science-ops-cli 0.3.0

A multi-discipline scientific CLI toolkit for physics, astronomy, biology, chemistry, and data analysis.

Science Ops CLI

A terminal-based Swiss army knife for scientists, engineers, students, and data nerds.

Think of it as a tiny multi-discipline lab that lives in your shell:

• Physical constants at your fingertips
• Unit conversions with dimensional sanity
• Basic statistics and probability tools
• Waveform generation and ASCII plotting
• A lab notebook that logs your commands and results
• Science modules (astronomy, chemistry, mechanics, optics, electromagnetism, relativity, biology)
• Quick CSV/TSV exploration and histograms
• Data analysis (regression), uncertainty, and lab calculators

This is designed to be extensible: new scientific domains can be added as tools/ modules with their own subcommands.

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Features

✅ Constants

Search a curated set of physical constants with proper units and references.

ops constants list
ops constants get c
ops constants get "planck"

✅ Units

Convert between common units using a small dimensional-analysis engine.

ops units convert 5.2 m/s mph
ops units convert 1 atm Pa
ops units list-dimensions

✅ Stats

Quick descriptive statistics and normal distribution helpers.

ops stats describe 1 2 3 4 5 6
ops stats normal-pdf 0 --mu 0 --sigma 1
ops stats normal-cdf 1.96 --mu 0 --sigma 1

✅ Waves

Generate simple waveforms and display them as ASCII plots.

ops waves sine --freq 1.0 --samples 40
ops waves square --freq 2.0 --samples 40

✅ Lab Notebook

Append timestamped notes and results to a Markdown file.

ops notebook log "Measured resistance: 4.7 kΩ ± 0.1 kΩ"
ops notebook show

✅ Mechanics (ops mech ...)

• ops mech projectile v0 angle – range, time of flight, max height
• ops mech work F d --angle θ – mechanical work
• ops mech pendulum L – small-angle period
• ops mech orbit-period a – Keplerian orbital period
• Use --body earth|moon|mars|jupiter|sun to pull preset gravity/μ.

🔭 Astro (preview)

Astronomy helpers: local sidereal time and coordinate transforms.

ops astro lst --lon -122.3 --datetime "2024-06-01T10:00:00Z"
ops astro altaz --ra "10h12m45s" --dec "-12d30m00s" --lat 37.8 --lon -122.3 --datetime "2024-06-01T10:00:00Z"

⚗️ Chem (preview)

Common lab calculations: molarity and dilution.

ops chem molarity --moles 0.25 --volume-l 0.5
ops chem dilute --c1 2.0 --v1 10 --c2 0.5

✅ Relativity (ops relativity ...)

• ops relativity gamma v
• ops relativity time-dilation Δτ v
• ops relativity energy m v
• ops relativity grav-dilation --body earth --altitude 0 (or custom mass/r)

✅ Biology (ops bio ...)

• ops bio hardy-weinberg --aa --ab --bb
• ops bio punnett Aa aa
• ops bio gc-content SEQUENCE
• ops bio translate SEQUENCE
• ops bio find-orfs SEQUENCE --min-aa 50 --frames 1,2,3

✅ Body presets

Use named bodies anywhere --body is supported:

ops mech projectile 20 45 --body moon
ops relativity grav-dilation --body jupiter --altitude 100000

Current presets: Earth, Venus, Moon, Mars, Jupiter, Saturn, Sun.

📈 Data (ops data ...)

• ops data summarize file.csv – stats for numeric columns
• ops data head file.csv --rows N – preview rows
• ops data hist file.csv col --bins 10 – ASCII histogram
• ops data plot file.csv x y – ASCII scatter/line plot

📊 Analysis (ops analysis ...)

• ops analysis regress file.csv x y – simple linear regression (slope/intercept/r/r^2)
• ops analysis uncertainty u1 u2 ... – combine independent uncertainties in quadrature

🔦 Optics (ops optics ...)

• ops optics snell n1 n2 theta1 – refraction / total internal reflection
• ops optics thin-lens f d_o – image distance and magnification

⚡ Electromagnetism (ops em ...)

• ops em coulomb q1 q2 r – Coulomb force magnitude and interaction type
• ops em reactance freq --L H --C F – reactive impedance for inductors/capacitors

🧪 Lab calculations (ops labcalc ...)

• ops labcalc stock-dilution C_stock C_final V_final – compute stock/solvent volumes
• ops labcalc percent-error measured true – quick percent error

🧬 Bio sequence files (ops bioseq ...)

• ops bioseq gc-file file.fa – GC content from FASTA/plain text
• ops bioseq translate-file file.fa – translate coding sequence (stop at first stop)

⚙️ Config (ops config ...)

• ops config show – view current config (notebook path, default body, color)
• ops config set KEY VALUE – change config values

🧭 Command index

• ops help-all – list all subcommands with their short descriptions

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Installation

From PyPI (recommended):

pip install -U science-ops-cli

Dev install from source:

git clone https://github.com/thatkidtk/science-ops-cli.git
cd science-ops-cli
pip install -e .

Either way you get a console script called ops.

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Usage

General help:

ops --help
ops constants --help
ops units --help
ops stats --help
ops waves --help
ops data --help
ops analysis --help
ops optics --help
ops em --help
ops labcalc --help
ops bioseq --help
ops config --help
ops help-all
ops notebook --help
ops astro --help
ops chem --help
ops mech --help
ops relativity --help
ops bio --help

Example:

# Convert 10 m/s to km/h
ops units convert 10 m/s km/h

# Look up Planck's constant
ops constants get planck

# Describe a dataset
ops stats describe 2.3 4.1 5.9 3.3 4.8

# Log an experiment step
ops notebook log "Ran titration trial 3, overshoot by ~0.2 mL"

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Project Structure

science_ops/
  cli.py        # Typer app entrypoint
  config.py     # Config handling (paths, defaults)
  tools/        # Individual scientific tool modules
  utils/        # Shared helpers (IO, math, display, etc.)

Each module under tools/ exposes a typer.Typer() app that gets mounted under the main ops CLI.

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Roadmap

See ROADMAP.md for what’s next (Phase 2/3) or open issues for ideas and bugs.

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Contributing

1. Add a new module under science_ops/tools/yourtool.py
2. Make a typer.Typer() instance in that file
3. Mount it in cli.py via app.add_typer(...)
4. Add tests in tests/
5. Open a PR

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License

MIT, because science should spread.