System utils

PeakMemoryProfiler

A context manager that monitors and tracks the peak memory usage of a process (and optionally its children) over a period of time. The memory usage can be reported in various units (bytes, MB, or GB).

Example:

with PeakMemoryProfiler() as profiler:
    # Code block to monitor memory usage
    ...

Class Attributes:

Attributes:

Name	Type	Description
pid		The PID of the process being monitored. Defaults to the current process.
interval		Time interval (in seconds) between memory checks. Defaults to 0.1.
include_children		Whether memory usage from child processes is included. Defaults to True.
unit		The unit used to report memory usage (either 'bytes', 'MB', or 'GB'). Defaults to 'MB'.
max_memory		The peak memory usage observed during the monitoring period.
monitoring_thread		Thread used for monitoring memory usage.
_stop_monitoring		Event used to signal when to stop monitoring.

Source code in magenpy/utils/system_utils.py

class PeakMemoryProfiler:
    """
    A context manager that monitors and tracks the peak memory usage of a process
    (and optionally its children) over a period of time. The memory usage can be
    reported in various units (bytes, MB, or GB).

    Example:

    ```
    with PeakMemoryProfiler() as profiler:
        # Code block to monitor memory usage
        ...
    ```

    Class Attributes:
    :ivar pid: The PID of the process being monitored. Defaults to the current process.
    :ivar interval: Time interval (in seconds) between memory checks. Defaults to 0.1.
    :ivar include_children: Whether memory usage from child processes is included. Defaults to True.
    :ivar unit: The unit used to report memory usage (either 'bytes', 'MB', or 'GB'). Defaults to 'MB'.
    :ivar max_memory: The peak memory usage observed during the monitoring period.
    :ivar monitoring_thread: Thread used for monitoring memory usage.
    :ivar _stop_monitoring: Event used to signal when to stop monitoring.
    """

    def __init__(self, pid=None, interval=0.1, include_children=True, unit="MB"):
        """
        Initializes the PeakMemoryProfiler instance with the provided parameters.

        :param pid: The PID of the process to monitor. Defaults to None (current process).
        :param interval: The interval (in seconds) between memory checks. Defaults to 0.1.
        :param include_children: Whether to include memory usage from child processes. Defaults to True.
        :param unit: The unit in which to report memory usage. Options are 'bytes', 'MB', or 'GB'. Defaults to 'MB'.
        """
        self.pid = pid or psutil.Process().pid  # Default to current process if no PID is provided
        self.interval = interval
        self.include_children = include_children
        self.unit = unit
        self.max_memory = 0
        self.monitoring_thread = None
        self._stop_monitoring = threading.Event()

    def __enter__(self):
        """
        Starts monitoring memory usage when entering the context block.

        :return: Returns the instance of PeakMemoryProfiler, so that we can access peak memory later.
        """
        self.process = psutil.Process(self.pid)
        self.max_memory = 0
        self._stop_monitoring.clear()  # Clear the stop flag to begin monitoring
        self.monitoring_thread = threading.Thread(target=self._monitor_memory)
        self.monitoring_thread.start()
        return self  # Return the instance so that the caller can access max_memory

    def __exit__(self, exc_type, exc_value, traceback):
        """
        Stops the memory monitoring when exiting the context block.

        :param exc_type: The exception type if an exception was raised in the block.
        :param exc_value: The exception instance if an exception was raised.
        :param traceback: The traceback object if an exception was raised.
        """
        self._stop_monitoring.set()  # Signal the thread to stop monitoring
        self.monitoring_thread.join()  # Wait for the monitoring thread to finish

    def get_curr_memory(self):
        """
        Get the current memory usage of the monitored process and its children.

        :return: The current memory usage in the specified unit (bytes, MB, or GB).
        :rtype: float
        """

        memory = self.process.memory_info().rss

        if self.include_children:
            # Include memory usage of child processes recursively
            for child in self.process.children(recursive=True):
                try:
                    memory += child.memory_info().rss
                except (psutil.NoSuchProcess, psutil.AccessDenied):
                    continue

        if self.unit == "MB":
            return memory / (1024 ** 2)  # Convert to MB
        elif self.unit == "GB":
            return memory / (1024 ** 3)  # Convert to GB
        else:
            return memory  # Return in bytes if no conversion is requested

    def _monitor_memory(self):
        """
        Monitors the memory usage of the process and its children continuously
        until the monitoring is stopped.

        This method runs in a separate thread and updates the peak memory usage
        as long as the monitoring flag is not set.
        """
        while not self._stop_monitoring.is_set():
            try:
                curr_memory = self.get_curr_memory()

                # Update max memory if a new peak is found
                self.max_memory = max(self.max_memory, curr_memory)
                time.sleep(self.interval)
            except psutil.NoSuchProcess:
                break  # Process no longer exists, stop monitoring

    def get_peak_memory(self):
        """
        Get the peak memory usage observed during the monitoring period.

        :return: The peak memory usage in the specified unit (bytes, MB, or GB).
        :rtype: float
        """
        return self.max_memory

__enter__()

Starts monitoring memory usage when entering the context block.

Returns:

Type	Description
	Returns the instance of PeakMemoryProfiler, so that we can access peak memory later.

Source code in magenpy/utils/system_utils.py

def __enter__(self):
    """
    Starts monitoring memory usage when entering the context block.

    :return: Returns the instance of PeakMemoryProfiler, so that we can access peak memory later.
    """
    self.process = psutil.Process(self.pid)
    self.max_memory = 0
    self._stop_monitoring.clear()  # Clear the stop flag to begin monitoring
    self.monitoring_thread = threading.Thread(target=self._monitor_memory)
    self.monitoring_thread.start()
    return self  # Return the instance so that the caller can access max_memory

__exit__(exc_type, exc_value, traceback)

Stops the memory monitoring when exiting the context block.

Parameters:

Name	Type	Description	Default
exc_type		The exception type if an exception was raised in the block.	required
exc_value		The exception instance if an exception was raised.	required
traceback		The traceback object if an exception was raised.	required

Source code in magenpy/utils/system_utils.py

def __exit__(self, exc_type, exc_value, traceback):
    """
    Stops the memory monitoring when exiting the context block.

    :param exc_type: The exception type if an exception was raised in the block.
    :param exc_value: The exception instance if an exception was raised.
    :param traceback: The traceback object if an exception was raised.
    """
    self._stop_monitoring.set()  # Signal the thread to stop monitoring
    self.monitoring_thread.join()  # Wait for the monitoring thread to finish

__init__(pid=None, interval=0.1, include_children=True, unit='MB')

Initializes the PeakMemoryProfiler instance with the provided parameters.

Parameters:

Name	Type	Description	Default
pid		The PID of the process to monitor. Defaults to None (current process).	None
interval		The interval (in seconds) between memory checks. Defaults to 0.1.	0.1
include_children		Whether to include memory usage from child processes. Defaults to True.	True
unit		The unit in which to report memory usage. Options are 'bytes', 'MB', or 'GB'. Defaults to 'MB'.	'MB'

Source code in magenpy/utils/system_utils.py

def __init__(self, pid=None, interval=0.1, include_children=True, unit="MB"):
    """
    Initializes the PeakMemoryProfiler instance with the provided parameters.

    :param pid: The PID of the process to monitor. Defaults to None (current process).
    :param interval: The interval (in seconds) between memory checks. Defaults to 0.1.
    :param include_children: Whether to include memory usage from child processes. Defaults to True.
    :param unit: The unit in which to report memory usage. Options are 'bytes', 'MB', or 'GB'. Defaults to 'MB'.
    """
    self.pid = pid or psutil.Process().pid  # Default to current process if no PID is provided
    self.interval = interval
    self.include_children = include_children
    self.unit = unit
    self.max_memory = 0
    self.monitoring_thread = None
    self._stop_monitoring = threading.Event()

get_curr_memory()

Get the current memory usage of the monitored process and its children.

Returns:

Type	Description
float	The current memory usage in the specified unit (bytes, MB, or GB).

Source code in magenpy/utils/system_utils.py

def get_curr_memory(self):
    """
    Get the current memory usage of the monitored process and its children.

    :return: The current memory usage in the specified unit (bytes, MB, or GB).
    :rtype: float
    """

    memory = self.process.memory_info().rss

    if self.include_children:
        # Include memory usage of child processes recursively
        for child in self.process.children(recursive=True):
            try:
                memory += child.memory_info().rss
            except (psutil.NoSuchProcess, psutil.AccessDenied):
                continue

    if self.unit == "MB":
        return memory / (1024 ** 2)  # Convert to MB
    elif self.unit == "GB":
        return memory / (1024 ** 3)  # Convert to GB
    else:
        return memory  # Return in bytes if no conversion is requested

get_peak_memory()

Get the peak memory usage observed during the monitoring period.

Returns:

Type	Description
float	The peak memory usage in the specified unit (bytes, MB, or GB).

Source code in magenpy/utils/system_utils.py

def get_peak_memory(self):
    """
    Get the peak memory usage observed during the monitoring period.

    :return: The peak memory usage in the specified unit (bytes, MB, or GB).
    :rtype: float
    """
    return self.max_memory

available_cpu()

Returns:

Type	Description
	The number of available cores on the system minus 1.

Source code in magenpy/utils/system_utils.py

def available_cpu():
    """
    :return: The number of available cores on the system minus 1.
    """
    return psutil.cpu_count() - 1

delete_temp_files(prefix)

Delete temporary files with the given prefix.

Parameters:

Name	Type	Description	Default
prefix		A string with the prefix of the temporary files to delete.	required

Source code in magenpy/utils/system_utils.py

def delete_temp_files(prefix):
    """
    Delete temporary files with the given `prefix`.
    :param prefix: A string with the prefix of the temporary files to delete.
    """
    for f in glob.glob(f"{prefix}*"):
        try:
            os.remove(f)
        except (OSError, FileNotFoundError):
            continue

get_filenames(path, extension=None)

Obtain valid and full path names given the provided path or prefix and extensions.

Parameters:

Name	Type	Description	Default
path		A string with the path prefix or full path.	required
extension		The extension for the class of files to search for.	None

Returns:

Type	Description
	A list of strings with the full paths of the files/folders.

Source code in magenpy/utils/system_utils.py

def get_filenames(path, extension=None):
    """
    Obtain valid and full path names given the provided `path` or prefix and extensions.

    :param path: A string with the path prefix or full path.
    :param extension: The extension for the class of files to search for.

    :return: A list of strings with the full paths of the files/folders.
    """

    if osp.isdir(path):
        if extension:
            if osp.isfile(osp.join(path, extension)):
                return [path]
            else:
                return [f for f in glob.glob(osp.join(path, '*/'))
                        if extension in f or osp.isfile(osp.join(f, extension))]
        else:
            return glob.glob(osp.join(path, '*'))
    else:
        if extension is None:
            return glob.glob(path + '*')
        elif extension in path:
            return glob.glob(path)
        elif osp.isfile(path + extension):
            return [path + extension]
        else:
            return (
                    glob.glob(osp.join(path, '*' + extension + '*')) +
                    glob.glob(osp.join(path, extension + '*')) +
                    glob.glob(path + '*' + extension + '*')
            )

get_memory_usage()

Returns:

Type	Description
	The current memory usage of the running process in Mega Bytes (MB)

Source code in magenpy/utils/system_utils.py

def get_memory_usage():
    """
    :return: The current memory usage of the running process in Mega Bytes (MB)
    """
    process = psutil.Process(os.getpid())
    mem_info = process.memory_info()
    return mem_info.rss / (1024 ** 2)

glob_s3_path(path)

Get the list of files/folders in the provided AWS S3 path. This works with wildcards.

Parameters:

Name	Type	Description	Default
path		A string with the S3 path to list files/folders from.	required

Returns:

Type	Description
	A list of strings with the full paths of the files/folders.

Source code in magenpy/utils/system_utils.py

def glob_s3_path(path):
    """
    Get the list of files/folders in the provided AWS S3 path. This works with wildcards.

    :param path: A string with the S3 path to list files/folders from.
    :return: A list of strings with the full paths of the files/folders.
    """

    import s3fs
    s3 = s3fs.S3FileSystem(anon=True)

    return s3.glob(path)

is_cmd_tool(name)

Check whether name is on PATH and marked as executable. From: https://stackoverflow.com/a/34177358

Parameters:

Name	Type	Description	Default
name		A string with the name of the command-line tool.	required

Returns:

Type	Description
	True if the command-line tool is available, False otherwise.

Source code in magenpy/utils/system_utils.py

def is_cmd_tool(name):
    """
    Check whether `name` is on PATH and marked as executable.
    From: https://stackoverflow.com/a/34177358
    :param name: A string with the name of the command-line tool.
    :return: True if the command-line tool is available, False otherwise.
    """
    from shutil import which

    return which(name) is not None

is_path_writable(path)

Check whether the user has write-access to the provided path. This function supports checking for nested directories (i.e., we iterate upwards until finding a parent directory that currently exists, and we check the write-access of that directory).

Parameters:

Name	Type	Description	Default
path		A string with the path to check.	required

Returns:

Type	Description
	True if the path is writable, False otherwise.

Source code in magenpy/utils/system_utils.py

def is_path_writable(path):
    """
    Check whether the user has write-access to the provided `path`.
    This function supports checking for nested directories (i.e.,
    we iterate upwards until finding a parent directory that currently
    exists, and we check the write-access of that directory).

    :param path: A string with the path to check.

    :return: True if the path is writable, False otherwise.
    """

    # Get the absolute path first:
    path = osp.abspath(path)

    while True:

        if osp.exists(path):
            return os.access(path, os.W_OK)
        else:
            path = osp.dirname(path)
            if path == '/' or len(path) == 0:
                return False

makedir(dirs)

Create directories on the filesystem, recursively.

Parameters:

Name	Type	Description	Default
dirs		A string or list of strings with the paths to create.	required

Source code in magenpy/utils/system_utils.py

def makedir(dirs):
    """
    Create directories on the filesystem, recursively.
    :param dirs: A string or list of strings with the paths to create.
    :raises: OSError if it fails to create the directory structure.
    """

    if isinstance(dirs, str):
        dirs = [dirs]

    for dir_l in dirs:
        try:
            os.makedirs(dir_l)
        except OSError as e:
            import errno
            if e.errno != errno.EEXIST:
                raise

run_shell_script(cmd)

Run the shell script given the command prompt in cmd.

Parameters:

Name	Type	Description	Default
cmd		A string with the shell command to run.	required

Returns:

Type	Description
	The result of the shell command.

Source code in magenpy/utils/system_utils.py

def run_shell_script(cmd):
    """
    Run the shell script given the command prompt in `cmd`.
    :param cmd: A string with the shell command to run.

    :return: The result of the shell command.
    :raises: subprocess.CalledProcessError if the shell command fails.
    """

    result = subprocess.run(cmd, shell=True, capture_output=True, check=True)

    if result.stderr:
        raise subprocess.CalledProcessError(
            returncode=result.returncode,
            cmd=result.args,
            stderr=result.stderr
        )

    return result

valid_url(path)

Check whether the provided path is a valid URL.

Parameters:

Name	Type	Description	Default
path		A string with the URL to check.	required

Returns:

Type	Description
	True if the URL is valid, False otherwise.

Source code in magenpy/utils/system_utils.py

def valid_url(path):
    """
    Check whether the provided `path` is a valid URL.
    :param path: A string with the URL to check.
    :return: True if the URL is valid, False otherwise.
    """

    import urllib.request

    try:
        with urllib.request.urlopen(path) as response:
            v_url = response.getcode() == 200  # Check if the response status is OK (HTTP 200)
        return v_url
    except Exception:
        return False