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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
325,700 | 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/cache/doi_cache.py | cache.doi_cache.DOICache | import os
from pathlib import Path
from .cache_utils import get_cache_dir, get_legacy_cache_dir, migrate_cache_file
import time
from typing import Any
import json
class DOICache:
"""Cache system for DOI metadata from CrossRef API."""
def __init__(self, cache_dir: str | None=None, cache_filename: str | None=No... |
class DOICache:
'''Cache system for DOI metadata from CrossRef API.'''
def __init__(self, cache_dir: str | None=None, cache_filename: str | None=None, manuscript_name: str | None=None):
'''Initialize DOI cache.
Args:
cache_dir: Directory to store cache files (if None, uses platform... | 19 | 19 | 28 | 4 | 17 | 7 | 4 | 0.4 | 0 | 13 | 0 | 0 | 18 | 8 | 18 | 18 | 516 | 97 | 303 | 100 | 279 | 120 | 244 | 89 | 225 | 10 | 0 | 5 | 79 |
325,701 | 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/cache/secure_cache_utils.py | cache.secure_cache_utils.SecurityError | class SecurityError(Exception):
"""Raised when a security violation is detected."""
pass | class SecurityError(Exception):
'''Raised when a security violation is detected.'''
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 |
325,702 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/examples/centralized_build_example.py | centralized_build_example.CentralizedBuildManager | from rxiv_maker.core.dependency_manager import DependencyManager
from rxiv_maker.core.execution_manager import ExecutionMode, ExecutionStep, create_execution_manager
from pathlib import Path
from rxiv_maker.core.validation_manager import ValidationContext, ValidationManager
import time
from rxiv_maker.core.resource_man... |
class CentralizedBuildManager:
'''Demonstration of centralized build management using all centralized components.
This replaces the scattered logic from the original BuildManager classes
with a clean, centralized approach using:
- ExecutionManager: Pipeline orchestration
- ResourceManager: Automati... | 13 | 13 | 28 | 6 | 17 | 6 | 2 | 0.43 | 0 | 8 | 1 | 0 | 7 | 6 | 7 | 7 | 245 | 54 | 139 | 42 | 125 | 60 | 103 | 41 | 89 | 5 | 0 | 3 | 25 |
325,703 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/scripts/check_performance_regression.py | check_performance_regression.PerformanceRegression | import json
from pathlib import Path
class PerformanceRegression:
"""Check for performance regressions in benchmark results."""
def __init__(self, baseline_file: str='performance_baseline.json', current_file: str='benchmark_results.json', regression_threshold: float=0.2):
self.baseline_file = Path(bas... |
class PerformanceRegression:
'''Check for performance regressions in benchmark results.'''
def __init__(self, baseline_file: str='performance_baseline.json', current_file: str='benchmark_results.json', regression_threshold: float=0.2):
pass
def load_benchmark_data(self, file_path: Path) -> dict |... | 6 | 5 | 21 | 3 | 18 | 1 | 4 | 0.09 | 0 | 8 | 0 | 0 | 5 | 3 | 5 | 5 | 114 | 18 | 90 | 31 | 79 | 8 | 59 | 24 | 53 | 7 | 0 | 2 | 18 |
325,704 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/scripts/cli_scanner.py | cli_scanner.CLIScanner | import json
from typing import Any, Dict, List, Optional
from pathlib import Path
class CLIScanner:
"""Main CLI scanner that discovers and analyzes CLI commands."""
def __init__(self, project_root: Path):
self.project_root = project_root
self.parser = ClickASTParser()
self.commands = {... |
class CLIScanner:
'''Main CLI scanner that discovers and analyzes CLI commands.'''
def __init__(self, project_root: Path):
pass
def scan_cli_files(self) -> Dict[str, ClickCommand]:
'''Scan all CLI files in the project.'''
pass
def _scan_directory(self, directory: Path, includ... | 9 | 8 | 32 | 4 | 26 | 3 | 7 | 0.13 | 0 | 6 | 2 | 0 | 8 | 3 | 8 | 8 | 266 | 41 | 205 | 50 | 194 | 27 | 147 | 48 | 136 | 15 | 0 | 7 | 53 |
325,705 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/scripts/cli_scanner.py | cli_scanner.ClickASTParser | import ast
from pathlib import Path
from typing import Any, Dict, List, Optional
class ClickASTParser:
"""Parses Python AST to extract Click decorators."""
def __init__(self):
self.commands = {}
def parse_file(self, file_path: Path) -> Dict[str, ClickCommand]:
"""Parse a Python file and e... |
class ClickASTParser:
'''Parses Python AST to extract Click decorators.'''
def __init__(self):
pass
def parse_file(self, file_path: Path) -> Dict[str, ClickCommand]:
'''Parse a Python file and extract Click commands.'''
pass
def _extract_commands(self, tree: ast.AST, file_pat... | 13 | 12 | 18 | 2 | 14 | 2 | 5 | 0.11 | 0 | 7 | 3 | 0 | 12 | 1 | 12 | 12 | 224 | 31 | 174 | 43 | 161 | 19 | 120 | 41 | 107 | 17 | 0 | 3 | 61 |
325,706 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/scripts/cli_scanner.py | cli_scanner.ClickArgument | from typing import Any, Dict, List, Optional
from dataclasses import dataclass
@dataclass
class ClickArgument:
"""Represents a Click argument decorator."""
name: str
help_text: Optional[str] = None
required: bool = True
option_type: Optional[str] = None | @dataclass
class ClickArgument:
'''Represents a Click argument decorator.'''
pass | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 0.2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 7 | 1 | 5 | 4 | 4 | 1 | 5 | 4 | 4 | 0 | 0 | 0 | 0 |
325,707 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/scripts/cli_scanner.py | cli_scanner.ClickCommand | from typing import Any, Dict, List, Optional
from dataclasses import dataclass
@dataclass
class ClickCommand:
"""Represents a Click command with its options and arguments."""
name: str
function_name: str
help_text: Optional[str] = None
options: List[ClickOption] = None
arguments: List[ClickArgu... | @dataclass
class ClickCommand:
'''Represents a Click command with its options and arguments.'''
def __post_init__(self):
pass | 3 | 1 | 5 | 0 | 5 | 0 | 3 | 0.08 | 0 | 0 | 0 | 0 | 1 | 0 | 1 | 1 | 16 | 2 | 13 | 7 | 11 | 1 | 13 | 7 | 11 | 3 | 0 | 1 | 3 |
325,708 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/scripts/cli_scanner.py | cli_scanner.ClickOption | from typing import Any, Dict, List, Optional
from dataclasses import dataclass
@dataclass
class ClickOption:
"""Represents a Click option decorator."""
name: str
short_name: Optional[str] = None
help_text: Optional[str] = None
default: Optional[Any] = None
is_flag: bool = False
option_type:... | @dataclass
class ClickOption:
'''Represents a Click option decorator.'''
pass | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 0.11 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 11 | 1 | 9 | 8 | 8 | 1 | 9 | 8 | 8 | 0 | 0 | 0 | 0 |
325,709 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/scripts/cli_verifier.py | cli_verifier.CLIDocumentationVerifier | from pathlib import Path
from cli_scanner import CLIScanner
import json
from docs_parser import DocumentationScanner
class CLIDocumentationVerifier:
"""Main verifier that compares CLI implementation with documentation."""
def __init__(self, project_root: Path):
self.project_root = project_root
... |
class CLIDocumentationVerifier:
'''Main verifier that compares CLI implementation with documentation.'''
def __init__(self, project_root: Path):
pass
def verify(self) -> VerificationReport:
'''Run complete verification and return report.'''
pass
def generate_report(self, repo... | 7 | 6 | 67 | 8 | 55 | 6 | 11 | 0.11 | 0 | 11 | 8 | 0 | 6 | 3 | 6 | 6 | 412 | 52 | 333 | 39 | 326 | 36 | 233 | 39 | 226 | 23 | 0 | 6 | 63 |
325,710 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/scripts/cli_verifier.py | cli_verifier.MismatchedDescription | from dataclasses import dataclass
@dataclass
class MismatchedDescription:
"""Represents an option with different descriptions in code vs docs."""
command_name: str
option_name: str
implementation_description: str
documentation_description: str
implemented_in: str
documented_in: str | @dataclass
class MismatchedDescription:
'''Represents an option with different descriptions in code vs docs.'''
pass | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 0.14 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 9 | 1 | 7 | 1 | 6 | 1 | 7 | 1 | 6 | 0 | 0 | 0 | 0 |
325,711 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/scripts/cli_verifier.py | cli_verifier.MissingCommand | from typing import List, Optional
from dataclasses import dataclass
@dataclass
class MissingCommand:
"""Represents a command that exists in implementation but not in docs."""
command_name: str
implemented_in: str
function_name: str
help_text: Optional[str] = None | @dataclass
class MissingCommand:
'''Represents a command that exists in implementation but not in docs.'''
pass | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 0.2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 7 | 1 | 5 | 2 | 4 | 1 | 5 | 2 | 4 | 0 | 0 | 0 | 0 |
325,712 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/scripts/cli_verifier.py | cli_verifier.MissingOption | from dataclasses import dataclass
from typing import List, Optional
@dataclass
class MissingOption:
"""Represents an implemented option not documented."""
command_name: str
option_name: str
implemented_in: str
line_number: int = 0
help_text: Optional[str] = None | @dataclass
class MissingOption:
'''Represents an implemented option not documented.'''
pass | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 0.17 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 8 | 1 | 6 | 3 | 5 | 1 | 6 | 3 | 5 | 0 | 0 | 0 | 0 |
325,713 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/scripts/cli_verifier.py | cli_verifier.PhantomCommand | from dataclasses import dataclass
from typing import List, Optional
@dataclass
class PhantomCommand:
"""Represents a command documented but not implemented."""
command_name: str
documented_in: str
description: Optional[str] = None | @dataclass
class PhantomCommand:
'''Represents a command documented but not implemented.'''
pass | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 0.25 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 6 | 1 | 4 | 2 | 3 | 1 | 4 | 2 | 3 | 0 | 0 | 0 | 0 |
325,714 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/scripts/cli_verifier.py | cli_verifier.PhantomOption | from dataclasses import dataclass
@dataclass
class PhantomOption:
"""Represents an option documented but not implemented."""
command_name: str
option_name: str
documented_in: str
line_number: int = 0 | @dataclass
class PhantomOption:
'''Represents an option documented but not implemented.'''
pass | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 0.2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 7 | 1 | 5 | 2 | 4 | 1 | 5 | 2 | 4 | 0 | 0 | 0 | 0 |
325,715 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/scripts/cli_verifier.py | cli_verifier.VerificationReport | from typing import List, Optional
from dataclasses import dataclass
@dataclass
class VerificationReport:
"""Complete verification report with all types of mismatches."""
phantom_options: List[PhantomOption]
missing_options: List[MissingOption]
mismatched_descriptions: List[MismatchedDescription]
mi... | @dataclass
class VerificationReport:
'''Complete verification report with all types of mismatches.'''
def __post_init__(self):
pass
@property
def has_issues(self) -> bool:
'''Check if any issues were found.'''
pass
@property
def critical_issues_count(self) -> int:
... | 9 | 4 | 8 | 0 | 7 | 1 | 2 | 0.12 | 0 | 2 | 0 | 0 | 4 | 0 | 4 | 4 | 53 | 6 | 42 | 12 | 34 | 5 | 27 | 9 | 22 | 6 | 0 | 1 | 9 |
325,716 | 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/common/config.py | common.config.ConfigLoader | from typing import Optional
from pathlib import Path
import os
import yaml
class ConfigLoader:
"""Loads and manages configuration from files and environment."""
def __init__(self, config_dir: Optional[Path]=None):
"""
Initialize config loader.
Args:
config_dir: Directory c... |
class ConfigLoader:
'''Loads and manages configuration from files and environment.'''
def __init__(self, config_dir: Optional[Path]=None):
'''
Initialize config loader.
Args:
config_dir: Directory containing config files. Defaults to .github/config
'''
pass
... | 5 | 5 | 19 | 3 | 13 | 4 | 3 | 0.29 | 0 | 6 | 2 | 0 | 4 | 1 | 4 | 4 | 81 | 14 | 52 | 18 | 47 | 15 | 34 | 16 | 29 | 4 | 0 | 2 | 11 |
325,717 | 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/common/config.py | common.config.MonitoringConfig | from dataclasses import dataclass
@dataclass
class MonitoringConfig:
"""Configuration for monitoring workflows."""
check_interval: int = 3600
alert_threshold: int = 3
repositories: list = None
def __post_init__(self):
if self.repositories is None:
self.repositories = ['rxiv-mak... | @dataclass
class MonitoringConfig:
'''Configuration for monitoring workflows.'''
def __post_init__(self):
pass | 3 | 1 | 3 | 0 | 3 | 0 | 2 | 0.43 | 0 | 0 | 0 | 0 | 1 | 0 | 1 | 1 | 10 | 2 | 7 | 5 | 5 | 3 | 7 | 5 | 5 | 2 | 0 | 1 | 2 |
325,718 | 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/common/config.py | common.config.ReleaseConfig | from dataclasses import dataclass
@dataclass
class ReleaseConfig:
"""Configuration for release workflows."""
package_name: str
pypi_timeout: int = 300
pypi_check_interval: int = 30
github_timeout: int = 120
homebrew_repo: str = 'homebrew-rxiv-maker'
apt_repo: str = 'apt-rxiv-maker'
cros... | @dataclass
class ReleaseConfig:
'''Configuration for release workflows.'''
def __post_init__(self):
'''Validate configuration after initialization.'''
pass | 3 | 2 | 6 | 0 | 5 | 1 | 3 | 0.46 | 0 | 1 | 0 | 0 | 1 | 0 | 1 | 1 | 17 | 2 | 13 | 8 | 11 | 6 | 13 | 8 | 11 | 3 | 0 | 1 | 3 |
325,719 | 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/common/utils.py | common.utils.RetryConfig | class RetryConfig:
"""Configuration for retry logic."""
def __init__(self, max_retries: int=3, backoff_factor: float=2.0, initial_delay: float=1.0, max_delay: float=60.0):
self.max_retries = max_retries
self.backoff_factor = backoff_factor
self.initial_delay = initial_delay
self... | class RetryConfig:
'''Configuration for retry logic.'''
def __init__(self, max_retries: int=3, backoff_factor: float=2.0, initial_delay: float=1.0, max_delay: float=60.0):
pass | 2 | 1 | 7 | 0 | 7 | 0 | 1 | 0.13 | 0 | 2 | 0 | 0 | 1 | 4 | 1 | 1 | 10 | 1 | 8 | 8 | 4 | 1 | 6 | 6 | 4 | 1 | 0 | 0 | 1 |
325,720 | 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/content_processor.py | content_processor.ContentProcessor | from ..converters.types import LatexContent, MarkdownContent, ProtectedContent
from .error_recovery import RecoveryEnhancedMixin
import re
import time
from typing import Any, Callable, Dict, List, Optional
from .managers.resource_manager import get_resource_manager, managed_resources
class ContentProcessor(RecoveryEnh... |
class ContentProcessor(RecoveryEnhancedMixin):
'''Enhanced centralized content processing pipeline.
Features:
- Structured processing pipeline with clear stages
- Dependency-aware processor execution
- State management for protected content
- Error recovery and rollback capabilities
- Progr... | 20 | 17 | 40 | 6 | 28 | 6 | 2 | 0.24 | 1 | 13 | 4 | 0 | 16 | 6 | 16 | 19 | 771 | 126 | 525 | 110 | 470 | 127 | 211 | 86 | 179 | 9 | 1 | 5 | 44 |
325,721 | 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/content_processor.py | content_processor.ProcessingResult | from typing import Any, Callable, Dict, List, Optional
from dataclasses import dataclass, field
from ..converters.types import LatexContent, MarkdownContent, ProtectedContent
@dataclass
class ProcessingResult:
"""Result from content processing."""
success: bool
content: LatexContent
duration: float
... | @dataclass
class ProcessingResult:
'''Result from content processing.'''
pass | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 0.1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 12 | 1 | 10 | 6 | 9 | 1 | 10 | 6 | 9 | 0 | 0 | 0 | 0 |
325,722 | 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/content_processor.py | content_processor.ProcessingStage | from enum import Enum
class ProcessingStage(Enum):
"""Content processing stages."""
PREPARATION = 'preparation'
PROTECTION = 'protection'
CONVERSION = 'conversion'
RESTORATION = 'restoration'
FINALIZATION = 'finalization' |
class ProcessingStage(Enum):
'''Content processing stages.'''
pass | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0.17 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 49 | 8 | 1 | 6 | 6 | 5 | 1 | 6 | 6 | 5 | 0 | 4 | 0 | 0 |
325,723 | 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/content_processor.py | content_processor.ProcessorConfig | from dataclasses import dataclass, field
from typing import Any, Callable, Dict, List, Optional
@dataclass
class ProcessorConfig:
"""Configuration for content processors."""
name: str
enabled: bool = True
priority: ProcessorPriority = ProcessorPriority.NORMAL
stage: ProcessingStage = ProcessingStag... | @dataclass
class ProcessorConfig:
'''Configuration for content processors.'''
pass | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 0.13 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 10 | 1 | 8 | 7 | 7 | 1 | 8 | 7 | 7 | 0 | 0 | 0 | 0 |
325,724 | 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/content_processor.py | content_processor.ProcessorPriority | from enum import Enum
class ProcessorPriority(Enum):
"""Processor execution priority."""
CRITICAL = 1
HIGH = 2
NORMAL = 3
LOW = 4
CLEANUP = 5 |
class ProcessorPriority(Enum):
'''Processor execution priority.'''
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 |
325,725 | 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/error_codes.py | core.error_codes.ErrorCategory | from enum import Enum
class ErrorCategory(Enum):
"""Error categories for organizational purposes."""
VALIDATION = 'validation'
FILESYSTEM = 'filesystem'
NETWORK = 'network'
COMPILATION = 'compilation'
CONFIGURATION = 'configuration'
AUTHENTICATION = 'authentication'
DEPENDENCY = 'depend... |
class ErrorCategory(Enum):
'''Error categories for organizational purposes.'''
pass | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0.1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 49 | 12 | 1 | 10 | 10 | 9 | 1 | 10 | 10 | 9 | 0 | 4 | 0 | 0 |
325,726 | 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/error_codes.py | core.error_codes.ErrorCode | from enum import Enum
class ErrorCode(Enum):
"""Comprehensive error codes for rxiv-maker."""
INVALID_DOI_FORMAT = 'E1001'
DOI_NOT_RESOLVABLE = 'E1002'
METADATA_MISMATCH = 'E1003'
METADATA_UNAVAILABLE = 'E1004'
INVALID_YAML_FORMAT = 'E1005'
MISSING_REQUIRED_FIELD = 'E1006'
INVALID_REFERE... |
class ErrorCode(Enum):
'''Comprehensive error codes for rxiv-maker.'''
@property
def category(self) -> ErrorCategory:
'''Get the category for this error code.'''
pass
@property
def description(self) -> str:
'''Get human-readable description of the error.'''
pass
... | 7 | 4 | 51 | 1 | 46 | 5 | 4 | 0.1 | 1 | 4 | 1 | 0 | 3 | 0 | 3 | 52 | 272 | 15 | 235 | 104 | 228 | 24 | 114 | 101 | 110 | 10 | 4 | 1 | 12 |
325,727 | 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/dependency_manager.py | dependency_manager.DependencyManager | import requests
import json
from typing import Any, Dict, List, Optional, Tuple
from pathlib import Path
from rxiv_maker.core.cache.advanced_cache import AdvancedCache
import subprocess
import re
class DependencyManager:
"""Manages dependency updates and security monitoring."""
def __init__(self, project_dir:... |
class DependencyManager:
'''Manages dependency updates and security monitoring.'''
def __init__(self, project_dir: Path, cache_enabled: bool=True):
'''Initialize dependency manager.
Args:
project_dir: Project root directory
cache_enabled: Whether to cache API responses
... | 21 | 21 | 30 | 5 | 22 | 5 | 5 | 0.22 | 0 | 9 | 1 | 0 | 20 | 6 | 20 | 20 | 631 | 117 | 434 | 134 | 400 | 95 | 308 | 113 | 283 | 14 | 0 | 4 | 100 |
325,728 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/scripts/docs_parser.py | docs_parser.DocumentationScanner | from pathlib import Path
from typing import Dict, List, Optional
import json
class DocumentationScanner:
"""Main documentation scanner that finds and analyzes CLI documentation."""
def __init__(self, project_root: Path):
self.project_root = project_root
self.parser = MarkdownCLIParser()
... |
class DocumentationScanner:
'''Main documentation scanner that finds and analyzes CLI documentation.'''
def __init__(self, project_root: Path):
pass
def scan_documentation_files(self) -> Dict[str, DocumentedCommand]:
'''Scan all documentation files in the project.'''
pass
def... | 9 | 8 | 21 | 2 | 18 | 2 | 5 | 0.12 | 0 | 4 | 2 | 0 | 8 | 3 | 8 | 8 | 179 | 25 | 143 | 33 | 134 | 17 | 110 | 33 | 101 | 15 | 0 | 4 | 42 |
325,729 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/scripts/docs_parser.py | docs_parser.DocumentedArgument | from typing import Dict, List, Optional
from dataclasses import dataclass
@dataclass
class DocumentedArgument:
"""Represents a CLI argument documented in markdown."""
name: str
description: Optional[str] = None
required: bool = True
source_file: str = ''
line_number: int = 0 | @dataclass
class DocumentedArgument:
'''Represents a CLI argument documented in markdown.'''
pass | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 0.17 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 8 | 1 | 6 | 5 | 5 | 1 | 6 | 5 | 5 | 0 | 0 | 0 | 0 |
325,730 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/scripts/docs_parser.py | docs_parser.DocumentedCommand | from typing import Dict, List, Optional
from dataclasses import dataclass
@dataclass
class DocumentedCommand:
"""Represents a CLI command documented in markdown."""
name: str
description: Optional[str] = None
options: List[DocumentedOption] = None
arguments: List[DocumentedArgument] = None
sour... | @dataclass
class DocumentedCommand:
'''Represents a CLI command documented in markdown.'''
def __post_init__(self):
pass | 3 | 1 | 7 | 0 | 7 | 0 | 4 | 0.07 | 0 | 0 | 0 | 0 | 1 | 0 | 1 | 1 | 17 | 2 | 14 | 7 | 12 | 1 | 14 | 7 | 12 | 4 | 0 | 1 | 4 |
325,731 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/scripts/docs_parser.py | docs_parser.DocumentedOption | from dataclasses import dataclass
from typing import Dict, List, Optional
@dataclass
class DocumentedOption:
"""Represents a CLI option documented in markdown."""
name: str
short_name: Optional[str] = None
description: Optional[str] = None
default: Optional[str] = None
is_flag: bool = False
... | @dataclass
class DocumentedOption:
'''Represents a CLI option documented in markdown.'''
pass | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 0.13 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 10 | 1 | 8 | 7 | 7 | 1 | 8 | 7 | 7 | 0 | 0 | 0 | 0 |
325,732 | HenriquesLab/rxiv-maker | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/HenriquesLab_rxiv-maker/scripts/docs_parser.py | docs_parser.MarkdownCLIParser | from typing import Dict, List, Optional
import re
from pathlib import Path
class MarkdownCLIParser:
"""Parses markdown documentation to extract CLI command information."""
def __init__(self):
self.commands = {}
self.command_header_pattern = re.compile('^#{1,4}\\s*`rxiv\\s+(\\w+(?:-\\w+)*)`\\s*... |
class MarkdownCLIParser:
'''Parses markdown documentation to extract CLI command information.'''
def __init__(self):
pass
def parse_file(self, file_path: Path) -> Dict[str, DocumentedCommand]:
'''Parse a markdown file and extract CLI documentation.'''
pass
def _extract_comman... | 10 | 9 | 23 | 4 | 15 | 4 | 4 | 0.29 | 0 | 8 | 3 | 0 | 9 | 5 | 9 | 9 | 217 | 46 | 140 | 68 | 128 | 40 | 107 | 64 | 97 | 8 | 0 | 3 | 34 |
325,733 | 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/environment_manager.py | environment_manager.EnvironmentManager | from typing import Any, Dict, Optional, Union
import os
from pathlib import Path
class EnvironmentManager:
"""Centralized environment variable management for rxiv-maker.
Provides consistent access to environment variables with proper
validation, type conversion, and default value handling.
"""
MAN... |
class EnvironmentManager:
'''Centralized environment variable management for rxiv-maker.
Provides consistent access to environment variables with proper
validation, type conversion, and default value handling.
'''
@classmethod
def get_manuscript_path(cls) -> Optional[str]:
'''Get ma... | 53 | 27 | 12 | 2 | 5 | 5 | 2 | 0.7 | 0 | 7 | 0 | 0 | 0 | 0 | 26 | 26 | 378 | 73 | 180 | 86 | 126 | 126 | 124 | 60 | 96 | 7 | 0 | 2 | 48 |
325,734 | 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/error_recovery.py | error_recovery.CircuitBreaker | import threading
from typing import Any, Callable, Dict, Generic, List, Optional, TypeVar
import time
class CircuitBreaker:
"""Circuit breaker pattern implementation for preventing cascading failures."""
def __init__(self, config: RecoveryConfig):
self.config = config
self.failure_count = 0
... |
class CircuitBreaker:
'''Circuit breaker pattern implementation for preventing cascading failures.'''
def __init__(self, config: RecoveryConfig):
pass
def call(self, operation: Callable[[], T]) -> T:
'''Execute operation with circuit breaker protection.'''
pass | 3 | 2 | 18 | 3 | 14 | 2 | 4 | 0.14 | 0 | 4 | 1 | 0 | 2 | 5 | 2 | 2 | 40 | 8 | 29 | 9 | 26 | 4 | 28 | 9 | 25 | 6 | 0 | 3 | 7 |
325,735 | 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/error_recovery.py | error_recovery.ErrorContext | from typing import Any, Callable, Dict, Generic, List, Optional, TypeVar
from dataclasses import dataclass, field
import time
@dataclass
class ErrorContext:
"""Context information for error analysis and recovery."""
error: Exception
operation: str
component: str
attempt_count: int = 0
timestamp... | @dataclass
class ErrorContext:
'''Context information for error analysis and recovery.'''
def add_recovery_attempt(self, strategy: RecoveryStrategy, success: bool, details: str='') -> None:
'''Record a recovery attempt.'''
pass | 3 | 2 | 7 | 0 | 6 | 1 | 3 | 0.13 | 0 | 3 | 1 | 0 | 1 | 0 | 1 | 1 | 19 | 2 | 15 | 9 | 13 | 2 | 15 | 9 | 13 | 3 | 0 | 1 | 3 |
325,736 | 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/error_recovery.py | error_recovery.ErrorRecoveryManager | from typing import Any, Callable, Dict, Generic, List, Optional, TypeVar
from contextlib import contextmanager
import time
import threading
class ErrorRecoveryManager:
"""Central manager for error recovery across all rxiv-maker components.
Features:
- Coordinated recovery strategies across components
... |
class ErrorRecoveryManager:
'''Central manager for error recovery across all rxiv-maker components.
Features:
- Coordinated recovery strategies across components
- Circuit breaker patterns for preventing cascading failures
- Transaction-like rollback capabilities
- Graceful degradation when com... | 14 | 12 | 17 | 2 | 9 | 6 | 2 | 0.74 | 0 | 21 | 5 | 0 | 11 | 5 | 11 | 11 | 211 | 38 | 100 | 30 | 86 | 74 | 86 | 25 | 74 | 5 | 0 | 4 | 26 |
325,737 | 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/error_recovery.py | error_recovery.ErrorSeverity | from enum import Enum
class ErrorSeverity(Enum):
"""Error severity levels for recovery decisions."""
LOW = 'low'
MEDIUM = 'medium'
HIGH = 'high'
CRITICAL = 'critical' |
class ErrorSeverity(Enum):
'''Error severity levels for recovery decisions.'''
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 |
325,738 | 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/error_recovery.py | error_recovery.FallbackAction | from typing import Any, Callable, Dict, Generic, List, Optional, TypeVar
class FallbackAction(RecoveryAction[T]):
"""Recovery action that uses an alternative approach."""
def __init__(self, fallback_func: Callable[[ErrorContext], T], config: RecoveryConfig):
self.fallback_func = fallback_func
... |
class FallbackAction(RecoveryAction[T]):
'''Recovery action that uses an alternative approach.'''
def __init__(self, fallback_func: Callable[[ErrorContext], T], config: RecoveryConfig):
pass
def can_handle(self, context: ErrorContext) -> bool:
'''Check if fallback is appropriate.'''
... | 4 | 3 | 6 | 1 | 5 | 1 | 2 | 0.19 | 1 | 7 | 4 | 0 | 3 | 2 | 3 | 27 | 24 | 5 | 16 | 8 | 12 | 3 | 16 | 7 | 12 | 3 | 5 | 2 | 5 |
325,739 | 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/error_recovery.py | error_recovery.RecoveryAction | from abc import ABC, abstractmethod
from typing import Any, Callable, Dict, Generic, List, Optional, TypeVar
class RecoveryAction(ABC, Generic[T]):
"""Abstract base class for recovery actions."""
@abstractmethod
def execute(self, context: ErrorContext) -> T:
"""Execute the recovery action.
... |
class RecoveryAction(ABC, Generic[T]):
'''Abstract base class for recovery actions.'''
@abstractmethod
def execute(self, context: ErrorContext) -> T:
'''Execute the recovery action.
Args:
context: Error context
Returns:
Recovery result
'''
pas... | 5 | 3 | 10 | 2 | 2 | 6 | 1 | 1.86 | 2 | 2 | 1 | 3 | 2 | 0 | 2 | 24 | 26 | 6 | 7 | 5 | 2 | 13 | 5 | 3 | 2 | 1 | 4 | 0 | 2 |
325,740 | 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/error_recovery.py | error_recovery.RecoveryConfig | from dataclasses import dataclass, field
@dataclass
class RecoveryConfig:
"""Configuration for error recovery behavior."""
max_retries: int = 3
retry_delay_base: float = 1.0
retry_delay_multiplier: float = 2.0
circuit_breaker_threshold: int = 5
circuit_breaker_timeout: float = 60.0
rollback... | @dataclass
class RecoveryConfig:
'''Configuration for error recovery behavior.'''
pass | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 0.1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 12 | 1 | 10 | 10 | 9 | 1 | 10 | 10 | 9 | 0 | 0 | 0 | 0 |
325,741 | 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/error_recovery.py | error_recovery.RecoveryEnhancedMixin | from typing import Any, Callable, Dict, Generic, List, Optional, TypeVar
class RecoveryEnhancedMixin:
"""Mixin class to add recovery capabilities to existing managers."""
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self._recovery_manager = get_error_recovery_manager(... |
class RecoveryEnhancedMixin:
'''Mixin class to add recovery capabilities to existing managers.'''
def __init__(self, *args, **kwargs):
pass
def execute_with_recovery(self, operation: str, func: Callable[[], T], **kwargs) -> T:
'''Execute operation with automatic recovery.
Args:
... | 4 | 3 | 9 | 1 | 3 | 4 | 1 | 1.27 | 0 | 3 | 0 | 7 | 3 | 2 | 3 | 3 | 32 | 7 | 11 | 7 | 7 | 14 | 11 | 7 | 7 | 1 | 0 | 1 | 3 |
325,742 | 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/error_recovery.py | error_recovery.RecoveryStrategy | from enum import Enum
class RecoveryStrategy(Enum):
"""Error recovery strategy types."""
RETRY = 'retry'
ROLLBACK = 'rollback'
FALLBACK = 'fallback'
CIRCUIT_BREAK = 'circuit_break'
GRACEFUL_DEGRADE = 'graceful_degrade' |
class RecoveryStrategy(Enum):
'''Error recovery strategy types.'''
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 |
325,743 | 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/error_recovery.py | error_recovery.RetryAction | from typing import Any, Callable, Dict, Generic, List, Optional, TypeVar
import time
class RetryAction(RecoveryAction[T]):
"""Recovery action that retries the original operation."""
def __init__(self, operation: Callable[[], T], config: RecoveryConfig):
self.operation = operation
self.config =... |
class RetryAction(RecoveryAction[T]):
'''Recovery action that retries the original operation.'''
def __init__(self, operation: Callable[[], T], config: RecoveryConfig):
pass
def can_handle(self, context: ErrorContext) -> bool:
'''Check if retry is appropriate.'''
pass
def exe... | 4 | 3 | 9 | 1 | 8 | 1 | 2 | 0.17 | 1 | 9 | 4 | 0 | 3 | 2 | 3 | 27 | 33 | 6 | 24 | 9 | 20 | 4 | 18 | 8 | 14 | 3 | 5 | 1 | 5 |
325,744 | 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/error_recovery.py | error_recovery.RollbackAction | from typing import Any, Callable, Dict, Generic, List, Optional, TypeVar
class RollbackAction(RecoveryAction[None]):
"""Recovery action that rolls back to a previous state."""
def __init__(self, rollback_func: Callable[[ErrorContext], None]):
self.rollback_func = rollback_func
def can_handle(self... |
class RollbackAction(RecoveryAction[None]):
'''Recovery action that rolls back to a previous state.'''
def __init__(self, rollback_func: Callable[[ErrorContext], None]):
pass
def can_handle(self, context: ErrorContext) -> bool:
'''Check if rollback is appropriate.'''
pass
def... | 4 | 3 | 6 | 1 | 4 | 1 | 1 | 0.21 | 1 | 6 | 3 | 0 | 3 | 1 | 3 | 27 | 22 | 5 | 14 | 6 | 10 | 3 | 14 | 5 | 10 | 2 | 5 | 1 | 4 |
325,745 | 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/error_recovery.py | error_recovery.TransactionContext | from typing import Any, Callable, Dict, Generic, List, Optional, TypeVar
class TransactionContext:
"""Context for transactional operations."""
def __init__(self, transaction_id: str, recovery_manager: ErrorRecoveryManager):
self.transaction_id = transaction_id
self.recovery_manager = recovery_... |
class TransactionContext:
'''Context for transactional operations.'''
def __init__(self, transaction_id: str, recovery_manager: ErrorRecoveryManager):
pass
def checkpoint(self, component: str, state: Dict[str, Any]) -> None:
'''Create a checkpoint for this component.
Args:
... | 3 | 2 | 6 | 1 | 3 | 3 | 1 | 1 | 0 | 3 | 1 | 0 | 2 | 2 | 2 | 2 | 15 | 3 | 6 | 5 | 3 | 6 | 6 | 5 | 3 | 1 | 0 | 0 | 2 |
325,746 | 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/global_container_manager.py | global_container_manager.GlobalContainerManager | import time
from typing import Any, Dict, Optional
from pathlib import Path
import threading
from ..engines.core.abstract import AbstractContainerEngine
import os
from ..engines.core.factory import get_container_engine
class GlobalContainerManager:
"""Singleton manager for container engines across CLI session."""
... |
class GlobalContainerManager:
'''Singleton manager for container engines across CLI session.'''
def __new__(cls):
'''Ensure singleton pattern.'''
pass
def __init__(self):
'''Initialize the global container manager.'''
pass
def _load_session_config(self) -> Dict[str, A... | 13 | 12 | 19 | 2 | 12 | 5 | 3 | 0.39 | 0 | 9 | 1 | 0 | 10 | 2 | 11 | 11 | 226 | 37 | 137 | 44 | 119 | 53 | 103 | 33 | 91 | 5 | 0 | 3 | 30 |
325,747 | 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/homebrew/formula_updater.py | homebrew.formula_updater.HomebrewFormulaUpdater | from logger import log_section, log_step, setup_logger
import tempfile
from config import get_current_version, get_github_token
from typing import Dict, Optional
from utils import create_http_session, run_command
from pathlib import Path
import hashlib
class HomebrewFormulaUpdater:
"""Homebrew formula updater."""
... |
class HomebrewFormulaUpdater:
'''Homebrew formula updater.'''
def __init__(self, tag: Optional[str]=None, force: bool=False, debug: bool=False, direct_commit: bool=False):
'''
Initialize Homebrew formula updater.
Args:
tag: Specific tag to update (overrides event-based dete... | 11 | 11 | 34 | 7 | 21 | 6 | 4 | 0.31 | 0 | 7 | 0 | 0 | 9 | 11 | 9 | 9 | 340 | 81 | 200 | 64 | 185 | 62 | 173 | 54 | 160 | 9 | 0 | 3 | 35 |
325,748 | 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/logging_config.py | logging_config.RxivLogger | from rich.console import Console
from rich.logging import RichHandler
from typing import Optional
from pathlib import Path
import logging
class RxivLogger:
"""Centralized logging configuration for rxiv-maker with Rich support."""
_instance: Optional['RxivLogger'] = None
_console: Console | None = None
... |
class RxivLogger:
'''Centralized logging configuration for rxiv-maker with Rich support.'''
def __new__(cls) -> 'RxivLogger':
'''Create a new instance of the singleton.'''
pass
def __init__(self) -> None:
'''Initialize the singleton instance only once.'''
pass
def _se... | 19 | 18 | 7 | 0 | 5 | 2 | 2 | 0.3 | 0 | 8 | 0 | 0 | 17 | 2 | 17 | 17 | 146 | 27 | 92 | 30 | 73 | 28 | 78 | 29 | 60 | 4 | 0 | 3 | 29 |
325,749 | 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/cache_manager.py | managers.cache_manager.CacheConfig | from dataclasses import dataclass, field
from typing import Any, Dict, Generic, List, Optional, TypeVar
@dataclass
class CacheConfig:
"""Configuration for cache instances."""
name: str
cache_type: CacheType = CacheType.DISK
serialization: SerializationFormat = SerializationFormat.JSON
ttl_seconds: ... | @dataclass
class CacheConfig:
'''Configuration for cache instances.'''
def __post_init__(self):
'''Validate configuration.'''
pass | 3 | 2 | 6 | 0 | 5 | 1 | 3 | 0.56 | 0 | 1 | 0 | 0 | 1 | 0 | 1 | 1 | 20 | 2 | 16 | 11 | 14 | 9 | 16 | 11 | 14 | 3 | 0 | 1 | 3 |
325,750 | 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/cache_manager.py | managers.cache_manager.CacheEntry | from dataclasses import dataclass, field
from typing import Any, Dict, Generic, List, Optional, TypeVar
import time
@dataclass
class CacheEntry:
"""A single cache entry with metadata."""
key: str
value: Any
timestamp: float = field(default_factory=time.time)
ttl: Optional[float] = None
access_c... | @dataclass
class CacheEntry:
'''A single cache entry with metadata.'''
def is_expired(self) -> bool:
'''Check if entry has expired.'''
pass
def touch(self) -> None:
'''Update access statistics.'''
pass | 4 | 3 | 5 | 0 | 4 | 1 | 2 | 0.25 | 0 | 1 | 0 | 0 | 2 | 0 | 2 | 2 | 22 | 3 | 16 | 9 | 13 | 4 | 16 | 9 | 13 | 2 | 0 | 1 | 3 |
325,751 | 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/cache_manager.py | managers.cache_manager.CacheInterface | from abc import ABC, abstractmethod
from typing import Any, Dict, Generic, List, Optional, TypeVar
class CacheInterface(ABC, Generic[T]):
"""Abstract interface for cache implementations."""
@abstractmethod
def get(self, key: str, default: Optional[T]=None) -> Optional[T]:
"""Get value from cache."... |
class CacheInterface(ABC, Generic[T]):
'''Abstract interface for cache implementations.'''
@abstractmethod
def get(self, key: str, default: Optional[T]=None) -> Optional[T]:
'''Get value from cache.'''
pass
@abstractmethod
def set(self, key: str, value: T, ttl: Optional[float]=None)... | 15 | 8 | 3 | 0 | 2 | 1 | 1 | 0.36 | 2 | 4 | 0 | 2 | 7 | 0 | 7 | 29 | 37 | 7 | 22 | 15 | 7 | 8 | 15 | 8 | 7 | 1 | 4 | 0 | 7 |
325,752 | 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/cache_manager.py | managers.cache_manager.CacheManager | import threading
from typing import Any, Dict, Generic, List, Optional, TypeVar
from ..error_recovery import RecoveryEnhancedMixin
class CacheManager(RecoveryEnhancedMixin):
"""Unified cache management system for rxiv-maker.
Features:
- Multiple cache instances with different configurations
- Memory, ... |
class CacheManager(RecoveryEnhancedMixin):
'''Unified cache management system for rxiv-maker.
Features:
- Multiple cache instances with different configurations
- Memory, disk, and hybrid caching strategies
- Automatic cleanup and eviction policies
- Thread-safe operations
- Performance mon... | 9 | 9 | 17 | 2 | 11 | 5 | 2 | 0.55 | 1 | 10 | 6 | 0 | 8 | 3 | 8 | 11 | 154 | 25 | 87 | 16 | 78 | 48 | 40 | 15 | 31 | 3 | 1 | 2 | 13 |
325,753 | 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/cache_manager.py | managers.cache_manager.CacheType | from enum import Enum
class CacheType(Enum):
"""Types of cache storage."""
MEMORY = 'memory'
DISK = 'disk'
HYBRID = 'hybrid' |
class CacheType(Enum):
'''Types of cache storage.'''
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 |
325,754 | 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/cache_manager.py | managers.cache_manager.DiskCache | import json
from pathlib import Path
from ..cache.cache_utils import get_cache_dir
import time
import threading
from typing import Any, Dict, Generic, List, Optional, TypeVar
import hashlib
import pickle
class DiskCache(CacheInterface[T]):
"""Disk-based cache implementation."""
def __init__(self, config: Cach... |
class DiskCache(CacheInterface[T]):
'''Disk-based cache implementation.'''
def __init__(self, config: CacheConfig, cache_dir: Optional[Path]=None):
pass
def get(self, key: str, default: Optional[T]=None) -> Optional[T]:
'''Get value from disk cache.'''
pass
def set(self, key:... | 17 | 16 | 11 | 1 | 9 | 1 | 3 | 0.16 | 1 | 10 | 2 | 0 | 16 | 5 | 16 | 45 | 200 | 37 | 142 | 43 | 125 | 23 | 125 | 34 | 108 | 5 | 5 | 3 | 40 |
325,755 | 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/cache_manager.py | managers.cache_manager.MemoryCache | from typing import Any, Dict, Generic, List, Optional, TypeVar
import threading
class MemoryCache(CacheInterface[T]):
"""In-memory cache implementation."""
def __init__(self, config: CacheConfig):
self.config = config
self._cache: Dict[str, CacheEntry] = {}
self._lock = threading.RLock... |
class MemoryCache(CacheInterface[T]):
'''In-memory cache implementation.'''
def __init__(self, config: CacheConfig):
pass
def get(self, key: str, default: Optional[T]=None) -> Optional[T]:
'''Get value from memory cache.'''
pass
def set(self, key: str, value: T, ttl: Optional... | 13 | 12 | 9 | 1 | 7 | 2 | 2 | 0.25 | 1 | 8 | 2 | 0 | 12 | 4 | 12 | 41 | 125 | 23 | 83 | 24 | 70 | 21 | 81 | 23 | 68 | 6 | 5 | 2 | 27 |
325,756 | 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/cache_manager.py | managers.cache_manager.SerializationFormat | from enum import Enum
class SerializationFormat(Enum):
"""Cache serialization formats."""
JSON = 'json'
PICKLE = 'pickle'
RAW = 'raw' |
class SerializationFormat(Enum):
'''Cache serialization formats.'''
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 |
325,757 | 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/config_manager.py | managers.config_manager.ConfigManager | import json
from ...config.validator import ConfigValidator
from typing import Any, Dict, List, Optional
from pathlib import Path
import os
from ..error_codes import ErrorCode, create_validation_error
import shutil
import yaml
class ConfigManager:
"""Centralized configuration management system."""
def __init_... |
class ConfigManager:
'''Centralized configuration management system.'''
def __init__(self, base_dir: Optional[Path]=None):
'''Initialize configuration manager.
Args:
base_dir: Base directory for configuration files
'''
pass
def load_config(self, config_path: Op... | 19 | 19 | 25 | 4 | 15 | 6 | 4 | 0.4 | 0 | 12 | 2 | 0 | 18 | 5 | 18 | 18 | 465 | 87 | 270 | 72 | 251 | 109 | 185 | 65 | 166 | 8 | 0 | 4 | 64 |
325,758 | 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/dependency_manager.py | managers.dependency_manager.DependencyChecker | from abc import ABC, abstractmethod
class DependencyChecker(ABC):
"""Abstract base class for dependency checkers."""
@abstractmethod
def check(self, spec: DependencySpec) -> DependencyResult:
"""Check if dependency is available.
Args:
spec: Dependency specification
Re... |
class DependencyChecker(ABC):
'''Abstract base class for dependency checkers.'''
@abstractmethod
def check(self, spec: DependencySpec) -> DependencyResult:
'''Check if dependency is available.
Args:
spec: Dependency specification
Returns:
Result of dependency... | 3 | 2 | 10 | 2 | 2 | 6 | 1 | 1.75 | 1 | 2 | 2 | 4 | 1 | 0 | 1 | 21 | 14 | 3 | 4 | 3 | 1 | 7 | 3 | 2 | 1 | 1 | 4 | 0 | 1 |
325,759 | 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/dependency_manager.py | managers.dependency_manager.DependencyManager | from .install_manager import InstallManager, InstallMode
from .resource_manager import get_resource_manager
from typing import Dict, List, Optional, Set
class DependencyManager:
"""Centralized dependency management for rxiv-maker.
Features:
- Unified dependency checking across all types
- Context-awar... |
class DependencyManager:
'''Centralized dependency management for rxiv-maker.
Features:
- Unified dependency checking across all types
- Context-aware dependency resolution (build, figures, validation, etc.)
- Parallel dependency checking
- Integration with InstallManager for missing dependenci... | 10 | 10 | 34 | 5 | 23 | 7 | 4 | 0.35 | 0 | 14 | 11 | 0 | 9 | 4 | 9 | 9 | 330 | 52 | 207 | 42 | 190 | 73 | 103 | 35 | 92 | 8 | 0 | 3 | 33 |
325,760 | 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/dependency_manager.py | managers.dependency_manager.DependencyResult | from dataclasses import dataclass, field
from typing import Dict, List, Optional, Set
@dataclass
class DependencyResult:
"""Result of dependency check."""
spec: DependencySpec
status: DependencyStatus
version: Optional[str] = None
error_message: Optional[str] = None
available_alternative: Optio... | @dataclass
class DependencyResult:
'''Result of dependency check.'''
pass | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 0.14 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 9 | 1 | 7 | 5 | 6 | 1 | 7 | 5 | 6 | 0 | 0 | 0 | 0 |
325,761 | 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/dependency_manager.py | managers.dependency_manager.DependencySpec | from dataclasses import dataclass, field
from typing import Dict, List, Optional, Set
@dataclass
class DependencySpec:
"""Specification for a dependency."""
name: str
type: DependencyType
required: bool = True
min_version: Optional[str] = None
max_version: Optional[str] = None
alternatives:... | @dataclass
class DependencySpec:
'''Specification for a dependency.'''
pass | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 0.18 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 13 | 1 | 11 | 9 | 10 | 2 | 11 | 9 | 10 | 0 | 0 | 0 | 0 |
325,762 | 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/dependency_manager.py | managers.dependency_manager.DependencyStatus | from enum import Enum
class DependencyStatus(Enum):
"""Dependency status states."""
AVAILABLE = 'available'
MISSING = 'missing'
VERSION_MISMATCH = 'version_mismatch'
ERROR = 'error'
UNKNOWN = 'unknown' |
class DependencyStatus(Enum):
'''Dependency status states.'''
pass | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0.17 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 49 | 8 | 1 | 6 | 6 | 5 | 1 | 6 | 6 | 5 | 0 | 4 | 0 | 0 |
325,763 | 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/dependency_manager.py | managers.dependency_manager.DependencyType | from enum import Enum
class DependencyType(Enum):
"""Types of dependencies."""
SYSTEM_BINARY = 'system_binary'
PYTHON_PACKAGE = 'python_package'
NODE_PACKAGE = 'node_package'
R_PACKAGE = 'r_package'
FONT = 'font'
DOCKER_IMAGE = 'docker_image'
ENVIRONMENT_VAR = 'environment_var' |
class DependencyType(Enum):
'''Types of dependencies.'''
pass | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 49 | 10 | 1 | 8 | 8 | 7 | 8 | 8 | 8 | 7 | 0 | 4 | 0 | 0 |
325,764 | 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/dependency_manager.py | managers.dependency_manager.DockerImageChecker | import subprocess
import shutil
class DockerImageChecker(DependencyChecker):
"""Checker for Docker images."""
def check(self, spec: DependencySpec) -> DependencyResult:
"""Check Docker image availability."""
try:
if not shutil.which('docker'):
return DependencyResul... |
class DockerImageChecker(DependencyChecker):
'''Checker for Docker images.'''
def check(self, spec: DependencySpec) -> DependencyResult:
'''Check Docker image availability.'''
pass | 2 | 2 | 24 | 3 | 18 | 3 | 4 | 0.21 | 1 | 5 | 3 | 0 | 1 | 0 | 1 | 22 | 27 | 4 | 19 | 4 | 17 | 4 | 11 | 3 | 9 | 4 | 5 | 2 | 4 |
325,765 | 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/dependency_manager.py | managers.dependency_manager.EnvironmentVarChecker | class EnvironmentVarChecker(DependencyChecker):
"""Checker for environment variables."""
def check(self, spec: DependencySpec) -> DependencyResult:
"""Check environment variable availability."""
import os
value = os.environ.get(spec.name)
if value:
return DependencyR... | class EnvironmentVarChecker(DependencyChecker):
'''Checker for environment variables.'''
def check(self, spec: DependencySpec) -> DependencyResult:
'''Check environment variable availability.'''
pass | 2 | 2 | 11 | 1 | 9 | 1 | 2 | 0.2 | 1 | 3 | 3 | 0 | 1 | 0 | 1 | 22 | 14 | 2 | 10 | 4 | 7 | 2 | 7 | 4 | 4 | 2 | 5 | 1 | 2 |
325,766 | 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/dependency_manager.py | managers.dependency_manager.PythonPackageChecker | from typing import Dict, List, Optional, Set
class PythonPackageChecker(DependencyChecker):
"""Checker for Python packages."""
def check(self, spec: DependencySpec) -> DependencyResult:
"""Check Python package availability."""
try:
__import__(spec.name)
version = self._... |
class PythonPackageChecker(DependencyChecker):
'''Checker for Python packages.'''
def check(self, spec: DependencySpec) -> DependencyResult:
'''Check Python package availability.'''
pass
def _get_package_version(self, package_name: str) -> Optional[str]:
'''Get package version.'''... | 3 | 3 | 14 | 1 | 11 | 2 | 3 | 0.17 | 1 | 6 | 3 | 0 | 2 | 0 | 2 | 23 | 31 | 4 | 23 | 7 | 19 | 4 | 18 | 6 | 14 | 3 | 5 | 2 | 5 |
325,767 | 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/dependency_manager.py | managers.dependency_manager.SystemBinaryChecker | from typing import Dict, List, Optional, Set
import shutil
import subprocess
class SystemBinaryChecker(DependencyChecker):
"""Checker for system binaries and executables."""
def check(self, spec: DependencySpec) -> DependencyResult:
"""Check system binary availability."""
for binary_name in [s... |
class SystemBinaryChecker(DependencyChecker):
'''Checker for system binaries and executables.'''
def check(self, spec: DependencySpec) -> DependencyResult:
'''Check system binary availability.'''
pass
def _get_version(self, binary_name: str, check_command: Optional[List[str]]) -> Optional... | 4 | 4 | 18 | 2 | 13 | 3 | 5 | 0.24 | 1 | 5 | 3 | 0 | 3 | 0 | 3 | 24 | 59 | 9 | 41 | 11 | 37 | 10 | 35 | 11 | 31 | 7 | 5 | 4 | 15 |
325,768 | 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/execution_manager.py | managers.execution_manager.AsyncLocalExecutionManager | import time
from typing import Any, Callable, Dict, List, Optional, Union
class AsyncLocalExecutionManager(LocalExecutionManager):
"""Async version of LocalExecutionManager with concurrent step execution.
Provides significant performance improvements for I/O-intensive operations
by executing independent p... |
class AsyncLocalExecutionManager(LocalExecutionManager):
'''Async version of LocalExecutionManager with concurrent step execution.
Provides significant performance improvements for I/O-intensive operations
by executing independent pipeline steps concurrently.
'''
def __init__(self, *args, **kwargs... | 7 | 7 | 48 | 8 | 31 | 10 | 6 | 0.35 | 1 | 16 | 4 | 0 | 6 | 2 | 6 | 38 | 302 | 53 | 186 | 59 | 165 | 65 | 131 | 46 | 121 | 12 | 6 | 6 | 34 |
325,769 | 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/execution_manager.py | managers.execution_manager.ContainerExecutionManager | class ContainerExecutionManager(ExecutionManager):
"""Container-based execution manager using Docker/Podman."""
def __init__(self, context: ExecutionContext, engine_type: str='docker', **kwargs):
"""Initialize container execution manager.
Args:
context: Execution context
... | class ContainerExecutionManager(ExecutionManager):
'''Container-based execution manager using Docker/Podman.'''
def __init__(self, context: ExecutionContext, engine_type: str='docker', **kwargs):
'''Initialize container execution manager.
Args:
context: Execution context
... | 4 | 4 | 16 | 3 | 6 | 7 | 1 | 1.11 | 1 | 6 | 3 | 0 | 3 | 2 | 3 | 33 | 53 | 13 | 19 | 9 | 14 | 21 | 19 | 9 | 14 | 2 | 5 | 1 | 4 |
325,770 | 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/execution_manager.py | managers.execution_manager.ExecutionContext | from typing import Any, Callable, Dict, List, Optional, Union
from pathlib import Path
from dataclasses import dataclass, field
@dataclass
class ExecutionContext:
"""Execution context containing shared state and configuration."""
mode: ExecutionMode
working_dir: Path
output_dir: Path
verbose: bool ... | @dataclass
class ExecutionContext:
'''Execution context containing shared state and configuration.'''
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 |
325,771 | 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/execution_manager.py | managers.execution_manager.ExecutionManager | from ..error_recovery import RecoveryEnhancedMixin
import time
from abc import ABC, abstractmethod
from ..path_manager import PathManager
from typing import Any, Callable, Dict, List, Optional, Union
class ExecutionManager(RecoveryEnhancedMixin, ABC):
"""Abstract base class for execution management.
Provides ... |
class ExecutionManager(RecoveryEnhancedMixin, ABC):
'''Abstract base class for execution management.
Provides consistent interface for complex multi-step operations with:
- Pipeline execution with dependencies
- Progress tracking and reporting
- Error handling and recovery
- Resource management... | 11 | 9 | 27 | 4 | 15 | 8 | 3 | 0.6 | 2 | 17 | 7 | 2 | 7 | 8 | 7 | 30 | 234 | 39 | 122 | 53 | 88 | 73 | 72 | 27 | 63 | 7 | 4 | 3 | 20 |
325,772 | 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/execution_manager.py | managers.execution_manager.ExecutionMode | from enum import Enum
class ExecutionMode(Enum):
"""Execution mode options."""
LOCAL = 'local'
DOCKER = 'docker'
PODMAN = 'podman' |
class ExecutionMode(Enum):
'''Execution mode options.'''
pass | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0.25 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 49 | 6 | 1 | 4 | 4 | 3 | 1 | 4 | 4 | 3 | 0 | 4 | 0 | 0 |
325,773 | 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/execution_manager.py | managers.execution_manager.ExecutionResult | from typing import Any, Callable, Dict, List, Optional, Union
from dataclasses import dataclass, field
@dataclass
class ExecutionResult:
"""Result of executing a pipeline."""
success: bool
total_duration: float
steps_completed: int
steps_failed: int
steps_skipped: int
error_message: Optiona... | @dataclass
class ExecutionResult:
'''Result of executing a pipeline.'''
pass | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 0.11 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 11 | 1 | 9 | 4 | 8 | 1 | 9 | 4 | 8 | 0 | 0 | 0 | 0 |
325,774 | 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/execution_manager.py | managers.execution_manager.ExecutionStep | from dataclasses import dataclass, field
from typing import Any, Callable, Dict, List, Optional, Union
@dataclass
class ExecutionStep:
"""Represents a single execution step in a pipeline."""
id: str
name: str
description: str
function: Callable[[Dict[str, Any]], StepResult]
dependencies: List[s... | @dataclass
class ExecutionStep:
'''Represents a single execution step in a pipeline.'''
pass | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 0.21 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 16 | 1 | 14 | 10 | 13 | 3 | 14 | 10 | 13 | 0 | 0 | 0 | 0 |
325,775 | 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/execution_manager.py | managers.execution_manager.LocalExecutionManager | import time
class LocalExecutionManager(ExecutionManager):
"""Local execution manager for running steps in the current process."""
def setup_pipeline(self) -> 'LocalExecutionManager':
"""Setup the local execution pipeline.
Returns:
Self for method chaining
"""
logg... |
class LocalExecutionManager(ExecutionManager):
'''Local execution manager for running steps in the current process.'''
def setup_pipeline(self) -> 'LocalExecutionManager':
'''Setup the local execution pipeline.
Returns:
Self for method chaining
'''
pass
def exe... | 3 | 3 | 54 | 9 | 38 | 8 | 6 | 0.21 | 1 | 5 | 3 | 1 | 2 | 1 | 2 | 32 | 112 | 19 | 77 | 20 | 74 | 16 | 50 | 19 | 47 | 10 | 5 | 5 | 12 |
325,776 | 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/execution_manager.py | managers.execution_manager.ProgressCallback | from typing import Any, Callable, Dict, List, Optional, Union
class ProgressCallback:
"""Progress reporting interface."""
def __init__(self, callback: Optional[Callable[[str, int, int], None]]=None):
self.callback = callback
def report(self, message: str, current: int, total: int) -> None:
... |
class ProgressCallback:
'''Progress reporting interface.'''
def __init__(self, callback: Optional[Callable[[str, int, int], None]]=None):
pass
def report(self, message: str, current: int, total: int) -> None:
'''Report progress.'''
pass | 3 | 2 | 4 | 0 | 4 | 1 | 2 | 0.25 | 0 | 2 | 0 | 0 | 2 | 1 | 2 | 2 | 12 | 2 | 8 | 4 | 5 | 2 | 7 | 4 | 4 | 2 | 0 | 1 | 3 |
325,777 | 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/execution_manager.py | managers.execution_manager.StepResult | from enum import Enum
class StepResult(Enum):
"""Step execution result."""
SUCCESS = 'success'
FAILURE = 'failure'
SKIP = 'skip' |
class StepResult(Enum):
'''Step execution result.'''
pass | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0.25 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 49 | 6 | 1 | 4 | 4 | 3 | 1 | 4 | 4 | 3 | 0 | 4 | 0 | 0 |
325,778 | 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/execution_manager.py | managers.execution_manager.StepStatus | from enum import Enum
class StepStatus(Enum):
"""Execution step status."""
PENDING = 'pending'
IN_PROGRESS = 'in_progress'
COMPLETED = 'completed'
FAILED = 'failed'
SKIPPED = 'skipped' |
class StepStatus(Enum):
'''Execution step status.'''
pass | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0.17 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 49 | 8 | 1 | 6 | 6 | 5 | 1 | 6 | 6 | 5 | 0 | 4 | 0 | 0 |
325,779 | 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/install_manager.py | managers.install_manager.InstallManager | from ...install.platform_installers import LinuxInstaller, MacOSInstaller, WindowsInstaller
from ...install.utils.progress import ProgressIndicator
from ...install.utils.verification import verify_installation
import platform
from pathlib import Path
from ...install.utils.logging import InstallLogger
import os
class I... |
class InstallManager:
'''Manages system dependency installation across platforms.'''
def __init__(self, mode: InstallMode=InstallMode.FULL, verbose: bool=False, force: bool=False, interactive: bool=True, log_file: Path | None=None):
'''Initialize the installation manager.
Args:
mod... | 16 | 16 | 24 | 4 | 17 | 4 | 4 | 0.24 | 0 | 16 | 6 | 0 | 15 | 10 | 15 | 15 | 384 | 69 | 255 | 68 | 227 | 62 | 213 | 59 | 192 | 12 | 0 | 4 | 63 |
325,780 | 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/install_manager.py | managers.install_manager.InstallMode | from enum import Enum
class InstallMode(Enum):
"""Installation mode options."""
FULL = 'full'
MINIMAL = 'minimal'
CORE = 'core'
SKIP_SYSTEM = 'skip-system' |
class InstallMode(Enum):
'''Installation mode options.'''
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 |
325,781 | 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/resource_manager.py | managers.resource_manager.ContainerCleaner | from typing import Any, Callable, Dict, List, Optional, Union
import subprocess
class ContainerCleaner(ResourceCleaner):
"""Cleaner for containers."""
def cleanup(self, resource: Any, metadata: Dict[str, Any]) -> bool:
"""Clean up container."""
try:
container_id = str(resource)
... |
class ContainerCleaner(ResourceCleaner):
'''Cleaner for containers.'''
def cleanup(self, resource: Any, metadata: Dict[str, Any]) -> bool:
'''Clean up container.'''
pass
def can_handle(self, resource_type: ResourceType) -> bool:
'''Check if can handle containers.'''
pass | 3 | 3 | 14 | 2 | 9 | 3 | 2 | 0.32 | 1 | 5 | 1 | 0 | 2 | 0 | 2 | 24 | 31 | 6 | 19 | 7 | 16 | 6 | 17 | 6 | 14 | 3 | 5 | 2 | 4 |
325,782 | 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/resource_manager.py | managers.resource_manager.FileHandleCleaner | from typing import Any, Callable, Dict, List, Optional, Union
class FileHandleCleaner(ResourceCleaner):
"""Cleaner for file handles."""
def cleanup(self, resource: Any, metadata: Dict[str, Any]) -> bool:
"""Clean up file handle."""
try:
if hasattr(resource, 'close'):
... |
class FileHandleCleaner(ResourceCleaner):
'''Cleaner for file handles.'''
def cleanup(self, resource: Any, metadata: Dict[str, Any]) -> bool:
'''Clean up file handle.'''
pass
def can_handle(self, resource_type: ResourceType) -> bool:
'''Check if can handle file handles.'''
... | 3 | 3 | 7 | 0 | 6 | 1 | 2 | 0.25 | 1 | 5 | 1 | 0 | 2 | 0 | 2 | 24 | 17 | 2 | 12 | 4 | 9 | 3 | 12 | 3 | 9 | 3 | 5 | 2 | 4 |
325,783 | 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/resource_manager.py | managers.resource_manager.ProcessCleaner | from typing import Any, Callable, Dict, List, Optional, Union
import psutil
import subprocess
class ProcessCleaner(ResourceCleaner):
"""Cleaner for processes."""
def cleanup(self, resource: Any, metadata: Dict[str, Any]) -> bool:
"""Clean up process."""
try:
if isinstance(resource,... |
class ProcessCleaner(ResourceCleaner):
'''Cleaner for processes.'''
def cleanup(self, resource: Any, metadata: Dict[str, Any]) -> bool:
'''Clean up process.'''
pass
def can_handle(self, resource_type: ResourceType) -> bool:
'''Check if can handle processes.'''
pass | 3 | 3 | 19 | 1 | 16 | 4 | 5 | 0.28 | 1 | 12 | 1 | 0 | 2 | 0 | 2 | 24 | 42 | 3 | 32 | 5 | 29 | 9 | 31 | 4 | 28 | 8 | 5 | 4 | 9 |
325,784 | 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/resource_manager.py | managers.resource_manager.ResourceCleaner | from typing import Any, Callable, Dict, List, Optional, Union
from abc import ABC, abstractmethod
class ResourceCleaner(ABC):
"""Abstract base class for resource cleaners."""
@abstractmethod
def cleanup(self, resource: Any, metadata: Dict[str, Any]) -> bool:
"""Clean up a resource.
Args:
... |
class ResourceCleaner(ABC):
'''Abstract base class for resource cleaners.'''
@abstractmethod
def cleanup(self, resource: Any, metadata: Dict[str, Any]) -> bool:
'''Clean up a resource.
Args:
resource: The resource to clean up
metadata: Resource metadata
Retur... | 5 | 3 | 11 | 2 | 2 | 7 | 1 | 2 | 1 | 4 | 1 | 4 | 2 | 0 | 2 | 22 | 27 | 6 | 7 | 5 | 2 | 14 | 5 | 3 | 2 | 1 | 4 | 0 | 2 |
325,785 | 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/resource_manager.py | managers.resource_manager.ResourceInfo | import time
from typing import Any, Callable, Dict, List, Optional, Union
from dataclasses import dataclass, field
@dataclass
class ResourceInfo:
"""Information about a managed resource."""
resource_id: str
resource_type: ResourceType
resource: Any
status: ResourceStatus = ResourceStatus.CREATED
... | @dataclass
class ResourceInfo:
'''Information about a managed resource.'''
pass | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 0.22 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 11 | 1 | 9 | 6 | 8 | 2 | 9 | 6 | 8 | 0 | 0 | 0 | 0 |
325,786 | 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/resource_manager.py | managers.resource_manager.ResourceManager | import threading
import tempfile
from contextlib import contextmanager
from typing import Any, Callable, Dict, List, Optional, Union
import os
import subprocess
import atexit
from pathlib import Path
import time
from ..error_recovery import RecoveryEnhancedMixin
import psutil
import shutil
class ResourceManager(Recove... |
class ResourceManager(RecoveryEnhancedMixin):
'''Centralized resource lifecycle management with automatic cleanup.
Features:
- Automatic registration and tracking of resources
- Context manager support for automatic cleanup
- Multiple cleanup strategies for different resource types
- Resource u... | 18 | 16 | 26 | 4 | 16 | 6 | 3 | 0.44 | 1 | 21 | 9 | 0 | 15 | 8 | 15 | 18 | 440 | 83 | 249 | 76 | 217 | 109 | 156 | 58 | 139 | 9 | 1 | 5 | 40 |
325,787 | 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/resource_manager.py | managers.resource_manager.ResourceStatus | from enum import Enum
class ResourceStatus(Enum):
"""Resource lifecycle status."""
CREATED = 'created'
ACTIVE = 'active'
CLEANING = 'cleaning'
CLEANED = 'cleaned'
FAILED = 'failed' |
class ResourceStatus(Enum):
'''Resource lifecycle status.'''
pass | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0.17 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 49 | 8 | 1 | 6 | 6 | 5 | 1 | 6 | 6 | 5 | 0 | 4 | 0 | 0 |
325,788 | 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/resource_manager.py | managers.resource_manager.ResourceType | from enum import Enum
class ResourceType(Enum):
"""Types of resources that can be managed."""
TEMP_FILE = 'temp_file'
TEMP_DIRECTORY = 'temp_directory'
PROCESS = 'process'
CONTAINER = 'container'
FILE_HANDLE = 'file_handle'
NETWORK_CONNECTION = 'network_connection'
CUSTOM = 'custom' |
class ResourceType(Enum):
'''Types of resources that can be managed.'''
pass | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0.13 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 49 | 10 | 1 | 8 | 8 | 7 | 1 | 8 | 8 | 7 | 0 | 4 | 0 | 0 |
325,789 | 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/resource_manager.py | managers.resource_manager.ResourceUsage | from dataclasses import dataclass, field
import time
@dataclass
class ResourceUsage:
"""Current resource usage metrics."""
memory_mb: float
cpu_percent: float
disk_usage_gb: float
open_files: int
running_processes: int
temporary_files: int
containers: int
timestamp: float = field(de... | @dataclass
class ResourceUsage:
'''Current resource usage metrics.'''
pass | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 0.11 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 11 | 1 | 9 | 2 | 8 | 1 | 9 | 2 | 8 | 0 | 0 | 0 | 0 |
325,790 | 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/resource_manager.py | managers.resource_manager.TempFileCleaner | import shutil
from pathlib import Path
from typing import Any, Callable, Dict, List, Optional, Union
class TempFileCleaner(ResourceCleaner):
"""Cleaner for temporary files and directories."""
def cleanup(self, resource: Any, metadata: Dict[str, Any]) -> bool:
"""Clean up temporary file or directory.""... |
class TempFileCleaner(ResourceCleaner):
'''Cleaner for temporary files and directories.'''
def cleanup(self, resource: Any, metadata: Dict[str, Any]) -> bool:
'''Clean up temporary file or directory.'''
pass
def can_handle(self, resource_type: ResourceType) -> bool:
'''Check if ca... | 3 | 3 | 9 | 0 | 8 | 1 | 3 | 0.18 | 1 | 6 | 1 | 0 | 2 | 0 | 2 | 24 | 22 | 2 | 17 | 5 | 14 | 3 | 16 | 4 | 13 | 5 | 5 | 3 | 6 |
325,791 | 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/state_manager.py | managers.state_manager.BuildPhase | from enum import Enum
class BuildPhase(Enum):
"""Build process phases."""
INITIALIZING = 'initializing'
VALIDATING = 'validating'
PREPROCESSING = 'preprocessing'
GENERATING_FIGURES = 'generating_figures'
CONVERTING_CONTENT = 'converting_content'
COMPILING_LATEX = 'compiling_latex'
FINAL... |
class BuildPhase(Enum):
'''Build process phases.'''
pass | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0.1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 49 | 12 | 1 | 10 | 10 | 9 | 1 | 10 | 10 | 9 | 0 | 4 | 0 | 0 |
325,792 | 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/state_manager.py | managers.state_manager.BuildState | from typing import Any, Dict, List, Optional, Set
from dataclasses import asdict, dataclass, field
@dataclass
class BuildState:
"""State tracking for build operations."""
phase: BuildPhase = BuildPhase.INITIALIZING
progress_percent: float = 0.0
current_step: str = ''
total_steps: int = 0
comple... | @dataclass
class BuildState:
'''State tracking for build operations.'''
pass | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 0.07 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 16 | 1 | 14 | 14 | 13 | 1 | 14 | 14 | 13 | 0 | 0 | 0 | 0 |
325,793 | 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/state_manager.py | managers.state_manager.SessionState | import time
from typing import Any, Dict, List, Optional, Set
from dataclasses import asdict, dataclass, field
@dataclass
class SessionState:
"""Current session state."""
session_id: str = ''
start_time: float = field(default_factory=time.time)
current_working_dir: Optional[str] = None
active_build... | @dataclass
class SessionState:
'''Current session state.'''
pass | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 0.13 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 10 | 1 | 8 | 8 | 7 | 1 | 8 | 8 | 7 | 0 | 0 | 0 | 0 |
325,794 | 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/state_manager.py | managers.state_manager.StateChangeListener | from abc import ABC, abstractmethod
from typing import Any, Dict, List, Optional, Set
class StateChangeListener(ABC):
"""Abstract base class for state change listeners."""
@abstractmethod
def on_state_changed(self, scope: StateScope, key: str, old_value: Any, new_value: Any) -> None:
"""Called whe... |
class StateChangeListener(ABC):
'''Abstract base class for state change listeners.'''
@abstractmethod
def on_state_changed(self, scope: StateScope, key: str, old_value: Any, new_value: Any) -> None:
'''Called when state changes.
Args:
scope: Scope of the changed state
... | 3 | 2 | 10 | 1 | 2 | 7 | 1 | 2 | 1 | 3 | 1 | 0 | 1 | 0 | 1 | 21 | 14 | 2 | 4 | 3 | 1 | 8 | 3 | 2 | 1 | 1 | 4 | 0 | 1 |
325,795 | 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/state_manager.py | managers.state_manager.StateManager | import json
from dataclasses import asdict, dataclass, field
from typing import Any, Dict, List, Optional, Set
from pathlib import Path
import threading
from contextlib import contextmanager
from ..error_recovery import RecoveryEnhancedMixin
import time
class StateManager(RecoveryEnhancedMixin):
"""Centralized app... |
class StateManager(RecoveryEnhancedMixin):
'''Centralized application state management.
Features:
- Multi-scope state management (session, persistent, global, local)
- Thread-safe operations with fine-grained locking
- State change notifications and listeners
- Automatic persistence and recover... | 24 | 23 | 16 | 3 | 8 | 5 | 2 | 0.72 | 1 | 15 | 6 | 0 | 22 | 7 | 22 | 25 | 393 | 96 | 173 | 61 | 149 | 124 | 162 | 49 | 139 | 5 | 1 | 4 | 51 |
325,796 | 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/state_manager.py | managers.state_manager.StateScope | from enum import Enum
class StateScope(Enum):
"""Scope of state management."""
SESSION = 'session'
PERSISTENT = 'persistent'
GLOBAL = 'global'
LOCAL = 'local' |
class StateScope(Enum):
'''Scope of state management.'''
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 |
325,797 | 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/state_manager.py | managers.state_manager.UserPreferences | from typing import Any, Dict, List, Optional, Set
from dataclasses import asdict, dataclass, field
@dataclass
class UserPreferences:
"""User preferences and settings."""
default_engine: str = 'LOCAL'
verbose_output: bool = False
auto_validate: bool = True
enable_caching: bool = True
default_out... | @dataclass
class UserPreferences:
'''User preferences and settings.'''
pass | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 0.09 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 13 | 1 | 11 | 11 | 10 | 1 | 11 | 11 | 10 | 0 | 0 | 0 | 0 |
325,798 | 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.CitationValidatorWrapper | 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 CitationValidatorWrapper(BaseValidator):
"""Wrapper for citation valid... |
class CitationValidatorWrapper(BaseValidator):
'''Wrapper for citation validator.'''
def __init__(self):
pass
def validate(self, manuscript_path: Path, context: ValidationContext, strictness: ValidationStrictness, **kwargs) -> ValidationResult:
'''Validate citations.'''
pass
... | 4 | 2 | 15 | 2 | 12 | 1 | 3 | 0.14 | 1 | 10 | 6 | 0 | 3 | 1 | 3 | 27 | 51 | 10 | 36 | 13 | 29 | 5 | 29 | 10 | 24 | 7 | 5 | 3 | 9 |
325,799 | 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.DOIValidatorWrapper | 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 DOIValidatorWrapper(BaseValidator):
"""Wrapper for DOI validator."""
... |
class DOIValidatorWrapper(BaseValidator):
'''Wrapper for DOI validator.'''
def __init__(self):
pass
def validate(self, manuscript_path: Path, context: ValidationContext, strictness: ValidationStrictness, **kwargs) -> ValidationResult:
'''Validate DOIs.'''
pass
def get_support... | 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 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.