DP-GEN Simplify Workflow
jinzhezenggroup/computational-chemistry-agent-skills
Prepares, validates and runs DP-GEN simplify jobs that thin out repeated or redundant DeepMD datasets, generating param.json and machine.json for local or scheduler runs.
Box Least Squares (BLS) periodogram for detecting transiting exoplanets and eclipsing binaries.
$ npx skills add benchflow-ai/skillsbench --skill box-least-squares -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install benchflow-ai/skillsbench box-least-squares --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/benchflow-ai/skillsbench.git skills-src && mkdir -p .claude/skills && cp -r skills-src/tasks/exoplanet-detection-period/environment/skills/box-least-squares .claude/skills/box-least-squares && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "box-least-squares" agent skill from https://github.com/benchflow-ai/skillsbench/tree/main/tasks/exoplanet-detection-period/environment/skills/box-least-squares into .claude/skills/box-least-squares/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "box-least-squares", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/benchflow-ai/skillsbench/tree/main/tasks/exoplanet-detection-period/environment/skills/box-least-squaresType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add benchflow-ai/skillsbench --skill box-least-squares -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install benchflow-ai/skillsbench box-least-squares --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/benchflow-ai/skillsbench.git skills-src && mkdir -p .agents/skills && cp -r skills-src/tasks/exoplanet-detection-period/environment/skills/box-least-squares .agents/skills/box-least-squares && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "box-least-squares" agent skill from https://github.com/benchflow-ai/skillsbench/tree/main/tasks/exoplanet-detection-period/environment/skills/box-least-squares into .agents/skills/box-least-squares/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "box-least-squares", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add benchflow-ai/skillsbench --skill box-least-squares -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install benchflow-ai/skillsbench box-least-squares --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/benchflow-ai/skillsbench.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/tasks/exoplanet-detection-period/environment/skills/box-least-squares .cursor/skills/box-least-squares && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "box-least-squares" agent skill from https://github.com/benchflow-ai/skillsbench/tree/main/tasks/exoplanet-detection-period/environment/skills/box-least-squares into .cursor/skills/box-least-squares/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "box-least-squares", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/benchflow-ai/skillsbench.git --path tasks/exoplanet-detection-period/environment/skills/box-least-squares--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add benchflow-ai/skillsbench --skill box-least-squares -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install benchflow-ai/skillsbench box-least-squares --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/benchflow-ai/skillsbench.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/tasks/exoplanet-detection-period/environment/skills/box-least-squares .gemini/skills/box-least-squares && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "box-least-squares" agent skill from https://github.com/benchflow-ai/skillsbench/tree/main/tasks/exoplanet-detection-period/environment/skills/box-least-squares into .gemini/skills/box-least-squares/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "box-least-squares", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install benchflow-ai/skillsbench box-least-squaresInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add benchflow-ai/skillsbench --skill box-least-squares -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/benchflow-ai/skillsbench.git skills-src && mkdir -p .github/skills && cp -r skills-src/tasks/exoplanet-detection-period/environment/skills/box-least-squares .github/skills/box-least-squares && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "box-least-squares" agent skill from https://github.com/benchflow-ai/skillsbench/tree/main/tasks/exoplanet-detection-period/environment/skills/box-least-squares into .github/skills/box-least-squares/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "box-least-squares", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add benchflow-ai/skillsbench --skill box-least-squares -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install benchflow-ai/skillsbench box-least-squares --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/benchflow-ai/skillsbench.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/tasks/exoplanet-detection-period/environment/skills/box-least-squares .opencode/skills/box-least-squares && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "box-least-squares" agent skill from https://github.com/benchflow-ai/skillsbench/tree/main/tasks/exoplanet-detection-period/environment/skills/box-least-squares into .opencode/skills/box-least-squares/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "box-least-squares", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
box-least-squaresBox Least Squares (BLS) periodogram for detecting transiting exoplanets and eclipsing binaries.
Box Least Squares is an agent skill from benchflow-ai/skillsbench. Box Least Squares (BLS) periodogram for detecting transiting exoplanets and eclipsing binaries. Use when searching for periodic box-shaped dips in light curves. Alternative to Transit Least Squares, available in astropy.timeseries. Based on Kovács et al. (2002).
Its SKILL.md is about 2.6k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.
It sits in Research & Science, covering Physical and earth sciences. The repository describes itself as: SkillsBench evaluates how well skills work and how effective agents are at using them. The licence is Apache-2.0.
2 steps, taken from the step headings in SKILL.md.
Read from SKILL.md and the folder at commit 9a1f4dd. It shows what the files ask for, not the result of running them.
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Shell commands in SKILL.md call:
pipFrom the folder's file list and the shell code blocks in SKILL.md.
Links to these hosts (documentation or services it may open):
docs.astropy.orgarxiv.orglightkurve.github.iogithub.comFrom URLs in SKILL.md, links to its own repository left out.
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Box Least Squares loads about 2.6k tokens when it runs. Until then it costs about 70 tokens; SKILL.md has 713 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.
The full file from benchflow-ai/skillsbench at commit 9a1f4dd, republished under its Apache-2.0 licence (© benchflow-ai). 713 words, ~2,570 tokens.
.claude/skills/box-least-squares/SKILL.md (or your agent's skills folder).The Box Least Squares (BLS) periodogram is a statistical tool for detecting transiting exoplanets and eclipsing binaries in photometric time series data. BLS models a transit as a periodic upside-down top hat (box shape) and finds the period, duration, depth, and reference time that best fit the data.
BLS is built into Astropy and provides an alternative to Transit Least Squares (TLS). Both search for transits, but with different implementations and performance characteristics.
Key parameters BLS searches for:
BLS is part of Astropy:
pip install astropyimport numpy as np
import astropy.units as u
from astropy.timeseries import BoxLeastSquares
# Prepare data
# time, flux, and flux_err should be numpy arrays or Quantities
t = time * u.day # Add units if not already present
y = flux
dy = flux_err # Optional but recommended
# Create BLS object
model = BoxLeastSquares(t, y, dy=dy)
# Automatic period search with specified duration
duration = 0.2 * u.day # Expected transit duration
periodogram = model.autopower(duration)
# Extract results
best_period = periodogram.period[np.argmax(periodogram.power)]
print(f"Best period: {best_period:.5f}")Recommended for initial searches. Automatically determines appropriate period grid:
# Specify duration (or multiple durations)
duration = 0.2 * u.day
periodogram = model.autopower(duration)
# Or search multiple durations
durations = [0.1, 0.15, 0.2, 0.25] * u.day
periodogram = model.autopower(durations)For more control over the search:
# Define custom period grid
periods = np.linspace(2.0, 10.0, 1000) * u.day
duration = 0.2 * u.day
periodogram = model.power(periods, duration)Warning: Period grid quality matters! Too coarse and you'll miss the true period.
BLS supports two objective functions:
Maximizes the statistical likelihood of the model fit:
periodogram = model.autopower(0.2 * u.day, objective='likelihood')Uses the SNR with which the transit depth is measured:
periodogram = model.autopower(0.2 * u.day, objective='snr')The SNR objective can improve reliability in the presence of correlated noise.
import numpy as np
import matplotlib.pyplot as plt
import astropy.units as u
from astropy.timeseries import BoxLeastSquares
# Load and prepare data
data = np.loadtxt('light_curve.txt')
time = data[:, 0] * u.day
flux = data[:, 1]
flux_err = data[:, 3]
# Create BLS model
model = BoxLeastSquares(time, flux, dy=flux_err)
# Run BLS with automatic period grid
# Try multiple durations to find best fit
durations = np.linspace(0.05, 0.3, 10) * u.day
periodogram = model.autopower(durations, objective='likelihood')
# Find peak
max_power_idx = np.argmax(periodogram.power)
best_period = periodogram.period[max_power_idx]
best_duration = periodogram.duration[max_power_idx]
best_t0 = periodogram.transit_time[max_power_idx]
max_power = periodogram.power[max_power_idx]
print(f"Period: {best_period:.5f}")
print(f"Duration: {best_duration:.5f}")
print(f"T0: {best_t0:.5f}")
print(f"Power: {max_power:.2f}")
# Plot periodogram
import matplotlib.pyplot as plt
plt.plot(periodogram.period, periodogram.power)
plt.xlabel('Period [days]')
plt.ylabel('BLS Power')
plt.show()Use compute_stats() to calculate detailed statistics about a candidate transit:
# Get statistics for the best period
stats = model.compute_stats(
periodogram.period[max_power_idx],
periodogram.duration[max_power_idx],
periodogram.transit_time[max_power_idx]
)
# Key statistics for validation
print(f"Depth: {stats['depth']:.6f}")
print(f"Depth uncertainty: {stats['depth_err']:.6f}")
print(f"SNR: {stats['depth_snr']:.2f}")
print(f"Odd/Even mismatch: {stats['depth_odd'] - stats['depth_even']:.6f}")
print(f"Number of transits: {stats['transit_count']}")
# Check for false positives
if abs(stats['depth_odd'] - stats['depth_even']) > 3 * stats['depth_err']:
print("Warning: Significant odd-even mismatch - may not be planetary")Validation criteria:
The BLS periodogram is sensitive to period grid spacing. The autoperiod() method provides a conservative grid:
# Get automatic period grid
periods = model.autoperiod(durations, minimum_period=1*u.day, maximum_period=10*u.day)
print(f"Period grid has {len(periods)} points")
# Use this grid with power()
periodogram = model.power(periods, durations)Tips:
autopower() for initial searchesTo compare multiple peaks:
# Find top 5 peaks
sorted_idx = np.argsort(periodogram.power)[::-1]
top_5 = sorted_idx[:5]
print("Top 5 candidates:")
for i, idx in enumerate(top_5):
period = periodogram.period[idx]
power = periodogram.power[idx]
duration = periodogram.duration[idx]
stats = model.compute_stats(period, duration, periodogram.transit_time[idx])
print(f"\n{i+1}. Period: {period:.5f}")
print(f" Power: {power:.2f}")
print(f" Duration: {duration:.5f}")
print(f" SNR: {stats['depth_snr']:.2f}")
print(f" Transits: {stats['transit_count']}")After finding a candidate, phase-fold to visualize the transit:
# Fold the light curve at the best period
phase = ((time.value - best_t0.value) % best_period.value) / best_period.value
# Plot to verify transit shape
import matplotlib.pyplot as plt
plt.plot(phase, flux, '.')
plt.xlabel('Phase')
plt.ylabel('Flux')
plt.show()Both methods search for transits, but differ in implementation:
Pros:
Cons:
Pros:
Cons:
Recommendation: Try both! TLS is often more sensitive, but BLS is faster and built-in.
BLS works best with preprocessed data. Consider this pipeline:
compute_stats() to check candidate qualityflatten())Causes:
Solutions:
flatten() windowCauses:
Solutions:
Cause:
Solution:
stats['depth_odd'] vs stats['depth_even']pip install astropy numpy matplotlib
# Optional: lightkurve for preprocessing
pip install lightkurveUse BLS when:
compute_stats)Use TLS when:
Use Lomb-Scargle when:
For exoplanet detection, both BLS and TLS are valid choices. Try both and compare results!
© benchflow-ai, Apache-2.0. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Just SKILL.md in tasks/exoplanet-detection-period/environment/skills/box-least-squares of benchflow-ai/skillsbench.
Open the folder on GitHubat commit 9a1f4dd
Box Least Squares next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Box Least Squares this skillbenchflow-ai/skillsbench | 1.8k | — | ~2.6k | Automated safety check: Pass | Apache-2.0 | |
| DP-GEN Simplify Workflowjinzhezenggroup/computational-chemistry-agent-skills | 148 | — | ~2.7k | Automated safety check: Pass | LGPL-3.0-or-later | |
| OpenpivK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~4.8k | Automated safety check: Notes | BSD-3-Clause | |
| Journal Of Climatebrycewang-stanford/Awesome-Journal-Skills | 1.2k | — | ~1.8k | Automated safety check: Pass | MIT | |
| Kidd Script Writinginfometa/workbuddyskills | 348 | — | ~1.3k | Automated safety check: Pass | None | |
| AstropyzLanqing/codex-claude-academic-skills | 4.7k | 13 repos | ~2.9k | Automated safety check: Pass | BSD-3-Clause |
jinzhezenggroup/computational-chemistry-agent-skills
Prepares, validates and runs DP-GEN simplify jobs that thin out repeated or redundant DeepMD datasets, generating param.json and machine.json for local or scheduler runs.
K-Dense-AI/scientific-agent-skills
Performs Particle Image Velocimetry (PIV) analysis with OpenPIV.
brycewang-stanford/Awesome-Journal-Skills
A skill your agent uses when targeting Journal of Climate or deciding whether a climate-dynamics or climate-variability manuscript fits this venue.
infometa/workbuddyskills
Creates deep-analysis short video scripts in "吟游诗人基德" (Minstrel Kidd) style.
zLanqing/codex-claude-academic-skills
Comprehensive Python library for astronomy and astrophysics.
zLanqing/codex-claude-academic-skills
Materials science toolkit. An agent skill from zLanqing/codex-claude-academic-skills.
benchflow-ai/skillsbench
This skill should be used when working on Lean 4 formalization projects to maintain persistent memory of successful proof patterns, failed approaches, project conventions, and user preferences…
benchflow-ai/skillsbench
World-class data engineering skill for building scalable data pipelines, ETL/ELT systems, real-time streaming, and data infrastructure.
benchflow-ai/skillsbench
AC branch pi-model power flow equations (P/Q and |S|) with transformer tap ratio and phase shift, matching acopf-math-model.md and MATPOWER branch fields.
benchflow-ai/skillsbench
Civilization 6 district mechanics library. An agent skill from benchflow-ai/skillsbench.
benchflow-ai/skillsbench
Build deterministic, verifiable data visualizations with D3.js (v6).
benchflow-ai/skillsbench
DC power flow analysis for power systems. An agent skill from benchflow-ai/skillsbench.
Categories
Box Least Squares (BLS) periodogram for detecting transiting exoplanets and eclipsing binaries. Box Least Squares is an agent skill from benchflow-ai/skillsbench. Box Least Squares (BLS) periodogram for detecting transiting exoplanets and eclipsing binaries.
Box Least Squares fits situations like: searching for periodic box-shaped dips in light curves; tasks that involve Physical and earth sciences.
Run `npx skills add benchflow-ai/skillsbench --skill box-least-squares -a claude-code`. Or copy the skill folder (tasks/exoplanet-detection-period/environment/skills/box-least-squares in benchflow-ai/skillsbench) into .claude/skills/box-least-squares in your project. Claude Code loads it when a task matches its description.
Run `npx skills add benchflow-ai/skillsbench --skill box-least-squares -a codex`. Or copy the skill folder (tasks/exoplanet-detection-period/environment/skills/box-least-squares in benchflow-ai/skillsbench) into .agents/skills/box-least-squares in your project. Codex loads it when a task matches its description.
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add benchflow-ai/skillsbench --skill box-least-squares -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/box-least-squares, .gemini/skills/box-least-squares, .github/skills/box-least-squares and .opencode/skills/box-least-squares in your project.
Going by SKILL.md and its folder, Box Least Squares needs the command-line tools its instructions call (pip). Our summary lists: Python 3.
SKILL.md names 4 domains. As links in the text: docs.astropy.org, arxiv.org, lightkurve.github.io and github.com. This is read from the text; nothing was executed.
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.
Box Least Squares is published under the Apache-2.0 licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
About 2.6k tokens (SKILL.md is roughly 10k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
Skills that share tags, products or a category with Box Least Squares: DP-GEN Simplify Workflow (jinzhezenggroup/computational-chemistry-agent-skills, 148 stars), Openpiv (K-Dense-AI/scientific-agent-skills, 48k stars), Journal Of Climate (brycewang-stanford/Awesome-Journal-Skills, 1.2k stars) and Kidd Script Writing (infometa/workbuddyskills, 348 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
benchflow-ai (a GitHub organization) maintains it in benchflow-ai/skillsbench, which has 1,835 GitHub stars. The repository holds 189 skills in this directory. The repository was last updated on July 23, 2026.
Source: benchflow-ai/skillsbench on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.