scitex_logging

scitex_logging.getLogger(name=None)[source]

Return a logger with the specified name, creating it if necessary.

If no name is specified, return the root logger.

scitex_logging.configure(level='info', log_file=None, enable_file=True, enable_console=True, capture_prints=True, max_file_size=10485760, backup_count=5)[source]

Configure logging for SciTeX with both console and file output.

Parameters:

level (Union[str, int]) – Log level (string or logging constant)
log_file (Optional[str]) – Path to log file (default: ~/.scitex/logging/runtime/scitex-YYYY-MM-DD.log)
enable_file (bool) – Whether to enable file logging
enable_console (bool) – Whether to enable console logging
capture_prints (bool) – Whether to capture print() statements to logs
max_file_size (int) – Maximum size of log file before rotation (default: 10MB)
backup_count (int) – Number of backup files to keep (default: 5)

scitex_logging.set_level(level)[source]: Set global log level for all SciTeX loggers.

scitex_logging.get_level()[source]: Get current global log level.

scitex_logging.enable_file_logging(enabled=True)[source]: Enable or disable file logging globally.

scitex_logging.is_file_logging_enabled()[source]: Check if file logging is enabled.

scitex_logging.get_log_path()[source]: Get the current log file path.

class scitex_logging.Tee(stream, log_path, verbose=True)[source]

Bases: object

__init__(stream, log_path, verbose=True)[source]

write(data)[source]

Return type:: None

flush()[source]

Return type:: None

isatty()[source]

Return type:: bool

fileno()[source]

Return type:: int

property buffer

close()[source]: Explicitly close the log file.

scitex_logging.tee(sys, sdir=None, verbose=True)[source]

Redirects stdout and stderr to both console and log files.

Example

>>> import sys
>>> sys.stdout, sys.stderr = tee(sys)
>>> print("abc")  # stdout
>>> print(1 / 0)  # stderr

Parameters:

sys_module (module) – System module containing stdout and stderr
sdir (str, optional) – Directory for log files
verbose (bool, default=True) – Whether to print log file locations

Returns:

Wrapped stdout and stderr objects

Return type:

tuple[Any, Any]

scitex_logging.log_to_file(file_path, level=10, mode='w', formatter=None)[source]

Context manager to temporarily log all output to a specific file.

Usage:

import scitex_logging as logging logger = logging.getLogger(__name__)

with logging.log_to_file(“/path/to/log.txt”):: logger.info(“This goes to both console and /path/to/log.txt”) logger.success(“This too!”)

Parameters:

file_path (Union[str, Path]) – Path to log file
level (int) – Logging level for this handler (default: DEBUG)
mode (str) – File mode (‘w’ for overwrite, ‘a’ for append)
formatter (Optional[Formatter]) – Custom formatter (default: SciTeXFileFormatter)

Yields:

The file handler (can be ignored)

exception scitex_logging.SciTeXWarning[source]

Bases: UserWarning

Base warning class for all SciTeX warnings.

exception scitex_logging.UnitWarning[source]

Bases: SciTeXWarning

Warning for axis label unit issues (educational for SI conventions).

Raised when: - Axis labels are missing units - Units use parentheses instead of brackets (SI prefers []) - Units use division instead of negative exponents (m/s vs m·s⁻¹)

exception scitex_logging.StyleWarning[source]

Bases: SciTeXWarning

Warning for style/formatting issues.

exception scitex_logging.SciTeXDeprecationWarning[source]

Bases: SciTeXWarning

Warning for deprecated SciTeX features.

exception scitex_logging.PerformanceWarning[source]

Bases: SciTeXWarning

Warning for performance issues.

exception scitex_logging.DataLossWarning[source]

Bases: SciTeXWarning

Warning for potential data loss.

scitex_logging.warn(message, category=<class 'scitex_logging._warnings.SciTeXWarning'>, stacklevel=2)[source]

Emit a warning (like warnings.warn but integrated with scitex.logging).

Parameters:

message (str) – Warning message
category (type) – Warning category (default: SciTeXWarning)
stacklevel (int) – Stack level for source location (default: 2 = caller)

Return type:

None

Examples

>>> import scitex.logging as logging
>>> from scitex.logging import UnitWarning
>>> logging.warn("X axis has no units", UnitWarning)

scitex_logging.filterwarnings(action, category=<class 'scitex_logging._warnings.SciTeXWarning'>, message=None)[source]

Control warning behavior (like warnings.filterwarnings).

Parameters:

action (str) – One of: - “ignore”: Never show this warning - “error”: Raise as exception - “always”: Always show - “default”: Show first occurrence per location - “once”: Show only once total - “module”: Show once per module
category (type) – Warning category (default: SciTeXWarning = all)
message (str, optional) – Regex pattern to match warning message (not implemented yet)

Return type:

None

Examples

>>> import scitex.logging as logging
>>> from scitex.logging import UnitWarning
>>> logging.filterwarnings("ignore", category=UnitWarning)

scitex_logging.resetwarnings()[source]

Reset all warning filters to default behavior.

Return type:: None

scitex_logging.warn_deprecated(old_name, new_name, version=None)[source]

Issue a deprecation warning.

Return type:: None

scitex_logging.warn_performance(operation, suggestion)[source]

Issue a performance warning.

Return type:: None

scitex_logging.warn_data_loss(operation, detail)[source]

Issue a data loss warning.

Return type:: None

exception scitex_logging.SciTeXError(message, context=None, suggestion=None)[source]

Bases: Exception

Base Exception class for all SciTeX errors.

__init__(message, context=None, suggestion=None)[source]

Initialize SciTeX error with detailed information.

Parameters:

message (str) – The error message
context (dict, optional) – Additional context information (e.g., file paths, variable values)
suggestion (str, optional) – Suggested fix or action

exception scitex_logging.ConfigurationError(message, context=None, suggestion=None)[source]

Bases: SciTeXError

Raised when there are issues with SciTeX configuration.

exception scitex_logging.ConfigFileNotFoundError(filepath)[source]

Bases: ConfigurationError

Raised when a required configuration file is not found.

__init__(filepath)[source]

Initialize SciTeX error with detailed information.

Parameters:

message (str) – The error message
context (dict, optional) – Additional context information (e.g., file paths, variable values)
suggestion (str, optional) – Suggested fix or action

exception scitex_logging.ConfigKeyError(key, available_keys=None)[source]

Bases: ConfigurationError

Raised when a required configuration key is missing.

__init__(key, available_keys=None)[source]

Initialize SciTeX error with detailed information.

Parameters:

message (str) – The error message
context (dict, optional) – Additional context information (e.g., file paths, variable values)
suggestion (str, optional) – Suggested fix or action

exception scitex_logging.IOError(message, context=None, suggestion=None)[source]

Bases: SciTeXError

Base class for input/output related errors.

exception scitex_logging.FileFormatError(filepath, expected_format=None, actual_format=None)[source]

Bases: IOError

Raised when file format is not supported or incorrect.

__init__(filepath, expected_format=None, actual_format=None)[source]

Initialize SciTeX error with detailed information.

Parameters:

message (str) – The error message
context (dict, optional) – Additional context information (e.g., file paths, variable values)
suggestion (str, optional) – Suggested fix or action

exception scitex_logging.SaveError(filepath, reason)[source]

Bases: IOError

Raised when saving data fails.

__init__(filepath, reason)[source]

Initialize SciTeX error with detailed information.

Parameters:

message (str) – The error message
context (dict, optional) – Additional context information (e.g., file paths, variable values)
suggestion (str, optional) – Suggested fix or action

exception scitex_logging.LoadError(filepath, reason)[source]

Bases: IOError

Raised when loading data fails.

__init__(filepath, reason)[source]

Initialize SciTeX error with detailed information.

Parameters:

message (str) – The error message
context (dict, optional) – Additional context information (e.g., file paths, variable values)
suggestion (str, optional) – Suggested fix or action

exception scitex_logging.ScholarError(message, context=None, suggestion=None)[source]

Bases: SciTeXError

Base class for scholar module errors.

exception scitex_logging.SearchError(query, source, reason)[source]

Bases: ScholarError

Raised when paper search fails.

__init__(query, source, reason)[source]

Initialize SciTeX error with detailed information.

Parameters:

message (str) – The error message
context (dict, optional) – Additional context information (e.g., file paths, variable values)
suggestion (str, optional) – Suggested fix or action

exception scitex_logging.EnrichmentError(paper_title, reason)[source]

Bases: ScholarError

Raised when paper enrichment fails.

__init__(paper_title, reason)[source]

Initialize SciTeX error with detailed information.

Parameters:

message (str) – The error message
context (dict, optional) – Additional context information (e.g., file paths, variable values)
suggestion (str, optional) – Suggested fix or action

exception scitex_logging.PDFDownloadError(url, reason)[source]

Bases: ScholarError

Raised when PDF download fails.

__init__(url, reason)[source]

Initialize SciTeX error with detailed information.

Parameters:

message (str) – The error message
context (dict, optional) – Additional context information (e.g., file paths, variable values)
suggestion (str, optional) – Suggested fix or action

exception scitex_logging.DOIResolutionError(doi, reason)[source]

Bases: ScholarError

Raised when DOI resolution fails.

__init__(doi, reason)[source]

Initialize SciTeX error with detailed information.

Parameters:

message (str) – The error message
context (dict, optional) – Additional context information (e.g., file paths, variable values)
suggestion (str, optional) – Suggested fix or action

exception scitex_logging.PDFExtractionError(filepath, reason)[source]

Bases: ScholarError

Raised when PDF text extraction fails.

__init__(filepath, reason)[source]

Initialize SciTeX error with detailed information.

Parameters:

message (str) – The error message
context (dict, optional) – Additional context information (e.g., file paths, variable values)
suggestion (str, optional) – Suggested fix or action

exception scitex_logging.BibTeXEnrichmentError(bibtex_file, reason)[source]

Bases: ScholarError

Raised when BibTeX enrichment fails.

__init__(bibtex_file, reason)[source]

Initialize SciTeX error with detailed information.

Parameters:

message (str) – The error message
context (dict, optional) – Additional context information (e.g., file paths, variable values)
suggestion (str, optional) – Suggested fix or action

exception scitex_logging.TranslatorError(translator_name, reason)[source]

Bases: ScholarError

Raised when Zotero translator operations fail.

__init__(translator_name, reason)[source]

Initialize SciTeX error with detailed information.

Parameters:

message (str) – The error message
context (dict, optional) – Additional context information (e.g., file paths, variable values)
suggestion (str, optional) – Suggested fix or action

exception scitex_logging.AuthenticationError(provider, reason='')[source]

Bases: ScholarError

Raised when authentication fails.

__init__(provider, reason='')[source]

Initialize SciTeX error with detailed information.

Parameters:

message (str) – The error message
context (dict, optional) – Additional context information (e.g., file paths, variable values)
suggestion (str, optional) – Suggested fix or action

exception scitex_logging.PlottingError(message, context=None, suggestion=None)[source]

Bases: SciTeXError

Base class for plotting-related errors.

exception scitex_logging.FigureNotFoundError(fig_id)[source]

Bases: PlottingError

Raised when attempting to operate on a non-existent figure.

__init__(fig_id)[source]

Initialize SciTeX error with detailed information.

Parameters:

message (str) – The error message
context (dict, optional) – Additional context information (e.g., file paths, variable values)
suggestion (str, optional) – Suggested fix or action

exception scitex_logging.AxisError(message, axis_info=None)[source]

Bases: PlottingError

Raised when there are issues with plot axes.

__init__(message, axis_info=None)[source]

Initialize SciTeX error with detailed information.

Parameters:

message (str) – The error message
context (dict, optional) – Additional context information (e.g., file paths, variable values)
suggestion (str, optional) – Suggested fix or action

exception scitex_logging.DataError(message, context=None, suggestion=None)[source]

Bases: SciTeXError

Base class for data processing errors.

exception scitex_logging.ShapeError(expected_shape, actual_shape, operation)[source]

Bases: DataError

Raised when data shapes are incompatible.

__init__(expected_shape, actual_shape, operation)[source]

Initialize SciTeX error with detailed information.

Parameters:

message (str) – The error message
context (dict, optional) – Additional context information (e.g., file paths, variable values)
suggestion (str, optional) – Suggested fix or action

exception scitex_logging.DTypeError(expected_dtype, actual_dtype, operation)[source]

Bases: DataError

Raised when data types are incompatible.

__init__(expected_dtype, actual_dtype, operation)[source]

Initialize SciTeX error with detailed information.

Parameters:

message (str) – The error message
context (dict, optional) – Additional context information (e.g., file paths, variable values)
suggestion (str, optional) – Suggested fix or action

exception scitex_logging.PathError(message, context=None, suggestion=None)[source]

Bases: SciTeXError

Base class for path-related errors.

exception scitex_logging.InvalidPathError(path, reason)[source]

Bases: PathError

Raised when a path is invalid or doesn’t follow SciTeX conventions.

__init__(path, reason)[source]

Initialize SciTeX error with detailed information.

Parameters:

message (str) – The error message
context (dict, optional) – Additional context information (e.g., file paths, variable values)
suggestion (str, optional) – Suggested fix or action

exception scitex_logging.PathNotFoundError(path)[source]

Bases: PathError

Raised when a required path doesn’t exist.

__init__(path)[source]

Initialize SciTeX error with detailed information.

Parameters:

message (str) – The error message
context (dict, optional) – Additional context information (e.g., file paths, variable values)
suggestion (str, optional) – Suggested fix or action

exception scitex_logging.TemplateError(message, context=None, suggestion=None)[source]

Bases: SciTeXError

Base class for template-related errors.

exception scitex_logging.TemplateViolationError(filepath, violation)[source]

Bases: TemplateError

Raised when SciTeX template is not followed.

__init__(filepath, violation)[source]

Initialize SciTeX error with detailed information.

Parameters:

message (str) – The error message
context (dict, optional) – Additional context information (e.g., file paths, variable values)
suggestion (str, optional) – Suggested fix or action

exception scitex_logging.NNError(message, context=None, suggestion=None)[source]

Bases: SciTeXError

Base class for neural network module errors.

exception scitex_logging.ModelError(model_name, reason)[source]

Bases: NNError

Raised when there are issues with neural network models.

__init__(model_name, reason)[source]

Initialize SciTeX error with detailed information.

Parameters:

message (str) – The error message
context (dict, optional) – Additional context information (e.g., file paths, variable values)
suggestion (str, optional) – Suggested fix or action

exception scitex_logging.StatsError(message, context=None, suggestion=None)[source]

Bases: SciTeXError

Base class for statistics module errors.

exception scitex_logging.TestError(test_name, reason)[source]

Bases: StatsError

Raised when statistical tests fail.

__init__(test_name, reason)[source]

Initialize SciTeX error with detailed information.

Parameters:

message (str) – The error message
context (dict, optional) – Additional context information (e.g., file paths, variable values)
suggestion (str, optional) – Suggested fix or action

scitex_logging.check_path(path)[source]

Validate a path according to SciTeX conventions.

Return type:: None

scitex_logging.check_file_exists(filepath)[source]

Check if a file exists.

Return type:: None

scitex_logging.check_shape_compatibility(shape1, shape2, operation)[source]

Check if two shapes are compatible for an operation.

Return type:: None