pybiolib 1.2.558__py3-none-any.whl → 1.2.565__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/compute_node/job_worker/executors/docker_executor.py

@@ -201,9 +201,6 @@ class DockerExecutor:
             stream=True,
         )
 
-        logger_no_user_data.debug(f'Running diff for Docker container for {job_uuid}')
-        pre_start_diff = self._container.diff()
-
         logger_no_user_data.debug(f'Starting Docker container for {job_uuid}')
         startup_error_string: Optional[str] = None
         try:
@@ -218,7 +215,6 @@ class DockerExecutor:
         self._metadata_for_save_output_on_cancel = MetadataToSaveOutput(
             arguments=module_input['arguments'],
             startup_error_string=startup_error_string,
-            pre_start_diff=pre_start_diff,
         )
 
         if self._options['job']['app_version'].get('stdout_render_type') != 'markdown':
@@ -264,7 +260,6 @@ class DockerExecutor:
             module_output_path=self._options['module_output_path'],
             stderr=full_stderr,
             stdout=full_stdout,
-            pre_start_diff=metadata['pre_start_diff'],
         )
 
     def cleanup(self):
@@ -532,12 +527,11 @@ class DockerExecutor:
         module_output_path: str,
         stderr: bytes,
         stdout: bytes,
-        pre_start_diff: List[Dict],
     ) -> None:
         mapped_files: List[FileInContainer] = []
         try:
             mappings = Mappings(mappings_list=self._options['module']['output_files_mappings'], arguments=arguments)
-            changed_files: List[FileInContainer] = self._get_changed_files_in_docker_container(pre_start_diff)
+            changed_files: List[FileInContainer] = self._get_changed_files_in_docker_container()
 
             for file in changed_files:
                 if file.is_file():
@@ -602,15 +596,13 @@ class DockerExecutor:
 
         return None
 
-    def _get_changed_files_in_docker_container(self, pre_start_diff: List[Dict]) -> List[FileInContainer]:
+    def _get_changed_files_in_docker_container(self) -> List[FileInContainer]:
         from_mappings = [mapping['from_path'] for mapping in self._options['module']['output_files_mappings']]
-        pre_start_diff_paths = [obj['Path'] for obj in pre_start_diff]
         post_run_diff = self._container.diff()
         run_diff_paths: List[str] = [
             obj['Path']
             for obj in post_run_diff
             if obj['Kind'] in (DockerDiffKind.CHANGED.value, DockerDiffKind.ADDED.value)
-            and obj['Path'] not in pre_start_diff_paths
         ]
 
         known_directories = set()

biolib/compute_node/job_worker/executors/types.py

@@ -46,4 +46,3 @@ class LocalExecutorOptions(TypedDict):
 class MetadataToSaveOutput(TypedDict):
     arguments: List[str]
     startup_error_string: Optional[str]
-    pre_start_diff: List[Dict]

{pybiolib-1.2.558.dist-info → pybiolib-1.2.565.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: pybiolib
-Version: 1.2.558
+Version: 1.2.565
 Summary: BioLib Python Client
 License: MIT
 Keywords: biolib

{pybiolib-1.2.558.dist-info → pybiolib-1.2.565.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
@@ -76,10 +76,10 @@ biolib/compute_node/job_worker/cache_state.py,sha256=MwjSRzcJJ_4jybqvBL4xdgnDYSI
 biolib/compute_node/job_worker/cache_types.py,sha256=ajpLy8i09QeQS9dEqTn3T6NVNMY_YsHQkSD5nvIHccQ,818
 biolib/compute_node/job_worker/docker_image_cache.py,sha256=ansHIkJIq_EMW1nZNlW-RRLVVeKWTbzNICYaOHpKiRE,7460
 biolib/compute_node/job_worker/executors/__init__.py,sha256=bW6t1qi3PZTlHM4quaTLa8EI4ALTCk83cqcVJfJfJfE,145
-biolib/compute_node/job_worker/executors/docker_executor.py,sha256=UxWUSk15mM_H73q2k5_kBB1IWGYGphyXbyC-Bm0QneU,31550
+biolib/compute_node/job_worker/executors/docker_executor.py,sha256=RBBPjxL-zqI77vHWG7ssrFGFSsHVob7TuIMw36URPQ0,31111
 biolib/compute_node/job_worker/executors/docker_types.py,sha256=VhsU1DKtJjx_BbCkVmiPZPH4ROiL1ygW1Y_s1Kbpa2o,216
 biolib/compute_node/job_worker/executors/tars/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-biolib/compute_node/job_worker/executors/types.py,sha256=gw_T-oq0lty8Hg8WsTrqhtV-kyOF_l5nr9Xe8-kzetc,1657
+biolib/compute_node/job_worker/executors/types.py,sha256=wbjWZZ2f9FttjqUCCOeZmn7n3L3Hu-7-2PZJ3BVf_Ps,1626
 biolib/compute_node/job_worker/job_legacy_input_wait_timeout_thread.py,sha256=_cvEiZbOwfkv6fYmfrvdi_FVviIEYr_dSClQcOQaUWM,1198
 biolib/compute_node/job_worker/job_max_runtime_timer_thread.py,sha256=K_xgz7IhiIjpLlXRk8sqaMyLoApcidJkgu29sJX0gb8,1174
 biolib/compute_node/job_worker/job_storage.py,sha256=lScHI3ubcHKagSEW243tgbIWXUfbWDHDjEOPMvXxJE8,4603
@@ -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-1.2.558.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.2.558.dist-info/METADATA,sha256=QO2zAOtRMRujoLhdT7UcWJqp3xx5lssaGVTbpcH2R-M,1570
-pybiolib-1.2.558.dist-info/WHEEL,sha256=XbeZDeTWKc1w7CSIyre5aMDU_-PohRwTQceYnisIYYY,88
-pybiolib-1.2.558.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.2.558.dist-info/RECORD,,
+pybiolib-1.2.565.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.2.565.dist-info/METADATA,sha256=_CM-jsOMgyM_KMENpfQz0auad3iMgTcoiGDKlvfTcC8,1570
+pybiolib-1.2.565.dist-info/WHEEL,sha256=XbeZDeTWKc1w7CSIyre5aMDU_-PohRwTQceYnisIYYY,88
+pybiolib-1.2.565.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.2.565.dist-info/RECORD,,