows/biolib.yml +21 -0
- biolib/_internal/templates/gitignore_template/.gitignore +10 -0
- biolib/_internal/templates/gui_template/.yarnrc.yml +1 -0
- biolib/_internal/templates/gui_template/App.tsx +53 -0
- biolib/_internal/templates/gui_template/Dockerfile +27 -0
- biolib/_internal/templates/gui_template/biolib-sdk.ts +82 -0
- biolib/_internal/templates/gui_template/dev-data/output.json +7 -0
- biolib/_internal/templates/gui_template/index.css +5 -0
- biolib/_internal/templates/gui_template/index.html +13 -0
- biolib/_internal/templates/gui_template/index.tsx +10 -0
- biolib/_internal/templates/gui_template/package.json +27 -0
- biolib/_internal/templates/gui_template/tsconfig.json +24 -0
- biolib/_internal/templates/gui_template/vite-plugin-dev-data.ts +50 -0
- biolib/_internal/templates/gui_template/vite.config.mts +10 -0
- biolib/_internal/templates/init_template/.biolib/config.yml +19 -0
- biolib/_internal/templates/init_template/Dockerfile +14 -0
- biolib/_internal/templates/init_template/requirements.txt +1 -0
- biolib/_internal/templates/init_template/run.py +12 -0
- biolib/_internal/templates/init_template/run.sh +4 -0
- biolib/_internal/templates/templates.py +25 -0
- biolib/_internal/tree_utils.py +106 -0
- biolib/_internal/utils/__init__.py +65 -0
- biolib/_internal/utils/auth.py +46 -0
- biolib/_internal/utils/job_url.py +33 -0
- biolib/_internal/utils/multinode.py +263 -0
- biolib/_runtime/runtime.py +157 -0
- biolib/_session/session.py +44 -0
- biolib/_shared/__init__.py +0 -0
- biolib/_shared/types/__init__.py +74 -0
- biolib/_shared/types/account.py +12 -0
- biolib/_shared/types/account_member.py +8 -0
- biolib/_shared/types/app.py +9 -0
- biolib/_shared/types/data_record.py +40 -0
- biolib/_shared/types/experiment.py +32 -0
- biolib/_shared/types/file_node.py +17 -0
- biolib/_shared/types/push.py +6 -0
- biolib/_shared/types/resource.py +37 -0
- biolib/_shared/types/resource_deploy_key.py +11 -0
- biolib/_shared/types/resource_permission.py +14 -0
- biolib/_shared/types/resource_version.py +19 -0
- biolib/_shared/types/result.py +14 -0
- biolib/_shared/types/typing.py +10 -0
- biolib/_shared/types/user.py +19 -0
- biolib/_shared/utils/__init__.py +7 -0
- biolib/_shared/utils/resource_uri.py +75 -0
- biolib/api/__init__.py +6 -0
- biolib/api/client.py +168 -0
- biolib/app/app.py +252 -49
- biolib/app/search_apps.py +45 -0
- biolib/biolib_api_client/api_client.py +126 -31
- biolib/biolib_api_client/app_types.py +24 -4
- biolib/biolib_api_client/auth.py +31 -8
- biolib/biolib_api_client/biolib_app_api.py +147 -52
- biolib/biolib_api_client/biolib_job_api.py +161 -141
- biolib/biolib_api_client/job_types.py +21 -5
- biolib/biolib_api_client/lfs_types.py +7 -23
- biolib/biolib_api_client/user_state.py +56 -0
- biolib/biolib_binary_format/__init__.py +1 -4
- biolib/biolib_binary_format/file_in_container.py +105 -0
- biolib/biolib_binary_format/module_input.py +24 -7
- biolib/biolib_binary_format/module_output_v2.py +149 -0
- biolib/biolib_binary_format/remote_endpoints.py +34 -0
- biolib/biolib_binary_format/remote_stream_seeker.py +59 -0
- biolib/biolib_binary_format/saved_job.py +3 -2
- biolib/biolib_binary_format/{attestation_document.py → stdout_and_stderr.py} +8 -8
- biolib/biolib_binary_format/system_status_update.py +3 -2
- biolib/biolib_binary_format/utils.py +175 -0
- biolib/biolib_docker_client/__init__.py +11 -2
- biolib/biolib_errors.py +36 -0
- biolib/biolib_logging.py +27 -10
- biolib/cli/__init__.py +38 -0
- biolib/cli/auth.py +46 -0
- biolib/cli/data_record.py +164 -0
- biolib/cli/index.py +32 -0
- biolib/cli/init.py +421 -0
- biolib/cli/lfs.py +101 -0
- biolib/cli/push.py +50 -0
- biolib/cli/run.py +63 -0
- biolib/cli/runtime.py +14 -0
- biolib/cli/sdk.py +16 -0
- biolib/cli/start.py +56 -0
- biolib/compute_node/cloud_utils/cloud_utils.py +110 -161
- biolib/compute_node/job_worker/cache_state.py +66 -88
- biolib/compute_node/job_worker/cache_types.py +1 -6
- biolib/compute_node/job_worker/docker_image_cache.py +112 -37
- biolib/compute_node/job_worker/executors/__init__.py +0 -3
- biolib/compute_node/job_worker/executors/docker_executor.py +532 -199
- biolib/compute_node/job_worker/executors/docker_types.py +9 -1
- biolib/compute_node/job_worker/executors/types.py +19 -9
- biolib/compute_node/job_worker/job_legacy_input_wait_timeout_thread.py +30 -0
- biolib/compute_node/job_worker/job_max_runtime_timer_thread.py +3 -5
- biolib/compute_node/job_worker/job_storage.py +108 -0
- biolib/compute_node/job_worker/job_worker.py +397 -212
- biolib/compute_node/job_worker/large_file_system.py +87 -38
- biolib/compute_node/job_worker/network_alloc.py +99 -0
- biolib/compute_node/job_worker/network_buffer.py +240 -0
- biolib/compute_node/job_worker/utilization_reporter_thread.py +197 -0
- biolib/compute_node/job_worker/utils.py +9 -24
- biolib/compute_node/remote_host_proxy.py +400 -98
- biolib/compute_node/utils.py +31 -9
- biolib/compute_node/webserver/compute_node_results_proxy.py +189 -0
- biolib/compute_node/webserver/proxy_utils.py +28 -0
- biolib/compute_node/webserver/webserver.py +130 -44
- biolib/compute_node/webserver/webserver_types.py +2 -6
- biolib/compute_node/webserver/webserver_utils.py +77 -12
- biolib/compute_node/webserver/worker_thread.py +183 -42
- biolib/experiments/__init__.py +0 -0
- biolib/experiments/experiment.py +356 -0
- biolib/jobs/__init__.py +1 -0
- biolib/jobs/job.py +741 -0
- biolib/jobs/job_result.py +185 -0
- biolib/jobs/types.py +50 -0
- biolib/py.typed +0 -0
- biolib/runtime/__init__.py +14 -0
- biolib/sdk/__init__.py +91 -0
- biolib/tables.py +34 -0
- biolib/typing_utils.py +2 -7
- biolib/user/__init__.py +1 -0
- biolib/user/sign_in.py +54 -0
- biolib/utils/__init__.py +162 -0
- biolib/utils/cache_state.py +94 -0
- biolib/utils/multipart_uploader.py +194 -0
- biolib/utils/seq_util.py +150 -0
- biolib/utils/zip/remote_zip.py +640 -0
- pybiolib-1.2.1890.dist-info/METADATA +41 -0
- pybiolib-1.2.1890.dist-info/RECORD +177 -0
- {pybiolib-0.2.951.dist-info → pybiolib-1.2.1890.dist-info}/WHEEL +1 -1
- pybiolib-1.2.1890.dist-info/entry_points.txt +2 -0
- README.md +0 -17
- biolib/app/app_result.py +0 -68
- biolib/app/utils.py +0 -62
- biolib/biolib-js/0-biolib.worker.js +0 -1
- biolib/biolib-js/1-biolib.worker.js +0 -1
- biolib/biolib-js/2-biolib.worker.js +0 -1
- biolib/biolib-js/3-biolib.worker.js +0 -1
- biolib/biolib-js/4-biolib.worker.js +0 -1
- biolib/biolib-js/5-biolib.worker.js +0 -1
- biolib/biolib-js/6-biolib.worker.js +0 -1
- biolib/biolib-js/index.html +0 -10
- biolib/biolib-js/main-biolib.js +0 -1
- biolib/biolib_api_client/biolib_account_api.py +0 -21
- biolib/biolib_api_client/biolib_large_file_system_api.py +0 -108
- biolib/biolib_binary_format/aes_encrypted_package.py +0 -42
- biolib/biolib_binary_format/module_output.py +0 -58
- biolib/biolib_binary_format/rsa_encrypted_aes_package.py +0 -57
- biolib/biolib_push.py +0 -114
- biolib/cli.py +0 -203
- biolib/cli_utils.py +0 -273
- biolib/compute_node/cloud_utils/enclave_parent_types.py +0 -7
- biolib/compute_node/enclave/__init__.py +0 -2
- biolib/compute_node/enclave/enclave_remote_hosts.py +0 -53
- biolib/compute_node/enclave/nitro_secure_module_utils.py +0 -64
- biolib/compute_node/job_worker/executors/base_executor.py +0 -18
- biolib/compute_node/job_worker/executors/pyppeteer_executor.py +0 -173
- biolib/compute_node/job_worker/executors/remote/__init__.py +0 -1
- biolib/compute_node/job_worker/executors/remote/nitro_enclave_utils.py +0 -81
- biolib/compute_node/job_worker/executors/remote/remote_executor.py +0 -51
- biolib/lfs.py +0 -196
- biolib/pyppeteer/.circleci/config.yml +0 -100
- biolib/pyppeteer/.coveragerc +0 -3
- biolib/pyppeteer/.gitignore +0 -89
- biolib/pyppeteer/.pre-commit-config.yaml +0 -28
- biolib/pyppeteer/CHANGES.md +0 -253
- biolib/pyppeteer/CONTRIBUTING.md +0 -26
- biolib/pyppeteer/LICENSE +0 -12
- biolib/pyppeteer/README.md +0 -137
- biolib/pyppeteer/docs/Makefile +0 -177
- biolib/pyppeteer/docs/_static/custom.css +0 -28
- biolib/pyppeteer/docs/_templates/layout.html +0 -10
- biolib/pyppeteer/docs/changes.md +0 -1
- biolib/pyppeteer/docs/conf.py +0 -299
- biolib/pyppeteer/docs/index.md +0 -21
- biolib/pyppeteer/docs/make.bat +0 -242
- biolib/pyppeteer/docs/reference.md +0 -211
- biolib/pyppeteer/docs/server.py +0 -60
- biolib/pyppeteer/poetry.lock +0 -1699
- biolib/pyppeteer/pyppeteer/__init__.py +0 -135
- biolib/pyppeteer/pyppeteer/accessibility.py +0 -286
- biolib/pyppeteer/pyppeteer/browser.py +0 -401
- biolib/pyppeteer/pyppeteer/browser_fetcher.py +0 -194
- biolib/pyppeteer/pyppeteer/command.py +0 -22
- biolib/pyppeteer/pyppeteer/connection/__init__.py +0 -242
- biolib/pyppeteer/pyppeteer/connection/cdpsession.py +0 -101
- biolib/pyppeteer/pyppeteer/coverage.py +0 -346
- biolib/pyppeteer/pyppeteer/device_descriptors.py +0 -787
- biolib/pyppeteer/pyppeteer/dialog.py +0 -79
- biolib/pyppeteer/pyppeteer/domworld.py +0 -597
- biolib/pyppeteer/pyppeteer/emulation_manager.py +0 -53
- biolib/pyppeteer/pyppeteer/errors.py +0 -48
- biolib/pyppeteer/pyppeteer/events.py +0 -63
- biolib/pyppeteer/pyppeteer/execution_context.py +0 -156
- biolib/pyppeteer/pyppeteer/frame/__init__.py +0 -299
- biolib/pyppeteer/pyppeteer/frame/frame_manager.py +0 -306
- biolib/pyppeteer/pyppeteer/helpers.py +0 -245
- biolib/pyppeteer/pyppeteer/input.py +0 -371
- biolib/pyppeteer/pyppeteer/jshandle.py +0 -598
- biolib/pyppeteer/pyppeteer/launcher.py +0 -683
- biolib/pyppeteer/pyppeteer/lifecycle_watcher.py +0 -169
- biolib/pyppeteer/pyppeteer/models/__init__.py +0 -103
- biolib/pyppeteer/pyppeteer/models/_protocol.py +0 -12460
- biolib/pyppeteer/pyppeteer/multimap.py +0 -82
- biolib/pyppeteer/pyppeteer/network_manager.py +0 -678
- biolib/pyppeteer/pyppeteer/options.py +0 -8
- biolib/pyppeteer/pyppeteer/page.py +0 -1728
- biolib/pyppeteer/pyppeteer/pipe_transport.py +0 -59
- biolib/pyppeteer/pyppeteer/target.py +0 -147
- biolib/pyppeteer/pyppeteer/task_queue.py +0 -24
- biolib/pyppeteer/pyppeteer/timeout_settings.py +0 -36
- biolib/pyppeteer/pyppeteer/tracing.py +0 -93
- biolib/pyppeteer/pyppeteer/us_keyboard_layout.py +0 -305
- biolib/pyppeteer/pyppeteer/util.py +0 -18
- biolib/pyppeteer/pyppeteer/websocket_transport.py +0 -47
- biolib/pyppeteer/pyppeteer/worker.py +0 -101
- biolib/pyppeteer/pyproject.toml +0 -97
- biolib/pyppeteer/spell.txt +0 -137
- biolib/pyppeteer/tox.ini +0 -72
- biolib/pyppeteer/utils/generate_protocol_types.py +0 -603
- biolib/start_cli.py +0 -7
- biolib/utils.py +0 -47
- biolib/validators/validate_app_version.py +0 -183
- biolib/validators/validate_argument.py +0 -134
- biolib/validators/validate_module.py +0 -323
- biolib/validators/validate_zip_file.py +0 -40
- biolib/validators/validator_utils.py +0 -103
- pybiolib-0.2.951.dist-info/LICENSE +0 -21
- pybiolib-0.2.951.dist-info/METADATA +0 -61
- pybiolib-0.2.951.dist-info/RECORD +0 -153
- pybiolib-0.2.951.dist-info/entry_points.txt +0 -3
- /LICENSE → /pybiolib-1.2.1890.dist-info/licenses/LICENSE +0 -0
biolib/pyppeteer/spell.txt
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webkit
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webpage
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websocket
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workercreated
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zipfile
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biolib/pyppeteer/tox.ini
DELETED
|
@@ -1,72 +0,0 @@
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1
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-
[tox]
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2
|
-
envlist = py3{6,7,8},pre-commit,mypy
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-
minversion = 3.4.0
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4
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isolated_build = True
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5
|
-
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-
[testenv]
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|
-
passenv:
|
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8
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-
PYTEST_ADDOPTS
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|
9
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-
CI*
|
|
10
|
-
MYPY_JUNIT_XML_PATH
|
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-
whitelist_external =
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poetry
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deps =
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py3{6,7,8},mypy: poetry
|
|
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-
skip_install = true
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|
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commands_pre:
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|
-
; mypy config doesn't play well when checking a dir, have to install the package and check it instead
|
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|
-
py3{6,7,8},mypy: poetry install -vv
|
|
19
|
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py3{6,7,8}: poetry run pyppeteer-install
|
|
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|
-
commands =
|
|
21
|
-
py3{6,7,8}: poetry run pytest {posargs}
|
|
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|
-
|
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23
|
-
|
|
24
|
-
[testenv:pre-commit]
|
|
25
|
-
deps = pre-commit
|
|
26
|
-
commands = pre-commit run --all-files --show-diff-on-failure
|
|
27
|
-
|
|
28
|
-
[testenv:mypy]
|
|
29
|
-
passenv = MYPY_JUNIT_XML_PATH
|
|
30
|
-
deps = mypy
|
|
31
|
-
whitelist_externals: poetry
|
|
32
|
-
commands = mypy pyppeteer --config-file ./tox.ini
|
|
33
|
-
|
|
34
|
-
[flake8]
|
|
35
|
-
max-line-length = 120
|
|
36
|
-
exclude = docs,.svn,CVS,.bzr,.hg,.git,__pycache__,.tox,.eggs,*.egg,out
|
|
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|
-
max-complexity = 7
|
|
38
|
-
|
|
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|
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[pydocstyle]
|
|
40
|
-
ignore = D105,D107,D203,D213,D402,D404
|
|
41
|
-
match_dir = (?!(tmp|docs|ja_docs|tests|\.)).*
|
|
42
|
-
|
|
43
|
-
[pytest]
|
|
44
|
-
; default number of workers for testing
|
|
45
|
-
; to change parallelism setting, export the PYTEST_ADDOPTS env variable
|
|
46
|
-
; (no need to change the next line, it's overridden by PYTEST_ADDOPTS)
|
|
47
|
-
;addopts = -n auto ; disabled till we have a good solution for debugging
|
|
48
|
-
timeout = 10
|
|
49
|
-
minversion = 5.0.0
|
|
50
|
-
; nicely formatted junit output for CI builds (must be enabled with flag: --junitxml=PATH)
|
|
51
|
-
junit_suite_name: pyppeteer tests
|
|
52
|
-
junit_log_passing_tests: True
|
|
53
|
-
junit_family = xunit2
|
|
54
|
-
|
|
55
|
-
;mypy config
|
|
56
|
-
;only mypy will be paying attention to this
|
|
57
|
-
;(hence the different env var interpolation format)
|
|
58
|
-
[mypy]
|
|
59
|
-
; this line is currently useless until this PR lands: https://github.com/python/mypy/pull/8479
|
|
60
|
-
junit_xml = $MYPY_JUNIT_XML_PATH
|
|
61
|
-
strict_optional = true
|
|
62
|
-
disallow_untyped_defs = true
|
|
63
|
-
disallow_untyped_calls = true
|
|
64
|
-
follow_imports = silent
|
|
65
|
-
ignore_missing_imports = true
|
|
66
|
-
mypy_path = out
|
|
67
|
-
|
|
68
|
-
[mypy-pyppeteer.tests.*,pyppeteer.docs.*]
|
|
69
|
-
ignore_errors = true
|
|
70
|
-
|
|
71
|
-
[mypy-typing_extensions]
|
|
72
|
-
ignore_missing_imports = true
|