14334168434

Committed 08 Apr 2025 12:59PM UTC coverage: 40.491% (+1.4%) from 39.089%

Build # 14334168434

Build Type

push

github

Committed by

web-flow

Commit Message

Merge pull request #84 from CCPBioSim/81-verbose-YAML-bug

Ensure verbose flag in YAML sets logging to DEBUG mode correctly

Coverage Stats

23 of 24 new or added lines in 3 files covered. (95.83%)

264 of 652 relevant lines covered (40.49%)

1.21 hits per line

Source File
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56.0

/CodeEntropy/config/data_logger.py

import json
import logging

from tabulate import tabulate

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


class DataLogger:
    def __init__(self):
        self.molecule_data = []
        self.residue_data = []

    def save_dataframes_as_json(self, molecule_df, residue_df, output_file):
        """Save multiple DataFrames into a single JSON file with separate keys"""
        data = {
            "molecule_data": molecule_df.to_dict(orient="records"),
            "residue_data": residue_df.to_dict(orient="records"),
        }

        # Write JSON data to file
        with open(output_file, "w") as out:
            json.dump(data, out, indent=4)

    def add_results_data(self, molecule, level, type, S_molecule):
        """Add data for molecule-level entries"""
        self.molecule_data.append([molecule, level, type, f"{S_molecule}"])

    def add_residue_data(self, molecule, residue, type, S_trans_residue):
        """Add data for residue-level entries"""
        self.residue_data.append([molecule, residue, type, f"{S_trans_residue}"])

    def log_tables(self):
        """Log both tables at once"""
        # Log molecule data
        if self.molecule_data:
            logger.info("Molecule Data Table:")
            table_str = tabulate(
                self.molecule_data,
                headers=["Molecule ID", "Level", "Type", "Result (J/mol/K)"],
                tablefmt="grid",
            )
            logger.info(f"\n{table_str}")

        # Log residue data
        if self.residue_data:
            logger.info("Residue Data Table:")
            table_str = tabulate(
                self.residue_data,
                headers=["Molecule ID", "Residue", "Type", "Result (J/mol/K)"],
                tablefmt="grid",
            )
            logger.info(f"\n{table_str}")

1	import json	3✔
2	import logging	3✔
3
4	from tabulate import tabulate	3✔
5
6	# Set up logger
7	logger = logging.getLogger(__name__)	3✔
8
9
10	class DataLogger:	3✔
11	def __init__(self):	3✔
12	self.molecule_data = []	3✔
13	self.residue_data = []	3✔
14
15	def save_dataframes_as_json(self, molecule_df, residue_df, output_file):	3✔
16	"""Save multiple DataFrames into a single JSON file with separate keys"""
17	data = {	×
18	"molecule_data": molecule_df.to_dict(orient="records"),
19	"residue_data": residue_df.to_dict(orient="records"),
20	}
21
22	# Write JSON data to file
NEW 23	with open(output_file, "w") as out:	×
24	json.dump(data, out, indent=4)	×
25
26	def add_results_data(self, molecule, level, type, S_molecule):	3✔
27	"""Add data for molecule-level entries"""
28	self.molecule_data.append([molecule, level, type, f"{S_molecule}"])	×
29
30	def add_residue_data(self, molecule, residue, type, S_trans_residue):	3✔
31	"""Add data for residue-level entries"""
32	self.residue_data.append([molecule, residue, type, f"{S_trans_residue}"])	×
33
34	def log_tables(self):	3✔
35	"""Log both tables at once"""
36	# Log molecule data
37	if self.molecule_data:	3✔
38	logger.info("Molecule Data Table:")	×
39	table_str = tabulate(	×
40	self.molecule_data,
41	headers=["Molecule ID", "Level", "Type", "Result (J/mol/K)"],
42	tablefmt="grid",
43	)
44	logger.info(f"\n{table_str}")	×
45
46	# Log residue data
47	if self.residue_data:	3✔
48	logger.info("Residue Data Table:")	×
49	table_str = tabulate(	×
50	self.residue_data,
51	headers=["Molecule ID", "Residue", "Type", "Result (J/mol/K)"],
52	tablefmt="grid",
53	)
54	logger.info(f"\n{table_str}")	×

CCPBioSim / CodeEntropy / 14334168434

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