instruction stringclasses 100
values | code stringlengths 78 193k | response stringlengths 259 170k | file stringlengths 59 203 |
|---|---|---|---|
Add docstrings to incomplete code | import os
import random
import sys
from collections import defaultdict
from collections.abc import Generator, Iterable, Mapping, Sequence
from functools import wraps
from typing import TYPE_CHECKING, Callable, Optional, Union
from dvc.exceptions import InvalidArgumentError
from dvc.repo.experiments.exceptions import A... | --- +++ @@ -77,6 +77,7 @@ def exp_refs(
scm: "Git", url: Optional[str] = None
) -> Generator["ExpRefInfo", None, None]:
+ """Iterate over all experiment refs."""
ref_gen = (
iter_remote_refs(scm, url, base=EXPS_NAMESPACE)
if url
@@ -89,6 +90,7 @@
def exp_refs_by_rev(scm: "Git", rev: ... | https://raw.githubusercontent.com/treeverse/dvc/HEAD/dvc/repo/experiments/utils.py |
Generate docstrings for each module | import os
import string
from collections import defaultdict
from collections.abc import Iterable
from contextlib import suppress
from dataclasses import dataclass
from typing import TYPE_CHECKING, Any, Optional, TypeVar, Union
from funcy import project
from dvc import prompt
from dvc.exceptions import CacheLinkError,... | --- +++ @@ -211,6 +211,10 @@
@property
def addressing(self) -> str:
+ """
+ Useful for alternative presentations where we don't need
+ `Stage:` prefix.
+ """
return self.relpath if self.path else "No path"
def __hash__(self):
@@ -233,18 +237,28 @@
@property
... | https://raw.githubusercontent.com/treeverse/dvc/HEAD/dvc/stage/__init__.py |
Generate consistent docstrings | import logging
import time
from collections import defaultdict
from collections.abc import Iterable, Iterator
from functools import partial
from itertools import chain
from typing import TYPE_CHECKING, Any, Callable, NamedTuple, Optional, Union
from funcy.debug import format_time
from dvc.dependency import ParamsDepe... | --- +++ @@ -47,6 +47,15 @@ def collect_files(
repo: "Repo", onerror: Optional[Callable[[str, Exception], None]] = None
):
+ """Collects all of the stages present in the DVC repo.
+
+ Args:
+ onerror (optional): callable that will be called with two args:
+ the filepath whose collection fai... | https://raw.githubusercontent.com/treeverse/dvc/HEAD/dvc/repo/index.py |
Generate docstrings for exported functions | from collections.abc import Iterable
from functools import partial
from typing import TYPE_CHECKING, Any, Optional, Union
from funcy import first
from dvc.log import logger
from dvc.stage.exceptions import StageUpdateError
if TYPE_CHECKING:
from dvc.data_cloud import Remote
from dvc.output import Output
... | --- +++ @@ -66,6 +66,14 @@ push: bool = False,
**kwargs: Any,
) -> "IndexView":
+ """Return view of data that can be stored in worktree remotes.
+
+ Args:
+ targets: Optional targets.
+ push: Whether the view should be restricted to pushable data only.
+
+ Additional kwargs will be pass... | https://raw.githubusercontent.com/treeverse/dvc/HEAD/dvc/repo/worktree.py |
Add missing documentation to my Python functions |
import hashlib
import os
import time
from abc import ABC, abstractmethod
from datetime import timedelta
from typing import Optional, Union
import flufl.lock
import zc.lockfile
from dvc.exceptions import DvcException
from dvc.progress import Tqdm
from dvc.utils import format_link
DEFAULT_TIMEOUT = 3
FAILED_TO_LOCK... | --- +++ @@ -1,3 +1,4 @@+"""Manages dvc lock file."""
import hashlib
import os
@@ -24,6 +25,7 @@
class LockError(DvcException):
+ """Thrown when unable to acquire the lock for DVC repo."""
class LockBase(ABC):
@@ -81,6 +83,10 @@
class Lock(LockBase):
+ """Class for DVC repo lock.
+
+ Uses zc.lo... | https://raw.githubusercontent.com/treeverse/dvc/HEAD/dvc/lock.py |
Add detailed documentation for each class | from collections import OrderedDict
from collections.abc import Iterable
from operator import attrgetter
from typing import TYPE_CHECKING, Any, Optional, Union, no_type_check
from funcy import post_processing
from dvc.dependency import ParamsDependency
from dvc.output import Annotation, Output
from dvc.utils.collecti... | --- +++ @@ -72,6 +72,14 @@
def _serialize_params_keys(params: Iterable["ParamsDependency"]):
+ """
+ Returns the following format of data:
+ ['lr', 'train', {'params2.yaml': ['lr']}]
+
+ The output is sorted, with keys of params from default params file being
+ at the first, and then followed by ent... | https://raw.githubusercontent.com/treeverse/dvc/HEAD/dvc/stage/serialize.py |
Write proper docstrings for these functions | import os
import tempfile
import threading
from typing import TYPE_CHECKING, Optional
from funcy import retry, wrap_with
from dvc.exceptions import NotDvcRepoError
from dvc.log import logger
from dvc.repo import Repo
from dvc.scm import CloneError, map_scm_exception
from dvc.utils import relpath
if TYPE_CHECKING:
... | --- +++ @@ -128,6 +128,11 @@
def _cached_clone(url, rev):
+ """Clone an external git repo to a temporary directory.
+
+ Returns the path to a local temporary directory with the specified
+ revision checked out.
+ """
from shutil import copytree
# even if we have already cloned this repo, we ... | https://raw.githubusercontent.com/treeverse/dvc/HEAD/dvc/repo/open_repo.py |
Add docstrings to existing functions | from typing import TYPE_CHECKING, Any, Optional
from celery import shared_task
from celery.utils.log import get_task_logger
from dvc.repo.experiments.executor.base import ExecutorInfo
from dvc.repo.experiments.executor.local import TempDirExecutor
from .base import BaseStashQueue, QueueEntry
if TYPE_CHECKING:
f... | --- +++ @@ -17,6 +17,14 @@
@shared_task
def setup_exp(entry_dict: dict[str, Any]) -> "BaseExecutor":
+ """Setup an experiment.
+
+ Arguments:
+ entry_dict: Serialized QueueEntry for this experiment.
+
+ Returns:
+ Root executor (temp) directory for this experiment.
+ """
from dvc.repo ... | https://raw.githubusercontent.com/treeverse/dvc/HEAD/dvc/repo/experiments/queue/tasks.py |
Generate NumPy-style docstrings | import os
import pathlib
from typing import TYPE_CHECKING, Any, Optional, Union
from funcy import concat, first, lsplit, rpartial
from dvc.annotations import ANNOTATION_FIELDS
from dvc.exceptions import InvalidArgumentError
from dvc_data.hashfile.meta import Meta
from .exceptions import (
MissingDataSource,
... | --- +++ @@ -221,6 +221,10 @@
def prepare_file_path(kwargs) -> str:
+ """Determine file path from the first output name.
+
+ Used in creating .dvc files.
+ """
from dvc.dvcfile import DVC_FILE_SUFFIX
out = first(
@@ -260,6 +264,7 @@ def validate_kwargs(
single_stage: bool = False, fname: Op... | https://raw.githubusercontent.com/treeverse/dvc/HEAD/dvc/stage/utils.py |
Write docstrings for algorithm functions | from collections.abc import Iterable, Iterator, Sequence
from contextlib import contextmanager, nullcontext
from typing import TYPE_CHECKING, Any, Callable, Optional, TextIO, Union
import colorama
from dvc.utils.objects import cached_property
if TYPE_CHECKING:
from rich.console import Console as RichConsole
... | --- +++ @@ -265,6 +265,11 @@ self.write(f"Your response must be one of: {choices}. Please try again.")
def confirm(self, statement: str) -> bool:
+ """Ask the user for confirmation about the specified statement.
+
+ Args:
+ statement: statement to ask the user confirmation ab... | https://raw.githubusercontent.com/treeverse/dvc/HEAD/dvc/ui/__init__.py |
Write docstrings describing functionality |
import re
import typing
from contextlib import suppress
from typing import TYPE_CHECKING, Any, Callable, Optional, TypeVar
from dvc.exceptions import PrettyDvcException
from dvc.ui import ui
from dvc.utils.serialize import (
EncodingError,
YAMLFileCorruptedError,
parse_yaml,
parse_yaml_for_update,
)
f... | --- +++ @@ -1,3 +1,11 @@+"""
+This module combines schema and yaml parser into one, to provide better error
+messages through a single entrypoint `load`.
+
+Used for parsing dvc.yaml, dvc.lock and .dvc files.
+
+Not to be confused with strictyaml, a python library with similar motivations.
+"""
import re
import typ... | https://raw.githubusercontent.com/treeverse/dvc/HEAD/dvc/utils/strictyaml.py |
Generate docstrings for each module | from typing import TYPE_CHECKING, Any
from rich.table import Table as RichTable
if TYPE_CHECKING:
from rich.console import Console, ConsoleOptions
class Table(RichTable):
def add_column(self, *args: Any, collapse: bool = False, **kwargs: Any) -> None:
super().add_column(*args, **kwargs)
self... | --- +++ @@ -14,6 +14,12 @@ def _calculate_column_widths(
self, console: "Console", options: "ConsoleOptions"
) -> list[int]:
+ """Calculate the widths of each column, including padding, not
+ including borders.
+
+ Adjacent collapsed columns will be removed until there is only a s... | https://raw.githubusercontent.com/treeverse/dvc/HEAD/dvc/utils/table.py |
Add docstrings with type hints explained |
import os
from contextlib import AbstractContextManager, contextmanager
from typing import TYPE_CHECKING, Any, Callable, Optional, Protocol, TextIO, Union
from funcy import reraise
from dvc.exceptions import DvcException
if TYPE_CHECKING:
from dvc.fs import FileSystem
from dvc.types import StrPath
class D... | --- +++ @@ -1,3 +1,4 @@+"""Common utilities for serialize."""
import os
from contextlib import AbstractContextManager, contextmanager
@@ -37,6 +38,7 @@
class ParseError(DvcException):
+ """Errors while parsing files"""
def __init__(self, path: "StrPath", message: str):
from dvc.utils import r... | https://raw.githubusercontent.com/treeverse/dvc/HEAD/dvc/utils/serialize/_common.py |
Add docstrings that explain inputs and outputs | from collections.abc import Iterable, Mapping
from typing import Union, no_type_check
@no_type_check
def apply_diff(src, dest): # noqa: C901
Seq = (list, tuple) # noqa: N806
Container = (Mapping, list, tuple) # noqa: N806
def is_same_type(a, b):
return any(
isinstance(a, t) and isi... | --- +++ @@ -4,6 +4,14 @@
@no_type_check
def apply_diff(src, dest): # noqa: C901
+ """Recursively apply changes from src to dest.
+
+ Preserves dest type and hidden info in dest structure,
+ like ruamel.yaml leaves when parses files. This includes comments,
+ ordering and line foldings.
+
+ Used in St... | https://raw.githubusercontent.com/treeverse/dvc/HEAD/dvc/utils/collections.py |
Add docstrings that explain inputs and outputs |
import hashlib
import json
import os
import re
import sys
from typing import TYPE_CHECKING, Optional
import colorama
from colorama import AnsiToWin32
if TYPE_CHECKING:
from typing import TextIO
LARGE_DIR_SIZE = 100
TARGET_REGEX = re.compile(r"(?P<path>.*?)(:(?P<name>[^\\/:]*))??$")
def bytes_hash(byts, typ):... | --- +++ @@ -1,3 +1,4 @@+"""Helpers for other modules."""
import hashlib
import json
@@ -24,6 +25,9 @@
def dict_filter(d, exclude=()):
+ """
+ Exclude specified keys from a nested dict
+ """
if not exclude or not isinstance(d, (list, dict)):
return d
@@ -61,6 +65,10 @@
def fix_env(en... | https://raw.githubusercontent.com/treeverse/dvc/HEAD/dvc/utils/__init__.py |
Document this module using docstrings |
import os
from collections.abc import Iterable, Iterator, Mapping
from contextlib import contextmanager
from functools import partial
from typing import TYPE_CHECKING, Literal, Optional, Union, overload
from funcy import group_by
from scmrepo.base import Base # noqa: TC002
from scmrepo.git import Git
from scmrepo.no... | --- +++ @@ -1,3 +1,4 @@+"""Manages source control systems (e.g. Git)."""
import os
from collections.abc import Iterable, Iterator, Mapping
@@ -23,6 +24,7 @@
class SCMError(DvcException):
+ """Base class for source control management errors."""
class CloneError(SCMError):
@@ -94,6 +96,18 @@
def SCM(r... | https://raw.githubusercontent.com/treeverse/dvc/HEAD/dvc/scm.py |
Create documentation for each function signature | import ast
from contextlib import contextmanager
from typing import Any
from funcy import reraise
from ._common import ParseError, _dump_data, _load_data, _modify_data
_PARAMS_KEY = "__params_old_key_for_update__"
_PARAMS_TEXT_KEY = "__params_text_key_for_update__"
class PythonFileCorruptedError(ParseError):
d... | --- +++ @@ -20,6 +20,7 @@
def parse_py(text, path):
+ """Parses text from .py file into Python structure."""
with reraise(SyntaxError, PythonFileCorruptedError(path)):
tree = ast.parse(text, filename=path)
@@ -27,6 +28,7 @@
def parse_py_for_update(text, path):
+ """Parses text into dict fo... | https://raw.githubusercontent.com/treeverse/dvc/HEAD/dvc/utils/serialize/_py.py |
Generate missing documentation strings | from pathlib import Path
from typing import TYPE_CHECKING, Optional
from dvc.exceptions import InvalidArgumentError
from dvc.log import logger
from .collections import merge_dicts, remove_missing_keys, to_omegaconf
if TYPE_CHECKING:
from dvc.types import StrPath
logger = logger.getChild(__name__)
def load_hy... | --- +++ @@ -33,6 +33,22 @@ plugins_path: str,
overrides: list[str],
) -> None:
+ """Compose Hydra config and dumpt it to `output_file`.
+
+ Args:
+ output_file: File where the composed config will be dumped.
+ config_dir: Folder containing the Hydra config files.
+ Must be absol... | https://raw.githubusercontent.com/treeverse/dvc/HEAD/dvc/utils/hydra.py |
Document this script properly | #!/usr/bin/env python3
import sys
import re
import argparse
from typing import List, Dict, Tuple
from collections import OrderedDict
class BibTeXFormatter:
def __init__(self):
# Standard field order for readability
self.field_order = [
'author', 'editor', 'title', 'booktitle', 'jo... | --- +++ @@ -1,4 +1,8 @@ #!/usr/bin/env python3
+"""
+BibTeX Formatter and Cleaner
+Format, clean, sort, and deduplicate BibTeX files.
+"""
import sys
import re
@@ -7,6 +11,7 @@ from collections import OrderedDict
class BibTeXFormatter:
+ """Format and clean BibTeX entries."""
def __init__(self):
... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/citation-management/scripts/format_bibtex.py |
Write docstrings for utility functions | #!/usr/bin/env python3
import argparse
import shutil
from pathlib import Path
TEMPLATES = {
"case_report": "case_report_template.md",
"soap_note": "soap_note_template.md",
"h_and_p": "history_physical_template.md",
"discharge_summary": "discharge_summary_template.md",
"consult_note": "consult_not... | --- +++ @@ -1,4 +1,13 @@ #!/usr/bin/env python3
+"""
+Interactive template generator for clinical reports.
+
+Helps users select and generate appropriate clinical report templates.
+
+Usage:
+ python generate_report_template.py
+ python generate_report_template.py --type case_report --output my_case_report.md
+""... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/clinical-reports/scripts/generate_report_template.py |
Add standardized docstrings across the file | #!/usr/bin/env python3
import requests
import json
from typing import Dict, List, Optional, Union
from urllib.parse import urlencode
BASE_URL = "https://clinicaltrials.gov/api/v2"
def search_studies(
condition: Optional[str] = None,
intervention: Optional[str] = None,
location: Optional[str] = None,
... | --- +++ @@ -1,4 +1,14 @@ #!/usr/bin/env python3
+"""
+ClinicalTrials.gov API Query Helper
+
+A comprehensive Python script for querying the ClinicalTrials.gov API v2.
+Provides convenient functions for common query patterns including searching
+by condition, intervention, location, sponsor, and retrieving specific tria... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/clinicaltrials-database/scripts/query_clinicaltrials.py |
Add docstrings to improve code quality | #!/usr/bin/env python3
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
from lifelines import KaplanMeierFitter
from lifelines.statistics import logrank_test, multivariate_logrank_test
from lifelines import CoxPHFitter
import argparse
from pathlib import Path
def load_survival_data(filepath):
... | --- +++ @@ -1,4 +1,17 @@ #!/usr/bin/env python3
+"""
+Generate Kaplan-Meier Survival Curves for Clinical Decision Support Documents
+
+This script creates publication-quality survival curves with:
+- Kaplan-Meier survival estimates
+- 95% confidence intervals
+- Log-rank test statistics
+- Hazard ratios with confidence... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/clinical-decision-support/scripts/generate_survival_analysis.py |
Generate consistent documentation across files | #!/usr/bin/env python3
import requests
import json
import argparse
from datetime import datetime, timedelta
from typing import List, Dict, Optional, Any
import time
import sys
from urllib.parse import quote
class BioRxivSearcher:
BASE_URL = "https://api.biorxiv.org"
# Valid bioRxiv categories
CATEGORIE... | --- +++ @@ -1,4 +1,11 @@ #!/usr/bin/env python3
+"""
+bioRxiv Search Tool
+A comprehensive Python tool for searching and retrieving preprints from bioRxiv.
+Supports keyword search, author search, date filtering, category filtering, and more.
+
+Note: This tool is focused exclusively on bioRxiv (life sciences preprints... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/biorxiv-database/scripts/biorxiv_search.py |
Turn comments into proper docstrings | #!/usr/bin/env python3
import requests
import time
import json
from pathlib import Path
from typing import Dict, List, Optional, Any
# API Configuration
BASE_URL = "https://api.clinpgx.org/v1/"
RATE_LIMIT_DELAY = 0.5 # 500ms delay = 2 requests/second
def rate_limited_request(url: str, params: Optional[Dict] = None... | --- +++ @@ -1,4 +1,14 @@ #!/usr/bin/env python3
+"""
+ClinPGx API Query Helper Script
+
+Provides ready-to-use functions for querying the ClinPGx database API.
+Includes rate limiting, error handling, and caching functionality.
+
+ClinPGx API: https://api.clinpgx.org/
+Rate limit: 2 requests per second
+License: Creati... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/clinpgx-database/scripts/query_clinpgx.py |
Add inline docstrings for readability | #!/usr/bin/env python3
import argparse
from pathlib import Path
import json
class DecisionNode:
def __init__(self, question, yes_path=None, no_path=None, node_id=None):
self.question = question
self.yes_path = yes_path
self.no_path = no_path
self.node_id = node_id or self._ge... | --- +++ @@ -1,4 +1,12 @@ #!/usr/bin/env python3
+"""
+Build Clinical Decision Tree Flowcharts in TikZ Format
+
+Generates LaTeX/TikZ code for clinical decision algorithms from
+simple text or YAML descriptions.
+
+Dependencies: pyyaml (optional, for YAML input)
+"""
import argparse
from pathlib import Path
@@ -6,6 ... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/clinical-decision-support/scripts/build_decision_tree.py |
Document classes and their methods | #!/usr/bin/env python3
import sys
import re
import requests
import argparse
import json
from typing import Dict, List, Tuple, Optional
from collections import defaultdict
class CitationValidator:
def __init__(self):
self.session = requests.Session()
self.session.headers.update({
'... | --- +++ @@ -1,4 +1,8 @@ #!/usr/bin/env python3
+"""
+Citation Validation Tool
+Validate BibTeX files for accuracy, completeness, and format compliance.
+"""
import sys
import re
@@ -9,6 +13,7 @@ from collections import defaultdict
class CitationValidator:
+ """Validate BibTeX entries for errors and inconsiste... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/citation-management/scripts/validate_citations.py |
Add docstrings to improve readability | #!/usr/bin/env python3
import sys
import os
import requests
import argparse
import json
import time
import xml.etree.ElementTree as ET
from typing import List, Dict, Optional
from datetime import datetime
class PubMedSearcher:
def __init__(self, api_key: Optional[str] = None, email: Optional[str] = None):
... | --- +++ @@ -1,4 +1,8 @@ #!/usr/bin/env python3
+"""
+PubMed Search Tool
+Search PubMed using E-utilities API and export results.
+"""
import sys
import os
@@ -11,8 +15,16 @@ from datetime import datetime
class PubMedSearcher:
+ """Search PubMed using NCBI E-utilities API."""
def __init__(self, api_... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/citation-management/scripts/search_pubmed.py |
Help me add docstrings to my project | #!/usr/bin/env python3
import argparse
import deepchem as dc
import sys
PRETRAINED_MODELS = {
'chemberta': {
'name': 'ChemBERTa',
'description': 'BERT pretrained on 77M molecules from ZINC15',
'model_id': 'seyonec/ChemBERTa-zinc-base-v1'
},
'grover': {
'name': 'GROVER',
... | --- +++ @@ -1,4 +1,14 @@ #!/usr/bin/env python3
+"""
+Transfer Learning Script for DeepChem
+
+Use pretrained models (ChemBERTa, GROVER, MolFormer) for molecular property prediction
+with transfer learning. Particularly useful for small datasets.
+
+Usage:
+ python transfer_learning.py --model chemberta --data my_da... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/deepchem/scripts/transfer_learning.py |
Replace inline comments with docstrings | #!/usr/bin/env python3
import argparse
import sys
WORKFLOWS = {
'chipseq_qc': {
'name': 'ChIP-seq Quality Control',
'description': 'Complete QC workflow for ChIP-seq experiments',
},
'chipseq_analysis': {
'name': 'ChIP-seq Complete Analysis',
'description': 'Full ChIP-seq ... | --- +++ @@ -1,4 +1,9 @@ #!/usr/bin/env python3
+"""
+deepTools Workflow Generator
+
+Generates bash script templates for common deepTools workflows.
+"""
import argparse
import sys
@@ -25,6 +30,7 @@
def generate_chipseq_qc_workflow(output_file, params):
+ """Generate ChIP-seq QC workflow script."""
sc... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/deeptools/scripts/workflow_generator.py |
Insert docstrings into my code |
import math
import numpy as np
from typing import List, Dict, Any, Optional, Tuple
import matplotlib.pyplot as plt
import seaborn as sns
from pathlib import Path
try:
import pandas as pd
PANDAS_AVAILABLE = True
except ImportError:
print("Warning: pandas not installed. Install with: uv pip install pandas")... | --- +++ @@ -1,3 +1,27 @@+"""
+BRENDA Database Visualization Utilities
+
+This module provides visualization functions for BRENDA enzyme data,
+including kinetic parameters, environmental conditions, and pathway analysis.
+
+Key features:
+- Plot Km, kcat, and Vmax distributions
+- Compare enzyme properties across organ... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/brenda-database/scripts/brenda_visualization.py |
Add docstrings for internal functions | #!/usr/bin/env python3
import argparse
import deepchem as dc
import numpy as np
import sys
def train_solubility_model(data_path=None, smiles_col='smiles', target_col='measured log solubility in mols per litre'):
print("=" * 60)
print("DeepChem Solubility Prediction")
print("=" * 60)
# Load data
... | --- +++ @@ -1,4 +1,14 @@ #!/usr/bin/env python3
+"""
+Molecular Solubility Prediction Script
+
+This script trains a model to predict aqueous solubility from SMILES strings
+using the Delaney (ESOL) dataset as an example. Can be adapted for custom datasets.
+
+Usage:
+ python predict_solubility.py --data custom_data... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/deepchem/scripts/predict_solubility.py |
Generate docstrings with parameter types | #!/usr/bin/env python3
import sys
import requests
import argparse
import time
import json
from typing import Optional, List
class DOIConverter:
def __init__(self):
self.session = requests.Session()
self.session.headers.update({
'User-Agent': 'DOIConverter/1.0 (Citation Management ... | --- +++ @@ -1,4 +1,8 @@ #!/usr/bin/env python3
+"""
+DOI to BibTeX Converter
+Quick utility to convert DOIs to BibTeX format using CrossRef API.
+"""
import sys
import requests
@@ -8,6 +12,7 @@ from typing import Optional, List
class DOIConverter:
+ """Convert DOIs to BibTeX entries using CrossRef API."""
... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/citation-management/scripts/doi_to_bibtex.py |
Improve documentation using docstrings | #!/usr/bin/env python3
import requests
import sys
import os
from typing import Optional
def download_cosmic_file(
email: str,
password: str,
filepath: str,
output_filename: Optional[str] = None,
genome_assembly: str = "GRCh38"
) -> bool:
base_url = "https://cancer.sanger.ac.uk/cosmic/file_dow... | --- +++ @@ -1,4 +1,25 @@ #!/usr/bin/env python3
+"""
+COSMIC Data Download Utility
+
+This script provides functions to download data from the COSMIC database
+(Catalogue of Somatic Mutations in Cancer).
+
+Usage:
+ from download_cosmic import download_cosmic_file, list_available_files
+
+ # Download a specific f... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/cosmic-database/scripts/download_cosmic.py |
Create simple docstrings for beginners | #!/usr/bin/env python3
import argparse
import os
import sys
import json
from pathlib import Path
from collections import defaultdict
import re
def parse_confidence_scores(results_dir):
results = {}
results_path = Path(results_dir)
# Check if this is a single complex or batch results
sdf_files = list... | --- +++ @@ -1,4 +1,15 @@ #!/usr/bin/env python3
+"""
+DiffDock Results Analysis Script
+
+This script analyzes DiffDock prediction results, extracting confidence scores,
+ranking predictions, and generating summary reports.
+
+Usage:
+ python analyze_results.py results/output_dir/
+ python analyze_results.py resu... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/diffdock/scripts/analyze_results.py |
Turn comments into proper docstrings | #!/usr/bin/env python3
import sys
import argparse
import csv
import time
from bioservices import UniProt
# Common database code mappings
DATABASE_CODES = {
'uniprot': 'UniProtKB_AC-ID',
'uniprotkb': 'UniProtKB_AC-ID',
'kegg': 'KEGG',
'geneid': 'GeneID',
'entrez': 'GeneID',
'ensembl': 'Ensembl... | --- +++ @@ -1,4 +1,33 @@ #!/usr/bin/env python3
+"""
+Batch Identifier Converter
+
+This script converts multiple identifiers between biological databases
+using UniProt's mapping service. Supports batch processing with
+automatic chunking and error handling.
+
+Usage:
+ python batch_id_converter.py INPUT_FILE --fro... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/bioservices/scripts/batch_id_converter.py |
Document functions with clear intent | #!/usr/bin/env python3
import argparse
import os
import sys
import pandas as pd
from pathlib import Path
try:
from rdkit import Chem
from rdkit import RDLogger
RDLogger.DisableLog('rdApp.*')
RDKIT_AVAILABLE = True
except ImportError:
RDKIT_AVAILABLE = False
print("Warning: RDKit not available.... | --- +++ @@ -1,4 +1,15 @@ #!/usr/bin/env python3
+"""
+DiffDock Batch CSV Preparation and Validation Script
+
+This script helps prepare and validate CSV files for DiffDock batch processing.
+It checks for required columns, validates file paths, and ensures SMILES strings
+are properly formatted.
+
+Usage:
+ python p... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/diffdock/scripts/prepare_batch_csv.py |
Write docstrings describing each step | #!/usr/bin/env python3
import argparse
import deepchem as dc
import sys
AVAILABLE_MODELS = {
'gcn': 'Graph Convolutional Network',
'gat': 'Graph Attention Network',
'attentivefp': 'Attentive Fingerprint',
'mpnn': 'Message Passing Neural Network',
'dmpnn': 'Directed Message Passing Neural Network'... | --- +++ @@ -1,4 +1,15 @@ #!/usr/bin/env python3
+"""
+Graph Neural Network Training Script
+
+This script demonstrates training Graph Convolutional Networks (GCNs) and other
+graph-based models for molecular property prediction.
+
+Usage:
+ python graph_neural_network.py --dataset tox21 --model gcn
+ python graph... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/deepchem/scripts/graph_neural_network.py |
Document functions with clear intent | #!/usr/bin/env python3
import sys
import time
import argparse
from bioservices import UniProt, KEGG, NCBIblast, PSICQUIC, QuickGO
def search_protein(query):
print(f"\n{'='*70}")
print("STEP 1: UniProt Search")
print(f"{'='*70}")
u = UniProt(verbose=False)
print(f"Searching for: {query}")
#... | --- +++ @@ -1,4 +1,24 @@ #!/usr/bin/env python3
+"""
+Complete Protein Analysis Workflow
+
+This script performs a comprehensive protein analysis pipeline:
+1. UniProt search and identifier retrieval
+2. FASTA sequence retrieval
+3. BLAST similarity search
+4. KEGG pathway discovery
+5. PSICQUIC interaction mapping
+6.... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/bioservices/scripts/protein_analysis_workflow.py |
Auto-generate documentation strings for this file | #!/usr/bin/env python3
import os
import sys
import argparse
from pathlib import Path
def check_file_exists(filepath):
if not os.path.exists(filepath):
return False, f"File not found: {filepath}"
if not os.access(filepath, os.R_OK):
return False, f"File not readable: {filepath}"
return Tru... | --- +++ @@ -1,4 +1,10 @@ #!/usr/bin/env python3
+"""
+deepTools File Validation Script
+
+Validates BAM, bigWig, and BED files for deepTools analysis.
+Checks for file existence, proper indexing, and basic format requirements.
+"""
import os
import sys
@@ -7,6 +13,7 @@
def check_file_exists(filepath):
+ """C... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/deeptools/scripts/validate_files.py |
Write beginner-friendly docstrings | #!/usr/bin/env python3
import argparse
import json
import re
from pathlib import Path
ICH_E3_SECTIONS = {
"title_page": "Title Page",
"synopsis": "Synopsis (2)",
"toc": "Table of Contents (3)",
"abbreviations": "List of Abbreviations (4)",
"ethics": "Ethics (Section 2)",
"investigators": "Inv... | --- +++ @@ -1,4 +1,12 @@ #!/usr/bin/env python3
+"""
+Validate clinical trial reports against ICH-E3 structure.
+
+Checks Clinical Study Reports (CSR) for ICH-E3 compliance.
+
+Usage:
+ python validate_trial_report.py <csr_file.md>
+"""
import argparse
import json
@@ -26,6 +34,7 @@
def validate_ich_e3(filena... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/clinical-reports/scripts/validate_trial_report.py |
Generate missing documentation strings | #!/usr/bin/env python3
import sys
import json
import base64
import argparse
from pathlib import Path
from typing import Optional
def check_env_file() -> Optional[str]:
# Look for .env in current directory and parent directories
current_dir = Path.cwd()
for parent in [current_dir] + list(current_dir.paren... | --- +++ @@ -1,4 +1,15 @@ #!/usr/bin/env python3
+"""
+Generate and edit images using OpenRouter API with various image generation models.
+
+Supports models like:
+- google/gemini-3.1-flash-image-preview (generation and editing)
+- black-forest-labs/flux.2-pro (generation and editing)
+- black-forest-labs/flux.2-flex (... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/generate-image/scripts/generate_image.py |
Add return value explanations in docstrings | #!/usr/bin/env python3
import sys
import os
import requests
import argparse
import time
import re
import json
import xml.etree.ElementTree as ET
from typing import Optional, Dict, List, Tuple
from urllib.parse import urlparse
class MetadataExtractor:
def __init__(self, email: Optional[str] = None):
s... | --- +++ @@ -1,4 +1,8 @@ #!/usr/bin/env python3
+"""
+Metadata Extraction Tool
+Extract citation metadata from DOI, PMID, arXiv ID, or URL using various APIs.
+"""
import sys
import os
@@ -12,8 +16,15 @@ from urllib.parse import urlparse
class MetadataExtractor:
+ """Extract metadata from various sources and g... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/citation-management/scripts/extract_metadata.py |
Write clean docstrings for readability | #!/usr/bin/env python3
import json
import os
import platform
import psutil
import subprocess
import sys
from pathlib import Path
from typing import Dict, List, Any, Optional
def get_cpu_info() -> Dict[str, Any]:
cpu_info = {
"physical_cores": psutil.cpu_count(logical=False),
"logical_cores": psut... | --- +++ @@ -1,4 +1,14 @@ #!/usr/bin/env python3
+"""
+System Resource Detection Script
+
+Detects available compute resources including CPU, GPU, memory, and disk space.
+Outputs a JSON file that Claude Code can use to make informed decisions about
+computational approaches (e.g., whether to use Dask, Zarr, Joblib, etc... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/get-available-resources/scripts/detect_resources.py |
Replace inline comments with docstrings |
import re
import json
import time
from typing import List, Dict, Any, Optional, Set, Tuple
from pathlib import Path
try:
import networkx as nx
NETWORKX_AVAILABLE = True
except ImportError:
print("Warning: networkx not installed. Install with: uv pip install networkx")
NETWORKX_AVAILABLE = False
try:
... | --- +++ @@ -1,3 +1,27 @@+"""
+Enzyme Pathway Builder for Retrosynthetic Analysis
+
+This module provides tools for constructing enzymatic pathways and
+retrosynthetic trees using BRENDA database information.
+
+Key features:
+- Find enzymatic pathways for target products
+- Build retrosynthetic trees from products
+- S... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/brenda-database/scripts/enzyme_pathway_builder.py |
Add well-formatted docstrings | #!/usr/bin/env python3
import argparse
import sys
from pathlib import Path
import gget
import pandas as pd
def read_gene_list(file_path):
file_path = Path(file_path)
if file_path.suffix == ".csv":
df = pd.read_csv(file_path)
# Assume first column contains gene names
genes = df.iloc[:... | --- +++ @@ -1,4 +1,8 @@ #!/usr/bin/env python3
+"""
+Enrichment Analysis Pipeline
+Perform comprehensive enrichment analysis on a gene list
+"""
import argparse
import sys
@@ -8,6 +12,7 @@
def read_gene_list(file_path):
+ """Read gene list from file (one gene per line or CSV)."""
file_path = Path(file_p... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/gget/scripts/enrichment_pipeline.py |
Document helper functions with docstrings | #!/usr/bin/env python3
import argparse
import sys
import os
from pathlib import Path
def check_python_version():
import sys
version = sys.version_info
print("Checking Python version...")
if version.major == 3 and version.minor >= 8:
print(f" ✓ Python {version.major}.{version.minor}.{version... | --- +++ @@ -1,4 +1,14 @@ #!/usr/bin/env python3
+"""
+DiffDock Environment Setup Checker
+
+This script verifies that the DiffDock environment is properly configured
+and all dependencies are available.
+
+Usage:
+ python setup_check.py
+ python setup_check.py --verbose
+"""
import argparse
import sys
@@ -7,6... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/diffdock/scripts/setup_check.py |
Add docstrings for production code | #!/usr/bin/env python3
import argparse
import pandas as pd
from arboreto.algo import grnboost2
from arboreto.utils import load_tf_names
def run_grn_inference(expression_file, output_file, tf_file=None, seed=777):
print(f"Loading expression data from {expression_file}...")
expression_data = pd.read_csv(expres... | --- +++ @@ -1,4 +1,19 @@ #!/usr/bin/env python3
+"""
+Basic GRN inference example using Arboreto.
+
+This script demonstrates the standard workflow for inferring gene regulatory
+networks from expression data using GRNBoost2.
+
+Usage:
+ python basic_grn_inference.py <expression_file> <output_file> [--tf-file TF_FIL... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/arboreto/scripts/basic_grn_inference.py |
Add return value explanations in docstrings | #!/usr/bin/env python3
import argparse
import base64
import json
import os
import re
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")
s... | --- +++ @@ -1,4 +1,23 @@ #!/usr/bin/env python3
+"""
+AI-powered infographic generation using Nano Banana Pro.
+
+This script uses a smart iterative refinement approach:
+1. (Optional) Research phase - gather facts and data using Perplexity Sonar
+2. Generate initial infographic with Nano Banana Pro
+3. AI quality revi... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/infographics/scripts/generate_infographic_ai.py |
Write docstrings describing each step | #!/usr/bin/env python3
import sys
import argparse
import json
import time
import random
from typing import List, Dict, Optional
try:
from scholarly import scholarly, ProxyGenerator
SCHOLARLY_AVAILABLE = True
except ImportError:
SCHOLARLY_AVAILABLE = False
print('Warning: scholarly library not installe... | --- +++ @@ -1,4 +1,11 @@ #!/usr/bin/env python3
+"""
+Google Scholar Search Tool
+Search Google Scholar and export results.
+
+Note: This script requires the 'scholarly' library.
+Install with: pip install scholarly
+"""
import sys
import argparse
@@ -15,8 +22,15 @@ print('Warning: scholarly library not install... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/citation-management/scripts/search_google_scholar.py |
Generate docstrings for script automation | #!/usr/bin/env python3
import argparse
import csv
from collections import defaultdict
from pathlib import Path
def format_ae_summary_table(data: list) -> str:
# Group by treatment arm
arm_stats = defaultdict(lambda: {
'total': 0,
'any_ae': 0,
'related_ae': 0,
'sae': 0,
... | --- +++ @@ -1,4 +1,12 @@ #!/usr/bin/env python3
+"""
+Format adverse event data into tables for clinical trial reports.
+
+Converts CSV or structured data into formatted AE summary tables.
+
+Usage:
+ python format_adverse_events.py <ae_data.csv>
+"""
import argparse
import csv
@@ -7,6 +15,7 @@
def format_ae... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/clinical-reports/scripts/format_adverse_events.py |
Document this script properly | #!/usr/bin/env python3
import argparse
import json
import sys
import urllib.parse
import urllib.request
from typing import Optional, Dict, Any, List
DATASETS_API_BASE = "https://api.ncbi.nlm.nih.gov/datasets/v2alpha/gene"
def get_taxon_id(taxon_name: str) -> Optional[str]:
# Common mappings
common_taxa = {... | --- +++ @@ -1,4 +1,10 @@ #!/usr/bin/env python3
+"""
+Fetch gene data from NCBI using the Datasets API.
+
+This script provides access to the NCBI Datasets API for retrieving
+comprehensive gene information including metadata and sequences.
+"""
import argparse
import json
@@ -12,6 +18,15 @@
def get_taxon_id(ta... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/gene-database/scripts/fetch_gene_data.py |
Write reusable docstrings | #!/usr/bin/env python3
import argparse
import sys
from pathlib import Path
import gget
def read_fasta(fasta_file):
sequences = []
current_id = None
current_seq = []
with open(fasta_file, "r") as f:
for line in f:
line = line.strip()
if line.startswith(">"):
... | --- +++ @@ -1,4 +1,8 @@ #!/usr/bin/env python3
+"""
+Batch Sequence Analysis Script
+Analyze multiple sequences: BLAST, alignment, and structure prediction
+"""
import argparse
import sys
@@ -7,6 +11,7 @@
def read_fasta(fasta_file):
+ """Read sequences from FASTA file."""
sequences = []
current_id ... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/gget/scripts/batch_sequence_analysis.py |
Write docstrings including parameters and return values | #!/usr/bin/env python3
import argparse
import sys
import gget
def analyze_gene(gene_name, species="homo_sapiens", output_prefix=None):
if output_prefix is None:
output_prefix = gene_name.lower()
print(f"Analyzing gene: {gene_name}")
print("=" * 60)
# Step 1: Search for the gene
print("\... | --- +++ @@ -1,4 +1,8 @@ #!/usr/bin/env python3
+"""
+Gene Analysis Script
+Quick analysis of a gene: search, info, sequences, expression, and enrichment
+"""
import argparse
import sys
@@ -6,6 +10,14 @@
def analyze_gene(gene_name, species="homo_sapiens", output_prefix=None):
+ """
+ Perform comprehensive ... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/gget/scripts/gene_analysis.py |
Add docstrings to existing functions | #!/usr/bin/env python3
import argparse
import json
import re
from pathlib import Path
from typing import Dict, List
# 18 HIPAA Identifiers patterns
HIPAA_IDENTIFIERS = {
"1_names": {
"description": "Names (patient, family, providers)",
"patterns": [
r"\b(Dr\.|Mr\.|Mrs\.|Ms\.)\s+[A-Z][... | --- +++ @@ -1,4 +1,13 @@ #!/usr/bin/env python3
+"""
+Check clinical reports for HIPAA identifiers that need removal.
+
+Scans text for 18 HIPAA identifiers and flags potential privacy violations.
+
+Usage:
+ python check_deidentification.py <input_file>
+ python check_deidentification.py <input_file> --output vi... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/clinical-reports/scripts/check_deidentification.py |
Create docstrings for reusable components | #!/usr/bin/env python3
import pandas as pd
import numpy as np
from scipy import stats
from pathlib import Path
import argparse
def calculate_p_value(data, variable, group_col='group', var_type='categorical'):
groups = data[group_col].unique()
if len(groups) != 2:
return np.nan # Only handl... | --- +++ @@ -1,4 +1,15 @@ #!/usr/bin/env python3
+"""
+Generate Clinical Cohort Tables for Baseline Characteristics and Outcomes
+
+Creates publication-ready tables with:
+- Baseline demographics (Table 1 style)
+- Efficacy outcomes
+- Safety/adverse events
+- Statistical comparisons between groups
+
+Dependencies: pand... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/clinical-decision-support/scripts/create_cohort_tables.py |
Generate docstrings with examples | #!/usr/bin/env python3
import argparse
import json
import re
from pathlib import Path
from typing import Dict, List, Tuple
class CareValidator:
# CARE checklist items with regex patterns
CARE_REQUIREMENTS = {
"title": {
"name": "Title contains 'case report'",
"pattern": r... | --- +++ @@ -1,4 +1,14 @@ #!/usr/bin/env python3
+"""
+Validate case reports against CARE (CAse REport) guidelines.
+
+This script checks a clinical case report for compliance with CARE guidelines
+and provides a checklist of required elements.
+
+Usage:
+ python validate_case_report.py <input_file.md|.txt>
+ pyth... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/clinical-reports/scripts/validate_case_report.py |
Write docstrings that follow conventions | #!/usr/bin/env python3
import pandas as pd
import numpy as np
from scipy import stats
import argparse
from pathlib import Path
def classify_binary_biomarker(data, biomarker_col, threshold,
above_label='Biomarker+', below_label='Biomarker-'):
data = data.copy()
data['biomar... | --- +++ @@ -1,4 +1,15 @@ #!/usr/bin/env python3
+"""
+Biomarker-Based Patient Stratification and Classification
+
+Performs patient stratification based on biomarker profiles with:
+- Binary classification (biomarker+/-)
+- Multi-class molecular subtypes
+- Continuous biomarker scoring
+- Correlation with clinical outc... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/clinical-decision-support/scripts/biomarker_classifier.py |
Create docstrings for API functions | #!/usr/bin/env python3
import argparse
import sys
import yaml
import os
from pathlib import Path
from datetime import datetime
def load_config(config_path='config.yaml'):
try:
with open(config_path, 'r') as f:
return yaml.safe_load(f)
except FileNotFoundError:
print(f"❌ Configurat... | --- +++ @@ -1,4 +1,9 @@ #!/usr/bin/env python3
+"""
+LabArchives Entry Operations
+
+Utilities for creating entries, uploading attachments, and managing notebook content.
+"""
import argparse
import sys
@@ -9,6 +14,7 @@
def load_config(config_path='config.yaml'):
+ """Load configuration from YAML file"""
... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/labarchive-integration/scripts/entry_operations.py |
Add docstrings to existing functions | #!/usr/bin/env python3
import requests
import json
import argparse
import xml.etree.ElementTree as ET
import time
import sys
import os
import re
from typing import List, Dict, Optional
from urllib.parse import quote
class ArxivSearcher:
BASE_URL = "http://export.arxiv.org/api/query"
ATOM_NS = "{http://www.w... | --- +++ @@ -1,4 +1,9 @@ #!/usr/bin/env python3
+"""
+arXiv Search Tool
+Search and retrieve preprints from arXiv via the Atom API.
+Supports keyword search, author search, category filtering, ID lookup, and PDF download.
+"""
import requests
import json
@@ -13,6 +18,7 @@
class ArxivSearcher:
+ """Search inte... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/arxiv-database/scripts/arxiv_search.py |
Create simple docstrings for beginners | #!/usr/bin/env python3
import argparse
import json
import re
# Common medical abbreviations that should be avoided (JCAHO "Do Not Use" list)
DO_NOT_USE = {
"U": "Unit",
"IU": "International Unit",
"QD": "daily",
"QOD": "every other day",
"MS": "morphine sulfate or magnesium sulfate",
"MSO4": ... | --- +++ @@ -1,4 +1,10 @@ #!/usr/bin/env python3
+"""
+Validate medical terminology and coding in clinical reports.
+
+Usage:
+ python terminology_validator.py <report_file>
+"""
import argparse
import json
@@ -21,6 +27,7 @@
def check_do_not_use_abbreviations(content: str) -> dict:
+ """Check for prohibite... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/clinical-reports/scripts/terminology_validator.py |
Add detailed documentation for each class | #!/usr/bin/env python3
import sys
import argparse
from bioservices import KEGG, UniChem, ChEBI, ChEMBL
def search_kegg_compound(compound_name):
print(f"\n{'='*70}")
print("STEP 1: KEGG Compound Search")
print(f"{'='*70}")
k = KEGG()
print(f"Searching KEGG for: {compound_name}")
try:
... | --- +++ @@ -1,4 +1,22 @@ #!/usr/bin/env python3
+"""
+Compound Cross-Database Search
+
+This script searches for a compound by name and retrieves identifiers
+from multiple databases:
+- KEGG Compound
+- ChEBI
+- ChEMBL (via UniChem)
+- Basic compound properties
+
+Usage:
+ python compound_cross_reference.py COMPOUN... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/bioservices/scripts/compound_cross_reference.py |
Create Google-style docstrings for my code | #!/usr/bin/env python3
import sys
import os
import argparse
import csv
from collections import Counter
from bioservices import KEGG
def get_all_pathways(kegg, organism):
print(f"\nRetrieving pathways for {organism}...")
kegg.organism = organism
pathway_ids = kegg.pathwayIds
print(f"✓ Found {len(pat... | --- +++ @@ -1,4 +1,27 @@ #!/usr/bin/env python3
+"""
+KEGG Pathway Network Analysis
+
+This script analyzes all pathways for an organism and extracts:
+- Pathway sizes (number of genes)
+- Protein-protein interactions
+- Interaction type distributions
+- Network data in various formats (CSV, SIF)
+
+Usage:
+ python ... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/bioservices/scripts/pathway_analysis.py |
Document all endpoints with docstrings | #!/usr/bin/env python3
import argparse
import json
import sys
import time
import urllib.parse
import urllib.request
from typing import Optional, Dict, List, Any
from xml.etree import ElementTree as ET
BASE_URL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/"
DB = "gene"
def esearch(query: str, retmax: int = 20, ... | --- +++ @@ -1,4 +1,10 @@ #!/usr/bin/env python3
+"""
+Query NCBI Gene database using E-utilities.
+
+This script provides access to ESearch, ESummary, and EFetch functions
+for searching and retrieving gene information.
+"""
import argparse
import json
@@ -15,6 +21,17 @@
def esearch(query: str, retmax: int = 20... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/gene-database/scripts/query_gene.py |
Add docstrings to improve readability | #!/usr/bin/env python3
import re
import argparse
from pathlib import Path
from collections import defaultdict
class CDSValidator:
def __init__(self, filepath):
self.filepath = filepath
with open(filepath, 'r', encoding='utf-8', errors='ignore') as f:
self.content = f.read()
... | --- +++ @@ -1,4 +1,17 @@ #!/usr/bin/env python3
+"""
+Validate Clinical Decision Support Documents for Quality and Completeness
+
+Checks for:
+- Evidence citations for all recommendations
+- Statistical reporting completeness
+- Biomarker nomenclature consistency
+- Required sections present
+- HIPAA de-identification... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/clinical-decision-support/scripts/validate_cds_document.py |
Create documentation for each function signature | #!/usr/bin/env python3
import yaml
import os
from pathlib import Path
def get_regional_endpoint():
print("\nSelect your regional API endpoint:")
print("1. US/International (mynotebook.labarchives.com)")
print("2. Australia (aunotebook.labarchives.com)")
print("3. UK (uknotebook.labarchives.com)")
... | --- +++ @@ -1,4 +1,10 @@ #!/usr/bin/env python3
+"""
+LabArchives Configuration Setup Script
+
+This script helps create a config.yaml file with necessary credentials
+for LabArchives API access.
+"""
import yaml
import os
@@ -6,6 +12,7 @@
def get_regional_endpoint():
+ """Prompt user to select regional API ... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/labarchive-integration/scripts/setup_config.py |
Add docstrings for better understanding | #!/usr/bin/env python3
import argparse
import os
import subprocess
import sys
from pathlib import Path
# Available options for quick reference
INFOGRAPHIC_TYPES = [
"statistical", "timeline", "process", "comparison", "list",
"geographic", "hierarchical", "anatomical", "resume", "social"
]
STYLE_PRESETS = [
... | --- +++ @@ -1,4 +1,18 @@ #!/usr/bin/env python3
+"""
+Generate professional infographics using Nano Banana Pro.
+
+This script generates infographics with smart iterative refinement:
+- Uses Nano Banana Pro (Gemini 3 Pro Image Preview) for generation
+- Uses Gemini 3 Pro for quality review
+- Only regenerates if qualit... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/infographics/scripts/generate_infographic.py |
Add missing documentation to my Python functions | #!/usr/bin/env python3
import json
import sys
from typing import Dict, List
from datetime import datetime
def format_search_results(results: List[Dict], output_format: str = 'json') -> str:
if output_format == 'json':
return json.dumps(results, indent=2)
elif output_format == 'markdown':
md =... | --- +++ @@ -1,4 +1,8 @@ #!/usr/bin/env python3
+"""
+Literature Database Search Script
+Searches multiple literature databases and aggregates results.
+"""
import json
import sys
@@ -6,6 +10,16 @@ from datetime import datetime
def format_search_results(results: List[Dict], output_format: str = 'json') -> str:
+ ... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/literature-review/scripts/search_databases.py |
Add documentation for all methods | #!/usr/bin/env python3
import os
import sys
import argparse
import json
from pathlib import Path
from typing import Dict, List, Set, Tuple
from datetime import datetime
# ISO 13485:2016 Required Documented Procedures
REQUIRED_PROCEDURES = {
"4.1.5": {
"title": "Risk Management",
"keywords": ["ris... | --- +++ @@ -1,4 +1,13 @@ #!/usr/bin/env python3
+"""
+ISO 13485 Gap Analysis Tool
+
+This script analyzes documentation provided by the user and identifies gaps
+against ISO 13485:2016 requirements.
+
+Usage:
+ python gap_analyzer.py --docs-dir <path> [--output <path>]
+"""
import os
import sys
@@ -153,13 +162,1... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/iso-13485-certification/scripts/gap_analyzer.py |
Insert docstrings into my code | #!/usr/bin/env python3
import argparse
import sys
import yaml
from datetime import datetime
from pathlib import Path
def load_config(config_path='config.yaml'):
try:
with open(config_path, 'r') as f:
return yaml.safe_load(f)
except FileNotFoundError:
print(f"❌ Configuration file n... | --- +++ @@ -1,4 +1,9 @@ #!/usr/bin/env python3
+"""
+LabArchives Notebook Operations
+
+Utilities for listing, backing up, and managing LabArchives notebooks.
+"""
import argparse
import sys
@@ -8,6 +13,7 @@
def load_config(config_path='config.yaml'):
+ """Load configuration from YAML file"""
try:
... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/labarchive-integration/scripts/notebook_operations.py |
Document this script properly | #!/usr/bin/env python3
import argparse
import os
import subprocess
import sys
from pathlib import Path
# Visual definitions with prompts
# Each tuple: (filename, tool, prompt_template, is_core)
# is_core=True for the 5-6 essential visuals to generate first
CORE_VISUALS = [
# Priority 1: Market Growth Trajectory... | --- +++ @@ -1,4 +1,23 @@ #!/usr/bin/env python3
+"""
+Market Research Report Visual Generator
+
+Batch generates visuals for a market research report using
+scientific-schematics and generate-image skills.
+
+Default behavior: Generate 5-6 core visuals only
+Use --all flag to generate all 28 extended visuals
+
+Usage:
... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/market-research-reports/scripts/generate_market_visuals.py |
Add docstrings to improve collaboration |
import urllib.request
import urllib.parse
import urllib.error
from typing import Optional, List, Union
KEGG_BASE_URL = "https://rest.kegg.jp"
def kegg_info(database: str) -> str:
url = f"{KEGG_BASE_URL}/info/{database}"
try:
with urllib.request.urlopen(url) as response:
return response.... | --- +++ @@ -1,3 +1,14 @@+"""
+KEGG REST API Helper Functions
+
+This module provides Python functions for interacting with the KEGG REST API.
+All functions return raw response text which can be parsed as needed.
+
+API Base URL: https://rest.kegg.jp
+Documentation: https://www.kegg.jp/kegg/rest/keggapi.html
+
+IMPORTA... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/kegg-database/scripts/kegg_api.py |
Can you add docstrings to this Python file? | #!/usr/bin/env python3
import subprocess
import sys
import os
from pathlib import Path
def generate_pdf(
markdown_file: str,
output_pdf: str = None,
citation_style: str = "apa",
template: str = None,
toc: bool = True,
number_sections: bool = True
) -> bool:
# Verify markdown file exists
... | --- +++ @@ -1,4 +1,8 @@ #!/usr/bin/env python3
+"""
+PDF Generation Script for Literature Reviews
+Converts markdown files to professionally formatted PDFs with proper styling.
+"""
import subprocess
import sys
@@ -13,6 +17,20 @@ toc: bool = True,
number_sections: bool = True
) -> bool:
+ """
+ Gene... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/literature-review/scripts/generate_pdf.py |
Can you add docstrings to this Python file? | #!/usr/bin/env python3
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.gridspec import GridSpec
import argparse
import os
# Predefined style presets
STYLE_PRESETS = {
'publication': {
'figure.figsize': (8, 6),
'figure.dpi': 100,
'savefig.dpi': 300,
'savefig.bbox... | --- +++ @@ -1,4 +1,17 @@ #!/usr/bin/env python3
+"""
+Matplotlib Style Configurator
+
+Interactive utility to configure matplotlib style preferences and generate
+custom style sheets. Creates a preview of the style and optionally saves
+it as a .mplstyle file.
+
+Usage:
+ python style_configurator.py [--preset PRESE... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/matplotlib/scripts/style_configurator.py |
Create structured documentation for my script | #!/usr/bin/env python3
import re
import requests
import json
from typing import Dict, List, Tuple
from urllib.parse import urlparse
import time
class CitationVerifier:
def __init__(self):
self.session = requests.Session()
self.session.headers.update({
'User-Agent': 'CitationVerifier/1.... | --- +++ @@ -1,4 +1,8 @@ #!/usr/bin/env python3
+"""
+Citation Verification Script
+Verifies DOIs, URLs, and citation metadata for accuracy.
+"""
import re
import requests
@@ -15,10 +19,15 @@ })
def extract_dois(self, text: str) -> List[str]:
+ """Extract all DOIs from text."""
doi_pat... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/literature-review/scripts/verify_citations.py |
Help me add docstrings to my project | #!/usr/bin/env python3
import argparse
import json
import re
import sys
from pathlib import Path
from typing import List, Dict, Optional
from markitdown import MarkItDown
from datetime import datetime
def extract_metadata_from_filename(filename: str) -> Dict[str, str]:
metadata = {}
# Remove extension
... | --- +++ @@ -1,4 +1,10 @@ #!/usr/bin/env python3
+"""
+Convert scientific literature PDFs to Markdown for analysis and review.
+
+This script is specifically designed for converting academic papers,
+organizing them, and preparing them for literature review workflows.
+"""
import argparse
import json
@@ -11,6 +17,10... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/markitdown/scripts/convert_literature.py |
Include argument descriptions in docstrings | #!/usr/bin/env python3
import argparse
from pathlib import Path
from typing import List, Optional
from markitdown import MarkItDown
from concurrent.futures import ThreadPoolExecutor, as_completed
import sys
def convert_file(md: MarkItDown, file_path: Path, output_dir: Path, verbose: bool = False) -> tuple[bool, str,... | --- +++ @@ -1,4 +1,10 @@ #!/usr/bin/env python3
+"""
+Batch convert multiple files to Markdown using MarkItDown.
+
+This script demonstrates how to efficiently convert multiple files
+in a directory to Markdown format.
+"""
import argparse
from pathlib import Path
@@ -9,6 +15,18 @@
def convert_file(md: MarkItDo... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/markitdown/scripts/batch_convert.py |
Add return value explanations in docstrings | #!/usr/bin/env python3
import argparse
import sys
from pathlib import Path
from typing import List, Dict, Optional, Tuple
import json
try:
import pandas as pd
import datamol as dm
import medchem as mc
from rdkit import Chem
from tqdm import tqdm
except ImportError as e:
print(f"Error: Missing ... | --- +++ @@ -1,4 +1,15 @@ #!/usr/bin/env python3
+"""
+Batch molecular filtering using medchem library.
+
+This script provides a production-ready workflow for filtering compound libraries
+using medchem rules, structural alerts, and custom constraints.
+
+Usage:
+ python filter_molecules.py input.csv --rules rule_of... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/medchem/scripts/filter_molecules.py |
Document this module using docstrings | #!/usr/bin/env python3
import argparse
import os
import sys
from pathlib import Path
from markitdown import MarkItDown
from openai import OpenAI
# Predefined prompts for different use cases
PROMPTS = {
'scientific': """
Analyze this scientific image or diagram. Provide:
1. Type of visualization (graph, chart, mi... | --- +++ @@ -1,4 +1,10 @@ #!/usr/bin/env python3
+"""
+Convert documents to Markdown with AI-enhanced image descriptions.
+
+This script demonstrates how to use MarkItDown with OpenRouter to generate
+detailed descriptions of images in documents (PowerPoint, PDFs with images, etc.)
+"""
import argparse
import os
@@ ... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/markitdown/scripts/convert_with_ai.py |
Write documentation strings for class attributes | #!/usr/bin/env python
import argparse
from pathlib import Path
import json
import pandas as pd
import spikeinterface.full as si
# Curation criteria presets
CURATION_CRITERIA = {
'allen': {
'snr': 3.0,
'isi_violations_ratio': 0.1,
'presence_ratio': 0.9,
'amplitude_cutoff': 0.1,
... | --- +++ @@ -1,4 +1,10 @@ #!/usr/bin/env python
+"""
+Compute quality metrics and curate units.
+
+Usage:
+ python compute_metrics.py sorting/ preprocessed/ --output metrics/
+"""
import argparse
from pathlib import Path
@@ -38,6 +44,7 @@ curation_method: str = 'allen',
n_jobs: int = -1,
):
+ """Comp... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/neuropixels-analysis/scripts/compute_metrics.py |
Help me add docstrings to my project | #!/usr/bin/env python3
import argparse
from pathlib import Path
import json
import spikeinterface.full as si
import numpy as np
def load_recording(data_path: str, stream_id: str = 'imec0.ap') -> si.BaseRecording:
data_path = Path(data_path)
# Auto-detect format
if any(data_path.rglob('*.ap.bin')) or an... | --- +++ @@ -1,4 +1,16 @@ #!/usr/bin/env python3
+"""
+Neuropixels Data Analysis Pipeline (Best Practices Version)
+
+Based on SpikeInterface, Allen Institute, and IBL recommendations.
+
+Usage:
+ python neuropixels_pipeline.py /path/to/spikeglx/data /path/to/output
+
+References:
+ - https://spikeinterface.readth... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/neuropixels-analysis/scripts/neuropixels_pipeline.py |
Write proper docstrings for these functions | #!/usr/bin/env python
# =============================================================================
# PARAMETERS - Customize these for your analysis
# =============================================================================
# Input/Output paths
DATA_PATH = '/path/to/your/spikeglx/data/'
OUTPUT_DIR = 'analysis_... | --- +++ @@ -1,4 +1,15 @@ #!/usr/bin/env python
+"""
+Neuropixels Analysis Template
+
+Complete analysis workflow from raw data to curated units.
+Copy and customize this template for your analysis.
+
+Usage:
+ 1. Copy this file to your analysis directory
+ 2. Update the PARAMETERS section
+ 3. Run: python anal... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/neuropixels-analysis/assets/analysis_template.py |
Add docstrings to meet PEP guidelines | #!/usr/bin/env python3
import argparse
import spikeinterface.full as si
import matplotlib.pyplot as plt
import numpy as np
def explore_recording(data_path: str, stream_id: str = 'imec0.ap'):
print(f"Loading: {data_path}")
recording = si.read_spikeglx(data_path, stream_id=stream_id)
# Basic info
pri... | --- +++ @@ -1,4 +1,10 @@ #!/usr/bin/env python3
+"""
+Quick exploration of Neuropixels recording.
+
+Usage:
+ python explore_recording.py /path/to/spikeglx/data
+"""
import argparse
import spikeinterface.full as si
@@ -7,6 +13,7 @@
def explore_recording(data_path: str, stream_id: str = 'imec0.ap'):
+ """E... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/neuropixels-analysis/scripts/explore_recording.py |
Add clean documentation to messy code |
import os
import time
import requests
BASE_URL = os.getenv("OPEN_NOTEBOOK_URL", "http://localhost:5055") + "/api"
def add_url_source(notebook_id, url, process_async=True):
response = requests.post(f"{BASE_URL}/sources", data={
"url": url,
"notebook_id": notebook_id,
"process_async": str(... | --- +++ @@ -1,3 +1,16 @@+"""
+Open Notebook - Source Ingestion Example
+
+Demonstrates ingesting various content types (URLs, files, text) into
+Open Notebook and monitoring processing status.
+
+Prerequisites:
+ pip install requests
+
+Usage:
+ export OPEN_NOTEBOOK_URL="http://localhost:5055"
+ python source_... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/open-notebook/scripts/source_ingestion.py |
Help me add docstrings to my project | #!/usr/bin/env python
import argparse
from pathlib import Path
import spikeinterface.full as si
def preprocess_recording(
input_path: str,
output_dir: str,
format: str = 'auto',
stream_id: str = None,
freq_min: float = 300,
freq_max: float = 6000,
phase_shift: bool = True,
common_ref... | --- +++ @@ -1,4 +1,10 @@ #!/usr/bin/env python
+"""
+Preprocess Neuropixels recording.
+
+Usage:
+ python preprocess_recording.py /path/to/data --output preprocessed/ --format spikeglx
+"""
import argparse
from pathlib import Path
@@ -18,6 +24,7 @@ detect_bad: bool = True,
n_jobs: int = -1,
):
+ """... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/neuropixels-analysis/scripts/preprocess_recording.py |
Add return value explanations in docstrings |
import os
import requests
BASE_URL = os.getenv("OPEN_NOTEBOOK_URL", "http://localhost:5055") + "/api"
def create_notebook(name, description=""):
response = requests.post(f"{BASE_URL}/notebooks", json={
"name": name,
"description": description,
})
response.raise_for_status()
notebook ... | --- +++ @@ -1,3 +1,16 @@+"""
+Open Notebook - Notebook Management Example
+
+Demonstrates creating, listing, updating, and deleting notebooks
+using the Open Notebook REST API.
+
+Prerequisites:
+ pip install requests
+
+Usage:
+ export OPEN_NOTEBOOK_URL="http://localhost:5055"
+ python notebook_management.py
... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/open-notebook/scripts/notebook_management.py |
Create docstrings for all classes and functions |
import os
import requests
BASE_URL = os.getenv("OPEN_NOTEBOOK_URL", "http://localhost:5055") + "/api"
def create_chat_session(notebook_id, title, model_override=None):
payload = {
"notebook_id": notebook_id,
"title": title,
}
if model_override:
payload["model_override"] = model_o... | --- +++ @@ -1,3 +1,16 @@+"""
+Open Notebook - Chat Interaction Example
+
+Demonstrates creating chat sessions, sending messages with context,
+and searching across research materials.
+
+Prerequisites:
+ pip install requests
+
+Usage:
+ export OPEN_NOTEBOOK_URL="http://localhost:5055"
+ python chat_interaction... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/open-notebook/scripts/chat_interaction.py |
Write docstrings for this repository | #!/usr/bin/env python3
import requests
import json
from typing import Dict, List, Optional, Any
# API endpoint
BASE_URL = "https://api.platform.opentargets.org/api/v4/graphql"
def execute_query(query: str, variables: Optional[Dict[str, Any]] = None) -> Dict[str, Any]:
payload = {"query": query}
if variable... | --- +++ @@ -1,4 +1,13 @@ #!/usr/bin/env python3
+"""
+Open Targets Platform GraphQL Query Helper
+
+This script provides reusable functions for querying the Open Targets Platform
+GraphQL API. Use these functions to retrieve target, disease, drug, and
+association data.
+
+Dependencies: requests (pip install requests)
... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/opentargets-database/scripts/query_opentargets.py |
Fill in missing docstrings in my code | #!/usr/bin/env python3
import os
import sys
import json
import argparse
from datetime import datetime
from typing import Any, Dict, List, Optional
def _get_api_key():
api_key = os.getenv("PARALLEL_API_KEY")
if not api_key:
raise ValueError(
"PARALLEL_API_KEY environment variable not set.\... | --- +++ @@ -1,4 +1,22 @@ #!/usr/bin/env python3
+"""
+Parallel Web Systems API Client
+
+Provides web search, URL content extraction, and deep research capabilities
+using the Parallel Web Systems APIs (https://docs.parallel.ai).
+
+Primary interface: Parallel Chat API (OpenAI-compatible) for search and research.
+Seco... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/parallel-web/scripts/parallel_web.py |
Write documentation strings for class attributes | #!/usr/bin/env python3
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.gridspec import GridSpec
import argparse
def set_publication_style():
plt.rcParams.update({
'figure.figsize': (10, 6),
'figure.dpi': 100,
'savefig.dpi': 300,
'savefig.bbox': 'tight',
... | --- +++ @@ -1,4 +1,16 @@ #!/usr/bin/env python3
+"""
+Matplotlib Plot Template
+
+Comprehensive template demonstrating various plot types and best practices.
+Use this as a starting point for creating publication-quality visualizations.
+
+Usage:
+ python plot_template.py [--plot-type TYPE] [--style STYLE] [--output... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/matplotlib/scripts/plot_template.py |
Add docstrings that explain inputs and outputs | #!/usr/bin/env python3
import time
import requests
from typing import Dict, List, Optional, Any
from urllib.parse import urljoin
class OpenAlexClient:
BASE_URL = "https://api.openalex.org"
def __init__(self, email: Optional[str] = None, requests_per_second: int = 10):
self.email = email
sel... | --- +++ @@ -1,4 +1,13 @@ #!/usr/bin/env python3
+"""
+OpenAlex API Client with rate limiting and error handling.
+
+Provides a robust client for interacting with the OpenAlex API with:
+- Automatic rate limiting (polite pool: 10 req/sec)
+- Exponential backoff retry logic
+- Pagination support
+- Batch operations suppo... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/openalex-database/scripts/openalex_client.py |
Create documentation for each function signature | #!/usr/bin/env python3
from typing import List, Dict, Optional, Any
from openalex_client import OpenAlexClient
def find_author_works(
author_name: str,
client: OpenAlexClient,
limit: Optional[int] = None
) -> List[Dict[str, Any]]:
# Step 1: Find author ID
author_response = client._make_request(
... | --- +++ @@ -1,4 +1,9 @@ #!/usr/bin/env python3
+"""
+Helper functions for common OpenAlex query patterns.
+
+Provides high-level functions for typical research queries.
+"""
from typing import List, Dict, Optional, Any
from openalex_client import OpenAlexClient
@@ -9,6 +14,17 @@ client: OpenAlexClient,
lim... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/openalex-database/scripts/query_helpers.py |
Insert docstrings into my code | #!/usr/bin/env python3
from opentrons import protocol_api
# Metadata
metadata = {
'protocolName': 'Basic Protocol Template',
'author': 'Your Name <email@example.com>',
'description': 'A basic protocol template for Opentrons',
'apiLevel': '2.19'
}
# Requirements
requirements = {
'robotType': 'Flex... | --- +++ @@ -1,4 +1,10 @@ #!/usr/bin/env python3
+"""
+Basic Opentrons Protocol Template
+
+This template provides a minimal starting point for creating Opentrons protocols.
+Replace the placeholder values and add your specific protocol logic.
+"""
from opentrons import protocol_api
@@ -17,6 +23,12 @@ }
def run(... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/opentrons-integration/scripts/basic_protocol_template.py |
Write proper docstrings for these functions | #!/usr/bin/env python3
from opentrons import protocol_api
metadata = {
'protocolName': 'Serial Dilution Template',
'author': 'Opentrons',
'description': 'Serial dilution protocol for creating concentration gradients',
'apiLevel': '2.19'
}
requirements = {
'robotType': 'Flex',
'apiLevel': '2.1... | --- +++ @@ -1,4 +1,10 @@ #!/usr/bin/env python3
+"""
+Serial Dilution Protocol Template
+
+This template demonstrates how to perform a serial dilution across a plate row.
+Useful for creating concentration gradients for assays.
+"""
from opentrons import protocol_api
@@ -15,6 +21,14 @@ }
def run(protocol: proto... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/opentrons-integration/scripts/serial_dilution_template.py |
Write docstrings for algorithm functions | #!/usr/bin/env python3
from opentrons import protocol_api
metadata = {
'protocolName': 'PCR Setup with Thermocycler',
'author': 'Opentrons',
'description': 'Automated PCR setup and cycling protocol',
'apiLevel': '2.19'
}
requirements = {
'robotType': 'Flex',
'apiLevel': '2.19'
}
def run(prot... | --- +++ @@ -1,4 +1,10 @@ #!/usr/bin/env python3
+"""
+PCR Setup Protocol Template
+
+This template demonstrates how to set up PCR reactions using the Thermocycler module.
+Includes master mix distribution, sample addition, and PCR cycling.
+"""
from opentrons import protocol_api
@@ -15,6 +21,14 @@ }
def run(pro... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/opentrons-integration/scripts/pcr_setup_template.py |
Insert docstrings into my code | #!/usr/bin/env python3
import os
import sys
import json
import argparse
from typing import Optional, Dict, Any, List
def check_dependencies():
try:
import litellm
return True
except ImportError:
print("Error: LiteLLM is not installed.", file=sys.stderr)
print("Install it with:... | --- +++ @@ -1,4 +1,20 @@ #!/usr/bin/env python3
+"""
+Perplexity Search via LitLLM and OpenRouter
+
+This script performs AI-powered web searches using Perplexity models through
+LiteLLM and OpenRouter. It provides real-time, grounded answers with source citations.
+
+Usage:
+ python perplexity_search.py "search que... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/perplexity-search/scripts/perplexity_search.py |
Generate documentation strings for clarity | #!/usr/bin/env python3
import os
import sys
import argparse
from pathlib import Path
def create_env_file(api_key: str, env_file: str = ".env") -> bool:
try:
env_path = Path(env_file)
# Read existing content if file exists
existing_content = []
if env_path.exists():
wi... | --- +++ @@ -1,4 +1,15 @@ #!/usr/bin/env python3
+"""
+Setup script for Perplexity Search environment configuration.
+
+This script helps users configure their OpenRouter API key and validates the setup.
+
+Usage:
+ python setup_env.py [--api-key YOUR_KEY] [--env-file .env]
+
+Author: Scientific Skills
+License: MIT
... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/perplexity-search/scripts/setup_env.py |
Write docstrings describing functionality |
import argparse
import os
import subprocess
import sys
from pathlib import Path
def check_dependencies():
tools = {
"mafft": "conda install -c bioconda mafft",
"iqtree2": "conda install -c bioconda iqtree",
}
missing = []
for tool, install_cmd in tools.items():
result = subpro... | --- +++ @@ -1,3 +1,16 @@+"""
+Phylogenetic Analysis Pipeline
+===============================
+Complete workflow: MAFFT alignment → IQ-TREE tree → ETE3 visualization.
+
+Requirements:
+ conda install -c bioconda mafft iqtree
+ pip install ete3
+
+Usage:
+ python phylogenetic_analysis.py sequences.fasta --type ... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/phylogenetics/scripts/phylogenetic_analysis.py |
Create simple docstrings for beginners | #!/usr/bin/env python3
from typing import Dict, List, Optional, Any
import xml.etree.ElementTree as ET
class DrugBankHelper:
NAMESPACE = {'db': 'http://www.drugbank.ca'}
def __init__(self, root=None):
self.root = root
self._drug_cache = {}
def _get_root(self):
if self.root is N... | --- +++ @@ -1,27 +1,61 @@ #!/usr/bin/env python3
+"""
+DrugBank Helper Functions
+
+Utility functions for common DrugBank operations including:
+- Drug information extraction
+- Interaction analysis
+- Target identification
+- Chemical property extraction
+
+Usage:
+ from drugbank_helper import DrugBankHelper
+
+ ... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/drugbank-database/scripts/drugbank_helper.py |
Provide docstrings following PEP 257 | #!/usr/bin/env python3
import argparse
import os
import pickle
import sys
from pathlib import Path
import pandas as pd
try:
from pydeseq2.dds import DeseqDataSet
from pydeseq2.ds import DeseqStats
except ImportError:
print("Error: pydeseq2 not installed. Install with: pip install pydeseq2")
sys.exit(... | --- +++ @@ -1,4 +1,20 @@ #!/usr/bin/env python3
+"""
+PyDESeq2 Analysis Script
+
+This script performs a complete differential expression analysis using PyDESeq2.
+It can be used as a template for standard RNA-seq DEA workflows.
+
+Usage:
+ python run_deseq2_analysis.py --counts counts.csv --metadata metadata.csv \
... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/pydeseq2/scripts/run_deseq2_analysis.py |
Add docstrings for better understanding | #!/usr/bin/env python3
import sys
import json
from typing import List, Dict, Optional, Union
try:
import pubchempy as pcp
except ImportError:
print("Error: pubchempy is not installed. Install it with: pip install pubchempy")
sys.exit(1)
def search_by_name(name: str, max_results: int = 10) -> List[pcp.Co... | --- +++ @@ -1,4 +1,10 @@ #!/usr/bin/env python3
+"""
+PubChem Compound Search Utility
+
+This script provides functions for searching and retrieving compound information
+from PubChem using the PubChemPy library.
+"""
import sys
import json
@@ -12,6 +18,16 @@
def search_by_name(name: str, max_results: int = 10)... | https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/HEAD/scientific-skills/pubchem-database/scripts/compound_search.py |
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