pybiolib 1.2.883__py3-none-any.whl → 1.2.1890__py3-none-any.whl

biolib/utils/multipart_uploader.py

@@ -10,7 +10,7 @@ from biolib._internal.http_client import HttpClient
 from biolib.biolib_api_client import BiolibApiClient
 from biolib.biolib_errors import BioLibError
 from biolib.biolib_logging import logger, logger_no_user_data
-from biolib.typing_utils import TypedDict, List, Iterator, Tuple, Optional, Dict
+from biolib.typing_utils import Callable, Dict, Iterator, List, Optional, Tuple, TypedDict
 
 
 def get_chunk_iterator_from_bytes(byte_buffer: bytes, chunk_size_in_bytes: int = 50_000_000) -> Iterator[bytes]:
@@ -45,19 +45,20 @@ _UploadChunkReturnType = Tuple[_PartMetadata, int]
 
 
 class MultiPartUploader:
-
     def __init__(
-            self,
-            complete_upload_request: RequestOptions,
-            get_presigned_upload_url_request: RequestOptions,
-            start_multipart_upload_request: Optional[RequestOptions] = None,
-            use_process_pool: Optional[bool] = None,
+        self,
+        complete_upload_request: RequestOptions,
+        get_presigned_upload_url_request: RequestOptions,
+        start_multipart_upload_request: Optional[RequestOptions] = None,
+        use_process_pool: Optional[bool] = None,
+        on_progress: Optional[Callable[[int, int], None]] = None,
     ):
         self._complete_upload_request = complete_upload_request
         self._get_presigned_upload_url_request = get_presigned_upload_url_request
         self._start_multipart_upload_request = start_multipart_upload_request
         self._bytes_uploaded: int = 0
         self._use_process_pool = use_process_pool
+        self._on_progress = on_progress
 
     def upload(self, payload_iterator: Iterator[bytes], payload_size_in_bytes: int) -> None:
         parts: List[_PartMetadata] = []
@@ -85,21 +86,22 @@ class MultiPartUploader:
                 self._update_progress_bar_and_parts(
                     upload_chunk_response=upload_chunk_response,
                     parts=parts,
-                    payload_size_in_bytes=payload_size_in_bytes
+                    payload_size_in_bytes=payload_size_in_bytes,
                 )
         else:
             # use 16 cores, unless less is available
             pool_size = min(16, multiprocessing.cpu_count() - 1)
-            process_pool = multiprocessing.Pool(pool_size) if self._use_process_pool else \
-                multiprocessing.pool.ThreadPool(pool_size)
+            process_pool = (
+                multiprocessing.Pool(pool_size)
+                if self._use_process_pool
+                else multiprocessing.pool.ThreadPool(pool_size)
+            )
 
             try:
                 response: _UploadChunkReturnType
                 for response in process_pool.imap(self._upload_chunk, iterator_with_index):
                     self._update_progress_bar_and_parts(
-                        upload_chunk_response=response,
-                        parts=parts,
-                        payload_size_in_bytes=payload_size_in_bytes
+                        upload_chunk_response=response, parts=parts, payload_size_in_bytes=payload_size_in_bytes
                     )
             finally:
                 logger_no_user_data.debug('Multipart upload closing process pool...')
@@ -148,8 +150,9 @@ class MultiPartUploader:
                     if app_caller_proxy_job_storage_base_url:
                         # Done to hit App Caller Proxy when uploading result from inside an app
                         parsed_url = urlparse(presigned_upload_url)
-                        presigned_upload_url = \
+                        presigned_upload_url = (
                             f'{app_caller_proxy_job_storage_base_url}{parsed_url.path}?{parsed_url.query}'
+                        )
 
                     put_chunk_response = HttpClient.request(
                         url=presigned_upload_url,
@@ -169,10 +172,10 @@ class MultiPartUploader:
         raise BioLibError(f'Max retries hit, when uploading part {part_number}. Exiting...')
 
     def _update_progress_bar_and_parts(
-            self,
-            upload_chunk_response: _UploadChunkReturnType,
-            parts: List[_PartMetadata],
-            payload_size_in_bytes: int,
+        self,
+        upload_chunk_response: _UploadChunkReturnType,
+        parts: List[_PartMetadata],
+        payload_size_in_bytes: int,
     ) -> None:
         part_metadata, chunk_byte_length = upload_chunk_response
         part_number = part_metadata['PartNumber']
@@ -180,6 +183,9 @@ class MultiPartUploader:
         parts.append(part_metadata)
         self._bytes_uploaded += chunk_byte_length
 
+        if self._on_progress is not None:
+            self._on_progress(self._bytes_uploaded, payload_size_in_bytes)
+
         approx_progress_percent = min(self._bytes_uploaded / (payload_size_in_bytes + 1) * 100, 100)
         approx_rounded_progress = round(approx_progress_percent, 2)
         logger_no_user_data.debug(

biolib/utils/seq_util.py

@@ -9,7 +9,7 @@ class SeqUtilRecord:
         self,
         sequence: str,
         sequence_id: str,
-        description: Optional['str'],
+        description: Optional['str'] = None,
         properties: Optional[Dict[str, str]] = None,
     ):
         self.sequence = sequence

pybiolib-1.2.1890.dist-info/METADATA

@@ -0,0 +1,41 @@
+Metadata-Version: 2.4
+Name: pybiolib
+Version: 1.2.1890
+Summary: BioLib Python Client
+Project-URL: Homepage, https://github.com/biolib
+Author-email: biolib <hello@biolib.com>
+License-Expression: MIT
+License-File: LICENSE
+Keywords: biolib
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.6.3
+Requires-Dist: appdirs>=1.4.3
+Requires-Dist: click>=8.0.0
+Requires-Dist: docker>=5.0.3
+Requires-Dist: importlib-metadata>=1.6.1
+Requires-Dist: pyyaml>=5.3.1
+Requires-Dist: rich>=12.4.4
+Requires-Dist: typing-extensions>=4.1.0; python_version < '3.11'
+Provides-Extra: compute-node
+Requires-Dist: flask>=2.0.1; extra == 'compute-node'
+Requires-Dist: gunicorn>=20.1.0; extra == 'compute-node'
+Description-Content-Type: text/markdown
+
+# PyBioLib
+
+PyBioLib is a Python package for running BioLib applications from Python scripts and the command line.
+
+### Python Example
+```python
+# pip3 install -U pybiolib
+import biolib
+samtools = biolib.load('samtools/samtools')
+print(samtools.cli(args='--help'))
+```
+
+### Command Line Example
+```bash
+pip3 install -U pybiolib
+biolib run samtools/samtools --help
+```

pybiolib-1.2.1890.dist-info/RECORD

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+pybiolib-1.2.1890.dist-info/entry_points.txt,sha256=YtPvuWP8ukZ3WwWH5_hQ6UGW6nDi54rcW2_bGQnbG7M,43
+pybiolib-1.2.1890.dist-info/licenses/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.2.1890.dist-info/RECORD,,

{pybiolib-1.2.883.dist-info → pybiolib-1.2.1890.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 2.1.3
+Generator: hatchling 1.28.0
 Root-Is-Purelib: true
 Tag: py3-none-any

pybiolib-1.2.1890.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+biolib = biolib:call_cli

biolib/_internal/llm_instructions/.github/instructions/style-react-ts.instructions.md

@@ -1,22 +0,0 @@
----
-applyTo: "**/*.ts,**/*.tsx"
----
-
-Apply the [general coding guidelines](./style-general.instructions.md) to all code.
-
-# General Project Guidelines
-- Use yarn instead of npm whenever relevant.
-- Prefer using `export default function` over exporting at the end of the file.
-
-# TypeScript Guidelines
-- Use TypeScript for all new code
-- Follow functional programming principles where possible
-- Use interfaces for data structures prefixed with I like `interface IRecord`
-- Prefer immutable data (const, readonly)
-- Use optional chaining (?.) and nullish coalescing (??) operators
-
-# React Guidelines
-- Use functional components with hooks
-- Follow the React hooks rules (no conditional hooks)
-- Prefer one component per file
-- Use Tailwindcss for styling

biolib/_internal/templates/init_template/.gitignore

@@ -1,2 +0,0 @@
-*__pycache__*
-*.pyc

biolib/_internal/types/__init__.py

@@ -1,6 +0,0 @@
-from .app import *  # noqa: F403
-from .data_record import *  # noqa: F403
-from .experiment import *  # noqa: F403
-from .resource import *  # noqa: F403
-from .resource_permission import *  # noqa: F403
-from .resource_version import *  # noqa: F403

biolib/_internal/types/resource.py

@@ -1,18 +0,0 @@
-from .app import AppSlimDict
-from .data_record import DataRecordSlimDict
-from .experiment import DeprecatedExperimentDict
-from .typing import Optional, TypedDict
-
-
-class ResourceDict(TypedDict):
-    uuid: str
-    uri: str
-    name: str
-    created_at: str
-    description: str
-
-
-class ResourceDetailedDict(ResourceDict):
-    app: Optional[AppSlimDict]
-    data_record: Optional[DataRecordSlimDict]
-    experiment: Optional[DeprecatedExperimentDict]

biolib/biolib_download_container.py

@@ -1,38 +0,0 @@
-from typing import Iterable
-from biolib.app import BioLibApp
-from biolib.biolib_api_client import JobState
-from biolib.biolib_docker_client import BiolibDockerClient
-from biolib.biolib_logging import logger
-from biolib._internal.push_application import DockerStatusUpdate, process_docker_status_updates
-from biolib.biolib_api_client.biolib_job_api import BiolibJobApi
-
-
-def download_container_from_uri(uri: str) -> None:
-    docker_client = BiolibDockerClient.get_docker_client()
-    app = BioLibApp(uri=uri)
-    job_response = BiolibJobApi.create(app_version_id=app.version["public_id"])
-    job_uuid = job_response["uuid"]
-    auth_config = {'username': 'biolib', 'password': f',{job_uuid}'}
-    try:
-        docker_image_uri = job_response["app_version"]["modules"][0]["absolute_image_uri"]
-
-        logger.info(msg=f"Pulling Docker image for {uri}...")
-
-        repo, tag = docker_image_uri.split(':')
-        pull_status_updates: Iterable[DockerStatusUpdate] = docker_client.api.pull(
-            decode=True,
-            repository=repo,
-            stream=True,
-            tag=tag,
-            auth_config=auth_config
-        )
-        process_docker_status_updates(status_updates=pull_status_updates, action='Pulling')
-        image = docker_client.images.get(docker_image_uri)
-        app_uri_repo, app_uri_tag = app.uri.lower().split(':')
-        image.tag(repository=app_uri_repo, tag=app_uri_tag)
-        docker_client.images.remove(docker_image_uri, force=True)
-        BiolibJobApi.update_state(job_uuid=job_response["public_id"], state=JobState.COMPLETED)
-
-    except Exception as error:
-        logger.error(msg=f"Could not pull Docker image for {uri} due to {error}")
-        BiolibJobApi.update_state(job_uuid=job_response["public_id"], state=JobState.FAILED)

biolib/cli/download_container.py

@@ -1,14 +0,0 @@
-import logging
-
-import click
-
-from biolib.biolib_download_container import download_container_from_uri
-from biolib.biolib_logging import logger, logger_no_user_data
-
-
-@click.command(help='Pull an application from BioLib', name='download-container', hidden=True)
-@click.argument('uri')
-def download_container(uri: str) -> None:
-    logger.configure(default_log_level=logging.INFO)
-    logger_no_user_data.configure(default_log_level=logging.INFO)
-    download_container_from_uri(uri)

biolib/utils/app_uri.py

@@ -1,57 +0,0 @@
-import re
-
-from biolib.biolib_errors import BioLibError
-from biolib.typing_utils import TypedDict, Optional
-
-
-class SemanticVersion(TypedDict):
-    major: int
-    minor: int
-    patch: int
-
-
-class AppUriParsed(TypedDict):
-    account_handle_normalized: str
-    app_name_normalized: Optional[str]
-    app_name: Optional[str]
-    resource_name_prefix: Optional[str]
-    version: Optional[SemanticVersion]
-
-
-def normalize(string: str) -> str:
-    return string.replace('-', '_').lower()
-
-
-# Mainly copied from backend
-def parse_app_uri(uri: str, use_account_as_name_default: bool = True) -> AppUriParsed:
-    uri_regex = r'^(@(?P<resource_name_prefix>[\w._-]+)/)?(?P<account_handle>[\w-]+)(/(?P<app_name>[\w-]+))?' \
-                r'(:(?P<version>(?P<major>0|[1-9]\d*)\.(?P<minor>0|[1-9]\d*)\.(?P<patch>0|[1-9]\d*)))?$'
-
-    uri_without_trailing_asterisk_version = uri[:-2] if uri.endswith(':*') else uri
-    matches = re.search(uri_regex, uri_without_trailing_asterisk_version)
-    if matches is None:
-        raise BioLibError(f"Could not parse app uri '{uri}', uri did not match regex")
-
-    resource_name_prefix: Optional[str] = matches.group('resource_name_prefix')
-    account_handle_normalized: str = normalize(matches.group('account_handle'))
-    app_name: Optional[str] = matches.group('app_name')
-
-    # Default to account_handle if app_name is not supplied
-    if app_name:
-        app_name_normalized = normalize(app_name)
-    elif use_account_as_name_default:
-        app_name_normalized = account_handle_normalized
-    else:
-        app_name_normalized = None
-
-    return AppUriParsed(
-        resource_name_prefix=resource_name_prefix.lower() if resource_name_prefix is not None else 'biolib.com',
-        account_handle_normalized=account_handle_normalized,
-        app_name_normalized=app_name_normalized,
-        app_name=app_name if app_name is not None or not use_account_as_name_default else account_handle_normalized,
-        version=None if not matches.group('version') else SemanticVersion(
-            major=int(matches.group('major')),
-            minor=int(matches.group('minor')),
-            patch=int(matches.group('patch')),
-        )
-    )

pybiolib-1.2.883.dist-info/METADATA

@@ -1,50 +0,0 @@
-Metadata-Version: 2.3
-Name: pybiolib
-Version: 1.2.883
-Summary: BioLib Python Client
-License: MIT
-Keywords: biolib
-Author: biolib
-Author-email: hello@biolib.com
-Requires-Python: >=3.6.3,<4.0.0
-Classifier: License :: OSI Approved :: MIT License
-Classifier: Operating System :: OS Independent
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.7
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-Classifier: Programming Language :: Python :: 3.13
-Provides-Extra: compute-node
-Requires-Dist: appdirs (>=1.4.3)
-Requires-Dist: click (>=8.0.0)
-Requires-Dist: docker (>=5.0.3)
-Requires-Dist: flask (>=2.0.1) ; extra == "compute-node"
-Requires-Dist: gunicorn (>=20.1.0) ; extra == "compute-node"
-Requires-Dist: importlib-metadata (>=1.6.1)
-Requires-Dist: pyyaml (>=5.3.1)
-Requires-Dist: rich (>=12.4.4)
-Requires-Dist: typing-extensions (>=4.1.0) ; python_version < "3.11"
-Project-URL: Homepage, https://github.com/biolib
-Description-Content-Type: text/markdown
-
-# PyBioLib
-
-PyBioLib is a Python package for running BioLib applications from Python scripts and the command line.
-
-### Python Example
-```python
-# pip3 install -U pybiolib
-import biolib
-samtools = biolib.load('samtools/samtools')
-print(samtools.cli(args='--help'))
-```
-
-### Command Line Example
-```bash
-pip3 install -U pybiolib
-biolib run samtools/samtools --help
-```
-