repo_full_name stringlengths 6 93 | repo_url stringlengths 25 112 | repo_api_url stringclasses 28
values | owner stringclasses 28
values | repo_name stringclasses 28
values | description stringclasses 28
values | stars int64 617 98.8k | forks int64 31 355 ⌀ | watchers int64 990 999 ⌀ | license stringclasses 2
values | default_branch stringclasses 2
values | repo_created_at timestamp[s]date 2012-07-24 23:12:50 2025-06-16 08:07:28 ⌀ | repo_updated_at timestamp[s]date 2026-02-23 15:23:15 2026-05-03 18:52:12 ⌀ | repo_topics listlengths 0 13 ⌀ | repo_languages unknown | is_fork bool 1
class | open_issues int64 3 104 ⌀ | file_path stringlengths 3 208 | file_name stringclasses 509
values | file_extension stringclasses 1
value | file_size_bytes int64 101 84k ⌀ | file_url stringclasses 627
values | file_raw_url stringclasses 627
values | file_sha stringclasses 624
values | language stringclasses 8
values | parsed_at stringdate 2026-05-04 01:12:36 2026-05-04 19:41:55 | text stringlengths 100 102k |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
foryourhealth111-pixel/Vibe-Skills | https://github.com/foryourhealth111-pixel/Vibe-Skills | null | null | null | null | 1,934 | null | null | apache-2.0 | null | null | null | null | null | null | null | apps/vgo-cli/src/vgo_cli/install_gates.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:34.719888 | from __future__ import annotations
from pathlib import Path
import subprocess
import sys
from .errors import CliError
from .process import (
choose_powershell,
print_process_output,
run_powershell_file,
run_subprocess,
)
from .repo import get_installed_runtime_config, resolve_canonical_repo_root
def... |
foryourhealth111-pixel/Vibe-Skills | https://github.com/foryourhealth111-pixel/Vibe-Skills | null | null | null | null | 1,934 | null | null | apache-2.0 | null | null | null | null | null | null | null | apps/vgo-cli/src/vgo_cli/commands.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:34.721230 | from __future__ import annotations
import argparse
from pathlib import Path
from .core_bridge import run_canonical_entry_core, run_installer_core, run_router_core, run_uninstaller_core
from .errors import CliError
from .external import maybe_install_external_dependencies
from .hosts import (
assert_target_root_ma... |
foryourhealth111-pixel/Vibe-Skills | https://github.com/foryourhealth111-pixel/Vibe-Skills | null | null | null | null | 1,934 | null | null | apache-2.0 | null | null | null | null | null | null | null | _python_source_roots.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:34.800650 | from vgo_python_source_roots import PYTHON_SOURCE_ROOTS, REPO_ROOT
__all__ = ["PYTHON_SOURCE_ROOTS", "REPO_ROOT"]
|
foryourhealth111-pixel/Vibe-Skills | https://github.com/foryourhealth111-pixel/Vibe-Skills | null | null | null | null | 1,934 | null | null | apache-2.0 | null | null | null | null | null | null | null | apps/vgo-cli/src/vgo_cli/core_bridge.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:34.802699 | from __future__ import annotations
from pathlib import Path
import subprocess
from typing import Sequence
from .process import invoke_python_core
from .workspace import extend_workspace_package_path
def run_installer_core(repo_root: Path, argv: Sequence[str]) -> subprocess.CompletedProcess[str]:
extend_workspac... |
foryourhealth111-pixel/Vibe-Skills | https://github.com/foryourhealth111-pixel/Vibe-Skills | null | null | null | null | 1,934 | null | null | apache-2.0 | null | null | null | null | null | null | null | apps/vgo-cli/src/vgo_cli/version_reminder.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:36.475223 | from __future__ import annotations
import argparse
from pathlib import Path
import sys
if __package__ in {None, ''}:
sys.path.insert(0, str(Path(__file__).resolve().parents[1]))
from vgo_cli.upgrade_service import has_recorded_install_truth, load_recorded_install_status, refresh_upstream_status
from vgo_cli.upg... |
foryourhealth111-pixel/Vibe-Skills | https://github.com/foryourhealth111-pixel/Vibe-Skills | null | null | null | null | 1,934 | null | null | apache-2.0 | null | null | null | null | null | null | null | apps/vgo-cli/src/vgo_cli/upgrade_service.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:36.476834 | from __future__ import annotations
import json
from pathlib import Path
import subprocess
from .core_bridge import run_installer_core
from .errors import CliError
from .external import maybe_install_external_dependencies
from .hosts import install_mode_for_host
from .install_support import reconcile_install_postcondi... |
foryourhealth111-pixel/Vibe-Skills | https://github.com/foryourhealth111-pixel/Vibe-Skills | null | null | null | null | 1,934 | null | null | apache-2.0 | null | null | null | null | null | null | null | apps/vgo-cli/src/vgo_cli/upgrade_state.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:36.612134 | from __future__ import annotations
from datetime import datetime, timedelta, timezone
import json
from pathlib import Path
from typing import Any
UPGRADE_STATUS_RELPATH = Path('.vibeskills') / 'upgrade-status.json'
UPSTREAM_CACHE_TTL = timedelta(hours=24)
def _utc_now() -> datetime:
return datetime.now(timezon... |
foryourhealth111-pixel/Vibe-Skills | https://github.com/foryourhealth111-pixel/Vibe-Skills | null | null | null | null | 1,934 | null | null | apache-2.0 | null | null | null | null | null | null | null | bundled/skills/.system/skill-creator/scripts/init_skill.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:37.201025 | #!/usr/bin/env python3
"""
Skill Initializer - Creates a new skill from template
Usage:
init_skill.py <skill-name> --path <path> [--resources scripts,references,assets] [--examples] [--interface key=value]
Examples:
init_skill.py my-new-skill --path skills/public
init_skill.py my-new-skill --path skills/p... |
foryourhealth111-pixel/Vibe-Skills | https://github.com/foryourhealth111-pixel/Vibe-Skills | null | null | null | null | 1,934 | null | null | apache-2.0 | null | null | null | null | null | null | null | bundled/skills/.system/skill-creator/scripts/generate_openai_yaml.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:37.244108 | #!/usr/bin/env python3
"""
OpenAI YAML Generator - Creates agents/openai.yaml for a skill folder.
Usage:
generate_openai_yaml.py <skill_dir> [--name <skill_name>] [--interface key=value]
"""
import argparse
import re
import sys
from pathlib import Path
import yaml
ACRONYMS = {
"GH",
"MCP",
"API",
... |
foryourhealth111-pixel/Vibe-Skills | https://github.com/foryourhealth111-pixel/Vibe-Skills | null | null | null | null | 1,934 | null | null | apache-2.0 | null | null | null | null | null | null | null | apps/vgo-cli/src/vgo_cli/workspace.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:37.384895 | from __future__ import annotations
import sys
from pathlib import Path
def extend_workspace_package_path(repo_root: Path) -> None:
for rel in (
'packages/contracts/src',
'packages/installer-core/src',
'packages/runtime-core/src',
'packages/verification-core/src',
):
sr... |
foryourhealth111-pixel/Vibe-Skills | https://github.com/foryourhealth111-pixel/Vibe-Skills | null | null | null | null | 1,934 | null | null | apache-2.0 | null | null | null | null | null | null | null | bundled/skills/.system/skill-creator/scripts/quick_validate.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:37.582859 | #!/usr/bin/env python3
"""
Quick validation script for skills - minimal version
"""
import re
import sys
from pathlib import Path
import yaml
MAX_SKILL_NAME_LENGTH = 64
def validate_skill(skill_path):
"""Basic validation of a skill"""
skill_path = Path(skill_path)
skill_md = skill_path / "SKILL.md"
... |
foryourhealth111-pixel/Vibe-Skills | https://github.com/foryourhealth111-pixel/Vibe-Skills | null | null | null | null | 1,934 | null | null | apache-2.0 | null | null | null | null | null | null | null | bundled/skills/.system/skill-installer/scripts/install-skill-from-github.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:37.951416 | #!/usr/bin/env python3
"""Install a skill from a GitHub repo path into $CODEX_HOME/skills."""
from __future__ import annotations
import argparse
from dataclasses import dataclass
import os
import shutil
import subprocess
import sys
import tempfile
import urllib.error
import urllib.parse
import zipfile
from github_ut... |
foryourhealth111-pixel/Vibe-Skills | https://github.com/foryourhealth111-pixel/Vibe-Skills | null | null | null | null | 1,934 | null | null | apache-2.0 | null | null | null | null | null | null | null | bundled/skills/.system/skill-installer/scripts/list-skills.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:38.095130 | #!/usr/bin/env python3
"""List skills from a GitHub repo path."""
from __future__ import annotations
import argparse
import json
import os
import sys
import urllib.error
from github_utils import github_api_contents_url, github_request
DEFAULT_REPO = "openai/skills"
DEFAULT_PATH = "skills/.curated"
DEFAULT_REF = "ma... |
foryourhealth111-pixel/Vibe-Skills | https://github.com/foryourhealth111-pixel/Vibe-Skills | null | null | null | null | 1,934 | null | null | apache-2.0 | null | null | null | null | null | null | null | bundled/skills/.system/skill-installer/scripts/github_utils.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:38.299699 | #!/usr/bin/env python3
"""Shared GitHub helpers for skill install scripts."""
from __future__ import annotations
import os
import urllib.request
def github_request(url: str, user_agent: str) -> bytes:
headers = {"User-Agent": user_agent}
token = os.environ.get("GITHUB_TOKEN") or os.environ.get("GH_TOKEN")
... |
foryourhealth111-pixel/Vibe-Skills | https://github.com/foryourhealth111-pixel/Vibe-Skills | null | null | null | null | 1,934 | null | null | apache-2.0 | null | null | null | null | null | null | null | bundled/skills/chembl-database/scripts/example_queries.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:38.505346 | #!/usr/bin/env python3
"""
ChEMBL Database Query Examples
This script demonstrates common query patterns for the ChEMBL database
using the chembl_webresource_client Python library.
Requirements:
pip install chembl_webresource_client
pip install pandas (optional, for data manipulation)
"""
from chembl_webreso... |
foryourhealth111-pixel/Vibe-Skills | https://github.com/foryourhealth111-pixel/Vibe-Skills | null | null | null | null | 1,934 | null | null | apache-2.0 | null | null | null | null | null | null | null | bundled/skills/citation-management/scripts/doi_to_bibtex.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:38.811090 | #!/usr/bin/env python3
"""
DOI to BibTeX Converter
Quick utility to convert DOIs to BibTeX format using CrossRef API.
"""
import sys
import requests
import argparse
import time
import json
from typing import Optional, List
class DOIConverter:
"""Convert DOIs to BibTeX entries using CrossRef API."""
def _... |
foryourhealth111-pixel/Vibe-Skills | https://github.com/foryourhealth111-pixel/Vibe-Skills | null | null | null | null | 1,934 | null | null | apache-2.0 | null | null | null | null | null | null | null | bundled/skills/citation-management/scripts/extract_metadata.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:39.023812 | #!/usr/bin/env python3
"""
Metadata Extraction Tool
Extract citation metadata from DOI, PMID, arXiv ID, or URL using various APIs.
"""
import sys
import os
import requests
import argparse
import time
import re
import json
import xml.etree.ElementTree as ET
from typing import Optional, Dict, List, Tuple
from urllib.par... |
foryourhealth111-pixel/Vibe-Skills | https://github.com/foryourhealth111-pixel/Vibe-Skills | null | null | null | null | 1,934 | null | null | apache-2.0 | null | null | null | null | null | null | null | bundled/skills/citation-management/scripts/search_google_scholar.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:39.222313 | #!/usr/bin/env python3
"""
Google Scholar Search Tool
Search Google Scholar and export results.
Note: This script requires the 'scholarly' library.
Install with: pip install scholarly
"""
import sys
import argparse
import json
import time
import random
from typing import List, Dict, Optional
try:
from scholarly ... |
foryourhealth111-pixel/Vibe-Skills | https://github.com/foryourhealth111-pixel/Vibe-Skills | null | null | null | null | 1,934 | null | null | apache-2.0 | null | null | null | null | null | null | null | bundled/skills/citation-management/scripts/format_bibtex.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:39.223412 | #!/usr/bin/env python3
"""
BibTeX Formatter and Cleaner
Format, clean, sort, and deduplicate BibTeX files.
"""
import sys
import re
import argparse
from typing import List, Dict, Tuple
from collections import OrderedDict
class BibTeXFormatter:
"""Format and clean BibTeX entries."""
def __init__(self):
... |
foryourhealth111-pixel/Vibe-Skills | https://github.com/foryourhealth111-pixel/Vibe-Skills | null | null | null | null | 1,934 | null | null | apache-2.0 | null | null | null | null | null | null | null | bundled/skills/citation-management/scripts/search_pubmed.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:39.648116 | #!/usr/bin/env python3
"""
PubMed Search Tool
Search PubMed using E-utilities API and export results.
"""
import sys
import os
import requests
import argparse
import json
import time
import xml.etree.ElementTree as ET
from typing import List, Dict, Optional
from datetime import datetime
class PubMedSearcher:
"""S... |
foryourhealth111-pixel/Vibe-Skills | https://github.com/foryourhealth111-pixel/Vibe-Skills | null | null | null | null | 1,934 | null | null | apache-2.0 | null | null | null | null | null | null | null | bundled/skills/citation-management/scripts/validate_citations.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:39.832010 | #!/usr/bin/env python3
"""
Citation Validation Tool
Validate BibTeX files for accuracy, completeness, and format compliance.
"""
import sys
import re
import requests
import argparse
import json
from typing import Dict, List, Tuple, Optional
from collections import defaultdict
class CitationValidator:
"""Validate ... |
foryourhealth111-pixel/Vibe-Skills | https://github.com/foryourhealth111-pixel/Vibe-Skills | null | null | null | null | 1,934 | null | null | apache-2.0 | null | null | null | null | null | null | null | bundled/skills/clinical-decision-support/scripts/build_decision_tree.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:39.941778 | #!/usr/bin/env python3
"""
Build Clinical Decision Tree Flowcharts in TikZ Format
Generates LaTeX/TikZ code for clinical decision algorithms from
simple text or YAML descriptions.
Dependencies: pyyaml (optional, for YAML input)
"""
import argparse
from pathlib import Path
import json
class DecisionNode:
"""Rep... |
foryourhealth111-pixel/Vibe-Skills | https://github.com/foryourhealth111-pixel/Vibe-Skills | null | null | null | null | 1,934 | null | null | apache-2.0 | null | null | null | null | null | null | null | bundled/skills/clinical-decision-support/scripts/biomarker_classifier.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:39.956530 | #!/usr/bin/env python3
"""
Biomarker-Based Patient Stratification and Classification
Performs patient stratification based on biomarker profiles with:
- Binary classification (biomarker+/-)
- Multi-class molecular subtypes
- Continuous biomarker scoring
- Correlation with clinical outcomes
Dependencies: pandas, numpy... |
foryourhealth111-pixel/Vibe-Skills | https://github.com/foryourhealth111-pixel/Vibe-Skills | null | null | null | null | 1,934 | null | null | apache-2.0 | null | null | null | null | null | null | null | apps/vgo-cli/src/vgo_cli/output.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:40.319880 | from __future__ import annotations
import json
from pathlib import Path
import shutil
import subprocess
from .errors import CliError
from .mcp_provision import manual_follow_up_servers
from .process import print_process_output
def parse_json_output(result: subprocess.CompletedProcess[str]) -> dict:
if result.re... |
foryourhealth111-pixel/Vibe-Skills | https://github.com/foryourhealth111-pixel/Vibe-Skills | null | null | null | null | 1,934 | null | null | apache-2.0 | null | null | null | null | null | null | null | apps/vgo-cli/src/vgo_cli/mcp_provision.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:40.340163 | from __future__ import annotations
from dataclasses import dataclass
import json
from pathlib import Path
import shutil
import subprocess
import sys
from typing import Any
from .repo import load_json
RECEIPT_RELPATH = Path(".vibeskills") / "mcp-auto-provision.json"
REQUIRED_SERVERS = ("github", "context7", "serena"... |
foryourhealth111-pixel/Vibe-Skills | https://github.com/foryourhealth111-pixel/Vibe-Skills | null | null | null | null | 1,934 | null | null | apache-2.0 | null | null | null | null | null | null | null | apps/vgo-cli/src/vgo_cli/main.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:40.364720 | from __future__ import annotations
import argparse
import sys
from .commands import canonical_entry_command, install_command, passthrough_command, route_command, runtime_command, uninstall_command, upgrade_command, verify_command
from .errors import CliError
def build_parser() -> argparse.ArgumentParser:
parser... |
foryourhealth111-pixel/Vibe-Skills | https://github.com/foryourhealth111-pixel/Vibe-Skills | null | null | null | null | 1,934 | null | null | apache-2.0 | null | null | null | null | null | null | null | bundled/skills/clinical-decision-support/scripts/create_cohort_tables.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:40.366318 | #!/usr/bin/env python3
"""
Generate Clinical Cohort Tables for Baseline Characteristics and Outcomes
Creates publication-ready tables with:
- Baseline demographics (Table 1 style)
- Efficacy outcomes
- Safety/adverse events
- Statistical comparisons between groups
Dependencies: pandas, numpy, scipy
"""
import pandas... |
foryourhealth111-pixel/Vibe-Skills | https://github.com/foryourhealth111-pixel/Vibe-Skills | null | null | null | null | 1,934 | null | null | apache-2.0 | null | null | null | null | null | null | null | apps/vgo-cli/src/vgo_cli/skill_surface.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:40.386314 | from __future__ import annotations
from datetime import datetime
from pathlib import Path
import shutil
from .errors import CliError
def resolve_codex_duplicate_skill_root(target_root: Path, host_id: str) -> Path | None:
if host_id != 'codex' or target_root.name.lower() != '.codex':
return None
pare... |
foryourhealth111-pixel/Vibe-Skills | https://github.com/foryourhealth111-pixel/Vibe-Skills | null | null | null | null | 1,934 | null | null | apache-2.0 | null | null | null | null | null | null | null | bundled/skills/clinical-decision-support/scripts/generate_survival_analysis.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:40.387602 | #!/usr/bin/env python3
"""
Generate Kaplan-Meier Survival Curves for Clinical Decision Support Documents
This script creates publication-quality survival curves with:
- Kaplan-Meier survival estimates
- 95% confidence intervals
- Log-rank test statistics
- Hazard ratios with confidence intervals
- Number at risk table... |
foryourhealth111-pixel/Vibe-Skills | https://github.com/foryourhealth111-pixel/Vibe-Skills | null | null | null | null | 1,934 | null | null | apache-2.0 | null | null | null | null | null | null | null | apps/vgo-cli/src/vgo_cli/repo.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:40.469814 | from __future__ import annotations
import json
from pathlib import Path
import subprocess
import sys
CONTRACTS_SRC = Path(__file__).resolve().parents[4] / 'packages' / 'contracts' / 'src'
if str(CONTRACTS_SRC) not in sys.path:
sys.path.insert(0, str(CONTRACTS_SRC))
from vgo_contracts.installed_runtime_contract ... |
foryourhealth111-pixel/Vibe-Skills | https://github.com/foryourhealth111-pixel/Vibe-Skills | null | null | null | null | 1,934 | null | null | apache-2.0 | null | null | null | null | null | null | null | apps/vgo-cli/src/vgo_cli/process.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:40.491509 | from __future__ import annotations
import contextlib
import io
import json
import os
from pathlib import Path
import shutil
import subprocess
import sys
from typing import Any, Callable, Sequence
import warnings
from .errors import CliError
REPO_ROOT = Path(__file__).resolve().parents[4]
POWERSHELL_HOST_POLICY_PATH... |
foryourhealth111-pixel/Vibe-Skills | https://github.com/foryourhealth111-pixel/Vibe-Skills | null | null | null | null | 1,934 | null | null | apache-2.0 | null | null | null | null | null | null | null | bundled/skills/clinical-decision-support/scripts/validate_cds_document.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:40.548737 | #!/usr/bin/env python3
"""
Validate Clinical Decision Support Documents for Quality and Completeness
Checks for:
- Evidence citations for all recommendations
- Statistical reporting completeness
- Biomarker nomenclature consistency
- Required sections present
- HIPAA de-identification
- GRADE recommendation format
De... |
foryourhealth111-pixel/Vibe-Skills | https://github.com/foryourhealth111-pixel/Vibe-Skills | null | null | null | null | 1,934 | null | null | apache-2.0 | null | null | null | null | null | null | null | bundled/skills/clinical-reports/scripts/check_deidentification.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:40.654443 | #!/usr/bin/env python3
"""
Check clinical reports for HIPAA identifiers that need removal.
Scans text for 18 HIPAA identifiers and flags potential privacy violations.
Usage:
python check_deidentification.py <input_file>
python check_deidentification.py <input_file> --output violations.json
"""
import argpars... |
foryourhealth111-pixel/Vibe-Skills | https://github.com/foryourhealth111-pixel/Vibe-Skills | null | null | null | null | 1,934 | null | null | apache-2.0 | null | null | null | null | null | null | null | bundled/skills/clinical-reports/scripts/extract_clinical_data.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:41.249773 | #!/usr/bin/env python3
"""
Extract structured clinical data from reports.
Usage:
python extract_clinical_data.py <report_file>
"""
import argparse
import json
import re
def extract_vital_signs(content: str) -> dict:
"""Extract vital signs."""
vitals = {}
patterns = {
"temperature": r"(?i)tem... |
foryourhealth111-pixel/Vibe-Skills | https://github.com/foryourhealth111-pixel/Vibe-Skills | null | null | null | null | 1,934 | null | null | apache-2.0 | null | null | null | null | null | null | null | bundled/skills/clinical-reports/scripts/compliance_checker.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:41.251909 | #!/usr/bin/env python3
"""
Check clinical reports for regulatory compliance (HIPAA, GCP, FDA).
Usage:
python compliance_checker.py <report_file>
"""
import argparse
import json
import re
COMPLIANCE_CHECKS = {
"hipaa": {
"consent_statement": r"(?i)(informed\s+consent|written\s+consent).*obtained",
... |
foryourhealth111-pixel/Vibe-Skills | https://github.com/foryourhealth111-pixel/Vibe-Skills | null | null | null | null | 1,934 | null | null | apache-2.0 | null | null | null | null | null | null | null | bundled/skills/clinical-reports/scripts/terminology_validator.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:41.252400 | #!/usr/bin/env python3
"""
Validate medical terminology and coding in clinical reports.
Usage:
python terminology_validator.py <report_file>
"""
import argparse
import json
import re
# Common medical abbreviations that should be avoided (JCAHO "Do Not Use" list)
DO_NOT_USE = {
"U": "Unit",
"IU": "Intern... |
foryourhealth111-pixel/Vibe-Skills | https://github.com/foryourhealth111-pixel/Vibe-Skills | null | null | null | null | 1,934 | null | null | apache-2.0 | null | null | null | null | null | null | null | bundled/skills/clinical-reports/scripts/format_adverse_events.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:41.252903 | #!/usr/bin/env python3
"""
Format adverse event data into tables for clinical trial reports.
Converts CSV or structured data into formatted AE summary tables.
Usage:
python format_adverse_events.py <ae_data.csv>
"""
import argparse
import csv
from collections import defaultdict
from pathlib import Path
def for... |
foryourhealth111-pixel/Vibe-Skills | https://github.com/foryourhealth111-pixel/Vibe-Skills | null | null | null | null | 1,934 | null | null | apache-2.0 | null | null | null | null | null | null | null | bundled/skills/clinical-reports/scripts/generate_report_template.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:41.253505 | #!/usr/bin/env python3
"""
Interactive template generator for clinical reports.
Helps users select and generate appropriate clinical report templates.
Usage:
python generate_report_template.py
python generate_report_template.py --type case_report --output my_case_report.md
"""
import argparse
import shutil
f... |
foryourhealth111-pixel/Vibe-Skills | https://github.com/foryourhealth111-pixel/Vibe-Skills | null | null | null | null | 1,934 | null | null | apache-2.0 | null | null | null | null | null | null | null | bundled/skills/clinicaltrials-database/scripts/query_clinicaltrials.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:41.426436 | #!/usr/bin/env python3
"""
ClinicalTrials.gov API Query Helper
A comprehensive Python script for querying the ClinicalTrials.gov API v2.
Provides convenient functions for common query patterns including searching
by condition, intervention, location, sponsor, and retrieving specific trials.
API Documentation: https:/... |
foryourhealth111-pixel/Vibe-Skills | https://github.com/foryourhealth111-pixel/Vibe-Skills | null | null | null | null | 1,934 | null | null | apache-2.0 | null | null | null | null | null | null | null | bundled/skills/clinical-reports/scripts/validate_trial_report.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:41.427842 | #!/usr/bin/env python3
"""
Validate clinical trial reports against ICH-E3 structure.
Checks Clinical Study Reports (CSR) for ICH-E3 compliance.
Usage:
python validate_trial_report.py <csr_file.md>
"""
import argparse
import json
import re
from pathlib import Path
ICH_E3_SECTIONS = {
"title_page": "Title Pa... |
foryourhealth111-pixel/Vibe-Skills | https://github.com/foryourhealth111-pixel/Vibe-Skills | null | null | null | null | 1,934 | null | null | apache-2.0 | null | null | null | null | null | null | null | bundled/skills/clinical-reports/scripts/validate_case_report.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:41.581513 | #!/usr/bin/env python3
"""
Validate case reports against CARE (CAse REport) guidelines.
This script checks a clinical case report for compliance with CARE guidelines
and provides a checklist of required elements.
Usage:
python validate_case_report.py <input_file.md|.txt>
python validate_case_report.py <input_... |
foryourhealth111-pixel/Vibe-Skills | https://github.com/foryourhealth111-pixel/Vibe-Skills | null | null | null | null | 1,934 | null | null | apache-2.0 | null | null | null | null | null | null | null | bundled/skills/code-reviewer/scripts/check_style.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:41.687648 | #!/usr/bin/env python3
"""Check Python code for style issues.
Usage:
echo "code here" | ./check_style.py
./check_style.py "def foo(): pass"
"""
import json
import sys
def check_style(code: str) -> dict:
"""Check code for common style issues."""
issues = []
lines = code.split("\n")
for i, li... |
foryourhealth111-pixel/Vibe-Skills | https://github.com/foryourhealth111-pixel/Vibe-Skills | null | null | null | null | 1,934 | null | null | apache-2.0 | null | null | null | null | null | null | null | bundled/skills/code-reviewer/scripts/code_quality_checker.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:42.190377 | #!/usr/bin/env python3
"""
Code Quality Checker
Automated tool for code reviewer tasks
"""
import os
import sys
import json
import argparse
from pathlib import Path
from typing import Dict, List, Optional
class CodeQualityChecker:
"""Main class for code quality checker functionality"""
def __init__(self,... |
foryourhealth111-pixel/Vibe-Skills | https://github.com/foryourhealth111-pixel/Vibe-Skills | null | null | null | null | 1,934 | null | null | apache-2.0 | null | null | null | null | null | null | null | bundled/skills/clinpgx-database/scripts/query_clinpgx.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:43.214372 | #!/usr/bin/env python3
"""
ClinPGx API Query Helper Script
Provides ready-to-use functions for querying the ClinPGx database API.
Includes rate limiting, error handling, and caching functionality.
ClinPGx API: https://api.clinpgx.org/
Rate limit: 2 requests per second
License: Creative Commons Attribution-ShareAlike ... |
showlab/computer_use_ootb | https://github.com/showlab/computer_use_ootb | null | null | null | null | 1,932 | null | null | apache-2.0 | null | null | null | null | null | null | null | computer_use_demo/gui_agent/llm_utils/llm_utils.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:46.980769 | import os
import re
import ast
import base64
def is_image_path(text):
# Checking if the input text ends with typical image file extensions
image_extensions = (".jpg", ".jpeg", ".png", ".gif", ".bmp", ".tiff", ".tif")
if text.endswith(image_extensions):
return True
else:
return False
... |
showlab/computer_use_ootb | https://github.com/showlab/computer_use_ootb | null | null | null | null | 1,932 | null | null | apache-2.0 | null | null | null | null | null | null | null | computer_use_demo/gui_agent/actor/showui_agent.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:46.983614 | import os
import ast
import base64
from io import BytesIO
from pathlib import Path
from uuid import uuid4
import pyautogui
import requests
import torch
from PIL import Image, ImageDraw
from qwen_vl_utils import process_vision_info
from transformers import AutoProcessor, Qwen2VLForConditionalGeneration
from computer_u... |
showlab/computer_use_ootb | https://github.com/showlab/computer_use_ootb | null | null | null | null | 1,932 | null | null | apache-2.0 | null | null | null | null | null | null | null | computer_use_demo/executor/anthropic_executor.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:46.987010 | import asyncio
from typing import Any, Dict, cast
from collections.abc import Callable
from anthropic.types.beta import (
BetaContentBlock,
BetaContentBlockParam,
BetaImageBlockParam,
BetaMessage,
BetaMessageParam,
BetaTextBlockParam,
BetaToolResultBlockParam,
)
from anthropic.types import T... |
showlab/computer_use_ootb | https://github.com/showlab/computer_use_ootb | null | null | null | null | 1,932 | null | null | apache-2.0 | null | null | null | null | null | null | null | computer_use_demo/gui_agent/llm_utils/run_llm.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:46.988370 | import base64
import logging
from .oai import run_oai_interleaved
from .gemini import run_gemini_interleaved
def run_llm(prompt, llm="gpt-4o-mini", max_tokens=256, temperature=0, stop=None):
log_prompt(prompt)
# turn string prompt into list
if isinstance(prompt, str):
prompt = [prompt]
eli... |
showlab/computer_use_ootb | https://github.com/showlab/computer_use_ootb | null | null | null | null | 1,932 | null | null | apache-2.0 | null | null | null | null | null | null | null | computer_use_demo/gui_agent/actor/uitars_agent.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:47.003611 | import json
import re
from openai import OpenAI
from computer_use_demo.gui_agent.llm_utils.oai import encode_image
from computer_use_demo.tools.screen_capture import get_screenshot
from computer_use_demo.tools.logger import logger, truncate_string
class UITARS_Actor:
"""
In OOTB, we use the default grounding... |
showlab/computer_use_ootb | https://github.com/showlab/computer_use_ootb | null | null | null | null | 1,932 | null | null | apache-2.0 | null | null | null | null | null | null | null | computer_use_demo/gui_agent/llm_utils/qwen.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:47.004685 |
import os
import logging
import base64
import requests
import dashscope
# from computer_use_demo.gui_agent.llm_utils import is_image_path, encode_image
def is_image_path(text):
return False
def encode_image(image_path):
return ""
def run_qwen(messages: list, system: str, llm: str, api_key: str, max_tok... |
showlab/computer_use_ootb | https://github.com/showlab/computer_use_ootb | null | null | null | null | 1,932 | null | null | apache-2.0 | null | null | null | null | null | null | null | computer_use_demo/gui_agent/llm_utils/oai.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:47.079026 | import os
import logging
import base64
import requests
from computer_use_demo.gui_agent.llm_utils.llm_utils import is_image_path, encode_image
def run_oai_interleaved(messages: list, system: str, llm: str, api_key: str, max_tokens=256, temperature=0):
api_key = api_key or os.environ.get("OPENAI_API_KEY")
if... |
showlab/computer_use_ootb | https://github.com/showlab/computer_use_ootb | null | null | null | null | 1,932 | null | null | apache-2.0 | null | null | null | null | null | null | null | computer_use_demo/executor/showui_executor.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:47.122436 | import ast
import asyncio
from typing import Any, Dict, cast, List, Union
from collections.abc import Callable
import uuid
from anthropic.types.beta import (
BetaContentBlock,
BetaContentBlockParam,
BetaImageBlockParam,
BetaMessage,
BetaMessageParam,
BetaTextBlockParam,
BetaToolResultBlockPa... |
showlab/computer_use_ootb | https://github.com/showlab/computer_use_ootb | null | null | null | null | 1,932 | null | null | apache-2.0 | null | null | null | null | null | null | null | app.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:47.143273 | """
Entrypoint for Gradio, see https://gradio.app/
"""
import platform
import asyncio
import base64
import os
import io
import json
from datetime import datetime
from enum import StrEnum
from functools import partial
from pathlib import Path
from typing import cast, Dict
from PIL import Image
import gradio as gr
from... |
showlab/computer_use_ootb | https://github.com/showlab/computer_use_ootb | null | null | null | null | 1,932 | null | null | apache-2.0 | null | null | null | null | null | null | null | computer_use_demo/gui_agent/planner/local_vlm_planner.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:47.548646 | import json
import asyncio
import platform
from collections.abc import Callable
from datetime import datetime
from enum import StrEnum
from typing import Any, cast, Dict, Callable
from anthropic import Anthropic, AnthropicBedrock, AnthropicVertex, APIResponse
from anthropic.types import TextBlock, ToolResultBlockParam... |
showlab/computer_use_ootb | https://github.com/showlab/computer_use_ootb | null | null | null | null | 1,932 | null | null | apache-2.0 | null | null | null | null | null | null | null | computer_use_demo/remote_inference.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:47.572602 | from contextlib import asynccontextmanager
from fastapi import FastAPI, HTTPException
from fastapi.middleware.cors import CORSMiddleware
from pydantic import BaseModel, field_validator
from typing import Optional, List, Union, Dict, Any
import torch
from transformers import (
Qwen2_5_VLForConditionalGeneration,
... |
showlab/computer_use_ootb | https://github.com/showlab/computer_use_ootb | null | null | null | null | 1,932 | null | null | apache-2.0 | null | null | null | null | null | null | null | computer_use_demo/gui_agent/planner/api_vlm_planner.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:47.574213 | import json
import asyncio
import platform
from collections.abc import Callable
from datetime import datetime
from enum import StrEnum
from typing import Any, cast, Dict, Callable
from anthropic import Anthropic, AnthropicBedrock, AnthropicVertex, APIResponse
from anthropic.types import TextBlock, ToolResultBlockParam... |
showlab/computer_use_ootb | https://github.com/showlab/computer_use_ootb | null | null | null | null | 1,932 | null | null | apache-2.0 | null | null | null | null | null | null | null | computer_use_demo/tools/__init__.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:47.603088 | from .base import CLIResult, ToolResult
from .bash import BashTool
from .collection import ToolCollection
from .computer import ComputerTool
from .edit import EditTool
from .screen_capture import get_screenshot
__ALL__ = [
BashTool,
CLIResult,
ComputerTool,
EditTool,
ToolCollection,
ToolResult,... |
showlab/computer_use_ootb | https://github.com/showlab/computer_use_ootb | null | null | null | null | 1,932 | null | null | apache-2.0 | null | null | null | null | null | null | null | computer_use_demo/loop.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:47.604665 | """
Agentic sampling loop that calls the Anthropic API and local implementation of computer use tools.
"""
import time
import json
from collections.abc import Callable
from enum import StrEnum
from anthropic import APIResponse
from anthropic.types.beta import BetaContentBlock, BetaMessage, BetaMessageParam
from comput... |
showlab/computer_use_ootb | https://github.com/showlab/computer_use_ootb | null | null | null | null | 1,932 | null | null | apache-2.0 | null | null | null | null | null | null | null | computer_use_demo/tools/bash.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:47.605886 | import asyncio
import os
from typing import ClassVar, Literal
from anthropic.types.beta import BetaToolBash20241022Param
from .base import BaseAnthropicTool, CLIResult, ToolError, ToolResult
class _BashSession:
"""A session of a bash shell."""
_started: bool
_process: asyncio.subprocess.Process
co... |
showlab/computer_use_ootb | https://github.com/showlab/computer_use_ootb | null | null | null | null | 1,932 | null | null | apache-2.0 | null | null | null | null | null | null | null | computer_use_demo/tools/colorful_text.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:47.678665 | """
Define some colorful stuffs for better visualization in the chat.
"""
# Define the RGB colors for each letter
colors = {
'S': 'rgb(106, 158, 210)',
'h': 'rgb(111, 163, 82)',
'o': 'rgb(209, 100, 94)',
'w': 'rgb(238, 171, 106)',
'U': 'rgb(0, 0, 0)',
'I': 'rgb(0, 0, 0)',
}
# Construct the... |
showlab/computer_use_ootb | https://github.com/showlab/computer_use_ootb | null | null | null | null | 1,932 | null | null | apache-2.0 | null | null | null | null | null | null | null | computer_use_demo/gui_agent/planner/anthropic_agent.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:47.709925 | """
Agentic sampling loop that calls the Anthropic API and local implementation of anthropic-defined computer use tools.
"""
import asyncio
import platform
from collections.abc import Callable
from datetime import datetime
from enum import StrEnum
from typing import Any, cast
from anthropic import Anthropic, Anthropic... |
showlab/computer_use_ootb | https://github.com/showlab/computer_use_ootb | null | null | null | null | 1,932 | null | null | apache-2.0 | null | null | null | null | null | null | null | computer_use_demo/tools/base.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:47.711034 | from abc import ABCMeta, abstractmethod
from dataclasses import dataclass, fields, replace
from typing import Any
from anthropic.types.beta import BetaToolUnionParam
class BaseAnthropicTool(metaclass=ABCMeta):
"""Abstract base class for Anthropic-defined tools."""
@abstractmethod
def __call__(self, **kw... |
showlab/computer_use_ootb | https://github.com/showlab/computer_use_ootb | null | null | null | null | 1,932 | null | null | apache-2.0 | null | null | null | null | null | null | null | computer_use_demo/tools/collection.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:47.734927 | """Collection classes for managing multiple tools."""
from typing import Any
from anthropic.types.beta import BetaToolUnionParam
from .base import (
BaseAnthropicTool,
ToolError,
ToolFailure,
ToolResult,
)
class ToolCollection:
"""A collection of anthropic-defined tools."""
def __init__(se... |
showlab/computer_use_ootb | https://github.com/showlab/computer_use_ootb | null | null | null | null | 1,932 | null | null | apache-2.0 | null | null | null | null | null | null | null | computer_use_demo/tools/computer.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:48.122703 | import subprocess
import platform
import pyautogui
import asyncio
import base64
import os
import time
if platform.system() == "Darwin":
import Quartz # uncomment this line if you are on macOS
from enum import StrEnum
from pathlib import Path
from typing import Literal, TypedDict
from uuid import uuid4
from screeni... |
showlab/computer_use_ootb | https://github.com/showlab/computer_use_ootb | null | null | null | null | 1,932 | null | null | apache-2.0 | null | null | null | null | null | null | null | computer_use_demo/tools/logger.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:48.206974 | import logging
def truncate_string(s, max_length=500):
"""Truncate long strings for concise printing."""
if isinstance(s, str) and len(s) > max_length:
return s[:max_length] + "..."
return s
# Configure logger
logger = logging.getLogger(__name__)
logger.setLevel(logging.INFO) # Choose your def... |
showlab/computer_use_ootb | https://github.com/showlab/computer_use_ootb | null | null | null | null | 1,932 | null | null | apache-2.0 | null | null | null | null | null | null | null | computer_use_demo/tools/edit.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:48.266680 | from collections import defaultdict
from pathlib import Path
from typing import Literal, get_args
from anthropic.types.beta import BetaToolTextEditor20241022Param
from .base import BaseAnthropicTool, CLIResult, ToolError, ToolResult
from .run import maybe_truncate, run
Command = Literal[
"view",
"create",
... |
showlab/computer_use_ootb | https://github.com/showlab/computer_use_ootb | null | null | null | null | 1,932 | null | null | apache-2.0 | null | null | null | null | null | null | null | install_tools/install_showui-awq-4bit.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:48.267582 | import os
from huggingface_hub import hf_hub_download, list_repo_files
# Specify the model repository and destination folder
model_repo = "yyyang/showui-2b-awq"
destination_folder = "./showui-2b-awq"
# Ensure the destination folder exists
os.makedirs(destination_folder, exist_ok=True)
# List all files in the reposit... |
showlab/computer_use_ootb | https://github.com/showlab/computer_use_ootb | null | null | null | null | 1,932 | null | null | apache-2.0 | null | null | null | null | null | null | null | install_tools/install_showui.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:48.279363 | import os
from huggingface_hub import hf_hub_download, list_repo_files
# Specify the model repository and destination folder
model_repo = "showlab/ShowUI-2B"
destination_folder = "./showui-2b"
# Ensure the destination folder exists
os.makedirs(destination_folder, exist_ok=True)
# List all files in the repository
fil... |
showlab/computer_use_ootb | https://github.com/showlab/computer_use_ootb | null | null | null | null | 1,932 | null | null | apache-2.0 | null | null | null | null | null | null | null | computer_use_demo/tools/screen_capture.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:48.279982 | import subprocess
import base64
from pathlib import Path
from PIL import ImageGrab
from uuid import uuid4
from screeninfo import get_monitors
import platform
if platform.system() == "Darwin":
import Quartz # uncomment this line if you are on macOS
from PIL import ImageGrab
from functools import partial
from .... |
showlab/computer_use_ootb | https://github.com/showlab/computer_use_ootb | null | null | null | null | 1,932 | null | null | apache-2.0 | null | null | null | null | null | null | null | install_tools/install_uitars-2b-sft.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:48.280574 | import os
from huggingface_hub import hf_hub_download, list_repo_files
# Specify the model repository and destination folder
model_repo = "bytedance-research/UI-TARS-2B-SFT"
destination_folder = "./ui-tars-2b-sft"
# Ensure the destination folder exists
os.makedirs(destination_folder, exist_ok=True)
# List all files ... |
showlab/computer_use_ootb | https://github.com/showlab/computer_use_ootb | null | null | null | null | 1,932 | null | null | apache-2.0 | null | null | null | null | null | null | null | computer_use_demo/tools/run.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:48.281368 | """Utility to run shell commands asynchronously with a timeout."""
import asyncio
TRUNCATED_MESSAGE: str = "<response clipped><NOTE>To save on context only part of this file has been shown to you. You should retry this tool after you have searched inside the file with `grep -n` in order to find the line numbers of wh... |
showlab/computer_use_ootb | https://github.com/showlab/computer_use_ootb | null | null | null | null | 1,932 | null | null | apache-2.0 | null | null | null | null | null | null | null | install_tools/test_ui-tars_server.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:48.311151 | from openai import OpenAI
from computer_use_demo.gui_agent.llm_utils.oai import encode_image
_NAV_SYSTEM_GROUNDING = """
You are a GUI agent. You are given a task and your action history, with screenshots. You need to perform the next action to complete the task.
## Output Format
```Action: ...```
## Action Space
c... |
chaidiscovery/chai-lab | https://github.com/chaidiscovery/chai-lab | null | null | null | null | 1,929 | null | null | apache-2.0 | null | null | null | null | null | null | null | chai_lab/data/dataset/all_atom_feature_context.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:50.679560 | # Copyright (c) 2024 Chai Discovery, Inc.
# Licensed under the Apache License, Version 2.0.
# See the LICENSE file for details.
import logging
from dataclasses import dataclass
from typing import Any, Final
from chai_lab.data.dataset.constraints.restraint_context import RestraintContext
from chai_lab.data.dataset.emb... |
chaidiscovery/chai-lab | https://github.com/chaidiscovery/chai-lab | null | null | null | null | 1,929 | null | null | apache-2.0 | null | null | null | null | null | null | null | chai_lab/data/dataset/__init__.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:50.680122 | # Copyright (c) 2024 Chai Discovery, Inc.
# Licensed under the Apache License, Version 2.0.
# See the LICENSE file for details.
|
chaidiscovery/chai-lab | https://github.com/chaidiscovery/chai-lab | null | null | null | null | 1,929 | null | null | apache-2.0 | null | null | null | null | null | null | null | chai_lab/data/collate/__init__.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:50.682231 | # Copyright (c) 2024 Chai Discovery, Inc.
# Licensed under the Apache License, Version 2.0.
# See the LICENSE file for details.
|
chaidiscovery/chai-lab | https://github.com/chaidiscovery/chai-lab | null | null | null | null | 1,929 | null | null | apache-2.0 | null | null | null | null | null | null | null | chai_lab/data/__init__.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:50.683750 | # Copyright (c) 2024 Chai Discovery, Inc.
# Licensed under the Apache License, Version 2.0.
# See the LICENSE file for details.
|
chaidiscovery/chai-lab | https://github.com/chaidiscovery/chai-lab | null | null | null | null | 1,929 | null | null | apache-2.0 | null | null | null | null | null | null | null | chai_lab/data/collate/collate.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:50.705537 | # Copyright (c) 2024 Chai Discovery, Inc.
# Licensed under the Apache License, Version 2.0.
# See the LICENSE file for details.
import dataclasses
import logging
from typing import Any
import torch
from chai_lab.data.collate.utils import get_pad_sizes
from chai_lab.data.dataset.all_atom_feature_context import AllAto... |
chaidiscovery/chai-lab | https://github.com/chaidiscovery/chai-lab | null | null | null | null | 1,929 | null | null | apache-2.0 | null | null | null | null | null | null | null | chai_lab/__init__.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:50.706064 | # Copyright (c) 2024 Chai Discovery, Inc.
# Licensed under the Apache License, Version 2.0.
# See the LICENSE file for details.
__version__ = "0.6.1"
|
chaidiscovery/chai-lab | https://github.com/chaidiscovery/chai-lab | null | null | null | null | 1,929 | null | null | apache-2.0 | null | null | null | null | null | null | null | chai_lab/data/collate/utils.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:50.707899 | # Copyright (c) 2024 Chai Discovery, Inc.
# Licensed under the Apache License, Version 2.0.
# See the LICENSE file for details.
from dataclasses import dataclass
from chai_lab.data.dataset.structure.all_atom_structure_context import (
AllAtomStructureContext,
)
# static graph is exported for different n_tokens,
... |
chaidiscovery/chai-lab | https://github.com/chaidiscovery/chai-lab | null | null | null | null | 1,929 | null | null | apache-2.0 | null | null | null | null | null | null | null | chai_lab/chai1.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:50.712914 | # Copyright (c) 2024 Chai Discovery, Inc.
# Licensed under the Apache License, Version 2.0.
# See the LICENSE file for details.
import itertools
import logging
import math
from collections import Counter
from contextlib import contextmanager
from dataclasses import dataclass
from pathlib import Path
from typing impor... |
chaidiscovery/chai-lab | https://github.com/chaidiscovery/chai-lab | null | null | null | null | 1,929 | null | null | apache-2.0 | null | null | null | null | null | null | null | chai_lab/data/dataset/constraints/__init__.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:50.743913 | # Copyright (c) 2024 Chai Discovery, Inc.
# Licensed under the Apache License, Version 2.0.
# See the LICENSE file for details.
|
chaidiscovery/chai-lab | https://github.com/chaidiscovery/chai-lab | null | null | null | null | 1,929 | null | null | apache-2.0 | null | null | null | null | null | null | null | chai_lab/data/dataset/constraints/restraint_context.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:50.744432 | # Copyright (c) 2024 Chai Discovery, Inc.
# Licensed under the Apache License, Version 2.0.
# See the LICENSE file for details.
import logging
from dataclasses import asdict, dataclass
from torch import Tensor
from typing_extensions import assert_never
from chai_lab.data import residue_constants as rc
from chai_lab.... |
chaidiscovery/chai-lab | https://github.com/chaidiscovery/chai-lab | null | null | null | null | 1,929 | null | null | apache-2.0 | null | null | null | null | null | null | null | chai_lab/data/dataset/embeddings/embedding_context.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:51.320288 | # Copyright (c) 2024 Chai Discovery, Inc.
# Licensed under the Apache License, Version 2.0.
# See the LICENSE file for details.
from dataclasses import asdict, dataclass
import torch
from torch import Tensor
from chai_lab.utils.typing import Float, typecheck
@typecheck
@dataclass
class EmbeddingContext:
esm_em... |
chaidiscovery/chai-lab | https://github.com/chaidiscovery/chai-lab | null | null | null | null | 1,929 | null | null | apache-2.0 | null | null | null | null | null | null | null | chai_lab/data/dataset/inference_dataset.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:51.342558 | # Copyright (c) 2024 Chai Discovery, Inc.
# Licensed under the Apache License, Version 2.0.
# See the LICENSE file for details.
import logging
import string
from dataclasses import dataclass
from datetime import datetime
from pathlib import Path
import gemmi
from chai_lab.data.dataset.structure.all_atom_residue_toke... |
chaidiscovery/chai-lab | https://github.com/chaidiscovery/chai-lab | null | null | null | null | 1,929 | null | null | apache-2.0 | null | null | null | null | null | null | null | chai_lab/data/dataset/embeddings/__init__.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:51.344281 | # Copyright (c) 2024 Chai Discovery, Inc.
# Licensed under the Apache License, Version 2.0.
# See the LICENSE file for details.
|
chaidiscovery/chai-lab | https://github.com/chaidiscovery/chai-lab | null | null | null | null | 1,929 | null | null | apache-2.0 | null | null | null | null | null | null | null | chai_lab/data/dataset/msas/__init__.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:51.345196 | # Copyright (c) 2024 Chai Discovery, Inc.
# Licensed under the Apache License, Version 2.0.
# See the LICENSE file for details.
|
chaidiscovery/chai-lab | https://github.com/chaidiscovery/chai-lab | null | null | null | null | 1,929 | null | null | apache-2.0 | null | null | null | null | null | null | null | chai_lab/data/dataset/embeddings/esm.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:51.346084 | # Copyright (c) 2024 Chai Discovery, Inc.
# Licensed under the Apache License, Version 2.0.
# See the LICENSE file for details.
import os
from contextlib import contextmanager
import torch
from chai_lab.data.dataset.embeddings.embedding_context import EmbeddingContext
from chai_lab.data.dataset.structure.chain impor... |
chaidiscovery/chai-lab | https://github.com/chaidiscovery/chai-lab | null | null | null | null | 1,929 | null | null | apache-2.0 | null | null | null | null | null | null | null | chai_lab/data/dataset/msas/load.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:51.380308 | # Copyright (c) 2024 Chai Discovery, Inc.
# Licensed under the Apache License, Version 2.0.
# See the LICENSE file for details.
import logging
from pathlib import Path
import torch
from chai_lab.data.dataset.msas.msa_context import MSAContext
from chai_lab.data.dataset.msas.preprocess import (
drop_duplicates,
... |
chaidiscovery/chai-lab | https://github.com/chaidiscovery/chai-lab | null | null | null | null | 1,929 | null | null | apache-2.0 | null | null | null | null | null | null | null | chai_lab/data/dataset/msas/msa_context.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:51.381400 | # Copyright (c) 2024 Chai Discovery, Inc.
# Licensed under the Apache License, Version 2.0.
# See the LICENSE file for details.
from dataclasses import dataclass
import torch
from einops import rearrange
from torch import Tensor
from chai_lab.data.parsing.msas.data_source import (
MSADataSource,
msa_dataset_... |
chaidiscovery/chai-lab | https://github.com/chaidiscovery/chai-lab | null | null | null | null | 1,929 | null | null | apache-2.0 | null | null | null | null | null | null | null | chai_lab/data/dataset/msas/utils.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:51.387350 | # Copyright (c) 2024 Chai Discovery, Inc.
# Licensed under the Apache License, Version 2.0.
# See the LICENSE file for details.
import logging
import torch
from einops import rearrange, reduce
from torch import Tensor
from torch.nn import functional as F
from chai_lab.utils.typing import Bool, Float, typecheck
@ty... |
chaidiscovery/chai-lab | https://github.com/chaidiscovery/chai-lab | null | null | null | null | 1,929 | null | null | apache-2.0 | null | null | null | null | null | null | null | chai_lab/data/dataset/msas/preprocess.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:51.388536 | # Copyright (c) 2024 Chai Discovery, Inc.
# Licensed under the Apache License, Version 2.0.
# See the LICENSE file for details.
import logging
from collections import Counter, defaultdict
import torch
from einops import reduce
from torch import Tensor
from chai_lab.data.dataset.msas.msa_context import NO_PAIRING_KEY,... |
chaidiscovery/chai-lab | https://github.com/chaidiscovery/chai-lab | null | null | null | null | 1,929 | null | null | apache-2.0 | null | null | null | null | null | null | null | chai_lab/data/dataset/msas/colabfold.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:51.417170 | # Copyright (c) 2024 Chai Discovery, Inc.
# Licensed under the Apache License, Version 2.0.
# See the LICENSE file for details.
import logging
import os
import random
import tarfile
import tempfile
import time
import typing
from pathlib import Path
import pandas as pd
import requests
from tqdm import tqdm
from chai_... |
chaidiscovery/chai-lab | https://github.com/chaidiscovery/chai-lab | null | null | null | null | 1,929 | null | null | apache-2.0 | null | null | null | null | null | null | null | chai_lab/data/dataset/structure/all_atom_residue_tokenizer.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:51.891352 | # Copyright (c) 2024 Chai Discovery, Inc.
# Licensed under the Apache License, Version 2.0.
# See the LICENSE file for details.
import logging
from dataclasses import dataclass
from itertools import chain
import torch
from einops import repeat
from torch import Tensor
from chai_lab.data.dataset.structure import util... |
chaidiscovery/chai-lab | https://github.com/chaidiscovery/chai-lab | null | null | null | null | 1,929 | null | null | apache-2.0 | null | null | null | null | null | null | null | chai_lab/data/dataset/structure/bond_utils.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:52.203128 | # Copyright (c) 2024 Chai Discovery, Inc.
# Licensed under the Apache License, Version 2.0.
# See the LICENSE file for details.
import torch
from einops import rearrange
from torch import Tensor
from chai_lab.data import residue_constants as rc
from chai_lab.data.parsing.glycans import _glycan_string_to_sugars_and_b... |
chaidiscovery/chai-lab | https://github.com/chaidiscovery/chai-lab | null | null | null | null | 1,929 | null | null | apache-2.0 | null | null | null | null | null | null | null | chai_lab/data/dataset/templates/align.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:52.203857 | # Copyright (c) 2024 Chai Discovery, Inc.
# Licensed under the Apache License, Version 2.0.
# See the LICENSE file for details.
"""Helper functions for aligning templates."""
import logging
from typing import Sequence
import torch
from torch import Tensor
from chai_lab.utils.typing import Shaped, typecheck
logger =... |
chaidiscovery/chai-lab | https://github.com/chaidiscovery/chai-lab | null | null | null | null | 1,929 | null | null | apache-2.0 | null | null | null | null | null | null | null | chai_lab/data/dataset/structure/utils.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:52.205956 | # Copyright (c) 2024 Chai Discovery, Inc.
# Licensed under the Apache License, Version 2.0.
# See the LICENSE file for details.
from functools import lru_cache
import torch
from torch import Tensor
import chai_lab.data.residue_constants as rc
from chai_lab.utils.typing import Bool, Int
def get_centre_atom_name(res... |
chaidiscovery/chai-lab | https://github.com/chaidiscovery/chai-lab | null | null | null | null | 1,929 | null | null | apache-2.0 | null | null | null | null | null | null | null | chai_lab/data/dataset/structure/chain.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:52.206832 | # Copyright (c) 2024 Chai Discovery, Inc.
# Licensed under the Apache License, Version 2.0.
# See the LICENSE file for details.
from dataclasses import dataclass
from chai_lab.data.dataset.structure.all_atom_structure_context import (
AllAtomStructureContext,
)
from chai_lab.data.parsing.structure.all_atom_entity... |
chaidiscovery/chai-lab | https://github.com/chaidiscovery/chai-lab | null | null | null | null | 1,929 | null | null | apache-2.0 | null | null | null | null | null | null | null | chai_lab/data/features/feature_factory.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:52.208076 | # Copyright (c) 2024 Chai Discovery, Inc.
# Licensed under the Apache License, Version 2.0.
# See the LICENSE file for details.
"""Helper methods for generating model input features"""
import logging
from torch import Tensor
from chai_lab.data.features.generators.base import FeatureGenerator
logger = logging.getLo... |
chaidiscovery/chai-lab | https://github.com/chaidiscovery/chai-lab | null | null | null | null | 1,929 | null | null | apache-2.0 | null | null | null | null | null | null | null | chai_lab/data/dataset/templates/context.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:52.209859 | # Copyright (c) 2024 Chai Discovery, Inc.
# Licensed under the Apache License, Version 2.0.
# See the LICENSE file for details.
import logging
import os
from dataclasses import asdict, dataclass
from pathlib import Path
from typing import Iterator
import torch
from torch import Tensor
from torch.nn import functional ... |
chaidiscovery/chai-lab | https://github.com/chaidiscovery/chai-lab | null | null | null | null | 1,929 | null | null | apache-2.0 | null | null | null | null | null | null | null | chai_lab/data/dataset/templates/load.py | null | null | null | null | null | null | Python | 2026-05-04T02:46:52.211098 | # Copyright (c) 2024 Chai Discovery, Inc.
# Licensed under the Apache License, Version 2.0.
# See the LICENSE file for details.
"""
Consider the following example:
Crop indices: |-------------------------------------|
Query: ------------------------------------------------------------------------
Hit on ... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.