14059657073

Committed 25 Mar 2025 12:31PM UTC coverage: 38.633% (+8.9%) from 29.725%

Build # 14059657073

Build Type

push

github

Committed by

web-flow

Commit Message

Merge pull request #73 from CCPBioSim/34-implement-python-logging

Implement Python Logging

Run Details

137 of 211 new or added lines in 9 files covered. (64.93%)

5 existing lines in 1 file now uncovered.

243 of 629 relevant lines covered (38.63%)

1.16 hits per line

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85.11

/CodeEntropy/config/arg_config_manager.py

import argparse
import logging
import os

import yaml

# Set up logger
logger = logging.getLogger(__name__)

arg_map = {
    "top_traj_file": {
        "type": str,
        "nargs": "+",
        "help": "Path to Structure/topology file followed by Trajectory file(s)",
        "default": [],
    },
    "selection_string": {
        "type": str,
        "help": "Selection string for CodeEntropy",
        "default": "all",
    },
    "start": {
        "type": int,
        "help": "Start analysing the trajectory from this frame index",
        "default": 0,
    },
    "end": {
        "type": int,
        "help": "Stop analysing the trajectory at this frame index",
        "default": -1,
    },
    "step": {
        "type": int,
        "help": "Interval between two consecutive frames to be read index",
        "default": 1,
    },
    "bin_width": {
        "type": int,
        "help": "Bin width in degrees for making the histogram",
        "default": 30,
    },
    "temperature": {
        "type": float,
        "help": "Temperature for entropy calculation (K)",
        "default": 298.0,
    },
    "verbose": {
        "action": "store_true",
        "help": "Enable verbose output",
    },
    "thread": {"type": int, "help": "How many multiprocess to use", "default": 1},
    "outfile": {
        "type": str,
        "help": "Name of the file where the output will be written",
        "default": "outfile.json",
    },
    "mout": {
        "type": str,
        "help": "Name of the file where certain matrices will be written",
        "default": None,
    },
    "force_partitioning": {"type": float, "help": "Force partitioning", "default": 0.5},
    "waterEntropy": {"type": bool, "help": "Calculate water entropy", "default": False},
}


class ConfigManager:
    def __init__(self):
        self.arg_map = arg_map

    def load_config(self, file_path):
        """Load YAML configuration file."""
        if not os.path.exists(file_path):
            raise FileNotFoundError(f"Configuration file '{file_path}' not found.")

        with open(file_path, "r") as file:
            config = yaml.safe_load(file)

            # If YAML content is empty, return an empty dictionary
            if config is None:
                config = {}

        return config

    def setup_argparse(self):
        """Setup argument parsing dynamically based on arg_map."""
        parser = argparse.ArgumentParser(
            description="CodeEntropy: Entropy calculation with MCC method."
        )

        for arg, properties in self.arg_map.items():
            kwargs = {key: properties[key] for key in properties if key != "help"}
            parser.add_argument(f"--{arg}", **kwargs, help=properties.get("help"))

        return parser

    def merge_configs(self, args, run_config):
        """Merge CLI arguments with YAML configuration and adjust logging level."""
        if run_config is None:
            run_config = {}

        if not isinstance(run_config, dict):
            raise TypeError("run_config must be a dictionary or None.")

        # Step 1: Merge YAML configuration into args
        for key, value in run_config.items():
            if getattr(args, key, None) is None:
                setattr(args, key, value)

        # Step 2: Set default values for any missing arguments from `arg_map`
        for key, params in self.arg_map.items():
            if getattr(args, key, None) is None:
                setattr(args, key, params.get("default"))

        # Step 3: Override with CLI values if provided
        for key in self.arg_map.keys():
            cli_value = getattr(args, key, None)
            if cli_value is not None:
                run_config[key] = cli_value

        # Adjust logging level based on 'verbose' flag
        if getattr(args, "verbose", False):
            logger.setLevel(logging.DEBUG)
            for handler in logger.handlers:
                handler.setLevel(logging.DEBUG)
            logger.debug("Verbose mode enabled. Logger set to DEBUG level.")
        else:
            logger.setLevel(logging.INFO)
            for handler in logger.handlers:
                handler.setLevel(logging.INFO)

        return args

1	import argparse	3✔
2	import logging	3✔
3	import os	3✔
4
5	import yaml	3✔
6
7	# Set up logger
8	logger = logging.getLogger(__name__)	3✔
9
10	arg_map = {	3✔
11	"top_traj_file": {
12	"type": str,
13	"nargs": "+",
14	"help": "Path to Structure/topology file followed by Trajectory file(s)",
15	"default": [],
16	},
17	"selection_string": {
18	"type": str,
19	"help": "Selection string for CodeEntropy",
20	"default": "all",
21	},
22	"start": {
23	"type": int,
24	"help": "Start analysing the trajectory from this frame index",
25	"default": 0,
26	},
27	"end": {
28	"type": int,
29	"help": "Stop analysing the trajectory at this frame index",
30	"default": -1,
31	},
32	"step": {
33	"type": int,
34	"help": "Interval between two consecutive frames to be read index",
35	"default": 1,
36	},
37	"bin_width": {
38	"type": int,
39	"help": "Bin width in degrees for making the histogram",
40	"default": 30,
41	},
42	"temperature": {
43	"type": float,
44	"help": "Temperature for entropy calculation (K)",
45	"default": 298.0,
46	},
47	"verbose": {
48	"action": "store_true",
49	"help": "Enable verbose output",
50	},
51	"thread": {"type": int, "help": "How many multiprocess to use", "default": 1},
52	"outfile": {
53	"type": str,
54	"help": "Name of the file where the output will be written",
55	"default": "outfile.json",
56	},
57	"mout": {
58	"type": str,
59	"help": "Name of the file where certain matrices will be written",
60	"default": None,
61	},
62	"force_partitioning": {"type": float, "help": "Force partitioning", "default": 0.5},
63	"waterEntropy": {"type": bool, "help": "Calculate water entropy", "default": False},
64	}
65
66
67	class ConfigManager:	3✔
68	def __init__(self):	3✔
69	self.arg_map = arg_map	3✔
70
71	def load_config(self, file_path):	3✔
72	"""Load YAML configuration file."""
73	if not os.path.exists(file_path):	3✔
NEW 74	raise FileNotFoundError(f"Configuration file '{file_path}' not found.")	×
75
76	with open(file_path, "r") as file:	3✔
77	config = yaml.safe_load(file)	3✔
78
79	# If YAML content is empty, return an empty dictionary
80	if config is None:	3✔
81	config = {}	3✔
82
83	return config	3✔
84
85	def setup_argparse(self):	3✔
86	"""Setup argument parsing dynamically based on arg_map."""
87	parser = argparse.ArgumentParser(	3✔
88	description="CodeEntropy: Entropy calculation with MCC method."
89	)
90
91	for arg, properties in self.arg_map.items():	3✔
92	kwargs = {key: properties[key] for key in properties if key != "help"}	3✔
93	parser.add_argument(f"--{arg}", **kwargs, help=properties.get("help"))	3✔
94
95	return parser	3✔
96
97	def merge_configs(self, args, run_config):	3✔
98	"""Merge CLI arguments with YAML configuration and adjust logging level."""
99	if run_config is None:	3✔
NEW 100	run_config = {}	×
101
102	if not isinstance(run_config, dict):	3✔
103	raise TypeError("run_config must be a dictionary or None.")	3✔
104
105	# Step 1: Merge YAML configuration into args
106	for key, value in run_config.items():	3✔
107	if getattr(args, key, None) is None:	3✔
108	setattr(args, key, value)	3✔
109
110	# Step 2: Set default values for any missing arguments from `arg_map`
111	for key, params in self.arg_map.items():	3✔
112	if getattr(args, key, None) is None:	3✔
113	setattr(args, key, params.get("default"))	3✔
114
115	# Step 3: Override with CLI values if provided
116	for key in self.arg_map.keys():	3✔
117	cli_value = getattr(args, key, None)	3✔
118	if cli_value is not None:	3✔
119	run_config[key] = cli_value	3✔
120
121	# Adjust logging level based on 'verbose' flag
122	if getattr(args, "verbose", False):	3✔
NEW 123	logger.setLevel(logging.DEBUG)	×
NEW 124	for handler in logger.handlers:	×
NEW 125	handler.setLevel(logging.DEBUG)	×
NEW 126	logger.debug("Verbose mode enabled. Logger set to DEBUG level.")	×
127	else:
128	logger.setLevel(logging.INFO)	3✔
129	for handler in logger.handlers:	3✔
NEW 130	handler.setLevel(logging.INFO)	×
131
132	return args	3✔

CCPBioSim / CodeEntropy / 14059657073

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