pybiolib 1.2.520__py3-none-any.whl → 1.2.561__py3-none-any.whl

biolib/__init__.py

@@ -29,6 +29,24 @@ def call_cli() -> None:
 
 
 def load(uri: str) -> _BioLibApp:
+    r"""Load a BioLib application by its URI or website URL.
+
+    Args:
+        uri (str): The URI or website URL of the application to load. Can be either:
+            - App URI (e.g., 'biolib/myapp:1.0.0')
+            - Website URL (e.g., 'https://biolib.com/biolib/myapp/')
+
+    Returns:
+        BioLibApp: The loaded application object
+
+    Example::
+
+        >>> # Load by URI
+        >>> app = biolib.load('biolib/myapp:1.0.0')
+        >>> # Load by website URL
+        >>> app = biolib.load('https://biolib.com/biolib/myapp/')
+        >>> result = app.cli('--help')
+    """
     return _BioLibApp(uri)
 
 
@@ -37,27 +55,126 @@ def search(
         team: Optional[str] = None,
         count: int = 100,
 ) -> List[str]:
+    r"""Search for BioLib applications.
+
+    Args:
+        search_query (str, optional): Search query string
+        team (str, optional): Filter by team name
+        count (int): Maximum number of results to return. Defaults to 100.
+
+    Returns:
+        List[str]: List of application URIs matching the search criteria
+
+    Example::
+
+        >>> # Search all apps
+        >>> apps = biolib.search()
+        >>> # Search by query
+        >>> alignment_apps = biolib.search('alignment')
+        >>> # Search team's apps
+        >>> team_apps = biolib.search(team='myteam')
+    """
     apps: List[str] = search_apps(search_query, team, count)
     return apps
 
 
 def get_job(job_id: str, job_token: Optional[str] = None) -> _Job:
+    r"""Get a job by its ID.
+
+    Args:
+        job_id (str): The UUID of the job to retrieve
+        job_token (str, optional): Authentication token for accessing the job.
+            Only needed for jobs that aren't owned by the current user.
+
+    Returns:
+        Job: The job object
+
+    Example::
+
+        >>> job = biolib.get_job('abc123')
+        >>> # Access shared job
+        >>> job = biolib.get_job('abc123', job_token='xyz789')
+    """
     return _Job.create_from_uuid(uuid=job_id, auth_token=job_token)
 
 
 def get_data_record(uri: str) -> _DataRecord:
+    r"""Get a data record by its URI.
+
+    Args:
+        uri (str): The URI of the data record to retrieve
+
+    Returns:
+        DataRecord: The data record object
+
+    Example::
+
+        >>> record = biolib.get_data_record('biolib/data/sequences:1.0.0')
+    """
     return _DataRecord.get_by_uri(uri)
 
 
 def fetch_jobs(count: int = 25, status: Optional[str] = None) -> List[_Job]:
+    r"""Fetch a list of jobs from the server.
+
+    Args:
+        count (int): Maximum number of jobs to fetch. Defaults to 25.
+        status (str, optional): Filter jobs by status. One of:
+            'in_progress', 'completed', 'failed', 'cancelled'
+
+    Returns:
+        List[Job]: List of job objects matching the criteria
+
+    Example::
+
+        >>> # Get last 10 completed jobs
+        >>> jobs = biolib.fetch_jobs(10, status='completed')
+        >>> # Get last 100 jobs of any status
+        >>> all_jobs = biolib.fetch_jobs(100)
+    """
     return _Job.fetch_jobs(count, status)
 
 
 def fetch_data_records(uri: Optional[str] = None, count: Optional[int] = None) -> List[_DataRecord]:
+    r"""Fetch a list of data records from the server.
+
+    Args:
+        uri (str, optional): Filter records by URI prefix
+        count (int, optional): Maximum number of records to fetch
+
+    Returns:
+        List[DataRecord]: List of data record objects matching the criteria
+
+    Example::
+
+        >>> # Get all records
+        >>> records = biolib.fetch_data_records()
+        >>> # Get records with URI prefix
+        >>> seq_records = biolib.fetch_data_records('biolib/data/sequences')
+    """
     return _DataRecord.fetch(uri, count)
 
 
 def get_experiment(uri: Optional[str] = None, name: Optional[str] = None) -> Experiment:
+    r"""Get an experiment by its URI or name.
+
+    Args:
+        uri (str, optional): The URI of the experiment
+        name (str, optional): The name of the experiment
+
+    Returns:
+        Experiment: The experiment object
+
+    Raises:
+        ValueError: If neither or both uri and name are provided
+
+    Example::
+
+        >>> # Get by URI
+        >>> exp = biolib.get_experiment(uri='biolib/experiments/analysis')
+        >>> # Get by name
+        >>> exp = biolib.get_experiment(name='sequence-analysis')
+    """
     if (not uri and not name) or (uri and name):
         raise ValueError('Must provide either uri or name')
 
@@ -65,10 +182,30 @@ def get_experiment(uri: Optional[str] = None, name: Optional[str] = None) -> Exp
 
 
 def show_jobs(count: int = 25) -> None:
+    r"""Display a table of recent jobs.
+
+    Args:
+        count (int): Maximum number of jobs to display. Defaults to 25.
+
+    Example::
+
+        >>> biolib.show_jobs()  # Show last 25 jobs
+        >>> biolib.show_jobs(100)  # Show last 100 jobs
+    """
     _Job.show_jobs(count=count)
 
 
 def show_experiments(count: int = 25) -> None:
+    r"""Display a table of experiments.
+
+    Args:
+        count (int): Maximum number of experiments to display. Defaults to 25.
+
+    Example::
+
+        >>> biolib.show_experiments()  # Show last 25 experiments
+        >>> biolib.show_experiments(100)  # Show last 100 experiments
+    """
     Experiment.show_experiments(count=count)
 
 
@@ -81,14 +218,39 @@ def sign_out() -> None:
 
 
 def login() -> None:
+    r"""Alias for :func:`sign_in`.
+
+    Example::
+
+        >>> biolib.login()  # Same as biolib.sign_in()
+    """
     sign_in()
 
 
 def logout() -> None:
+    r"""Alias for :func:`sign_out`.
+
+    Example::
+
+        >>> biolib.logout()  # Same as biolib.sign_out()
+    """
     sign_out()
 
 
 def set_api_base_url(api_base_url: str) -> None:
+    r"""Set the base URL for the BioLib API.
+
+    Args:
+        api_base_url (str): The base URL for the BioLib API
+
+    Example::
+
+        >>> biolib.set_api_base_url('https://biolib.com')
+
+    Note:
+        This will also update related configuration like site hostname
+        and environment flags.
+    """
     _BioLibApiClient.initialize(base_url=api_base_url)
     biolib.utils.BIOLIB_BASE_URL = api_base_url
     biolib.utils.BIOLIB_SITE_HOSTNAME = _urlparse(api_base_url).hostname
@@ -98,15 +260,46 @@ def set_api_base_url(api_base_url: str) -> None:
 
 
 def set_base_url(base_url: str) -> None:
+    r"""Alias for :func:`set_api_base_url`.
+
+    Args:
+        base_url (str): The base URL for the BioLib API
+
+    Example::
+
+        >>> biolib.set_base_url('https://biolib.com')
+    """
     return set_api_base_url(base_url)
 
 
 def set_api_token(api_token: str) -> None:
+    r"""Sign in using an API token.
+
+    Args:
+        api_token (str): The API token to authenticate with
+
+    Example::
+
+        >>> biolib.set_api_token('my-api-token')
+        # Signed in using API token
+    """
     api_client = _BioLibApiClient.get()
     api_client.sign_in_with_api_token(api_token)
 
 
 def set_log_level(level: _typing_utils.Union[str, int]) -> None:
+    r"""Set the logging level for BioLib.
+
+    Args:
+        level (Union[str, int]): The log level to use. Can be a string
+            ('DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL') or an integer
+            level from the logging module.
+
+    Example::
+
+        >>> biolib.set_log_level('DEBUG')  # Enable debug logging
+        >>> biolib.set_log_level('WARNING')  # Only show warnings and errors
+    """
     _logger.setLevel(level)
     _logger_no_user_data.setLevel(level)
 

biolib/_internal/types/resource_version.py

@@ -1,7 +1,13 @@
-from .typing import Literal, TypedDict
+from .typing import Literal, NotRequired, TypedDict
 
 
-class ResourceVersionDetailedDict(TypedDict):
+class ResourceVersionDict(TypedDict):
+    uuid: str
     semantic_version: str
     state: Literal['published', 'unpublished']
-    uuid: str
+    created_at: str
+    git_branch_name: NotRequired[str]
+
+
+class ResourceVersionDetailedDict(ResourceVersionDict):
+    pass

biolib/_internal/types/typing.py

@@ -5,3 +5,6 @@ from typing import *  # noqa:F403 pylint: disable=wildcard-import, unused-wildca
 
 if sys.version_info < (3, 8):  # noqa: UP036
     from typing_extensions import Literal, TypedDict  # pylint: disable=unused-import
+
+if sys.version_info < (3, 11):  # noqa: UP036
+    from typing_extensions import NotRequired  # pylint: disable=unused-import

biolib/app/app.py

@@ -108,7 +108,7 @@ class BioLibApp:
                 (utils.STREAM_STDOUT or stream_logs)
                 and (self._app_version.get('main_output_file') or self._app_version.get('stdout_render_type') == 'text')
             )
-            job._stream_logs(enable_print=enable_print) # pylint: disable=protected-access
+            job._stream_logs(enable_print=enable_print)  # pylint: disable=protected-access
 
             if check:
                 exit_code = job.get_exit_code()

{pybiolib-1.2.520.dist-info → pybiolib-1.2.561.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: pybiolib
-Version: 1.2.520
+Version: 1.2.561
 Summary: BioLib Python Client
 License: MIT
 Keywords: biolib
@@ -26,7 +26,7 @@ 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 (>=3.10.0) ; python_version < "3.8"
+Requires-Dist: typing-extensions (>=4.1.0) ; python_version < "3.11"
 Project-URL: Homepage, https://github.com/biolib
 Description-Content-Type: text/markdown
 

{pybiolib-1.2.520.dist-info → pybiolib-1.2.561.dist-info}/RECORD

@@ -1,4 +1,4 @@
-biolib/__init__.py,sha256=4Rfa0AJKztqkCG5D67kFgSwdOUiBTa5HkAzIOqHNREU,4431
+biolib/__init__.py,sha256=nPgMXXoJ4wqGwDqMgwtAYrw_-GVMdaWwKemOpRKKljU,9774
 biolib/_data_record/data_record.py,sha256=zKvnh5T-dIVY46-kgVzMBoZ666ZhcTCFQnWvZT0D6RM,12026
 biolib/_internal/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biolib/_internal/data_record/__init__.py,sha256=fGdME6JGRU_2VxpJbYpGXYndjN-feUkmKY4fuMyq3cg,76
@@ -21,15 +21,15 @@ biolib/_internal/types/data_record.py,sha256=9r_vdhVs60YTnzU4XQFXfDrfS2P2MqD3BH2
 biolib/_internal/types/experiment.py,sha256=D94iBdn2nS92lRW-TOs1a2WKXJD5ZtmzL4ypggKX2ys,176
 biolib/_internal/types/file_node.py,sha256=T6BIqo662f3nwMBRqtBHYsg6YuuUaKpiokHcVjv9_ME,283
 biolib/_internal/types/resource.py,sha256=uUI9Rt5ehkXv9NEDW9zsaPXiTXxnj811rSUW3g_joJw,437
-biolib/_internal/types/resource_version.py,sha256=sLxViYXloDDUhTDFgjegiQCj097OM1Ih1-uqlC_4ULA,174
-biolib/_internal/types/typing.py,sha256=D4EKKEe7kDx0K6lJi-H_XLtk-8w6nu2fdqn9bvzI-Xo,288
+biolib/_internal/types/resource_version.py,sha256=cU0YFHqxO-wX_Y6CoeK0Iei61gFwVoyR_kPOSTQ4mCs,304
+biolib/_internal/types/typing.py,sha256=qrsk8hHcGEbDpU1QQFzHAKnhQxkMe7uJ6pxHeAnfv1Y,414
 biolib/_internal/utils/__init__.py,sha256=p5vsIFyu-zYqBgdSMfwW9NC_jk7rXvvCbV4Bzd3As7c,630
 biolib/_internal/utils/multinode.py,sha256=-J3PEAK3NaOwCn--5T7vWHkA3yu5w9QhmuhkQcH-2wY,8229
 biolib/_runtime/runtime.py,sha256=bZQ0m39R9jOBVAtlyvzDnOobKueOAQUCwMUZjDQnO7E,4439
 biolib/api/__init__.py,sha256=mQ4u8FijqyLzjYMezMUUbbBGNB3iFmkNdjXnWPZ7Jlw,138
 biolib/api/client.py,sha256=EN3lDbbgWxw3aPDe8W5XIU6WkMfOHW7Dmsz-R6QqxAw,4176
 biolib/app/__init__.py,sha256=cdPtcfb_U-bxb9iSL4fCEq2rpD9OjkyY4W-Zw60B0LI,37
-biolib/app/app.py,sha256=U7PzLxDjYc73ZVcL1f-hKgwdroLqyvE0TiDa5xK0kzM,9621
+biolib/app/app.py,sha256=-Ed4wV3RSMIq7DgQqCHkzkooyr2RRzoUuOAtJRl3E5E,9622
 biolib/app/search_apps.py,sha256=K4a41f5XIWth2BWI7OffASgIsD0ko8elCax8YL2igaY,1470
 biolib/biolib_api_client/__init__.py,sha256=E5EMa19wJoblwSdQPYrxc_BtIeRsAuO0L_jQweWw-Yk,182
 biolib/biolib_api_client/api_client.py,sha256=ohvbWbpresxLHFGPkvXACfmiTYsBk8RBx5XsBbLYg_M,7546
@@ -119,8 +119,8 @@ biolib/utils/cache_state.py,sha256=u256F37QSRIVwqKlbnCyzAX4EMI-kl6Dwu6qwj-Qmag,3
 biolib/utils/multipart_uploader.py,sha256=XvGP1I8tQuKhAH-QugPRoEsCi9qvbRk-DVBs5PNwwJo,8452
 biolib/utils/seq_util.py,sha256=Ozk0blGtPur_D9MwShD02r_mphyQmgZkx-lOHOwnlIM,6730
 biolib/utils/zip/remote_zip.py,sha256=0wErYlxir5921agfFeV1xVjf29l9VNgGQvNlWOlj2Yc,23232
-pybiolib-1.2.520.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.2.520.dist-info/METADATA,sha256=P8QqYdoshoaytFWMOg3byel-wiDde7-iS7YnHgSiYag,1570
-pybiolib-1.2.520.dist-info/WHEEL,sha256=XbeZDeTWKc1w7CSIyre5aMDU_-PohRwTQceYnisIYYY,88
-pybiolib-1.2.520.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.2.520.dist-info/RECORD,,
+pybiolib-1.2.561.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.2.561.dist-info/METADATA,sha256=vK5utD-3vpUDsQfgH-j7GEhFqqRpCmHWxS1D7uz3jRM,1570
+pybiolib-1.2.561.dist-info/WHEEL,sha256=XbeZDeTWKc1w7CSIyre5aMDU_-PohRwTQceYnisIYYY,88
+pybiolib-1.2.561.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.2.561.dist-info/RECORD,,