|
2 | 2 | # ruff: noqa: F403 |
3 | 3 | """mBuild: a hierarchical, component based molecule builder.""" |
4 | 4 |
|
| 5 | +import logging |
| 6 | +import sys |
| 7 | +from logging.handlers import RotatingFileHandler |
| 8 | + |
5 | 9 | from mbuild.box import Box |
6 | 10 | from mbuild.coarse_graining import coarse_grain |
7 | 11 | from mbuild.compound import * |
|
10 | 14 | from mbuild.lattice import Lattice |
11 | 15 | from mbuild.packing import * |
12 | 16 | from mbuild.pattern import * |
| 17 | +from mbuild.polymer import Polymer |
13 | 18 | from mbuild.port import Port |
14 | 19 | from mbuild.recipes import recipes |
15 | 20 |
|
16 | | -__version__ = "1.2.0" |
| 21 | +__version__ = "1.3.0" |
17 | 22 | __date__ = "2025-01-23" |
| 23 | + |
| 24 | + |
| 25 | +class DeduplicationFilter(logging.Filter): |
| 26 | + """A logging filter that suppresses duplicate messages.""" |
| 27 | + |
| 28 | + def __init__(self): |
| 29 | + super().__init__() |
| 30 | + self.logged_messages = set() |
| 31 | + |
| 32 | + def filter(self, record): |
| 33 | + log_entry = (record.name, record.levelno, record.msg) |
| 34 | + if log_entry not in self.logged_messages: |
| 35 | + self.logged_messages.add(log_entry) |
| 36 | + return True |
| 37 | + return False |
| 38 | + |
| 39 | + |
| 40 | +class HeaderRotatingFileHandler(RotatingFileHandler): |
| 41 | + def __init__( |
| 42 | + self, |
| 43 | + filename, |
| 44 | + mode="w", |
| 45 | + maxBytes=0, |
| 46 | + backupCount=0, |
| 47 | + encoding=None, |
| 48 | + delay=False, |
| 49 | + header="", |
| 50 | + ): |
| 51 | + self.header = header |
| 52 | + super().__init__(filename, mode, maxBytes, backupCount, encoding, delay) |
| 53 | + |
| 54 | + def _open(self): |
| 55 | + """ |
| 56 | + Open the current base log file, with the header written. |
| 57 | + """ |
| 58 | + stream = super()._open() |
| 59 | + if stream.tell() == 0 and self.header: # Only write header if file is empty |
| 60 | + stream.write(self.header + "\n") |
| 61 | + return stream |
| 62 | + |
| 63 | + |
| 64 | +class mBuildLogger: |
| 65 | + def __init__(self): |
| 66 | + self.library_logger = logging.getLogger("mbuild") |
| 67 | + self.library_logger.setLevel(logging.DEBUG) |
| 68 | + |
| 69 | + # Create handlers |
| 70 | + self.console_handler = logging.StreamHandler(sys.stdout) |
| 71 | + self.console_handler.setLevel(logging.WARNING) |
| 72 | + |
| 73 | + # Create a formatter |
| 74 | + self.formatter = logging.Formatter( |
| 75 | + "%(asctime)s - %(name)s - %(levelname)s - %(message)s" |
| 76 | + ) |
| 77 | + |
| 78 | + # Add formatter to handlers |
| 79 | + self.console_handler.setFormatter(self.formatter) |
| 80 | + |
| 81 | + # Initialize and add the deduplication filter |
| 82 | + self.dedup_filter = DeduplicationFilter() |
| 83 | + self.console_handler.addFilter(self.dedup_filter) |
| 84 | + |
| 85 | + # Clear any previous handlers to avoid duplicates in Jupyter |
| 86 | + self._clear_handlers() |
| 87 | + |
| 88 | + # Add handlers to the library logger |
| 89 | + self.library_logger.addHandler(self.console_handler) |
| 90 | + |
| 91 | + def _clear_handlers(self): |
| 92 | + handlers = self.library_logger.handlers[:] |
| 93 | + for handler in handlers: |
| 94 | + self.library_logger.removeHandler(handler) |
| 95 | + |
| 96 | + def debug_file(self, filename: str): |
| 97 | + """Print logging Debug messages to file `filename`.""" |
| 98 | + # Get the path to the Python interpreter |
| 99 | + python_executable = sys.executable |
| 100 | + |
| 101 | + # Get the list of command-line arguments |
| 102 | + command_arguments = sys.argv |
| 103 | + |
| 104 | + # Construct the full command |
| 105 | + full_command = [python_executable] + command_arguments |
| 106 | + header = f"Log details for mBuild {__version__} from running \n{full_command}" |
| 107 | + self.file_handler = HeaderRotatingFileHandler( |
| 108 | + filename, mode="a", maxBytes=10**6, backupCount=2, header=header |
| 109 | + ) |
| 110 | + self.file_handler.setLevel(logging.DEBUG) |
| 111 | + |
| 112 | + self.file_handler.addFilter(DeduplicationFilter()) # fresh duplication handler |
| 113 | + self.file_handler.setFormatter(self.formatter) |
| 114 | + self.library_logger.addHandler(self.file_handler) |
| 115 | + |
| 116 | + def print_level(self, level: str): |
| 117 | + """Print sys.stdout screen based on the logging `level` passed.""" |
| 118 | + levelDict = { |
| 119 | + "notset": logging.NOTSET, |
| 120 | + "debug": logging.DEBUG, |
| 121 | + "info": logging.INFO, |
| 122 | + "warning": logging.WARNING, |
| 123 | + "error": logging.ERROR, |
| 124 | + "critical": logging.CRITICAL, |
| 125 | + } |
| 126 | + logLevel = levelDict.get(level.lower()) |
| 127 | + if logLevel: |
| 128 | + self.console_handler.setLevel(logLevel) # sets stdout |
| 129 | + else: |
| 130 | + raise ValueError( |
| 131 | + f"INCORRECT {level=}. Please set level of {levelDict.keys()}" |
| 132 | + ) |
| 133 | + |
| 134 | + |
| 135 | +# Example usage in __init__.py |
| 136 | +mbuild_logger = mBuildLogger() |
| 137 | +mbuild_logger.library_logger.setLevel(logging.INFO) |
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