Merge pull request #16 from alan-turing-institute/13-clarifying-environment-setup-in-readme

13 clarifying environment setup in readme

Author: MaxBalmus

.github/workflows/ci.yml

@@ -4,31 +4,76 @@ on:
   push:
     branches:
       - main
-      - tests_ci
+      - dev
   pull_request:
     branches:
       - main
-      - tests_ci
+      - dev
 
 jobs:
-  build:
+
+  build-conda:
+    name: Conda environment
+    runs-on: "ubuntu-latest"
+    defaults:
+      run:
+        shell: bash -el {0}
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Create environment.yml
+        run: |
+          echo "name: myenv" > environment.yml
+          echo "channels:" >> environment.yml
+          echo "  - conda-forge" >> environment.yml
+          echo "  - defaults" >> environment.yml
+          echo "dependencies:" >> environment.yml
+          echo "  - pip" >> environment.yml
+
+      - name: Set up Conda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          activate-environment: myenv
+          environment-file: environment.yml
+          python-version: '3.10'
+          auto-activate-base: false
+      
+      - name: Install dependencies
+        run: | 
+          python -m pip install --upgrade pip
+          pip install setuptools --upgrade
+          pip install ./
+
+      - name: Run tests
+        run: |    
+          python -m unittest discover -s tests
+
+  build-venv:
+    name: Python virtual environment
     runs-on: ubuntu-latest
 
     steps:
     - name: Checkout code
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: '3.x'
+        python-version: '3.10'
+
+    - name: Set up environment
+      run: |
+        python -m venv venv
+        source venv/bin/activate
 
     - name: Install dependencies
       run: |
+        source venv/bin/activate
         python -m pip install --upgrade pip
-        pip install -r requirements.txt
+        pip install ./
 
     - name: Run tests
       run: |
-        python -m unittest discover -s tests
-
+        source venv/bin/activate
+        python -m unittest discover -s tests

README.md

@@ -5,11 +5,50 @@ The scope of this package is to provide a framework for building **0D models** a
 2. **Valves**
 3. **Vessels**
 
+## Clone the ModularCirc GitHub repo locally
+
+Run:
+
+```
+git clone https://github.com/alan-turing-institute/ModularCirc
+cd ModularCirc
+```
+
+## Setup Conda or python virtual environment
+
+Before installation of the ModularCirc package, please setup a virtual environment using either Conda or python virtual environment.
+
+### Conda setup
+
+Install Conda from https://docs.conda.io/projects/conda/en/stable/user-guide/install/index.html
+
+Run: 
+
+```
+conda create --name <yourenvname>
+conda activate <yourenvname>
+```
+
+Proceed to installing the ModularCirc package.
+
+### Python virtual environment setup
+
+Run `python3 -m venv venv`. This creates a virtual environment called `venv` in your base directory. 
+
+Activate the python environment: `source venv/bin/activate`
+
+Proceed to installing the ModularCirc package.
+
 ## Installation
+
+From the repo directory, run:
+
 ```bash
-pip install git+https://github.com/alan-turing-institute/ModularCirc.git
+pip install ./
 ```
 
+This will install the package based on the `pyproject.toml` file specifications. 
+
 ## Steps for running basic models
 1. Load the classes for the model of interest and the parameter object used to paramterise the said model:
 ```python
@@ -76,4 +115,4 @@ You can run locally the tests by running the following command:
 ```bash
   python -m unittest discover -s tests
 ```
-there is also a autamtated test pipeline that runs the tests on every push to the repository (see [here](.github/workflows/ci.yml)).
+there is also a autamtated test pipeline that runs the tests on every push to the repository (see [here](.github/workflows/ci.yml)).

pyproject.toml

@@ -0,0 +1,36 @@
+[build-system]
+requires = ["setuptools>=42", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "ModularCirc"
+version = "0.1.1"
+description = "A python package for creating and running 0D models of the cardiovascular system"
+readme = "README.md"
+requires-python = ">=3.10"
+license = {text = "MIT" }
+authors = [
+    {name = "Maximilian Balmus", email = "[email protected]"}
+]
+
+dependencies = [
+    "matplotlib",
+    "numba",
+    "numpy",
+    "pandas",
+    "scipy",
+    "joblib",
+    "pandera",
+    "tdqm"
+]
+
+[project.optional-dependencies]
+notebooks = ["ipykernel"]
+
+[project.urls]
+"Homepage" = "https://github.com/alan-turing-institute/ModularCirc"
+"Source Code" = "https://github.com/alan-turing-institute/ModularCirc"
+"Bug Tracker" = "https://github.com/alan-turing-institute/ModularCirc/issues"
+
+[tool.setuptools]
+packages = ["ModularCirc"]