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/open-notebook/scripts/notebook_management.py | .py | """
Open Notebook - Notebook Management Example
Demonstrates creating, listing, updating, and deleting notebooks
using the Open Notebook REST API.
Prerequisites:
uv pip install requests
Usage:
export OPEN_NOTEBOOK_URL="http://localhost:5055"
python notebook_management.py
"""
import os
import requests
B... | 143 | 4,173 |
scientific-agent-skills | skills/open-notebook/scripts/source_ingestion.py | .py | """
Open Notebook - Source Ingestion Example
Demonstrates ingesting various content types (URLs, files, text) into
Open Notebook and monitoring processing status.
Prerequisites:
uv pip install requests
Usage:
export OPEN_NOTEBOOK_URL="http://localhost:5055"
python source_ingestion.py
"""
import os
impor... | 161 | 4,904 |
scientific-agent-skills | skills/open-notebook/scripts/chat_interaction.py | .py | """
Open Notebook - Chat Interaction Example
Demonstrates creating chat sessions, sending messages with context,
and searching across research materials.
Prerequisites:
uv pip install requests
Usage:
export OPEN_NOTEBOOK_URL="http://localhost:5055"
python chat_interaction.py
"""
import os
import request... | 191 | 6,230 |
scientific-agent-skills | skills/ncats-arax/scripts/arax_client.py | .py | #!/usr/bin/env python3
"""Bounded, provenance-preserving client for the NCATS Translator ARAX API."""
from __future__ import annotations
import argparse
import email.utils
import hashlib
import ipaddress
import json
import os
import re
import socket
import sys
import tempfile
import time
import urllib.error
import ur... | 2,088 | 84,320 |
scientific-agent-skills | skills/get-available-resources/scripts/detect_resources.py | .py | #!/usr/bin/env python3
"""Collect a conservative, privacy-preserving resource snapshot.
The script performs only bounded, read-only probes. It never stress-tests the
machine, allocates a large buffer, changes affinity, or changes accelerator
state. JSON is written to stdout unless a private local filename is explicitl... | 1,768 | 59,840 |
scientific-agent-skills | skills/get-available-resources/scripts/_common.py | .py | #!/usr/bin/env python3
"""Shared, dependency-free safety and JSON helpers."""
from __future__ import annotations
import argparse
import json
import math
import os
import stat
import sys
from pathlib import Path
from typing import Any
SCHEMA_VERSION = "1.1"
MAX_SNAPSHOT_BYTES = 1_048_576
MAX_WORKERS = 1_024
MAX_TASKS... | 191 | 6,068 |
scientific-agent-skills | skills/get-available-resources/scripts/plan_workload.py | .py | #!/usr/bin/env python3
"""Build a conservative worker and memory plan from a validated snapshot."""
from __future__ import annotations
import argparse
import math
from typing import Any, Mapping, Sequence
from _common import (
MAX_BYTES,
MAX_TASKS,
MAX_WORKERS,
SCHEMA_VERSION,
ResourceToolError,
... | 312 | 10,799 |
scientific-agent-skills | skills/get-available-resources/scripts/accelerator_diagnostics.py | .py | #!/usr/bin/env python3
"""Generate, but never execute, a read-only accelerator diagnostic plan."""
from __future__ import annotations
import argparse
from typing import Any, Mapping, Sequence
from _common import (
SCHEMA_VERSION,
ResourceToolError,
cli_error,
emit_json,
read_json_file,
)
from sna... | 152 | 4,623 |
scientific-agent-skills | skills/get-available-resources/scripts/snapshot_tools.py | .py | #!/usr/bin/env python3
"""Validate or deterministically diff resource snapshots."""
from __future__ import annotations
import argparse
import copy
from typing import Any, Mapping, Sequence
from _common import (
MAX_BYTES,
SCHEMA_VERSION,
ResourceToolError,
bounded_number,
cli_error,
emit_json... | 487 | 16,960 |
scientific-agent-skills | skills/dnanexus-integration/scripts/validate_dxapp.py | .py | #!/usr/bin/env python3
"""Offline validation and safety linting for a DNAnexus dxapp.json file."""
from __future__ import annotations
import argparse
import json
import re
import sys
from dataclasses import asdict, dataclass
from pathlib import Path
from typing import Any, Iterable, Optional
NAME_RE = re.compile(r"... | 797 | 26,829 |
scientific-agent-skills | skills/dnanexus-integration/scripts/inspect_dxpy.py | .py | #!/usr/bin/env python3
"""Inspect local dxpy symbols and signatures without authentication or network."""
from __future__ import annotations
import argparse
import importlib
import inspect
import json
import platform
import re
import sys
from importlib.metadata import PackageNotFoundError, version
from typing import ... | 367 | 10,347 |
scientific-agent-skills | skills/arbor/scripts/tree.py | .py | #!/usr/bin/env python3
"""
tree.py — persistent hypothesis-tree state manager for Arbor-style
Hypothesis Tree Refinement (HTR).
The hypothesis tree is the durable research state for an Autonomous
Optimization (AO) run. This script owns the *mechanical* parts of that state
— creating nodes, writing back evidence, propa... | 565 | 22,130 |
scientific-agent-skills | skills/scientific-visualization/scripts/image_metadata.py | .py | #!/usr/bin/env python3
"""Inspect figure/image metadata and screen it against explicit constraints.
The tool is network-free. Pillow is loaded only for raster inputs and pypdf is
loaded only for PDF inputs. A successful screen is not a journal-compliance
claim.
"""
from __future__ import annotations
import argparse
... | 732 | 25,029 |
scientific-agent-skills | skills/scientific-visualization/scripts/figure_export.py | .py | #!/usr/bin/env python3
"""Safe Matplotlib export helpers with explicit, auditable settings.
This module does not certify journal compliance. Publisher profiles are dated
planning snapshots and must be confirmed against the target journal.
"""
from __future__ import annotations
import argparse
import importlib.metada... | 643 | 22,256 |
scientific-agent-skills | skills/scientific-visualization/scripts/style_presets.py | .py | #!/usr/bin/env python3
"""Scoped Matplotlib style presets for scientific figures.
Presets are visual starting points, not journal-compliance profiles. Matplotlib
is imported lazily so listing and help work in a standard-library environment.
"""
from __future__ import annotations
import argparse
import importlib.util... | 502 | 16,123 |
scientific-agent-skills | skills/scientific-visualization/scripts/_common.py | .py | #!/usr/bin/env python3
"""Shared, network-free safety helpers for visualization command-line tools."""
from __future__ import annotations
import json
import os
import stat
import tempfile
from pathlib import Path
from typing import Any
MAX_INPUT_BYTES = 200 * 1024 * 1024
MAX_REPORT_BYTES = 4 * 1024 * 1024
class Cl... | 137 | 4,351 |
scientific-agent-skills | skills/scientific-visualization/scripts/palette_audit.py | .py | #!/usr/bin/env python3
"""Audit palette contrast and heuristic grayscale distinguishability.
WCAG contrast calculations are exact for the supplied sRGB values. Whether a
specific WCAG success criterion applies depends on how a color is used. The
grayscale delta-L* threshold is a screening heuristic, not a standard.
""... | 328 | 11,654 |
scientific-agent-skills | skills/scientific-visualization/scripts/style_preview.py | .py | #!/usr/bin/env python3
"""Generate a deterministic preview for a bundled scientific figure style."""
from __future__ import annotations
import argparse
import math
import sys
from typing import Any
from _common import CliError, emit_json, positive_float
def build_preview(style_name: str, palette_name: str) -> tupl... | 233 | 7,762 |
scientific-agent-skills | skills/scientific-visualization/scripts/export_plan.py | .py | #!/usr/bin/env python3
"""Build and screen against dated publication-export planning snapshots."""
from __future__ import annotations
import argparse
import json
import math
import sys
from pathlib import Path
from typing import Any
from _common import CliError, emit_json, positive_float
SCHEMA_VERSION = "1.0"
PROF... | 494 | 16,700 |
scientific-agent-skills | skills/scientific-visualization/assets/color_palettes.py | .py | """Curated sRGB palettes for scientific figures.
Sources were checked 2026-07-23. Palette selection alone never establishes
accessibility: audit the rendered foreground/background contrast and add
redundant encodings.
Paul Tol values and recommended fixed order:
https://sronpersonalpages.nl/~pault/data/colourschemes.... | 264 | 6,756 |
scientific-agent-skills | skills/docx/scripts/office/soffice.py | .py | """
Helper for running LibreOffice (soffice) in environments where AF_UNIX
sockets may be blocked (e.g., sandboxed VMs). Detects the restriction
at runtime and applies an LD_PRELOAD shim if needed.
Usage:
from office.soffice import run_soffice
result = run_soffice(["--headless", "--convert-to", "pdf", "input... | 233 | 8,012 |
scientific-agent-skills | skills/pymc/scripts/model_comparison.py | .py | """
PyMC Model Comparison Script
Utilities for comparing multiple Bayesian models using information criteria
and cross-validation metrics.
Usage:
from scripts.model_comparison import compare_models, plot_model_comparison
# Compare multiple models
comparison = compare_models(
{'model1': idata1, 'm... | 410 | 13,731 |
scientific-agent-skills | skills/pymc/scripts/model_diagnostics.py | .py | """
PyMC Model Diagnostics Script
Comprehensive diagnostic checks for PyMC models.
Run this after sampling to validate results before interpretation.
Usage:
from scripts.model_diagnostics import check_diagnostics, create_diagnostic_report
# Quick check
check_diagnostics(idata)
# Full report with plo... | 329 | 10,970 |
scientific-agent-skills | skills/pymc/assets/hierarchical_model_template.py | .py | """
PyMC Hierarchical/Multilevel Model Template
This template provides a complete workflow for Bayesian hierarchical models,
useful for grouped/nested data (e.g., students within schools, patients within hospitals).
Customize the sections marked with # TODO
"""
import pymc as pm
import arviz as az
import numpy as np... | 333 | 11,902 |
scientific-agent-skills | skills/pymc/assets/linear_regression_template.py | .py | """
PyMC Linear Regression Template
This template provides a complete workflow for Bayesian linear regression,
including data preparation, model building, diagnostics, and predictions.
Customize the sections marked with # TODO
"""
import pymc as pm
import arviz as az
import numpy as np
import pandas as pd
import mat... | 245 | 8,277 |
scientific-agent-skills | skills/fluidsim/scripts/budget_summary.py | .py | #!/usr/bin/env python3
"""Summarize bounded FluidSim scalar and spectral diagnostics."""
from __future__ import annotations
import argparse
import math
import re
from pathlib import Path
from typing import Any
try:
from ._common import (
MAX_FILES,
MAX_RECORDS,
MAX_TEXT_BYTES,
Too... | 397 | 13,373 |
scientific-agent-skills | skills/fluidsim/scripts/_schema.py | .py | #!/usr/bin/env python3
"""Static FluidSim 0.9 configuration schema and scientific guardrails."""
from __future__ import annotations
import re
from collections.abc import Mapping
from copy import deepcopy
from typing import Any
try:
from ._common import (
MAX_CPU_CORES,
MAX_DIMENSION,
MAX_... | 873 | 28,807 |
scientific-agent-skills | skills/fluidsim/scripts/solver_config_validator.py | .py | #!/usr/bin/env python3
"""Validate a bounded FluidSim 0.9 JSON simulation plan."""
from __future__ import annotations
import argparse
try:
from ._common import ToolError, checked_input, emit_json, fail_json, load_json
from ._schema import example_config, validate_config
except ImportError: # Direct script e... | 71 | 2,107 |
scientific-agent-skills | skills/fluidsim/scripts/grid_resource_estimator.py | .py | #!/usr/bin/env python3
"""Estimate bounded FluidSim grid memory and output storage envelopes."""
from __future__ import annotations
import argparse
import math
from typing import Any
try:
from ._common import (
GIB,
ToolError,
bounded_int,
checked_input,
emit_json,
... | 287 | 9,047 |
scientific-agent-skills | skills/fluidsim/scripts/_common.py | .py | #!/usr/bin/env python3
"""Shared dependency-free safety and JSON helpers for FluidSim skill CLIs."""
from __future__ import annotations
import hashlib
import json
import math
import os
import re
import stat
import sys
import tempfile
from collections.abc import Iterable, Mapping
from pathlib import Path, PurePath
fro... | 492 | 15,595 |
scientific-agent-skills | skills/fluidsim/scripts/output_inventory.py | .py | #!/usr/bin/env python3
"""Inventory bounded FluidSim output and HDF5/netCDF4 metadata lazily."""
from __future__ import annotations
import argparse
import os
from pathlib import Path
from typing import Any
try:
from ._common import (
MAX_ATTRIBUTES,
MAX_DATASETS,
MAX_FILES,
MAX_HD... | 354 | 11,198 |
scientific-agent-skills | skills/fluidsim/scripts/simulation_dry_run.py | .py | #!/usr/bin/env python3
"""Generate a reviewable, opt-in FluidSim launch script without running it."""
from __future__ import annotations
import argparse
import hashlib
import json
from pathlib import Path
from typing import Any
try:
from ._common import (
ToolError,
atomic_write,
checked_... | 247 | 7,813 |
scientific-agent-skills | skills/fluidsim/scripts/restart_compatibility.py | .py | #!/usr/bin/env python3
"""Check FluidSim restart metadata against a validated target configuration."""
from __future__ import annotations
import argparse
import re
from collections.abc import Mapping
from pathlib import Path
from typing import Any
try:
from ._common import (
GIB,
ToolError,
... | 425 | 15,757 |
scientific-agent-skills | skills/diffdock/scripts/setup_check.py | .py | #!/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
import os
from pathlib import Path
def chec... | 284 | 8,216 |
scientific-agent-skills | skills/diffdock/scripts/prepare_batch_csv.py | .py | #!/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 prepare_batch_csv.py input.csv --va... | 258 | 8,976 |
scientific-agent-skills | skills/diffdock/scripts/analyze_results.py | .py | #!/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 results/ --top 50 --threshold 0.0
... | 347 | 11,693 |
scientific-agent-skills | skills/matlab/scripts/scan_m_code.py | .py | #!/usr/bin/env python3
"""Bounded static risk triage for MATLAB source and opaque artifacts."""
from __future__ import annotations
import argparse
import re
import sys
from collections import Counter
from pathlib import Path
from typing import Any
from _common import (
CliError,
bounded_int,
checked_inpu... | 434 | 13,951 |
scientific-agent-skills | skills/matlab/scripts/validate_project_manifest.py | .py | #!/usr/bin/env python3
"""Validate a bounded MATLAB/Octave project and product manifest."""
from __future__ import annotations
import argparse
import re
import sys
from pathlib import Path
from typing import Any
from _common import (
CliError,
checked_input,
checked_root,
emit_json,
fail_json,
... | 349 | 12,255 |
scientific-agent-skills | skills/matlab/scripts/inventory_mat_file.py | .py | #!/usr/bin/env python3
"""Inventory bounded MAT/HDF5 metadata without deserializing object values."""
from __future__ import annotations
import argparse
import hashlib
import sys
from collections import Counter
from pathlib import Path
from typing import Any
from _common import (
CliError,
bounded_int,
c... | 352 | 12,357 |
scientific-agent-skills | skills/matlab/scripts/plan_python_compatibility.py | .py | #!/usr/bin/env python3
"""Plan MATLAB R2026a Python compatibility without importing or starting Engine."""
from __future__ import annotations
import argparse
import re
import sys
from pathlib import Path
from typing import Any
from _common import (
CliError,
checked_input,
checked_root,
emit_json,
... | 177 | 6,566 |
scientific-agent-skills | skills/matlab/scripts/plan_batch_command.py | .py | #!/usr/bin/env python3
"""Create a bounded MATLAB or Octave command plan without executing it."""
from __future__ import annotations
import argparse
import math
import re
import sys
from pathlib import Path
from typing import Any
from _common import (
CliError,
checked_input,
checked_root,
emit_json,... | 258 | 8,967 |
scientific-agent-skills | skills/matlab/scripts/_common.py | .py | #!/usr/bin/env python3
"""Shared bounded local-only helpers for the MATLAB skill CLIs."""
from __future__ import annotations
import hashlib
import json
import re
import sys
from pathlib import Path
from typing import Any, Iterable
MAX_INPUT_BYTES = 64 * 1024 * 1024
MAX_TEXT_BYTES = 4 * 1024 * 1024
MAX_JSON_BYTES = 2... | 264 | 8,703 |
scientific-agent-skills | skills/matlab/scripts/generate_function_scaffold.py | .py | #!/usr/bin/env python3
"""Dry-run or write deterministic MATLAB function and unit-test scaffolds."""
from __future__ import annotations
import argparse
import re
import sys
from pathlib import Path
from typing import Any
from _common import (
CliError,
checked_input,
checked_root,
emit_json,
fail... | 166 | 4,955 |
scientific-agent-skills | skills/matlab/scripts/reproducibility_report.py | .py | #!/usr/bin/env python3
"""Create a deterministic named-file reproducibility report."""
from __future__ import annotations
import argparse
import json
import math
import re
import sys
from pathlib import Path
from typing import Any
from _common import (
CliError,
checked_input,
checked_output,
checked... | 234 | 7,966 |
scientific-agent-skills | skills/ontology-term-resolution/scripts/validate_terms.py | .py | #!/usr/bin/env python3
# /// script
# requires-python = ">=3.11"
# dependencies = []
# ///
"""Validate ontology CURIEs against EBI OLS4 before they leave the machine.
This is the gate that catches invented IDs. For each term it reports whether the
ID exists at all, whether it has been obsoleted (and what replaced it),... | 298 | 9,746 |
scientific-agent-skills | skills/ontology-term-resolution/scripts/ols_client.py | .py | #!/usr/bin/env python3
# /// script
# requires-python = ">=3.11"
# dependencies = []
# ///
"""Minimal EBI OLS4 client plus the pure helpers the two CLIs share.
Standard library only. Network access to https://www.ebi.ac.uk/ols4 is required
for the request functions; every helper below the ``--- pure helpers ---`` mark... | 342 | 12,458 |
scientific-agent-skills | skills/ontology-term-resolution/scripts/resolve_terms.py | .py | #!/usr/bin/env python3
# /// script
# requires-python = ">=3.11"
# dependencies = []
# ///
"""Resolve free-text labels to ontology terms via EBI OLS4.
Never emit an ontology ID from memory -- run this instead. Each input string is
searched with an escalating strategy and every returned candidate is labelled
with how i... | 256 | 8,160 |
scientific-agent-skills | skills/generate-image/scripts/generate_image.py | .py | #!/usr/bin/env python3
"""
Generate and edit images through the OpenRouter Image API (POST /api/v1/images).
The Image API is model-agnostic: the same request shape reaches Gemini,
Seedream, Recraft, GPT-Image, Riverflow, and the rest of the image catalogue.
Responses carry base64 payloads in ``data[].b64_json`` alongs... | 753 | 29,113 |
scientific-agent-skills | skills/hypogenic/scripts/inspect_outputs.py | .py | #!/usr/bin/env python3
"""Inspect local HypoGeniC hypothesis/result JSON without echoing raw content."""
from __future__ import annotations
import argparse
from collections import Counter
from collections.abc import Sequence
if __package__:
from ._common import (
MAX_JSON_BYTES,
MISSING_PREDICTIO... | 167 | 5,771 |
scientific-agent-skills | skills/hypogenic/scripts/validate_config.py | .py | #!/usr/bin/env python3
"""Validate HypoGeniC task configs and the skill's plan-only run policy."""
from __future__ import annotations
import argparse
from collections.abc import Sequence
if __package__:
from ._common import (
MAX_CONFIG_BYTES,
MAX_JSON_BYTES,
CliError,
checked_inp... | 193 | 5,878 |
scientific-agent-skills | skills/hypogenic/scripts/audit_dataset.py | .py | #!/usr/bin/env python3
"""Audit pinned HypoGeniC dataset files, schemas, splits, and duplicates."""
from __future__ import annotations
import argparse
import hashlib
from collections import Counter, defaultdict
from collections.abc import Mapping, Sequence
from pathlib import Path
from typing import Any
if __package... | 411 | 13,628 |
scientific-agent-skills | skills/hypogenic/scripts/_common.py | .py | """Shared, dependency-light helpers for the HypoGeniC skill CLIs.
The helpers perform bounded local file I/O only. They never import HypoGeniC,
contact a network service, enumerate environment variables, load ``.env``
files, or execute text from configs, datasets, hypotheses, or results.
"""
from __future__ import an... | 1,313 | 45,534 |
scientific-agent-skills | skills/hypogenic/scripts/plan_run.py | .py | #!/usr/bin/env python3
"""Create a deterministic token/cost preflight without calling any model."""
from __future__ import annotations
import argparse
from collections.abc import Sequence
from decimal import Decimal, ROUND_HALF_UP
if __package__:
from ._common import (
HYPOGENIC_COMMIT,
HYPOGENIC... | 248 | 8,417 |
scientific-agent-skills | skills/hypogenic/scripts/evaluate_local.py | .py | #!/usr/bin/env python3
"""Create an evaluation plan or score saved predictions without model calls."""
from __future__ import annotations
import argparse
from collections.abc import Sequence
if __package__:
from ._common import (
MAX_CONFIG_BYTES,
MAX_JSON_BYTES,
SPLIT_NAMES,
CliE... | 251 | 7,925 |
scientific-agent-skills | skills/statistical-power/scripts/simulate_power.py | .py | """Monte Carlo power for designs with no closed-form formula.
Closed-form power covers a handful of standard tests. For anything else --
logistic/Poisson regression, mixed-effects models, cluster-randomized trials,
survival analysis, mediation, interactions -- you estimate power by simulation:
1. simulate a datas... | 218 | 8,009 |
scientific-agent-skills | skills/statistical-power/scripts/power.py | .py | """Unified closed-form power / sample-size interface over statsmodels and scipy.
One function each for the three things people actually want:
- sample_size(...) : solve for n given effect size, alpha, power
- power(...) : solve for achieved power given n and effect size
- mde(...) : solve for th... | 321 | 12,490 |
scientific-agent-skills | skills/etetoolkit/scripts/tree_operations.py | .py | #!/usr/bin/env python3
"""Validated command-line tree operations for ETE 4."""
from __future__ import annotations
import argparse
import json
import statistics
import sys
from collections import Counter
from pathlib import Path
from typing import Any
try:
import ete4
from ete4 import Tree
from ete4.parse... | 447 | 15,763 |
scientific-agent-skills | skills/etetoolkit/scripts/quick_visualize.py | .py | #!/usr/bin/env python3
"""Interactive or static ETE 4 tree visualization."""
from __future__ import annotations
import argparse
import ipaddress
import sys
from pathlib import Path
try:
import ete4
from ete4 import Tree
from ete4.parser.newick import NewickError
except ImportError as exc:
raise Syste... | 456 | 15,016 |
scientific-agent-skills | skills/pymatgen/scripts/composition_structure_validator.py | .py | #!/usr/bin/env python3
"""Validate a composition or local periodic structure without modifying it."""
from __future__ import annotations
import argparse
import math
from typing import Any
from _common import (
ABSOLUTE_MAX_PAIRWISE_SITES,
CliError,
DEFAULT_MAX_INPUT_BYTES,
DEFAULT_MAX_OUTPUT_BYTES,
... | 301 | 11,521 |
scientific-agent-skills | skills/pymatgen/scripts/mp_query.py | .py | #!/usr/bin/env python3
"""Plan or explicitly execute one bounded Materials Project summary query."""
from __future__ import annotations
import argparse
import math
import os
import re
from datetime import datetime, timezone
from typing import Any
from _common import (
CliError,
DEFAULT_MAX_OUTPUT_BYTES,
... | 417 | 15,087 |
scientific-agent-skills | skills/pymatgen/scripts/symmetry_sensitivity_report.py | .py | #!/usr/bin/env python3
"""Report space-group sensitivity across explicit symmetry tolerances."""
from __future__ import annotations
import argparse
import math
from typing import Any
from _common import (
CliError,
DEFAULT_MAX_INPUT_BYTES,
DEFAULT_MAX_OUTPUT_BYTES,
DEFAULT_MAX_SITES,
checked_outp... | 213 | 7,659 |
scientific-agent-skills | skills/pymatgen/scripts/io_conversion_plan.py | .py | #!/usr/bin/env python3
"""Create a dependency-free, non-executing structure conversion plan."""
from __future__ import annotations
import argparse
from _common import (
CliError,
DEFAULT_MAX_OUTPUT_BYTES,
checked_output_file,
emit_json,
positive_int,
write_json_new,
)
FORMAT_CAPABILITIES = ... | 205 | 6,970 |
scientific-agent-skills | skills/pymatgen/scripts/_common.py | .py | #!/usr/bin/env python3
"""Shared, standard-library-first helpers for the bundled pymatgen CLIs."""
from __future__ import annotations
import hashlib
import json
import math
import os
import warnings
from importlib.metadata import PackageNotFoundError, version
from pathlib import Path
from typing import Any
PYMATGEN... | 317 | 10,658 |
scientific-agent-skills | skills/pymatgen/scripts/phase_diagram_generator.py | .py | #!/usr/bin/env python3
"""Build a local phase diagram from a strict, provenance-bearing JSON dataset."""
from __future__ import annotations
import argparse
import math
import tempfile
from pathlib import Path
from typing import Any
from _common import (
ABSOLUTE_MAX_OUTPUT_BYTES,
CliError,
DEFAULT_MAX_IN... | 416 | 14,650 |
scientific-agent-skills | skills/pymatgen/scripts/structure_analyzer.py | .py | #!/usr/bin/env python3
"""Produce a bounded JSON analysis of one local periodic structure."""
from __future__ import annotations
import argparse
import math
import warnings
from typing import Any
from _common import (
ABSOLUTE_MAX_PAIRWISE_SITES,
CliError,
DEFAULT_MAX_INPUT_BYTES,
DEFAULT_MAX_OUTPUT_... | 294 | 11,051 |
scientific-agent-skills | skills/pymatgen/scripts/artifact_manifest.py | .py | #!/usr/bin/env python3
"""Create a bounded checksum and provenance manifest for explicit local files."""
from __future__ import annotations
import argparse
import mimetypes
import platform
import re
from datetime import datetime, timezone
from _common import (
CliError,
DEFAULT_MAX_OUTPUT_BYTES,
MP_API_V... | 173 | 5,659 |
scientific-agent-skills | skills/pymatgen/scripts/structure_converter.py | .py | #!/usr/bin/env python3
"""Convert one local periodic structure with explicit loss acknowledgement."""
from __future__ import annotations
import argparse
import warnings
from _common import (
CliError,
DEFAULT_MAX_INPUT_BYTES,
DEFAULT_MAX_OUTPUT_BYTES,
DEFAULT_MAX_SITES,
checked_output_file,
e... | 220 | 7,596 |
scientific-agent-skills | skills/scientific-slides/scripts/generate_schematic.py | .py | #!/usr/bin/env python3
"""
Scientific schematic generation using Nano Banana 2.
Generate any scientific diagram by describing it in natural language.
Nano Banana 2 handles everything automatically with smart iterative refinement.
Smart iteration: Only regenerates if quality is below threshold for your document type.
... | 199 | 7,600 |
scientific-agent-skills | skills/scientific-slides/scripts/pdf_to_images.py | .py | #!/usr/bin/env python3
"""
PDF to Images Converter for Presentations
Converts presentation PDFs to images for visual inspection and review.
Supports multiple output formats and resolutions.
Uses PyMuPDF (fitz) as the primary conversion method - no external
dependencies required (no poppler, ghostscript, or ImageMagic... | 222 | 6,650 |
scientific-agent-skills | skills/scientific-slides/scripts/generate_slide_image_ai.py | .py | #!/usr/bin/env python3
"""
AI-powered slide image generation using Nano Banana Pro.
This script generates presentation slides or slide visuals using AI:
- full_slide mode: Generate complete slides with title, content, and visuals (for PDF workflow)
- visual_only mode: Generate just images/figures to place on slides (f... | 878 | 34,505 |
scientific-agent-skills | skills/scientific-slides/scripts/validate_presentation.py | .py | #!/usr/bin/env python3
"""
Presentation Validation Script
Validates scientific presentations for common issues:
- Slide count vs. duration
- LaTeX compilation
- File size checks
- Basic format validation
"""
import sys
import os
import argparse
import subprocess
from pathlib import Path
from typing import Dict, List,... | 409 | 13,367 |
scientific-agent-skills | skills/scientific-slides/scripts/slides_to_pdf.py | .py | #!/usr/bin/env python3
"""
Combine slide images into a single PDF presentation.
This script takes multiple slide images (PNG, JPG) and combines them
into a single PDF file, maintaining aspect ratio and quality.
Usage:
# Combine all PNG files in a directory
python slides_to_pdf.py slides/*.png -o presentation.... | 236 | 7,426 |
scientific-agent-skills | skills/scientific-slides/scripts/generate_schematic_ai.py | .py | #!/usr/bin/env python3
"""
AI-powered scientific schematic generation using Nano Banana 2.
This script uses a smart iterative refinement approach:
1. Generate initial image with Nano Banana 2
2. AI quality review using Gemini 3.6 Flash for scientific critique
3. Only regenerate if quality is below threshold for docume... | 951 | 38,534 |
scientific-agent-skills | skills/scientific-slides/scripts/generate_slide_image.py | .py | #!/usr/bin/env python3
"""
Slide image generation using Nano Banana Pro.
Generate presentation slides or visuals by describing them in natural language.
Nano Banana Pro handles everything automatically with smart iterative refinement.
Two modes:
- Default (full slide): Generate complete slides with title, content, vi... | 198 | 7,754 |
scientific-agent-skills | skills/pacsomatic/scripts/run_pacsomatic.py | .py | """Prepare, validate, and optionally launch nf-core/pacsomatic across platforms."""
import argparse
import csv
import os
import re
import shlex
import shutil
import subprocess
import sys
from pathlib import Path
from urllib.parse import urlparse
SCHEDULER_CMDS = {
"lsf": "bsub",
"slurm": "sbatch",
"pbs": ... | 795 | 29,233 |
scientific-agent-skills | skills/exploratory-data-analysis/scripts/eda_analyzer.py | .py | #!/usr/bin/env python3
"""Closed, bounded exploratory analyzer for explicitly supported local formats."""
from __future__ import annotations
import argparse
import json
from pathlib import Path
from typing import Any
from _capabilities import capability_for_path
from _common import (
DEFAULT_MAX_FILE_BYTES,
... | 346 | 10,547 |
scientific-agent-skills | skills/exploratory-data-analysis/scripts/report_scaffold.py | .py | #!/usr/bin/env python3
"""Generate a rigorous, redacted EDA Markdown report scaffold."""
from __future__ import annotations
import argparse
from pathlib import Path
from _common import (
DEFAULT_MAX_FILE_BYTES,
CliError,
bounded_file_limit,
checked_input_file,
emit_markdown,
markdown_scalar,
... | 144 | 4,247 |
scientific-agent-skills | skills/exploratory-data-analysis/scripts/_capabilities.py | .py | #!/usr/bin/env python3
"""Closed capability registry and lightweight format checks for EDA tools."""
from __future__ import annotations
import itertools
import zipfile
from pathlib import Path
from typing import Any
from _common import (
MAX_COMPRESSION_RATIO,
MAX_NPZ_MEMBERS,
MAX_NPZ_UNCOMPRESSED_BYTES,... | 577 | 20,714 |
scientific-agent-skills | skills/exploratory-data-analysis/scripts/_tabular.py | .py | #!/usr/bin/env python3
"""Bounded, redacted tabular profiling and EDA sensitivity calculations."""
from __future__ import annotations
import csv
import hashlib
import heapq
import math
import statistics
from collections import Counter
from collections.abc import Callable, Iterable, Sequence
from dataclasses import da... | 906 | 32,695 |
scientific-agent-skills | skills/exploratory-data-analysis/scripts/_common.py | .py | #!/usr/bin/env python3
"""Shared local-only, bounded-I/O helpers for the EDA command-line tools."""
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, PurePath
from typing import Any
... | 461 | 14,039 |
scientific-agent-skills | skills/exploratory-data-analysis/scripts/_structured.py | .py | #!/usr/bin/env python3
"""Bounded inspectors for JSON, NumPy containers, and HDF5 metadata."""
from __future__ import annotations
import itertools
import math
from pathlib import Path
from typing import Any
from _capabilities import preflight_npz
from _common import (
MAX_JSON_BYTES,
CliError,
display_id... | 392 | 14,584 |
scientific-agent-skills | skills/exploratory-data-analysis/scripts/distribution_sensitivity.py | .py | #!/usr/bin/env python3
"""Bounded distribution, transformation, and outlier sensitivity CLI."""
from __future__ import annotations
import argparse
from _capabilities import capability_for_path
from _common import (
DEFAULT_MAX_FILE_BYTES,
DEFAULT_MAX_ROWS,
bounded_file_limit,
checked_input_file,
... | 118 | 3,304 |
scientific-agent-skills | skills/exploratory-data-analysis/scripts/missingness_leakage_audit.py | .py | #!/usr/bin/env python3
"""Bounded missingness, group structure, and split leakage audit for CSV/TSV."""
from __future__ import annotations
import argparse
from _capabilities import capability_for_path
from _common import (
DEFAULT_MAX_FILE_BYTES,
DEFAULT_MAX_ROWS,
bounded_file_limit,
checked_input_fi... | 131 | 3,904 |
scientific-agent-skills | skills/exploratory-data-analysis/scripts/image_inspector.py | .py | #!/usr/bin/env python3
"""Metadata-only PNG/JPEG/TIFF inspector; pixel arrays are never decoded."""
from __future__ import annotations
import argparse
import itertools
import warnings
from pathlib import Path
from typing import Any
from _capabilities import capability_for_path, validate_magic
from _common import (
... | 215 | 7,298 |
scientific-agent-skills | skills/exploratory-data-analysis/scripts/capability_manifest.py | .py | #!/usr/bin/env python3
"""Emit the closed capability matrix or a redacted local-file manifest."""
from __future__ import annotations
import argparse
from pathlib import Path
from typing import Any
from _capabilities import (
REFERENCE_ONLY_FORMATS,
automated_capability_rows,
capability_for_path,
vali... | 185 | 5,433 |
scientific-agent-skills | skills/exploratory-data-analysis/scripts/tabular_profile.py | .py | #!/usr/bin/env python3
"""Bounded aggregate schema/profile CLI for local CSV and TSV files."""
from __future__ import annotations
import argparse
from _capabilities import capability_for_path
from _common import (
DEFAULT_MAX_FILE_BYTES,
DEFAULT_MAX_ROWS,
CliError,
bounded_file_limit,
checked_inp... | 110 | 3,077 |
scientific-agent-skills | skills/exploratory-data-analysis/scripts/sequence_inspector.py | .py | #!/usr/bin/env python3
"""Bounded FASTA/FASTQ aggregate inspector with no identifier or sequence output."""
from __future__ import annotations
import argparse
import math
from pathlib import Path
from typing import Any
from _capabilities import capability_for_path, validate_magic
from _common import (
DEFAULT_MA... | 256 | 8,621 |
scientific-agent-skills | skills/pytdc/scripts/cache_audit.py | .py | #!/usr/bin/env python3
"""Create a bounded, read-only manifest of a local PyTDC data directory."""
from __future__ import annotations
import argparse
import heapq
import os
import sys
from collections import Counter
from pathlib import Path
from typing import Any
from _common import CliError, bounded_int, emit_json,... | 147 | 4,574 |
scientific-agent-skills | skills/pytdc/scripts/discover_metadata.py | .py | #!/usr/bin/env python3
"""Discover PyTDC registries without constructing loaders or downloading data."""
from __future__ import annotations
import argparse
import sys
from typing import Any, Iterable
from _common import (
CliError,
bounded_int,
canonical_name,
emit_json,
load_pytdc_metadata,
)
... | 175 | 5,066 |
scientific-agent-skills | skills/pytdc/scripts/load_and_split_data.py | .py | #!/usr/bin/env python3
"""Plan or explicitly execute one bounded PyTDC dataset split."""
from __future__ import annotations
import argparse
import importlib
import itertools
import sys
from pathlib import Path
from typing import Any
from _common import (
CliError,
bounded_int,
canonical_name,
emit_js... | 375 | 12,594 |
scientific-agent-skills | skills/pytdc/scripts/molecular_generation.py | .py | #!/usr/bin/env python3
"""Safely plan PyTDC molecule data access or bounded oracle scoring."""
from __future__ import annotations
import argparse
import contextlib
import os
import sys
from pathlib import Path
from typing import Any, Iterator
from _common import (
CliError,
bounded_int,
canonical_name,
... | 418 | 13,619 |
scientific-agent-skills | skills/pytdc/scripts/benchmark_evaluation.py | .py | #!/usr/bin/env python3
"""Plan or explicitly evaluate user-supplied TDC benchmark predictions."""
from __future__ import annotations
import argparse
import importlib
import math
import sys
from pathlib import Path
from typing import Any
from _common import (
CliError,
bounded_int,
canonical_name,
emi... | 368 | 12,498 |
scientific-agent-skills | skills/pytdc/scripts/_common.py | .py | #!/usr/bin/env python3
"""Shared, standard-library-only helpers for the bundled PyTDC CLIs."""
from __future__ import annotations
import importlib
import json
import math
import os
import tempfile
from importlib.metadata import PackageNotFoundError, version
from pathlib import Path
from typing import Any, Iterable, S... | 206 | 7,346 |
scientific-agent-skills | skills/omero-integration/scripts/inventory.py | .py | #!/usr/bin/env python3
"""Produce a bounded, read-only OMERO object inventory."""
from __future__ import annotations
import argparse
import sys
from datetime import datetime, timezone
from typing import Any
from omero_common import (
ConfigError,
DependencyError,
OutputPathError,
bounded_int,
con... | 303 | 8,364 |
scientific-agent-skills | skills/omero-integration/scripts/export_image_metadata.py | .py | #!/usr/bin/env python3
"""Export bounded annotations and ROI geometry for explicit image IDs."""
from __future__ import annotations
import argparse
import json
import sys
from datetime import datetime, timezone
from typing import Any
from omero_common import (
ConfigError,
DependencyError,
OutputPathErro... | 561 | 16,731 |
scientific-agent-skills | skills/omero-integration/scripts/validate_config.py | .py | #!/usr/bin/env python3
"""Validate named OMERO endpoint/auth variables without contacting OMERO."""
from __future__ import annotations
import argparse
import json
import socket
import sys
from typing import Any
from omero_common import (
ConfigError,
config_summary,
load_connection_config,
scrubbed_e... | 141 | 4,146 |
scientific-agent-skills | skills/omero-integration/scripts/omero_common.py | .py | #!/usr/bin/env python3
"""Shared safety utilities for the bundled OMERO client helpers."""
from __future__ import annotations
import argparse
import contextlib
import json
import math
import os
import tempfile
from collections.abc import Iterable, Iterator, Mapping
from dataclasses import dataclass
from datetime impo... | 491 | 14,257 |
scientific-agent-skills | skills/omero-integration/scripts/plan_transfer.py | .py | #!/usr/bin/env python3
"""Build a local-only, bounded OMERO import or export plan."""
from __future__ import annotations
import argparse
import os
import re
import sys
from datetime import datetime, timezone
from pathlib import Path
from typing import Any
from omero_common import (
OutputPathError,
bounded_i... | 394 | 11,861 |
scientific-agent-skills | skills/analytical-method-validation/scripts/check_detection_limits.py | .py | #!/usr/bin/env python3
"""Estimate DL and QL by every approach ICH Q2(R2) 3.2.3 allows, and compare them.
The four approaches routinely disagree by a factor of two or more on the same
data. Reporting one number without naming the approach is the finding an
assessor raises, so this script computes all of the applicable... | 311 | 13,215 |
scientific-agent-skills | skills/analytical-method-validation/scripts/_catalog.py | .py | #!/usr/bin/env python3
"""Framework catalogue for analytical method validation.
Content sourced 2026-07-27 from the freely published ICH guidelines, which ICH
licenses for reuse with acknowledgement. Compendial (USP) and CLSI documents are
copyrighted and paywalled: they are referenced here by designation, title, and
... | 500 | 23,838 |
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