SYMBOL INDEX (1486 symbols across 201 files)

FILE: scientific-skills/arboreto/scripts/basic_grn_inference.py
  function run_grn_inference (line 24) | def run_grn_inference(expression_file, output_file, tf_file=None, seed=7...

FILE: scientific-skills/arxiv-database/scripts/arxiv_search.py
  class ArxivSearcher (line 20) | class ArxivSearcher:
    method __init__ (line 31) | def __init__(self, verbose: bool = False, delay: float = 3.0):
    method _log (line 40) | def _log(self, message: str):
    method _rate_limit (line 44) | def _rate_limit(self):
    method _parse_entry (line 53) | def _parse_entry(self, entry: ET.Element) -> Dict:
    method _fetch (line 112) | def _fetch(self, params: Dict) -> List[Dict]:
    method search (line 138) | def search(
    method get_by_ids (line 176) | def get_by_ids(self, arxiv_ids: List[str]) -> List[Dict]:
    method download_pdf (line 200) | def download_pdf(self, arxiv_id: str, output_path: str) -> bool:
    method build_query (line 239) | def build_query(
  function main (line 274) | def main():

FILE: scientific-skills/biorxiv-database/scripts/biorxiv_search.py
  class BioRxivSearcher (line 20) | class BioRxivSearcher:
    method __init__ (line 37) | def __init__(self, verbose: bool = False):
    method _log (line 45) | def _log(self, message: str):
    method _make_request (line 50) | def _make_request(self, endpoint: str, params: Optional[Dict] = None) ...
    method search_by_date_range (line 67) | def search_by_date_range(
    method search_by_interval (line 99) | def search_by_interval(
    method get_paper_details (line 119) | def get_paper_details(self, doi: str) -> Dict:
    method search_by_author (line 143) | def search_by_author(
    method search_by_keywords (line 182) | def search_by_keywords(
    method download_pdf (line 231) | def download_pdf(self, doi: str, output_path: str) -> bool:
    method format_result (line 264) | def format_result(self, paper: Dict, include_abstract: bool = True) ->...
  function main (line 301) | def main():

FILE: scientific-skills/bioservices/scripts/batch_id_converter.py
  function normalize_database_code (line 63) | def normalize_database_code(code):
  function read_ids_from_file (line 78) | def read_ids_from_file(filename):
  function batch_convert (line 94) | def batch_convert(ids, from_db, to_db, chunk_size=100, delay=0.5):
  function save_mapping_csv (line 164) | def save_mapping_csv(mapping, output_file, from_db, to_db):
  function save_failed_ids (line 188) | def save_failed_ids(failed_ids, output_file):
  function print_mapping_summary (line 202) | def print_mapping_summary(mapping, from_db, to_db):
  function list_common_databases (line 241) | def list_common_databases():
  function main (line 257) | def main():

FILE: scientific-skills/bioservices/scripts/compound_cross_reference.py
  function search_kegg_compound (line 26) | def search_kegg_compound(compound_name):
  function get_kegg_info (line 66) | def get_kegg_info(kegg, kegg_id):
  function get_chembl_id (line 147) | def get_chembl_id(kegg_id):
  function get_chebi_info (line 172) | def get_chebi_info(chebi_id):
  function get_chembl_info (line 222) | def get_chembl_info(chembl_id):
  function save_results (line 278) | def save_results(compound_name, kegg_info, chembl_id, output_file):
  function main (line 315) | def main():

FILE: scientific-skills/bioservices/scripts/pathway_analysis.py
  function get_all_pathways (line 34) | def get_all_pathways(kegg, organism):
  function analyze_pathway (line 46) | def analyze_pathway(kegg, pathway_id):
  function analyze_all_pathways (line 89) | def analyze_all_pathways(kegg, pathway_ids, limit=None):
  function save_pathway_summary (line 110) | def save_pathway_summary(results, output_file):
  function save_interactions_sif (line 150) | def save_interactions_sif(results, output_file):
  function save_detailed_pathway_info (line 169) | def save_detailed_pathway_info(results, output_dir):
  function print_statistics (line 195) | def print_statistics(results):
  function main (line 237) | def main():

FILE: scientific-skills/bioservices/scripts/protein_analysis_workflow.py
  function search_protein (line 29) | def search_protein(query):
  function retrieve_sequence (line 86) | def retrieve_sequence(uniprot, uniprot_id):
  function run_blast (line 116) | def run_blast(sequence, email, skip=False):
  function discover_pathways (line 186) | def discover_pathways(uniprot, kegg, uniprot_id):
  function find_interactions (line 243) | def find_interactions(protein_query):
  function get_go_annotations (line 289) | def get_go_annotations(uniprot_id):
  function main (line 346) | def main():

FILE: scientific-skills/brenda-database/scripts/brenda_queries.py
  function validate_dependencies (line 67) | def validate_dependencies():
  function parse_km_entry (line 80) | def parse_km_entry(entry: str) -> Dict[str, Any]:
  function parse_reaction_entry (line 115) | def parse_reaction_entry(entry: str) -> Dict[str, Any]:
  function extract_organism_data (line 147) | def extract_organism_data(entry: str) -> Dict[str, Any]:
  function search_enzymes_by_substrate (line 167) | def search_enzymes_by_substrate(substrate: str, limit: int = 50) -> List...
  function search_enzymes_by_product (line 204) | def search_enzymes_by_product(product: str, limit: int = 50) -> List[Dic...
  function compare_across_organisms (line 236) | def compare_across_organisms(ec_number: str, organisms: List[str]) -> Li...
  function get_organisms_for_enzyme (line 295) | def get_organisms_for_enzyme(ec_number: str) -> List[str]:
  function get_environmental_parameters (line 316) | def get_environmental_parameters(ec_number: str) -> Dict[str, Any]:
  function get_cofactor_requirements (line 369) | def get_cofactor_requirements(ec_number: str) -> List[Dict[str, Any]]:
  function get_substrate_specificity (line 419) | def get_substrate_specificity(ec_number: str) -> List[Dict[str, Any]]:
  function compare_substrate_affinity (line 472) | def compare_substrate_affinity(ec_number: str) -> List[Dict[str, Any]]:
  function get_inhibitors (line 477) | def get_inhibitors(ec_number: str) -> List[Dict[str, Any]]:
  function get_activators (line 528) | def get_activators(ec_number: str) -> List[Dict[str, Any]]:
  function find_thermophilic_homologs (line 580) | def find_thermophilic_homologs(ec_number: str, min_temp: int = 50) -> Li...
  function find_ph_stable_variants (line 623) | def find_ph_stable_variants(ec_number: str, min_ph: float = 8.0, max_ph:...
  function get_modeling_parameters (line 668) | def get_modeling_parameters(ec_number: str, substrate: str = None) -> Di...
  function export_kinetic_data (line 732) | def export_kinetic_data(ec_number: str, format: str = 'csv', filename: s...
  function search_by_pattern (line 784) | def search_by_pattern(pattern: str, limit: int = 50) -> List[Dict[str, A...

FILE: scientific-skills/brenda-database/scripts/brenda_visualization.py
  function validate_dependencies (line 58) | def validate_dependencies():
  function plot_kinetic_parameters (line 69) | def plot_kinetic_parameters(ec_number: str, save_path: str = None, show_...
  function plot_organism_comparison (line 159) | def plot_organism_comparison(ec_number: str, organisms: List[str], save_...
  function plot_pH_profiles (line 235) | def plot_pH_profiles(ec_number: str, save_path: str = None, show_plot: b...
  function plot_temperature_profiles (line 311) | def plot_temperature_profiles(ec_number: str, save_path: str = None, sho...
  function plot_substrate_specificity (line 393) | def plot_substrate_specificity(ec_number: str, save_path: str = None, sh...
  function plot_michaelis_menten (line 471) | def plot_michaelis_menten(ec_number: str, substrate: str = None, save_pa...
  function create_heatmap_data (line 581) | def create_heatmap_data(ec_number: str, parameters: List[str] = None) ->...
  function plot_heatmap (line 618) | def plot_heatmap(ec_number: str, save_path: str = None, show_plot: bool ...
  function generate_summary_plots (line 681) | def generate_summary_plots(ec_number: str, save_dir: str = None) -> List...

FILE: scientific-skills/brenda-database/scripts/enzyme_pathway_builder.py
  function validate_dependencies (line 66) | def validate_dependencies():
  function identify_metabolite (line 180) | def identify_metabolite(metabolite_name: str) -> Dict[str, Any]:
  function infer_transformation_type (line 232) | def infer_transformation_type(substrate: str, product: str) -> List[str]:
  function find_enzymes_for_transformation (line 274) | def find_enzymes_for_transformation(substrate: str, product: str, limit:...
  function find_pathway_for_product (line 348) | def find_pathway_for_product(product: str, max_steps: int = 3, starting_...
  function build_retrosynthetic_tree (line 450) | def build_retrosynthetic_tree(target: str, depth: int = 2) -> Dict[str, ...
  function suggest_enzyme_substitutions (line 533) | def suggest_enzyme_substitutions(ec_number: str, criteria: Dict[str, Any...
  function calculate_pathway_feasibility (line 596) | def calculate_pathway_feasibility(pathway: Dict[str, Any]) -> Dict[str, ...
  function optimize_pathway_conditions (line 696) | def optimize_pathway_conditions(pathway: Dict[str, Any]) -> Dict[str, Any]:
  function generate_pathway_report (line 805) | def generate_pathway_report(pathway: Dict[str, Any], filename: str = Non...
  function visualize_pathway (line 932) | def visualize_pathway(pathway: Dict[str, Any], save_path: str = None) ->...

FILE: scientific-skills/chembl-database/scripts/example_queries.py
  function get_molecule_info (line 16) | def get_molecule_info(chembl_id):
  function search_molecules_by_name (line 30) | def search_molecules_by_name(name_pattern):
  function find_molecules_by_properties (line 45) | def find_molecules_by_properties(max_mw=500, min_logp=None, max_logp=None):
  function get_target_info (line 72) | def get_target_info(target_chembl_id):
  function search_targets_by_name (line 86) | def search_targets_by_name(target_name):
  function get_bioactivity_data (line 104) | def get_bioactivity_data(target_chembl_id, activity_type='IC50', max_val...
  function find_similar_compounds (line 126) | def find_similar_compounds(smiles, similarity_threshold=85):
  function substructure_search (line 145) | def substructure_search(smiles):
  function get_drug_info (line 160) | def get_drug_info(molecule_chembl_id):
  function find_kinase_inhibitors (line 185) | def find_kinase_inhibitors(max_ic50=100):
  function get_compound_bioactivities (line 218) | def get_compound_bioactivities(molecule_chembl_id):
  function export_to_dataframe (line 236) | def export_to_dataframe(data):

FILE: scientific-skills/citation-management/scripts/doi_to_bibtex.py
  class DOIConverter (line 14) | class DOIConverter:
    method __init__ (line 17) | def __init__(self):
    method doi_to_bibtex (line 23) | def doi_to_bibtex(self, doi: str) -> Optional[str]:
    method convert_multiple (line 72) | def convert_multiple(self, dois: List[str], delay: float = 0.5) -> Lis...
  function main (line 99) | def main():

FILE: scientific-skills/citation-management/scripts/extract_metadata.py
  class MetadataExtractor (line 18) | class MetadataExtractor:
    method __init__ (line 21) | def __init__(self, email: Optional[str] = None):
    method identify_type (line 34) | def identify_type(self, identifier: str) -> Tuple[str, str]:
    method _parse_url (line 70) | def _parse_url(self, url: str) -> Tuple[str, str]:
    method extract_from_doi (line 98) | def extract_from_doi(self, doi: str) -> Optional[Dict]:
    method extract_from_pmid (line 141) | def extract_from_pmid(self, pmid: str) -> Optional[Dict]:
    method extract_from_arxiv (line 213) | def extract_from_arxiv(self, arxiv_id: str) -> Optional[Dict]:
    method metadata_to_bibtex (line 283) | def metadata_to_bibtex(self, metadata: Dict, citation_key: Optional[st...
    method _crossref_type_to_bibtex (line 348) | def _crossref_type_to_bibtex(self, crossref_type: str) -> str:
    method _format_authors_crossref (line 361) | def _format_authors_crossref(self, authors: List[Dict]) -> str:
    method _format_authors_pubmed (line 378) | def _format_authors_pubmed(self, authors: List) -> str:
    method _extract_year_crossref (line 392) | def _extract_year_crossref(self, message: Dict) -> str:
    method _extract_year_pubmed (line 403) | def _extract_year_pubmed(self, article: ET.Element) -> str:
    method _generate_citation_key (line 414) | def _generate_citation_key(self, metadata: Dict) -> str:
    method _protect_title (line 442) | def _protect_title(self, title: str) -> str:
    method extract (line 455) | def extract(self, identifier: str) -> Optional[str]:
  function main (line 487) | def main():

FILE: scientific-skills/citation-management/scripts/format_bibtex.py
  class BibTeXFormatter (line 13) | class BibTeXFormatter:
    method __init__ (line 16) | def __init__(self):
    method parse_bibtex_file (line 27) | def parse_bibtex_file(self, filepath: str) -> List[Dict]:
    method format_entry (line 78) | def format_entry(self, entry: Dict) -> str:
    method fix_common_issues (line 119) | def fix_common_issues(self, entry: Dict) -> Dict:
    method deduplicate_entries (line 166) | def deduplicate_entries(self, entries: List[Dict]) -> List[Dict]:
    method sort_entries (line 201) | def sort_entries(self, entries: List[Dict], sort_by: str = 'key', desc...
    method format_file (line 233) | def format_file(self, filepath: str, output: str = None,
  function main (line 292) | def main():

FILE: scientific-skills/citation-management/scripts/search_google_scholar.py
  class GoogleScholarSearcher (line 24) | class GoogleScholarSearcher:
    method __init__ (line 27) | def __init__(self, use_proxy: bool = False):
    method search (line 47) | def search(self, query: str, max_results: int = 50,
    method metadata_to_bibtex (line 119) | def metadata_to_bibtex(self, metadata: Dict) -> str:
  function main (line 179) | def main():

FILE: scientific-skills/citation-management/scripts/search_pubmed.py
  class PubMedSearcher (line 17) | class PubMedSearcher:
    method __init__ (line 20) | def __init__(self, api_key: Optional[str] = None, email: Optional[str]...
    method search (line 36) | def search(self, query: str, max_results: int = 100,
    method fetch_metadata (line 98) | def fetch_metadata(self, pmids: List[str]) -> List[Dict]:
    method _extract_metadata_from_xml (line 154) | def _extract_metadata_from_xml(self, article: ET.Element) -> Optional[...
    method metadata_to_bibtex (line 214) | def metadata_to_bibtex(self, metadata: Dict) -> str:
  function main (line 269) | def main():

FILE: scientific-skills/citation-management/scripts/validate_citations.py
  class CitationValidator (line 15) | class CitationValidator:
    method __init__ (line 18) | def __init__(self):
    method parse_bibtex_file (line 43) | def parse_bibtex_file(self, filepath: str) -> List[Dict]:
    method validate_entry (line 95) | def validate_entry(self, entry: Dict) -> Tuple[List[Dict], List[Dict]]:
    method verify_doi (line 201) | def verify_doi(self, doi: str) -> Tuple[bool, Optional[Dict]]:
    method detect_duplicates (line 239) | def detect_duplicates(self, entries: List[Dict]) -> List[Dict]:
    method validate_file (line 303) | def validate_file(self, filepath: str, check_dois: bool = False) -> Dict:
    method _extract_year_crossref (line 377) | def _extract_year_crossref(self, message: Dict) -> str:
    method _format_authors_crossref (line 387) | def _format_authors_crossref(self, authors: List[Dict]) -> str:
  function main (line 405) | def main():

FILE: scientific-skills/clinical-decision-support/scripts/biomarker_classifier.py
  function classify_binary_biomarker (line 21) | def classify_binary_biomarker(data, biomarker_col, threshold,
  function classify_pd_l1_tps (line 45) | def classify_pd_l1_tps(data, pd_l1_col='pd_l1_tps'):
  function classify_her2_status (line 77) | def classify_her2_status(data, ihc_col='her2_ihc', fish_col='her2_fish'):
  function classify_breast_cancer_subtype (line 130) | def classify_breast_cancer_subtype(data, er_col='er_positive', pr_col='p...
  function correlate_biomarker_outcome (line 169) | def correlate_biomarker_outcome(data, biomarker_col, outcome_col, biomar...
  function stratify_cohort_report (line 229) | def stratify_cohort_report(data, stratification_var, output_dir='stratif...
  function main (line 296) | def main():

FILE: scientific-skills/clinical-decision-support/scripts/build_decision_tree.py
  class DecisionNode (line 16) | class DecisionNode:
    method __init__ (line 19) | def __init__(self, question, yes_path=None, no_path=None, node_id=None):
    method _generate_id (line 25) | def _generate_id(self, text):
  class ActionNode (line 30) | class ActionNode:
    method __init__ (line 33) | def __init__(self, action, urgency='routine', node_id=None):
    method _generate_id (line 38) | def _generate_id(self, text):
  function generate_tikz_header (line 42) | def generate_tikz_header():
  function generate_tikz_footer (line 90) | def generate_tikz_footer():
  function simple_algorithm_to_tikz (line 102) | def simple_algorithm_to_tikz(algorithm_text, output_file='algorithm.tex'):
  function json_to_tikz (line 230) | def json_to_tikz(json_file, output_file='algorithm.tex'):
  function create_example_json (line 337) | def create_example_json():
  function main (line 390) | def main():

FILE: scientific-skills/clinical-decision-support/scripts/create_cohort_tables.py
  function calculate_p_value (line 21) | def calculate_p_value(data, variable, group_col='group', var_type='categ...
  function format_continuous_variable (line 72) | def format_continuous_variable(data, variable, group_col, distribution='...
  function format_categorical_variable (line 106) | def format_categorical_variable(data, variable, group_col):
  function generate_baseline_table (line 138) | def generate_baseline_table(data, group_col='group', output_file='table1...
  function generate_efficacy_table (line 197) | def generate_efficacy_table(data, group_col='group', output_file='table2...
  function generate_safety_table (line 282) | def generate_safety_table(data, ae_columns, group_col='group', output_fi...
  function generate_latex_table (line 333) | def generate_latex_table(df, caption, label='table'):
  function _binomial_ci (line 371) | def _binomial_ci(successes, trials, confidence=0.95):
  function create_example_data (line 400) | def create_example_data():
  function main (line 422) | def main():

FILE: scientific-skills/clinical-decision-support/scripts/generate_survival_analysis.py
  function load_survival_data (line 26) | def load_survival_data(filepath):
  function calculate_median_survival (line 54) | def calculate_median_survival(kmf):
  function generate_kaplan_meier_plot (line 71) | def generate_kaplan_meier_plot(data, time_col='time', event_col='event',
  function generate_number_at_risk_table (line 186) | def generate_number_at_risk_table(data, time_col='time', event_col='event',
  function calculate_hazard_ratio (line 218) | def calculate_hazard_ratio(data, time_col='time', event_col='event', gro...
  function generate_report (line 257) | def generate_report(data, output_dir, prefix='survival'):
  function main (line 375) | def main():

FILE: scientific-skills/clinical-decision-support/scripts/validate_cds_document.py
  class CDSValidator (line 22) | class CDSValidator:
    method __init__ (line 25) | def __init__(self, filepath):
    method validate_all (line 34) | def validate_all(self):
    method check_required_sections (line 49) | def check_required_sections(self):
    method check_evidence_citations (line 90) | def check_evidence_citations(self):
    method check_recommendation_grading (line 121) | def check_recommendation_grading(self):
    method check_statistical_reporting (line 145) | def check_statistical_reporting(self):
    method check_hipaa_identifiers (line 178) | def check_hipaa_identifiers(self):
    method check_biomarker_nomenclature (line 206) | def check_biomarker_nomenclature(self):
    method generate_report (line 237) | def generate_report(self):
    method save_report (line 271) | def save_report(self, output_file):
  function main (line 300) | def main():

FILE: scientific-skills/clinical-reports/scripts/check_deidentification.py
  function check_identifiers (line 159) | def check_identifiers(text: str) -> Dict:
  function check_age_compliance (line 188) | def check_age_compliance(text: str) -> Dict:
  function generate_report (line 202) | def generate_report(filename: str) -> Dict:
  function get_recommendation (line 243) | def get_recommendation(status: str, identifiers: Dict, ages: Dict) -> str:
  function print_report (line 263) | def print_report(report: Dict):
  function main (line 310) | def main():

FILE: scientific-skills/clinical-reports/scripts/compliance_checker.py
  function check_compliance (line 31) | def check_compliance(filename: str) -> dict:
  function main (line 46) | def main():

FILE: scientific-skills/clinical-reports/scripts/extract_clinical_data.py
  function extract_vital_signs (line 14) | def extract_vital_signs(content: str) -> dict:
  function extract_demographics (line 33) | def extract_demographics(content: str) -> dict:
  function extract_medications (line 49) | def extract_medications(content: str) -> list:
  function main (line 67) | def main():

FILE: scientific-skills/clinical-reports/scripts/format_adverse_events.py
  function format_ae_summary_table (line 17) | def format_ae_summary_table(data: list) -> str:
  function main (line 70) | def main():

FILE: scientific-skills/clinical-reports/scripts/generate_report_template.py
  function get_template_dir (line 44) | def get_template_dir() -> Path:
  function list_templates (line 51) | def list_templates():
  function generate_template (line 60) | def generate_template(template_type: str, output_file: str = None):
  function interactive_mode (line 82) | def interactive_mode():
  function main (line 121) | def main():

FILE: scientific-skills/clinical-reports/scripts/terminology_validator.py
  function check_do_not_use_abbreviations (line 29) | def check_do_not_use_abbreviations(content: str) -> dict:
  function check_ambiguous_abbreviations (line 47) | def check_ambiguous_abbreviations(content: str) -> dict:
  function validate_icd10_format (line 63) | def validate_icd10_format(content: str) -> list:
  function main (line 71) | def main():

FILE: scientific-skills/clinical-reports/scripts/validate_case_report.py
  class CareValidator (line 20) | class CareValidator:
    method __init__ (line 109) | def __init__(self, filename: str):
    method _read_file (line 115) | def _read_file(self) -> str:
    method validate_care_compliance (line 125) | def validate_care_compliance(self) -> Dict[str, Dict]:
    method check_deidentification (line 144) | def check_deidentification(self) -> Dict[str, List[str]]:
    method check_word_count (line 156) | def check_word_count(self) -> Dict[str, int]:
    method check_references (line 170) | def check_references(self) -> Dict[str, any]:
    method generate_report (line 191) | def generate_report(self) -> Dict:
    method print_report (line 217) | def print_report(self):
  function main (line 286) | def main():

FILE: scientific-skills/clinical-reports/scripts/validate_trial_report.py
  function validate_ich_e3 (line 36) | def validate_ich_e3(filename: str) -> dict:
  function main (line 58) | def main():

FILE: scientific-skills/clinicaltrials-database/scripts/query_clinicaltrials.py
  function search_studies (line 22) | def search_studies(
  function get_study_details (line 96) | def get_study_details(nct_id: str, format: str = "json") -> Dict:
  function search_with_all_results (line 119) | def search_with_all_results(
  function extract_study_summary (line 170) | def extract_study_summary(study: Dict) -> Dict:

FILE: scientific-skills/clinpgx-database/scripts/query_clinpgx.py
  function rate_limited_request (line 24) | def rate_limited_request(url: str, params: Optional[Dict] = None, delay:...
  function safe_api_call (line 41) | def safe_api_call(url: str, params: Optional[Dict] = None, max_retries: ...
  function cached_query (line 81) | def cached_query(cache_file: str, query_func, *args, **kwargs) -> Any:
  function get_gene_info (line 114) | def get_gene_info(gene_symbol: str) -> Optional[Dict]:
  function get_drug_info (line 132) | def get_drug_info(drug_name: str) -> Optional[List[Dict]]:
  function get_gene_drug_pairs (line 152) | def get_gene_drug_pairs(gene: Optional[str] = None, drug: Optional[str] ...
  function get_cpic_guidelines (line 180) | def get_cpic_guidelines(gene: Optional[str] = None, drug: Optional[str] ...
  function get_alleles (line 208) | def get_alleles(gene: str) -> Optional[List[Dict]]:
  function get_allele_info (line 228) | def get_allele_info(allele_name: str) -> Optional[Dict]:
  function get_clinical_annotations (line 246) | def get_clinical_annotations(
  function get_drug_labels (line 281) | def get_drug_labels(drug: str, source: Optional[str] = None) -> Optional...
  function search_variants (line 307) | def search_variants(rsid: Optional[str] = None, chromosome: Optional[str...
  function get_pathway_info (line 342) | def get_pathway_info(pathway_id: Optional[str] = None, drug: Optional[st...
  function export_to_dataframe (line 374) | def export_to_dataframe(data: List[Dict], output_file: Optional[str] = N...
  function batch_gene_query (line 405) | def batch_gene_query(gene_list: List[str], delay: float = 0.5) -> Dict[s...
  function find_actionable_gene_drug_pairs (line 437) | def find_actionable_gene_drug_pairs(cpic_level: str = "A") -> Optional[L...

FILE: scientific-skills/cosmic-database/scripts/download_cosmic.py
  function download_cosmic_file (line 30) | def download_cosmic_file(
  function get_common_file_path (line 131) | def get_common_file_path(
  function main (line 163) | def main():

FILE: scientific-skills/deepchem/scripts/graph_neural_network.py
  function create_model (line 38) | def create_model(model_type, n_tasks, mode='classification'):
  function train_on_molnet (line 90) | def train_on_molnet(dataset_name, model_type, n_epochs=50):
  function train_on_custom_data (line 164) | def train_on_custom_data(data_path, model_type, task_type, target_cols, ...
  function main (line 244) | def main():

FILE: scientific-skills/deepchem/scripts/predict_solubility.py
  function train_solubility_model (line 19) | def train_solubility_model(data_path=None, smiles_col='smiles', target_c...
  function predict_new_molecules (line 119) | def predict_new_molecules(model, smiles_list, transformers=None):
  function main (line 158) | def main():

FILE: scientific-skills/deepchem/scripts/transfer_learning.py
  function train_chemberta (line 37) | def train_chemberta(train_dataset, valid_dataset, test_dataset, task_typ...
  function train_grover (line 100) | def train_grover(train_dataset, test_dataset, task_type='classification'...
  function load_molnet_dataset (line 159) | def load_molnet_dataset(dataset_name, model_type):
  function load_custom_dataset (line 203) | def load_custom_dataset(data_path, target_cols, smiles_col, model_type):
  function main (line 252) | def main():

FILE: scientific-skills/deeptools/scripts/validate_files.py
  function check_file_exists (line 15) | def check_file_exists(filepath):
  function check_bam_index (line 24) | def check_bam_index(bam_file):
  function check_bigwig_file (line 37) | def check_bigwig_file(bw_file):
  function check_bed_file (line 46) | def check_bed_file(bed_file):
  function validate_files (line 76) | def validate_files(bam_files=None, bigwig_files=None, bed_files=None):
  function main (line 145) | def main():

FILE: scientific-skills/deeptools/scripts/workflow_generator.py
  function generate_chipseq_qc_workflow (line 32) | def generate_chipseq_qc_workflow(output_file, params):
  function generate_chipseq_analysis_workflow (line 107) | def generate_chipseq_analysis_workflow(output_file, params):
  function generate_rnaseq_coverage_workflow (line 226) | def generate_rnaseq_coverage_workflow(output_file, params):
  function generate_atacseq_workflow (line 275) | def generate_atacseq_workflow(output_file, params):
  function main (line 361) | def main():

FILE: scientific-skills/diffdock/scripts/analyze_results.py
  function parse_confidence_scores (line 23) | def parse_confidence_scores(results_dir):
  function parse_single_complex (line 53) | def parse_single_complex(complex_dir):
  function extract_confidence_score (line 82) | def extract_confidence_score(sdf_file, complex_dir):
  function classify_confidence (line 125) | def classify_confidence(score):
  function print_summary (line 137) | def print_summary(results, top_n=None, min_confidence=None):
  function export_to_csv (line 210) | def export_to_csv(results, output_path):
  function get_top_predictions (line 236) | def get_top_predictions(results, n=10, sort_by='confidence'):
  function print_top_predictions (line 255) | def print_top_predictions(results, n=10):
  function main (line 271) | def main():

FILE: scientific-skills/diffdock/scripts/prepare_batch_csv.py
  function validate_smiles (line 30) | def validate_smiles(smiles_string):
  function validate_file_path (line 44) | def validate_file_path(file_path, base_dir=None):
  function validate_csv (line 61) | def validate_csv(csv_path, base_dir=None):
  function create_template_csv (line 159) | def create_template_csv(output_path, num_examples=3):
  function main (line 183) | def main():

FILE: scientific-skills/diffdock/scripts/setup_check.py
  function check_python_version (line 19) | def check_python_version():
  function check_package (line 34) | def check_package(package_name, import_name=None, version_attr='__versio...
  function check_pytorch (line 49) | def check_pytorch():
  function check_pytorch_geometric (line 70) | def check_pytorch_geometric():
  function check_core_dependencies (line 88) | def check_core_dependencies():
  function check_esm (line 114) | def check_esm():
  function check_diffdock_installation (line 127) | def check_diffdock_installation():
  function print_installation_instructions (line 169) | def print_installation_instructions():
  function print_performance_notes (line 198) | def print_performance_notes(has_cuda):
  function main (line 228) | def main():

FILE: scientific-skills/docx/scripts/accept_changes.py
  function accept_changes (line 36) | def accept_changes(
  function _setup_libreoffice_macro (line 91) | def _setup_libreoffice_macro() -> bool:

FILE: scientific-skills/docx/scripts/comment.py
  function _generate_hex_id (line 68) | def _generate_hex_id() -> str:
  function _encode_smart_quotes (line 80) | def _encode_smart_quotes(text: str) -> str:
  function _append_xml (line 86) | def _append_xml(xml_path: Path, root_tag: str, content: str) -> None:
  function _find_para_id (line 98) | def _find_para_id(comments_path: Path, comment_id: int) -> str | None:
  function _get_next_rid (line 108) | def _get_next_rid(rels_path: Path) -> int:
  function _has_relationship (line 121) | def _has_relationship(rels_path: Path, target: str) -> bool:
  function _has_content_type (line 129) | def _has_content_type(ct_path: Path, part_name: str) -> bool:
  function _ensure_comment_relationships (line 137) | def _ensure_comment_relationships(unpacked_dir: Path) -> None:
  function _ensure_comment_content_types (line 179) | def _ensure_comment_content_types(unpacked_dir: Path) -> None:
  function add_comment (line 218) | def add_comment(

FILE: scientific-skills/docx/scripts/office/helpers/merge_runs.py
  function merge_runs (line 16) | def merge_runs(input_dir: str) -> tuple[int, str]:
  function _find_elements (line 44) | def _find_elements(root, tag: str) -> list:
  function _get_child (line 59) | def _get_child(parent, tag: str):
  function _get_children (line 68) | def _get_children(parent, tag: str) -> list:
  function _is_adjacent (line 78) | def _is_adjacent(elem1, elem2) -> bool:
  function _remove_elements (line 93) | def _remove_elements(root, tag: str):
  function _strip_run_rsid_attrs (line 99) | def _strip_run_rsid_attrs(root):
  function _merge_runs_in (line 108) | def _merge_runs_in(container) -> int:
  function _first_child_run (line 128) | def _first_child_run(container):
  function _next_element_sibling (line 135) | def _next_element_sibling(node):
  function _next_sibling_run (line 144) | def _next_sibling_run(node):
  function _is_run (line 154) | def _is_run(node) -> bool:
  function _can_merge (line 159) | def _can_merge(run1, run2) -> bool:
  function _merge_run_content (line 170) | def _merge_run_content(target, source):
  function _consolidate_text (line 178) | def _consolidate_text(run):

FILE: scientific-skills/docx/scripts/office/helpers/simplify_redlines.py
  function simplify_redlines (line 22) | def simplify_redlines(input_dir: str) -> tuple[int, str]:
  function _merge_tracked_changes_in (line 47) | def _merge_tracked_changes_in(container, tag: str) -> int:
  function _is_element (line 75) | def _is_element(node, tag: str) -> bool:
  function _get_author (line 80) | def _get_author(elem) -> str:
  function _can_merge_tracked (line 89) | def _can_merge_tracked(elem1, elem2) -> bool:
  function _merge_tracked_content (line 104) | def _merge_tracked_content(target, source):
  function _find_elements (line 111) | def _find_elements(root, tag: str) -> list:
  function get_tracked_change_authors (line 126) | def get_tracked_change_authors(doc_xml_path: Path) -> dict[str, int]:
  function _get_authors_from_docx (line 149) | def _get_authors_from_docx(docx_path: Path) -> dict[str, int]:
  function infer_author (line 172) | def infer_author(modified_dir: Path, original_docx: Path, default: str =...

FILE: scientific-skills/docx/scripts/office/pack.py
  function pack (line 24) | def pack(
  function _run_validation (line 69) | def _run_validation(
  function _condense_xml (line 108) | def _condense_xml(xml_file: Path) -> None:

FILE: scientific-skills/docx/scripts/office/soffice.py
  function get_soffice_env (line 24) | def get_soffice_env() -> dict:
  function run_soffice (line 35) | def run_soffice(args: list[str], **kwargs) -> subprocess.CompletedProcess:
  function _needs_shim (line 44) | def _needs_shim() -> bool:
  function _ensure_shim (line 53) | def _ensure_shim() -> Path:

FILE: scientific-skills/docx/scripts/office/unpack.py
  function unpack (line 34) | def unpack(
  function _pretty_print_xml (line 82) | def _pretty_print_xml(xml_file: Path) -> None:
  function _escape_smart_quotes (line 91) | def _escape_smart_quotes(xml_file: Path) -> None:

FILE: scientific-skills/docx/scripts/office/validate.py
  function main (line 25) | def main():

FILE: scientific-skills/docx/scripts/office/validators/base.py
  class BaseSchemaValidator (line 12) | class BaseSchemaValidator:
    method __init__ (line 94) | def __init__(self, unpacked_dir, original_file=None, verbose=False):
    method validate (line 109) | def validate(self):
    method repair (line 112) | def repair(self) -> int:
    method repair_whitespace_preservation (line 115) | def repair_whitespace_preservation(self) -> int:
    method validate_xml (line 143) | def validate_xml(self):
    method validate_namespaces (line 170) | def validate_namespaces(self):
    method validate_unique_ids (line 199) | def validate_unique_ids(self):
    method validate_file_references (line 289) | def validate_file_references(self):
    method validate_all_relationship_ids (line 385) | def validate_all_relationship_ids(self):
    method _get_expected_relationship_type (line 469) | def _get_expected_relationship_type(self, element_name):
    method validate_content_types (line 492) | def validate_content_types(self):
    method validate_file_against_xsd (line 598) | def validate_file_against_xsd(self, xml_file, verbose=False):
    method validate_against_xsd (line 636) | def validate_against_xsd(self):
    method _get_schema_path (line 685) | def _get_schema_path(self, xml_file):
    method _clean_ignorable_namespaces (line 703) | def _clean_ignorable_namespaces(self, xml_doc):
    method _remove_ignorable_elements (line 723) | def _remove_ignorable_elements(self, root):
    method _preprocess_for_mc_ignorable (line 742) | def _preprocess_for_mc_ignorable(self, xml_doc):
    method _validate_single_file_xsd (line 750) | def _validate_single_file_xsd(self, xml_file, base_path):
    method _get_original_file_errors (line 787) | def _get_original_file_errors(self, xml_file):
    method _remove_template_tags_from_text_nodes (line 814) | def _remove_template_tags_from_text_nodes(self, xml_doc):

FILE: scientific-skills/docx/scripts/office/validators/docx.py
  class DOCXSchemaValidator (line 16) | class DOCXSchemaValidator(BaseSchemaValidator):
    method validate (line 24) | def validate(self):
    method validate_whitespace_preservation (line 66) | def validate_whitespace_preservation(self):
    method validate_deletions (line 112) | def validate_deletions(self):
    method count_paragraphs_in_unpacked (line 163) | def count_paragraphs_in_unpacked(self):
    method count_paragraphs_in_original (line 179) | def count_paragraphs_in_original(self):
    method validate_insertions (line 202) | def validate_insertions(self):
    method compare_paragraph_counts (line 243) | def compare_paragraph_counts(self):
    method _parse_id_value (line 251) | def _parse_id_value(self, val: str, base: int = 16) -> int:
    method validate_id_constraints (line 254) | def validate_id_constraints(self):
    method validate_comment_markers (line 298) | def validate_comment_markers(self):
    method repair (line 386) | def repair(self) -> int:
    method repair_durableId (line 391) | def repair_durableId(self) -> int:

FILE: scientific-skills/docx/scripts/office/validators/pptx.py
  class PPTXSchemaValidator (line 10) | class PPTXSchemaValidator(BaseSchemaValidator):
    method validate (line 25) | def validate(self):
    method validate_uuid_ids (line 62) | def validate_uuid_ids(self):
    method _looks_like_uuid (line 100) | def _looks_like_uuid(self, value):
    method validate_slide_layout_ids (line 104) | def validate_slide_layout_ids(self):
    method validate_no_duplicate_slide_layouts (line 172) | def validate_no_duplicate_slide_layouts(self):
    method validate_notes_slide_references (line 210) | def validate_notes_slide_references(self):

FILE: scientific-skills/docx/scripts/office/validators/redlining.py
  class RedliningValidator (line 11) | class RedliningValidator:
    method __init__ (line 13) | def __init__(self, unpacked_dir, original_docx, verbose=False, author=...
    method repair (line 22) | def repair(self) -> int:
    method validate (line 25) | def validate(self):
    method _generate_detailed_diff (line 104) | def _generate_detailed_diff(self, original_text, modified_text):
    method _get_git_word_diff (line 127) | def _get_git_word_diff(self, original_text, modified_text):
    method _remove_author_tracked_changes (line 198) | def _remove_author_tracked_changes(self, root):
    method _extract_text_content (line 229) | def _extract_text_content(self, root):

FILE: scientific-skills/drugbank-database/scripts/drugbank_helper.py
  class DrugBankHelper (line 23) | class DrugBankHelper:
    method __init__ (line 28) | def __init__(self, root=None):
    method _get_root (line 38) | def _get_root(self):
    method _get_text_safe (line 45) | def _get_text_safe(self, element) -> Optional[str]:
    method find_drug (line 49) | def find_drug(self, drugbank_id: str):
    method get_drug_info (line 70) | def get_drug_info(self, drugbank_id: str) -> Dict[str, Any]:
    method get_interactions (line 97) | def get_interactions(self, drugbank_id: str) -> List[Dict[str, str]]:
    method get_targets (line 124) | def get_targets(self, drugbank_id: str) -> List[Dict[str, Any]]:
    method get_properties (line 169) | def get_properties(self, drugbank_id: str) -> Dict[str, Dict[str, Any]]:
    method check_interaction (line 205) | def check_interaction(self, drug1_id: str, drug2_id: str) -> Optional[...
    method check_polypharmacy (line 229) | def check_polypharmacy(self, drug_ids: List[str]) -> List[Dict[str, An...
    method get_smiles (line 251) | def get_smiles(self, drugbank_id: str) -> Optional[str]:
    method get_inchi (line 264) | def get_inchi(self, drugbank_id: str) -> Optional[str]:
    method search_by_name (line 277) | def search_by_name(self, name: str, exact: bool = False) -> List[Dict[...

FILE: scientific-skills/ensembl-database/scripts/ensembl_query.py
  class EnsemblAPIClient (line 19) | class EnsemblAPIClient:
    method __init__ (line 22) | def __init__(self, server: str = "https://rest.ensembl.org", rate_limi...
    method _rate_limit_check (line 35) | def _rate_limit_check(self):
    method _make_request (line 50) | def _make_request(
    method lookup_gene_by_symbol (line 105) | def lookup_gene_by_symbol(self, species: str, symbol: str, expand: boo...
    method lookup_by_id (line 121) | def lookup_by_id(self, ensembl_id: str, expand: bool = False) -> Dict:
    method get_sequence (line 136) | def get_sequence(
    method get_region_sequence (line 164) | def get_region_sequence(
    method get_variant (line 191) | def get_variant(self, species: str, variant_id: str, include_pops: boo...
    method predict_variant_effect (line 207) | def predict_variant_effect(
    method find_orthologs (line 225) | def find_orthologs(
    method get_region_features (line 246) | def get_region_features(
    method get_species_info (line 267) | def get_species_info(self) -> List[Dict]:
    method get_assembly_info (line 278) | def get_assembly_info(self, species: str) -> Dict:
    method map_coordinates (line 291) | def map_coordinates(
  function main (line 314) | def main():

FILE: scientific-skills/etetoolkit/scripts/quick_visualize.py
  function create_tree_style (line 20) | def create_tree_style(args):
  function apply_node_styling (line 53) | def apply_node_styling(tree, args):
  function visualize_tree (line 79) | def visualize_tree(tree_file, output, args):
  function main (line 117) | def main():

FILE: scientific-skills/etetoolkit/scripts/tree_operations.py
  function load_tree (line 24) | def load_tree(tree_file, format_num=0):
  function convert_format (line 33) | def convert_format(tree_file, output, in_format=0, out_format=1):
  function reroot_tree (line 40) | def reroot_tree(tree_file, output, outgroup=None, midpoint=False, format...
  function prune_tree (line 64) | def prune_tree(tree_file, output, keep_taxa, preserve_length=True, forma...
  function tree_stats (line 88) | def tree_stats(tree_file, format_num=0):
  function show_ascii (line 120) | def show_ascii(tree_file, format_num=0, show_internal=True):
  function list_leaves (line 126) | def list_leaves(tree_file, format_num=0):
  function main (line 133) | def main():

FILE: scientific-skills/exploratory-data-analysis/scripts/eda_analyzer.py
  function detect_file_type (line 14) | def detect_file_type(filepath):
  function get_file_basic_info (line 136) | def get_file_basic_info(filepath):
  function format_bytes (line 151) | def format_bytes(size):
  function load_reference_info (line 160) | def load_reference_info(category, extension):
  function analyze_file (line 215) | def analyze_file(filepath):
  function analyze_general_scientific (line 251) | def analyze_general_scientific(filepath, extension):
  function analyze_bioinformatics (line 335) | def analyze_bioinformatics(filepath, extension):
  function analyze_imaging (line 381) | def analyze_imaging(filepath, extension):
  function generate_markdown_report (line 421) | def generate_markdown_report(analysis, output_path=None):
  function main (line 517) | def main():

FILE: scientific-skills/fda-database/scripts/fda_examples.py
  function example_drug_safety_profile (line 15) | def example_drug_safety_profile(fda, drug_name):
  function example_device_surveillance (line 68) | def example_device_surveillance(fda, device_name):
  function example_food_recall_monitoring (line 109) | def example_food_recall_monitoring(fda, allergen):
  function example_substance_lookup (line 144) | def example_substance_lookup(fda, substance_name):
  function example_comparative_drug_analysis (line 202) | def example_comparative_drug_analysis(fda, drug_list):
  function example_veterinary_analysis (line 252) | def example_veterinary_analysis(fda, species, drug_name):
  function main (line 296) | def main():

FILE: scientific-skills/fda-database/scripts/fda_query.py
  class RateLimiter (line 25) | class RateLimiter:
    method __init__ (line 28) | def __init__(self, max_per_minute: int = 240):
    method wait_if_needed (line 32) | def wait_if_needed(self):
  class FDACache (line 51) | class FDACache:
    method __init__ (line 54) | def __init__(self, cache_dir: str = "fda_cache", ttl: int = 3600):
    method _get_cache_key (line 59) | def _get_cache_key(self, url: str, params: Dict) -> str:
    method get (line 64) | def get(self, url: str, params: Dict) -> Optional[Dict]:
    method set (line 76) | def set(self, url: str, params: Dict, data: Dict):
  class FDAQuery (line 84) | class FDAQuery:
    method __init__ (line 89) | def __init__(self, api_key: Optional[str] = None, use_cache: bool = True,
    method _build_url (line 104) | def _build_url(self, category: str, endpoint: str) -> str:
    method _make_request (line 108) | def _make_request(self, url: str, params: Dict, use_cache: bool = True...
    method query (line 160) | def query(self, category: str, endpoint: str, search: Optional[str] = ...
    method query_all (line 194) | def query_all(self, category: str, endpoint: str, search: str,
    method query_drug_events (line 239) | def query_drug_events(self, drug_name: str, limit: int = 100) -> Dict:
    method query_drug_label (line 244) | def query_drug_label(self, drug_name: str, brand: bool = True) -> Dict:
    method query_drug_ndc (line 250) | def query_drug_ndc(self, ndc: Optional[str] = None,
    method query_drug_recalls (line 262) | def query_drug_recalls(self, drug_name: Optional[str] = None,
    method query_device_events (line 277) | def query_device_events(self, device_name: str, limit: int = 100) -> D...
    method query_device_510k (line 282) | def query_device_510k(self, applicant: Optional[str] = None,
    method query_device_classification (line 294) | def query_device_classification(self, product_code: str) -> Dict:
    method query_food_events (line 301) | def query_food_events(self, product_name: Optional[str] = None,
    method query_food_recalls (line 313) | def query_food_recalls(self, product: Optional[str] = None,
    method query_animal_events (line 331) | def query_animal_events(self, species: Optional[str] = None,
    method query_substance_by_unii (line 345) | def query_substance_by_unii(self, unii: str) -> Dict:
    method query_substance_by_name (line 350) | def query_substance_by_name(self, name: str) -> Dict:
    method count_by_field (line 357) | def count_by_field(self, category: str, endpoint: str,
    method get_date_range_data (line 375) | def get_date_range_data(self, category: str, endpoint: str,
  function main (line 403) | def main():

FILE: scientific-skills/fred-economic-data/scripts/fred_examples.py
  function example_basic_series (line 16) | def example_basic_series():
  function example_transformations (line 42) | def example_transformations():
  function example_search (line 76) | def example_search():
  function example_categories (line 107) | def example_categories():
  function example_releases (line 135) | def example_releases():
  function example_economic_indicators (line 174) | def example_economic_indicators():
  function example_time_series_analysis (line 203) | def example_time_series_analysis():
  function example_vintage_data (line 240) | def example_vintage_data():
  function example_sources (line 265) | def example_sources():
  function example_regional_data (line 288) | def example_regional_data():
  function main (line 314) | def main():

FILE: scientific-skills/fred-economic-data/scripts/fred_query.py
  class FREDQuery (line 14) | class FREDQuery:
    method __init__ (line 27) | def __init__(
    method _make_request (line 54) | def _make_request(
    method get_series (line 99) | def get_series(self, series_id: str, **kwargs) -> Dict[str, Any]:
    method get_observations (line 113) | def get_observations(
    method search_series (line 162) | def search_series(
    method get_series_categories (line 211) | def get_series_categories(self, series_id: str, **kwargs) -> Dict[str,...
    method get_series_release (line 216) | def get_series_release(self, series_id: str, **kwargs) -> Dict[str, Any]:
    method get_series_tags (line 221) | def get_series_tags(self, series_id: str, **kwargs) -> Dict[str, Any]:
    method get_series_updates (line 226) | def get_series_updates(
    method get_vintage_dates (line 242) | def get_vintage_dates(self, series_id: str, **kwargs) -> Dict[str, Any]:
    method get_category (line 249) | def get_category(self, category_id: int = 0, **kwargs) -> Dict[str, Any]:
    method get_category_children (line 259) | def get_category_children(self, category_id: int = 0, **kwargs) -> Dic...
    method get_category_series (line 264) | def get_category_series(
    method get_category_tags (line 284) | def get_category_tags(self, category_id: int, **kwargs) -> Dict[str, A...
    method get_releases (line 291) | def get_releases(
    method get_release_dates (line 309) | def get_release_dates(
    method get_release (line 335) | def get_release(self, release_id: int, **kwargs) -> Dict[str, Any]:
    method get_release_series (line 340) | def get_release_series(
    method get_release_sources (line 356) | def get_release_sources(self, release_id: int, **kwargs) -> Dict[str, ...
    method get_release_tables (line 361) | def get_release_tables(self, release_id: int, **kwargs) -> Dict[str, A...
    method get_tags (line 368) | def get_tags(
    method get_related_tags (line 392) | def get_related_tags(
    method get_series_by_tags (line 408) | def get_series_by_tags(
    method get_sources (line 443) | def get_sources(
    method get_source (line 461) | def get_source(self, source_id: int, **kwargs) -> Dict[str, Any]:
    method get_source_releases (line 466) | def get_source_releases(
    method get_shapes (line 484) | def get_shapes(self, shape: str) -> Dict[str, Any]:
    method get_series_group (line 494) | def get_series_group(self, series_id: str) -> Dict[str, Any]:
    method get_series_data (line 499) | def get_series_data(
    method get_regional_data (line 513) | def get_regional_data(
    method clear_cache (line 555) | def clear_cache(self):
  function query_fred (line 561) | def query_fred(series_id: str, api_key: Optional[str] = None, **kwargs) ...

FILE: scientific-skills/gene-database/scripts/batch_gene_lookup.py
  function read_gene_list (line 18) | def read_gene_list(filepath: str) -> List[str]:
  function batch_esearch (line 40) | def batch_esearch(queries: List[str], organism: Optional[str] = None,
  function batch_esummary (line 96) | def batch_esummary(gene_ids: List[str], api_key: Optional[str] = None,
  function batch_lookup_by_ids (line 147) | def batch_lookup_by_ids(gene_ids: List[str], api_key: Optional[str] = No...
  function batch_lookup_by_symbols (line 182) | def batch_lookup_by_symbols(gene_symbols: List[str], organism: str,
  function main (line 240) | def main():

FILE: scientific-skills/gene-database/scripts/fetch_gene_data.py
  function get_taxon_id (line 20) | def get_taxon_id(taxon_name: str) -> Optional[str]:
  function fetch_gene_by_id (line 56) | def fetch_gene_by_id(gene_id: str, api_key: Optional[str] = None) -> Dic...
  function fetch_gene_by_symbol (line 87) | def fetch_gene_by_symbol(symbol: str, taxon: str, api_key: Optional[str]...
  function fetch_multiple_genes (line 125) | def fetch_multiple_genes(gene_ids: List[str], api_key: Optional[str] = N...
  function display_gene_info (line 157) | def display_gene_info(data: Dict[str, Any], verbose: bool = False) -> None:
  function main (line 216) | def main():

FILE: scientific-skills/gene-database/scripts/query_gene.py
  function esearch (line 23) | def esearch(query: str, retmax: int = 20, api_key: Optional[str] = None)...
  function esummary (line 65) | def esummary(gene_ids: List[str], api_key: Optional[str] = None) -> Dict...
  function efetch (line 99) | def efetch(gene_ids: List[str], retmode: str = 'xml', api_key: Optional[...
  function search_and_summarize (line 133) | def search_and_summarize(query: str, organism: Optional[str] = None,
  function fetch_by_id (line 182) | def fetch_by_id(gene_ids: List[str], output_format: str = 'json',
  function main (line 205) | def main():

FILE: scientific-skills/generate-image/scripts/generate_image.py
  function check_env_file (line 22) | def check_env_file() -> Optional[str]:
  function load_image_as_base64 (line 38) | def load_image_as_base64(image_path: str) -> str:
  function save_base64_image (line 63) | def save_base64_image(base64_data: str, output_path: str) -> None:
  function generate_image (line 75) | def generate_image(
  function main (line 209) | def main():

FILE: scientific-skills/get-available-resources/scripts/detect_resources.py
  function get_cpu_info (line 23) | def get_cpu_info() -> Dict[str, Any]:
  function get_memory_info (line 45) | def get_memory_info() -> Dict[str, Any]:
  function get_disk_info (line 60) | def get_disk_info(path: str = None) -> Dict[str, Any]:
  function detect_nvidia_gpus (line 81) | def detect_nvidia_gpus() -> List[Dict[str, Any]]:
  function detect_amd_gpus (line 116) | def detect_amd_gpus() -> List[Dict[str, Any]]:
  function detect_apple_silicon_gpu (line 149) | def detect_apple_silicon_gpu() -> Optional[Dict[str, Any]]:
  function get_gpu_info (line 204) | def get_gpu_info() -> Dict[str, Any]:
  function get_os_info (line 230) | def get_os_info() -> Dict[str, Any]:
  function detect_all_resources (line 241) | def detect_all_resources(output_path: str = None) -> Dict[str, Any]:
  function generate_recommendations (line 273) | def generate_recommendations(resources: Dict[str, Any]) -> Dict[str, Any]:
  function main (line 351) | def main():

FILE: scientific-skills/gget/scripts/batch_sequence_analysis.py
  function read_fasta (line 13) | def read_fasta(fasta_file):
  function analyze_sequences (line 36) | def analyze_sequences(
  function main (line 141) | def main():

FILE: scientific-skills/gget/scripts/enrichment_pipeline.py
  function read_gene_list (line 14) | def read_gene_list(file_path):
  function enrichment_pipeline (line 30) | def enrichment_pipeline(
  function main (line 169) | def main():

FILE: scientific-skills/gget/scripts/gene_analysis.py
  function analyze_gene (line 12) | def analyze_gene(gene_name, species="homo_sapiens", output_prefix=None):
  function main (line 132) | def main():

FILE: scientific-skills/infographics/scripts/generate_infographic.py
  function list_options (line 42) | def list_options():
  function main (line 98) | def main():

FILE: scientific-skills/infographics/scripts/generate_infographic_ai.py
  function _load_env_file (line 39) | def _load_env_file():
  class InfographicGenerator (line 272) | class InfographicGenerator:
    method __init__ (line 339) | def __init__(self, api_key: Optional[str] = None, verbose: bool = False):
    method _log (line 364) | def _log(self, message: str):
    method research_topic (line 371) | def research_topic(self, topic: str, infographic_type: Optional[str] =...
    method web_search (line 481) | def web_search(self, query: str) -> Dict[str, Any]:
    method _enhance_prompt_with_research (line 555) | def _enhance_prompt_with_research(self, user_prompt: str, research_dat...
    method _make_request (line 581) | def _make_request(self, model: str, messages: List[Dict[str, Any]],
    method _extract_image_from_response (line 625) | def _extract_image_from_response(self, response: Dict[str, Any]) -> Op...
    method _image_to_base64 (line 683) | def _image_to_base64(self, image_path: str) -> str:
    method _build_generation_prompt (line 700) | def _build_generation_prompt(self, user_prompt: str,
    method generate_image (line 738) | def generate_image(self, prompt: str) -> Optional[bytes]:
    method review_image (line 786) | def review_image(self, image_path: str, original_prompt: str,
    method improve_prompt (line 936) | def improve_prompt(self, original_prompt: str, critique: str,
    method generate_iterative (line 983) | def generate_iterative(self, user_prompt: str, output_path: str,
  function main (line 1173) | def main():

FILE: scientific-skills/iso-13485-certification/scripts/gap_analyzer.py
  class GapAnalyzer (line 164) | class GapAnalyzer:
    method __init__ (line 167) | def __init__(self, docs_dir: str):
    method analyze (line 173) | def analyze(self) -> Dict:
    method _scan_documents (line 198) | def _scan_documents(self) -> List[Tuple[Path, str]]:
    method _search_for_procedure (line 223) | def _search_for_procedure(self, documents: List[Tuple[Path, str]],
    method _search_for_document (line 238) | def _search_for_document(self, documents: List[Tuple[Path, str]],
    method _generate_report (line 249) | def _generate_report(self) -> Dict:
    method _generate_recommendations (line 292) | def _generate_recommendations(self, missing_procedures: List[Dict],
  function print_report (line 331) | def print_report(report: Dict):
  function save_report (line 400) | def save_report(report: Dict, output_path: str):
  function main (line 407) | def main():

FILE: scientific-skills/kegg-database/scripts/kegg_api.py
  function kegg_info (line 22) | def kegg_info(database: str) -> str:
  function kegg_list (line 43) | def kegg_list(database: str, org: Optional[str] = None) -> str:
  function kegg_find (line 71) | def kegg_find(database: str, query: str, option: Optional[str] = None) -...
  function kegg_get (line 110) | def kegg_get(entries: Union[str, List[str]], option: Optional[str] = Non...
  function kegg_conv (line 157) | def kegg_conv(target_db: str, source_db: str) -> str:
  function kegg_link (line 186) | def kegg_link(target_db: str, source_db: str) -> str:
  function kegg_ddi (line 215) | def kegg_ddi(drug_entries: Union[str, List[str]]) -> str:

FILE: scientific-skills/labarchive-integration/scripts/entry_operations.py
  function load_config (line 16) | def load_config(config_path='config.yaml'):
  function init_client (line 30) | def init_client(config):
  function get_user_id (line 45) | def get_user_id(client, config):
  function create_entry (line 70) | def create_entry(client, uid, nbid, title, content=None, date=None):
  function create_comment (line 119) | def create_comment(client, uid, nbid, entry_id, comment):
  function upload_attachment (line 145) | def upload_attachment(client, config, uid, nbid, entry_id, file_path):
  function batch_upload (line 187) | def batch_upload(client, config, uid, nbid, entry_id, directory):
  function create_entry_with_attachments (line 218) | def create_entry_with_attachments(client, config, uid, nbid, title, cont...
  function main (line 235) | def main():

FILE: scientific-skills/labarchive-integration/scripts/notebook_operations.py
  function load_config (line 15) | def load_config(config_path='config.yaml'):
  function init_client (line 29) | def init_client(config):
  function get_user_id (line 44) | def get_user_id(client, config):
  function list_notebooks (line 69) | def list_notebooks(client, uid):
  function backup_notebook (line 113) | def backup_notebook(client, uid, nbid, output_dir='backups', json_format...
  function backup_all_notebooks (line 165) | def backup_all_notebooks(client, uid, output_dir='backups', json_format=...
  function main (line 197) | def main():

FILE: scientific-skills/labarchive-integration/scripts/setup_config.py
  function get_regional_endpoint (line 14) | def get_regional_endpoint():
  function get_credentials (line 39) | def get_credentials():
  function create_config_file (line 70) | def create_config_file(config_data, output_path='config.yaml'):
  function verify_config (line 82) | def verify_config(config_path='config.yaml'):
  function test_authentication (line 105) | def test_authentication(config_path='config.yaml'):
  function main (line 161) | def main():

FILE: scientific-skills/literature-review/scripts/generate_pdf.py
  function generate_pdf (line 12) | def generate_pdf(
  function check_dependencies (line 100) | def check_dependencies():
  function main (line 128) | def main():

FILE: scientific-skills/literature-review/scripts/search_databases.py
  function format_search_results (line 12) | def format_search_results(results: List[Dict], output_format: str = 'jso...
  function deduplicate_results (line 83) | def deduplicate_results(results: List[Dict]) -> List[Dict]:
  function rank_results (line 119) | def rank_results(results: List[Dict], criteria: str = 'citations') -> Li...
  function filter_by_year (line 139) | def filter_by_year(results: List[Dict], start_year: int = None, end_year...
  function generate_search_summary (line 167) | def generate_search_summary(results: List[Dict]) -> Dict:
  function main (line 209) | def main():

FILE: scientific-skills/literature-review/scripts/verify_citations.py
  class CitationVerifier (line 14) | class CitationVerifier:
    method __init__ (line 15) | def __init__(self):
    method extract_dois (line 21) | def extract_dois(self, text: str) -> List[str]:
    method verify_doi (line 26) | def verify_doi(self, doi: str) -> Tuple[bool, Dict]:
    method _get_crossref_metadata (line 44) | def _get_crossref_metadata(self, doi: str) -> Dict:
    method _format_authors (line 69) | def _format_authors(self, authors: List[Dict]) -> str:
    method _extract_year (line 86) | def _extract_year(self, message: Dict) -> str:
    method verify_url (line 96) | def verify_url(self, url: str) -> Tuple[bool, int]:
    method verify_citations_in_file (line 108) | def verify_citations_in_file(self, filepath: str) -> Dict:
    method format_citation_apa (line 139) | def format_citation_apa(self, metadata: Dict) -> str:
    method format_citation_nature (line 161) | def format_citation_nature(self, metadata: Dict) -> str:
  function main (line 182) | def main():

FILE: scientific-skills/market-research-reports/scripts/generate_market_visuals.py
  function get_script_path (line 312) | def get_script_path(tool: str) -> Path:
  function generate_visual (line 324) | def generate_visual(
  function main (line 400) | def main():

FILE: scientific-skills/markitdown/scripts/batch_convert.py
  function convert_file (line 17) | def convert_file(md: MarkItDown, file_path: Path, output_dir: Path, verb...
  function batch_convert (line 54) | def batch_convert(
  function main (line 136) | def main():

FILE: scientific-skills/markitdown/scripts/convert_literature.py
  function extract_metadata_from_filename (line 19) | def extract_metadata_from_filename(filename: str) -> Dict[str, str]:
  function convert_paper (line 45) | def convert_paper(
  function create_index (line 127) | def create_index(papers: List[Dict], output_dir: Path):
  function main (line 180) | def main():

FILE: scientific-skills/markitdown/scripts/convert_with_ai.py
  function convert_with_ai (line 70) | def convert_with_ai(
  function main (line 140) | def main():

FILE: scientific-skills/matplotlib/scripts/plot_template.py
  function set_publication_style (line 21) | def set_publication_style():
  function generate_sample_data (line 39) | def generate_sample_data():
  function create_line_plot (line 64) | def create_line_plot(data, ax=None):
  function create_scatter_plot (line 88) | def create_scatter_plot(data, ax=None):
  function create_bar_chart (line 115) | def create_bar_chart(data, ax=None):
  function create_histogram (line 148) | def create_histogram(data, ax=None):
  function create_heatmap (line 174) | def create_heatmap(data, ax=None):
  function create_contour_plot (line 201) | def create_contour_plot(data, ax=None):
  function create_box_plot (line 231) | def create_box_plot(data, ax=None):
  function create_violin_plot (line 255) | def create_violin_plot(data, ax=None):
  function create_3d_plot (line 284) | def create_3d_plot():
  function create_comprehensive_figure (line 316) | def create_comprehensive_figure():
  function main (line 350) | def main():

FILE: scientific-skills/matplotlib/scripts/style_configurator.py
  function generate_preview_data (line 114) | def generate_preview_data():
  function create_style_preview (line 132) | def create_style_preview(style_dict=None):
  function save_style_file (line 196) | def save_style_file(style_dict, filename):
  function print_style_info (line 235) | def print_style_info(style_dict):
  function list_available_presets (line 261) | def list_available_presets():
  function interactive_mode (line 277) | def interactive_mode():
  function main (line 339) | def main():

FILE: scientific-skills/medchem/scripts/filter_molecules.py
  function load_molecules (line 32) | def load_molecules(input_file: Path, smiles_column: str = "smiles") -> T...
  function apply_rule_filters (line 98) | def apply_rule_filters(mols: List[Chem.Mol], rules: List[str], n_jobs: i...
  function apply_structural_alerts (line 114) | def apply_structural_alerts(mols: List[Chem.Mol], alert_type: str, n_job...
  function apply_complexity_filter (line 159) | def apply_complexity_filter(mols: List[Chem.Mol], max_complexity: float,...
  function apply_constraints (line 176) | def apply_constraints(mols: List[Chem.Mol], constraints: Dict, n_jobs: i...
  function apply_chemical_groups (line 191) | def apply_chemical_groups(mols: List[Chem.Mol], groups: List[str]) -> pd...
  function generate_summary (line 205) | def generate_summary(df: pd.DataFrame, output_file: Path):
  function main (line 289) | def main():

FILE: scientific-skills/neuropixels-analysis/assets/analysis_template.py
  function main (line 59) | def main():

FILE: scientific-skills/neuropixels-analysis/scripts/compute_metrics.py
  function compute_metrics (line 40) | def compute_metrics(
  function main (line 157) | def main():

FILE: scientific-skills/neuropixels-analysis/scripts/explore_recording.py
  function explore_recording (line 15) | def explore_recording(data_path: str, stream_id: str = 'imec0.ap'):
  function plot_probe (line 69) | def plot_probe(recording, output_path=None):
  function plot_traces (line 82) | def plot_traces(recording, duration=1.0, output_path=None):
  function plot_power_spectrum (line 110) | def plot_power_spectrum(recording, output_path=None):

FILE: scientific-skills/neuropixels-analysis/scripts/export_to_phy.py
  function export_phy (line 16) | def export_phy(
  function main (line 57) | def main():

FILE: scientific-skills/neuropixels-analysis/scripts/neuropixels_pipeline.py
  function load_recording (line 22) | def load_recording(data_path: str, stream_id: str = 'imec0.ap') -> si.Ba...
  function preprocess (line 47) | def preprocess(
  function check_drift (line 87) | def check_drift(recording: si.BaseRecording, output_folder: str) -> dict:
  function correct_motion (line 152) | def correct_motion(
  function run_spike_sorting (line 174) | def run_spike_sorting(
  function postprocess (line 197) | def postprocess(
  function curate_units (line 236) | def curate_units(qm, method: str = 'allen') -> dict:
  function export_results (line 300) | def export_results(
  function run_pipeline (line 348) | def run_pipeline(

FILE: scientific-skills/neuropixels-analysis/scripts/preprocess_recording.py
  function preprocess_recording (line 15) | def preprocess_recording(
  function main (line 92) | def main():

FILE: scientific-skills/neuropixels-analysis/scripts/run_sorting.py
  function run_sorting (line 36) | def run_sorting(
  function main (line 79) | def main():

FILE: scientific-skills/open-notebook/scripts/chat_interaction.py
  function create_chat_session (line 21) | def create_chat_session(notebook_id, title, model_override=None):
  function list_chat_sessions (line 36) | def list_chat_sessions(notebook_id):
  function send_chat_message (line 51) | def send_chat_message(session_id, message, include_sources=True,
  function get_session_history (line 72) | def get_session_history(session_id):
  function build_context (line 86) | def build_context(notebook_id, source_ids=None, note_ids=None):
  function search_knowledge_base (line 101) | def search_knowledge_base(query, search_type="vector", limit=5):
  function ask_question (line 118) | def ask_question(query):
  function delete_chat_session (line 130) | def delete_chat_session(session_id):

FILE: scientific-skills/open-notebook/scripts/notebook_management.py
  function create_notebook (line 21) | def create_notebook(name, description=""):
  function list_notebooks (line 33) | def list_notebooks(archived=False):
  function get_notebook (line 48) | def get_notebook(notebook_id):
  function update_notebook (line 55) | def update_notebook(notebook_id, name=None, description=None, archived=N...
  function delete_notebook (line 73) | def delete_notebook(notebook_id, delete_sources=False):
  function link_source_to_notebook (line 90) | def link_source_to_notebook(notebook_id, source_id):
  function unlink_source_from_notebook (line 99) | def unlink_source_from_notebook(notebook_id, source_id):

FILE: scientific-skills/open-notebook/scripts/source_ingestion.py
  function add_url_source (line 22) | def add_url_source(notebook_id, url, process_async=True):
  function add_text_source (line 35) | def add_text_source(notebook_id, title, text):
  function upload_file_source (line 48) | def upload_file_source(notebook_id, file_path, process_async=True):
  function wait_for_processing (line 66) | def wait_for_processing(source_id, poll_interval=5, timeout=300):
  function list_sources (line 85) | def list_sources(notebook_id=None, limit=20):
  function get_source_insights (line 99) | def get_source_insights(source_id):
  function retry_failed_source (line 106) | def retry_failed_source(source_id):
  function delete_source (line 114) | def delete_source(source_id):

FILE: scientific-skills/open-notebook/scripts/test_open_notebook_skill.py
  class TestSkillDirectoryStructure (line 26) | class TestSkillDirectoryStructure(unittest.TestCase):
    method test_skill_directory_exists (line 29) | def test_skill_directory_exists(self):
    method test_skill_md_exists (line 36) | def test_skill_md_exists(self):
    method test_references_directory_exists (line 43) | def test_references_directory_exists(self):
    method test_scripts_directory_exists (line 50) | def test_scripts_directory_exists(self):
  class TestSkillMdFrontmatter (line 58) | class TestSkillMdFrontmatter(unittest.TestCase):
    method setUpClass (line 62) | def setUpClass(cls):
    method test_has_yaml_frontmatter (line 69) | def test_has_yaml_frontmatter(self):
    method test_frontmatter_has_name (line 81) | def test_frontmatter_has_name(self):
    method test_frontmatter_has_description (line 86) | def test_frontmatter_has_description(self):
    method test_frontmatter_has_license (line 99) | def test_frontmatter_has_license(self):
    method test_frontmatter_has_metadata_author (line 104) | def test_frontmatter_has_metadata_author(self):
  class TestSkillMdContent (line 111) | class TestSkillMdContent(unittest.TestCase):
    method setUpClass (line 115) | def setUpClass(cls):
    method test_has_title_heading (line 119) | def test_has_title_heading(self):
    method test_has_overview_section (line 126) | def test_has_overview_section(self):
    method test_has_quick_start_section (line 134) | def test_has_quick_start_section(self):
    method test_has_docker_setup (line 142) | def test_has_docker_setup(self):
    method test_has_api_base_url (line 147) | def test_has_api_base_url(self):
    method test_mentions_notebooklm_alternative (line 151) | def test_mentions_notebooklm_alternative(self):
    method test_mentions_self_hosted (line 159) | def test_mentions_self_hosted(self):
    method test_mentions_multiple_ai_providers (line 167) | def test_mentions_multiple_ai_providers(self):
    method test_has_core_features_section (line 181) | def test_has_core_features_section(self):
    method test_has_api_reference_section (line 192) | def test_has_api_reference_section(self):
    method test_has_python_code_examples (line 200) | def test_has_python_code_examples(self):
    method test_has_bash_code_examples (line 204) | def test_has_bash_code_examples(self):
    method test_has_installation_instructions (line 211) | def test_has_installation_instructions(self):
    method test_has_environment_variable_info (line 219) | def test_has_environment_variable_info(self):
    method test_has_kdense_suggestion (line 227) | def test_has_kdense_suggestion(self):
    method test_content_length_sufficient (line 235) | def test_content_length_sufficient(self):
  class TestReferenceFiles (line 244) | class TestReferenceFiles(unittest.TestCase):
    method _read_reference (line 247) | def _read_reference(self, filename):
    method test_api_reference_exists_and_comprehensive (line 257) | def test_api_reference_exists_and_comprehensive(self):
    method test_api_reference_has_http_methods (line 269) | def test_api_reference_has_http_methods(self):
    method test_examples_reference_exists (line 279) | def test_examples_reference_exists(self):
    method test_configuration_reference_exists (line 285) | def test_configuration_reference_exists(self):
    method test_architecture_reference_exists (line 299) | def test_architecture_reference_exists(self):
  class TestExampleScripts (line 312) | class TestExampleScripts(unittest.TestCase):
    method _check_script (line 315) | def _check_script(self, filename):
    method test_notebook_management_script_exists (line 330) | def test_notebook_management_script_exists(self):
    method test_source_ingestion_script_exists (line 336) | def test_source_ingestion_script_exists(self):
    method test_chat_interaction_script_exists (line 341) | def test_chat_interaction_script_exists(self):
  class TestMarketplaceJson (line 347) | class TestMarketplaceJson(unittest.TestCase):
    method setUpClass (line 351) | def setUpClass(cls):
    method test_marketplace_has_open_notebook_skill (line 355) | def test_marketplace_has_open_notebook_skill(self):
    method test_marketplace_valid_json (line 365) | def test_marketplace_valid_json(self):
  class TestSkillMdApiEndpointCoverage (line 373) | class TestSkillMdApiEndpointCoverage(unittest.TestCase):
    method setUpClass (line 377) | def setUpClass(cls):
    method test_covers_notebook_endpoints (line 385) | def test_covers_notebook_endpoints(self):
    method test_covers_source_endpoints (line 389) | def test_covers_source_endpoints(self):
    method test_covers_note_endpoints (line 393) | def test_covers_note_endpoints(self):
    method test_covers_chat_endpoints (line 397) | def test_covers_chat_endpoints(self):
    method test_covers_search_endpoints (line 401) | def test_covers_search_endpoints(self):
    method test_covers_podcast_endpoints (line 405) | def test_covers_podcast_endpoints(self):
    method test_covers_transformation_endpoints (line 409) | def test_covers_transformation_endpoints(self):
    method test_covers_model_management (line 413) | def test_covers_model_management(self):
    method test_covers_credential_management (line 417) | def test_covers_credential_management(self):

FILE: scientific-skills/openalex-database/scripts/openalex_client.py
  class OpenAlexClient (line 18) | class OpenAlexClient:
    method __init__ (line 23) | def __init__(self, email: Optional[str] = None, requests_per_second: i...
    method _rate_limit (line 36) | def _rate_limit(self):
    method _make_request (line 44) | def _make_request(
    method search_works (line 101) | def search_works(
    method get_entity (line 144) | def get_entity(self, entity_type: str, entity_id: str) -> Dict[str, Any]:
    method batch_lookup (line 158) | def batch_lookup(
    method paginate_all (line 192) | def paginate_all(
    method sample_works (line 238) | def sample_works(
    method group_by (line 295) | def group_by(

FILE: scientific-skills/openalex-database/scripts/query_helpers.py
  function find_author_works (line 12) | def find_author_works(
  function find_institution_works (line 58) | def find_institution_works(
  function find_highly_cited_recent_papers (line 103) | def find_highly_cited_recent_papers(
  function get_open_access_papers (line 140) | def get_open_access_papers(
  function get_publication_trends (line 176) | def get_publication_trends(
  function analyze_research_output (line 208) | def analyze_research_output(

FILE: scientific-skills/opentargets-database/scripts/query_opentargets.py
  function execute_query (line 21) | def execute_query(query: str, variables: Optional[Dict[str, Any]] = None...
  function search_entities (line 53) | def search_entities(query_string: str, entity_types: Optional[List[str]]...
  function get_target_info (line 85) | def get_target_info(ensembl_id: str, include_diseases: bool = False) -> ...
  function get_disease_info (line 156) | def get_disease_info(efo_id: str, include_targets: bool = False) -> Dict...
  function get_target_disease_evidence (line 206) | def get_target_disease_evidence(ensembl_id: str, efo_id: str,
  function get_known_drugs_for_disease (line 245) | def get_known_drugs_for_disease(efo_id: str) -> Dict[str, Any]:
  function get_drug_info (line 285) | def get_drug_info(chembl_id: str) -> Dict[str, Any]:
  function get_target_associations (line 330) | def get_target_associations(ensembl_id: str, min_score: float = 0.0) -> ...

FILE: scientific-skills/opentrons-integration/scripts/basic_protocol_template.py
  function run (line 25) | def run(protocol: protocol_api.ProtocolContext):

FILE: scientific-skills/opentrons-integration/scripts/pcr_setup_template.py
  function run (line 23) | def run(protocol: protocol_api.ProtocolContext):

FILE: scientific-skills/opentrons-integration/scripts/serial_dilution_template.py
  function run (line 23) | def run(protocol: protocol_api.ProtocolContext):

FILE: scientific-skills/parallel-web/scripts/parallel_web.py
  function _get_api_key (line 29) | def _get_api_key():
  function _get_extract_client (line 41) | def _get_extract_client():
  class ParallelChat (line 53) | class ParallelChat:
    method __init__ (line 66) | def __init__(self):
    method query (line 80) | def query(
    method _extract_basis (line 135) | def _extract_basis(self, response) -> List[Dict[str, str]]:
  class ParallelSearch (line 165) | class ParallelSearch:
    method __init__ (line 181) | def __init__(self):
    method search (line 184) | def search(
  class ParallelExtract (line 224) | class ParallelExtract:
    method __init__ (line 232) | def __init__(self):
    method extract (line 235) | def extract(
  class ParallelDeepResearch (line 300) | class ParallelDeepResearch:
    method __init__ (line 319) | def __init__(self):
    method research (line 322) | def research(
  function _print_search_results (line 371) | def _print_search_results(result: Dict[str, Any], output_file=None):
  function _print_extract_results (line 401) | def _print_extract_results(result: Dict[str, Any], output_file=None):
  function _print_research_results (line 432) | def _print_research_results(result: Dict[str, Any], output_file=None):
  function main (line 467) | def main():

FILE: scientific-skills/pdf/scripts/check_bounding_boxes.py
  class RectAndField (line 9) | class RectAndField:
  function get_bounding_box_messages (line 15) | def get_bounding_box_messages(fields_json_stream) -> list[str]:

FILE: scientific-skills/pdf/scripts/convert_pdf_to_images.py
  function convert (line 9) | def convert(pdf_path, output_dir, max_dim=1000):

FILE: scientific-skills/pdf/scripts/create_validation_image.py
  function create_validation_image (line 9) | def create_validation_image(page_number, fields_json_path, input_path, o...

FILE: scientific-skills/pdf/scripts/extract_form_field_info.py
  function get_full_annotation_field_id (line 9) | def get_full_annotation_field_id(annotation):
  function make_field_dict (line 19) | def make_field_dict(field, field_id):
  function get_field_info (line 47) | def get_field_info(reader: PdfReader):
  function write_field_info (line 110) | def write_field_info(pdf_path: str, json_output_path: str):

FILE: scientific-skills/pdf/scripts/extract_form_structure.py
  function extract_form_structure (line 20) | def extract_form_structure(pdf_path):
  function main (line 91) | def main():

FILE: scientific-skills/pdf/scripts/fill_fillable_fields.py
  function fill_pdf_fields (line 11) | def fill_pdf_fields(input_pdf_path: str, fields_json_path: str, output_p...
  function validation_error_for_field_value (line 55) | def validation_error_for_field_value(field_info, field_value):
  function monkeypatch_pydpf_method (line 74) | def monkeypatch_pydpf_method():

FILE: scientific-skills/pdf/scripts/fill_pdf_form_with_annotations.py
  function transform_from_image_coords (line 10) | def transform_from_image_coords(bbox, image_width, image_height, pdf_wid...
  function transform_from_pdf_coords (line 23) | def transform_from_pdf_coords(bbox, pdf_height):
  function fill_pdf_form (line 33) | def fill_pdf_form(input_pdf_path, fields_json_path, output_pdf_path):

FILE: scientific-skills/perplexity-search/scripts/perplexity_search.py
  function check_dependencies (line 26) | def check_dependencies():
  function check_api_key (line 37) | def check_api_key() -> Optional[str]:
  function search_with_perplexity (line 52) | def search_with_perplexity(
  function main (line 135) | def main():

FILE: scientific-skills/perplexity-search/scripts/setup_env.py
  function create_env_file (line 20) | def create_env_file(api_key: str, env_file: str = ".env") -> bool:
  function validate_setup (line 61) | def validate_setup() -> bool:
  function main (line 104) | def main():

FILE: scientific-skills/phylogenetics/scripts/phylogenetic_analysis.py
  function check_dependencies (line 22) | def check_dependencies():
  function count_sequences (line 42) | def count_sequences(fasta_file: str) -> int:
  function run_mafft (line 48) | def run_mafft(input_fasta: str, output_fasta: str, n_threads: int = 4,
  function run_iqtree (line 79) | def run_iqtree(aligned_fasta: str, prefix: str, seq_type: str = "nt",
  function run_fasttree (line 118) | def run_fasttree(aligned_fasta: str, output_tree: str, seq_type: str = "...
  function visualize_tree (line 137) | def visualize_tree(tree_file: str, output_png: str, outgroup: str = None...
  function tree_summary (line 174) | def tree_summary(tree_file: str) -> dict:
  function main (line 204) | def main():

FILE: scientific-skills/pptx/scripts/add_slide.py
  function get_next_slide_number (line 27) | def get_next_slide_number(slides_dir: Path) -> int:
  function create_slide_from_layout (line 33) | def create_slide_from_layout(unpacked_dir: Path, layout_file: str) -> None:
  function duplicate_slide (line 90) | def duplicate_slide(unpacked_dir: Path, source: str) -> None:
  function _add_to_content_types (line 130) | def _add_to_content_types(unpacked_dir: Path, dest: str) -> None:
  function _add_to_presentation_rels (line 141) | def _add_to_presentation_rels(unpacked_dir: Path, dest: str) -> str:
  function _get_next_slide_id (line 158) | def _get_next_slide_id(unpacked_dir: Path) -> int:
  function parse_source (line 165) | def parse_source(source: str) -> tuple[str, str | None]:

FILE: scientific-skills/pptx/scripts/clean.py
  function get_slides_in_sldidlst (line 27) | def get_slides_in_sldidlst(unpacked_dir: Path) -> set[str]:
  function remove_orphaned_slides (line 49) | def remove_orphaned_slides(unpacked_dir: Path) -> list[str]:
  function remove_trash_directory (line 91) | def remove_trash_directory(unpacked_dir: Path) -> list[str]:
  function get_slide_referenced_files (line 106) | def get_slide_referenced_files(unpacked_dir: Path) -> set:
  function remove_orphaned_rels_files (line 128) | def remove_orphaned_rels_files(unpacked_dir: Path) -> list[str]:
  function get_referenced_files (line 153) | def get_referenced_files(unpacked_dir: Path) -> set:
  function remove_orphaned_files (line 171) | def remove_orphaned_files(unpacked_dir: Path, referenced: set) -> list[s...
  function update_content_types (line 221) | def update_content_types(unpacked_dir: Path, removed_files: list[str]) -...
  function clean_unused_files (line 241) | def clean_unused_files(unpacked_dir: Path) -> list[str]:

FILE: scientific-skills/pptx/scripts/office/helpers/merge_runs.py
  function merge_runs (line 16) | def merge_runs(input_dir: str) -> tuple[int, str]:
  function _find_elements (line 44) | def _find_elements(root, tag: str) -> list:
  function _get_child (line 59) | def _get_child(parent, tag: str):
  function _get_children (line 68) | def _get_children(parent, tag: str) -> list:
  function _is_adjacent (line 78) | def _is_adjacent(elem1, elem2) -> bool:
  function _remove_elements (line 93) | def _remove_elements(root, tag: str):
  function _strip_run_rsid_attrs (line 99) | def _strip_run_rsid_attrs(root):
  function _merge_runs_in (line 108) | def _merge_runs_in(container) -> int:
  function _first_child_run (line 128) | def _first_child_run(container):
  function _next_element_sibling (line 135) | def _next_element_sibling(node):
  function _next_sibling_run (line 144) | def _next_sibling_run(node):
  function _is_run (line 154) | def _is_run(node) -> bool:
  function _can_merge (line 159) | def _can_merge(run1, run2) -> bool:
  function _merge_run_content (line 170) | def _merge_run_content(target, source):
  function _consolidate_text (line 178) | def _consolidate_text(run):

FILE: scientific-skills/pptx/scripts/office/helpers/simplify_redlines.py
  function simplify_redlines (line 22) | def simplify_redlines(input_dir: str) -> tuple[int, str]:
  function _merge_tracked_changes_in (line 47) | def _merge_tracked_changes_in(container, tag: str) -> int:
  function _is_element (line 75) | def _is_element(node, tag: str) -> bool:
  function _get_author (line 80) | def _get_author(elem) -> str:
  function _can_merge_tracked (line 89) | def _can_merge_tracked(elem1, elem2) -> bool:
  function _merge_tracked_content (line 104) | def _merge_tracked_content(target, source):
  function _find_elements (line 111) | def _find_elements(root, tag: str) -> list:
  function get_tracked_change_authors (line 126) | def get_tracked_change_authors(doc_xml_path: Path) -> dict[str, int]:
  function _get_authors_from_docx (line 149) | def _get_authors_from_docx(docx_path: Path) -> dict[str, int]:
  function infer_author (line 172) | def infer_author(modified_dir: Path, original_docx: Path, default: str =...

FILE: scientific-skills/pptx/scripts/office/pack.py
  function pack (line 24) | def pack(
  function _run_validation (line 69) | def _run_validation(
  function _condense_xml (line 108) | def _condense_xml(xml_file: Path) -> None:

FILE: scientific-skills/pptx/scripts/office/soffice.py
  function get_soffice_env (line 24) | def get_soffice_env() -> dict:
  function run_soffice (line 35) | def run_soffice(args: list[str], **kwargs) -> subprocess.CompletedProcess:
  function _needs_shim (line 44) | def _needs_shim() -> bool:
  function _ensure_shim (line 53) | def _ensure_shim() -> Path:

FILE: scientific-skills/pptx/scripts/office/unpack.py
  function unpack (line 34) | def unpack(
  function _pretty_print_xml (line 82) | def _pretty_print_xml(xml_file: Path) -> None:
  function _escape_smart_quotes (line 91) | def _escape_smart_quotes(xml_file: Path) -> None:

FILE: scientific-skills/pptx/scripts/office/validate.py
  function main (line 25) | def main():

FILE: scientific-skills/pptx/scripts/office/validators/base.py
  class BaseSchemaValidator (line 12) | class BaseSchemaValidator:
    method __init__ (line 94) | def __init__(self, unpacked_dir, original_file=None, verbose=False):
    method validate (line 109) | def validate(self):
    method repair (line 112) | def repair(self) -> int:
    method repair_whitespace_preservation (line 115) | def repair_whitespace_preservation(self) -> int:
    method validate_xml (line 143) | def validate_xml(self):
    method validate_namespaces (line 170) | def validate_namespaces(self):
    method validate_unique_ids (line 199) | def validate_unique_ids(self):
    method validate_file_references (line 289) | def validate_file_references(self):
    method validate_all_relationship_ids (line 385) | def validate_all_relationship_ids(self):
    method _get_expected_relationship_type (line 469) | def _get_expected_relationship_type(self, element_name):
    method validate_content_types (line 492) | def validate_content_types(self):
    method validate_file_against_xsd (line 598) | def validate_file_against_xsd(self, xml_file, verbose=False):
    method validate_against_xsd (line 636) | def validate_against_xsd(self):
    method _get_schema_path (line 685) | def _get_schema_path(self, xml_file):
    method _clean_ignorable_namespaces (line 703) | def _clean_ignorable_namespaces(self, xml_doc):
    method _remove_ignorable_elements (line 723) | def _remove_ignorable_elements(self, root):
    method _preprocess_for_mc_ignorable (line 742) | def _preprocess_for_mc_ignorable(self, xml_doc):
    method _validate_single_file_xsd (line 750) | def _validate_single_file_xsd(self, xml_file, base_path):
    method _get_original_file_errors (line 787) | def _get_original_file_errors(self, xml_file):
    method _remove_template_tags_from_text_nodes (line 814) | def _remove_template_tags_from_text_nodes(self, xml_doc):

FILE: scientific-skills/pptx/scripts/office/validators/docx.py
  class DOCXSchemaValidator (line 16) | class DOCXSchemaValidator(BaseSchemaValidator):
    method validate (line 24) | def validate(self):
    method validate_whitespace_preservation (line 66) | def validate_whitespace_preservation(self):
    method validate_deletions (line 112) | def validate_deletions(self):
    method count_paragraphs_in_unpacked (line 163) | def count_paragraphs_in_unpacked(self):
    method count_paragraphs_in_original (line 179) | def count_paragraphs_in_original(self):
    method validate_insertions (line 202) | def validate_insertions(self):
    method compare_paragraph_counts (line 243) | def compare_paragraph_counts(self):
    method _parse_id_value (line 251) | def _parse_id_value(self, val: str, base: int = 16) -> int:
    method validate_id_constraints (line 254) | def validate_id_constraints(self):
    method validate_comment_markers (line 298) | def validate_comment_markers(self):
    method repair (line 386) | def repair(self) -> int:
    method repair_durableId (line 391) | def repair_durableId(self) -> int:

FILE: scientific-skills/pptx/scripts/office/validators/pptx.py
  class PPTXSchemaValidator (line 10) | class PPTXSchemaValidator(BaseSchemaValidator):
    method validate (line 25) | def validate(self):
    method validate_uuid_ids (line 62) | def validate_uuid_ids(self):
    method _looks_like_uuid (line 100) | def _looks_like_uuid(self, value):
    method validate_slide_layout_ids (line 104) | def validate_slide_layout_ids(self):
    method validate_no_duplicate_slide_layouts (line 172) | def validate_no_duplicate_slide_layouts(self):
    method validate_notes_slide_references (line 210) | def validate_notes_slide_references(self):

FILE: scientific-skills/pptx/scripts/office/validators/redlining.py
  class RedliningValidator (line 11) | class RedliningValidator:
    method __init__ (line 13) | def __init__(self, unpacked_dir, original_docx, verbose=False, author=...
    method repair (line 22) | def repair(self) -> int:
    method validate (line 25) | def validate(self):
    method _generate_detailed_diff (line 104) | def _generate_detailed_diff(self, original_text, modified_text):
    method _get_git_word_diff (line 127) | def _get_git_word_diff(self, original_text, modified_text):
    method _remove_author_tracked_changes (line 198) | def _remove_author_tracked_changes(self, root):
    method _extract_text_content (line 229) | def _extract_text_content(self, root):

FILE: scientific-skills/pptx/scripts/thumbnail.py
  function main (line 40) | def main():
  function get_slide_info (line 95) | def get_slide_info(pptx_path: Path) -> list[dict]:
  function build_slide_list (line 121) | def build_slide_list(
  function create_hidden_placeholder (line 149) | def create_hidden_placeholder(size: tuple[int, int]) -> Image.Image:
  function convert_to_images (line 158) | def convert_to_images(pptx_path: Path, temp_dir: Path) -> list[Path]:
  function create_grids (line 196) | def create_grids(
  function create_grid (line 225) | def create_grid(

FILE: scientific-skills/primekg/scripts/query_primekg.py
  function _load_kg (line 9) | def _load_kg():
  function search_nodes (line 17) | def search_nodes(name_query: str, node_type: Optional[str] = None) -> Li...
  function get_neighbors (line 46) | def get_neighbors(node_id: Union[str, int], relation_type: Optional[str]...
  function find_paths (line 76) | def find_paths(start_node_id: str, end_node_id: str, max_depth: int = 2)...
  function get_disease_context (line 105) | def get_disease_context(disease_name: str) -> Dict:

FILE: scientific-skills/pubchem-database/scripts/bioactivity_query.py
  function rate_limited_request (line 28) | def rate_limited_request(url: str, method: str = 'GET', **kwargs) -> Opt...
  function get_bioassay_summary (line 55) | def get_bioassay_summary(cid: int) -> Optional[Dict]:
  function get_compound_bioactivities (line 73) | def get_compound_bioactivities(
  function get_assay_description (line 110) | def get_assay_description(aid: int) -> Optional[Dict]:
  function get_assay_targets (line 128) | def get_assay_targets(aid: int) -> List[str]:
  function search_assays_by_target (line 160) | def search_assays_by_target(
  function get_active_compounds_in_assay (line 185) | def get_active_compounds_in_assay(aid: int, max_results: int = 1000) -> ...
  function get_compound_annotations (line 206) | def get_compound_annotations(cid: int, section: Optional[str] = None) ->...
  function get_drug_information (line 229) | def get_drug_information(cid: int) -> Optional[Dict]:
  function get_safety_hazards (line 242) | def get_safety_hazards(cid: int) -> Optional[Dict]:
  function summarize_bioactivities (line 255) | def summarize_bioactivities(cid: int) -> Dict:
  function find_compounds_by_bioactivity (line 291) | def find_compounds_by_bioactivity(
  function main (line 336) | def main():

FILE: scientific-skills/pubchem-database/scripts/compound_search.py
  function search_by_name (line 20) | def search_by_name(name: str, max_results: int = 10) -> List[pcp.Compound]:
  function search_by_smiles (line 39) | def search_by_smiles(smiles: str) -> Optional[pcp.Compound]:
  function get_compound_by_cid (line 57) | def get_compound_by_cid(cid: int) -> Optional[pcp.Compound]:
  function get_compound_properties (line 74) | def get_compound_properties(
  function similarity_search (line 110) | def similarity_search(
  function substructure_search (line 140) | def substructure_search(
  function get_synonyms (line 167) | def get_synonyms(identifier: Union[str, int], namespace: str = 'name') -...
  function batch_search (line 188) | def batch_search(
  function download_structure (line 213) | def download_structure(
  function print_compound_info (line 242) | def print_compound_info(compound: pcp.Compound) -> None:
  function main (line 265) | def main():

FILE: scientific-skills/pufferlib/scripts/env_template.py
  class MyEnvironment (line 14) | class MyEnvironment(PufferEnv):
    method __init__ (line 21) | def __init__(self, buf=None, grid_size=10, max_steps=1000):
    method reset (line 66) | def reset(self):
    method step (line 81) | def step(self, action):
    method _apply_action (line 119) | def _apply_action(self, action):
    method _compute_reward (line 131) | def _compute_reward(self):
    method _is_done (line 145) | def _is_done(self):
    method _get_observation (line 154) | def _get_observation(self):
  class MultiAgentEnvironment (line 165) | class MultiAgentEnvironment(PufferEnv):
    method __init__ (line 172) | def __init__(self, buf=None, num_agents=4, grid_size=10, max_steps=1000):
    method reset (line 196) | def reset(self):
    method step (line 212) | def step(self, actions):
    method _apply_action (line 250) | def _apply_action(self, agent_idx, action):
    method _compute_reward (line 269) | def _compute_reward(self, agent_idx):
    method _is_done (line 276) | def _is_done(self, agent_idx):
    method _get_obs (line 283) | def _get_obs(self, agent_idx):
  function test_environment (line 299) | def test_environment():

FILE: scientific-skills/pufferlib/scripts/train_template.py
  class Policy (line 18) | class Policy(nn.Module):
    method __init__ (line 21) | def __init__(self, observation_space, action_space, hidden_size=256):
    method forward (line 41) | def forward(self, observations):
  function make_env (line 49) | def make_env():
  function create_policy (line 62) | def create_policy(env):
  function train (line 71) | def train(args):
  function main (line 166) | def main():

FILE: scientific-skills/pydeseq2/scripts/run_deseq2_analysis.py
  function load_and_validate_data (line 35) | def load_and_validate_data(counts_path, metadata_path, transpose_counts=...
  function filter_data (line 66) | def filter_data(counts_df, metadata, min_counts=10, condition_col=None):
  function run_deseq2 (line 93) | def run_deseq2(counts_df, metadata, design, n_cpus=1):
  function run_statistical_tests (line 122) | def run_statistical_tests(dds, contrast, alpha=0.05, shrink_lfc=True):
  function save_results (line 155) | def save_results(ds, dds, output_dir, shrink_lfc=True):
  function create_plots (line 202) | def create_plots(ds, output_dir):
  function main (line 268) | def main():

FILE: scientific-skills/pydicom/scripts/anonymize_dicom.py
  function anonymize_dicom (line 40) | def anonymize_dicom(input_path, output_path, patient_id='ANONYMOUS', pat...
  function main (line 91) | def main():

FILE: scientific-skills/pydicom/scripts/dicom_to_image.py
  function apply_windowing (line 25) | def apply_windowing(pixel_array, ds):
  function normalize_to_uint8 (line 34) | def normalize_to_uint8(pixel_array):
  function convert_dicom_to_image (line 52) | def convert_dicom_to_image(input_path, output_path, image_format='PNG',
  function main (line 113) | def main():

FILE: scientific-skills/pydicom/scripts/extract_metadata.py
  function format_value (line 23) | def format_value(value):
  function extract_metadata_text (line 38) | def extract_metadata_text(ds, show_sequences=False):
  function extract_metadata_json (line 102) | def extract_metadata_json(ds):
  function main (line 121) | def main():

FILE: scientific-skills/pymatgen/scripts/phase_diagram_generator.py
  function get_api_key (line 37) | def get_api_key() -> str:
  function generate_phase_diagram (line 48) | def generate_phase_diagram(chemsys: str, args):
  function main (line 169) | def main():

FILE: scientific-skills/pymatgen/scripts/structure_analyzer.py
  function analyze_structure (line 36) | def analyze_structure(struct: Structure, args) -> dict:
  function main (line 194) | def main():

FILE: scientific-skills/pymatgen/scripts/structure_converter.py
  function convert_structure (line 31) | def convert_structure(input_path: Path, output_path: Path = None, output...
  function batch_convert (line 66) | def batch_convert(input_files: List[Path], output_dir: Path, output_form...
  function main (line 87) | def main():

FILE: scientific-skills/pymc/scripts/model_comparison.py
  function compare_models (line 27) | def compare_models(models_dict: Dict[str, az.InferenceData],
  function check_loo_reliability (line 120) | def check_loo_reliability(models_dict: Dict[str, az.InferenceData],
  function plot_model_comparison (line 195) | def plot_model_comparison(comparison, output_path=None, show=True):
  function model_averaging (line 230) | def model_averaging(models_dict: Dict[str, az.InferenceData],
  function cross_validation_comparison (line 291) | def cross_validation_comparison(models_dict: Dict[str, az.InferenceData],

FILE: scientific-skills/pymc/scripts/model_diagnostics.py
  function check_diagnostics (line 23) | def check_diagnostics(idata, var_names=None, ess_threshold=400, rhat_thr...
  function create_diagnostic_report (line 171) | def create_diagnostic_report(idata, var_names=None, output_dir='diagnost...
  function compare_prior_posterior (line 269) | def compare_prior_posterior(idata, prior_idata, var_names=None, output_p...

FILE: scientific-skills/pymoo/scripts/custom_problem_example.py
  class MyBiObjectiveProblem (line 15) | class MyBiObjectiveProblem(ElementwiseProblem):
    method __init__ (line 28) | def __init__(self):
    method _evaluate (line 38) | def _evaluate(self, x, out, *args, **kwargs):
  class ConstrainedProblem (line 50) | class ConstrainedProblem(ElementwiseProblem):
    method __init__ (line 65) | def __init__(self):
    method _evaluate (line 74) | def _evaluate(self, x, out, *args, **kwargs):
  function solve_custom_problem (line 92) | def solve_custom_problem():
  function solve_constrained_problem (line 127) | def solve_constrained_problem():

FILE: scientific-skills/pymoo/scripts/decision_making_example.py
  function run_optimization_for_decision_making (line 17) | def run_optimization_for_decision_making():
  function apply_pseudo_weights (line 39) | def apply_pseudo_weights(result, weights):
  function compare_different_preferences (line 61) | def compare_different_preferences(result):
  function visualize_selected_solutions (line 95) | def visualize_selected_solutions(result, selections):
  function find_extreme_solutions (line 115) | def find_extreme_solutions(result):
  function main (line 135) | def main():

FILE: scientific-skills/pymoo/scripts/many_objective_example.py
  function run_many_objective_optimization (line 16) | def run_many_objective_optimization():

FILE: scientific-skills/pymoo/scripts/multi_objective_example.py
  function run_multi_objective_optimization (line 15) | def run_multi_objective_optimization():

FILE: scientific-skills/pymoo/scripts/single_objective_example.py
  function run_single_objective_optimization (line 18) | def run_single_objective_optimization():

FILE: scientific-skills/pytdc/scripts/benchmark_evaluation.py
  function load_benchmark_group (line 18) | def load_benchmark_group():
  function single_dataset_evaluation (line 43) | def single_dataset_evaluation(group, dataset_name='Caco2_Wang'):
  function multiple_datasets_evaluation (line 102) | def multiple_datasets_evaluation(group):
  function custom_model_template (line 168) | def custom_model_template():
  function multi_seed_statistics (line 221) | def multi_seed_statistics(predictions_dict):
  function leaderboard_submission_guide (line 247) | def leaderboard_submission_guide():
  function main (line 290) | def main():

FILE: scientific-skills/pytdc/scripts/load_and_split_data.py
  function load_single_pred_example (line 18) | def load_single_pred_example():
  function load_multi_pred_example (line 60) | def load_multi_pred_example():
  function evaluation_example (line 123) | def evaluation_example(split):
  function custom_split_example (line 163) | def custom_split_example():
  function main (line 188) | def main():

FILE: scientific-skills/pytdc/scripts/molecular_generation.py
  function load_generation_dataset (line 17) | def load_generation_dataset():
  function single_oracle_example (line 43) | def single_oracle_example():
  function multiple_oracles_example (line 71) | def multiple_oracles_example():
  function batch_evaluation_example (line 118) | def batch_evaluation_example():
  function goal_directed_generation_template (line 156) | def goal_directed_generation_template():
  function distribution_learning_example (line 220) | def distribution_learning_example(train_smiles):
  function available_oracles_info (line 272) | def available_oracles_info():
  function constraint_satisfaction_example (line 309) | def constraint_satisfaction_example():
  function main (line 360) | def main():

FILE: scientific-skills/pytorch-lightning/scripts/quick_trainer_setup.py
  function basic_trainer (line 24) | def basic_trainer():
  function debug_trainer (line 43) | def debug_trainer():
  function production_single_gpu_trainer (line 62) | def production_single_gpu_trainer(
  function multi_gpu_ddp_trainer (line 121) | def multi_gpu_ddp_trainer(
  function large_model_fsdp_trainer (line 183) | def large_model_fsdp_trainer(
  function deepspeed_trainer (line 244) | def deepspeed_trainer(
  function hyperparameter_tuning_trainer (line 299) | def hyperparameter_tuning_trainer(max_epochs=50):
  function overfit_test_trainer (line 321) | def overfit_test_trainer(num_batches=10):
  function time_limited_trainer (line 341) | def time_limited_trainer(
  function reproducible_trainer (line 375) | def reproducible_trainer(seed=42, max_epochs=100):

FILE: scientific-skills/pytorch-lightning/scripts/template_datamodule.py
  class CustomDataset (line 13) | class CustomDataset(Dataset):
    method __init__ (line 20) | def __init__(self, data_path, transform=None):
    method __len__ (line 39) | def __len__(self):
    method __getitem__ (line 43) | def __getitem__(self, idx):
  class TemplateDataModule (line 62) | class TemplateDataModule(L.LightningDataModule):
    method __init__ (line 79) | def __init__(
    method prepare_data (line 98) | def prepare_data(self):
    method setup (line 120) | def setup(self, stage: str = None):
    method _get_train_transforms (line 167) | def _get_train_transforms(self):
    method _get_test_transforms (line 185) | def _get_test_transforms(self):
    method train_dataloader (line 201) | def train_dataloader(self):
    method val_dataloader (line 218) | def val_dataloader(self):
    method test_dataloader (line 234) | def test_dataloader(self):
    method predict_dataloader (line 248) | def predict_dataloader(self):
    method state_dict (line 264) | def state_dict(self):
    method load_state_dict (line 273) | def load_state_dict(self, state_dict):
    method teardown (line 284) | def teardown(self, stage: str = None):

FILE: scientific-skills/pytorch-lightning/scripts/template_lightning_module.py
  class TemplateLightningModule (line 16) | class TemplateLightningModule(L.LightningModule):
    method __init__ (line 26) | def __init__(
    method forward (line 50) | def forward(self, x):
    method training_step (line 62) | def training_step(self, batch, batch_idx):
    method validation_step (line 90) | def validation_step(self, batch, batch_idx):
    method test_step (line 112) | def test_step(self, batch, batch_idx):
    method predict_step (line 134) | def predict_step(self, batch, batch_idx, dataloader_idx=0):
    method configure_optimizers (line 151) | def configure_optimizers(self):
    method on_train_epoch_end (line 187) | def on_train_epoch_end(self):
    method on_validation_epoch_end (line 192) | def on_validation_epoch_end(self):

FILE: scientific-skills/rdkit/scripts/molecular_properties.py
  function calculate_properties (line 25) | def calculate_properties(mol):
  function process_single_molecule (line 92) | def process_single_molecule(smiles):
  function process_file (line 103) | def process_file(input_file, output_file=None):
  function write_csv (line 145) | def write_csv(results, output_file):
  function print_properties (line 160) | def print_properties(props):
  function main (line 205) | def main():

FILE: scientific-skills/rdkit/scripts/similarity_search.py
  function generate_fingerprint (line 35) | def generate_fingerprint(mol, method='morgan', radius=2, n_bits=2048):
  function load_molecules (line 60) | def load_molecules(file_path):
  function similarity_search (line 97) | def similarity_search(query_mol, database, method='morgan', threshold=0.7,
  function write_results (line 157) | def write_results(hits, output_file):
  function print_results (line 176) | def print_results(hits, max_display=20):
  function main (line 198) | def main():

FILE: scientific-skills/rdkit/scripts/substructure_filter.py
  function load_molecules (line 67) | def load_molecules(file_path, keep_props=True):
  function create_pattern_query (line 95) | def create_pattern_query(pattern_string):
  function filter_molecules (line 111) | def filter_molecules(molecules, include_patterns=None, exclude_patterns=...
  function write_molecules (line 191) | def write_molecules(molecules, output_file):
  function write_report (line 213) | def write_report(match_info, output_file):
  function print_summary (line 231) | def print_summary(total, filtered, match_info):
  function main (line 254) | def main():

FILE: scientific-skills/reactome-database/scripts/reactome_query.py
  class ReactomeClient (line 28) | class ReactomeClient:
    method get_version (line 34) | def get_version(self) -> str:
    method query_pathway (line 40) | def query_pathway(self, pathway_id: str) -> Dict:
    method get_pathway_entities (line 46) | def get_pathway_entities(self, pathway_id: str) -> List[Dict]:
    method search_pathways (line 54) | def search_pathways(self, term: str) -> List[Dict]:
    method analyze_genes (line 63) | def analyze_genes(self, gene_list: List[str]) -> Dict:
    method get_analysis_by_token (line 74) | def get_analysis_by_token(self, token: str) -> Dict:
  function print_json (line 81) | def print_json(data):
  function command_version (line 86) | def command_version():
  function command_query (line 93) | def command_query(pathway_id: str):
  function command_entities (line 121) | def command_entities(pathway_id: str):
  function command_search (line 153) | def command_search(term: str):
  function command_analyze (line 176) | def command_analyze(gene_file: str):
  function print_usage (line 236) | def print_usage():
  function main (line 241) | def main():

FILE: scientific-skills/research-lookup/examples.py
  function example_automatic_selection (line 16) | def example_automatic_selection():
  function example_manual_override (line 42) | def example_manual_override():
  function example_batch_queries (line 67) | def example_batch_queries():
  function example_scientific_writing_workflow (line 96) | def example_scientific_writing_workflow():
  function main (line 132) | def main():

FILE: scientific-skills/research-lookup/lookup.py
  function format_response (line 17) | def format_response(result: Dict) -> str:
  function _detect_venue_tier (line 90) | def _detect_venue_tier(url: str) -> Optional[str]:
  function main (line 149) | def main():

FILE: scientific-skills/research-lookup/research_lookup.py
  class ResearchLookup (line 24) | class ResearchLookup:
    method __init__ (line 61) | def __init__(self, force_backend: Optional[str] = None):
    method _select_backend (line 79) | def _select_backend(self, query: str) -> str:
    method _get_chat_client (line 105) | def _get_chat_client(self):
    method _parallel_lookup (line 121) | def _parallel_lookup(self, query: str) -> Dict[str, Any]:
    method _extract_basis_citations (line 168) | def _extract_basis_citations(self, response) -> List[Dict[str, str]]:
    method _perplexity_lookup (line 201) | def _perplexity_lookup(self, query: str) -> Dict[str, Any]:
    method _format_academic_prompt (line 299) | def _format_academic_prompt(self, query: str) -> str:
    method _extract_api_citations (line 328) | def _extract_api_citations(self, response: Dict[str, Any], choice: Dic...
    method _extract_citations_from_text (line 370) | def _extract_citations_from_text(self, text: str) -> List[Dict[str, st...
    method lookup (line 408) | def lookup(self, query: str) -> Dict[str, Any]:
    method batch_lookup (line 422) | def batch_lookup(self, queries: List[str], delay: float = 1.0) -> List...
  function main (line 438) | def main():

FILE: scientific-skills/research-lookup/scripts/research_lookup.py
  class ResearchLookup (line 24) | class ResearchLookup:
    method __init__ (line 61) | def __init__(self, force_backend: Optional[str] = None):
    method _select_backend (line 79) | def _select_backend(self, query: str) -> str:
    method _get_chat_client (line 105) | def _get_chat_client(self):
    method _parallel_lookup (line 121) | def _parallel_lookup(self, query: str) -> Dict[str, Any]:
    method _extract_basis_citations (line 168) | def _extract_basis_citations(self, response) -> List[Dict[str, str]]:
    method _perplexity_lookup (line 201) | def _perplexity_lookup(self, query: str) -> Dict[str, Any]:
    method _format_academic_prompt (line 299) | def _format_academic_prompt(self, query: str) -> str:
    method _extract_api_citations (line 328) | def _extract_api_citations(self, response: Dict[str, Any], choice: Dic...
    method _extract_citations_from_text (line 370) | def _extract_citations_from_text(self, text: str) -> List[Dict[str, st...
    method lookup (line 408) | def lookup(self, query: str) -> Dict[str, Any]:
    method batch_lookup (line 422) | def batch_lookup(self, queries: List[str], delay: float = 1.0) -> List...
  function main (line 438) | def main():

FILE: scientific-skills/scanpy/scripts/qc_analysis.py
  function calculate_qc_metrics (line 17) | def calculate_qc_metrics(adata, mt_threshold=5, min_genes=200, min_cells...
  function generate_qc_plots (line 54) | def generate_qc_plots(adata, output_prefix='qc'):
  function filter_data (line 86) | def filter_data(adata, mt_threshold=5, min_genes=200, max_genes=None,
  function main (line 138) | def main():

FILE: scientific-skills/scholar-evaluation/scripts/calculate_scores.py
  function load_scores (line 47) | def load_scores(filepath: Path) -> Dict[str, float]:
  function load_weights (line 70) | def load_weights(filepath: Optional[Path] = None) -> Dict[str, float]:
  function calculate_weighted_average (line 96) | def calculate_weighted_average(scores: Dict[str, float], weights: Dict[s...
  function get_quality_level (line 115) | def get_quality_level(score: float) -> tuple:
  function generate_bar_chart (line 123) | def generate_bar_chart(scores: Dict[str, float], max_width: int = 50) ->...
  function identify_strengths_weaknesses (line 137) | def identify_strengths_weaknesses(scores: Dict[str, float]) -> tuple:
  function generate_report (line 147) | def generate_report(scores: Dict[str, float], weights: Dict[str, float],
  function interactive_mode (line 245) | def interactive_mode():
  function main (line 305) | def main():

FILE: scientific-skills/scientific-schematics/scripts/generate_schematic.py
  function main (line 29) | def main():

FILE: scientific-skills/scientific-schematics/scripts/generate_schematic_ai.py
  function _load_env_file (line 37) | def _load_env_file():
  class ScientificSchematicGenerator (line 79) | class ScientificSchematicGenerator:
    method __init__ (line 146) | def __init__(self, api_key: Optional[str] = None, verbose: bool = False):
    method _log (line 180) | def _log(self, message: str):
    method _make_request (line 185) | def _make_request(self, model: str, messages: List[Dict[str, Any]],
    method _extract_image_from_response (line 241) | def _extract_image_from_response(self, response: Dict[str, Any]) -> Op...
    method _image_to_base64 (line 322) | def _image_to_base64(self, image_path: str) -> str:
    method generate_image (line 348) | def generate_image(self, prompt: str) -> Optional[bytes]:
    method review_image (line 426) | def review_image(self, image_path: str, original_prompt: str,
    method improve_prompt (line 580) | def improve_prompt(self, original_prompt: str, critique: str,
    method generate_iterative (line 604) | def generate_iterative(self, user_prompt: str, output_path: str,
  function main (line 753) | def main():

FILE: scientific-skills/scientific-slides/scripts/generate_slide_image.py
  function main (line 32) | def main():

FILE: scientific-skills/scientific-slides/scripts/generate_slide_image_ai.py
  function _load_env_file (line 49) | def _load_env_file():
  class SlideImageGenerator (line 87) | class SlideImageGenerator:
    method __init__ (line 170) | def __init__(self, api_key: Optional[str] = None, verbose: bool = False):
    method _log (line 201) | def _log(self, message: str):
    method _make_request (line 206) | def _make_request(self, model: str, messages: List[Dict[str, Any]],
    method _extract_image_from_response (line 250) | def _extract_image_from_response(self, response: Dict[str, Any]) -> Op...
    method _image_to_base64 (line 308) | def _image_to_base64(self, image_path: str) -> str:
    method generate_image (line 325) | def generate_image(self, prompt: str, attachments: Optional[List[str]]...
    method review_image (line 404) | def review_image(self, image_path: str, original_prompt: str,
    method improve_prompt (line 518) | def improve_prompt(self, original_prompt: str, critique: str,
    method generate_slide (line 532) | def generate_slide(self, user_prompt: str, output_path: str,
  function main (line 682) | def main():

FILE: scientific-skills/scientific-slides/scripts/pdf_to_images.py
  class PDFToImagesConverter (line 25) | class PDFToImagesConverter:
    method __init__ (line 28) | def __init__(
    method convert (line 48) | def convert(self) -> List[Path]:
    method _convert_with_pymupdf (line 67) | def _convert_with_pymupdf(self) -> List[Path]:
  function main (line 108) | def main():

FILE: scientific-skills/scientific-slides/scripts/slides_to_pdf.py
  function get_image_files (line 31) | def get_image_files(paths: List[str]) -> List[Path]:
  function combine_images_to_pdf (line 74) | def combine_images_to_pdf(image_paths: List[Path], output_path: Path,
  function main (line 162) | def main():

FILE: scientific-skills/scientific-slides/scripts/validate_presentation.py
  class PresentationValidator (line 34) | class PresentationValidator:
    method __init__ (line 48) | def __init__(self, filepath: str, duration: Optional[int] = None):
    method validate (line 56) | def validate(self) -> Dict:
    method _check_file_size (line 82) | def _check_file_size(self):
    method _validate_pdf (line 98) | def _validate_pdf(self):
    method _validate_pptx (line 147) | def _validate_pptx(self):
    method _check_pptx_content (line 181) | def _check_pptx_content(self, prs):
    method _validate_latex (line 220) | def _validate_latex(self):
    method _try_compile_latex (line 243) | def _try_compile_latex(self) -> bool:
    method _check_slide_count (line 257) | def _check_slide_count(self, num_slides: int):
    method _format_results (line 291) | def _format_results(self) -> Dict:
  function print_results (line 303) | def print_results(results: Dict):
  function main (line 340) | def main():

FILE: scientific-skills/scientific-visualization/assets/color_palettes.py
  function apply_palette (line 111) | def apply_palette(palette_name='okabe_ito'):
  function get_palette (line 156) | def get_palette(palette_name='okabe_ito'):

FILE: scientific-skills/scientific-visualization/scripts/figure_export.py
  function save_publication_figure (line 14) | def save_publication_figure(
  function save_for_journal (line 98) | def save_for_journal(
  function check_figure_size (line 187) | def check_figure_size(fig: plt.Figure, journal: str = 'nature') -> dict:
  function verify_font_embedding (line 281) | def verify_font_embedding(pdf_path: Union[str, Path]) -> bool:

FILE: scientific-skills/scientific-visualization/scripts/style_presets.py
  function get_base_style (line 35) | def get_base_style() -> Dict[str, Any]:
  function apply_publication_style (line 111) | def apply_publication_style(style_name: str = 'default') -> None:
  function set_color_palette (line 195) | def set_color_palette(palette_name: str = 'okabe_ito') -> None:
  function configure_for_journal (line 234) | def configure_for_journal(journal: str, figure_width: str = 'single') ->...
  function create_style_template (line 303) | def create_style_template(output_file: str = 'publication.mplstyle') -> ...
  function show_color_palettes (line 335) | def show_color_palettes() -> None:
  function reset_to_default (line 367) | def reset_to_default() -> None:

FILE: scientific-skills/scikit-learn/scripts/classification_pipeline.py
  function create_preprocessing_pipeline (line 23) | def create_preprocessing_pipeline(numeric_features, categorical_features):
  function train_and_evaluate_model (line 62) | def train_and_evaluate_model(X, y, numeric_features, categorical_features,

FILE: scientific-skills/scikit-learn/scripts/clustering_analysis.py
  function preprocess_for_clustering (line 19) | def preprocess_for_clustering(X, scale=True, pca_components=None):
  function find_optimal_k_kmeans (line 51) | def find_optimal_k_kmeans(X, k_range=range(2, 11)):
  function compare_clustering_algorithms (line 111) | def compare_clustering_algorithms(X, n_clusters=3):
  function visualize_clusters (line 201) | def visualize_clusters(X, results, true_labels=None):
  function complete_clustering_analysis (line 277) | def complete_clustering_analysis(X, true_labels=None, scale=True,

FILE: scientific-skills/scvelo/scripts/rna_velocity_workflow.py
  function run_velocity_analysis (line 21) | def run_velocity_analysis(
  function load_from_loom (line 179) | def load_from_loom(loom_path, processed_h5ad=None):

FILE: scientific-skills/simpy/scripts/basic_simulation_template.py
  class SimulationConfig (line 13) | class SimulationConfig:
    method __init__ (line 16) | def __init__(self):
  class SimulationStats (line 26) | class SimulationStats:
    method __init__ (line 29) | def __init__(self):
    method record_arrival (line 36) | def record_arrival(self, time):
    method record_service_start (line 39) | def record_service_start(self, time):
    method record_departure (line 42) | def record_departure(self, time):
    method record_wait_time (line 45) | def record_wait_time(self, wait_time):
    method record_service_time (line 48) | def record_service_time(self, service_time):
    method report (line 51) | def report(self):
  function customer_process (line 72) | def customer_process(env, name, resource, stats, config):
  function customer_generator (line 114) | def customer_generator(env, resource, stats, config):
  function run_simulation (line 137) | def run_simulation(config):
  function main (line 174) | def main():

FILE: scientific-skills/simpy/scripts/resource_monitor.py
  class ResourceMonitor (line 15) | class ResourceMonitor:
    method __init__ (line 26) | def __init__(self, env: simpy.Environment, resource: simpy.Resource, n...
    method _patch_resource (line 49) | def _patch_resource(self):
    method average_queue_length (line 100) | def average_queue_length(self) -> float:
    method average_utilization (line 117) | def average_utilization(self) -> float:
    method average_wait_time (line 134) | def average_wait_time(self) -> float:
    method max_queue_length (line 138) | def max_queue_length(self) -> int:
    method report (line 142) | def report(self):
    method export_csv (line 170) | def export_csv(self, filename: str):
  class MultiResourceMonitor (line 194) | class MultiResourceMonitor:
    method __init__ (line 197) | def __init__(self, env: simpy.Environment):
    method add_resource (line 207) | def add_resource(self, resource: simpy.Resource, name: str):
    method report_all (line 219) | def report_all(self):
    method summary (line 224) | def summary(self):
  class ContainerMonitor (line 240) | class ContainerMonitor:
    method __init__ (line 243) | def __init__(self, env: simpy.Environment, container: simpy.Container,...
    method _patch_container (line 259) | def _patch_container(self):
    method average_level (line 285) | def average_level(self) -> float:
    method report (line 302) | def report(self):
  function example_process (line 322) | def example_process(env, name, resource, duration):

FILE: scientific-skills/stable-baselines3/scripts/custom_env_template.py
  class CustomEnv (line 17) | class CustomEnv(gym.Env):
    method __init__ (line 32) | def __init__(self, grid_size=5, render_mode=None):
    method reset (line 78) | def reset(self, seed=None, options=None):
    method step (line 106) | def step(self, action):
    method _get_obs (line 154) | def _get_obs(self):
    method _get_info (line 170) | def _get_info(self):
    method render (line 185) | def render(self):
    method close (line 216) | def close(self):
  function validate_environment (line 232) | def validate_environment():
  function test_environment (line 244) | def test_environment():
  function train_on_custom_env (line 275) | def train_on_custom_env():

FILE: scientific-skills/stable-baselines3/scripts/evaluate_agent.py
  function evaluate_agent (line 19) | def evaluate_agent(
  function watch_agent (line 97) | def watch_agent(
  function compare_models (line 162) | def compare_models(

FILE: scientific-skills/stable-baselines3/scripts/train_rl_agent.py
  function train_agent (line 24) | def train_agent(

FILE: scientific-skills/statistical-analysis/scripts/assumption_checks.py
  function check_normality (line 20) | def check_normality(
  function check_normality_per_group (line 95) | def check_normality_per_group(
  function check_homogeneity_of_variance (line 156) | def check_homogeneity_of_variance(
  function check_linearity (line 236) | def check_linearity(
  function detect_outliers (line 308) | def detect_outliers(
  function comprehensive_assumption_check (line 409) | def comprehensive_assumption_check(

FILE: scientific-skills/string-database/scripts/string_api.py
  function string_map_ids (line 24) | def string_map_ids(identifiers: Union[str, List[str]],
  function string_network (line 72) | def string_network(identifiers: Union[str, List[str]],
  function string_network_image (line 125) | def string_network_image(identifiers: Union[str, List[str]],
  function string_interaction_partners (line 174) | def string_interaction_partners(identifiers: Union[str, List[str]],
  function string_enrichment (line 218) | def string_enrichment(identifiers: Union[str, List[str]],
  function string_ppi_enrichment (line 257) | def string_ppi_enrichment(identifiers: Union[str, List[str]],
  function string_homology (line 299) | def string_homology(identifiers: Union[str, List[str]],
  function string_version (line 337) | def string_version() -> str:

FILE: scientific-skills/timesfm-forecasting/examples/anomaly-detection/detect_anomalies.py
  function detect_context_anomalies (line 50) | def detect_context_anomalies(
  function build_synthetic_future (line 98) | def build_synthetic_future(
  function detect_forecast_anomalies (line 121) | def detect_forecast_anomalies(
  function plot_results (line 172) | def plot_results(
  function main (line 391) | def main() -> None:

FILE: scientific-skills/timesfm-forecasting/examples/covariates-forecasting/demo_covariates.py
  function generate_sales_data (line 49) | def generate_sales_data() -> dict:
  function create_visualization (line 132) | def create_visualization(data: dict) -> None:
  function demonstrate_api (line 405) | def demonstrate_api() -> None:
  function explain_xreg_modes (line 431) | def explain_xreg_modes() -> None:
  function main (line 450) | def main() -> None:

FILE: scientific-skills/timesfm-forecasting/examples/global-temperature/generate_animation_data.py
  function main (line 30) | def main() -> None:

FILE: scientific-skills/timesfm-forecasting/examples/global-temperature/generate_gif.py
  function create_frame (line 26) | def create_frame(
  function main (line 157) | def main() -> None:

FILE: scientific-skills/timesfm-forecasting/examples/global-temperature/generate_html.py
  function main (line 521) | def main() -> None:

FILE: scientific-skills/timesfm-forecasting/examples/global-temperature/visualize_forecast.py
  function main (line 30) | def main() -> None:

FILE: scientific-skills/timesfm-forecasting/scripts/check_system.py
  class CheckResult (line 74) | class CheckResult:
    method icon (line 81) | def icon(self) -> str:
    method __str__ (line 84) | def __str__(self) -> str:
  class SystemReport (line 89) | class SystemReport:
    method passed (line 98) | def passed(self) -> bool:
    method to_dict (line 101) | def to_dict(self) -> dict[str, Any]:
  function _get_total_ram_gb (line 126) | def _get_total_ram_gb() -> float:
  function _get_available_ram_gb (line 173) | def _get_available_ram_gb() -> float:
  function check_ram (line 222) | def check_ram(profile: dict[str, Any]) -> CheckResult:
  function check_gpu (line 262) | def check_gpu() -> CheckResult:
  function check_disk (line 303) | def check_disk(profile: dict[str, Any]) -> CheckResult:
  function check_python (line 336) | def check_python() -> CheckResult:
  function check_package (line 357) | def check_package(pkg_name: str, import_name: str | None = None) -> Chec...
  function recommend_batch_size (line 383) | def recommend_batch_size(report: SystemReport) -> int:
  function run_checks (line 432) | def run_checks(model_version: str = "v2.5") -> SystemReport:
  function print_report (line 474) | def print_report(report: SystemReport) -> None:
  function main (line 491) | def main() -> None:

FILE: scientific-skills/timesfm-forecasting/scripts/forecast_csv.py
  function run_preflight (line 32) | def run_preflight() -> dict:
  function load_model (line 49) | def load_model(batch_size: int = 32):
  function load_csv (line 78) | def load_csv(
  function forecast_series (line 118) | def forecast_series(
  function write_csv_output (line 144) | def write_csv_output(
  function write_json_output (line 187) | def write_json_output(results: dict[str, dict], output_path: str) -> None:
  function main (line 194) | def main() -> None:

FILE: scientific-skills/torch-geometric/scripts/benchmark_model.py
  class GCN (line 24) | class GCN(torch.nn.Module):
    method __init__ (line 25) | def __init__(self, num_features, hidden_channels, num_classes, dropout...
    method forward (line 31) | def forward(self, x, edge_index, batch=None):
  class GAT (line 41) | class GAT(torch.nn.Module):
    method __init__ (line 42) | def __init__(self, num_features, hidden_channels, num_classes, heads=8...
    method forward (line 49) | def forward(self, x, edge_index, batch=None):
  class GraphSAGE (line 59) | class GraphSAGE(torch.nn.Module):
    method __init__ (line 60) | def __init__(self, num_features, hidden_channels, num_classes, dropout...
    method forward (line 66) | def forward(self, x, edge_index, batch=None):
  function train_node_classification (line 83) | def train_node_classification(model, data, optimizer):
  function test_node_classification (line 95) | def test_node_classification(model, data):
  function train_graph_classification (line 109) | def train_graph_classification(model, loader, optimizer, device):
  function test_graph_classification (line 127) | def test_graph_classification(model, loader, device):
  function benchmark_node_classification (line 141) | def benchmark_node_classification(model_name, dataset_name, epochs, lr, ...
  function benchmark_graph_classification (line 180) | def benchmark_graph_classification(model_name, dataset_name, epochs, lr,...
  function run_benchmark (line 221) | def run_benchmark(args):
  function main (line 289) | def main():

FILE: scientific-skills/torch-geometric/scripts/create_gnn_template.py
  function generate_template (line 452) | def generate_template(model_type: str, task: str, output_path: str):
  function list_templates (line 476) | def list_templates():
  function main (line 488) | def main():

FILE: scientific-skills/torch-geometric/scripts/visualize_graph.py
  function visualize_data (line 27) | def visualize_data(
  function is_undirected (line 150) | def is_undirected(edge_index):
  function plot_degree_distribution (line 163) | def plot_degree_distribution(data, output_path: Optional[str] = None):
  function plot_graph_statistics (line 198) | def plot_graph_statistics(data, output_path: Optional[str] = None):
  function main (line 248) | def main():

FILE: scientific-skills/treatment-plans/scripts/check_completeness.py
  function read_file (line 42) | def read_file(filepath: Path) -> str:
  function check_sections (line 55) | def check_sections(content: str) -> Tuple[List[bool], List[str]]:
  function check_smart_goals (line 73) | def check_smart_goals(content: str) -> Tuple[bool, List[str]]:
  function check_hipaa_notice (line 95) | def check_hipaa_notice(content: str) -> bool:
  function check_provider_signature (line 101) | def check_provider_signature(content: str) -> bool:
  function check_placeholders_remaining (line 107) | def check_placeholders_remaining(content: str) -> Tuple[int, List[str]]:
  function display_results (line 127) | def display_results(filepath: Path, checklist: List[bool], missing: List...
  function main (line 247) | def main():

FILE: scientific-skills/treatment-plans/scripts/generate_template.py
  function get_templates_dir (line 49) | def get_templates_dir():
  function list_templates (line 57) | def list_templates():
  function interactive_selection (line 72) | def interactive_selection():
  function get_output_filename (line 95) | def get_output_filename(template_key, custom_name=None):
  function copy_template (line 108) | def copy_template(template_key, output_path):
  function display_success (line 127) | def display_success(output_path, template_key):
  function main (line 161) | def main():

FILE: scientific-skills/treatment-plans/scripts/timeline_generator.py
  function extract_timeline_info (line 24) | def extract_timeline_info(content: str) -> Dict[str, List[Tuple[str, str...
  function parse_timeframe_to_days (line 75) | def parse_timeframe_to_days(timeframe: str) -> Tuple[int, int]:
  function create_text_timeline (line 117) | def create_text_timeline(timeline_data: Dict, output_file: Path = None):
  function create_visual_timeline (line 161) | def create_visual_timeline(timeline_data: Dict, output_file: Path, start...
  function main (line 267) | def main():

FILE: scientific-skills/uniprot-database/scripts/uniprot_client.py
  function search_proteins (line 35) | def search_proteins(query: str, format: str = "json",
  function get_protein (line 70) | def get_protein(accession: str, format: str = "json") -> str:
  function batch_retrieve (line 92) | def batch_retrieve(accessions: List[str], format: str = "json",
  function stream_results (line 109) | def stream_results(query: str, format: str = "fasta",
  function map_ids (line 142) | def map_ids(ids: List[str], from_db: str, to_db: str,
  function get_available_fields (line 203) | def get_available_fields() -> List[Dict]:
  function get_id_mapping_databases (line 218) | def get_id_mapping_databases() -> Dict:
  function main (line 233) | def main():

FILE: scientific-skills/uspto-database/scripts/patent_search.py
  class PatentSearchClient (line 24) | class PatentSearchClient:
    method __init__ (line 29) | def __init__(self, api_key: Optional[str] = None):
    method _request (line 45) | def _request(self, endpoint: str, query: Dict, fields: Optional[List[s...
    method search_patents (line 75) | def search_patents(self, query: Dict, fields: Optional[List[str]] = None,
    method get_patent (line 116) | def get_patent(self, patent_number: str) -> Optional[Dict]:
    method search_by_inventor (line 142) | def search_by_inventor(self, inventor_name: str, **kwargs) -> Dict:
    method search_by_assignee (line 156) | def search_by_assignee(self, assignee_name: str, **kwargs) -> Dict:
    method search_by_classification (line 170) | def search_by_classification(self, cpc_code: str, **kwargs) -> Dict:
    method search_by_date_range (line 184) | def search_by_date_range(self, start_date: str, end_date: str, **kwarg...
    method advanced_search (line 204) | def advanced_search(self, keywords: List[str], assignee: Optional[str]...
  function main (line 252) | def main():

FILE: scientific-skills/uspto-database/scripts/peds_client.py
  class PEDSHelper (line 29) | class PEDSHelper:
    method __init__ (line 32) | def __init__(self):
    method get_application (line 38) | def get_application(self, application_number: str) -> Optional[Dict]:
    method get_patent (line 61) | def get_patent(self, patent_number: str) -> Optional[Dict]:
    method get_transaction_history (line 78) | def get_transaction_history(self, application_number: str) -> List[Dict]:
    method get_office_actions (line 93) | def get_office_actions(self, application_number: str) -> List[Dict]:
    method get_status_summary (line 115) | def get_status_summary(self, application_number: str) -> Dict[str, Any]:
    method analyze_prosecution (line 155) | def analyze_prosecution(self, application_number: str) -> Dict[str, Any]:
    method _format_application_data (line 207) | def _format_application_data(self, raw_data: Dict) -> Dict:
  function main (line 214) | def main():

FILE: scientific-skills/uspto-database/scripts/trademark_client.py
  class TrademarkClient (line 23) | class TrademarkClient:
    method __init__ (line 29) | def __init__(self, api_key: Optional[str] = None):
    method get_trademark_by_serial (line 42) | def get_trademark_by_serial(self, serial_number: str) -> Optional[Dict]:
    method get_trademark_by_registration (line 63) | def get_trademark_by_registration(self, registration_number: str) -> O...
    method get_trademark_status (line 84) | def get_trademark_status(self, serial_or_registration: str) -> Dict[st...
    method get_goods_and_services (line 123) | def get_goods_and_services(self, serial_or_registration: str) -> List[...
    method get_owner_info (line 143) | def get_owner_info(self, serial_or_registration: str) -> List[Dict]:
    method get_prosecution_history (line 163) | def get_prosecution_history(self, serial_or_registration: str) -> List...
    method check_trademark_health (line 183) | def check_trademark_health(self, serial_or_registration: str) -> Dict[...
  function main (line 226) | def main():