Set up automated tests via Github Actions

.github/workflows/tests.yaml

@@ -0,0 +1,72 @@
+name: Tests for PROTEUS
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+    types:
+      - opened
+      - reopened
+      - synchronize
+      - ready_for_review
+  workflow_dispatch:
+
+jobs:
+  test:
+    if: github.event.pull_request.draft == false
+    name: Run Coverage and Tests
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.10']
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          submodules: 'true'
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - uses: actions/cache@v3
+        id: cache-virtualenv
+        with:
+          path: ${{ env.pythonLocation }}
+          key: ${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }}
+
+      - name: Install dependencies
+        if: steps.cache-virtualenv.outputs.cache-hit != 'true'
+        run: |
+          python -m pip install -e .[develop]
+
+      - name: Test with pytest
+        run: |
+          coverage run -m pytest
+
+      - name: Report coverage
+        run: |
+          coverage json
+          export TOTAL=$(python -c "import json;print(json.load(open('coverage.json'))['totals']['percent_covered_display'])")
+          echo "total=$TOTAL" >> $GITHUB_ENV
+          echo "### Total coverage: ${TOTAL}%" >> $GITHUB_STEP_SUMMARY
+          echo $'\n```' >> $GITHUB_STEP_SUMMARY
+          coverage report >> $GITHUB_STEP_SUMMARY
+          echo $'\n```' >> $GITHUB_STEP_SUMMARY
+
+      - name: Make coverage badge
+        if: ${{ github.ref == 'refs/heads/master' && matrix.python-version == '3.10' }}
+        uses: schneegans/[email protected]
+        with:
+          auth: ${{ secrets.GIST_TOKEN }}
+          gistID: b4ee7dab92e20644bcb3a5ad09f71165
+          filename: covbadge.svg
+          label: Coverage
+          message: ${{ env.total }}%
+          minColorRange: 50
+          maxColorRange: 90
+          valColorRange: ${{ env.total }}

CONTRIBUTING.md

@@ -13,7 +13,7 @@ git clone https://github.com/FormingWorlds/PROTEUS proteus
 Install using `virtualenv`:
 
 ```console
-cd gemdat
+cd proteus
 python3 -m venv .venv
 source .venv/bin/activate
 python3 -m pip install -e .[develop]
@@ -28,6 +28,23 @@ conda activate proteus
 pip install -e .[develop]
 ```
 
+### Running tests
+
+PROTEUS uses [pytest](https://docs.pytest.org/en/latest/) to run the tests.
+You can run the tests for yourself using:
+
+```console
+pytest
+```
+
+To check coverage:
+
+```console
+coverage run -m pytest
+coverage report  # to output to terminal
+coverage html    # to generate html report
+```
+
 ### Building the documentation
 
 The documentation is written in [markdown](https://www.markdownguide.org/basic-syntax/), and uses [mkdocs](https://www.mkdocs.org/) to generate the pages.

README.md

@@ -1,4 +1,6 @@
-[![Documentation Status](https://readthedocs.org/projects/fwl-proteus/badge/?version=latest)](https://fwl-proteus.readthedocs.io/en/latest/?badge=latest) 
+[![Tests for PROTEUS](https://github.com/FormingWorlds/actions/workflows/tests.yaml/badge.svg)](https://github.com/FormingWorlds/actions/workflows/tests.yaml)
+![Coverage](https://gist.githubusercontent.com/stefsmeets/b4ee7dab92e20644bcb3a5ad09f71165/raw/covbadge.svg)
+[![Documentation Status](https://readthedocs.org/projects/fwl-proteus/badge/?version=latest)](https://fwl-proteus.readthedocs.io/en/latest/?badge=latest)
 [![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
 
 ![PROTEUS banner](https://raw.githubusercontent.com/FormingWorlds/PROTEUS/master/docs/images/PROTEUS_white.png#gh-light-mode-only)
@@ -9,17 +11,17 @@
 **PROTEUS** is a Python framework that simulates the coupled evolution
 of the atmospheres and interiors of rocky planets.
 
-## Installation instructions   
+## Installation instructions
 
 Click [here](https://fwl-proteus.readthedocs.io/en/latest/installation.html) for steps and troubleshooting advice.
 
 ## Run instructions
 
-Only attempt to run PROTEUS after you have followed all of the installation instructions.    
-If using a fresh shell, it is necessary to perform the following steps:     
-1. `conda activate proteus` (if using Anaconda/Miniconda)     
-2. `source PROTEUS.env`      
-Then you can start the model by running: `proteus.py`. See the ReadTheDocs pages for more information.    
+Only attempt to run PROTEUS after you have followed all of the installation instructions.
+If using a fresh shell, it is necessary to perform the following steps:
+1. `conda activate proteus` (if using Anaconda/Miniconda)
+2. `source PROTEUS.env`
+Then you can start the model by running: `start_proteus.py`. See the ReadTheDocs pages for more information.
 
 ## Updating the code
 
@@ -29,7 +31,7 @@ Run `git submodule update --recursive --remote`
 
 | Name  | Email address |
 | -     | -             |
-Tim Lichtenberg         | tim.lichtenberg[at]rug.nl | 
+Tim Lichtenberg         | tim.lichtenberg[at]rug.nl |
 Harrison Nicholls       | harrison.nicholls[at]physics.ox.ac.uk |
 Laurent Soucasse        | l.soucasse[at]esciencecenter.nl |
 Stef Smeets             | s.smeets[at]esciencecenter.nl |
@@ -45,18 +47,19 @@ Hamish Innes            | hamish.innes[at]fu-berlin.de |
 
 | Object                | Description                                               |
 | -                     | -                                                         |
-| `proteus.py`          | Main PROTEUS Python script                                |
+| `start_proteus.py`    | Main PROTEUS Python script                                |
 | `README.md`           | Overview file                                             |
-| `pyproject.toml`	    | Documentation file                                        |
+| `pyproject.toml`	    | Project configuration file                                |
 | `CODE_OF_CONDUCT.md`	| Project code of conduct                                   |
 | `LICENSE.txt`         | Project license                                           |
-| `JANUS/`              | Submodule JANUS                                          |
+| `src/proteus`         | Source code for PROTEUS                                   |
+| `JANUS/`              | Submodule JANUS                                           |
 | `SPIDER/`             | Submodule SPIDER                                          |
 | `VULCAN/`             | Submodule VULCAN                                          |
 | `Mors/`               | Submodule Mors                                            |
 | `utils/`              | Code used for running PROTEUS and its submodules          |
 | `plot/`               | Code used for plotting results                            |
 | `output/`             | Output folder with subfolders for each model run          |
 | `input/`              | Input folder (e.g. stellar spectra, example configs)      |
-| `docs/`			    | Documentation source files                                |
-| `examples/`           | Example cases that the model should be able to reproduce     |
+| `docs/`			          | Documentation source files                                |
+| `examples/`           | Example cases that the model should be able to reproduce  |