sl-shared-assets 1.0.0rc14__py3-none-any.whl → 1.0.0rc15__py3-none-any.whl

sl_shared_assets/tools/__init__.py

@@ -0,0 +1,8 @@
+"""This package provides helper tools used to automate routine operations, such as transferring or verifying the
+integrity of the data. The tools from this package are used by most other data processing libraries in the lab."""
+
+from .transfer_tools import transfer_directory
+from .ascension_tools import ascend_tyche_data
+from .packaging_tools import calculate_directory_checksum
+
+__all__ = ["transfer_directory", "calculate_directory_checksum", "ascend_tyche_data"]

sl_shared_assets/tools/__init__.pyi

@@ -0,0 +1,5 @@
+from .transfer_tools import transfer_directory as transfer_directory
+from .ascension_tools import ascend_tyche_data as ascend_tyche_data
+from .packaging_tools import calculate_directory_checksum as calculate_directory_checksum
+
+__all__ = ["transfer_directory", "calculate_directory_checksum", "ascend_tyche_data"]

sl_shared_assets/{ascension_tools.py → tools/ascension_tools.py}

@@ -1,6 +1,7 @@
 """This module provides tools for translating ('ascending') old Tyche data to use the modern data structure used in the
 Sun lab. The tools from this module will not work for any other data and also assume that the Tyche data has been
-preprocessed with an early version of the Sun lab mesoscope processing pipeline."""
+preprocessed with an early version of the Sun lab mesoscope processing pipeline. However, this module can be used as
+an example for how to convert other data formats to match use the Sun lab data structure."""
 
 from pathlib import Path
 import datetime
@@ -10,7 +11,7 @@ import numpy as np
 from ataraxis_base_utilities import LogLevel, console
 from ataraxis_time.time_helpers import extract_timestamp_from_bytes
 
-from .data_classes import SessionData, ProjectConfiguration
+from ..data_classes import SessionData, ProjectConfiguration
 from .transfer_tools import transfer_directory
 from .packaging_tools import calculate_directory_checksum
 

sl_shared_assets/{ascension_tools.pyi → tools/ascension_tools.pyi}

@@ -1,6 +1,6 @@
 from pathlib import Path
 
-from .data_classes import (
+from ..data_classes import (
     SessionData as SessionData,
     ProjectConfiguration as ProjectConfiguration,
 )

{sl_shared_assets-1.0.0rc14.dist-info → sl_shared_assets-1.0.0rc15.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: sl-shared-assets
-Version: 1.0.0rc14
+Version: 1.0.0rc15
 Summary: Stores assets shared between multiple Sun (NeuroAI) lab data pipelines.
 Project-URL: Homepage, https://github.com/Sun-Lab-NBB/sl-shared-assets
 Project-URL: Documentation, https://sl-shared-assets-api-docs.netlify.app/

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sl_shared_assets/server.py

@@ -1,300 +0,0 @@
-"""This module provides the tools for working with the Sun lab BioHPC cluster. Specifically, the classes from this
-module establish an API for submitting jobs to the shared data processing cluster (managed via SLURM) and monitoring
-the running job status. All lab processing and analysis pipelines use this interface for accessing shared compute
-resources.
-"""
-
-import re
-import time
-from pathlib import Path
-import datetime
-from dataclasses import dataclass
-
-import paramiko
-
-# noinspection PyProtectedMember
-from simple_slurm import Slurm  # type: ignore
-from paramiko.client import SSHClient
-from ataraxis_base_utilities import LogLevel, console
-from ataraxis_data_structures import YamlConfig
-
-
-def generate_server_credentials(
-    output_directory: Path, username: str, password: str, host: str = "cbsuwsun.biohpc.cornell.edu"
-) -> None:
-    """Generates a new server_credentials.yaml file under the specified directory, using input information.
-
-    This function provides a convenience interface for generating new BioHPC server credential files. Generally, this is
-    only used when setting up new host-computers in the lab.
-    """
-    ServerCredentials(username=username, password=password, host=host).to_yaml(
-        file_path=output_directory.joinpath("server_credentials.yaml")
-    )
-
-
-@dataclass()
-class ServerCredentials(YamlConfig):
-    """This class stores the hostname and credentials used to log into the BioHPC cluster to run Sun lab processing
-    pipelines.
-
-    Primarily, this is used as part of the sl-experiment library runtime to start data processing once it is
-    transferred to the BioHPC server during preprocessing. However, the same file can be used together with the Server
-    class API to run any computation jobs on the lab's BioHPC server.
-    """
-
-    username: str = "YourNetID"
-    """The username to use for server authentication."""
-    password: str = "YourPassword"
-    """The password to use for server authentication."""
-    host: str = "cbsuwsun.biohpc.cornell.edu"
-    """The hostname or IP address of the server to connect to."""
-
-
-class Server:
-    """Encapsulates access to the Sun lab BioHPC processing server.
-
-    This class provides the API that allows accessing the BioHPC server to create and submit various SLURM-managed jobs
-    to the server. It functions as the central interface used by all processing pipelines in the lab to execute costly
-    data processing on the server.
-
-    Notes:
-        All lab processing pipelines expect the data to be stored on the server and all processing logic to be packaged
-        and installed into dedicated conda environments on the server.
-
-        This class assumes that the target server has SLURM job manager installed and accessible to the user whose
-        credentials are used to connect to the server as part of this class instantiation.
-
-    Args:
-        credentials_path: The path to the locally stored .yaml file that contains the server hostname and access
-            credentials.
-
-        Attributes:
-            _open: Tracks whether the connection to the server is open or not.
-            _client: Stores the initialized SSHClient instance used to interface with the server.
-    """
-
-    def __init__(self, credentials_path: Path) -> None:
-        # Tracker used to prevent __del__ from classing stop() for a partially initialized class.
-        self._open: bool = False
-
-        # Loads the credentials from the provided .yaml file
-        self._credentials: ServerCredentials = ServerCredentials.from_yaml(credentials_path)  # type: ignore
-
-        # Establishes the SSH connection to the specified processing server. At most, attempts to connect to the server
-        # 30 times before terminating with an error
-        attempt = 0
-        while True:
-            console.echo(
-                f"Trying to connect to {self._credentials.host} (attempt {attempt}/30)...", level=LogLevel.INFO
-            )
-            try:
-                self._client: SSHClient = paramiko.SSHClient()
-                self._client.set_missing_host_key_policy(paramiko.AutoAddPolicy())
-                self._client.connect(
-                    self._credentials.host, username=self._credentials.username, password=self._credentials.password
-                )
-                console.echo(f"Connected to {self._credentials.host}", level=LogLevel.SUCCESS)
-                break
-            except paramiko.AuthenticationException:
-                message = (
-                    f"Authentication failed when connecting to {self._credentials.host} using "
-                    f"{self._credentials.username} user."
-                )
-                console.error(message, RuntimeError)
-                raise RuntimeError
-            except:
-                if attempt == 30:
-                    message = f"Could not connect to {self._credentials.host} after 30 attempts. Aborting runtime."
-                    console.error(message, RuntimeError)
-                    raise RuntimeError
-
-                console.echo(
-                    f"Could not SSH to {self._credentials.host}, retrying after a 2-second delay...",
-                    level=LogLevel.WARNING,
-                )
-                attempt += 1
-                time.sleep(2)
-
-    def __del__(self) -> None:
-        """If the instance is connected to the server, terminates the connection before the instance is destroyed."""
-        self.close()
-
-    @staticmethod
-    def generate_slurm_header(
-        job_name: str, output_log: Path, error_log: Path, cpus_to_use: int = 10, ram_gb: int = 10, time_limit: int = 60
-    ) -> Slurm:
-        """Creates a SLURM command object and fills it with initial job configuration data.
-
-        This method is used to generate the initial SLURM command object and fill it with job (SLURM) configuration and
-        conda shell initialization data. It is used by all processing pipelines in the lab as the initial configuration
-        point when writing job shell scripts.
-
-        Notes:
-            The command header generated by this method does not contain the command to initialize the specific conda
-            environment to be used during processing. This has to be provided as part of the additional command
-            configuration, typically by adding the "source activate {ENV_NAME}" subcommand to the end of the header
-            returned by this method.
-
-        Args:
-            job_name: The descriptive name of the SLURM job to be created.
-            output_log: The absolute path to the .txt file on the processing server, where to store the standard output
-                data of the job.
-            error_log: The absolute path to the .txt file on the processing server, where to store the standard error
-                data of the job.
-            cpus_to_use: The number of CPUs to use for the job.
-            ram_gb: The amount of RAM to allocate for the job in Gigabytes.
-            time_limit: The maximum time limit for the job, in minutes. It is highly advised to set an adequate maximum
-                runtime limit to prevent jobs from hogging the server for a long period of time.
-        """
-
-        # Builds the slurm command object filled with configuration information
-        slurm_command = Slurm(
-            cpus_per_task=cpus_to_use,
-            job_name=job_name,
-            output=str(output_log),
-            error=str(error_log),
-            mem=f"{ram_gb}G",
-            time=datetime.timedelta(minutes=time_limit),
-        )
-
-        # Adds commands to initialize conda shell as part of the job runtime
-        slurm_command.add_cmd("eval $(conda shell.bash hook)")
-        slurm_command.add_cmd("conda init bash")
-
-        return slurm_command
-
-    def submit_job(self, slurm_command: Slurm, working_directory: Path) -> str:
-        """Submits the input SLURM command to the managed BioHPC server via the shell script.
-
-        This method submits various commands for execution via SLURM-managed BioHPC cluster. As part of its runtime, the
-        method translates the Slurm object into the shell script, moves the script to the target working directory on
-        the server, and instructs the server to execute the shell script (via SLURM).
-
-        Args:
-            slurm_command: The Slurm (command) object containing the job configuration and individual commands to run
-                as part of the processing pipeline.
-            working_directory: The path to the working directory on the server where the shell script is moved
-                and executed.
-
-        Returns:
-            The job ID assigned to the job by SLURM manager if the command submission is successful.
-
-        Raises:
-            RuntimeError: If the command submission to the server fails.
-        """
-
-        # Extracts the job name from the slurm command text and uses it to generate the name for the remote script
-        job_name_pattern = r"#SBATCH\s+--job-name\s+(\S+)"
-        match = re.search(job_name_pattern, str(slurm_command))
-        if match is None:
-            message = (
-                f"Failed to submit the job to the BioHPC cluster. It appears that the job does not contain the "
-                f"expected SLURM job header. All jobs submitted via this method have to be initialized using the "
-                f"generate_slurm_header() class method."
-            )
-            console.error(message, RuntimeError)
-            raise RuntimeError(message)  # This is a fallback to appease mypy. It should not be reachable.
-        job_name = match.group(1)
-
-        # Resolves the paths to the local and remote (server-side) .sh script files.
-        local_script_path = Path("temp_script.sh")
-        remote_script_path = str(working_directory.joinpath(f"{job_name}.sh"))
-
-        # Appends the command to clean up (remove) the temporary script file after processing runtime is over
-        slurm_command.add_cmd(f"rm -f {remote_script_path}")
-
-        # Translates the command to string format
-        script_content = str(slurm_command)
-
-        # Replaces escaped $ (/$) with $. This is essential, as without this correction things like conda
-        # initialization would not work as expected.
-        fixed_script_content = script_content.replace("\\$", "$")
-
-        # Creates a temporary script file locally and dumps translated command data into the file
-        with open(local_script_path, "w") as f:
-            f.write(fixed_script_content)
-
-        # Uploads the command script to the server
-        sftp = self._client.open_sftp()
-        sftp.put(localpath=local_script_path, remotepath=remote_script_path)
-        sftp.close()
-
-        # Removes the temporary local .sh file
-        local_script_path.unlink()
-
-        # Makes the server-side script executable
-        self._client.exec_command(f"chmod +x {remote_script_path}")
-
-        # Submits the job to SLURM with sbatch and verifies submission state by returning either the ID of the job or
-        # None to indicate no job has been submitted.
-        job_output = self._client.exec_command(f"sbatch {remote_script_path}")[1].read().strip().decode()
-        if "Submitted batch job" in job_output:
-            return job_output.split()[-1]
-        else:
-            message = f"Failed to submit the {job_name} job to the BioHPC cluster."
-            console.error(message, RuntimeError)
-
-            # Fallback to appease mypy, should not be reachable
-            raise RuntimeError(message)
-
-    def job_complete(self, job_id: str) -> bool:
-        """Returns True if the job with the given ID has been completed or terminated its runtime due to an error.
-
-        If the job is still running or is waiting inside the execution queue, returns False.
-
-        Args:
-            job_id: The numeric ID of the job to check, assigned by SLURM.
-        """
-        if j_id not in self._client.exec_command(f"squeue -j {job_id}")[1].read().decode().strip():
-            return True
-        else:
-            return False
-
-    def close(self) -> None:
-        """Closes the SSH connection to the server.
-
-        This method has to be called before destroying the class instance to ensure proper resource cleanup.
-        """
-        # Prevents closing already closed connections
-        if self._open:
-            self._client.close()
-
-
-if __name__ == "__main__":
-    # Creates SSHClient for server access
-    console.enable()
-    cred_path = Path("/home/cyberaxolotl/Desktop/test/server_credentials.yaml")
-    server = Server(credentials_path=cred_path)
-
-    # Generates SLURM job header
-    slurm = server.generate_slurm_header(
-        job_name="test_job",
-        output_log=Path("/workdir/cbsuwsun/test_job_stdout.txt"),
-        error_log=Path("/workdir/cbsuwsun/test_job_stderr.txt"),
-        cpus_to_use=1,
-    )
-
-    # Adds test runtime command
-    slurm.add_cmd("python --version > /workdir/cbsuwsun/mamba_version.txt")
-
-    # Submits the job to the server
-    j_id = server.submit_job(slurm_command=slurm, working_directory=Path("/workdir/cbsuwsun/"))
-
-    if j_id:
-        console.echo(f"Successfully submitted job with ID {j_id} to the server.", level=LogLevel.SUCCESS)
-
-        max_wait_time = 60  # Maximum wait time in seconds
-        wait_interval = 1  # Check every 1 second
-        elapsed_time = 0
-
-        while elapsed_time < max_wait_time:
-            if server.job_complete(job_id=j_id):
-                console.echo("Job completed", level=LogLevel.SUCCESS)
-                break
-
-            console.echo(f"Job still running. Waiting {wait_interval} seconds...", level=LogLevel.INFO)
-            time.sleep(wait_interval)
-            elapsed_time += wait_interval
-
-    # Close the connection
-    server.close()

sl_shared_assets/server.pyi

@@ -1,117 +0,0 @@
-from pathlib import Path
-from dataclasses import dataclass
-
-from simple_slurm import Slurm
-from paramiko.client import SSHClient as SSHClient
-from ataraxis_data_structures import YamlConfig
-
-def generate_server_credentials(
-    output_directory: Path, username: str, password: str, host: str = "cbsuwsun.biohpc.cornell.edu"
-) -> None:
-    """Generates a new server_credentials.yaml file under the specified directory, using input information.
-
-    This function provides a convenience interface for generating new BioHPC server credential files. Generally, this is
-    only used when setting up new host-computers in the lab.
-    """
-@dataclass()
-class ServerCredentials(YamlConfig):
-    """This class stores the hostname and credentials used to log into the BioHPC cluster to run Sun lab processing
-    pipelines.
-
-    Primarily, this is used as part of the sl-experiment library runtime to start data processing once it is
-    transferred to the BioHPC server during preprocessing. However, the same file can be used together with the Server
-    class API to run any computation jobs on the lab's BioHPC server.
-    """
-
-    username: str = ...
-    password: str = ...
-    host: str = ...
-
-class Server:
-    """Encapsulates access to the Sun lab BioHPC processing server.
-
-    This class provides the API that allows accessing the BioHPC server to create and submit various SLURM-managed jobs
-    to the server. It functions as the central interface used by all processing pipelines in the lab to execute costly
-    data processing on the server.
-
-    Notes:
-        All lab processing pipelines expect the data to be stored on the server and all processing logic to be packaged
-        and installed into dedicated conda environments on the server.
-
-        This class assumes that the target server has SLURM job manager installed and accessible to the user whose
-        credentials are used to connect to the server as part of this class instantiation.
-
-    Args:
-        credentials_path: The path to the locally stored .yaml file that contains the server hostname and access
-            credentials.
-
-        Attributes:
-            _open: Tracks whether the connection to the server is open or not.
-            _client: Stores the initialized SSHClient instance used to interface with the server.
-    """
-
-    _open: bool
-    _credentials: ServerCredentials
-    _client: SSHClient
-    def __init__(self, credentials_path: Path) -> None: ...
-    def __del__(self) -> None:
-        """If the instance is connected to the server, terminates the connection before the instance is destroyed."""
-    @staticmethod
-    def generate_slurm_header(
-        job_name: str, output_log: Path, error_log: Path, cpus_to_use: int = 10, ram_gb: int = 10, time_limit: int = 60
-    ) -> Slurm:
-        """Creates a SLURM command object and fills it with initial job configuration data.
-
-        This method is used to generate the initial SLURM command object and fill it with job (SLURM) configuration and
-        conda shell initialization data. It is used by all processing pipelines in the lab as the initial configuration
-        point when writing job shell scripts.
-
-        Notes:
-            The command header generated by this method does not contain the command to initialize the specific conda
-            environment to be used during processing. This has to be provided as part of the additional command
-            configuration, typically by adding the "source activate {ENV_NAME}" subcommand to the end of the header
-            returned by this method.
-
-        Args:
-            job_name: The descriptive name of the SLURM job to be created.
-            output_log: The absolute path to the .txt file on the processing server, where to store the standard output
-                data of the job.
-            error_log: The absolute path to the .txt file on the processing server, where to store the standard error
-                data of the job.
-            cpus_to_use: The number of CPUs to use for the job.
-            ram_gb: The amount of RAM to allocate for the job in Gigabytes.
-            time_limit: The maximum time limit for the job, in minutes. It is highly advised to set an adequate maximum
-                runtime limit to prevent jobs from hogging the server for a long period of time.
-        """
-    def submit_job(self, slurm_command: Slurm, working_directory: Path) -> str:
-        """Submits the input SLURM command to the managed BioHPC server via the shell script.
-
-        This method submits various commands for execution via SLURM-managed BioHPC cluster. As part of its runtime, the
-        method translates the Slurm object into the shell script, moves the script to the target working directory on
-        the server, and instructs the server to execute the shell script (via SLURM).
-
-        Args:
-            slurm_command: The Slurm (command) object containing the job configuration and individual commands to run
-                as part of the processing pipeline.
-            working_directory: The path to the working directory on the server where the shell script is moved
-                and executed.
-
-        Returns:
-            The job ID assigned to the job by SLURM manager if the command submission is successful.
-
-        Raises:
-            RuntimeError: If the command submission to the server fails.
-        """
-    def job_complete(self, job_id: str) -> bool:
-        """Returns True if the job with the given ID has been completed or terminated its runtime due to an error.
-
-        If the job is still running or is waiting inside the execution queue, returns False.
-
-        Args:
-            job_id: The numeric ID of the job to check, assigned by SLURM.
-        """
-    def close(self) -> None:
-        """Closes the SSH connection to the server.
-
-        This method has to be called before destroying the class instance to ensure proper resource cleanup.
-        """

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