pybiolib 1.1.1874__tar.gz → 1.1.1881__tar.gz

{pybiolib-1.1.1874 → pybiolib-1.1.1881}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pybiolib
-Version: 1.1.1874
+Version: 1.1.1881
 Summary: BioLib Python Client
 Home-page: https://github.com/biolib
 License: MIT

{pybiolib-1.1.1874 → pybiolib-1.1.1881}/biolib/_internal/data_record/data_record.py

@@ -3,16 +3,16 @@ from collections import namedtuple
 from datetime import datetime
 from fnmatch import fnmatch
 from struct import Struct
-from typing import Optional, List, Dict, Union, Callable, cast
+from typing import Callable, Dict, List, Optional, Union, cast
 
 from biolib import lfs
 from biolib._internal.data_record.remote_storage_endpoint import DataRecordRemoteStorageEndpoint
 from biolib._internal.http_client import HttpClient
+from biolib.api import client as api_client
 from biolib.biolib_api_client import AppGetResponse
 from biolib.biolib_binary_format import LazyLoadedFile
 from biolib.biolib_binary_format.utils import RemoteIndexableBuffer
 from biolib.biolib_logging import logger
-from biolib.api import client as api_client
 from biolib.utils.app_uri import parse_app_uri
 from biolib.utils.zip.remote_zip import RemoteZip  # type: ignore
 
@@ -20,7 +20,6 @@ PathFilter = Union[str, Callable[[str], bool]]
 
 
 class DataRecord:
-
     def __init__(self, uri: str):
         self._uri = uri
         uri_parsed = parse_app_uri(uri, use_account_as_name_default=False)
@@ -97,18 +96,21 @@ class DataRecord:
     def _get_file(remote_storage_endpoint: DataRecordRemoteStorageEndpoint, file_info: Dict) -> LazyLoadedFile:
         local_file_header_signature_bytes = b'\x50\x4b\x03\x04'
         local_file_header_struct = Struct('<H2sHHHIIIHH')
-        LocalFileHeader = namedtuple('LocalFileHeader', (
-            'version',
-            'flags',
-            'compression_raw',
-            'mod_time',
-            'mod_date',
-            'crc_32_expected',
-            'compressed_size_raw',
-            'uncompressed_size_raw',
-            'file_name_len',
-            'extra_field_len',
-        ))
+        LocalFileHeader = namedtuple(
+            'LocalFileHeader',
+            (
+                'version',
+                'flags',
+                'compression_raw',
+                'mod_time',
+                'mod_date',
+                'crc_32_expected',
+                'compressed_size_raw',
+                'uncompressed_size_raw',
+                'file_name_len',
+                'extra_field_len',
+            ),
+        )
 
         local_file_header_start = file_info['header_offset'] + len(local_file_header_signature_bytes)
         local_file_header_end = local_file_header_start + local_file_header_struct.size
@@ -120,11 +122,10 @@ class DataRecord:
                 timeout_in_seconds=300,
             )
             local_file_header = LocalFileHeader._make(
-                local_file_header_struct.unpack(local_file_header_response.content))
+                local_file_header_struct.unpack(local_file_header_response.content)
+            )
             file_start: int = (
-                    local_file_header_end +
-                    local_file_header.file_name_len +
-                    local_file_header.extra_field_len
+                local_file_header_end + local_file_header.file_name_len + local_file_header.extra_field_len
             )
             return file_start
 

{pybiolib-1.1.1874 → pybiolib-1.1.1881}/biolib/_internal/http_client.py

@@ -1,25 +1,24 @@
 import json
 import platform
-import time
 import socket
 import ssl
 import subprocess
-import urllib.request
+import time
 import urllib.error
 import urllib.parse
+import urllib.request
 
 from biolib.biolib_logging import logger_no_user_data
-from biolib.typing_utils import Dict, Optional, Union, Literal, cast
+from biolib.typing_utils import Dict, Literal, Optional, Union, cast
+
+_HttpMethod = Literal['GET', 'POST', 'PATCH', 'PUT']
 
 
 def _create_ssl_context():
     context = ssl.create_default_context()
     try:
         if platform.system() == 'Darwin':
-            certificates = subprocess.check_output(
-                "security find-certificate -a -p",
-                shell=True
-            ).decode('utf-8')
+            certificates = subprocess.check_output('security find-certificate -a -p', shell=True).decode('utf-8')
             context.load_verify_locations(cadata=certificates)
     except BaseException:
         pass
@@ -33,7 +32,7 @@ class HttpError(urllib.error.HTTPError):
             code=http_error.code,
             msg=http_error.msg,  # type: ignore
             hdrs=http_error.hdrs,  # type: ignore
-            fp=http_error.fp
+            fp=http_error.fp,
         )
 
     def __str__(self):
@@ -61,12 +60,12 @@ class HttpClient:
 
     @staticmethod
     def request(
-            url: str,
-            method: Optional[Literal['GET', 'POST', 'PATCH', 'PUT']] = None,
-            data: Optional[Union[Dict, bytes]] = None,
-            headers: Optional[Dict[str, str]] = None,
-            retries: int = 5,
-            timeout_in_seconds: Optional[int] = None,
+        url: str,
+        method: Optional[_HttpMethod] = None,
+        data: Optional[Union[Dict, bytes]] = None,
+        headers: Optional[Dict[str, str]] = None,
+        retries: int = 5,
+        timeout_in_seconds: Optional[int] = None,
     ) -> HttpResponse:
         if not HttpClient.ssl_context:
             HttpClient.ssl_context = _create_ssl_context()
@@ -91,9 +90,9 @@ class HttpClient:
                 logger_no_user_data.debug(f'Retrying HTTP {method} request...')
             try:
                 with urllib.request.urlopen(
-                        request,
-                        context=HttpClient.ssl_context,
-                        timeout=timeout_in_seconds,
+                    request,
+                    context=HttpClient.ssl_context,
+                    timeout=timeout_in_seconds,
                 ) as response:
                     return HttpResponse(response)
 

{pybiolib-1.1.1874 → pybiolib-1.1.1881}/biolib/_internal/push_application.py

@@ -1,17 +1,18 @@
 import os
 import re
 from pathlib import Path
-import yaml
+
 import rich.progress
+import yaml
 
-from biolib.lfs.utils import get_iterable_zip_stream, get_files_and_size_of_directory
-from biolib.typing_utils import Optional, Set, TypedDict, Iterable
+from biolib import api, utils
 from biolib.biolib_api_client import BiolibApiClient
-from biolib.biolib_docker_client import BiolibDockerClient
 from biolib.biolib_api_client.biolib_app_api import BiolibAppApi
+from biolib.biolib_docker_client import BiolibDockerClient
 from biolib.biolib_errors import BioLibError
 from biolib.biolib_logging import logger
-from biolib import utils, api
+from biolib.lfs.utils import get_files_and_size_of_directory, get_iterable_zip_stream
+from biolib.typing_utils import Iterable, Optional, Set, TypedDict
 
 REGEX_MARKDOWN_INLINE_IMAGE = re.compile(r'!\[(?P<alt>.*)\]\((?P<src>.*)\)')
 
@@ -38,9 +39,7 @@ def process_docker_status_updates(status_updates: Iterable[DockerStatusUpdate],
                 progress_detail = update['progressDetail']
 
                 if layer_id not in layer_id_to_task_id:
-                    layer_id_to_task_id[layer_id] = progress.add_task(
-                        description=f'[cyan]{action} layer {layer_id}'
-                    )
+                    layer_id_to_task_id[layer_id] = progress.add_task(description=f'[cyan]{action} layer {layer_id}')
 
                 if progress_detail and 'current' in progress_detail and 'total' in progress_detail:
                     progress.update(
@@ -60,7 +59,7 @@ def process_docker_status_updates(status_updates: Iterable[DockerStatusUpdate],
 
 
 def set_app_version_as_active(
-        app_version_uuid: str,
+    app_version_uuid: str,
 ):
     logger.debug(f'Setting app version {app_version_uuid} as active.')
     api.client.patch(
@@ -70,10 +69,10 @@ def set_app_version_as_active(
 
 
 def push_application(
-        app_uri: str,
-        app_path: str,
-        app_version_to_copy_images_from: Optional[str],
-        is_dev_version: Optional[bool],
+    app_uri: str,
+    app_path: str,
+    app_version_to_copy_images_from: Optional[str],
+    is_dev_version: Optional[bool],
 ):
     app_path_absolute = Path(app_path).resolve()
 
@@ -96,7 +95,7 @@ def push_application(
 
     input_files_maps_to_root = False
     try:
-        with open(config_yml_path, mode='r') as config_yml_file:
+        with open(config_yml_path) as config_yml_file:
             config = yaml.safe_load(config_yml_file.read())
 
         license_file_relative_path = config.get('license_file', 'LICENSE')
@@ -109,7 +108,7 @@ def push_application(
             raise BioLibError(f'Could not find {description_file_relative_path}')
 
         zip_filters.add(description_file_relative_path)
-        with open(description_file_absolute_path, mode='r') as description_file:
+        with open(description_file_absolute_path) as description_file:
             description_file_content = description_file.read()
 
         for _, img_src_path in re.findall(REGEX_MARKDOWN_INLINE_IMAGE, description_file_content):
@@ -171,8 +170,9 @@ def push_application(
         author=app['account_handle'],
         set_as_active=False,
         zip_binary=source_files_zip_bytes,
-        app_version_id_to_copy_images_from=app_response['app_version']['public_id'] if app_version_to_copy_images_from
-        else None
+        app_version_id_to_copy_images_from=app_response['app_version']['public_id']
+        if app_version_to_copy_images_from
+        else None,
     )
 
     #  Don't push docker images if copying from another app version
@@ -180,18 +180,6 @@ def push_application(
     if not app_version_to_copy_images_from and docker_tags:
         logger.info('Found docker images to push.')
 
-        try:
-            yaml_file = open(f'{app_path}/.biolib/config.yml', 'r', encoding='utf-8')
-
-        except Exception as error:  # pylint: disable=broad-except
-            raise BioLibError('Could not open the config file .biolib/config.yml') from error
-
-        try:
-            config_data = yaml.safe_load(yaml_file)
-
-        except Exception as error:  # pylint: disable=broad-except
-            raise BioLibError('Could not parse .biolib/config.yml. Please make sure it is valid YAML') from error
-
         # Auth to be sent to proxy
         # The tokens are sent as "{access_token},{job_id}". We leave job_id blank on push.
         tokens = f'{BiolibApiClient.get().access_token},'
@@ -200,14 +188,12 @@ def push_application(
         docker_client = BiolibDockerClient.get_docker_client()
 
         for module_name, repo_and_tag in docker_tags.items():
-            docker_image_definition = config_data['modules'][module_name]['image']
+            docker_image_definition = config['modules'][module_name]['image']
             repo, tag = repo_and_tag.split(':')
 
             if docker_image_definition.startswith('dockerhub://'):
                 docker_image_name = docker_image_definition.replace('dockerhub://', 'docker.io/', 1)
-                logger.info(
-                    f'Pulling image {docker_image_name} defined on module {module_name} from Dockerhub.'
-                )
+                logger.info(f'Pulling image {docker_image_name} defined on module {module_name} from Dockerhub.')
                 dockerhub_repo, dockerhub_tag = docker_image_name.split(':')
                 pull_status_updates: Iterable[DockerStatusUpdate] = docker_client.api.pull(
                     decode=True,
@@ -238,7 +224,7 @@ def push_application(
 
                 process_docker_status_updates(push_status_updates, action='Pushing')
 
-            except Exception as exception:  # pylint: disable=broad-except
+            except Exception as exception:
                 raise BioLibError(f'Failed to tag and push image {docker_image_name}.') from exception
 
             logger.info(f'Successfully pushed {docker_image_name}')
@@ -249,10 +235,9 @@ def push_application(
         data={'set_as_active': not is_dev_version},
     )
 
-    sematic_version = \
-        f"{new_app_version_json['major']}.{new_app_version_json['minor']}.{new_app_version_json['patch']}"
+    sematic_version = f"{new_app_version_json['major']}.{new_app_version_json['minor']}.{new_app_version_json['patch']}"
     logger.info(
         f"Successfully pushed new {'development ' if is_dev_version else ''}version {sematic_version} of {app_uri}."
     )
 
-    return {"app_uri": app_uri, "sematic_version": sematic_version}
+    return {'app_uri': app_uri, 'sematic_version': sematic_version}

{pybiolib-1.1.1874 → pybiolib-1.1.1881}/biolib/_internal/runtime.py

@@ -1,6 +1,7 @@
 import json
-from biolib.typing_utils import TypedDict, Optional, cast
+
 from biolib import api
+from biolib.typing_utils import Optional, TypedDict, cast
 
 
 class RuntimeJobDataDict(TypedDict):
@@ -52,7 +53,7 @@ class Runtime:
     def _try_to_get_job_data() -> Optional[RuntimeJobDataDict]:
         if not Runtime._job_data:
             try:
-                with open('/biolib/secrets/biolib_system_secret', mode='r') as file:
+                with open('/biolib/secrets/biolib_system_secret') as file:
                     job_data: RuntimeJobDataDict = json.load(file)
             except BaseException:
                 return None

{pybiolib-1.1.1874 → pybiolib-1.1.1881}/biolib/runtime/__init__.py

@@ -6,7 +6,7 @@ def set_main_result_prefix(result_prefix: str) -> None:
     warnings.warn(
         'The "biolib.runtime.set_main_result_prefix" function is deprecated. '
         'It will be removed in future releases from mid 2024. '
-        'Please use "biolib.sdk.runtime.set_main_result_prefix" instead.',
+        'Please use "from biolib.sdk import Runtime" and then "Runtime.set_main_result_prefix" instead.',
         DeprecationWarning,
         stacklevel=2,
     )

{pybiolib-1.1.1874 → pybiolib-1.1.1881}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pybiolib"
-version = "1.1.1874"
+version = "1.1.1881"
 description = "BioLib Python Client"
 readme = "README.md"
 license = "MIT"

{pybiolib-1.1.1874 → pybiolib-1.1.1881}/biolib/_internal/utils/__init__.py

@@ -5,8 +5,8 @@ import uuid
 def open_browser_window_from_notebook(url_to_open: str) -> None:
     try:
         from IPython.display import (  # type:ignore # pylint: disable=import-error, import-outside-toplevel
-            display,
             Javascript,
+            display,
             update_display,
         )
     except ImportError as error: