repo stringclasses 454
values | file_path stringlengths 5 201 | extension stringclasses 1
value | content stringlengths 8 509k | num_lines int64 3 16.9k | size_bytes int64 8 511k |
|---|---|---|---|---|---|
scientific-agent-skills | skills/analytical-method-validation/scripts/_common.py | .py | #!/usr/bin/env python3
"""Shared statistics and I/O for analytical method validation checks.
Standard library only. Every distribution function here is implemented from the
regularised incomplete beta and gamma functions so the scripts run in any
Python 3.11+ interpreter without numpy or scipy.
These helpers compute ... | 956 | 32,420 |
scientific-agent-skills | skills/analytical-method-validation/scripts/check_bioanalytical_run.py | .py | #!/usr/bin/env python3
"""Apply ICH M10 acceptance criteria to a bioanalytical run or an ISR dataset.
Chromatographic assays and ligand binding assays carry DIFFERENT numeric
criteria in ICH M10, and conflating them is the most common error in this area.
--modality is therefore mandatory: nothing here has a default.
... | 294 | 11,344 |
scientific-agent-skills | skills/analytical-method-validation/scripts/compare_methods.py | .py | #!/usr/bin/env python3
"""Compare two analytical procedures for a transfer, bridging, or bias study.
Uses the regressions that belong to method comparison -- Deming and
Passing-Bablok, which allow error in both measurements -- rather than ordinary
least squares, which assumes the comparative procedure is error-free an... | 216 | 9,105 |
scientific-agent-skills | skills/analytical-method-validation/scripts/plan_validation.py | .py | #!/usr/bin/env python3
"""Design a validation study: which framework, which tests, what study layout.
Answers the first question of any validation exercise -- what am I required to
demonstrate, and with how much data -- before any sample is injected.
python3 plan_validation.py --framework ich-q2r2 --attribute ass... | 382 | 15,414 |
scientific-agent-skills | skills/analytical-method-validation/scripts/check_response.py | .py | #!/usr/bin/env python3
"""Evaluate a calibration response (linearity) the way ICH Q2(R2) 3.2.2 asks.
Reports what the guideline asks to be reported -- slope, intercept, coefficient
of determination, and an analysis of the deviation of points from the line --
and adds the diagnostics that actually detect an unsuitable ... | 244 | 9,858 |
scientific-agent-skills | skills/analytical-method-validation/scripts/check_accuracy_precision.py | .py | #!/usr/bin/env python3
"""Evaluate accuracy and precision per ICH Q2(R2) 3.3.
Accuracy is reported as mean recovery with a confidence interval, which is what
Q2(R2) 3.3.1.4 asks for -- a bare mean is not sufficient. Precision is
decomposed into repeatability and intermediate precision by a one-way
random-effects model... | 329 | 14,263 |
scientific-agent-skills | skills/pathml/scripts/image_qc.py | .py | #!/usr/bin/env python3
"""Compute bounded synthetic/local image QC and a coarse tissue-like mask."""
from __future__ import annotations
import argparse
import math
from pathlib import Path
from typing import Any
from _common import (
CliError,
MAX_IMAGE_BYTES,
MAX_PIXELS,
atomic_write_bytes,
chec... | 326 | 11,127 |
scientific-agent-skills | skills/pathml/scripts/validate_spatial_schema.py | .py | #!/usr/bin/env python3
"""Validate bounded graph JSON and multiplex cell-table CSV schemas."""
from __future__ import annotations
import argparse
import csv
import math
import re
from collections import Counter
from pathlib import Path
from typing import Any
from _common import (
CliError,
MAX_CSV_BYTES,
... | 421 | 16,044 |
scientific-agent-skills | skills/pathml/scripts/plan_pipeline.py | .py | #!/usr/bin/env python3
"""Plan bounded PathML tiling and pipeline work without opening a slide."""
from __future__ import annotations
import argparse
import math
from typing import Any
from _common import CliError, emit_json, parse_name_list, run_cli
TRANSFORM_KINDS = {
"AdaptiveHistogramEqualization": "image"... | 240 | 9,054 |
scientific-agent-skills | skills/pathml/scripts/_common.py | .py | #!/usr/bin/env python3
"""Shared bounded-I/O helpers for the PathML skill CLIs."""
from __future__ import annotations
import hashlib
import json
import math
import os
import stat
import tempfile
from collections.abc import Iterable, Mapping
from pathlib import Path
from typing import Any
PATHML_VERSION = "3.0.5"
PI... | 386 | 12,105 |
scientific-agent-skills | skills/pathml/scripts/plan_inference.py | .py | #!/usr/bin/env python3
"""Plan bounded inference batches from numbers or a JSON model card only."""
from __future__ import annotations
import argparse
import math
import re
from pathlib import Path
from typing import Any
from _common import (
CliError,
MAX_JSON_BYTES,
emit_json,
finite_float,
loa... | 283 | 9,691 |
scientific-agent-skills | skills/pathml/scripts/slide_manifest.py | .py | #!/usr/bin/env python3
"""Validate local slide manifests and inspect allowlisted technical metadata."""
from __future__ import annotations
import argparse
import csv
import math
import re
from collections import Counter
from pathlib import Path
from typing import Any
from _common import (
CliError,
MAX_CSV_B... | 406 | 14,065 |
scientific-agent-skills | skills/gget/scripts/gene_analysis.py | .py | #!/usr/bin/env python3
"""
Gene Analysis Script
Quick analysis of a gene: search, info, sequences, expression, and enrichment
"""
import argparse
import sys
import gget
def fasta_text(sequences):
"""Render what gget.seq returned as FASTA text.
gget.seq returns a list of FASTA lines (header, sequence, ...); ... | 176 | 6,297 |
scientific-agent-skills | skills/gget/scripts/batch_sequence_analysis.py | .py | #!/usr/bin/env python3
"""
Batch Sequence Analysis Script
Analyze multiple sequences: BLAST, alignment, and structure prediction
"""
import argparse
import sys
from pathlib import Path
import gget
def read_fasta(fasta_file):
"""Read sequences from FASTA file."""
sequences = []
current_id = None
curre... | 193 | 6,119 |
scientific-agent-skills | skills/gget/scripts/enrichment_pipeline.py | .py | #!/usr/bin/env python3
"""
Enrichment Analysis Pipeline
Perform comprehensive enrichment analysis on a gene list
"""
import argparse
import sys
from pathlib import Path
import gget
import pandas as pd
def read_gene_list(file_path):
"""Read gene list from file (one gene per line or CSV)."""
file_path = Path(f... | 236 | 7,201 |
scientific-agent-skills | skills/scikit-learn/scripts/clustering_analysis.py | .py | """
Clustering analysis example with multiple algorithms, evaluation, and visualization.
"""
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
... | 387 | 11,396 |
scientific-agent-skills | skills/scikit-learn/scripts/classification_pipeline.py | .py | """
Complete classification pipeline example with preprocessing, model training,
hyperparameter tuning, and evaluation.
"""
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 skl... | 258 | 8,044 |
scientific-agent-skills | skills/medchem/scripts/filter_molecules.py | .py | #!/usr/bin/env python3
"""
Batch molecular filtering using the medchem library.
Usage:
uv run python filter_molecules.py input.csv --rules rule_of_five,rule_of_cns --pains --output filtered.csv
uv run python filter_molecules.py input.sdf --rules rule_of_veber --nibr --complexity 99 --output results.csv
uv ... | 303 | 12,336 |
scientific-agent-skills | skills/infographics/scripts/generate_infographic_ai.py | .py | #!/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 review using Gemini 3.6 Flash for in... | 1,447 | 57,598 |
scientific-agent-skills | skills/infographics/scripts/generate_infographic.py | .py | #!/usr/bin/env python3
"""
Generate professional infographics using Nano Banana Pro.
This script generates infographics with smart iterative refinement:
- Uses Nano Banana Pro (Gemini 3.1 Flash Image) for generation
- Uses Gemini 3.6 Flash for quality review
- Only regenerates if quality is below threshold
- Supports ... | 292 | 12,643 |
scientific-agent-skills | skills/pymoo/scripts/many_objective_example.py | .py | """
Many-objective optimization example using pymoo.
This script demonstrates many-objective optimization (4+ objectives)
using NSGA-III on the DTLZ2 benchmark problem.
"""
from pymoo.algorithms.moo.nsga3 import NSGA3
from pymoo.problems import get_problem
from pymoo.optimize import minimize
from pymoo.util.ref_dirs ... | 75 | 2,227 |
scientific-agent-skills | skills/pymoo/scripts/decision_making_example.py | .py | """
Multi-criteria decision making example using pymoo.
This script demonstrates how to select preferred solutions from
a Pareto front using various MCDM methods.
"""
from pymoo.algorithms.moo.nsga2 import NSGA2
from pymoo.problems import get_problem
from pymoo.optimize import minimize
from pymoo.mcdm.pseudo_weights ... | 162 | 4,588 |
scientific-agent-skills | skills/pymoo/scripts/custom_problem_example.py | .py | """
Custom problem definition example using pymoo.
This script demonstrates how to define a custom optimization problem
and solve it using pymoo.
"""
from pymoo.core.problem import ElementwiseProblem
from pymoo.algorithms.moo.nsga2 import NSGA2
from pymoo.optimize import minimize
from pymoo.visualization.scatter impo... | 182 | 4,770 |
scientific-agent-skills | skills/pymoo/scripts/multi_objective_example.py | .py | """
Multi-objective optimization example using pymoo.
This script demonstrates multi-objective optimization using
NSGA-II on the ZDT1 benchmark problem.
"""
from pymoo.algorithms.moo.nsga2 import NSGA2
from pymoo.problems import get_problem
from pymoo.optimize import minimize
from pymoo.visualization.scatter import S... | 64 | 1,731 |
scientific-agent-skills | skills/pymoo/scripts/single_objective_example.py | .py | """
Single-objective optimization example using pymoo.
This script demonstrates basic single-objective optimization
using the Genetic Algorithm on the Sphere function.
"""
from pymoo.algorithms.soo.nonconvex.ga import GA
from pymoo.problems import get_problem
from pymoo.optimize import minimize
from pymoo.operators.c... | 60 | 1,620 |
scientific-agent-skills | skills/market-research-reports/scripts/generate_report_scaffold.py | .py | #!/usr/bin/env python3
"""Generate a bounded local evidence-first market-report workspace."""
from __future__ import annotations
import argparse
import csv
import json
import re
from pathlib import Path
from typing import Any
from _common import (
ValidationError,
error_exit,
parse_currency,
parse_is... | 445 | 14,779 |
scientific-agent-skills | skills/market-research-reports/scripts/calculate_market_sizing.py | .py | #!/usr/bin/env python3
"""Calculate bounded TAM/SAM/SOM scenarios and reconcile two sizing methods."""
from __future__ import annotations
import argparse
from pathlib import Path
from typing import Any
from _common import (
ValidationError,
error_exit,
parse_currency,
parse_fraction,
parse_iso_da... | 390 | 13,738 |
scientific-agent-skills | skills/market-research-reports/scripts/check_unit_consistency.py | .py | #!/usr/bin/env python3
"""Check units, currency, base year, taxonomy, and denominator consistency."""
from __future__ import annotations
import argparse
import re
from typing import Any
from _common import (
ValidationError,
error_exit,
parse_currency,
parse_number,
parse_year,
read_csv_recor... | 218 | 6,943 |
scientific-agent-skills | skills/market-research-reports/scripts/_common.py | .py | #!/usr/bin/env python3
"""Shared, dependency-free validation helpers for local market-research CLIs."""
from __future__ import annotations
import csv
import json
import math
import os
import re
import tempfile
from datetime import date
from pathlib import Path
from typing import Any, Iterable
MAX_FILE_BYTES = 5 * 10... | 313 | 11,093 |
scientific-agent-skills | skills/market-research-reports/scripts/validate_evidence_ledger.py | .py | #!/usr/bin/env python3
"""Validate a local market-research source/evidence ledger."""
from __future__ import annotations
import argparse
from datetime import date
from pathlib import Path, PurePosixPath
from typing import Any
from urllib.parse import urlsplit
from _common import (
MAX_ROWS,
ValidationError,
... | 292 | 9,202 |
scientific-agent-skills | skills/market-research-reports/scripts/forecast_sensitivity.py | .py | #!/usr/bin/env python3
"""Generate deterministic scenario forecasts and one-way growth sensitivity."""
from __future__ import annotations
import argparse
from typing import Any
from _common import (
ValidationError,
error_exit,
parse_currency,
parse_iso_date,
parse_number,
parse_year,
rea... | 327 | 11,102 |
scientific-agent-skills | skills/market-research-reports/scripts/validate_competitor_matrix.py | .py | #!/usr/bin/env python3
"""Validate a complete, evidence-linked competitor-feature matrix CSV."""
from __future__ import annotations
import argparse
from pathlib import Path
from typing import Any
from _common import (
MAX_ROWS,
ValidationError,
error_exit,
parse_iso_date,
read_csv_records,
re... | 224 | 7,807 |
scientific-agent-skills | skills/market-research-reports/scripts/audit_claim_citations.py | .py | #!/usr/bin/env python3
"""Audit claim-to-source mappings in local CSV ledgers."""
from __future__ import annotations
import argparse
from pathlib import Path
from typing import Any
from _common import (
MAX_ROWS,
ValidationError,
error_exit,
parse_currency,
parse_iso_date,
parse_year,
rea... | 327 | 11,051 |
scientific-agent-skills | skills/markitdown/scripts/convert_literature.py | .py | #!/usr/bin/env python3
"""Convert a trusted local PDF collection into provenance-rich Markdown."""
from __future__ import annotations
import argparse
import json
import re
from dataclasses import asdict, dataclass
from datetime import datetime, timezone
from hashlib import sha256
from importlib.metadata import versio... | 406 | 12,069 |
scientific-agent-skills | skills/markitdown/scripts/inspect_installation.py | .py | #!/usr/bin/env python3
"""Inspect a MarkItDown installation without loading plugins or using network."""
from __future__ import annotations
import argparse
import json
import platform
import shutil
from importlib.metadata import (
PackageNotFoundError,
entry_points,
metadata,
version,
)
from typing im... | 163 | 4,889 |
scientific-agent-skills | skills/markitdown/scripts/batch_convert.py | .py | #!/usr/bin/env python3
"""Batch-convert trusted local files with Microsoft MarkItDown 0.1.6.
The script deliberately uses convert_local(), skips symlinks, preserves relative
directories, and keeps plugins disabled unless explicitly requested.
"""
from __future__ import annotations
import argparse
import json
import ... | 355 | 10,522 |
scientific-agent-skills | skills/scvelo/scripts/rna_velocity_workflow.py | .py | """
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 as scv
import scanpy as sc
import num... | 241 | 8,440 |
scientific-agent-skills | skills/peer-review/scripts/select_reporting_guidelines.py | .py | #!/usr/bin/env python3
"""Select bundled reporting guidance and audit checklist coverage locally."""
from __future__ import annotations
import argparse
import re
from collections import Counter
from pathlib import Path
from typing import Any
from _common import (
ValidationError,
error_exit,
issue,
r... | 384 | 13,594 |
scientific-agent-skills | skills/peer-review/scripts/_common.py | .py | #!/usr/bin/env python3
"""Shared, dependency-free safety helpers for local peer-review CLIs."""
from __future__ import annotations
import csv
import json
import os
import re
import tempfile
from datetime import date
from pathlib import Path
from typing import Any, Iterable
MAX_INPUT_BYTES = 4 * 1024 * 1024
MAX_ROWS ... | 399 | 13,896 |
scientific-agent-skills | skills/peer-review/scripts/audit_statistics_reproducibility.py | .py | #!/usr/bin/env python3
"""Audit a structured statistics and reproducibility checklist locally."""
from __future__ import annotations
import argparse
from collections import Counter
from typing import Any
from _common import (
ValidationError,
error_exit,
issue,
read_json,
require_bool,
requir... | 306 | 10,455 |
scientific-agent-skills | skills/peer-review/scripts/validate_claim_evidence.py | .py | #!/usr/bin/env python3
"""Validate a bounded claim-evidence alignment matrix without echoing prose."""
from __future__ import annotations
import argparse
from collections import Counter
from typing import Any
from _common import (
ValidationError,
error_exit,
issue,
read_csv_records,
require_enum... | 222 | 7,083 |
scientific-agent-skills | skills/peer-review/scripts/audit_citations.py | .py | #!/usr/bin/env python3
"""Audit Markdown citation keys against a local reference CSV without network use."""
from __future__ import annotations
import argparse
import re
from collections import Counter
from typing import Any
from _common import (
ValidationError,
error_exit,
issue,
read_csv_records,
... | 208 | 7,097 |
scientific-agent-skills | skills/peer-review/scripts/generate_review_scaffold.py | .py | #!/usr/bin/env python3
"""Generate a local structured peer-review draft scaffold from validated intake."""
from __future__ import annotations
import argparse
import re
from pathlib import Path
from typing import Any
from _common import (
ValidationError,
error_exit,
read_markdown,
write_markdown,
)
f... | 82 | 2,634 |
scientific-agent-skills | skills/peer-review/scripts/validate_review_intake.py | .py | #!/usr/bin/env python3
"""Validate peer-review scope, authorization, conflicts, and handling controls."""
from __future__ import annotations
import argparse
from typing import Any
from _common import (
ValidationError,
error_exit,
issue,
read_json,
require_bool,
require_enum,
require_exac... | 453 | 14,466 |
scientific-agent-skills | skills/peer-review/scripts/lint_review.py | .py | #!/usr/bin/env python3
"""Lint a structured review for channel separation, tone, and actionability."""
from __future__ import annotations
import argparse
import re
from typing import Any
from _common import (
ValidationError,
error_exit,
issue,
read_markdown,
write_json_report,
)
AUTHOR_HEADING ... | 255 | 9,085 |
scientific-agent-skills | skills/onekgpd/scripts/onekgpd_meta.py | .py | # /// script
# requires-python = ">=3.11"
# dependencies = []
# ///
"""OneKGPd — sample & population metadata (offline) over the 1000 Genomes Project.
Six commands answering population/pedigree questions from a data file bundled in
the skill (``onekgpd/assets/kgpe.json``): no network, no credentials, and no
third-part... | 486 | 19,389 |
scientific-agent-skills | skills/onekgpd/scripts/onekgpd_api.py | .py | # /// script
# requires-python = ">=3.11"
# dependencies = ["dnaerys>=0.2.1,<0.3.0"]
# ///
"""OneKGPd — individual-level queries over the 1000 Genomes Project.
A single command-line wrapper exposing ten subcommands over the 1000 Genomes
Project cohort (3,202 whole-genome-sequenced individuals, GRCh38): selecting and
c... | 795 | 30,403 |
scientific-agent-skills | skills/autoskill/scripts/backends.py | .py | import ipaddress
import os
import sys
from urllib.parse import urlparse
import httpx
def _is_loopback(host):
if host in ("localhost", ""):
return True
try:
return ipaddress.ip_address(host).is_loopback
except ValueError:
return False
def check_remote_endpoint(endpoint, label):
... | 117 | 3,936 |
scientific-agent-skills | skills/autoskill/scripts/autoskill.py | .py | """Unified CLI for the autoskill skill.
Subcommands:
run — detect workflows and draft proposed skills
doctor — verify screenpipe + LM Studio + config + skills dir
promote — move an approved proposal into skills/
"""
import argparse
import sys
def main(argv=None):
parser = argparse.ArgumentParser(p... | 36 | 1,158 |
scientific-agent-skills | skills/autoskill/scripts/cluster.py | .py | from collections import defaultdict
def segment_sessions(events, idle_gap_seconds, min_session_seconds):
if not events:
return []
events = sorted(events, key=lambda e: e["ts"])
groups = [[events[0]]]
for prev, curr in zip(events, events[1:]):
if curr["ts"] - prev["ts"] > idle_gap_secon... | 55 | 1,723 |
scientific-agent-skills | skills/autoskill/scripts/promote.py | .py | import argparse
import shutil
import sys
from pathlib import Path
class PromoteError(Exception):
pass
_KINDS = ("new-skills", "composition-recipes")
def promote(proposed_path, skills_dir, name):
proposed_path = Path(proposed_path)
skills_dir = Path(skills_dir)
source = None
for kind in _KINDS... | 59 | 1,559 |
scientific-agent-skills | skills/autoskill/scripts/run.py | .py | import datetime as _dt
from pathlib import Path
import httpx
from cluster import cluster_sessions, segment_sessions
from fetch_window import fetch_window
from match_skills import load_skill_descriptions, top_k_matches
from redact import redact
from synthesize import synthesize
class ScreenpipeUnreachable(RuntimeErr... | 195 | 7,370 |
scientific-agent-skills | skills/autoskill/scripts/fetch_window.py | .py | _MAX_PAGES = 10_000 # bounded exit: hard ceiling so the loop cannot spin forever
def fetch_window(client, start_time, end_time, page_size=50, token=None):
events = []
offset = 0
headers = {"Authorization": f"Bearer {token}"} if token else {}
for _page in range(_MAX_PAGES):
response = client.g... | 34 | 1,172 |
scientific-agent-skills | skills/autoskill/scripts/match_skills.py | .py | import math
from pathlib import Path
def _parse_frontmatter(content: str) -> dict:
if not content.startswith("---"):
return {}
_, _, rest = content.partition("---\n")
block, _, _ = rest.partition("\n---")
out = {}
for line in block.splitlines():
if ":" not in line:
cont... | 47 | 1,316 |
scientific-agent-skills | skills/autoskill/scripts/synthesize.py | .py | import json
import re
VALID_VERDICTS = {"reuse", "compose", "novel"}
class SynthesisError(Exception):
pass
def _build_prompt(cluster, top_k_skills):
apps = ", ".join(cluster["apps"])
titles = "; ".join(cluster.get("example_titles", []))
candidates = "\n".join(
f"- {s['name']} (score={s['sco... | 73 | 2,378 |
scientific-agent-skills | skills/autoskill/scripts/doctor.py | .py | import argparse
import os
import sys
from pathlib import Path
import httpx
_VALID_BACKENDS = {"local", "claude", "foundry"}
def default_screenpipe_probe(config):
sp = config.get("screenpipe", {})
url = sp.get("url", "http://localhost:3030")
token = sp.get("token") or os.environ.get("SCREENPIPE_TOKEN")
... | 109 | 3,501 |
scientific-agent-skills | skills/autoskill/scripts/redact.py | .py | import re
# Order matters: multi-line and prefixed patterns run before narrower ones.
_PATTERNS = [
(re.compile(r"-----BEGIN [A-Z ]+PRIVATE KEY-----[\s\S]*?-----END [A-Z ]+PRIVATE KEY-----"),
"[REDACTED:private_key]"),
# Known-env-var secret assignments: NAME=value (catches long values only)
(re.com... | 41 | 1,634 |
scientific-agent-skills | skills/geniml/scripts/bed_validator.py | .py | #!/usr/bin/env python3
"""Validate one local BED file and emit a non-mutating normalization plan."""
from __future__ import annotations
import argparse
import re
import sys
from collections import Counter
from pathlib import Path
from _common import (
HARD_MAX_BYTES,
HARD_MAX_RECORDS,
MAX_COORDINATE,
... | 364 | 11,186 |
scientific-agent-skills | skills/geniml/scripts/_common.py | .py | #!/usr/bin/env python3
"""Shared, dependency-free safety helpers for local Geniml skill CLIs."""
from __future__ import annotations
import csv
import gzip
import hashlib
import io
import json
import os
import re
import stat
import sys
from pathlib import Path
from typing import Any, Iterator
HARD_MAX_FILES = 100_00... | 400 | 13,387 |
scientific-agent-skills | skills/geniml/scripts/corpus_auditor.py | .py | #!/usr/bin/env python3
"""Audit a local interval manifest without exposing sample metadata values."""
from __future__ import annotations
import argparse
import sys
from collections import Counter, defaultdict
from pathlib import Path
from _common import (
HARD_MAX_BYTES,
HARD_MAX_FILES,
SafetyError,
... | 305 | 10,637 |
scientific-agent-skills | skills/geniml/scripts/tokenizer_compatibility.py | .py | #!/usr/bin/env python3
"""Plan local tokenizer/universe/model compatibility checks without imports."""
from __future__ import annotations
import argparse
import os
import stat
import sys
from collections import Counter
from pathlib import Path
from _common import (
HARD_MAX_BYTES,
HARD_MAX_RECORDS,
MAX_C... | 322 | 10,994 |
scientific-agent-skills | skills/geniml/scripts/embedding_plan.py | .py | #!/usr/bin/env python3
"""Plan a bounded local Geniml embedding run without importing ML packages."""
from __future__ import annotations
import argparse
import os
import stat
import sys
from collections import Counter
from pathlib import Path
from _common import (
HARD_MAX_BYTES,
HARD_MAX_EPOCHS,
HARD_MA... | 477 | 17,044 |
scientific-agent-skills | skills/geniml/scripts/model_artifact_inspector.py | .py | #!/usr/bin/env python3
"""Inspect local model artifacts and checksums without deserialization."""
from __future__ import annotations
import argparse
import json
import os
import re
import sys
from collections import Counter
from pathlib import Path
from _common import (
HARD_MAX_BYTES,
HARD_MAX_FILES,
Sa... | 359 | 12,111 |
scientific-agent-skills | skills/geniml/scripts/consensus_plan.py | .py | #!/usr/bin/env python3
"""Create a bounded, local-only Geniml consensus-universe execution plan."""
from __future__ import annotations
import argparse
import re
import sys
from collections import Counter
from pathlib import Path
from _common import (
HARD_MAX_BYTES,
HARD_MAX_FILES,
SafetyError,
add_p... | 417 | 14,245 |
scientific-agent-skills | skills/arboreto/scripts/basic_grn_inference.py | .py | #!/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_FILE] [--seed SEED] [--limit LIMIT]
... | 108 | 3,318 |
scientific-agent-skills | skills/labarchive-integration/scripts/setup_config.py | .py | #!/usr/bin/env python3
"""Validate LabArchives regional endpoints and named environment variables.
This utility never reads .env files, writes configuration, authenticates, or
prints credential values.
"""
from __future__ import annotations
import argparse
import getpass
import json
import os
import sys
from collect... | 259 | 8,570 |
scientific-agent-skills | skills/labarchive-integration/scripts/entry_operations.py | .py | #!/usr/bin/env python3
"""Offline LabArchives request-signing helpers and redacted request plans.
The CLI performs no network requests and never prints credentials or reusable
signatures. Import the functions into institution-reviewed HTTP code when
needed, and pass returned authentication material directly to the cli... | 382 | 12,784 |
scientific-agent-skills | skills/labarchive-integration/scripts/notebook_operations.py | .py | #!/usr/bin/env python3
"""Safely inspect a local LabArchives LA container ZIP without extracting it.
An LA container is an attachment packaging format with lamanifest.xml. It is
not a notebook backup. This script performs no network or remote write.
"""
from __future__ import annotations
import argparse
import json
... | 452 | 15,659 |
scientific-agent-skills | skills/hugging-science/scripts/fetch_catalog.py | .py | #!/usr/bin/env python3
"""
Fetch and parse content from the Hugging Science catalog (huggingscience.co).
The catalog ships LLM-friendly markdown at three endpoints:
- https://huggingscience.co/llms.txt (compact index)
- https://huggingscience.co/llms-full.txt (every entry, every domain)
- https://huggin... | 359 | 13,350 |
scientific-agent-skills | skills/pufferlib/scripts/benchmark_vectorization.py | .py | #!/usr/bin/env python3
"""Bounded synthetic vectorization benchmark with no PufferLib import."""
from __future__ import annotations
import argparse
import multiprocessing as mp
import os
import platform
import statistics
import time
from typing import Any
try:
from ._common import UserInputError, bounded_int, em... | 245 | 8,332 |
scientific-agent-skills | skills/pufferlib/scripts/validate_plan.py | .py | #!/usr/bin/env python3
"""Strict, dependency-free validator for PufferLib training plans."""
from __future__ import annotations
import argparse
import copy
import re
from typing import Any
try:
from ._common import (
LOGGER_CREDENTIAL_ENV,
MAX_ENVS,
MAX_EVAL_EPISODES,
MAX_STEPS,
... | 571 | 18,466 |
scientific-agent-skills | skills/pufferlib/scripts/_common.py | .py | #!/usr/bin/env python3
"""Shared safety and strict-JSON helpers for bundled PufferLib CLIs."""
from __future__ import annotations
import json
import math
import re
from pathlib import Path
from typing import Any
MAX_JSON_BYTES = 1_048_576
MAX_STEPS = 1_000_000_000
MAX_ENVS = 65_536
MAX_WORKERS = 256
MAX_EVAL_EPISODE... | 200 | 6,668 |
scientific-agent-skills | skills/pufferlib/scripts/env_contract_validator.py | .py | #!/usr/bin/env python3
"""Validate a built-in synthetic environment without importing plug-ins."""
from __future__ import annotations
import argparse
import math
import random
from typing import Any
try:
from ._common import UserInputError, bounded_int, emit_json
from .env_template import SyntheticGymEnv
exc... | 199 | 6,892 |
scientific-agent-skills | skills/pufferlib/scripts/inspect_checkpoint.py | .py | #!/usr/bin/env python3
"""Inspect checkpoint file metadata without deserializing checkpoint contents."""
from __future__ import annotations
import argparse
import hashlib
import os
import stat
from pathlib import Path
from typing import Any, BinaryIO
try:
from ._common import (
UserInputError,
bo... | 226 | 6,832 |
scientific-agent-skills | skills/pufferlib/scripts/train_template.py | .py | #!/usr/bin/env python3
"""Safe PufferLib training-plan template.
This script never imports PufferLib, starts training, loads checkpoints, uses a
GPU, or contacts an external logger. It emits a validated argv preview for a
human to review in an appropriately sandboxed, pinned environment.
"""
from __future__ import an... | 283 | 9,975 |
scientific-agent-skills | skills/pufferlib/scripts/repro_plan.py | .py | #!/usr/bin/env python3
"""Generate a bounded reproducibility and held-out evaluation plan."""
from __future__ import annotations
import argparse
from typing import Any
try:
from ._common import (
SOURCE_4_COMMIT,
STABLE_SDIST_SHA256,
UserInputError,
bounded_int,
emit_json,... | 178 | 6,027 |
scientific-agent-skills | skills/pufferlib/scripts/env_template.py | .py | #!/usr/bin/env python3
"""Dependency-free synthetic Gymnasium-style environment template.
This module is intentionally local and synthetic. It does not import PufferLib,
Gymnasium, environment plug-ins, native extensions, or ROMs. Port the contract
to a separately reviewed Gymnasium or PufferLib environment only after... | 211 | 7,251 |
scientific-agent-skills | skills/genomic-coordinates/scripts/check_contigs.py | .py | #!/usr/bin/env python3
"""Identify the assembly behind a file, and check that two files can be joined.
The two ways a genomics pipeline produces confident nonsense are a chr-prefix
mismatch (the join returns nothing, or worse, returns only the contigs that
happen to agree) and an assembly mismatch (the join succeeds a... | 383 | 16,049 |
scientific-agent-skills | skills/genomic-coordinates/scripts/normalize_variant.py | .py | #!/usr/bin/env python3
"""Normalise VCF-style variants: check REF, trim, and left-align.
Two variant records can describe exactly the same change to the genome and share
no field values at all. Comparing, joining, or deduplicating variants without
normalising first silently loses real matches. This implements the pars... | 291 | 9,962 |
scientific-agent-skills | skills/genomic-coordinates/scripts/_common.py | .py | """Shared helpers for the genomic-coordinates scripts.
Everything here is standard library only. The single organising idea is that all
intervals are converted to one canonical form on the way in and back out again on
the way out, so no script ever has to reason about two conventions at once.
Canonical form: ``(start... | 336 | 13,550 |
scientific-agent-skills | skills/genomic-coordinates/scripts/audit_intervals.py | .py | #!/usr/bin/env python3
"""Check an interval or variant file against its own format's conventions.
A BED file holding 1-based coordinates parses cleanly, sorts cleanly, and
intersects cleanly. Nothing downstream complains; every result is shifted by one
base. These checks look for the evidence that survives that kind o... | 512 | 19,077 |
scientific-agent-skills | skills/genomic-coordinates/scripts/convert_coords.py | .py | #!/usr/bin/env python3
"""Convert intervals between genomic coordinate conventions.
Every conversion goes through one canonical form (0-based half-open), so the
answer never depends on remembering which pair of formats is involved.
python3 convert_coords.py --from bed --to gff chr1 999 1000
python3 convert_co... | 181 | 6,618 |
scientific-agent-skills | skills/neuropixels-analysis/scripts/compute_metrics.py | .py | #!/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
import json
import pandas as pd
import spikeinterface.full as si
# Curation criteria presets. snr and presence_ratio are min... | 183 | 5,588 |
scientific-agent-skills | skills/neuropixels-analysis/scripts/neuropixels_pipeline.py | .py | #!/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.readthedocs.io/en/stable/how_to/analyze_n... | 443 | 13,808 |
scientific-agent-skills | skills/neuropixels-analysis/scripts/preprocess_recording.py | .py | #!/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
import spikeinterface.full as si
def preprocess_recording(
input_path: str,
output_dir: str,
format: ... | 123 | 4,279 |
scientific-agent-skills | skills/neuropixels-analysis/scripts/run_sorting.py | .py | #!/usr/bin/env python
"""
Run spike sorting on preprocessed recording.
Usage:
python run_sorting.py preprocessed/ --sorter kilosort4 --output sorting/
"""
import argparse
from pathlib import Path
import spikeinterface.full as si
# Default parameters for each sorter
SORTER_DEFAULTS = {
'kilosort4': {
... | 99 | 2,573 |
scientific-agent-skills | skills/neuropixels-analysis/scripts/export_to_phy.py | .py | #!/usr/bin/env python
"""
Export sorting results to Phy for manual curation.
Usage:
python export_to_phy.py metrics/analyzer --output phy_export/
"""
import argparse
from pathlib import Path
import spikeinterface.full as si
from spikeinterface.exporters import export_to_phy
def export_phy(
analyzer_path: s... | 80 | 2,477 |
scientific-agent-skills | skills/neuropixels-analysis/scripts/explore_recording.py | .py | #!/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
import matplotlib.pyplot as plt
import numpy as np
def explore_recording(data_path: str, stream_name: str = 'imec0.ap'):
"""Ex... | 169 | 5,553 |
scientific-agent-skills | skills/neuropixels-analysis/assets/analysis_template.py | .py | #!/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 analysis_template.py
"""
# ===========... | 272 | 9,009 |
scientific-agent-skills | skills/imaging-data-commons/scripts/check_version.py | .py | #!/usr/bin/env python3
"""Check the idc-index package and this skill for required/available updates.
Run FIRST at the start of an IDC session: python scripts/check_version.py
- Verifies that idc-index is installed and at least MIN_VERSION. It never
installs or upgrades anything itself: if the requirement is not me... | 133 | 5,381 |
scientific-agent-skills | skills/scientific-writing/scripts/select_reporting_guidelines.py | .py | """Select reporting guidance and check non-scoring coverage metadata."""
from __future__ import annotations
import argparse
from pathlib import Path
from typing import Any
from _common import (
InputError,
Issue,
emit_report,
is_nonempty_string,
issue,
read_json,
require_list,
require... | 215 | 7,580 |
scientific-agent-skills | skills/scientific-writing/scripts/validate_manifest.py | .py | """Validate bounded manuscript and source manifests without network access."""
from __future__ import annotations
import argparse
import re
from typing import Any
from _common import (
InputError,
Issue,
emit_report,
is_nonempty_string,
is_placeholder,
issue,
read_json,
require_list,
... | 461 | 14,514 |
scientific-agent-skills | skills/scientific-writing/scripts/check_consistency.py | .py | """Check numeric and methods-results consistency in a bounded JSON registry."""
from __future__ import annotations
import argparse
import math
import re
from typing import Any
from _common import (
InputError,
Issue,
emit_report,
is_nonempty_string,
is_placeholder,
issue,
read_json,
r... | 409 | 14,209 |
scientific-agent-skills | skills/scientific-writing/scripts/_common.py | .py | """Shared, dependency-free safety helpers for scientific-writing CLIs."""
from __future__ import annotations
import csv
import io
import json
import sys
from collections.abc import Iterable
from dataclasses import asdict, dataclass
from pathlib import Path
from typing import Any
MAX_FILE_BYTES = 5_000_000
MAX_RECORD... | 241 | 7,670 |
scientific-agent-skills | skills/scientific-writing/scripts/lint_manuscript.py | .py | """Lint manuscript Markdown for placeholders, language risks, and sensitive content."""
from __future__ import annotations
import argparse
import re
from typing import Any
from _common import (
Issue,
emit_report,
issue,
read_json,
read_text,
require_object,
run,
)
TOOL = "lint_manuscrip... | 172 | 5,881 |
scientific-agent-skills | skills/scientific-writing/scripts/validate_authorship.py | .py | """Validate human authorship, CRediT roles, accountability, and AI disclosure."""
from __future__ import annotations
import argparse
import re
from typing import Any
from _common import (
InputError,
Issue,
emit_report,
is_nonempty_string,
is_placeholder,
issue,
read_json,
require_lis... | 323 | 11,498 |
scientific-agent-skills | skills/scientific-writing/scripts/scaffold_manuscript.py | .py | """Generate a local, explicitly incomplete manuscript workspace."""
from __future__ import annotations
import argparse
import json
import re
from pathlib import Path
from typing import Any
from _common import (
InputError,
emit_report,
read_json,
read_text,
require_object,
run,
write_new_... | 144 | 4,328 |
scientific-agent-skills | skills/scientific-writing/scripts/audit_claims.py | .py | """Audit claim-to-evidence mappings and local citation markers."""
from __future__ import annotations
import argparse
import re
from typing import Any
from _common import (
InputError,
Issue,
emit_report,
is_nonempty_string,
issue,
read_csv,
read_json,
read_text,
require_list,
... | 242 | 8,834 |
scientific-agent-skills | skills/scientific-writing/scripts/check_references.py | .py | """Check local reference identifiers and duplicates without resolving them."""
from __future__ import annotations
import argparse
import re
import unicodedata
from typing import Any
from _common import (
InputError,
Issue,
emit_report,
is_nonempty_string,
issue,
read_json,
require_list,
... | 220 | 7,075 |
scientific-agent-skills | skills/exa-search/scripts/exa_extract.py | .py | #!/usr/bin/env python3
# /// script
# requires-python = ">=3.11"
# dependencies = ["exa-py>=1.14.0"]
# ///
"""Fetch and extract content from URLs using Exa's /contents endpoint.
Example:
uv run exa_extract.py \\
https://arxiv.org/abs/2401.04088 \\
https://www.nature.com/articles/s41586-024-07566-y ... | 118 | 3,529 |
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