instruction stringclasses 100
values | code stringlengths 78 193k | response stringlengths 259 170k | file stringlengths 59 203 |
|---|---|---|---|
Generate missing documentation strings | #!/usr/bin/env python3
import requests
import time
import json
import argparse
from typing import Dict, List, Optional, Any
class EnsemblAPIClient:
def __init__(self, server: str = "https://rest.ensembl.org", rate_limit: int = 15):
self.server = server
self.rate_limit = rate_limit
self.r... | --- +++ @@ -1,4 +1,13 @@ #!/usr/bin/env python3
+"""
+Ensembl REST API Query Script
+Reusable functions for common Ensembl database queries with built-in rate limiting and error handling.
+
+Usage:
+ python ensembl_query.py --gene BRCA2 --species human
+ python ensembl_query.py --variant rs699 --species human
+ ... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/ensembl-database/scripts/ensembl_query.py |
Add docstrings to my Python code | #!/usr/bin/env python3
import argparse
import torch
import torch.nn as nn
import pufferlib
from pufferlib import PuffeRL
from pufferlib.pytorch import layer_init
class Policy(nn.Module):
def __init__(self, observation_space, action_space, hidden_size=256):
super().__init__()
self.observation_sp... | --- +++ @@ -1,4 +1,11 @@ #!/usr/bin/env python3
+"""
+PufferLib Training Template
+
+This template provides a complete training script for reinforcement learning
+with PufferLib. Customize the environment, policy, and training configuration
+as needed for your use case.
+"""
import argparse
import torch
@@ -9,6 +16... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/pufferlib/scripts/train_template.py |
Generate docstrings with examples | #!/usr/bin/env python3
import numpy as np
import pufferlib
from pufferlib import PufferEnv
class MyEnvironment(PufferEnv):
def __init__(self, buf=None, grid_size=10, max_steps=1000):
super().__init__(buf)
self.grid_size = grid_size
self.max_steps = max_steps
# Define observatio... | --- +++ @@ -1,4 +1,10 @@ #!/usr/bin/env python3
+"""
+PufferLib Environment Template
+
+This template provides a starting point for creating custom PufferEnv environments.
+Customize the observation space, action space, and environment logic for your task.
+"""
import numpy as np
import pufferlib
@@ -6,8 +12,21 @@ ... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/pufferlib/scripts/env_template.py |
Add docstrings that explain purpose and usage | #!/usr/bin/env python3
import sys
import json
import time
from typing import Dict, List, Optional
try:
import requests
except ImportError:
print("Error: requests is not installed. Install it with: pip install requests")
sys.exit(1)
BASE_URL = "https://pubchem.ncbi.nlm.nih.gov/rest/pug"
PUG_VIEW_URL = "h... | --- +++ @@ -1,4 +1,10 @@ #!/usr/bin/env python3
+"""
+PubChem Bioactivity Data Retrieval
+
+This script provides functions for retrieving biological activity data
+from PubChem for compounds and assays.
+"""
import sys
import json
@@ -20,6 +26,17 @@
def rate_limited_request(url: str, method: str = 'GET', **kwar... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/pubchem-database/scripts/bioactivity_query.py |
Add docstrings for production code | import pandas as pd
import os
import json
from typing import List, Dict, Optional, Union
# Default data path
DATA_PATH = "/mnt/c/Users/eamon/Documents/Data/PrimeKG/kg.csv"
def _load_kg():
if not os.path.exists(DATA_PATH):
raise FileNotFoundError(f"PrimeKG data not found at {DATA_PATH}. Please ensure the f... | --- +++ @@ -7,6 +7,7 @@ DATA_PATH = "/mnt/c/Users/eamon/Documents/Data/PrimeKG/kg.csv"
def _load_kg():
+ """Internal helper to load the KG efficiently."""
if not os.path.exists(DATA_PATH):
raise FileNotFoundError(f"PrimeKG data not found at {DATA_PATH}. Please ensure the file is downloaded.")
#... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/primekg/scripts/query_primekg.py |
Improve documentation using docstrings |
import arviz as az
import numpy as np
import matplotlib.pyplot as plt
from pathlib import Path
def check_diagnostics(idata, var_names=None, ess_threshold=400, rhat_threshold=1.01):
print("="*70)
print(" " * 20 + "MCMC DIAGNOSTICS REPORT")
print("="*70)
# Get summary statistics
summary = az.summa... | --- +++ @@ -1,3 +1,18 @@+"""
+PyMC Model Diagnostics Script
+
+Comprehensive diagnostic checks for PyMC models.
+Run this after sampling to validate results before interpretation.
+
+Usage:
+ from scripts.model_diagnostics import check_diagnostics, create_diagnostic_report
+
+ # Quick check
+ check_diagnostics... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/pymc/scripts/model_diagnostics.py |
Write docstrings for backend logic |
import arviz as az
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from typing import Dict
def compare_models(models_dict: Dict[str, az.InferenceData],
ic='loo',
scale='deviance',
verbose=True):
if verbose:
print("="*70)
... | --- +++ @@ -1,3 +1,21 @@+"""
+PyMC Model Comparison Script
+
+Utilities for comparing multiple Bayesian models using information criteria
+and cross-validation metrics.
+
+Usage:
+ from scripts.model_comparison import compare_models, plot_model_comparison
+
+ # Compare multiple models
+ comparison = compare_mo... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/pymc/scripts/model_comparison.py |
Create Google-style docstrings for my code |
import os
import time
import requests
from typing import Optional, Dict, Any, List
from functools import lru_cache
class FREDQuery:
BASE_URL = "https://api.stlouisfed.org/fred"
GEOFRED_URL = "https://api.stlouisfed.org/geofred"
def __init__(
self,
api_key: Optional[str] = None,
... | --- +++ @@ -1,3 +1,8 @@+"""
+FRED API Query Module
+
+Provides a unified interface to query the Federal Reserve Economic Data (FRED) API.
+"""
import os
import time
@@ -7,6 +12,14 @@
class FREDQuery:
+ """
+ Client for querying the FRED API.
+
+ Example:
+ >>> fred = FREDQuery(api_key="your_key"... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/fred-economic-data/scripts/fred_query.py |
Add docstrings that explain logic | #!/usr/bin/env python3
import argparse
import sys
from pathlib import Path
try:
import pydicom
import numpy as np
from PIL import Image
except ImportError as e:
print(f"Error: Required package not installed: {e}")
print("Install with: pip install pydicom pillow numpy")
sys.exit(1)
def apply_... | --- +++ @@ -1,4 +1,12 @@ #!/usr/bin/env python3
+"""
+Convert DICOM files to common image formats (PNG, JPEG, TIFF).
+
+Usage:
+ python dicom_to_image.py input.dcm output.png
+ python dicom_to_image.py input.dcm output.jpg --format JPEG
+ python dicom_to_image.py input.dcm output.tiff --apply-windowing
+"""
... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/pydicom/scripts/dicom_to_image.py |
Write reusable docstrings | #!/usr/bin/env python3
import argparse
import json
import sys
import time
import urllib.parse
import urllib.request
from typing import Optional, List, Dict, Any
def read_gene_list(filepath: str) -> List[str]:
try:
with open(filepath, 'r') as f:
genes = [line.strip() for line in f if line.stri... | --- +++ @@ -1,4 +1,10 @@ #!/usr/bin/env python3
+"""
+Batch gene lookup using NCBI APIs.
+
+This script efficiently processes multiple gene queries with proper
+rate limiting and error handling.
+"""
import argparse
import json
@@ -10,6 +16,15 @@
def read_gene_list(filepath: str) -> List[str]:
+ """
+ Rea... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/gene-database/scripts/batch_gene_lookup.py |
Can you add docstrings to this Python file? | #!/usr/bin/env python3
import os
import sys
from pathlib import Path
from datetime import datetime
import json
def detect_file_type(filepath):
file_path = Path(filepath)
extension = file_path.suffix.lower()
name = file_path.name.lower()
# Map extensions to categories and reference files
extensio... | --- +++ @@ -1,4 +1,8 @@ #!/usr/bin/env python3
+"""
+Exploratory Data Analysis Analyzer
+Analyzes scientific data files and generates comprehensive markdown reports
+"""
import os
import sys
@@ -8,6 +12,12 @@
def detect_file_type(filepath):
+ """
+ Detect the file type based on extension and content.
+
+ ... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/exploratory-data-analysis/scripts/eda_analyzer.py |
Create documentation for each function signature | #!/usr/bin/env python3
import argparse
import sys
from pathlib import Path
try:
import pydicom
except ImportError:
print("Error: pydicom is not installed. Install it with: pip install pydicom")
sys.exit(1)
# Tags commonly containing PHI (Protected Health Information)
PHI_TAGS = [
'PatientName', 'Pat... | --- +++ @@ -1,4 +1,11 @@ #!/usr/bin/env python3
+"""
+Anonymize DICOM files by removing or replacing Protected Health Information (PHI).
+
+Usage:
+ python anonymize_dicom.py input.dcm output.dcm
+ python anonymize_dicom.py input.dcm output.dcm --patient-id ANON001
+"""
import argparse
import sys
@@ -31,6 +38... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/pydicom/scripts/anonymize_dicom.py |
Write clean docstrings for readability | #!/usr/bin/env python3
import argparse
import sys
from pathlib import Path
try:
from ete3 import Tree
except ImportError:
print("Error: ete3 not installed. Install with: pip install ete3")
sys.exit(1)
def load_tree(tree_file, format_num=0):
try:
return Tree(str(tree_file), format=format_num)... | --- +++ @@ -1,4 +1,14 @@ #!/usr/bin/env python3
+"""
+Tree operations helper script for common ETE toolkit tasks.
+
+Provides command-line interface for basic tree operations like:
+- Format conversion
+- Rooting (outgroup, midpoint)
+- Pruning
+- Basic statistics
+- ASCII visualization
+"""
import argparse
import ... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/etetoolkit/scripts/tree_operations.py |
Add docstrings to make code maintainable | #!/usr/bin/env python3
import argparse
import scanpy as sc
import matplotlib.pyplot as plt
def calculate_qc_metrics(adata, mt_threshold=5, min_genes=200, min_cells=3):
# Identify mitochondrial genes (assumes gene names follow standard conventions)
adata.var['mt'] = adata.var_names.str.startswith(('MT-', 'mt-... | --- +++ @@ -1,4 +1,13 @@ #!/usr/bin/env python3
+"""
+Quality Control Analysis Script for Scanpy
+
+Performs comprehensive quality control on single-cell RNA-seq data,
+including calculating metrics, generating QC plots, and filtering cells.
+
+Usage:
+ python qc_analysis.py <input_file> [--output <output_file>]
+""... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/scanpy/scripts/qc_analysis.py |
Add docstrings that explain inputs and outputs | #!/usr/bin/env python3
import argparse
import sys
import json
from pathlib import Path
try:
import pydicom
except ImportError:
print("Error: pydicom is not installed. Install it with: pip install pydicom")
sys.exit(1)
def format_value(value):
if isinstance(value, bytes):
try:
ret... | --- +++ @@ -1,4 +1,12 @@ #!/usr/bin/env python3
+"""
+Extract and display DICOM metadata in a readable format.
+
+Usage:
+ python extract_metadata.py file.dcm
+ python extract_metadata.py file.dcm --output metadata.txt
+ python extract_metadata.py file.dcm --format json --output metadata.json
+"""
import ar... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/pydicom/scripts/extract_metadata.py |
Document classes and their methods | #!/usr/bin/env python3
import argparse
import sys
from pathlib import Path
try:
from rdkit import Chem
except ImportError:
print("Error: RDKit not installed. Install with: conda install -c conda-forge rdkit")
sys.exit(1)
# Common SMARTS pattern libraries
PATTERN_LIBRARIES = {
'functional-groups': {
... | --- +++ @@ -1,4 +1,14 @@ #!/usr/bin/env python3
+"""
+Substructure Filter
+
+Filter molecules based on substructure patterns using SMARTS.
+Supports inclusion and exclusion filters, and custom pattern libraries.
+
+Usage:
+ python substructure_filter.py molecules.smi --pattern "c1ccccc1" --output filtered.smi
+ p... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/rdkit/scripts/substructure_filter.py |
Add docstrings to make code maintainable | #!/usr/bin/env python3
import argparse
import sys
from pathlib import Path
try:
from rdkit import Chem
from rdkit.Chem import Descriptors, Lipinski
except ImportError:
print("Error: RDKit not installed. Install with: conda install -c conda-forge rdkit")
sys.exit(1)
def calculate_properties(mol):
... | --- +++ @@ -1,4 +1,14 @@ #!/usr/bin/env python3
+"""
+Molecular Properties Calculator
+
+Calculate comprehensive molecular properties and descriptors for molecules.
+Supports single molecules or batch processing from files.
+
+Usage:
+ python molecular_properties.py "CCO"
+ python molecular_properties.py --file m... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/rdkit/scripts/molecular_properties.py |
Add well-formatted docstrings |
import lightning as L
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.optim import Adam
from torch.optim.lr_scheduler import ReduceLROnPlateau
class TemplateLightningModule(L.LightningModule):
def __init__(
self,
learning_rate: float = 0.001,
hidden_dim: int... | --- +++ @@ -1,3 +1,9 @@+"""
+Template for creating a PyTorch Lightning Module.
+
+This template provides a complete boilerplate for building a LightningModule
+with all essential methods and best practices.
+"""
import lightning as L
import torch
@@ -8,6 +14,14 @@
class TemplateLightningModule(L.LightningModule... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/pytorch-lightning/scripts/template_lightning_module.py |
Document classes and their methods | #!/usr/bin/env python3
import os
import sys
import json
from typing import Dict, List, Optional
# Import the main research lookup class
sys.path.append(os.path.join(os.path.dirname(os.path.abspath(__file__)), 'scripts'))
from research_lookup import ResearchLookup
def format_response(result: Dict) -> str:
if not... | --- +++ @@ -1,4 +1,8 @@ #!/usr/bin/env python3
+"""
+Research Lookup Tool for Claude Code
+Performs research queries using Perplexity Sonar Pro Search via OpenRouter.
+"""
import os
import sys
@@ -11,6 +15,7 @@
def format_response(result: Dict) -> str:
+ """Format the research result for display."""
if ... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/research-lookup/lookup.py |
Add professional docstrings to my codebase | #!/usr/bin/env python3
import os
import sys
import json
import re
import time
import requests
from datetime import datetime
from typing import Any, Dict, List, Optional
class ResearchLookup:
ACADEMIC_KEYWORDS = [
"find papers", "find paper", "find articles", "find article",
"cite ", "citation", ... | --- +++ @@ -1,4 +1,15 @@ #!/usr/bin/env python3
+"""
+Research Information Lookup Tool
+
+Routes research queries to the best backend:
+ - Parallel Chat API (core model): Default for all general research queries
+ - Perplexity sonar-pro-search (via OpenRouter): Academic-specific paper searches
+
+Environment variable... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/research-lookup/research_lookup.py |
Add return value explanations in docstrings | #!/usr/bin/env python3
from tdc.benchmark_group import admet_group
from tdc import Evaluator
import numpy as np
import pandas as pd
def load_benchmark_group():
print("=" * 60)
print("Loading ADMET Benchmark Group")
print("=" * 60)
# Initialize benchmark group
group = admet_group(path='data/')
... | --- +++ @@ -1,4 +1,13 @@ #!/usr/bin/env python3
+"""
+TDC Benchmark Group Evaluation Template
+
+This script demonstrates how to use TDC benchmark groups for systematic
+model evaluation following the required 5-seed protocol.
+
+Usage:
+ python benchmark_evaluation.py
+"""
from tdc.benchmark_group import admet_g... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/pytdc/scripts/benchmark_evaluation.py |
Add return value explanations in docstrings | #!/usr/bin/env python3
from tdc.single_pred import ADME
from tdc.multi_pred import DTI
from tdc import Evaluator
import pandas as pd
def load_single_pred_example():
print("=" * 60)
print("Example 1: Single-Prediction Task (ADME)")
print("=" * 60)
# Load Caco2 dataset (intestinal permeability)
pr... | --- +++ @@ -1,4 +1,13 @@ #!/usr/bin/env python3
+"""
+TDC Data Loading and Splitting Template
+
+This script demonstrates how to load TDC datasets and apply different
+splitting strategies for model training and evaluation.
+
+Usage:
+ python load_and_split_data.py
+"""
from tdc.single_pred import ADME
from tdc.... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/pytdc/scripts/load_and_split_data.py |
Add docstrings including usage examples | #!/usr/bin/env python3
import requests
import time
import json
import hashlib
from pathlib import Path
from datetime import datetime, timedelta
from collections import deque, Counter
from typing import Dict, List, Optional, Any
class RateLimiter:
def __init__(self, max_per_minute: int = 240):
self.max_p... | --- +++ @@ -1,4 +1,16 @@ #!/usr/bin/env python3
+"""
+FDA API Query Helper
+
+Comprehensive utility for querying FDA databases through openFDA API.
+Includes error handling, rate limiting, caching, and common query patterns.
+
+Usage:
+ from fda_query import FDAQuery
+
+ fda = FDAQuery(api_key="YOUR_API_KEY")
+ ... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/fda-database/scripts/fda_query.py |
Help me add docstrings to my project | #!/usr/bin/env python3
import argparse
import json
import sys
from pathlib import Path
try:
from pymatgen.core import Structure
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from pymatgen.analysis.local_env import CrystalNN
except ImportError:
print("Error: pymatgen is not installed. Insta... | --- +++ @@ -1,4 +1,23 @@ #!/usr/bin/env python3
+"""
+Structure analysis tool using pymatgen.
+
+Analyzes crystal structures and provides comprehensive information including:
+- Composition and formula
+- Space group and symmetry
+- Lattice parameters
+- Density
+- Coordination environment
+- Bond lengths and angles
+
... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/pymatgen/scripts/structure_analyzer.py |
Document helper functions with docstrings | #!/usr/bin/env python3
import sys
import json
import requests
from typing import List, Dict, Optional
class ReactomeClient:
CONTENT_BASE = "https://reactome.org/ContentService"
ANALYSIS_BASE = "https://reactome.org/AnalysisService"
def get_version(self) -> str:
response = requests.get(f"{self.C... | --- +++ @@ -1,4 +1,23 @@ #!/usr/bin/env python3
+"""
+Reactome Database Query Helper Script
+
+This script provides convenient command-line access to common Reactome operations.
+
+Usage:
+ python reactome_query.py version
+ python reactome_query.py query <pathway_id>
+ python reactome_query.py analyze <gene_l... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/reactome-database/scripts/reactome_query.py |
Document functions with clear intent | #!/usr/bin/env python3
import argparse
import sys
from pathlib import Path
try:
from ete3 import Tree, TreeStyle, NodeStyle
except ImportError:
print("Error: ete3 not installed. Install with: pip install ete3")
sys.exit(1)
def create_tree_style(args):
ts = TreeStyle()
# Basic display options
... | --- +++ @@ -1,4 +1,10 @@ #!/usr/bin/env python3
+"""
+Quick tree visualization script with common customization options.
+
+Provides command-line interface for rapid tree visualization with
+customizable styles, layouts, and output formats.
+"""
import argparse
import sys
@@ -12,6 +18,7 @@
def create_tree_style... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/etetoolkit/scripts/quick_visualize.py |
Write documentation strings for class attributes |
import lightning as L
from lightning.pytorch.callbacks import (
ModelCheckpoint,
EarlyStopping,
LearningRateMonitor,
DeviceStatsMonitor,
RichProgressBar,
)
from lightning.pytorch import loggers as pl_loggers
from lightning.pytorch.strategies import DDPStrategy, FSDPStrategy
# ====================... | --- +++ @@ -1,3 +1,9 @@+"""
+Quick Trainer Setup Examples for PyTorch Lightning.
+
+This script provides ready-to-use Trainer configurations for common use cases.
+Copy and modify these configurations for your specific needs.
+"""
import lightning as L
from lightning.pytorch.callbacks import (
@@ -16,6 +22,10 @@ # ... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/pytorch-lightning/scripts/quick_trainer_setup.py |
Add docstrings with type hints explained |
import scvelo as scv
import scanpy as sc
import numpy as np
import matplotlib
matplotlib.use('Agg') # Non-interactive backend
import matplotlib.pyplot as plt
import os
def run_velocity_analysis(
adata,
groupby="leiden",
n_top_genes=2000,
n_neighbors=30,
mode="dynamical",
n_jobs=4,
output... | --- +++ @@ -1,3 +1,13 @@+"""
+RNA Velocity Analysis Workflow using scVelo
+===========================================
+Complete pipeline from raw data to velocity visualization.
+
+Usage:
+ python rna_velocity_workflow.py
+
+Or import and use run_velocity_analysis() with your AnnData object.
+"""
import scvelo a... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/scvelo/scripts/rna_velocity_workflow.py |
Create documentation for each function signature | #!/usr/bin/env python3
from tdc.generation import MolGen
from tdc import Oracle
import numpy as np
def load_generation_dataset():
print("=" * 60)
print("Loading Molecular Generation Dataset")
print("=" * 60)
# Load ChEMBL dataset
data = MolGen(name='ChEMBL_V29')
# Get training molecules
... | --- +++ @@ -1,4 +1,13 @@ #!/usr/bin/env python3
+"""
+TDC Molecular Generation with Oracles Template
+
+This script demonstrates how to use TDC oracles for molecular generation
+tasks including goal-directed generation and distribution learning.
+
+Usage:
+ python molecular_generation.py
+"""
from tdc.generation ... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/pytdc/scripts/molecular_generation.py |
Write docstrings for data processing functions | #!/usr/bin/env python3
import argparse
import os
import sys
from pathlib import Path
try:
from pymatgen.core import Composition
from pymatgen.analysis.phase_diagram import PhaseDiagram, PDPlotter
except ImportError:
print("Error: pymatgen is not installed. Install with: pip install pymatgen")
sys.exit... | --- +++ @@ -1,4 +1,19 @@ #!/usr/bin/env python3
+"""
+Phase diagram generator using Materials Project data.
+
+This script generates phase diagrams for chemical systems using data from the
+Materials Project database via pymatgen's MPRester.
+
+Usage:
+ python phase_diagram_generator.py chemical_system [options]
+
+... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/pymatgen/scripts/phase_diagram_generator.py |
Add professional docstrings to my codebase |
import gymnasium as gym
from gymnasium import spaces
import numpy as np
class CustomEnv(gym.Env):
# Optional: Provide metadata for rendering modes
metadata = {"render_modes": ["human", "rgb_array"], "render_fps": 30}
def __init__(self, grid_size=5, render_mode=None):
super().__init__()
... | --- +++ @@ -1,3 +1,13 @@+"""
+Template for creating custom Gymnasium environments compatible with Stable Baselines3.
+
+This template demonstrates:
+- Proper Gymnasium environment structure
+- Observation and action space definition
+- Step and reset implementation
+- Validation with SB3's env_checker
+- Registration w... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/stable-baselines3/scripts/custom_env_template.py |
Document my Python code with docstrings |
import gymnasium as gym
import numpy as np
from stable_baselines3 import PPO
from stable_baselines3.common.evaluation import evaluate_policy
from stable_baselines3.common.vec_env import DummyVecEnv, VecVideoRecorder, VecNormalize
import os
def evaluate_agent(
model_path,
env_id="CartPole-v1",
n_eval_epis... | --- +++ @@ -1,3 +1,12 @@+"""
+Template script for evaluating trained RL agents with Stable Baselines3.
+
+This template demonstrates:
+- Loading trained models
+- Evaluating performance with statistics
+- Recording videos of agent behavior
+- Visualizing agent performance
+"""
import gymnasium as gym
import numpy a... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/stable-baselines3/scripts/evaluate_agent.py |
Add docstrings for utility scripts |
import gymnasium as gym
from stable_baselines3 import PPO
from stable_baselines3.common.env_util import make_vec_env
from stable_baselines3.common.callbacks import (
EvalCallback,
CheckpointCallback,
CallbackList,
)
from stable_baselines3.common.vec_env import SubprocVecEnv, VecNormalize
import os
def tr... | --- +++ @@ -1,3 +1,13 @@+"""
+Template script for training RL agents with Stable Baselines3.
+
+This template demonstrates best practices for:
+- Setting up training with proper monitoring
+- Using callbacks for evaluation and checkpointing
+- Vectorized environments for efficiency
+- TensorBoard integration
+- Model s... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/stable-baselines3/scripts/train_rl_agent.py |
Write reusable docstrings | #!/usr/bin/env python3
import simpy
import random
class SimulationConfig:
def __init__(self):
self.random_seed = 42
self.num_resources = 2
self.num_processes = 10
self.sim_time = 100
self.arrival_rate = 5.0 # Average time between arrivals
self.service_time_mean =... | --- +++ @@ -1,10 +1,17 @@ #!/usr/bin/env python3
+"""
+Basic SimPy Simulation Template
+
+This template provides a starting point for building SimPy simulations.
+Customize the process functions and parameters for your specific use case.
+"""
import simpy
import random
class SimulationConfig:
+ """Configura... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/simpy/scripts/basic_simulation_template.py |
Document all public functions with docstrings | #!/usr/bin/env python3
import argparse
import sys
from pathlib import Path
try:
from rdkit import Chem
from rdkit.Chem import AllChem, MACCSkeys, rdFingerprintGenerator
from rdkit import DataStructs
except ImportError:
print("Error: RDKit not installed. Install with: conda install -c conda-forge rdkit... | --- +++ @@ -1,4 +1,14 @@ #!/usr/bin/env python3
+"""
+Molecular Similarity Search
+
+Perform fingerprint-based similarity screening against a database of molecules.
+Supports multiple fingerprint types and similarity metrics.
+
+Usage:
+ python similarity_search.py "CCO" database.smi --threshold 0.7
+ python simi... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/rdkit/scripts/similarity_search.py |
Add docstrings to make code maintainable |
import lightning as L
from torch.utils.data import Dataset, DataLoader, random_split
import torch
class CustomDataset(Dataset):
def __init__(self, data_path, transform=None):
self.data_path = data_path
self.transform = transform
# Load your data here
# self.data = load_data(data... | --- +++ @@ -1,3 +1,9 @@+"""
+Template for creating a PyTorch Lightning DataModule.
+
+This template provides a complete boilerplate for building a LightningDataModule
+with all essential methods and best practices for data handling.
+"""
import lightning as L
from torch.utils.data import Dataset, DataLoader, random... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/pytorch-lightning/scripts/template_datamodule.py |
Add structured docstrings to improve clarity | #!/usr/bin/env python3
import simpy
from collections import defaultdict
from typing import List, Tuple, Dict, Any
class ResourceMonitor:
def __init__(self, env: simpy.Environment, resource: simpy.Resource, name: str = "Resource"):
self.env = env
self.resource = resource
self.name = name
... | --- +++ @@ -1,4 +1,11 @@ #!/usr/bin/env python3
+"""
+SimPy Resource Monitoring Utilities
+
+This module provides reusable classes and functions for monitoring
+SimPy resources during simulation. Includes utilities for tracking
+queue lengths, utilization, wait times, and generating reports.
+"""
import simpy
from ... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/simpy/scripts/resource_monitor.py |
Add documentation for all methods | #!/usr/bin/env python3
import argparse
import sys
from pathlib import Path
from typing import List
try:
from PIL import Image
except ImportError:
print("Error: Pillow library not found. Install with: pip install Pillow")
sys.exit(1)
def get_image_files(paths: List[str]) -> List[Path]:
image_extensio... | --- +++ @@ -1,4 +1,20 @@ #!/usr/bin/env python3
+"""
+Combine slide images into a single PDF presentation.
+
+This script takes multiple slide images (PNG, JPG) and combines them
+into a single PDF file, maintaining aspect ratio and quality.
+
+Usage:
+ # Combine all PNG files in a directory
+ python slides_to_pd... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/scientific-slides/scripts/slides_to_pdf.py |
Write beginner-friendly docstrings | #!/usr/bin/env python3
import sys
import re
import argparse
from pathlib import Path
from typing import Dict, List, Tuple
# Validation criteria and patterns
VALIDATION_CHECKS = {
'smart_goals': {
'name': 'SMART Goals Criteria',
'patterns': [
(r'\bspecific\b', 'Specific criterion'),
... | --- +++ @@ -1,4 +1,8 @@ #!/usr/bin/env python3
+"""
+Validate Treatment Plan Quality
+Comprehensive validation of treatment plan content quality and compliance.
+"""
import sys
import re
@@ -51,6 +55,7 @@
def read_file(filepath: Path) -> str:
+ """Read and return file contents."""
try:
with ope... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/treatment-plans/scripts/validate_treatment_plan.py |
Write reusable docstrings | #!/usr/bin/env python3
import sys
import re
import argparse
from pathlib import Path
from datetime import datetime, timedelta
from typing import List, Dict, Tuple
# Try to import matplotlib, but make it optional
try:
import matplotlib.pyplot as plt
import matplotlib.dates as mdates
from matplotlib.patches... | --- +++ @@ -1,4 +1,8 @@ #!/usr/bin/env python3
+"""
+Treatment Timeline Generator
+Generates visual treatment timelines from treatment plan files.
+"""
import sys
import re
@@ -18,6 +22,10 @@
def extract_timeline_info(content: str) -> Dict[str, List[Tuple[str, str]]]:
+ """
+ Extract timeline and schedule... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/treatment-plans/scripts/timeline_generator.py |
Generate docstrings for exported functions | #!/usr/bin/env python3
import argparse
import base64
import json
import os
import sys
import time
from pathlib import Path
from typing import Optional, Dict, Any, List, Tuple
try:
import requests
except ImportError:
print("Error: requests library not found. Install with: pip install requests")
sys.exit(1)... | --- +++ @@ -1,4 +1,22 @@ #!/usr/bin/env python3
+"""
+AI-powered scientific schematic generation using Nano Banana 2.
+
+This script uses a smart iterative refinement approach:
+1. Generate initial image with Nano Banana 2
+2. AI quality review using Gemini 3.1 Pro Preview for scientific critique
+3. Only regenerate if... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/scientific-schematics/scripts/generate_schematic_ai.py |
Add docstrings to clarify complex logic | #!/usr/bin/env python3
import matplotlib.pyplot as plt
import matplotlib as mpl
from typing import Optional, Dict, Any
# Okabe-Ito colorblind-friendly palette
OKABE_ITO_COLORS = [
'#E69F00', # Orange
'#56B4E9', # Sky Blue
'#009E73', # Bluish Green
'#F0E442', # Yellow
'#0072B2', # Blue
'#... | --- +++ @@ -1,4 +1,10 @@ #!/usr/bin/env python3
+"""
+Matplotlib Style Presets for Publication-Ready Scientific Figures
+
+This module provides pre-configured matplotlib styles optimized for
+different journals and use cases.
+"""
import matplotlib.pyplot as plt
import matplotlib as mpl
@@ -27,6 +33,14 @@
def g... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/scientific-visualization/scripts/style_presets.py |
Add concise docstrings to each method |
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from sklearn.preprocessing import StandardScaler
from sklearn.decomposition import PCA
from sklearn.cluster import KMeans, DBSCAN, AgglomerativeClustering
from sklearn.mixture import GaussianMixture
from sklearn.metrics import (
silhouette_scor... | --- +++ @@ -1,3 +1,6 @@+"""
+Clustering analysis example with multiple algorithms, evaluation, and visualization.
+"""
import numpy as np
import pandas as pd
@@ -14,6 +17,23 @@
def preprocess_for_clustering(X, scale=True, pca_components=None):
+ """
+ Preprocess data for clustering.
+
+ Parameters:
+ ... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/scikit-learn/scripts/clustering_analysis.py |
Please document this code using docstrings | #!/usr/bin/env python3
import argparse
import base64
import json
import os
import sys
import time
from pathlib import Path
from typing import Optional, Dict, Any, List, Tuple
try:
import requests
except ImportError:
print("Error: requests library not found. Install with: pip install requests")
sys.exit(1... | --- +++ @@ -1,4 +1,33 @@ #!/usr/bin/env python3
+"""
+AI-powered slide image generation using Nano Banana Pro.
+
+This script generates presentation slides or slide visuals using AI:
+- full_slide mode: Generate complete slides with title, content, and visuals (for PDF workflow)
+- visual_only mode: Generate just image... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/scientific-slides/scripts/generate_slide_image_ai.py |
Add missing documentation to my Python functions | #!/usr/bin/env python3
import sys
import argparse
from pathlib import Path
from typing import Optional, List
# Try to import pymupdf (preferred - no external dependencies)
try:
import fitz # PyMuPDF
HAS_PYMUPDF = True
except ImportError:
HAS_PYMUPDF = False
class PDFToImagesConverter:
def __in... | --- +++ @@ -1,4 +1,13 @@ #!/usr/bin/env python3
+"""
+PDF to Images Converter for Presentations
+
+Converts presentation PDFs to images for visual inspection and review.
+Supports multiple output formats and resolutions.
+
+Uses PyMuPDF (fitz) as the primary conversion method - no external
+dependencies required (no po... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/scientific-slides/scripts/pdf_to_images.py |
Add docstrings including usage examples | #!/usr/bin/env python3
import sys
import re
import argparse
from pathlib import Path
from typing import List, Tuple
# Required sections for all treatment plans
REQUIRED_SECTIONS = [
r'\\section\*\{.*Patient Information',
r'\\section\*\{.*Diagnosis.*Assessment',
r'\\section\*\{.*Goals',
r'\\section\*\{... | --- +++ @@ -1,4 +1,8 @@ #!/usr/bin/env python3
+"""
+Check Treatment Plan Completeness
+Validates that all required sections are present in a treatment plan.
+"""
import sys
import re
@@ -36,6 +40,7 @@
def read_file(filepath: Path) -> str:
+ """Read and return file contents."""
try:
with open(f... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/treatment-plans/scripts/check_completeness.py |
Document all public functions with docstrings | #!/usr/bin/env python3
import argparse
import matplotlib.pyplot as plt
import networkx as nx
import torch
from typing import Optional, Union
import numpy as np
def visualize_data(
data,
title: str = "Graph Visualization",
node_color_attr: Optional[str] = None,
edge_color_attr: Optional[str] = None,
... | --- +++ @@ -1,4 +1,20 @@ #!/usr/bin/env python3
+"""
+Visualize PyTorch Geometric graph structures using networkx and matplotlib.
+
+This script provides utilities to visualize Data objects, including:
+- Graph structure (nodes and edges)
+- Node features (as colors)
+- Edge attributes (as edge colors/widths)
+- Commun... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/torch-geometric/scripts/visualize_graph.py |
Generate docstrings for this script | #!/usr/bin/env python3
import json
import argparse
import sys
from typing import Dict, List, Optional
from pathlib import Path
# Default dimension weights (total = 100%)
DEFAULT_WEIGHTS = {
"problem_formulation": 0.15,
"literature_review": 0.15,
"methodology": 0.20,
"data_collection": 0.10,
"anal... | --- +++ @@ -1,4 +1,18 @@ #!/usr/bin/env python3
+"""
+ScholarEval Score Calculator
+
+Calculate aggregate evaluation scores from dimension-level ratings.
+Supports weighted averaging, threshold analysis, and score visualization.
+
+Usage:
+ python calculate_scores.py --scores <dimension_scores.json> --output <report... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/scholar-evaluation/scripts/calculate_scores.py |
Write documentation strings for class attributes |
import urllib.request
import urllib.parse
import urllib.error
import json
from typing import Optional, List, Union, Dict
STRING_BASE_URL = "https://string-db.org/api"
def string_map_ids(identifiers: Union[str, List[str]],
species: int = 9606,
limit: int = 1,
... | --- +++ @@ -1,3 +1,15 @@+"""
+STRING Database REST API Helper Functions
+
+This module provides Python functions for interacting with the STRING database API.
+All functions return raw response text or JSON which can be parsed as needed.
+
+API Base URL: https://string-db.org/api
+Documentation: https://string-db.org/h... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/string-database/scripts/string_api.py |
Add docstrings that explain logic | #!/usr/bin/env python3
import os
import sys
import shutil
import argparse
from pathlib import Path
from datetime import datetime
# Template types and descriptions
TEMPLATES = {
'general_medical': {
'name': 'General Medical Treatment Plan',
'file': 'general_medical_treatment_plan.tex',
'des... | --- +++ @@ -1,4 +1,8 @@ #!/usr/bin/env python3
+"""
+Generate Treatment Plan Template
+Interactive script to select and generate treatment plan templates.
+"""
import os
import sys
@@ -43,6 +47,7 @@
def get_templates_dir():
+ """Get the path to the templates directory."""
# Assume script is in .claude/s... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/treatment-plans/scripts/generate_template.py |
Generate docstrings for this script | #!/usr/bin/env python3
import sys
import os
import argparse
import subprocess
from pathlib import Path
from typing import Dict, List, Tuple, Optional
# Try to import PyPDF2 for PDF analysis
try:
import PyPDF2
HAS_PYPDF2 = True
except ImportError:
HAS_PYPDF2 = False
# Try to import python-pptx for PowerPo... | --- +++ @@ -1,4 +1,13 @@ #!/usr/bin/env python3
+"""
+Presentation Validation Script
+
+Validates scientific presentations for common issues:
+- Slide count vs. duration
+- LaTeX compilation
+- File size checks
+- Basic format validation
+"""
import sys
import os
@@ -23,6 +32,7 @@
class PresentationValidator:
+... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/scientific-slides/scripts/validate_presentation.py |
Create docstrings for all classes and functions |
# Okabe-Ito Palette (2008)
# The most widely recommended colorblind-friendly palette
OKABE_ITO = {
'orange': '#E69F00',
'sky_blue': '#56B4E9',
'bluish_green': '#009E73',
'yellow': '#F0E442',
'blue': '#0072B2',
'vermillion': '#D55E00',
'reddish_purple': '#CC79A7',
'black': '#000000'
}
O... | --- +++ @@ -1,3 +1,16 @@+"""
+Colorblind-Friendly Color Palettes for Scientific Visualization
+
+This module provides carefully curated color palettes optimized for
+scientific publications and accessibility.
+
+Usage:
+ from color_palettes import OKABE_ITO, apply_palette
+ import matplotlib.pyplot as plt
+
+ ... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/scientific-visualization/assets/color_palettes.py |
Create documentation strings for testing functions | #!/usr/bin/env python3
import sys
import json
from typing import Dict, List, Optional, Any
from datetime import datetime
try:
from uspto.peds import PEDSClient as OriginalPEDSClient
HAS_USPTO_LIB = True
except ImportError:
HAS_USPTO_LIB = False
print("Warning: uspto-opendata-python not installed.", fi... | --- +++ @@ -1,4 +1,16 @@ #!/usr/bin/env python3
+"""
+USPTO Patent Examination Data System (PEDS) Helper
+
+Provides functions for retrieving patent examination data using the
+uspto-opendata-python library.
+
+Requires:
+ - uspto-opendata-python: pip install uspto-opendata-python
+
+Note: This script provides a sim... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/uspto-database/scripts/peds_client.py |
Generate docstrings with parameter types | #!/usr/bin/env python3
import argparse
import re
from pathlib import Path
def get_skill_path():
script_dir = Path(__file__).parent
skill_dir = script_dir.parent
return skill_dir
def find_template(template_name):
skill_path = get_skill_path()
assets_path = skill_path / "assets"
# Search i... | --- +++ @@ -1,15 +1,26 @@ #!/usr/bin/env python3
+"""
+Customize Template Script
+Customize LaTeX templates with author information and project details.
+
+Usage:
+ python customize_template.py --template nature_article.tex --output my_paper.tex
+ python customize_template.py --template nature_article.tex --title... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/venue-templates/scripts/customize_template.py |
Write docstrings for data processing functions | #!/usr/bin/env python3
import os
import sys
import json
import requests
from typing import Dict, List, Optional, Any
from datetime import datetime
class PatentSearchClient:
BASE_URL = "https://search.patentsview.org/api/v1"
def __init__(self, api_key: Optional[str] = None):
self.api_key = api_key o... | --- +++ @@ -1,4 +1,17 @@ #!/usr/bin/env python3
+"""
+USPTO PatentSearch API Helper
+
+Provides functions for searching and retrieving patent data using the USPTO
+PatentSearch API (ElasticSearch-based system, replaced legacy PatentsView in May 2025).
+
+Requires:
+ - requests library: pip install requests
+ - US... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/uspto-database/scripts/patent_search.py |
Add docstrings with type hints explained | #!/usr/bin/env python3
from __future__ import annotations
import argparse
import json
import sys
from pathlib import Path
import numpy as np
import pandas as pd
def run_preflight() -> dict:
# Import the check_system module from the same directory
script_dir = Path(__file__).parent
sys.path.insert(0, st... | --- +++ @@ -1,4 +1,22 @@ #!/usr/bin/env python3
+"""End-to-end CSV forecasting with TimesFM.
+
+Loads a CSV, runs the system preflight check, loads TimesFM, forecasts
+the requested columns, and writes results to a new CSV or JSON.
+
+Usage:
+ python forecast_csv.py input.csv --horizon 24
+ python forecast_csv.py... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/timesfm-forecasting/scripts/forecast_csv.py |
Add docstrings that explain purpose and usage | #!/usr/bin/env python3
import argparse
import os
import json
from pathlib import Path
# Template database
TEMPLATES = {
"journals": {
"nature": {
"file": "nature_article.tex",
"full_name": "Nature",
"description": "Top-tier multidisciplinary science journal",
... | --- +++ @@ -1,4 +1,14 @@ #!/usr/bin/env python3
+"""
+Query Template Script
+Search and retrieve venue-specific templates by name, type, or keywords.
+
+Usage:
+ python query_template.py --venue "Nature" --type "article"
+ python query_template.py --keyword "machine learning"
+ python query_template.py --list-... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/venue-templates/scripts/query_template.py |
Add return value explanations in docstrings | #!/usr/bin/env python3
import requests
import sys
import time
import json
from typing import List, Dict, Optional, Generator
from urllib.parse import urlencode
BASE_URL = "https://rest.uniprot.org"
POLLING_INTERVAL = 3 # seconds
def search_proteins(query: str, format: str = "json",
fields: Optio... | --- +++ @@ -1,4 +1,25 @@ #!/usr/bin/env python3
+"""
+UniProt REST API Client
+
+A Python client for interacting with the UniProt REST API.
+Provides helper functions for common operations including search,
+retrieval, ID mapping, and streaming.
+
+Usage examples:
+ # Search for proteins
+ results = search_protei... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/uniprot-database/scripts/uniprot_client.py |
Add docstrings to make code maintainable | #!/usr/bin/env python3
import matplotlib.pyplot as plt
from pathlib import Path
from typing import List, Optional, Union
def save_publication_figure(
fig: plt.Figure,
filename: Union[str, Path],
formats: List[str] = ['pdf', 'png'],
dpi: int = 300,
transparent: bool = False,
bbox_inches: str =... | --- +++ @@ -1,4 +1,10 @@ #!/usr/bin/env python3
+"""
+Figure Export Utilities for Publication-Ready Scientific Figures
+
+This module provides utilities to export matplotlib figures in publication-ready
+formats with appropriate settings for various journals.
+"""
import matplotlib.pyplot as plt
from pathlib import... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/scientific-visualization/scripts/figure_export.py |
Help me comply with documentation standards | #!/usr/bin/env python3
import argparse
import subprocess
from pathlib import Path
import re
# Venue requirements database
VENUE_REQUIREMENTS = {
"nature": {
"page_limit": 5, # Approximate for ~3000 words
"margins": {"top": 2.5, "bottom": 2.5, "left": 2.5, "right": 2.5}, # cm
"font_size":... | --- +++ @@ -1,4 +1,13 @@ #!/usr/bin/env python3
+"""
+Validate Format Script
+Check if document meets venue-specific formatting requirements.
+
+Usage:
+ python validate_format.py --file my_paper.pdf --venue "Nature" --check-all
+ python validate_format.py --file my_paper.pdf --venue "NeurIPS" --check page-count,... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/venue-templates/scripts/validate_format.py |
Expand my code with proper documentation strings |
import numpy as np
import pandas as pd
from scipy import stats
import matplotlib.pyplot as plt
import seaborn as sns
from typing import Dict, List, Tuple, Optional, Union
def check_normality(
data: Union[np.ndarray, pd.Series, List],
name: str = "data",
alpha: float = 0.05,
plot: bool = True
) -> Dic... | --- +++ @@ -1,3 +1,13 @@+"""
+Comprehensive statistical assumption checking utilities.
+
+This module provides functions to check common statistical assumptions:
+- Normality
+- Homogeneity of variance
+- Independence
+- Linearity
+- Outliers
+"""
import numpy as np
import pandas as pd
@@ -13,6 +23,25 @@ alpha:... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/statistical-analysis/scripts/assumption_checks.py |
Add verbose docstrings with examples | #!/usr/bin/env python3
import argparse
import sys
from pathlib import Path
from typing import List
try:
from pymatgen.core import Structure
except ImportError:
print("Error: pymatgen is not installed. Install with: pip install pymatgen")
sys.exit(1)
def convert_structure(input_path: Path, output_path: P... | --- +++ @@ -1,4 +1,20 @@ #!/usr/bin/env python3
+"""
+Structure file format converter using pymatgen.
+
+This script converts between different structure file formats supported by pymatgen.
+Supports automatic format detection and batch conversion.
+
+Usage:
+ python structure_converter.py input_file output_file
+ ... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/pymatgen/scripts/structure_converter.py |
Write docstrings for algorithm functions | #!/usr/bin/env python3
import argparse
import torch
import torch.nn.functional as F
from torch_geometric.nn import GCNConv, GATConv, SAGEConv, GINConv
from torch_geometric.datasets import Planetoid, TUDataset
from torch_geometric.loader import DataLoader
from torch_geometric.nn import global_mean_pool
import time
impo... | --- +++ @@ -1,4 +1,14 @@ #!/usr/bin/env python3
+"""
+Benchmark GNN models on standard datasets.
+
+This script provides a simple way to benchmark different GNN architectures
+on common datasets and compare their performance.
+
+Usage:
+ python benchmark_model.py --models gcn gat --dataset Cora
+ python benchmark... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/torch-geometric/scripts/benchmark_model.py |
Document this code for team use | import signal
import threading
from invoke import Runner, pty_size, Result as InvokeResult
def cares_about_SIGWINCH():
return (
hasattr(signal, "SIGWINCH")
and threading.current_thread() is threading.main_thread()
)
class Remote(Runner):
def __init__(self, *args, **kwargs):
sel... | --- +++ @@ -12,8 +12,36 @@
class Remote(Runner):
+ """
+ Run a shell command over an SSH connection.
+
+ This class subclasses `invoke.runners.Runner`; please see its documentation
+ for most public API details.
+
+ .. note::
+ `.Remote`'s ``__init__`` method expects a `.Connection` (or subcla... | https://raw.githubusercontent.com/fabric/fabric/HEAD/fabric/runners.py |
Add detailed documentation for each class |
import os
import posixpath
import stat
from pathlib import Path
from .util import debug # TODO: actual logging! LOL
# TODO: figure out best way to direct folks seeking rsync, to patchwork's rsync
# call (which needs updating to use invoke.run() & fab 2 connection methods,
# but is otherwise suitable).
# UNLESS we ... | --- +++ @@ -1,3 +1,6 @@+"""
+File transfer via SFTP and/or SCP.
+"""
import os
import posixpath
@@ -16,6 +19,11 @@
class Transfer:
+ """
+ `.Connection`-wrapping class responsible for managing file upload/download.
+
+ .. versionadded:: 2.0
+ """
# TODO: SFTP clear default, but how to do SCP?... | https://raw.githubusercontent.com/fabric/fabric/HEAD/fabric/transfer.py |
Add docstrings to clarify complex logic | #!/usr/bin/env python3
from __future__ import annotations
import argparse
import json
import os
import platform
import shutil
import struct
import sys
from dataclasses import dataclass, field
from pathlib import Path
from typing import Any
# --------------------------------------------------------------------------... | --- +++ @@ -1,4 +1,17 @@ #!/usr/bin/env python3
+"""TimesFM System Requirements Preflight Checker.
+
+MANDATORY: Run this script before loading TimesFM for the first time.
+It checks RAM, GPU/VRAM, disk space, Python version, and package
+installation so the agent never crashes a user's machine.
+
+Usage:
+ python c... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/timesfm-forecasting/scripts/check_system.py |
Add return value explanations in docstrings |
import numpy as np
import pandas as pd
from sklearn.model_selection import train_test_split, GridSearchCV, cross_val_score
from sklearn.preprocessing import StandardScaler, OneHotEncoder
from sklearn.impute import SimpleImputer
from sklearn.compose import ColumnTransformer
from sklearn.pipeline import Pipeline
from sk... | --- +++ @@ -1,3 +1,7 @@+"""
+Complete classification pipeline example with preprocessing, model training,
+hyperparameter tuning, and evaluation.
+"""
import numpy as np
import pandas as pd
@@ -17,6 +21,21 @@
def create_preprocessing_pipeline(numeric_features, categorical_features):
+ """
+ Create a prepr... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/scikit-learn/scripts/classification_pipeline.py |
Turn comments into proper docstrings | import os
import time
from io import StringIO
from invoke import pty_size, CommandTimedOut
from invocations.environment import in_ci
from pytest import skip, raises
from pytest_relaxed import trap
from fabric import Connection, Config
# TODO: use pytest markers
def skip_outside_ci():
if not in_ci():
sk... | --- +++ @@ -36,12 +36,18 @@
class run:
def simple_command_on_host(self):
+ """
+ Run command on localhost
+ """
result = Connection("localhost").run("echo foo", hide=True)
assert result.stdout == "foo\n"
assert result.exited == 0
... | https://raw.githubusercontent.com/fabric/fabric/HEAD/integration/connection.py |
Write beginner-friendly docstrings | #!/usr/bin/env python3
import os
import sys
import json
import requests
from typing import Dict, List, Optional, Any
class TrademarkClient:
TSDR_BASE_URL = "https://tsdrapi.uspto.gov/ts/cd"
ASSIGNMENT_BASE_URL = "https://assignment-api.uspto.gov/trademark"
def __init__(self, api_key: Optional[str] = No... | --- +++ @@ -1,4 +1,17 @@ #!/usr/bin/env python3
+"""
+USPTO Trademark API Helper
+
+Provides functions for searching and retrieving trademark data using USPTO
+Trademark Status & Document Retrieval (TSDR) API.
+
+Requires:
+ - requests library: pip install requests
+ - USPTO API key from https://account.uspto.gov... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/uspto-database/scripts/trademark_client.py |
Add standardized docstrings across the file | import invoke
from .connection import Connection
class Task(invoke.Task):
def __init__(self, *args, **kwargs):
# Pull out our own kwargs before hitting super, which will TypeError on
# anything it doesn't know about.
self.hosts = kwargs.pop("hosts", None)
super().__init__(*args, ... | --- +++ @@ -4,6 +4,15 @@
class Task(invoke.Task):
+ """
+ Extends `invoke.tasks.Task` with knowledge of target hosts and similar.
+
+ As `invoke.tasks.Task` relegates documentation responsibility to its `@task
+ <invoke.tasks.task>` expression, so we relegate most details to our version
+ of `@task <... | https://raw.githubusercontent.com/fabric/fabric/HEAD/fabric/tasks.py |
Write docstrings describing each step | from queue import Queue
from invoke.util import ExceptionHandlingThread
from .connection import Connection
from .exceptions import GroupException
class Group(list):
def __init__(self, *hosts, **kwargs):
# TODO: #563, #388 (could be here or higher up in Program area)
self.extend([Connection(host... | --- +++ @@ -7,13 +7,89 @@
class Group(list):
+ """
+ A collection of `.Connection` objects whose API operates on its contents.
+
+ .. warning::
+ **This is a partially abstract class**; you need to use one of its
+ concrete subclasses (such as `.SerialGroup` or `.ThreadingGroup`) or
+ ... | https://raw.githubusercontent.com/fabric/fabric/HEAD/fabric/group.py |
Create docstrings for each class method | import copy
import errno
import os
from invoke.config import Config as InvokeConfig, merge_dicts
from paramiko.config import SSHConfig
from .runners import Remote, RemoteShell
from .util import get_local_user, debug
class Config(InvokeConfig):
prefix = "fabric"
@classmethod
def from_v1(cls, env, **kwa... | --- +++ @@ -10,11 +10,59 @@
class Config(InvokeConfig):
+ """
+ An `invoke.config.Config` subclass with extra Fabric-related behavior.
+
+ This class behaves like `invoke.config.Config` in every way, with the
+ following exceptions:
+
+ - its `global_defaults` staticmethod has been extended to add/mo... | https://raw.githubusercontent.com/fabric/fabric/HEAD/fabric/config.py |
Add docstrings to meet PEP guidelines | from functools import partial
from getpass import getpass
from pathlib import Path
from paramiko import Agent, PKey
from paramiko.auth_strategy import (
AuthStrategy,
Password,
InMemoryPrivateKey,
OnDiskPrivateKey,
)
from .util import win32
class OpenSSHAuthStrategy(AuthStrategy):
# Skimming op... | --- +++ @@ -14,6 +14,28 @@
class OpenSSHAuthStrategy(AuthStrategy):
+ """
+ Auth strategy that tries very hard to act like the OpenSSH client.
+
+ .. warning::
+ As of version 3.1, this class is **EXPERIMENTAL** and **incomplete**.
+ It works best with passphraseless (eg ssh-agent) private ke... | https://raw.githubusercontent.com/fabric/fabric/HEAD/fabric/auth.py |
Replace inline comments with docstrings | from contextlib import contextmanager
from io import StringIO
from threading import Event
import socket
from decorator import decorator
from invoke import Context
from invoke.exceptions import ThreadException
from paramiko.agent import AgentRequestHandler
from paramiko.client import SSHClient, AutoAddPolicy
from param... | --- +++ @@ -47,6 +47,79 @@
class Connection(Context):
+ """
+ A connection to an SSH daemon, with methods for commands and file transfer.
+
+ **Basics**
+
+ This class inherits from Invoke's `~invoke.context.Context`, as it is a
+ context within which commands, tasks etc can operate. It also encapsul... | https://raw.githubusercontent.com/fabric/fabric/HEAD/fabric/connection.py |
Create docstrings for all classes and functions | import invoke
from invoke import Call, Task
from .tasks import ConnectionCall
from .exceptions import NothingToDo
from .util import debug
class Executor(invoke.Executor):
def normalize_hosts(self, hosts):
dicts = []
for value in hosts or []:
# Assume first posarg to Connection() if n... | --- +++ @@ -7,8 +7,38 @@
class Executor(invoke.Executor):
+ """
+ `~invoke.executor.Executor` subclass which understands Fabric concepts.
+
+ Designed to work in tandem with Fabric's `@task
+ <fabric.tasks.task>`/`~fabric.tasks.Task`, and is capable of acting on
+ information stored on the resulting ... | https://raw.githubusercontent.com/fabric/fabric/HEAD/fabric/executor.py |
Generate NumPy-style docstrings | # TODO: this may want to move to Invoke if we can find a use for it there too?
# Or make it _more_ narrowly focused and stay here?
class NothingToDo(Exception):
pass
class GroupException(Exception):
def __init__(self, result):
#: The `.GroupResult` object which would have been returned, had there
... | --- +++ @@ -5,6 +5,11 @@
class GroupException(Exception):
+ """
+ Lightweight exception wrapper for `.GroupResult` when one contains errors.
+
+ .. versionadded:: 2.0
+ """
def __init__(self, result):
#: The `.GroupResult` object which would have been returned, had there
@@ -14,5 +19,8 @... | https://raw.githubusercontent.com/fabric/fabric/HEAD/fabric/exceptions.py |
Add detailed documentation for each class |
import select
import socket
import time
from threading import Event
from invoke.exceptions import ThreadException
from invoke.util import ExceptionHandlingThread
class TunnelManager(ExceptionHandlingThread):
def __init__(
self,
local_host,
local_port,
remote_host,
remote... | --- +++ @@ -1,3 +1,9 @@+"""
+Tunnel and connection forwarding internals.
+
+If you're looking for simple, end-user-focused connection forwarding, please
+see `.Connection`, e.g. `.Connection.forward_local`.
+"""
import select
import socket
@@ -9,6 +15,19 @@
class TunnelManager(ExceptionHandlingThread):
+ """... | https://raw.githubusercontent.com/fabric/fabric/HEAD/fabric/tunnels.py |
Insert docstrings into my code | from os import getcwd
import sys
from invocations import ci
from invocations import checks
from invocations.docs import docs, www, sites, watch_docs
from invocations.pytest import (
test,
integration as integration_,
coverage as coverage_,
)
from invocations.packaging import release
from invoke import Col... | --- +++ @@ -16,6 +16,11 @@
@task
def safety_test_v1_to_v2_shim(c):
+ """
+ Run some very quick in-process safety checks on a dual fabric1-v-2 env.
+
+ Assumes Fabric 2+ is already installed as 'fabric2'.
+ """
c.run("pip install 'fabric<2'")
# Make darn sure the two copies of fabric are coming ... | https://raw.githubusercontent.com/fabric/fabric/HEAD/tasks.py |
Add docstrings to my Python code |
from typing import Optional, Tuple, Union
import torch
import torch.utils.checkpoint
from torch import nn
from torch.nn import CrossEntropyLoss
from transformers.activations import ACT2FN
from transformers.modeling_utils import PreTrainedModel
from transformers.modeling_outputs import BaseModelOutputWithPast, Causal... | --- +++ @@ -1,3 +1,4 @@+""" PyTorch Moss model."""
from typing import Optional, Tuple, Union
@@ -91,6 +92,9 @@ return reshaped
def _merge_heads(self, tensor, num_attention_heads, attn_head_size):
+ """
+ Merges attn_head_size dim and num_attn_heads dim into n_ctx
+ """
... | https://raw.githubusercontent.com/GaiZhenbiao/ChuanhuChatGPT/HEAD/modules/models/modeling_moss.py |
Document classes and their methods | import base64
import json
import logging
import os
import textwrap
import requests
from typing import List, Dict, Any, Generator
from ..utils import count_token
from ..index_func import construct_index
from ..presets import i18n
from .base_model import BaseLLMModel
class GoogleGeminiClient(BaseLLMModel):
def __i... | --- +++ @@ -37,10 +37,12 @@ self.frequencyPenalty = None
def _encode_image_to_base64(self, image_path: str) -> str:
+ """Encode an image file to base64 string"""
with open(image_path, "rb") as image_file:
return base64.b64encode(image_file.read()).decode("utf-8")
def _... | https://raw.githubusercontent.com/GaiZhenbiao/ChuanhuChatGPT/HEAD/modules/models/GoogleGemini.py |
Turn comments into proper docstrings | from types import SimpleNamespace
import pdfplumber
import logging
from langchain.docstore.document import Document
def prepare_table_config(crop_page):
page = crop_page.root_page # root/parent
cs = page.curves + page.edges
def curves_to_edges():
edges = []
for c in cs:
edges +=... | --- +++ @@ -4,9 +4,14 @@ from langchain.docstore.document import Document
def prepare_table_config(crop_page):
+ """Prepare table查找边界, 要求page为原始page
+
+ From https://github.com/jsvine/pdfplumber/issues/242
+ """
page = crop_page.root_page # root/parent
cs = page.curves + page.edges
def curves... | https://raw.githubusercontent.com/GaiZhenbiao/ChuanhuChatGPT/HEAD/modules/pdf_func.py |
Add docstrings that explain logic | # 代码主要来源于 https://github.com/Shawn-Inspur/Yuan-1.0/blob/main/yuan_api/inspurai.py
import hashlib
import json
import os
import time
import uuid
from datetime import datetime
import pytz
import requests
from modules.presets import NO_APIKEY_MSG
from modules.models.base_model import BaseLLMModel
class Example:
d... | --- +++ @@ -15,6 +15,7 @@
class Example:
+ """ store some examples(input, output pairs and formats) for few-shots to prime the model."""
def __init__(self, inp, out):
self.input = inp
@@ -22,12 +23,15 @@ self.id = uuid.uuid4().hex
def get_input(self):
+ """return the input o... | https://raw.githubusercontent.com/GaiZhenbiao/ChuanhuChatGPT/HEAD/modules/models/inspurai.py |
Generate helpful docstrings for debugging | # -*- coding:utf-8 -*-
from __future__ import annotations
from typing import TYPE_CHECKING, Any, Callable, Dict, List, Tuple, Type
from enum import Enum
import logging
import commentjson as json
import os
import datetime
import csv
import threading
import requests
import hmac
import html
import hashlib
import gradio a... | --- +++ @@ -306,6 +306,9 @@
def convert_bot_before_marked(chat_message):
+ """
+ 注意不能给输出加缩进, 否则会被marked解析成代码块
+ """
if '<div class="md-message">' in chat_message:
return chat_message
else:
@@ -335,6 +338,9 @@
def escape_markdown(text):
+ """
+ Escape Markdown special characters... | https://raw.githubusercontent.com/GaiZhenbiao/ChuanhuChatGPT/HEAD/modules/utils.py |
Provide docstrings following PEP 257 | from __future__ import annotations
import base64
import json
import time
import logging
import os
import shutil
import time
import traceback
from collections import deque
from enum import Enum
from io import BytesIO
from itertools import islice
from threading import Condition, Thread
from typing import Any, Dict, List... | --- +++ @@ -81,6 +81,7 @@
class ChuanhuCallbackHandler(BaseCallbackHandler):
def __init__(self, callback) -> None:
+ """Initialize callback handler."""
self.callback = callback
def on_agent_action(
@@ -96,6 +97,7 @@ llm_prefix: Optional[str] = None,
**kwargs: Any,
) -... | https://raw.githubusercontent.com/GaiZhenbiao/ChuanhuChatGPT/HEAD/modules/models/base_model.py |
Annotate my code with docstrings | # 代码主要来源于 https://github.com/OpenLMLab/MOSS/blob/main/moss_inference.py
import os
import torch
import warnings
import platform
import time
from typing import Union, List, Tuple, Optional, Dict
from huggingface_hub import snapshot_download
from transformers.generation.utils import logger
from accelerate import init_em... | --- +++ @@ -137,6 +137,15 @@ yield i
def preprocess(self, raw_text: str) -> Tuple[torch.Tensor, torch.Tensor]:
+ """
+ Preprocesses the raw input text by adding the prefix and tokenizing it.
+
+ Args:
+ raw_text (str): The raw input text.
+
+ Returns:
+ ... | https://raw.githubusercontent.com/GaiZhenbiao/ChuanhuChatGPT/HEAD/modules/models/MOSS.py |
Add standardized docstrings across the file | import base64
import io
import json
import logging
import os
import pathlib
import tempfile
import time
from datetime import datetime
import requests
import tiktoken
from PIL import Image
from modules.config import retrieve_proxy
from modules.models.XMChat import XMChat
mj_proxy_api_base = os.getenv("MIDJOURNEY_PROX... | --- +++ @@ -23,6 +23,9 @@ class Midjourney_Client(XMChat):
class FetchDataPack:
+ """
+ A class to store data for current fetching data from Midjourney API
+ """
action: str # current action, e.g. "IMAGINE", "UPSCALE", "VARIATION"
prefix_content: str # prefix content, t... | https://raw.githubusercontent.com/GaiZhenbiao/ChuanhuChatGPT/HEAD/modules/models/midjourney.py |
Replace inline comments with docstrings |
import json
import os
import numpy as np
import regex as re
from functools import lru_cache
from typing import TYPE_CHECKING, List, Optional, Tuple, Union
from transformers.utils import is_tf_available, is_torch_available, logging
from transformers.tokenization_utils import AddedToken, PreTrainedTokenizer
if TYPE_... | --- +++ @@ -1,3 +1,4 @@+"""Tokenization classes for Moss"""
import json
import os
@@ -47,6 +48,15 @@
@lru_cache()
def bytes_to_unicode():
+ """
+ Returns list of utf-8 byte and a mapping to unicode strings. We specifically avoids mapping to whitespace/control
+ characters the bpe code barfs on.
+
+ T... | https://raw.githubusercontent.com/GaiZhenbiao/ChuanhuChatGPT/HEAD/modules/models/tokenization_moss.py |
Add docstrings for better understanding |
import json
import os
from pathlib import Path
from claude_code_sdk import ClaudeCodeOptions, ClaudeSDKClient
from claude_code_sdk.types import HookMatcher
from security import bash_security_hook
# Puppeteer MCP tools for browser automation
PUPPETEER_TOOLS = [
"mcp__puppeteer__puppeteer_navigate",
"mcp__pu... | --- +++ @@ -1,3 +1,9 @@+"""
+Claude SDK Client Configuration
+===============================
+
+Functions for creating and configuring the Claude Agent SDK client.
+"""
import json
import os
@@ -32,6 +38,22 @@
def create_client(project_dir: Path, model: str) -> ClaudeSDKClient:
+ """
+ Create a Claude Ag... | https://raw.githubusercontent.com/anthropics/claude-quickstarts/HEAD/autonomous-coding/client.py |
Write docstrings for algorithm functions | #!/usr/bin/env python3
import math
from mcp.server import FastMCP
mcp = FastMCP("Calculator")
@mcp.tool(name="calculator")
def calculator(number1: float, number2: float, operator: str) -> str:
try:
if operator == "+":
result = number1 + number2
elif operator == "-":
res... | --- +++ @@ -1,5 +1,6 @@ #!/usr/bin/env python3
+"""Simple calculator tool for basic math operations."""
import math
@@ -10,6 +11,17 @@
@mcp.tool(name="calculator")
def calculator(number1: float, number2: float, operator: str) -> str:
+ """Performs basic calculations with two numbers.
+
+ Args:
+ ... | https://raw.githubusercontent.com/anthropics/claude-quickstarts/HEAD/agents/tools/calculator_mcp.py |
Add docstrings to make code maintainable |
import asyncio
import os
from contextlib import AsyncExitStack
from dataclasses import dataclass
from typing import Any
from anthropic import Anthropic
from .tools.base import Tool
from .utils.connections import setup_mcp_connections
from .utils.history_util import MessageHistory
from .utils.tool_util import execute... | --- +++ @@ -1,3 +1,4 @@+"""Agent implementation with Claude API and tools."""
import asyncio
import os
@@ -15,6 +16,7 @@
@dataclass
class ModelConfig:
+ """Configuration settings for Claude model parameters."""
# Available models include:
# - claude-sonnet-4-20250514 (default)
@@ -29,6 +31,7 @@
... | https://raw.githubusercontent.com/anthropics/claude-quickstarts/HEAD/agents/agent.py |
Write clean docstrings for readability |
from typing import Any
class MessageHistory:
def __init__(
self,
model: str,
system: str,
context_window_tokens: int,
client: Any,
enable_caching: bool = True,
):
self.model = model
self.system = system
self.context_window_tokens = cont... | --- +++ @@ -1,8 +1,10 @@+"""Message history with token tracking and prompt caching."""
from typing import Any
class MessageHistory:
+ """Manages chat history with token tracking and context management."""
def __init__(
self,
@@ -45,6 +47,7 @@ content: str | list[dict[str, Any]],
... | https://raw.githubusercontent.com/anthropics/claude-quickstarts/HEAD/agents/utils/history_util.py |
Add detailed docstrings explaining each function |
import json
from pathlib import Path
def count_passing_tests(project_dir: Path) -> tuple[int, int]:
tests_file = project_dir / "feature_list.json"
if not tests_file.exists():
return 0, 0
try:
with open(tests_file, "r") as f:
tests = json.load(f)
total = len(tests)
... | --- +++ @@ -1,9 +1,24 @@+"""
+Progress Tracking Utilities
+===========================
+
+Functions for tracking and displaying progress of the autonomous coding agent.
+"""
import json
from pathlib import Path
def count_passing_tests(project_dir: Path) -> tuple[int, int]:
+ """
+ Count passing and total... | https://raw.githubusercontent.com/anthropics/claude-quickstarts/HEAD/autonomous-coding/progress.py |
Provide docstrings following PEP 257 |
from dataclasses import dataclass
from typing import Any
@dataclass
class CodeExecutionServerTool:
name: str = "code_execution"
type: str = "code_execution_20250522"
def to_dict(self) -> dict[str, Any]:
return {
"type": self.type,
"name": self.name,
} | --- +++ @@ -1,3 +1,4 @@+"""Code execution server tool for the agent framework."""
from dataclasses import dataclass
from typing import Any
@@ -5,11 +6,13 @@
@dataclass
class CodeExecutionServerTool:
+ """Code execution server tool that uses Anthropic's server tool format."""
name: str = "code_execu... | https://raw.githubusercontent.com/anthropics/claude-quickstarts/HEAD/agents/tools/code_execution.py |
Write reusable docstrings |
from dataclasses import dataclass
from typing import Any
@dataclass
class Tool:
name: str
description: str
input_schema: dict[str, Any]
def to_dict(self) -> dict[str, Any]:
return {
"name": self.name,
"description": self.description,
"input_schema": self.... | --- +++ @@ -1,3 +1,4 @@+"""Base tool definitions for the agent framework."""
from dataclasses import dataclass
from typing import Any
@@ -5,12 +6,14 @@
@dataclass
class Tool:
+ """Base class for all agent tools."""
name: str
description: str
input_schema: dict[str, Any]
def to_dict(sel... | https://raw.githubusercontent.com/anthropics/claude-quickstarts/HEAD/agents/tools/base.py |
Document all public functions with docstrings |
from dataclasses import dataclass
from typing import Any, Optional
@dataclass
class WebSearchServerTool:
name: str = "web_search"
type: str = "web_search_20250305"
max_uses: Optional[int] = None
allowed_domains: Optional[list[str]] = None
blocked_domains: Optional[list[str]] = None
user_... | --- +++ @@ -1,3 +1,4 @@+"""Web search server tool for the agent framework."""
from dataclasses import dataclass
from typing import Any, Optional
@@ -5,6 +6,7 @@
@dataclass
class WebSearchServerTool:
+ """Web search server tool that uses Anthropic's server tool format."""
name: str = "web_search"
... | https://raw.githubusercontent.com/anthropics/claude-quickstarts/HEAD/agents/tools/web_search.py |
Generate helpful docstrings for debugging |
import os
import shlex
# Allowed commands for development tasks
# Minimal set needed for the autonomous coding demo
ALLOWED_COMMANDS = {
# File inspection
"ls",
"cat",
"head",
"tail",
"wc",
"grep",
# File operations (agent uses SDK tools for most file ops, but cp/mkdir needed occasion... | --- +++ @@ -1,3 +1,10 @@+"""
+Security Hooks for Autonomous Coding Agent
+==========================================
+
+Pre-tool-use hooks that validate bash commands for security.
+Uses an allowlist approach - only explicitly permitted commands can run.
+"""
import os
import shlex
@@ -38,6 +45,17 @@
def split_... | https://raw.githubusercontent.com/anthropics/claude-quickstarts/HEAD/autonomous-coding/security.py |
Document all public functions with docstrings |
import asyncio
from pathlib import Path
from typing import Optional
from claude_code_sdk import ClaudeSDKClient
from client import create_client
from progress import print_session_header, print_progress_summary
from prompts import get_initializer_prompt, get_coding_prompt, copy_spec_to_project
# Configuration
AUTO... | --- +++ @@ -1,3 +1,9 @@+"""
+Agent Session Logic
+===================
+
+Core agent interaction functions for running autonomous coding sessions.
+"""
import asyncio
from pathlib import Path
@@ -19,6 +25,19 @@ message: str,
project_dir: Path,
) -> tuple[str, str]:
+ """
+ Run a single agent session ... | https://raw.githubusercontent.com/anthropics/claude-quickstarts/HEAD/autonomous-coding/agent.py |
Add docstrings following best practices |
from abc import ABC, abstractmethod
from contextlib import AsyncExitStack
from typing import Any
from mcp import ClientSession, StdioServerParameters
from mcp.client.sse import sse_client
from mcp.client.stdio import stdio_client
from ..tools.mcp_tool import MCPTool
class MCPConnection(ABC):
def __init__(self... | --- +++ @@ -1,3 +1,4 @@+"""Connection handling for MCP servers."""
from abc import ABC, abstractmethod
from contextlib import AsyncExitStack
@@ -11,6 +12,7 @@
class MCPConnection(ABC):
+ """Base class for MCP server connections."""
def __init__(self):
self.session = None
@@ -19,8 +21,10 @@
... | https://raw.githubusercontent.com/anthropics/claude-quickstarts/HEAD/agents/utils/connections.py |
Add docstrings to improve code quality |
import shutil
from pathlib import Path
PROMPTS_DIR = Path(__file__).parent / "prompts"
def load_prompt(name: str) -> str:
prompt_path = PROMPTS_DIR / f"{name}.md"
return prompt_path.read_text()
def get_initializer_prompt() -> str:
return load_prompt("initializer_prompt")
def get_coding_prompt() -> ... | --- +++ @@ -1,3 +1,9 @@+"""
+Prompt Loading Utilities
+========================
+
+Functions for loading prompt templates from the prompts directory.
+"""
import shutil
from pathlib import Path
@@ -7,21 +13,25 @@
def load_prompt(name: str) -> str:
+ """Load a prompt template from the prompts directory."""
... | https://raw.githubusercontent.com/anthropics/claude-quickstarts/HEAD/autonomous-coding/prompts.py |
Create documentation for each function signature |
from typing import Any
from .base import Tool
from ..utils.connections import MCPConnection
class MCPTool(Tool):
def __init__(
self,
name: str,
description: str,
input_schema: dict[str, Any],
connection: "MCPConnection",
):
super().__init__(
name=na... | --- +++ @@ -1,3 +1,4 @@+"""Tools that interface with MCP servers."""
from typing import Any
from .base import Tool
@@ -18,6 +19,8 @@ self.connection = connection
async def execute(self, **kwargs) -> str:
+ """Execute the MCP tool with the given input_schema.
+ Note: Currently only suppo... | https://raw.githubusercontent.com/anthropics/claude-quickstarts/HEAD/agents/tools/mcp_tool.py |
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