id int64 0 328k | repository_name stringlengths 7 58 | file_path stringlengths 9 302 | class_name stringlengths 5 256 | human_written_code stringlengths 16 2.16M | class_skeleton stringlengths 18 1.49M ⌀ | total_program_units int64 1 1.76k | total_doc_str int64 0 771 | AvgCountLine float64 0 7.89k | AvgCountLineBlank float64 0 297 | AvgCountLineCode float64 0 7.89k | AvgCountLineComment float64 0 7.89k | AvgCyclomatic float64 0 130 | CommentToCodeRatio float64 0 168 | CountClassBase float64 0 40 | CountClassCoupled float64 0 583 | CountClassCoupledModified float64 0 575 | CountClassDerived float64 0 5.35k | CountDeclInstanceMethod float64 0 529 | CountDeclInstanceVariable float64 0 296 | CountDeclMethod float64 0 599 | CountDeclMethodAll float64 0 1.12k | CountLine float64 1 40.4k | CountLineBlank float64 0 8.16k | CountLineCode float64 1 25.7k | CountLineCodeDecl float64 1 8.15k | CountLineCodeExe float64 0 24.2k | CountLineComment float64 0 16.5k | CountStmt float64 1 9.71k | CountStmtDecl float64 1 8.15k | CountStmtExe float64 0 9.69k | MaxCyclomatic float64 0 759 | MaxInheritanceTree float64 0 16 | MaxNesting float64 0 34 | SumCyclomatic float64 0 2.9k |
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325,800 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/core/managers/validation_manager.py | managers.validation_manager.FigureValidatorWrapper | from ..error_codes import ErrorCode, create_validation_error
from typing import Any, Callable, Dict, List, Optional, Set, Union
import time
from pathlib import Path
from ...validators.base_validator import ValidationError, ValidationLevel
class FigureValidatorWrapper(BaseValidator):
"""Wrapper for figure validator... |
class FigureValidatorWrapper(BaseValidator):
'''Wrapper for figure validator.'''
def __init__(self):
pass
def validate(self, manuscript_path: Path, context: ValidationContext, strictness: ValidationStrictness, **kwargs) -> ValidationResult:
'''Validate figures.'''
pass
def ge... | 4 | 2 | 14 | 2 | 11 | 1 | 3 | 0.12 | 1 | 10 | 6 | 0 | 3 | 1 | 3 | 27 | 48 | 10 | 34 | 13 | 27 | 4 | 29 | 10 | 24 | 7 | 5 | 3 | 9 |
325,801 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/core/managers/validation_manager.py | managers.validation_manager.MathValidatorWrapper | from ..error_codes import ErrorCode, create_validation_error
from typing import Any, Callable, Dict, List, Optional, Set, Union
import time
from pathlib import Path
from ...validators.base_validator import ValidationError, ValidationLevel
class MathValidatorWrapper(BaseValidator):
"""Wrapper for math validator."""... |
class MathValidatorWrapper(BaseValidator):
'''Wrapper for math validator.'''
def __init__(self):
pass
def validate(self, manuscript_path: Path, context: ValidationContext, strictness: ValidationStrictness, **kwargs) -> ValidationResult:
'''Validate mathematical expressions.'''
pas... | 4 | 2 | 14 | 2 | 11 | 1 | 3 | 0.12 | 1 | 10 | 6 | 0 | 3 | 1 | 3 | 27 | 48 | 10 | 34 | 13 | 27 | 4 | 29 | 10 | 24 | 7 | 5 | 3 | 9 |
325,802 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/core/managers/validation_manager.py | managers.validation_manager.SyntaxValidatorWrapper | from ..error_codes import ErrorCode, create_validation_error
from typing import Any, Callable, Dict, List, Optional, Set, Union
import time
from pathlib import Path
from ...validators.base_validator import ValidationError, ValidationLevel
class SyntaxValidatorWrapper(BaseValidator):
"""Wrapper for syntax validator... |
class SyntaxValidatorWrapper(BaseValidator):
'''Wrapper for syntax validator.'''
def __init__(self):
pass
def validate(self, manuscript_path: Path, context: ValidationContext, strictness: ValidationStrictness, **kwargs) -> ValidationResult:
'''Validate syntax.'''
pass
def get... | 4 | 2 | 14 | 2 | 11 | 1 | 3 | 0.12 | 1 | 10 | 6 | 0 | 3 | 1 | 3 | 27 | 48 | 10 | 34 | 13 | 27 | 4 | 29 | 10 | 24 | 7 | 5 | 3 | 9 |
325,803 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/core/managers/validation_manager.py | managers.validation_manager.ValidationContext | from enum import Enum
class ValidationContext(Enum):
"""Different validation contexts for different scenarios."""
FULL = 'full'
QUICK = 'quick'
BUILD = 'build'
PUBLISH = 'publish'
DEVELOPMENT = 'development'
CI = 'ci' |
class ValidationContext(Enum):
'''Different validation contexts for different scenarios.'''
pass | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 49 | 9 | 1 | 7 | 7 | 6 | 7 | 7 | 7 | 6 | 0 | 4 | 0 | 0 |
325,804 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/core/managers/validation_manager.py | managers.validation_manager.ValidationManager | from ..error_recovery import RecoveryEnhancedMixin
from typing import Any, Callable, Dict, List, Optional, Set, Union
import time
from pathlib import Path
import concurrent.futures
from ..path_manager import PathManager
class ValidationManager(RecoveryEnhancedMixin):
"""Centralized validation orchestration with co... |
class ValidationManager(RecoveryEnhancedMixin):
'''Centralized validation orchestration with configurable validation levels.
Features parallel execution and comprehensive reporting.
Features:
- Multiple validation contexts (full, quick, build, etc.)
- Configurable strictness levels
- Parallel e... | 14 | 14 | 30 | 5 | 18 | 7 | 3 | 0.43 | 1 | 22 | 12 | 0 | 13 | 6 | 13 | 16 | 411 | 80 | 232 | 88 | 197 | 100 | 147 | 63 | 133 | 10 | 1 | 4 | 42 |
325,805 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/core/managers/validation_manager.py | managers.validation_manager.ValidationResult | from ...validators.base_validator import ValidationError, ValidationLevel
from typing import Any, Callable, Dict, List, Optional, Set, Union
from dataclasses import dataclass, field
@dataclass
class ValidationResult:
"""Result from a single validator."""
validator_name: str
success: bool
duration: floa... | @dataclass
class ValidationResult:
'''Result from a single validator.'''
pass | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 0.11 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 11 | 1 | 9 | 6 | 8 | 1 | 9 | 6 | 8 | 0 | 0 | 0 | 0 |
325,806 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/core/managers/validation_manager.py | managers.validation_manager.ValidationStrictness | from enum import Enum
class ValidationStrictness(Enum):
"""Validation strictness levels."""
STRICT = 'strict'
NORMAL = 'normal'
LENIENT = 'lenient'
PERMISSIVE = 'permissive' |
class ValidationStrictness(Enum):
'''Validation strictness levels.'''
pass | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 49 | 7 | 1 | 5 | 5 | 4 | 5 | 5 | 5 | 4 | 0 | 4 | 0 | 0 |
325,807 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/core/managers/validation_manager.py | managers.validation_manager.ValidationSummary | from typing import Any, Callable, Dict, List, Optional, Set, Union
from dataclasses import dataclass, field
@dataclass
class ValidationSummary:
"""Summary of complete validation run."""
success: bool
total_duration: float
context: ValidationContext
strictness: ValidationStrictness
validators_ru... | @dataclass
class ValidationSummary:
'''Summary of complete validation run.'''
pass | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 0.07 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 16 | 1 | 14 | 3 | 13 | 1 | 14 | 3 | 13 | 0 | 0 | 0 | 0 |
325,808 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/core/managers/validation_manager.py | managers.validation_manager.ValidatorConfig | from dataclasses import dataclass, field
from typing import Any, Callable, Dict, List, Optional, Set, Union
@dataclass
class ValidatorConfig:
"""Configuration for individual validators."""
validator_name: str
enabled: bool = True
required: bool = True
timeout: Optional[int] = None
retry_count: ... | @dataclass
class ValidatorConfig:
'''Configuration for individual validators.'''
pass | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 0.1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 12 | 1 | 10 | 9 | 9 | 1 | 10 | 9 | 9 | 0 | 0 | 0 | 0 |
325,809 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/core/managers/workflow_manager.py | managers.workflow_manager.CommandStep | import subprocess
from typing import Any, Callable, Dict, List, Optional, Set
class CommandStep(WorkflowStep):
"""Workflow step that executes a shell command."""
def __init__(self, config: StepConfig, command: str, shell: bool=True):
"""Initialize command step.
Args:
config: Step ... |
class CommandStep(WorkflowStep):
'''Workflow step that executes a shell command.'''
def __init__(self, config: StepConfig, command: str, shell: bool=True):
'''Initialize command step.
Args:
config: Step configuration
command: Shell command to execute
shell: ... | 3 | 3 | 13 | 2 | 7 | 4 | 2 | 0.53 | 1 | 7 | 1 | 0 | 2 | 2 | 2 | 27 | 29 | 6 | 15 | 7 | 12 | 8 | 13 | 6 | 10 | 3 | 5 | 2 | 4 |
325,810 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/core/managers/workflow_manager.py | managers.workflow_manager.ExecutionMode | from enum import Enum
class ExecutionMode(Enum):
"""Workflow execution modes."""
SEQUENTIAL = 'sequential'
PARALLEL = 'parallel'
ADAPTIVE = 'adaptive' |
class ExecutionMode(Enum):
'''Workflow execution modes.'''
pass | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 49 | 6 | 1 | 4 | 4 | 3 | 4 | 4 | 4 | 3 | 0 | 4 | 0 | 0 |
325,811 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/core/managers/workflow_manager.py | managers.workflow_manager.FunctionStep | from typing import Any, Callable, Dict, List, Optional, Set
class FunctionStep(WorkflowStep):
"""Workflow step that wraps a function."""
def __init__(self, config: StepConfig, function: Callable):
"""Initialize function step.
Args:
config: Step configuration
function: ... |
class FunctionStep(WorkflowStep):
'''Workflow step that wraps a function.'''
def __init__(self, config: StepConfig, function: Callable):
'''Initialize function step.
Args:
config: Step configuration
function: Function to execute
'''
pass
def execute... | 3 | 3 | 6 | 1 | 3 | 3 | 1 | 1.17 | 1 | 4 | 1 | 0 | 2 | 1 | 2 | 27 | 16 | 3 | 6 | 4 | 3 | 7 | 6 | 4 | 3 | 1 | 5 | 0 | 2 |
325,812 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/core/managers/workflow_manager.py | managers.workflow_manager.StepConfig | from dataclasses import dataclass, field
from typing import Any, Callable, Dict, List, Optional, Set
@dataclass
class StepConfig:
"""Configuration for workflow steps."""
name: str
description: str = ''
dependencies: List[str] = field(default_factory=list)
condition: Optional[Callable[[], bool]] = N... | @dataclass
class StepConfig:
'''Configuration for workflow steps.'''
pass | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 0.33 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 14 | 1 | 12 | 11 | 11 | 4 | 12 | 11 | 11 | 0 | 0 | 0 | 0 |
325,813 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/core/managers/workflow_manager.py | managers.workflow_manager.StepResult | from typing import Any, Callable, Dict, List, Optional, Set
from dataclasses import dataclass, field
@dataclass
class StepResult:
"""Result of step execution."""
status: StepStatus
output: Any = None
error: Optional[Exception] = None
duration: float = 0.0
retries: int = 0
metadata: Dict[str... | @dataclass
class StepResult:
'''Result of step execution.'''
@property
def success(self) -> bool:
'''Check if step was successful.'''
pass
@property
def failed(self) -> bool:
'''Check if step failed.'''
pass | 6 | 3 | 3 | 0 | 2 | 1 | 1 | 0.23 | 0 | 2 | 1 | 0 | 2 | 0 | 2 | 2 | 19 | 3 | 13 | 10 | 8 | 3 | 11 | 8 | 8 | 1 | 0 | 0 | 2 |
325,814 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/core/managers/workflow_manager.py | managers.workflow_manager.StepStatus | from enum import Enum
class StepStatus(Enum):
"""Individual step execution status."""
PENDING = 'pending'
READY = 'ready'
RUNNING = 'running'
COMPLETED = 'completed'
FAILED = 'failed'
SKIPPED = 'skipped'
RETRYING = 'retrying' |
class StepStatus(Enum):
'''Individual step execution status.'''
pass | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0.25 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 49 | 10 | 1 | 8 | 8 | 7 | 2 | 8 | 8 | 7 | 0 | 4 | 0 | 0 |
325,815 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/core/managers/workflow_manager.py | managers.workflow_manager.Workflow | import time
import threading
from .cache_manager import get_cache_manager
from .resource_manager import get_resource_manager, managed_resources
from typing import Any, Callable, Dict, List, Optional, Set
from .state_manager import get_state_manager
class Workflow:
"""Configurable multi-step workflow orchestrator.
... |
class Workflow:
'''Configurable multi-step workflow orchestrator.
Features:
- Dependency-based step ordering
- Parallel execution of independent steps
- Conditional step execution
- Retry mechanisms with exponential backoff
- Comprehensive error handling and recovery
- Progress tracking... | 16 | 16 | 26 | 5 | 14 | 7 | 4 | 0.56 | 0 | 15 | 9 | 0 | 15 | 12 | 15 | 15 | 425 | 89 | 218 | 82 | 199 | 121 | 200 | 75 | 183 | 12 | 0 | 5 | 67 |
325,816 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/core/managers/workflow_manager.py | managers.workflow_manager.WorkflowConfig | from dataclasses import dataclass, field
from typing import Any, Callable, Dict, List, Optional, Set
@dataclass
class WorkflowConfig:
"""Configuration for workflows."""
name: str
description: str = ''
execution_mode: ExecutionMode = ExecutionMode.ADAPTIVE
max_parallel_steps: int = 4
overall_tim... | @dataclass
class WorkflowConfig:
'''Configuration for workflows.'''
pass | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 0.4 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 12 | 1 | 10 | 9 | 9 | 4 | 10 | 9 | 9 | 0 | 0 | 0 | 0 |
325,817 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/core/managers/workflow_manager.py | managers.workflow_manager.WorkflowManager | from typing import Any, Callable, Dict, List, Optional, Set
from ..error_recovery import RecoveryEnhancedMixin
class WorkflowManager(RecoveryEnhancedMixin):
"""Central manager for workflow definitions and execution.
Features:
- Workflow template library
- Execution history and analytics
- Workflow... |
class WorkflowManager(RecoveryEnhancedMixin):
'''Central manager for workflow definitions and execution.
Features:
- Workflow template library
- Execution history and analytics
- Workflow composition and reuse
- Integration with state and resource management
'''
def __init__(self):
... | 12 | 11 | 15 | 2 | 9 | 3 | 1 | 0.62 | 1 | 7 | 3 | 0 | 10 | 3 | 10 | 13 | 142 | 30 | 69 | 19 | 57 | 43 | 44 | 19 | 32 | 2 | 1 | 1 | 12 |
325,818 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/core/managers/workflow_manager.py | managers.workflow_manager.WorkflowStatus | from enum import Enum
class WorkflowStatus(Enum):
"""Workflow execution status."""
PENDING = 'pending'
RUNNING = 'running'
COMPLETED = 'completed'
FAILED = 'failed'
CANCELLED = 'cancelled'
PAUSED = 'paused' |
class WorkflowStatus(Enum):
'''Workflow execution status.'''
pass | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0.14 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 49 | 9 | 1 | 7 | 7 | 6 | 1 | 7 | 7 | 6 | 0 | 4 | 0 | 0 |
325,819 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/core/managers/workflow_manager.py | managers.workflow_manager.WorkflowStep | from abc import ABC, abstractmethod
from typing import Any, Callable, Dict, List, Optional, Set
import threading
class WorkflowStep(ABC):
"""Abstract base class for workflow steps."""
def __init__(self, config: StepConfig):
"""Initialize workflow step.
Args:
config: Step configura... |
class WorkflowStep(ABC):
'''Abstract base class for workflow steps.'''
def __init__(self, config: StepConfig):
'''Initialize workflow step.
Args:
config: Step configuration
'''
pass
@abstractmethod
def execute(self, context: Dict[str, Any]) -> Any:
'... | 8 | 6 | 10 | 1 | 4 | 5 | 1 | 1.19 | 1 | 6 | 2 | 2 | 5 | 3 | 5 | 25 | 58 | 12 | 21 | 12 | 13 | 25 | 19 | 9 | 13 | 3 | 4 | 2 | 7 |
325,820 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/security/monitor.py | monitor.SecurityEvent | from dataclasses import dataclass, field
from typing import Any, Dict, List, Optional, Set
import time
from datetime import datetime
@dataclass
class SecurityEvent:
"""Represents a security event."""
event_type: SecurityEventType
severity: SecuritySeverity
timestamp: float = field(default_factory=time.... | @dataclass
class SecurityEvent:
'''Represents a security event.'''
def to_dict(self) -> Dict[str, Any]:
'''Convert event to dictionary for serialization.'''
pass | 3 | 2 | 14 | 0 | 13 | 1 | 1 | 0.09 | 0 | 3 | 0 | 0 | 1 | 0 | 1 | 1 | 27 | 2 | 23 | 9 | 21 | 2 | 12 | 9 | 10 | 1 | 0 | 0 | 1 |
325,821 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/security/monitor.py | monitor.SecurityEventType | from enum import Enum
class SecurityEventType(Enum):
"""Types of security events to monitor."""
PATH_TRAVERSAL_ATTEMPT = 'path_traversal_attempt'
SYMLINK_ATTACK = 'symlink_attack'
PERMISSION_VIOLATION = 'permission_violation'
DISK_EXHAUSTION = 'disk_exhaustion'
LARGE_FILE_ATTEMPT = 'large_file_... |
class SecurityEventType(Enum):
'''Types of security events to monitor.'''
pass | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0.09 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 49 | 13 | 1 | 11 | 11 | 10 | 1 | 11 | 11 | 10 | 0 | 4 | 0 | 0 |
325,822 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/security/monitor.py | monitor.SecurityMonitor | import json
from datetime import datetime
from pathlib import Path
from typing import Any, Dict, List, Optional, Set
import time
import logging
import hashlib
class SecurityMonitor:
"""Main security monitoring system."""
def __init__(self, log_dir: Optional[Path]=None, alert_threshold: SecuritySeverity=Securi... |
class SecurityMonitor:
'''Main security monitoring system.'''
def __init__(self, log_dir: Optional[Path]=None, alert_threshold: SecuritySeverity=SecuritySeverity.HIGH, max_events: int=10000, rate_limit_window: int=60, rate_limit_max: int=100):
'''Initialize security monitor.
Args:
... | 13 | 13 | 27 | 4 | 17 | 6 | 2 | 0.4 | 0 | 14 | 3 | 0 | 12 | 14 | 12 | 12 | 344 | 60 | 204 | 56 | 183 | 82 | 105 | 46 | 91 | 4 | 0 | 3 | 27 |
325,823 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/security/monitor.py | monitor.SecuritySeverity | from enum import Enum
class SecuritySeverity(Enum):
"""Security event severity levels."""
CRITICAL = 'critical'
HIGH = 'high'
MEDIUM = 'medium'
LOW = 'low'
INFO = 'info' |
class SecuritySeverity(Enum):
'''Security event severity levels.'''
pass | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 49 | 8 | 1 | 6 | 6 | 5 | 6 | 6 | 6 | 5 | 0 | 4 | 0 | 0 |
325,824 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/.github/scripts/monitoring/cross_repo_health.py | monitoring.cross_repo_health.CrossRepoHealthMonitor | import aiohttp
from config import get_github_token
from typing import Dict, List, Optional
import asyncio
from datetime import datetime, timedelta
from logger import setup_logger
class CrossRepoHealthMonitor:
"""Monitor health across all rxiv-maker repositories."""
def __init__(self, debug: bool=False):
... |
class CrossRepoHealthMonitor:
'''Monitor health across all rxiv-maker repositories.'''
def __init__(self, debug: bool=False):
pass
async def check_repository_health(self, session: aiohttp.ClientSession, repo_name: str, repo_path: str) -> Dict:
'''Check health of a single repository.'''
... | 9 | 8 | 26 | 4 | 20 | 2 | 5 | 0.11 | 0 | 7 | 0 | 0 | 8 | 4 | 8 | 8 | 220 | 38 | 164 | 58 | 155 | 18 | 129 | 48 | 120 | 8 | 0 | 4 | 36 |
325,825 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/nox_utils/cleanup.py | nox_utils.cleanup.CleanupError | class CleanupError(Exception):
"""Exception raised when cleanup operations fail."""
pass | class CleanupError(Exception):
'''Exception raised when cleanup operations fail.'''
pass | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0.5 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 10 | 4 | 1 | 2 | 1 | 1 | 1 | 2 | 1 | 1 | 0 | 3 | 0 | 0 |
325,826 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/nox_utils/cleanup.py | nox_utils.cleanup.CleanupManager | from typing import Dict, List, Tuple
import shutil
from pathlib import Path
class CleanupManager:
"""Comprehensive cleanup manager for test environments."""
def __init__(self):
self.engines = []
self.disk_monitor = DiskSpaceMonitor()
for engine_type in ['docker', 'podman']:
... |
class CleanupManager:
'''Comprehensive cleanup manager for test environments.'''
def __init__(self):
pass
def pre_test_cleanup(self, aggressive: bool=False) -> Dict[str, any]:
'''Perform cleanup before running tests.'''
pass
def post_test_cleanup(self, aggressive: bool=True) ... | 6 | 5 | 33 | 6 | 24 | 3 | 7 | 0.13 | 0 | 6 | 2 | 0 | 5 | 2 | 5 | 5 | 173 | 35 | 122 | 37 | 116 | 16 | 111 | 35 | 105 | 10 | 0 | 3 | 37 |
325,827 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/nox_utils/cleanup.py | nox_utils.cleanup.ContainerEngine | from typing import Dict, List, Tuple
import subprocess
class ContainerEngine:
"""Base class for container engine operations."""
def __init__(self, engine_type: str):
self.engine_type = engine_type.lower()
if self.engine_type not in ['docker', 'podman']:
raise ValueError(f'Unsupport... |
class ContainerEngine:
'''Base class for container engine operations.'''
def __init__(self, engine_type: str):
pass
def is_available(self) -> bool:
'''Check if the container engine is available.'''
pass
def run_command(self, args: List[str], timeout: int=30) -> Tuple[bool, st... | 12 | 11 | 14 | 2 | 11 | 1 | 4 | 0.12 | 0 | 8 | 0 | 0 | 11 | 1 | 11 | 11 | 163 | 29 | 120 | 42 | 106 | 14 | 114 | 41 | 100 | 6 | 0 | 4 | 45 |
325,828 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/nox_utils/cleanup.py | nox_utils.cleanup.DiskSpaceMonitor | from typing import Dict, List, Tuple
import shutil
class DiskSpaceMonitor:
"""Monitor and report disk space usage."""
@staticmethod
def get_disk_usage(path: str='.') -> Tuple[int, int, int]:
"""Get disk usage statistics for a path.
Returns:
Tuple of (total, used, free) space i... |
class DiskSpaceMonitor:
'''Monitor and report disk space usage.'''
@staticmethod
def get_disk_usage(path: str='.') -> Tuple[int, int, int]:
'''Get disk usage statistics for a path.
Returns:
Tuple of (total, used, free) space in bytes
'''
pass
@staticmethod
... | 9 | 5 | 10 | 1 | 8 | 2 | 2 | 0.23 | 0 | 5 | 0 | 0 | 0 | 0 | 4 | 4 | 51 | 8 | 35 | 17 | 26 | 8 | 27 | 12 | 22 | 3 | 0 | 2 | 9 |
325,829 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/core/path_manager.py | path_manager.PathManager | import os
from pathlib import Path
from typing import Optional, Union
from ..utils.platform import platform_detector
class PathManager:
"""Centralized path management for rxiv-maker operations.
Handles:
- Manuscript path resolution with proper trailing slash handling
- Cross-platform path normalizatio... |
class PathManager:
'''Centralized path management for rxiv-maker operations.
Handles:
- Manuscript path resolution with proper trailing slash handling
- Cross-platform path normalization
- Docker container path translation
- Style directory auto-detection (dev vs installed)
- Output directo... | 30 | 23 | 14 | 2 | 6 | 6 | 2 | 0.87 | 0 | 5 | 1 | 0 | 22 | 8 | 22 | 22 | 342 | 64 | 150 | 58 | 115 | 130 | 118 | 46 | 95 | 5 | 0 | 2 | 43 |
325,830 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/core/path_manager.py | path_manager.PathResolutionError | class PathResolutionError(Exception):
"""Exception raised when path resolution fails."""
pass | class PathResolutionError(Exception):
'''Exception raised when path resolution fails.'''
pass | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0.5 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 10 | 4 | 1 | 2 | 1 | 1 | 1 | 2 | 1 | 1 | 0 | 3 | 0 | 0 |
325,831 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/.github/scripts/release/orchestrator.py | release.orchestrator.ReleaseOrchestrator | from config import ConfigLoader, get_current_version, get_github_token, get_pypi_token
import os
from utils import check_github_release_exists, check_pypi_package_available, validate_environment, wait_for_condition
from logger import log_section, log_step, setup_logger
class ReleaseOrchestrator:
"""Main release or... |
class ReleaseOrchestrator:
'''Main release orchestration class.'''
def __init__(self, dry_run: bool=False, force: bool=False, debug: bool=False):
'''
Initialize release orchestrator.
Args:
dry_run: Skip actual publishing steps
force: Force release even if valida... | 13 | 12 | 38 | 7 | 25 | 6 | 5 | 0.24 | 0 | 5 | 1 | 0 | 11 | 10 | 11 | 11 | 466 | 92 | 304 | 65 | 286 | 72 | 225 | 59 | 207 | 8 | 0 | 5 | 54 |
325,832 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/cli/config.py | rxiv_maker.cli.config.Config | from pathlib import Path
from typing import Any
from rxiv_maker.utils.unicode_safe import console_error, console_success, console_warning, safe_console_print
class Config:
"""Configuration manager for rxiv-maker."""
def __init__(self):
"""Initialize configuration manager."""
self.config_dir = ... |
class Config:
'''Configuration manager for rxiv-maker.'''
def __init__(self):
'''Initialize configuration manager.'''
pass
def load_config(self) -> None:
'''Load configuration from file.'''
pass
def get_default_config(self) -> dict[str, Any]:
'''Get default co... | 12 | 11 | 15 | 1 | 13 | 1 | 3 | 0.12 | 0 | 8 | 0 | 0 | 10 | 3 | 10 | 10 | 175 | 24 | 136 | 38 | 121 | 16 | 82 | 35 | 67 | 5 | 0 | 3 | 28 |
325,833 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/cli/framework.py | rxiv_maker.cli.framework.BaseCommand | from abc import ABC, abstractmethod
from ..core.path_manager import PathManager, PathResolutionError
from typing import Any, Optional
from rich.console import Console
from rich.progress import Progress, SpinnerColumn, TextColumn
from ..core.environment_manager import EnvironmentManager
import sys
import click
class Ba... |
class BaseCommand(ABC):
'''Base class for rxiv-maker CLI commands.
Features:
- Consistent path resolution and validation
- Standardized error handling and exit codes
- Progress reporting utilities
- Environment variable integration
- Docker readiness checking
- Common logging and consol... | 12 | 11 | 18 | 3 | 8 | 7 | 3 | 1.04 | 1 | 14 | 4 | 2 | 10 | 4 | 10 | 30 | 200 | 41 | 78 | 22 | 65 | 81 | 72 | 18 | 60 | 8 | 4 | 3 | 27 |
325,834 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/cli/framework.py | rxiv_maker.cli.framework.CommandExecutionError | class CommandExecutionError(Exception):
"""Exception raised during command execution."""
def __init__(self, message: str, exit_code: int=1):
super().__init__(message)
self.exit_code = exit_code | class CommandExecutionError(Exception):
'''Exception raised during command execution.'''
def __init__(self, message: str, exit_code: int=1):
pass | 2 | 1 | 3 | 0 | 3 | 0 | 1 | 0.25 | 1 | 3 | 0 | 0 | 1 | 1 | 1 | 11 | 6 | 1 | 4 | 3 | 2 | 1 | 4 | 3 | 2 | 1 | 3 | 0 | 1 |
325,835 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/cli/framework.py | rxiv_maker.cli.framework.FiguresCommand | from typing import Any, Optional
class FiguresCommand(BaseCommand):
"""Figures command implementation using the framework."""
def execute_operation(self, force: bool=False, figures_dir: Optional[str]=None) -> None:
"""Execute figure generation.
Args:
force: Force regeneration of a... |
class FiguresCommand(BaseCommand):
'''Figures command implementation using the framework.'''
def execute_operation(self, force: bool=False, figures_dir: Optional[str]=None) -> None:
'''Execute figure generation.
Args:
force: Force regeneration of all figures
figures_dir... | 2 | 2 | 51 | 10 | 34 | 7 | 9 | 0.23 | 1 | 5 | 2 | 0 | 1 | 1 | 1 | 31 | 54 | 11 | 35 | 9 | 32 | 8 | 27 | 6 | 24 | 9 | 5 | 3 | 9 |
325,836 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/cli/framework.py | rxiv_maker.cli.framework.ValidationCommand | class ValidationCommand(BaseCommand):
"""Validation command implementation using the framework."""
def execute_operation(self, detailed: bool=False, no_doi: bool=False) -> bool:
"""Execute manuscript validation.
Args:
detailed: Show detailed validation report
no_doi: Sk... | class ValidationCommand(BaseCommand):
'''Validation command implementation using the framework.'''
def execute_operation(self, detailed: bool=False, no_doi: bool=False) -> bool:
'''Execute manuscript validation.
Args:
detailed: Show detailed validation report
no_doi: Ski... | 2 | 2 | 43 | 7 | 26 | 10 | 4 | 0.41 | 1 | 3 | 1 | 0 | 1 | 1 | 1 | 31 | 46 | 8 | 27 | 8 | 24 | 11 | 16 | 6 | 13 | 4 | 5 | 2 | 4 |
325,837 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/cli/main.py | rxiv_maker.cli.main.UpdateCheckGroup | import rich_click as click
from ..utils.update_checker import check_for_updates_async, show_update_notification
class UpdateCheckGroup(click.Group):
"""Custom Click group that handles update checking and Docker cleanup."""
def invoke(self, ctx):
"""Invoke command and handle update checking and Docker ... |
class UpdateCheckGroup(click.Group):
'''Custom Click group that handles update checking and Docker cleanup.'''
def invoke(self, ctx):
'''Invoke command and handle update checking and Docker cleanup.'''
pass | 2 | 2 | 47 | 10 | 28 | 9 | 11 | 0.34 | 1 | 2 | 0 | 0 | 1 | 0 | 1 | 1 | 50 | 11 | 29 | 10 | 25 | 10 | 27 | 9 | 23 | 11 | 1 | 4 | 11 |
325,838 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/converters/python_executor.py | rxiv_maker.converters.python_executor.PythonExecutionError | class PythonExecutionError(Exception):
"""Exception raised during Python code execution."""
pass | class PythonExecutionError(Exception):
'''Exception raised during Python code execution.'''
pass | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0.5 | 1 | 0 | 0 | 1 | 0 | 0 | 0 | 10 | 4 | 1 | 2 | 1 | 1 | 1 | 2 | 1 | 1 | 0 | 3 | 0 | 0 |
325,839 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/converters/python_executor.py | rxiv_maker.converters.python_executor.PythonExecutor | import tempfile
import json
import io
from typing import Any, Dict, Optional, Tuple
import subprocess
import sys
import ast
from pathlib import Path
class PythonExecutor:
"""Secure Python code executor for markdown commands."""
def __init__(self, timeout: int=10, max_output_length: int=10000):
"""Init... |
class PythonExecutor:
'''Secure Python code executor for markdown commands.'''
def __init__(self, timeout: int=10, max_output_length: int=10000):
'''Initialize Python executor.
Args:
timeout: Maximum execution time in seconds
max_output_length: Maximum length of capture... | 8 | 8 | 51 | 7 | 33 | 12 | 5 | 0.37 | 0 | 28 | 2 | 0 | 7 | 3 | 7 | 7 | 366 | 55 | 230 | 46 | 220 | 84 | 108 | 41 | 98 | 14 | 0 | 5 | 37 |
325,840 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/converters/python_executor.py | rxiv_maker.converters.python_executor.SecurityError | class SecurityError(PythonExecutionError):
"""Exception raised when code violates security restrictions."""
pass | class SecurityError(PythonExecutionError):
'''Exception raised when code violates security restrictions.'''
pass | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0.5 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 10 | 4 | 1 | 2 | 1 | 1 | 1 | 2 | 1 | 1 | 0 | 4 | 0 | 0 |
325,841 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/docker/build_manager.py | rxiv_maker.docker.build_manager.DockerBuildManager | import time
from typing import Any, Dict, List, Optional, Tuple
from .optimization import DockerBuildOptimizer, DockerResourceManager
import shutil
import subprocess
import platform
from ..utils.platform import platform_detector
from pathlib import Path
import os
class DockerBuildManager:
"""Unified Docker build m... |
class DockerBuildManager:
'''Unified Docker build manager with acceleration and safety features.'''
def __init__(self, mode: str=DockerBuildMode.BALANCED, image_name: str='henriqueslab/rxiv-maker-base:latest', dockerfile_path: Optional[Path]=None, build_context: Optional[Path]=None, max_build_time: int=7200, ... | 12 | 12 | 46 | 7 | 32 | 7 | 7 | 0.21 | 0 | 12 | 3 | 0 | 11 | 16 | 11 | 11 | 515 | 86 | 356 | 90 | 331 | 76 | 257 | 69 | 244 | 14 | 0 | 4 | 74 |
325,842 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/docker/build_manager.py | rxiv_maker.docker.build_manager.DockerBuildMode | class DockerBuildMode:
"""Build mode configuration."""
ACCELERATED = 'accelerated'
SAFE = 'safe'
BALANCED = 'balanced' | class DockerBuildMode:
'''Build mode configuration.'''
pass | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0.25 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 6 | 1 | 4 | 4 | 3 | 1 | 4 | 4 | 3 | 0 | 0 | 0 | 0 |
325,843 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/docker/manager.py | rxiv_maker.docker.manager.DockerManager | from pathlib import Path
import logging
from typing import Any
from ..core.environment_manager import EnvironmentManager
import platform
from ..utils.platform import platform_detector
import subprocess
import time
import contextlib
class DockerManager:
"""Centralized Docker operations manager with session reuse an... | null | 28 | 28 | 33 | 4 | 24 | 6 | 4 | 0.25 | 0 | 18 | 2 | 0 | 27 | 15 | 27 | 27 | 933 | 134 | 656 | 176 | 578 | 161 | 341 | 124 | 310 | 10 | 0 | 5 | 103 |
325,844 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/docker/manager.py | rxiv_maker.docker.manager.DockerSession | from pathlib import Path
import time
import subprocess
class DockerSession:
"""Manages a persistent Docker container session for multiple operations."""
def __init__(self, container_id: str, image: str, workspace_dir: Path):
"""Initialize Docker session.
Args:
container_id: Docker... |
class DockerSession:
'''Manages a persistent Docker container session for multiple operations.'''
def __init__(self, container_id: str, image: str, workspace_dir: Path):
'''Initialize Docker session.
Args:
container_id: Docker container ID
image: Docker image name
... | 4 | 4 | 20 | 2 | 14 | 3 | 3 | 0.25 | 0 | 5 | 0 | 0 | 3 | 5 | 3 | 3 | 64 | 9 | 44 | 11 | 40 | 11 | 30 | 11 | 26 | 5 | 0 | 3 | 9 |
325,845 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/docker/optimization.py | rxiv_maker.docker.optimization.DockerBuildOptimizer | from pathlib import Path
import platform
from rxiv_maker.core.cache.advanced_cache import AdvancedCache
import subprocess
from typing import Any, Dict, List, Optional, Tuple
import tempfile
import os
class DockerBuildOptimizer:
"""Optimizes Docker builds with advanced caching and resource management."""
def _... |
class DockerBuildOptimizer:
'''Optimizes Docker builds with advanced caching and resource management.'''
def __init__(self, cache_dir: Optional[Path]=None):
'''Initialize Docker build optimizer.
Args:
cache_dir: Directory for build caches
'''
pass
def get_optim... | 12 | 12 | 35 | 5 | 25 | 6 | 6 | 0.24 | 0 | 9 | 1 | 0 | 11 | 2 | 11 | 11 | 401 | 65 | 278 | 70 | 258 | 66 | 175 | 62 | 162 | 14 | 0 | 5 | 62 |
325,846 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/docker/optimization.py | rxiv_maker.docker.optimization.DockerResourceManager | import os
from typing import Any, Dict, List, Optional, Tuple
import platform
class DockerResourceManager:
"""Manages Docker container resources and limits."""
def __init__(self):
self.system_info = self._get_system_info()
def _get_system_info(self) -> Dict[str, Any]:
"""Get system resour... |
class DockerResourceManager:
'''Manages Docker container resources and limits.'''
def __init__(self):
pass
def _get_system_info(self) -> Dict[str, Any]:
'''Get system resource information.'''
pass
def get_optimal_container_limits(self, operation_type: str='general', priority:... | 5 | 4 | 28 | 5 | 16 | 8 | 4 | 0.51 | 0 | 4 | 1 | 0 | 4 | 1 | 4 | 4 | 116 | 25 | 65 | 16 | 58 | 33 | 47 | 14 | 42 | 10 | 0 | 1 | 16 |
325,847 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/engines/core/abstract.py | rxiv_maker.engines.core.abstract.AbstractContainerEngine | from typing import Any, Dict, List, Optional
from abc import ABC, abstractmethod
from pathlib import Path
import subprocess
class AbstractContainerEngine(ABC):
"""Abstract base class for container engines (Docker, Podman, etc.)."""
def __init__(self, default_image: str='henriqueslab/rxiv-maker-base:latest', w... | null | 25 | 22 | 43 | 6 | 30 | 8 | 5 | 0.25 | 1 | 19 | 6 | 2 | 21 | 12 | 21 | 41 | 935 | 147 | 638 | 194 | 538 | 161 | 340 | 130 | 299 | 12 | 4 | 4 | 104 |
325,848 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/engines/core/abstract.py | rxiv_maker.engines.core.abstract.ContainerSession | from typing import Any, Dict, List, Optional
from pathlib import Path
import subprocess
class ContainerSession:
"""Represents a persistent container session for multiple operations."""
def __init__(self, container_id: str, image: str, workspace_dir: Path, engine_type: str):
"""Initialize container ses... |
class ContainerSession:
'''Represents a persistent container session for multiple operations.'''
def __init__(self, container_id: str, image: str, workspace_dir: Path, engine_type: str):
'''Initialize container session.
Args:
container_id: Container ID
image: Container ... | 4 | 4 | 31 | 3 | 24 | 5 | 4 | 0.2 | 0 | 6 | 0 | 2 | 3 | 6 | 3 | 3 | 97 | 11 | 74 | 17 | 69 | 15 | 43 | 16 | 38 | 6 | 0 | 3 | 12 |
325,849 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/engines/core/docker_engine.py | rxiv_maker.engines.core.docker_engine.DockerEngine | from .abstract import AbstractContainerEngine, ContainerSession
from pathlib import Path
class DockerEngine(AbstractContainerEngine):
"""Docker container engine implementation."""
@property
def engine_name(self) -> str:
"""Return the name of the container engine."""
return 'docker'
de... |
class DockerEngine(AbstractContainerEngine):
'''Docker container engine implementation.'''
@property
def engine_name(self) -> str:
'''Return the name of the container engine.'''
pass
def _create_session_instance(self, container_id: str, image: str, workspace_dir: Path) -> 'DockerSessio... | 4 | 3 | 3 | 0 | 2 | 1 | 1 | 1.17 | 1 | 3 | 1 | 0 | 2 | 0 | 2 | 43 | 19 | 6 | 6 | 4 | 2 | 7 | 5 | 3 | 2 | 1 | 5 | 0 | 2 |
325,850 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/engines/core/docker_engine.py | rxiv_maker.engines.core.docker_engine.DockerSession | import time
from .abstract import AbstractContainerEngine, ContainerSession
from pathlib import Path
class DockerSession(ContainerSession):
"""Docker-specific container session implementation."""
def __init__(self, container_id: str, image: str, workspace_dir: Path):
super().__init__(container_id, ima... |
class DockerSession(ContainerSession):
'''Docker-specific container session implementation.'''
def __init__(self, container_id: str, image: str, workspace_dir: Path):
pass | 2 | 1 | 3 | 0 | 3 | 0 | 1 | 0.25 | 1 | 3 | 0 | 0 | 1 | 1 | 1 | 4 | 6 | 1 | 4 | 3 | 2 | 1 | 4 | 3 | 2 | 1 | 1 | 0 | 1 |
325,851 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/engines/core/exceptions.py | rxiv_maker.engines.core.exceptions.ContainerEngineError | from typing import Optional
class ContainerEngineError(Exception):
"""Base exception for container engine errors."""
def __init__(self, message: str, engine_type: str, suggestion: Optional[str]=None):
"""Initialize container engine error.
Args:
message: Error message
e... |
class ContainerEngineError(Exception):
'''Base exception for container engine errors.'''
def __init__(self, message: str, engine_type: str, suggestion: Optional[str]=None):
'''Initialize container engine error.
Args:
message: Error message
engine_type: Type of engine (d... | 2 | 2 | 16 | 3 | 7 | 6 | 2 | 0.88 | 1 | 2 | 0 | 7 | 1 | 2 | 1 | 11 | 19 | 4 | 8 | 5 | 6 | 7 | 8 | 5 | 6 | 2 | 3 | 1 | 2 |
325,852 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/engines/core/exceptions.py | rxiv_maker.engines.core.exceptions.ContainerEngineNotFoundError | import platform
class ContainerEngineNotFoundError(ContainerEngineError):
"""Exception raised when container engine binary is not found."""
def __init__(self, engine_type: str):
"""Initialize not found error with installation suggestions."""
system = platform.system().lower()
if engine... |
class ContainerEngineNotFoundError(ContainerEngineError):
'''Exception raised when container engine binary is not found.'''
def __init__(self, engine_type: str):
'''Initialize not found error with installation suggestions.'''
pass | 2 | 2 | 34 | 2 | 31 | 2 | 8 | 0.09 | 1 | 2 | 0 | 0 | 1 | 0 | 1 | 12 | 37 | 3 | 32 | 4 | 30 | 3 | 15 | 4 | 13 | 8 | 4 | 2 | 8 |
325,853 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/engines/core/exceptions.py | rxiv_maker.engines.core.exceptions.ContainerEngineNotRunningError | import platform
class ContainerEngineNotRunningError(ContainerEngineError):
"""Exception raised when container engine daemon is not running."""
def __init__(self, engine_type: str):
"""Initialize not running error with startup suggestions."""
system = platform.system().lower()
if engin... |
class ContainerEngineNotRunningError(ContainerEngineError):
'''Exception raised when container engine daemon is not running.'''
def __init__(self, engine_type: str):
'''Initialize not running error with startup suggestions.'''
pass | 2 | 2 | 29 | 2 | 26 | 2 | 8 | 0.11 | 1 | 2 | 0 | 0 | 1 | 0 | 1 | 12 | 32 | 3 | 27 | 4 | 25 | 3 | 15 | 4 | 13 | 8 | 4 | 2 | 8 |
325,854 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/engines/core/exceptions.py | rxiv_maker.engines.core.exceptions.ContainerImagePullError | from typing import Optional
class ContainerImagePullError(ContainerEngineError):
"""Exception raised when container image pull fails."""
def __init__(self, engine_type: str, image: str, details: Optional[str]=None):
"""Initialize image pull error.
Args:
engine_type: Type of engine... |
class ContainerImagePullError(ContainerEngineError):
'''Exception raised when container image pull fails.'''
def __init__(self, engine_type: str, image: str, details: Optional[str]=None):
'''Initialize image pull error.
Args:
engine_type: Type of engine (docker, podman)
... | 2 | 2 | 18 | 3 | 9 | 6 | 2 | 0.7 | 1 | 2 | 0 | 0 | 1 | 0 | 1 | 12 | 21 | 4 | 10 | 4 | 8 | 7 | 7 | 4 | 5 | 2 | 4 | 1 | 2 |
325,855 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/engines/core/exceptions.py | rxiv_maker.engines.core.exceptions.ContainerPermissionError | import platform
class ContainerPermissionError(ContainerEngineError):
"""Exception raised when container operations fail due to permissions."""
def __init__(self, engine_type: str, operation: str):
"""Initialize permission error.
Args:
engine_type: Type of engine (docker, podman)
... |
class ContainerPermissionError(ContainerEngineError):
'''Exception raised when container operations fail due to permissions.'''
def __init__(self, engine_type: str, operation: str):
'''Initialize permission error.
Args:
engine_type: Type of engine (docker, podman)
opera... | 2 | 2 | 23 | 3 | 15 | 5 | 3 | 0.38 | 1 | 2 | 0 | 0 | 1 | 0 | 1 | 12 | 26 | 4 | 16 | 4 | 14 | 6 | 8 | 4 | 6 | 3 | 4 | 1 | 3 |
325,856 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/engines/core/exceptions.py | rxiv_maker.engines.core.exceptions.ContainerResourceError | from typing import Optional
class ContainerResourceError(ContainerEngineError):
"""Exception raised when container operations fail due to resource constraints."""
def __init__(self, engine_type: str, resource_type: str, details: Optional[str]=None):
"""Initialize resource error.
Args:
... |
class ContainerResourceError(ContainerEngineError):
'''Exception raised when container operations fail due to resource constraints.'''
def __init__(self, engine_type: str, resource_type: str, details: Optional[str]=None):
'''Initialize resource error.
Args:
engine_type: Type of eng... | 2 | 2 | 30 | 3 | 21 | 6 | 5 | 0.32 | 1 | 2 | 0 | 0 | 1 | 0 | 1 | 12 | 33 | 4 | 22 | 4 | 20 | 7 | 11 | 4 | 9 | 5 | 4 | 1 | 5 |
325,857 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/engines/core/exceptions.py | rxiv_maker.engines.core.exceptions.ContainerSessionError | from typing import Optional
class ContainerSessionError(ContainerEngineError):
"""Exception raised when container session operations fail."""
def __init__(self, engine_type: str, operation: str, container_id: Optional[str]=None, details: Optional[str]=None):
"""Initialize session error.
Args:... |
class ContainerSessionError(ContainerEngineError):
'''Exception raised when container session operations fail.'''
def __init__(self, engine_type: str, operation: str, container_id: Optional[str]=None, details: Optional[str]=None):
'''Initialize session error.
Args:
engine_type: Typ... | 2 | 2 | 24 | 3 | 14 | 7 | 4 | 0.53 | 1 | 2 | 0 | 0 | 1 | 0 | 1 | 12 | 27 | 4 | 15 | 7 | 11 | 8 | 10 | 5 | 8 | 4 | 4 | 1 | 4 |
325,858 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/engines/core/exceptions.py | rxiv_maker.engines.core.exceptions.ContainerTimeoutError | class ContainerTimeoutError(ContainerEngineError):
"""Exception raised when container operations timeout."""
def __init__(self, engine_type: str, operation: str, timeout_seconds: int):
"""Initialize timeout error.
Args:
engine_type: Type of engine (docker, podman)
opera... | class ContainerTimeoutError(ContainerEngineError):
'''Exception raised when container operations timeout.'''
def __init__(self, engine_type: str, operation: str, timeout_seconds: int):
'''Initialize timeout error.
Args:
engine_type: Type of engine (docker, podman)
operat... | 2 | 2 | 17 | 3 | 8 | 6 | 1 | 0.78 | 1 | 3 | 0 | 0 | 1 | 0 | 1 | 12 | 20 | 4 | 9 | 4 | 7 | 7 | 5 | 4 | 3 | 1 | 4 | 0 | 1 |
325,859 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/engines/core/factory.py | rxiv_maker.engines.core.factory.ContainerEngineFactory | from .docker_engine import DockerEngine
import atexit
from .podman_engine import PodmanEngine
import weakref
from .exceptions import ContainerEngineError
from pathlib import Path
from .abstract import AbstractContainerEngine
import os
import logging
from typing import Dict, Optional, Set, Type
class ContainerEngineFac... |
class ContainerEngineFactory:
'''Factory class for creating container engine instances.'''
@classmethod
def create_engine(cls, engine_type: str, default_image: str='henriqueslab/rxiv-maker-base:latest', workspace_dir: Optional[Path]=None, enable_session_reuse: bool=True, memory_limit: str='2g', cpu_limit: ... | 17 | 9 | 25 | 4 | 12 | 9 | 3 | 0.65 | 0 | 10 | 2 | 0 | 0 | 0 | 8 | 8 | 230 | 42 | 114 | 58 | 80 | 74 | 77 | 30 | 68 | 6 | 0 | 3 | 25 |
325,860 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/engines/core/podman_engine.py | rxiv_maker.engines.core.podman_engine.PodmanEngine | from pathlib import Path
from .abstract import AbstractContainerEngine, ContainerSession
class PodmanEngine(AbstractContainerEngine):
"""Podman container engine implementation.
Podman has a Docker-compatible API but needs its own engine implementation
to handle rootless containers and other Podman-specifi... |
class PodmanEngine(AbstractContainerEngine):
'''Podman container engine implementation.
Podman has a Docker-compatible API but needs its own engine implementation
to handle rootless containers and other Podman-specific behavior.
'''
@property
def engine_name(self) -> str:
'''Return the ... | 4 | 3 | 3 | 0 | 2 | 1 | 1 | 1.5 | 1 | 3 | 1 | 0 | 2 | 0 | 2 | 43 | 21 | 6 | 6 | 4 | 2 | 9 | 5 | 3 | 2 | 1 | 5 | 0 | 2 |
325,861 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/engines/core/podman_engine.py | rxiv_maker.engines.core.podman_engine.PodmanSession | from pathlib import Path
import time
from .abstract import AbstractContainerEngine, ContainerSession
class PodmanSession(ContainerSession):
"""Podman-specific container session implementation."""
def __init__(self, container_id: str, image: str, workspace_dir: Path):
super().__init__(container_id, ima... |
class PodmanSession(ContainerSession):
'''Podman-specific container session implementation.'''
def __init__(self, container_id: str, image: str, workspace_dir: Path):
pass | 2 | 1 | 3 | 0 | 3 | 0 | 1 | 0.25 | 1 | 3 | 0 | 0 | 1 | 1 | 1 | 4 | 6 | 1 | 4 | 3 | 2 | 1 | 4 | 3 | 2 | 1 | 1 | 0 | 1 |
325,862 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/engines/operations/add_bibliography.py | rxiv_maker.engines.operations.add_bibliography.BibliographyAdder | import re
import requests
from pathlib import Path
import time
from rxiv_maker.core.cache.doi_cache import DOICache
from crossref_commons.retrieval import get_publication_as_json
from typing import Any
class BibliographyAdder:
"""Add bibliography entries from DOI to bibliography file."""
DOI_REGEX = re.compile... |
class BibliographyAdder:
'''Add bibliography entries from DOI to bibliography file.'''
def __init__(self, manuscript_path: str):
'''Initialize bibliography adder.
Args:
manuscript_path: Path to manuscript directory
'''
pass
def add_entries(self, doi_inputs: lis... | 14 | 14 | 38 | 7 | 21 | 10 | 7 | 0.49 | 0 | 13 | 1 | 0 | 13 | 3 | 13 | 13 | 507 | 101 | 274 | 71 | 259 | 135 | 240 | 67 | 225 | 29 | 0 | 5 | 89 |
325,863 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/engines/operations/build_manager.py | rxiv_maker.engines.operations.build_manager.BuildManager | from ...core.path_manager import PathManager
from datetime import datetime
import subprocess
from ...utils.performance import get_performance_tracker
from ...core.global_container_manager import get_global_container_manager
import os
from ...utils.operation_ids import create_operation
from ...core.logging_config import... |
class BuildManager:
'''Manage the complete build process.'''
def __init__(self, manuscript_path: str | None=None, output_dir: str='output', force_figures: bool=False, skip_validation: bool=False, skip_pdf_validation: bool=False, verbose: bool=False, track_changes_tag: str | None=None, engine: str='local'):
... | 30 | 30 | 36 | 5 | 26 | 5 | 6 | 0.2 | 0 | 11 | 2 | 0 | 28 | 20 | 28 | 28 | 1,076 | 179 | 752 | 196 | 699 | 150 | 618 | 164 | 575 | 25 | 0 | 5 | 167 |
325,864 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/engines/operations/cleanup.py | rxiv_maker.engines.operations.cleanup.CleanupManager | from pathlib import Path
import os
from ...utils.platform import platform_detector
class CleanupManager:
"""Handle cleanup operations."""
def __init__(self, manuscript_path: str | None=None, output_dir: str='output', verbose: bool=False):
"""Initialize cleanup manager.
Args:
manus... |
class CleanupManager:
'''Handle cleanup operations.'''
def __init__(self, manuscript_path: str | None=None, output_dir: str='output', verbose: bool=False):
'''Initialize cleanup manager.
Args:
manuscript_path: Path to manuscript directory
output_dir: Output directory to... | 10 | 10 | 40 | 5 | 30 | 5 | 9 | 0.16 | 0 | 5 | 0 | 0 | 9 | 6 | 9 | 9 | 371 | 58 | 269 | 63 | 248 | 44 | 214 | 48 | 202 | 18 | 0 | 7 | 84 |
325,865 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/engines/operations/fix_bibliography.py | rxiv_maker.engines.operations.fix_bibliography.BibliographyFixer | import re
from typing import Any, Dict
import time
from rxiv_maker.core.cache.doi_cache import DOICache
from pathlib import Path
from difflib import SequenceMatcher
import requests
from rxiv_maker.validators.doi_validator import DOIValidator
class BibliographyFixer:
"""Tool for automatically fixing bibliography is... |
class BibliographyFixer:
'''Tool for automatically fixing bibliography issues.'''
def __init__(self, manuscript_path: str, backup: bool=True):
'''Initialize bibliography fixer.
Args:
manuscript_path: Path to manuscript directory
backup: Whether to create backup before m... | 17 | 17 | 31 | 6 | 21 | 4 | 4 | 0.21 | 0 | 13 | 2 | 0 | 16 | 4 | 16 | 16 | 516 | 112 | 336 | 118 | 318 | 71 | 254 | 116 | 236 | 10 | 0 | 3 | 71 |
325,866 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/engines/operations/generate_figures.py | rxiv_maker.engines.operations.generate_figures.FigureGenerator | from pathlib import Path
import base64
from typing import Optional
import logging
import os
import re
class FigureGenerator:
"""Main class for generating figures from various source formats."""
def __init__(self, figures_dir='FIGURES', output_dir='FIGURES', output_format='png', r_only=False, engine=None, enab... |
class FigureGenerator:
'''Main class for generating figures from various source formats.'''
def __init__(self, figures_dir='FIGURES', output_dir='FIGURES', output_format='png', r_only=False, engine=None, enable_content_caching=True, manuscript_path=None):
'''Initialize the figure generator.
Ar... | 21 | 20 | 44 | 7 | 31 | 7 | 7 | 0.24 | 0 | 22 | 3 | 0 | 18 | 13 | 18 | 18 | 883 | 148 | 594 | 155 | 552 | 145 | 449 | 131 | 416 | 24 | 0 | 5 | 134 |
325,867 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/engines/operations/setup_environment.py | rxiv_maker.engines.operations.setup_environment.EnvironmentSetup | from rxiv_maker.utils.dependency_checker import DependencyChecker
from pathlib import Path
import subprocess
from rxiv_maker.utils.platform import platform_detector
class EnvironmentSetup:
"""Handle environment setup operations."""
def __init__(self, reinstall: bool=False, verbose: bool=False, check_system_de... |
class EnvironmentSetup:
'''Handle environment setup operations.'''
def __init__(self, reinstall: bool=False, verbose: bool=False, check_system_deps: bool=True):
'''Initialize environment setup.
Args:
reinstall: Whether to reinstall (remove existing .venv)
verbose: Wheth... | 11 | 11 | 27 | 3 | 21 | 4 | 5 | 0.17 | 0 | 7 | 1 | 0 | 10 | 5 | 10 | 10 | 283 | 37 | 213 | 40 | 197 | 37 | 162 | 32 | 151 | 9 | 0 | 3 | 46 |
325,868 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/engines/operations/track_changes.py | rxiv_maker.engines.operations.track_changes.TrackChangesManager | import builtins
from pathlib import Path
import subprocess
import tempfile
import sys
import contextlib
import shutil
import os
class TrackChangesManager:
"""Manage change tracking between current manuscript and a git tag."""
def __init__(self, manuscript_path: str, output_dir: str='output', git_tag: str='', ... |
class TrackChangesManager:
'''Manage change tracking between current manuscript and a git tag.'''
def __init__(self, manuscript_path: str, output_dir: str='output', git_tag: str='', verbose: bool=False):
'''Initialize track changes manager.
Args:
manuscript_path: Path to manuscript... | 12 | 12 | 43 | 7 | 27 | 9 | 5 | 0.34 | 0 | 8 | 0 | 0 | 11 | 5 | 11 | 11 | 489 | 88 | 299 | 75 | 281 | 102 | 215 | 62 | 203 | 15 | 0 | 4 | 53 |
325,869 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/install/dependency_handlers/latex.py | rxiv_maker.install.dependency_handlers.latex.LaTeXHandler | from ..utils.logging import InstallLogger
import subprocess
class LaTeXHandler:
"""Handler for LaTeX-specific operations."""
def __init__(self, logger: InstallLogger):
"""Initialize LaTeX handler.
Args:
logger: Logger instance
"""
self.logger = logger
def veri... |
class LaTeXHandler:
'''Handler for LaTeX-specific operations.'''
def __init__(self, logger: InstallLogger):
'''Initialize LaTeX handler.
Args:
logger: Logger instance
'''
pass
def verify_installation(self) -> bool:
'''Verify LaTeX installation.'''
... | 6 | 6 | 21 | 2 | 17 | 2 | 3 | 0.13 | 0 | 9 | 1 | 0 | 5 | 1 | 5 | 5 | 110 | 14 | 85 | 15 | 79 | 11 | 41 | 14 | 35 | 5 | 0 | 4 | 15 |
325,870 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/install/dependency_handlers/nodejs.py | rxiv_maker.install.dependency_handlers.nodejs.NodeJSHandler | from ..utils.logging import InstallLogger
import subprocess
class NodeJSHandler:
"""Handler for Node.js-specific operations."""
def __init__(self, logger: InstallLogger):
"""Initialize Node.js handler.
Args:
logger: Logger instance
"""
self.logger = logger
def... |
class NodeJSHandler:
'''Handler for Node.js-specific operations.'''
def __init__(self, logger: InstallLogger):
'''Initialize Node.js handler.
Args:
logger: Logger instance
'''
pass
def verify_installation(self) -> bool:
'''Verify Node.js installation.''... | 8 | 8 | 15 | 2 | 11 | 2 | 2 | 0.22 | 0 | 9 | 1 | 0 | 7 | 1 | 7 | 7 | 112 | 18 | 78 | 18 | 70 | 17 | 50 | 17 | 42 | 6 | 0 | 3 | 17 |
325,871 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/install/dependency_handlers/r_lang.py | rxiv_maker.install.dependency_handlers.r_lang.RLanguageHandler | from ..utils.logging import InstallLogger
import subprocess
class RLanguageHandler:
"""Handler for R language-specific operations."""
def __init__(self, logger: InstallLogger):
"""Initialize R language handler.
Args:
logger: Logger instance
"""
self.logger = logger... |
class RLanguageHandler:
'''Handler for R language-specific operations.'''
def __init__(self, logger: InstallLogger):
'''Initialize R language handler.
Args:
logger: Logger instance
'''
pass
def verify_installation(self) -> bool:
'''Verify R installation... | 7 | 7 | 18 | 2 | 15 | 2 | 3 | 0.13 | 0 | 9 | 1 | 0 | 6 | 1 | 6 | 6 | 114 | 15 | 88 | 19 | 81 | 11 | 48 | 18 | 41 | 5 | 0 | 4 | 16 |
325,872 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/install/dependency_handlers/system_libs.py | rxiv_maker.install.dependency_handlers.system_libs.SystemLibsHandler | import sys
import subprocess
from ..utils.logging import InstallLogger
class SystemLibsHandler:
"""Handler for system libraries verification."""
def __init__(self, logger: InstallLogger):
"""Initialize system libraries handler.
Args:
logger: Logger instance
"""
sel... |
class SystemLibsHandler:
'''Handler for system libraries verification.'''
def __init__(self, logger: InstallLogger):
'''Initialize system libraries handler.
Args:
logger: Logger instance
'''
pass
def verify_installation(self) -> bool:
'''Verify system l... | 8 | 8 | 15 | 2 | 10 | 3 | 2 | 0.35 | 0 | 7 | 1 | 0 | 7 | 1 | 7 | 7 | 114 | 22 | 68 | 25 | 59 | 24 | 48 | 24 | 39 | 3 | 0 | 2 | 16 |
325,873 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/install/platform_installers/base.py | rxiv_maker.install.platform_installers.base.BaseInstaller | from ..utils.logging import InstallLogger
from abc import ABC, abstractmethod
from ..utils.progress import ProgressIndicator
class BaseInstaller(ABC):
"""Abstract base class for platform-specific installers."""
def __init__(self, logger: InstallLogger, progress: ProgressIndicator):
"""Initialize base ... |
class BaseInstaller(ABC):
'''Abstract base class for platform-specific installers.'''
def __init__(self, logger: InstallLogger, progress: ProgressIndicator):
'''Initialize base installer.
Args:
logger: Logger instance
progress: Progress indicator instance
'''
... | 11 | 7 | 8 | 1 | 2 | 5 | 1 | 1.47 | 1 | 4 | 2 | 0 | 6 | 2 | 6 | 26 | 61 | 14 | 19 | 14 | 7 | 28 | 15 | 10 | 7 | 1 | 4 | 0 | 6 |
325,874 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/install/platform_installers/linux.py | rxiv_maker.install.platform_installers.linux.LinuxInstaller | import os
import subprocess
from ..utils.progress import ProgressIndicator
from pathlib import Path
from ..utils.logging import InstallLogger
import shutil
class LinuxInstaller:
"""Linux-specific installer for rxiv-maker dependencies."""
def __init__(self, logger: InstallLogger, progress: ProgressIndicator):
... |
class LinuxInstaller:
'''Linux-specific installer for rxiv-maker dependencies.'''
def __init__(self, logger: InstallLogger, progress: ProgressIndicator):
'''Initialize Linux installer.
Args:
logger: Logger instance
progress: Progress indicator instance
'''
... | 15 | 15 | 28 | 3 | 23 | 3 | 3 | 0.13 | 0 | 12 | 2 | 0 | 13 | 4 | 13 | 13 | 385 | 49 | 297 | 35 | 283 | 40 | 126 | 33 | 112 | 9 | 0 | 3 | 43 |
325,875 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/install/platform_installers/macos.py | rxiv_maker.install.platform_installers.macos.MacOSInstaller | import urllib.request
import subprocess
from ..utils.progress import ProgressIndicator
from ..utils.logging import InstallLogger
from pathlib import Path
class MacOSInstaller:
"""macOS-specific installer for rxiv-maker dependencies."""
def __init__(self, logger: InstallLogger, progress: ProgressIndicator):
... |
class MacOSInstaller:
'''macOS-specific installer for rxiv-maker dependencies.'''
def __init__(self, logger: InstallLogger, progress: ProgressIndicator):
'''Initialize macOS installer.
Args:
logger: Logger instance
progress: Progress indicator instance
'''
... | 23 | 23 | 22 | 3 | 17 | 3 | 4 | 0.16 | 0 | 6 | 2 | 0 | 22 | 4 | 22 | 22 | 508 | 82 | 367 | 87 | 343 | 59 | 275 | 71 | 251 | 6 | 0 | 5 | 77 |
325,876 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/install/platform_installers/windows.py | rxiv_maker.install.platform_installers.windows.WindowsInstaller | from ..utils.logging import InstallLogger
import subprocess
from ..utils.progress import ProgressIndicator
from pathlib import Path
import urllib.request
class WindowsInstaller:
"""Windows-specific installer for rxiv-maker dependencies."""
def __init__(self, logger: InstallLogger, progress: ProgressIndicator)... |
class WindowsInstaller:
'''Windows-specific installer for rxiv-maker dependencies.'''
def __init__(self, logger: InstallLogger, progress: ProgressIndicator):
'''Initialize Windows installer.
Args:
logger: Logger instance
progress: Progress indicator instance
'''... | 20 | 20 | 24 | 3 | 19 | 3 | 3 | 0.13 | 0 | 10 | 2 | 0 | 19 | 3 | 19 | 19 | 484 | 69 | 366 | 69 | 345 | 49 | 228 | 56 | 207 | 5 | 0 | 3 | 58 |
325,877 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/install/utils/logging.py | rxiv_maker.install.utils.logging.InstallLogger | from pathlib import Path
from datetime import datetime
from rxiv_maker.utils.unicode_safe import get_safe_icon
import logging
import sys
class InstallLogger:
"""Logger for installation process with file and console output."""
def __init__(self, log_file: Path | None=None, verbose: bool=False):
"""Init... |
class InstallLogger:
'''Logger for installation process with file and console output.'''
def __init__(self, log_file: Path | None=None, verbose: bool=False):
'''Initialize the logger.
Args:
log_file: Path to log file (auto-generated if None)
verbose: Enable verbose cons... | 8 | 8 | 8 | 1 | 5 | 2 | 1 | 0.43 | 0 | 7 | 0 | 0 | 7 | 3 | 7 | 7 | 66 | 13 | 37 | 20 | 29 | 16 | 37 | 20 | 29 | 3 | 0 | 1 | 9 |
325,878 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/install/utils/progress.py | rxiv_maker.install.utils.progress.ProgressIndicator | from rxiv_maker.utils.unicode_safe import get_safe_icon
import time
import threading
import sys
class ProgressIndicator:
"""Progress indicator for installation tasks."""
def __init__(self, verbose: bool=False):
"""Initialize progress indicator.
Args:
verbose: Enable verbose output... |
class ProgressIndicator:
'''Progress indicator for installation tasks.'''
def __init__(self, verbose: bool=False):
'''Initialize progress indicator.
Args:
verbose: Enable verbose output
'''
pass
def start_task(self, task_name: str):
'''Start a new task ... | 9 | 9 | 13 | 1 | 8 | 3 | 2 | 0.4 | 0 | 4 | 0 | 0 | 8 | 5 | 8 | 8 | 112 | 19 | 67 | 21 | 58 | 27 | 59 | 21 | 50 | 6 | 0 | 3 | 19 |
325,879 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/services/base.py | rxiv_maker.services.base.BaseService | from pathlib import Path
from typing import Any, Dict, Generic, List, Optional, TypeVar
from abc import ABC, abstractmethod
from ..core.managers.config_manager import ConfigManager
from ..utils.platform import safe_console_print, safe_print
import logging
from ..core.cache import get_cache_dir
class BaseService(ABC):
... |
class BaseService(ABC):
'''Base class for all rxiv-maker services.
Provides common functionality including:
- Consistent logging
- Configuration management
- Error handling patterns
- Cache access
- Validation utilities
'''
def __init__(self, config: Optional[ConfigManager]=None, l... | 11 | 9 | 9 | 2 | 5 | 3 | 2 | 0.82 | 1 | 12 | 5 | 5 | 8 | 3 | 8 | 28 | 94 | 21 | 40 | 20 | 27 | 33 | 36 | 15 | 27 | 5 | 4 | 2 | 15 |
325,880 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/services/base.py | rxiv_maker.services.base.ConfigurationError | class ConfigurationError(ServiceError):
"""Raised when configuration is invalid."""
pass | class ConfigurationError(ServiceError):
'''Raised when configuration is invalid.'''
pass | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0.5 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 11 | 4 | 1 | 2 | 1 | 1 | 1 | 2 | 1 | 1 | 0 | 4 | 0 | 0 |
325,881 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/services/base.py | rxiv_maker.services.base.ProcessingError | class ProcessingError(ServiceError):
"""Raised when processing operations fail."""
pass | class ProcessingError(ServiceError):
'''Raised when processing operations fail.'''
pass | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0.5 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 11 | 4 | 1 | 2 | 1 | 1 | 1 | 2 | 1 | 1 | 0 | 4 | 0 | 0 |
325,882 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/services/base.py | rxiv_maker.services.base.ServiceError | from typing import Any, Dict, Generic, List, Optional, TypeVar
class ServiceError(Exception):
"""Base exception for service layer errors."""
def __init__(self, message: str, details: Optional[Dict[str, Any]]=None):
super().__init__(message)
self.details = details or {} |
class ServiceError(Exception):
'''Base exception for service layer errors.'''
def __init__(self, message: str, details: Optional[Dict[str, Any]]=None):
pass | 2 | 1 | 3 | 0 | 3 | 0 | 1 | 0.25 | 1 | 3 | 0 | 3 | 1 | 1 | 1 | 11 | 6 | 1 | 4 | 3 | 2 | 1 | 4 | 3 | 2 | 1 | 3 | 0 | 1 |
325,883 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/services/base.py | rxiv_maker.services.base.ServiceResult | from typing import Any, Dict, Generic, List, Optional, TypeVar
class ServiceResult(Generic[T]):
"""Standardized service operation result."""
def __init__(self, success: bool, data: Optional[T]=None, errors: Optional[List[str]]=None, warnings: Optional[List[str]]=None, metadata: Optional[Dict[str, Any]]=None):... |
class ServiceResult(Generic[T]):
'''Standardized service operation result.'''
def __init__(self, success: bool, data: Optional[T]=None, errors: Optional[List[str]]=None, warnings: Optional[List[str]]=None, metadata: Optional[Dict[str, Any]]=None):
pass
@classmethod
def success_result(cls, data... | 8 | 5 | 5 | 0 | 4 | 1 | 1 | 0.2 | 1 | 3 | 0 | 0 | 3 | 5 | 5 | 7 | 35 | 5 | 25 | 20 | 10 | 5 | 16 | 11 | 10 | 1 | 1 | 0 | 5 |
325,884 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/services/base.py | rxiv_maker.services.base.ValidationError | class ValidationError(ServiceError):
"""Raised when validation fails."""
pass | class ValidationError(ServiceError):
'''Raised when validation fails.'''
pass | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0.5 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 11 | 4 | 1 | 2 | 1 | 1 | 1 | 2 | 1 | 1 | 0 | 4 | 0 | 0 |
325,885 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/services/build_service.py | rxiv_maker.services.build_service.BuildService | from pathlib import Path
from typing import Any, Dict, Optional
from .manuscript_service import ManuscriptService
from .base import BaseService, ServiceResult
class BuildService(BaseService):
"""Service for orchestrating manuscript build processes."""
def __init__(self, *args, **kwargs):
super().__ini... |
class BuildService(BaseService):
'''Service for orchestrating manuscript build processes.'''
def __init__(self, *args, **kwargs):
pass
def build_pdf(self, manuscript_path: Optional[str]=None, output_dir: str='./output', engine: str='LOCAL', skip_validation: bool=False) -> ServiceResult[Path]:
... | 4 | 3 | 15 | 2 | 8 | 4 | 1 | 0.56 | 1 | 8 | 2 | 0 | 3 | 1 | 3 | 31 | 49 | 10 | 25 | 15 | 15 | 14 | 15 | 8 | 11 | 2 | 5 | 1 | 4 |
325,886 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/services/configuration_service.py | rxiv_maker.services.configuration_service.ConfigurationService | from .base import BaseService, ServiceResult
from typing import Any, Dict, Optional
from pathlib import Path
class ConfigurationService(BaseService):
"""Service for configuration management and environment setup."""
def load_manuscript_config(self, manuscript_path: Optional[str]=None, config_file: str='00_CON... |
class ConfigurationService(BaseService):
'''Service for configuration management and environment setup.'''
def load_manuscript_config(self, manuscript_path: Optional[str]=None, config_file: str='00_CONFIG.yml') -> ServiceResult[Dict[str, Any]]:
'''Load manuscript configuration.
Args:
... | 4 | 4 | 32 | 7 | 19 | 6 | 5 | 0.31 | 1 | 5 | 1 | 0 | 3 | 0 | 3 | 31 | 100 | 24 | 58 | 21 | 50 | 18 | 50 | 16 | 44 | 5 | 5 | 3 | 14 |
325,887 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/services/manuscript_service.py | rxiv_maker.services.manuscript_service.ManuscriptMetadata | from ..processors.yaml_processor import extract_yaml_metadata, get_doi_validation_setting
from pathlib import Path
from typing import Any, Dict, Optional
class ManuscriptMetadata:
"""Structured representation of manuscript metadata."""
def __init__(self, raw_metadata: Dict[str, Any], manuscript_path: Path):
... |
class ManuscriptMetadata:
'''Structured representation of manuscript metadata.'''
def __init__(self, raw_metadata: Dict[str, Any], manuscript_path: Path):
pass
@property
def has_authors(self) -> bool:
'''Check if manuscript has authors defined.'''
pass
@property
def aut... | 7 | 4 | 5 | 0 | 3 | 1 | 1 | 0.31 | 0 | 6 | 0 | 0 | 4 | 6 | 4 | 4 | 26 | 5 | 16 | 13 | 9 | 5 | 14 | 11 | 9 | 2 | 0 | 0 | 5 |
325,888 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/services/manuscript_service.py | rxiv_maker.services.manuscript_service.ManuscriptService | from ..processors.template_processor import generate_supplementary_tex, get_template_path, process_template_replacements
from ..utils import create_output_dir, find_manuscript_md, write_manuscript_output
from ..processors.yaml_processor import extract_yaml_metadata, get_doi_validation_setting
from .base import BaseServ... |
class ManuscriptService(BaseService):
'''Service for manuscript discovery, metadata extraction, and processing.'''
def discover_manuscript(self, manuscript_path: Optional[str]=None) -> ServiceResult[Path]:
'''Discover manuscript file in the given path.
Args:
manuscript_path: Option... | 6 | 6 | 48 | 10 | 29 | 9 | 6 | 0.3 | 1 | 6 | 2 | 0 | 5 | 0 | 5 | 33 | 247 | 55 | 148 | 44 | 142 | 45 | 115 | 38 | 109 | 12 | 5 | 3 | 29 |
325,889 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/services/publication_service.py | rxiv_maker.services.publication_service.PublicationService | from typing import Any, Dict, Optional
from pathlib import Path
from .base import BaseService, ServiceResult
class PublicationService(BaseService):
"""Service for preparing manuscripts for publication."""
def prepare_arxiv_submission(self, manuscript_path: Optional[str]=None, output_dir: str='./output', arxiv... |
class PublicationService(BaseService):
'''Service for preparing manuscripts for publication.'''
def prepare_arxiv_submission(self, manuscript_path: Optional[str]=None, output_dir: str='./output', arxiv_dir: Optional[str]=None) -> ServiceResult[Path]:
'''Prepare arXiv submission package.
Args:
... | 3 | 3 | 17 | 3 | 9 | 5 | 2 | 0.61 | 1 | 5 | 1 | 0 | 2 | 0 | 2 | 30 | 37 | 8 | 18 | 9 | 13 | 11 | 12 | 6 | 9 | 3 | 5 | 1 | 4 |
325,890 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/services/validation_service.py | rxiv_maker.services.validation_service.ValidationConfig | from dataclasses import dataclass, field
@dataclass
class ValidationConfig:
"""Configuration for validation operations."""
verbose: bool = False
include_info: bool = False
check_latex: bool = True
enable_doi_validation: bool = True
validation_level: str = 'ERROR'
stop_on_first_error: bool =... | @dataclass
class ValidationConfig:
'''Configuration for validation operations.'''
def __post_init__(self):
'''Validate configuration after initialization.'''
pass | 3 | 2 | 5 | 0 | 4 | 1 | 2 | 0.25 | 0 | 1 | 0 | 0 | 1 | 0 | 1 | 1 | 16 | 2 | 12 | 10 | 10 | 3 | 12 | 10 | 10 | 2 | 0 | 1 | 2 |
325,891 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/services/validation_service.py | rxiv_maker.services.validation_service.ValidationService | from pathlib import Path
from .manuscript_service import ManuscriptService
from typing import Any, Dict, List, Optional
from .base import BaseService, ServiceResult
class ValidationService(BaseService):
"""Service for comprehensive manuscript validation."""
def __init__(self, *args, **kwargs):
super()... |
class ValidationService(BaseService):
'''Service for comprehensive manuscript validation.'''
def __init__(self, *args, **kwargs):
pass
def check_validator_availability(self) -> ServiceResult[Dict[str, bool]]:
'''Check which validators are available.'''
pass
def validate_manus... | 8 | 7 | 40 | 7 | 29 | 4 | 7 | 0.14 | 1 | 19 | 13 | 0 | 7 | 1 | 7 | 35 | 289 | 56 | 204 | 60 | 190 | 29 | 145 | 50 | 135 | 15 | 5 | 5 | 51 |
325,892 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/services/validation_service.py | rxiv_maker.services.validation_service.ValidationSummary | from dataclasses import dataclass, field
from typing import Any, Dict, List, Optional
@dataclass
class ValidationSummary:
"""Summary of all validation results."""
total_validators: int
successful_validators: int
total_errors: int
total_warnings: int
total_info: int
execution_time: float
... | null | 6 | 3 | 3 | 0 | 2 | 1 | 1 | 0.21 | 0 | 1 | 0 | 0 | 2 | 0 | 2 | 2 | 20 | 3 | 14 | 6 | 9 | 3 | 12 | 4 | 9 | 1 | 0 | 0 | 2 |
325,893 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/services/validation_service.py | rxiv_maker.services.validation_service.ValidatorResult | from typing import Any, Dict, List, Optional
from dataclasses import dataclass, field
@dataclass
class ValidatorResult:
"""Result from a single validator."""
name: str
success: bool
errors: List[str] = field(default_factory=list)
warnings: List[str] = field(default_factory=list)
info: List[str]... | @dataclass
class ValidatorResult:
'''Result from a single validator.'''
pass | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 0.13 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 10 | 1 | 8 | 6 | 7 | 1 | 8 | 6 | 7 | 0 | 0 | 0 | 0 |
325,894 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/utils/bibliography_checksum.py | rxiv_maker.utils.bibliography_checksum.BibliographyChecksumManager | import json
from typing import Any
import time
from pathlib import Path
from ..core.cache.cache_utils import get_cache_dir, get_legacy_cache_dir, migrate_cache_file
import hashlib
class BibliographyChecksumManager:
"""Manages checksums for bibliography files to enable efficient DOI validation."""
def __init__... |
class BibliographyChecksumManager:
'''Manages checksums for bibliography files to enable efficient DOI validation.'''
def __init__(self, manuscript_path: str, cache_dir: str | None=None):
'''Initialize the bibliography checksum manager.
Args:
manuscript_path: Path to the manuscript... | 14 | 14 | 19 | 3 | 12 | 4 | 3 | 0.34 | 0 | 11 | 0 | 0 | 13 | 6 | 13 | 13 | 257 | 48 | 157 | 55 | 142 | 53 | 136 | 44 | 121 | 5 | 0 | 3 | 37 |
325,895 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/utils/dependency_checker.py | rxiv_maker.utils.dependency_checker.DependencyChecker | import subprocess
import shutil
class DependencyChecker:
"""Check system dependencies for Rxiv-Maker."""
def __init__(self, verbose: bool=False):
"""Initialize dependency checker.
Args:
verbose: Whether to show verbose output
"""
self.verbose = verbose
self... |
class DependencyChecker:
'''Check system dependencies for Rxiv-Maker.'''
def __init__(self, verbose: bool=False):
'''Initialize dependency checker.
Args:
verbose: Whether to show verbose output
'''
pass
def log(self, message: str, level: str='INFO'):
''... | 17 | 17 | 20 | 3 | 14 | 3 | 3 | 0.21 | 0 | 8 | 1 | 0 | 16 | 3 | 16 | 16 | 338 | 65 | 227 | 61 | 208 | 48 | 138 | 59 | 121 | 10 | 0 | 2 | 42 |
325,896 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/utils/dependency_checker.py | rxiv_maker.utils.dependency_checker.DependencyInfo | from dataclasses import dataclass
@dataclass
class DependencyInfo:
"""Information about a system dependency."""
name: str
required: bool
found: bool
version: str | None = None
path: str | None = None
install_commands: dict[str, str] | None = None
description: str = ''
alternative: s... | @dataclass
class DependencyInfo:
'''Information about a system dependency.'''
pass | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 0.11 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 11 | 1 | 9 | 6 | 8 | 1 | 9 | 6 | 8 | 0 | 0 | 0 | 0 |
325,897 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/utils/figure_checksum.py | rxiv_maker.utils.figure_checksum.FigureChecksumManager | import hashlib
from pathlib import Path
from typing import Any
from ..core.cache.cache_utils import get_cache_dir, get_legacy_cache_dir, migrate_cache_file
import json
class FigureChecksumManager:
"""Manages checksums for figure source files to enable efficient regeneration."""
def __init__(self, manuscript_p... |
class FigureChecksumManager:
'''Manages checksums for figure source files to enable efficient regeneration.'''
def __init__(self, manuscript_path: str, cache_dir: str | None=None):
'''Initialize the checksum manager.
Args:
manuscript_path: Path to the manuscript directory
... | 16 | 16 | 17 | 2 | 11 | 4 | 3 | 0.34 | 0 | 10 | 0 | 0 | 15 | 6 | 15 | 15 | 269 | 52 | 163 | 62 | 147 | 56 | 151 | 55 | 135 | 6 | 0 | 3 | 46 |
325,898 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/utils/operation_ids.py | rxiv_maker.utils.operation_ids.OperationContext | import time
import random
from typing import Any
import string
class OperationContext:
"""Context manager for operation tracking with unique IDs."""
def __init__(self, operation_type: str, metadata: dict[str, Any] | None=None):
"""Initialize operation context.
Args:
operation_type... |
class OperationContext:
'''Context manager for operation tracking with unique IDs.'''
def __init__(self, operation_type: str, metadata: dict[str, Any] | None=None):
'''Initialize operation context.
Args:
operation_type: Type of operation (e.g., "pdf_build", "validation")
... | 7 | 7 | 8 | 1 | 5 | 2 | 1 | 0.45 | 0 | 7 | 0 | 0 | 6 | 6 | 6 | 6 | 54 | 10 | 31 | 16 | 24 | 14 | 30 | 16 | 23 | 2 | 0 | 1 | 7 |
325,899 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/src/rxiv_maker/utils/operation_ids.py | rxiv_maker.utils.operation_ids.OperationHistory | from typing import Any
class OperationHistory:
"""Manages history of operations for debugging."""
def __init__(self, max_operations: int=100):
"""Initialize operation history.
Args:
max_operations: Maximum operations to keep in history
"""
self.max_operations = max... |
class OperationHistory:
'''Manages history of operations for debugging.'''
def __init__(self, max_operations: int=100):
'''Initialize operation history.
Args:
max_operations: Maximum operations to keep in history
'''
pass
def add_operation(self, operation: Oper... | 9 | 9 | 9 | 1 | 6 | 2 | 2 | 0.33 | 0 | 6 | 1 | 0 | 8 | 3 | 8 | 8 | 79 | 15 | 48 | 17 | 39 | 16 | 36 | 17 | 27 | 5 | 0 | 2 | 14 |
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