optimization-project-structure

optimization-project-structure is a skill for Claude Code from hajibabaie/combinatorial-optimization-skills. It costs 134 tokens per session (10,201 once invoked), scanned A, original, MIT.

A guide to structuring optimization experiments so that code, settings, random seeds, and results remain reproducible. It covers package layouts, configuration files, algorithm and problem selection, safe result writing, and basic tests.

In plain words
What is it for?
Use it to organize thesis or paper projects, run many experiment variations, support more than one computer, and connect each result to its source code and settings.
Why use it?
It prevents research projects from becoming collections of scripts where results are hard to repeat, compare, or explain later.

Skill for Claude Code

Written for Claude Code: shipped in a Claude Code plugin.

Not installable: its command points at a path on the author’s own machine, so it runs nowhere else. The line is /home/alice/....

Part of the combinatorial-optimization plugin — 76 skills shipped together

Good fit Use it to organize thesis or paper projects, run many experiment variations, support more than one computer, and connect each result to its source code and settings.

Compare 6 skills from other repositories ↓
Install

Getting it into your agent

This one installs as part of its plugin. Adding the marketplace and installing the plugin brings it with everything else the plugin ships.

Claude Code
/plugin marketplace add hajibabaie/combinatorial-optimization-skills
Claude Code
/plugin install combinatorial-optimization

Made for: Claude Code.

Or install combinatorial-optimization, the plugin that ships this one along with the rest of its 76 skills.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for optimization-project-structure

README.md
[![agentmods](https://agentmods.dev/badge/skills/hajibabaie/combinatorial-optimization-skills/optimization-project-structure/github.svg)](https://agentmods.dev/skills/hajibabaie/combinatorial-optimization-skills/optimization-project-structure)
Your own site
<a href="https://agentmods.dev/skills/hajibabaie/combinatorial-optimization-skills/optimization-project-structure"><img src="https://agentmods.dev/badge/skills/hajibabaie/combinatorial-optimization-skills/optimization-project-structure/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for optimization-project-structure

Your own site · 80×15
<a href="https://agentmods.dev/skills/hajibabaie/combinatorial-optimization-skills/optimization-project-structure"><img src="https://agentmods.dev/badge/skills/hajibabaie/combinatorial-optimization-skills/optimization-project-structure.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 134 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 10,201 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 1 finding. A grade says what 26 rules found in the file — not that it is safe.
Origin original No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00134 $0.10201
Opus 5.5 $0.00054 $0.04080
Sonnet 5.5 $0.00027 $0.02040
Haiku 4.5 $0.00013 $0.01020

Measured 1mo ago against content hash d92fd2efcfde, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

optimization-project-structure scanned grade A with 1 finding against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 1mo ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Runs shell commandslowCapability

Expected in a hook, worth knowing in a rule or an instructions file.

head = subprocess.run(["git", "rev-parse", "--short", "HEAD"],
skills/optimization-project-structure/SKILL.md · 901 lines

How it starts

The opening of the file, as written. The whole thing — 901 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Optimization Project Structure

You are an expert in structuring research code for combinatorial optimization: package layout, configuration systems, algorithm/problem factories, seeding discipline, atomic result writing, and a light testing tier. This skill is a pattern catalog: each pattern gives a short motivation, a complete implementation, and the pitfall that most often invalidates experiments. Use the framework below to size the structure to the project, then adapt the matching patterns.

Initial Assessment

Establish the following before recommending any structure:

  • Project lifetime and stakes. A one-week exploration tolerates a single script. A thesis or paper project will produce thousands of runs over months and must support the question "which code and parameters produced this number in Table 3?"
  • Count the axes of variation. How many problems, algorithms, parameter settings, instances, and seeds will be combined? The product of these axes is the number of runs the structure must name, store, and aggregate without collisions.
  • Compute environment. Laptop only, or also a cluster/colleague's machine? Anything beyond one machine forbids absolute paths, machine-local state, and manual run bookkeeping.
  • Current state of the code. Greenfield, a pile of notebooks, or a working flat script? Migration order matters: extract the library first, configs second, orchestration last.
  • Result volume and format. Hundreds of scalar records fit JSON-per-run plus a CSV aggregate. Millions of rows or per-iteration traces need parquet and a separate trace directory from day one.
  • Failure tolerance of campaigns. Will runs take seconds or hours? Long campaigns need resumability (skip completed runs) and per-run failure isolation; short ones do not.
  • Sources of randomness. List them: metaheuristic moves, instance generation, tie-breaking, solver internals. Every source must trace back to a recorded seed.
  • External solvers and licenses. Solver version and parameter files are part of provenance; a Gurobi version bump can change every number in a results table.
  • Who else runs this code. Solo use allows conventions in your head; a second user (advisor, reviewer, future you in 18 months) requires the conventions to be in the repository: README, configs, and tests.
  • What the paper needs. Identify the final artifacts (tables, figures, per-instance bests) and design the results directory and record schema backward from them.

Read the full file on GitHub · 901 lines

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 1mo ago First seen · 901 lines · 134 tokens per session scan A d92fd2efcfde

Subscribe to this mod's changes

optimization-project-structure is a skill published in the GitHub repository hajibabaie/combinatorial-optimization-skills (14 stars, last pushed 4mo ago), licensed MIT. It adds 134 tokens to every session and 10,201 once invoked, about $0.0005 per session on Opus 5.5. A static security scan graded it A with 1 finding (runs shell commands). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.

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