sciencehub-team/manifestoPublic

import marimo

__generated_with = "0.25.1"
app = marimo.App(width="medium")


@app.cell(hide_code=True)
def _(mo):
    mo.md(
        r"""
        # Science that runs

        *Why we are building ScienceHub. This page is a notebook: the numbers
        and the chart below are computed while you read.*

        ## Science is computation now

        In 1665 the first scientific journals turned letters between scholars
        into a public record. In 1991 arXiv put that record online, free and
        within a day. Both carried the same thing: a description of work.

        The work itself has changed. A climate projection, a protein structure,
        a gravitational-wave detection, a clinical trial's statistics: each is
        a computation, and the paper describes it from the outside. The code
        that produced the figure is usually somewhere else, if it is anywhere.

        And the cost of writing that code is falling fast. AI systems now write
        much of the code a researcher needs, so a biologist, a historian, or a
        physician can turn an idea into a working analysis in an afternoon.
        Soon most new science will be done as computation, by people who never
        trained as programmers.
        """
    )
    return


@app.cell
def _():
    import marimo as mo
    import numpy as np
    import matplotlib.pyplot as plt
    return mo, np, plt


@app.cell(hide_code=True)
def _(mo):
    mo.md(
        r"""
        ## Most published computations do not run

        Code that exists is not code that works. In 2019 Pimentel and
        colleagues collected more than a million Jupyter notebooks from GitHub
        and ran the ones whose dependencies they could reconstruct. About a
        quarter finished without an error. About 4 percent reproduced the
        results their authors had saved.
        """
    )
    return


@app.cell
def _(plt):
    stages = ["ran without\nan error", "gave the\nsame results"]
    share = [24.1, 4.0]
    fig, ax = plt.subplots(figsize=(6, 2.4))
    ax.barh(stages[::-1], share[::-1], color=["#9a6700", "#0969da"])
    for _y, _v in enumerate(share[::-1]):
        ax.text(_v + 1, _y, f"{_v:.0f} %", va="center")
    ax.set_xlim(0, 100)
    ax.set_xlabel("share of executed notebooks (Pimentel et al. 2019)")
    for _side in ("top", "right"):
        ax.spines[_side].set_visible(False)
    fig.tight_layout()
    fig
    return


@app.cell(hide_code=True)
def _(mo):
    mo.md(
        r"""
        Hidden state is a large part of the reason. A classic notebook remembers
        whatever ran last, in whatever order it ran, and saves outputs that the
        code on the page may no longer produce. A marimo notebook does not: it
        knows which cell reads which variable and reruns everything that
        depends on a change. Move the slider and watch.
        """
    )
    return


@app.cell
def _(mo):
    trials = mo.ui.slider(10, 5000, step=10, value=200, label="Coin flips")
    trials
    return (trials,)


@app.cell
def _(mo, np, trials):
    flips = np.random.default_rng(1665).integers(0, 2, trials.value)
    heads = flips.mean()
    mo.md(
        f"""
        {trials.value:,} flips, **{heads:.1%} heads**. The interval
        {heads - 1.96 * np.sqrt(heads * (1 - heads) / trials.value):.1%} to
        {heads + 1.96 * np.sqrt(heads * (1 - heads) / trials.value):.1%} covers
        the true 50% about 95 times in 100. This sentence was recomputed when
        you moved the slider, and so would every figure that depends on it.
        """
    )
    return


@app.cell(hide_code=True)
def _(mo):
    mo.md(
        r"""
        ## What we believe

        **A result is the computation that produced it.** Publishing the
        description without the computation leaves out the part that can be
        checked. We publish both together, as one file.

        **Reading is free and needs nothing.** A public notebook runs in the
        reader's browser, with no account, no installation, and no cost to
        anyone. A student with a phone can rerun the calculation behind a published figure.

        **Your work is a plain Python file.** It diffs, imports, and runs
        anywhere marimo runs. You can take it with you.

        **Every version is kept and can be cited.** The notebook a paper cites
        is the notebook a reader gets, years later. Forks link back, so credit
        follows the work.

        **We do not sell attention.** No advertising, no paid ranking. We
        charge for compute when a browser is not enough, at a price shown
        before you use it.

        ## What comes after the paper

        Papers will not disappear; neither did letters. But the record of
        science is becoming something you can run, change, and build on. The
        place where that record lives should be public, permanent, and owned by
        the people who make it. That is what we are building.

        Fork this notebook and write your own answer. Or publish the
        computation behind your last paper, so that the next person can start
        where you stopped.
        """
    )
    return


@app.cell(hide_code=True)
def _(mo):
    mo.md(
        r"""
        ---
        **References.** J. F. Pimentel, L. Murta, V. Braganholo, J. Freire,
        "A Large-scale Study about Quality and Reproducibility of Jupyter
        Notebooks", MSR 2019.
        """
    )
    return


if __name__ == "__main__":
    app.run()