Initial commit

.github/dependabot.yml

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+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "monthly"

.github/workflows/publish.yml

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+name: Publish
+
+on: push
+
+jobs:
+  publish:
+    name: Publish reveal.js slides
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: 3.9
+      - run: pip install -r requirements.txt
+      - run: sudo apt update -qy && sudo apt install ffmpeg -qy
+      - run: jupyter nbconvert *.ipynb --to slides --execute
+      - run: mkdir dist && mv *.slides.html dist/index.html
+      - uses: JamesIves/[email protected]
+        if: github.event_name == 'push' && github.ref == 'refs/heads/master'
+        name: Deploy to gh-pages
+        with:
+          branch: gh-pages
+          folder: dist
+          single-commit: true

.pre-commit-config.yaml

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+repos:
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.0.1
+    hooks:
+    - id: check-yaml
+    - id: end-of-file-fixer
+    - id: trailing-whitespace
+    - id: mixed-line-ending
+
+  - repo: https://github.com/psf/black
+    rev: 21.8b0
+    hooks:
+    - id: black
+
+  - repo: https://github.com/dfm/black_nbconvert
+    rev: v0.3.0
+    hooks:
+    - id: black_nbconvert
+
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.5.0
+    hooks:
+    - id: nbstripout

LICENSE

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+MIT License
+
+Copyright (c) 2021 Liam Keegan
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

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+# [ssciwr.github.io/jupyter-slides-template](https://ssciwr.github.io/jupyter-slides-template)
+
+A simple way to convert a jupyter notebook into an online web presentation.
+
+The notebook [jupyter-slides-template.ipynb](jupyter-slides-template.ipynb) is converted into [reveal.js](https://revealjs.com/) html slides and hosted by github pages at [ssciwr.github.io/jupyter-slides-template](https://ssciwr.github.io/jupyter-slides-template)
+
+## Quickstart
+
+- click the 'Use this template' button to create your own repo based on this one
+- enable gh-pages for your repo: Settings -> Pages -> Source branch: gh-pages
+- slides will appear at `YOUR_USERNAME.github.io/YOUR_REPO_NAME`
+
+## Optional extras
+
+- add any additional Python libraries your notebook needs to [requirements.txt](requirements.txt)
+- go to https://pre-commit.ci/ to enable automatic code formatting for your repo
+- install pre-commit to also do this on your computer
+  - `pip install pre-commit`
+  - `pre-commit install`

jupyter-slides-template.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "1e4bbd6c",
+   "metadata": {
+    "slideshow": {
+     "slide_type": "slide"
+    }
+   },
+   "source": [
+    "# jupyter-slides-template\n",
+    "\n",
+    "- Automatically generated from this [jupyter notebook](https://github.com/ssciwr/jupyter-slides-template/blob/master/jupyter-slides-template.ipynb)\n",
+    "- Press `Space` or `Right`to move to the next page\n",
+    "- Press `Escape` to zoom out\n",
+    "- Make your own at [github.com/ssciwr/jupyter-slides-template](https://github.com/ssciwr/jupyter-slides-template)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "189a6a56",
+   "metadata": {
+    "slideshow": {
+     "slide_type": "slide"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "import sme\n",
+    "\n",
+    "model = sme.open_example_model()\n",
+    "print(model)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "1ae11bfc",
+   "metadata": {
+    "slideshow": {
+     "slide_type": "slide"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "import matplotlib.pyplot as plt\n",
+    "\n",
+    "plt.title(model.name)\n",
+    "plt.imshow(model.compartment_image)\n",
+    "plt.show()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "d9d162e3",
+   "metadata": {
+    "slideshow": {
+     "slide_type": "slide"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "import sme_contrib.plot as smeplot\n",
+    "from IPython.display import HTML\n",
+    "\n",
+    "results = model.simulate(100, 10)\n",
+    "anim = smeplot.concentration_heatmap_animation(results, [\"B_cell\"])\n",
+    "HTML(anim.to_html5_video())"
+   ]
+  }
+ ],
+ "metadata": {
+  "celltoolbar": "Slideshow",
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.4"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

requirements.txt

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+jupyter
+sme
+sme_contrib
+matplotlib