pybiolib 1.2.558__tar.gz → 1.2.565__tar.gz

{pybiolib-1.2.558 → pybiolib-1.2.565}/PKG-INFO

@@ -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-1.2.565/biolib/__init__.py

@@ -0,0 +1,338 @@
+# Imports to hide
+import os
+from urllib.parse import urlparse as _urlparse
+
+from biolib import typing_utils as _typing_utils
+from biolib.app import BioLibApp as _BioLibApp
+# TODO: Fix ignore of type
+from biolib.app.search_apps import search_apps  # type: ignore
+from biolib.biolib_errors import BioLibError
+from biolib.biolib_logging import logger as _logger, logger_no_user_data as _logger_no_user_data
+from biolib.experiments.experiment import Experiment
+from biolib.biolib_api_client import BiolibApiClient as _BioLibApiClient, App
+from biolib.jobs import Job as _Job
+from biolib import user as _user
+from biolib.typing_utils import List, Optional, cast as _cast
+from biolib._data_record.data_record import DataRecord as _DataRecord
+
+import biolib.api
+import biolib.app
+import biolib.cli
+import biolib.sdk
+import biolib.utils
+
+
+# ------------------------------------ Function definitions for public Python API ------------------------------------
+
+def call_cli() -> None:
+    biolib.cli.cli()
+
+
+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)
+
+
+def search(
+        search_query: Optional[str] = None,
+        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')
+
+    return Experiment.get_by_uri(uri=_cast(str, uri or name))
+
+
+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)
+
+
+def sign_in() -> None:
+    _user.sign_in()
+
+
+def sign_out() -> None:
+    _user.sign_out()
+
+
+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
+    biolib.utils.BASE_URL_IS_PUBLIC_BIOLIB = api_base_url.endswith('biolib.com') or (
+            os.environ.get('BIOLIB_ENVIRONMENT_IS_PUBLIC_BIOLIB', '').upper() == 'TRUE'
+    )
+
+
+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)
+
+
+def _configure_requests_certificates():
+    if os.getenv('REQUESTS_CA_BUNDLE'):
+        if not os.getenv('SSL_CERT_FILE'):
+            # set SSL_CERT_FILE to urllib use same certs
+            os.environ['SSL_CERT_FILE'] = os.getenv('REQUESTS_CA_BUNDLE')
+        return  # don't change REQUESTS_CA_BUNDLE if manually configured
+
+    certs_to_check = [
+        '/etc/ssl/certs/ca-certificates.crt',
+        '/etc/pki/tls/certs/ca-bundle.crt',
+        '/etc/ssl/ca-bundle.pem',
+        '/etc/pki/tls/cacert.pem',
+        '/etc/pki/ca-trust/extracted/pem/tls-ca-bundle.pem',
+        '/etc/ssl/cert.pem',
+    ]
+
+    for cert in certs_to_check:
+        if os.path.exists(cert):
+            os.environ['REQUESTS_CA_BUNDLE'] = cert
+            if not os.getenv('SSL_CERT_FILE'):
+                os.environ['SSL_CERT_FILE'] = cert
+            return
+
+
+# -------------------------------------------------- Configuration ---------------------------------------------------
+__version__ = biolib.utils.BIOLIB_PACKAGE_VERSION
+_DEFAULT_LOG_LEVEL = 'INFO' if biolib.utils.IS_RUNNING_IN_NOTEBOOK else 'WARNING'
+_logger.configure(default_log_level=_DEFAULT_LOG_LEVEL)
+_logger_no_user_data.configure(default_log_level=_DEFAULT_LOG_LEVEL)
+_configure_requests_certificates()
+
+set_api_base_url(biolib.utils.load_base_url_from_env())

{pybiolib-1.2.558 → pybiolib-1.2.565}/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()

{pybiolib-1.2.558 → pybiolib-1.2.565}/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 → pybiolib-1.2.565}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pybiolib"
-version = "1.2.558"
+version = "1.2.565"
 description = "BioLib Python Client"
 readme = "PYPI_README.md"
 license = "MIT"

pybiolib-1.2.558/biolib/__init__.py

@@ -1,145 +0,0 @@
-# Imports to hide
-import os
-from urllib.parse import urlparse as _urlparse
-
-from biolib import typing_utils as _typing_utils
-from biolib.app import BioLibApp as _BioLibApp
-# TODO: Fix ignore of type
-from biolib.app.search_apps import search_apps  # type: ignore
-from biolib.biolib_errors import BioLibError
-from biolib.biolib_logging import logger as _logger, logger_no_user_data as _logger_no_user_data
-from biolib.experiments.experiment import Experiment
-from biolib.biolib_api_client import BiolibApiClient as _BioLibApiClient, App
-from biolib.jobs import Job as _Job
-from biolib import user as _user
-from biolib.typing_utils import List, Optional, cast as _cast
-from biolib._data_record.data_record import DataRecord as _DataRecord
-
-import biolib.api
-import biolib.app
-import biolib.cli
-import biolib.sdk
-import biolib.utils
-
-
-# ------------------------------------ Function definitions for public Python API ------------------------------------
-
-def call_cli() -> None:
-    biolib.cli.cli()
-
-
-def load(uri: str) -> _BioLibApp:
-    return _BioLibApp(uri)
-
-
-def search(
-        search_query: Optional[str] = None,
-        team: Optional[str] = None,
-        count: int = 100,
-) -> List[str]:
-    apps: List[str] = search_apps(search_query, team, count)
-    return apps
-
-
-def get_job(job_id: str, job_token: Optional[str] = None) -> _Job:
-    return _Job.create_from_uuid(uuid=job_id, auth_token=job_token)
-
-
-def get_data_record(uri: str) -> _DataRecord:
-    return _DataRecord.get_by_uri(uri)
-
-
-def fetch_jobs(count: int = 25, status: Optional[str] = None) -> List[_Job]:
-    return _Job.fetch_jobs(count, status)
-
-
-def fetch_data_records(uri: Optional[str] = None, count: Optional[int] = None) -> List[_DataRecord]:
-    return _DataRecord.fetch(uri, count)
-
-
-def get_experiment(uri: Optional[str] = None, name: Optional[str] = None) -> Experiment:
-    if (not uri and not name) or (uri and name):
-        raise ValueError('Must provide either uri or name')
-
-    return Experiment.get_by_uri(uri=_cast(str, uri or name))
-
-
-def show_jobs(count: int = 25) -> None:
-    _Job.show_jobs(count=count)
-
-
-def show_experiments(count: int = 25) -> None:
-    Experiment.show_experiments(count=count)
-
-
-def sign_in() -> None:
-    _user.sign_in()
-
-
-def sign_out() -> None:
-    _user.sign_out()
-
-
-def login() -> None:
-    sign_in()
-
-
-def logout() -> None:
-    sign_out()
-
-
-def set_api_base_url(api_base_url: str) -> None:
-    _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
-    biolib.utils.BASE_URL_IS_PUBLIC_BIOLIB = api_base_url.endswith('biolib.com') or (
-            os.environ.get('BIOLIB_ENVIRONMENT_IS_PUBLIC_BIOLIB', '').upper() == 'TRUE'
-    )
-
-
-def set_base_url(base_url: str) -> None:
-    return set_api_base_url(base_url)
-
-
-def set_api_token(api_token: str) -> None:
-    api_client = _BioLibApiClient.get()
-    api_client.sign_in_with_api_token(api_token)
-
-
-def set_log_level(level: _typing_utils.Union[str, int]) -> None:
-    _logger.setLevel(level)
-    _logger_no_user_data.setLevel(level)
-
-
-def _configure_requests_certificates():
-    if os.getenv('REQUESTS_CA_BUNDLE'):
-        if not os.getenv('SSL_CERT_FILE'):
-            # set SSL_CERT_FILE to urllib use same certs
-            os.environ['SSL_CERT_FILE'] = os.getenv('REQUESTS_CA_BUNDLE')
-        return  # don't change REQUESTS_CA_BUNDLE if manually configured
-
-    certs_to_check = [
-        '/etc/ssl/certs/ca-certificates.crt',
-        '/etc/pki/tls/certs/ca-bundle.crt',
-        '/etc/ssl/ca-bundle.pem',
-        '/etc/pki/tls/cacert.pem',
-        '/etc/pki/ca-trust/extracted/pem/tls-ca-bundle.pem',
-        '/etc/ssl/cert.pem',
-    ]
-
-    for cert in certs_to_check:
-        if os.path.exists(cert):
-            os.environ['REQUESTS_CA_BUNDLE'] = cert
-            if not os.getenv('SSL_CERT_FILE'):
-                os.environ['SSL_CERT_FILE'] = cert
-            return
-
-
-# -------------------------------------------------- Configuration ---------------------------------------------------
-__version__ = biolib.utils.BIOLIB_PACKAGE_VERSION
-_DEFAULT_LOG_LEVEL = 'INFO' if biolib.utils.IS_RUNNING_IN_NOTEBOOK else 'WARNING'
-_logger.configure(default_log_level=_DEFAULT_LOG_LEVEL)
-_logger_no_user_data.configure(default_log_level=_DEFAULT_LOG_LEVEL)
-_configure_requests_certificates()
-
-set_api_base_url(biolib.utils.load_base_url_from_env())