Merge pull request #55 from alan-turing-institute/45-publish-in-pypi

Merging a release branch off of dev into main, to publish on PyPI. Will keep the branch alive for further updates

Author: LevanBokeria

.github/workflows/ci.yml

@@ -0,0 +1,79 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+      - dev
+  pull_request:
+    branches:
+      - main
+      - dev
+
+jobs:
+
+  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@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        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 ./
+
+    - name: Run tests
+      run: |
+        source venv/bin/activate
+        python -m unittest discover -s tests

.gitignore

@@ -163,3 +163,12 @@ cython_debug/
 *.csv
 /Tutorials
 .DS_Store
+/playground_files
+
+*.pyc
+
+# Ignore the PyPI configuration file
+.pypirc
+
+# Ignore vscode settings
+.vscode/

README.md

@@ -1,15 +1,67 @@
 # ModularCirc
 
+[![Actions Status][actions-badge]][actions-link]
+[![PyPI version][pypi-version]][pypi-link]
+[![PyPI platforms][pypi-platforms]][pypi-link]
+
 The scope of this package is to provide a framework for building **0D models** and **simulating cardiovascular flow** and **mechanics**. Conceptually, the models can be split into three types of components:
 1. **Heart chambers**
 2. **Valves**
-3. **Vessels**
+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
+
+To install the pip package: 
+
+```bash
+python -m pip install ModularCirc_LevanBokeria
+```
+
+From source:
+
+After downloading the GitHub repository, 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
@@ -63,9 +115,25 @@ solver.solve()
 
 8. Extract the state variable values of interest.
 ```python
-v_lv = solver.model.commponents['lv'].V.values
-p_lv = solver.model.commponents['lv'].P_i.values
+v_lv = solver.model.components['lv'].V.values
+p_lv = solver.model.components['lv'].P_i.values
 ```
 
 ## Example values pv loops for all 4 chambers:
 ![Example PV loops!](Figures/PV_loops.png)
+
+## Run tests
+
+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)).
+
+<!-- prettier-ignore-start -->
+[actions-badge]:            https://github.com/alan-turing-institute/ModularCirc/workflows/CI/badge.svg
+[actions-link]:             https://github.com/alan-turing-institute/ModularCirc/actions
+[pypi-link]:                https://test.pypi.org/project/ModularCirc-LevanBokeria/
+[pypi-platforms]:           https://img.shields.io/pypi/pyversions/ModularCirc-LevanBokeria
+[pypi-version]:             https://img.shields.io/pypi/v/ModularCirc-LevanBokeria
+<!-- prettier-ignore-end -->

Tutorials/Tutorial_01/circ_utils.py

@@ -97,7 +97,7 @@ def run_case(row, output_path, N_cycles, dt):
     ind = model.time_object.n_c
 
     # Get the raw pressure signal...
-    raw_signal = model.commponents["ao"].P[-ind:]
+    raw_signal = model.components["ao"].P[-ind:]
 
     # Resamples the raw signals (variable length) to a standard 100 time points resolution
     resampled_dt, resampled_signal = signal_get_pulse(raw_signal, model.time_object.dt)