Create google colab 'sandbox' environment for Biosimulators interaction

.github/workflows/ci.yml

@@ -26,6 +26,12 @@ jobs:
       - name: Checkout repository
         uses: actions/[email protected]
 
+      # Install dependencies
+      - name: Install dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libglpk-dev build-essential
+
       # Build Docker image
       - id: get-timestamp
         name: Get timestamp
@@ -37,14 +43,14 @@ jobs:
         uses: whoan/docker-build-with-cache-action@v5
         with:
           dockerfile: Dockerfile
-          build_extra_args: "--compress=true --label org.opencontainers.image.revision=${{github.sha}} --label org.opencontainers.image.created=${{steps.get-timestamp.outputs.timestamp}}"
+          build_extra_args: '--compress=true --label org.opencontainers.image.revision=${{github.sha}} --label org.opencontainers.image.created=${{steps.get-timestamp.outputs.timestamp}}'
           registry: ghcr.io
           stages_image_name: biosimulators/tutorials-stages
           image_name: biosimulators/tutorials-stages
           image_tag: ${{github.sha}}
           push_image_and_stages: true
           username: ${{ secrets.DOCKER_REGISTRY_USERNAME }}
-          password: "${{ secrets.DOCKER_REGISTRY_TOKEN }}"
+          password: '${{ secrets.DOCKER_REGISTRY_TOKEN }}'
 
       - name: Label Docker image
         run: |

Dockerfile

@@ -10,6 +10,8 @@ LABEL \
     org.opencontainers.image.vendor="BioSimulators Team"
 
 COPY requirements.txt /tmp/requirements.txt
+RUN pip install --upgrade pip 
+RUN pip install --upgrade setuptools wheel
 RUN pip install -r /tmp/requirements.txt \
     && rm /tmp/requirements.txt \
     && pip uninstall -y ipyparallel

README.md

@@ -1,31 +1,42 @@
+[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1aI7Z6ZBcQzOc9PJllW9N9oeTcFtXfhTd#offline=true&sandboxMode=true)
+
 [![Binder](https://mybinder.org/badge_logo.svg)](https://tutorial.biosimulators.org/)
 [![All Contributors](https://img.shields.io/github/all-contributors/biosimulators/Biosimulators_tutorials/HEAD)](#contributors-)
 
 ![Logo](https://raw.githubusercontent.com/biosimulations/Biosimulations/dev/libs/shared/assets/src/assets/images/biosimulators-logo/logo-white.svg)
 
 # BioSimulators tutorials
 
-This repository contains Jupyter notebooks with tutorials for the Python APIs for the simulation tools registered with BioSimulators and a Jupyter notebook server for running the notebooks.
+This repository contains Jupyter notebooks with tutorials for the Python APIs for the simulation tools registered with BioSimulators and a Jupyter notebook server for running the notebooks. NEW: As an alternative to the Jupyter Notebooks and relative Jupyter Notebook server, we have added a [Google Colab Notebook](https://colab.research.google.com/drive/1aI7Z6ZBcQzOc9PJllW9N9oeTcFtXfhTd#offline=true&sandboxMode=true) for users that are more comfortable with a shareable, annotatable "sandbox environment". Complete with the required dependencies, input data, and explicitly-defined methods that are essential to interacting with `Biosimulators`, this Google Colab notebook serves as "click and play" experience.
 
 The tutorials are located in the [`tutorials`](tutorials) subdirectory. The [README](tutorials/README.md) in this directory summarizes the content of the tutorials.
 
 ## Getting started
 
+### Running the tutorials online with Google Colab (web-based, minimal setup)
+
+Simply open [the Colab notebook](https://colab.research.google.com/drive/1aI7Z6ZBcQzOc9PJllW9N9oeTcFtXfhTd#offline=true&sandboxMode=true) in your browser or click on the above Colab badge.
+
 ### Running the tutorials online with Binder
-The easiest way to run the tutorials is with Binder. Simply open https://tutorial.biosimulators.org/ in your browser.
+
+Simply open https://tutorial.biosimulators.org/ in your browser or click on the above Binder Badge.
 
 ### Running the tutorials on your own machine
+
 Run the following command to download the tutorials:
+
 ```
 docker pull ghcr.io/biosimulators/tutorials
 ```
 
 Run the following command to launch a Jupyter notebook server at http://localhost:8888 for the tutorials in this repository:
+
 ```
 docker run -it --rm -p 8888:8888 ghcr.io/biosimulators/tutorials jupyter notebook --ip=0.0.0.0 --port=8888
 ```
 
 Alternatively, run the following command to launch a Jupyter lab server at http://localhost:8888 for the tutorials in this repository:
+
 ```
 docker run -it --rm -p 8888:8888 ghcr.io/biosimulators/tutorials jupyter lab --ip=0.0.0.0 --port=8888
 ```

pyproject.toml

@@ -0,0 +1,10 @@
+[build-system]
+requires = ["setuptools", "wheel", "cython"]
+build-backend = "setuptools.build_meta"
+
+[tool.cythondialect]
+include_dirs = ["include"]
+
+[tool.glpk]
+include_dirs = ["include"]
+library_dirs = ["lib"]

pytest.ini

@@ -0,0 +1,3 @@
+[pytest]
+filterwarnings =
+    ignore::ImportWarning:evalidate

requirements.tests.txt

@@ -1,3 +1,4 @@
 pytest
 nbmake
+nbconvert
 pytest-forked

requirements.txt

@@ -9,7 +9,7 @@ biosimulators-cbmpy
 biosimulators-copasi
 biosimulators-cobrapy
 biosimulators-tellurium
-biosimulators-utils[sbml,logging,containers]>=0.1.152
+biosimulators-utils[sbml,logging,containers]>=0.1.175
 ipython
 kisao
 numpy