https://github.com/maurosilber/simbio-paper

https://github.com/maurosilber/simbio-paper

Last synced: 17 days ago
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• Host: GitHub
• URL: https://github.com/maurosilber/simbio-paper
• Owner: maurosilber
• Created: 2023-12-13T13:40:15.000Z (about 1 year ago)
• Default Branch: main
• Last Pushed: 2024-08-14T14:30:26.000Z (5 months ago)
• Last Synced: 2024-10-29T16:59:30.154Z (2 months ago)
• Language: TeX
• Size: 1.12 MB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# SimBio paper

To read the current HTML version, visit:

https://maurosilber.github.io/simbio-paper

The following instructions assume you have cloned the repository

```bash

git clone https://github.com/maurosilber/simbio-paper

```

and are inside the `simbio-paper` directory.

## Install dependencies

To run the benchmarking code and compile the article,

you must install some dependencies.

If you have `conda` installed,

create an environment from the included `environment.yml` file:

```bash

conda env create

```

and install the Python package included in the repository:

```bash

pip install -e .

```

To compile the article,

you must also install Quarto:

https://quarto.org

## Run benchmarks and compile article

```bash

make

```

> Note:

> as `src/perfomance/figures/performance.png` was commited to the repository,

> the benchmarking code is not actually triggered by the Makefile.

> Remove that file to re-run the benchmarks with `make`.