Merging dev to Fay's branch

.github/workflows/ci.yml

@@ -38,15 +38,15 @@ jobs:
           environment-file: environment.yml
           python-version: '3.10'
           auto-activate-base: false
-      
+
       - name: Install dependencies
-        run: | 
+        run: |
           python -m pip install --upgrade pip
           pip install setuptools --upgrade
           pip install ./
 
       - name: Run tests
-        run: |    
+        run: |
           python -m unittest discover -s tests
 
   build-venv:
@@ -76,4 +76,4 @@ jobs:
     - name: Run tests
       run: |
         source venv/bin/activate
-        python -m unittest discover -s tests
+        python -m unittest discover -s tests

.github/workflows/publish.yml

@@ -0,0 +1,30 @@
+name: Upload Python Package to PyPI when a Release is Created
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  pypi-publish:
+    name: Publish release to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi_release
+      url: https://pypi.org/p/ModularCirc
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install setuptools wheel build
+      - name: Build package
+        run: |
+          python -m build
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.gitignore

@@ -164,3 +164,11 @@ cython_debug/
 /Tutorials
 .DS_Store
 /playground_files
+
+*.pyc
+
+# Ignore the PyPI configuration file
+.pypirc
+
+# Ignore vscode settings
+.vscode/

.pre-commit-config.yaml

@@ -0,0 +1,56 @@
+ci:
+  autoupdate_commit_msg: "chore: update pre-commit hooks"
+  autofix_commit_msg: "style: pre-commit fixes"
+
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v5.0.0
+  hooks:
+    - id: trailing-whitespace # remove trailing whitespace
+    - id: end-of-file-fixer # ensure files end with a newline
+    - id: check-yaml # check YAML files for syntax errors
+    - id: check-json # check JSON files for syntax errors
+    - id: check-added-large-files # check for large files
+      args: ['--maxkb=500'] # set the max file size to 500KB
+    - id: check-case-conflict # check for case conflicts in filenames.
+    - id: check-merge-conflict # This hook checks for merge conflict markers in files.
+    # It ensures that there are no unresolved merge conflicts in the codebase.
+    - id: check-symlinks # check for broken symlinks
+    # - id: debug-statements
+    - id: mixed-line-ending # check for mixed line endings, meaning that
+      # a file contains both CRLF and LF line endings. This can cause issues
+      # when working with files across different operating systems.
+
+# - repo: https://github.com/psf/black
+#   rev: 25.1.0  # Use the latest stable version
+#   hooks:
+#     - id: black
+
+# - repo: https://github.com/PyCQA/flake8
+#   rev: 7.1.1  # Use the latest stable version
+#   hooks:
+#     - id: flake8
+
+# - repo: https://github.com/pre-commit/mirrors-isort
+#   rev: 6.0.0  # Use the latest stable version
+#   hooks:
+#     - id: isort
+
+# - repo: https://github.com/astral-sh/ruff-pre-commit
+#   rev: "v0.11.5"
+#   hooks:
+#     # first, lint + autofix
+#     - id: ruff
+#       types_or: [python, pyi, jupyter]
+#       args: ["--fix", "--show-fixes"]
+#     # then, format
+#     - id: ruff-format
+
+# - repo: https://github.com/pre-commit/mirrors-mypy
+#   rev: "v1.15.0"
+#   hooks:
+#     - id: mypy
+#       files: src
+#       args: []
+#       additional_dependencies:
+#         - pytest

CONTRIBUTING.md

@@ -0,0 +1,47 @@
+See the [Scientific Python Developer Guide][spc-dev-intro] for a detailed
+description of best practices for developing scientific packages.
+
+[spc-dev-intro]: https://learn.scientific-python.org/development/
+
+# Setting up a development environment manually
+
+You can set up a development environment by running:
+
+```zsh
+python3 -m venv venv          # create a virtualenv called venv
+source ./venv/bin/activate   # now `python` points to the virtualenv python
+pip install -v -e ".[dev]"    # -v for verbose, -e for editable, [dev] for dev dependencies
+```
+
+# Post setup
+
+You should prepare pre-commit, which will help you by checking that commits pass
+required checks:
+
+```bash
+pip install pre-commit # or brew install pre-commit on macOS
+pre-commit install # this will install a pre-commit hook into the git repo
+```
+
+You can also/alternatively run `pre-commit run` (changes only) or
+`pre-commit run --all-files` to check even without installing the hook.
+
+# Testing
+
+This repo uses `unittest` for testing. 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)).
+
+
+# Pre-commit
+
+This project uses pre-commit for all style checking. Install pre-commit and run:
+
+```bash
+pre-commit run -a
+```
+
+to check all files.

README.md

@@ -1,5 +1,9 @@
 # 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**
@@ -22,7 +26,7 @@ Before installation of the ModularCirc package, please setup a virtual environme
 
 Install Conda from https://docs.conda.io/projects/conda/en/stable/user-guide/install/index.html
 
-Run: 
+Run:
 
 ```
 conda create --name <yourenvname>
@@ -33,21 +37,30 @@ 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. 
+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:
+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 ./
 ```
 
-This will install the package based on the `pyproject.toml` file specifications. 
+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:
@@ -66,14 +79,14 @@ TEMPLATE_TIME_SETUP_DICT = {
     'name'       :  'TimeTest',
     'ncycles'    :  40,
     'tcycle'     :  1.0,
-    'dt'         :  0.001, 
+    'dt'         :  0.001,
     'export_min' :  1
  }
 ```
 Here, `ncycles` indicates the maximum number of heart cycles to run, before the simulation finishes.
-If the simulation reaches steady state faster than that, the simulation will end provided the number of cycles is higher than `export_min`. 
-`tcycle` indicates the duration of the heart beat and `dt` represent the time step size used in the temporal discretization. 
-These measurements assume that time is measured in **seconds**. 
+If the simulation reaches steady state faster than that, the simulation will end provided the number of cycles is higher than `export_min`.
+`tcycle` indicates the duration of the heart beat and `dt` represent the time step size used in the temporal discretization.
+These measurements assume that time is measured in **seconds**.
 If the units used are different, ensure this is done consistently in line with other parameters.
 
 4. Create an instance of the parameter object and used it to change the default values:
@@ -116,3 +129,11 @@ You can run locally the tests by running the following command:
   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://pypi.org/project/ModularCirc
+[pypi-platforms]:           https://img.shields.io/pypi/pyversions/ModularCirc
+[pypi-version]:             https://img.shields.io/pypi/v/ModularCirc
+<!-- prettier-ignore-end -->

Tutorials/Tutorial_01/README.md

@@ -6,7 +6,7 @@ Involved in a larger project involving patients with pulmonary arterial hyperten
 
 Currently, while the monitors provide a lot of cardiac data, the usefulness of the data that they provide is limited, as it is difficult to interpret and use the information to make approprate changes to patient management.
 
-The project focuses on the development of a digital twin to aid with interpretation of the cardiac data from these monitors. 
+The project focuses on the development of a digital twin to aid with interpretation of the cardiac data from these monitors.
 
 The sensitivity analysis aims to focus in on the parameters from the model that most affect pulmonary arterial pressure and cardiac output.
 
@@ -28,4 +28,4 @@ Using a reduced set of parameters, you can more efficiently fit the model to pat
  4) Complete K fold cross validation.
  5) Retrain model on all the data with the new reduced number of components.
  6) Use the reduced PCA results as output and the original parameter set you created as input for emulation - use [Autoemulate](https://github.com/alan-turing-institute/autoemulate)  to find the best emulator for the data, this uses the "step3" notebook.
- 7) Conduct a sensitivity analysis using the results from emulation using SAlib.
+ 7) Conduct a sensitivity analysis using the results from emulation using SAlib.

Tutorials/Tutorial_01/circ_utils.py

@@ -26,8 +26,8 @@ def signal_get_pulse(signal, dt, num=100):
     Returns:
             _type_: _description_
     """
-    
-    ind = np.argmin(signal)        
+
+    ind = np.argmin(signal)
     ncycle = len(signal)
     new_signal = np.interp(np.linspace(0, ncycle, num), np.arange(ncycle), np.roll(signal, -ind))
     new_dt = ncycle / (num - 1) * dt
@@ -80,8 +80,8 @@ def run_case(row, output_path, N_cycles, dt):
     )  # replace the .. with the correct Class and inputs if applicable
 
     solver.setup(
-        suppress_output=True, 
-        optimize_secondary_sv=False, 
+        suppress_output=True,
+        optimize_secondary_sv=False,
         conv_cols=["p_ao"],
         method='LSODA'
         )
@@ -138,7 +138,7 @@ def simulation_loader(input_directory):
 
     file_series.sort_values('Index', inplace=True)
     file_series.set_index('Index', inplace=True)
-    
+
     # Define a dataframe for the values collected from the simulation...
     signal_df  = file_series.apply(
         lambda row: list(pd.read_csv(os.path.join(input_directory, row['file']), index_col='Index').to_numpy().reshape((-1))),
@@ -147,7 +147,7 @@ def simulation_loader(input_directory):
     signal_df.rename(columns=template_columns, inplace=True)
 
     return signal_df
- 
+
 
 dict_parameters_condensed_range = dict()
 dict_parameters_condensed_single = dict()
@@ -166,7 +166,7 @@ def condense_dict_parameters(dict_param:dict, prev=""):
                 dict_parameters_condensed_range[new_key] = tuple(np.array(r) * value)
             else:
                 dict_parameters_condensed_single[new_key] = val[0]
-    return  
+    return
 
 
 ######## DEFINED A FUNCTION TO PLOT THE VARIANCE
@@ -186,7 +186,7 @@ def plot_variance(pca, width=8, dpi=100):
     cumulative_explained_variance = np.cumsum(explained_variance_ratio)
     axs[1].semilogy(grid, cumulative_explained_variance, "o-")
     axs[1].set(
-        xlabel="Component", title="% Cumulative Variance", 
+        xlabel="Component", title="% Cumulative Variance",
     )
     # Set up figure
     fig.set(figwidth=8, dpi=100)
@@ -207,13 +207,13 @@ def scale_time_parameters_and_asign_to_components(df):
 # 800 ms in this case
 
     df['la.delay'] = df['la.delay'] * df['T'] / 800.
-    
+
     df['la.t_tr'] = df['la.t_tr'] * df['T'] / 800.
     df['lv.t_tr'] = df['lv.t_tr'] * df['T'] / 800.
-    
+
     df['la.tau'] = df['la.tau'] * df['T'] / 800.
     df['lv.tau'] = df['lv.tau'] * df['T'] / 800.
 
     df['la.t_max'] = df['la.t_max']  * df['T'] / 800.
     df['lv.t_max'] = df['lv.t_max']  * df['T'] / 800.
-    return 
+    return