Add support for publishing to PyPI

.github/workflows/build.yml

@@ -5,30 +5,34 @@ on: [push]
 jobs:
   build-linux:
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [ '3.8', '3.9', '3.10' ]
+    name: Python ${{ matrix.python-version }}
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.8
-      uses: actions/setup-python@v2
-      with:
-        python-version: 3.8
-    - name: Install MPI
-      run: |
-        sudo apt install -y -q mpich libmpich-dev
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        make install
-    - name: Lint
-      run: |
-        make lint
-    - name: Type-check
-      run: |
-        make type-check
-    - name: Test
-      run: |
-        make coverage
-    - name: Scan
-      uses: SonarSource/sonarcloud-github-action@master
-      env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install MPI
+        run: |
+          sudo apt install -y -q mpich libmpich-dev
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          make install
+      - name: Lint
+        run: |
+          make lint
+      - name: Type-check
+        run: |
+          make type-check
+      - name: Test
+        run: |
+          make coverage
+      - name: Scan
+        uses: SonarSource/sonarcloud-github-action@master
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}

MANIFEST.in

@@ -0,0 +1,4 @@
+include README.md
+include LICENSE
+include MANIFEST.in
+include requirements.txt

Makefile

@@ -1,6 +1,15 @@
 setup:
 	python setup.py install
 
+package:
+	python setup.py sdist bdist_wheel
+
+publish-test:
+	python -m twine upload --repository testpypi dist/*
+
+publish:
+	python -m twine upload dist/*
+
 install:
 	pip3 install -r requirements.txt
 

README.md

@@ -1,10 +1,18 @@
-# PararealML [![Build Status](https://github.com/ViktorC/PararealML/actions/workflows/build.yml/badge.svg)](https://github.com/ViktorC/PararealML/actions/workflows/build.yml) [![Quality Gate Status](https://sonarcloud.io/api/project_badges/measure?project=net.viktorc%3Apararealml&metric=alert_status)](https://sonarcloud.io/dashboard?id=net.viktorc%3Apararealml) [![Docs](https://img.shields.io/badge/docs-latest-blue.svg)](https://pararealml.readthedocs.io/en/latest/index.html) [![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT)
+# PararealML
+
+[![Build Status](https://github.com/ViktorC/PararealML/actions/workflows/build.yml/badge.svg)](https://github.com/ViktorC/PararealML/actions/workflows/build.yml)
+[![Quality Gate Status](https://sonarcloud.io/api/project_badges/measure?project=net.viktorc%3Apararealml&metric=alert_status)](https://sonarcloud.io/dashboard?id=net.viktorc%3Apararealml)
+[![PyPI Version](https://badge.fury.io/py/pararealml.svg)](https://badge.fury.io/py/pararealml)
+[![Docs](https://img.shields.io/badge/docs-latest-blue.svg)](https://pararealml.readthedocs.io/en/latest/index.html)
+[![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT)
 
 PararealML is a differential equation solver library featuring a [Parareal](https://en.wikipedia.org/wiki/Parareal) framework based on a unified interface for initial value problems and various solvers including a number of machine learning accelerated ones. The library's main purpose is to provide a toolset to investigate the properties of the Parareal algorithm, especially when using machine learning accelerated coarse operators, across various problems. The library's implementation of the Parareal algorithm uses [MPI](https://en.wikipedia.org/wiki/Message_Passing_Interface) via [mpi4py](https://mpi4py.readthedocs.io/en/stable/).
 
 ## Main components
 The library has a modular design to allow for easy extensibility. The main components that enable this are described below.
 
+<img src="https://user-images.githubusercontent.com/12938964/156269280-58213998-58c2-45f1-aabb-7441ac4aa33e.png" alt="pararealml"/>
+
 ### Differential equation
 Differential equations extend the `DifferentialEquation` base class. In PararealML, all differential equations are time-dependent. Moreover, the unknown variables of differential equations are by definition vector-valued to support systems of differential equations. Both ordinary and partial differential equations are supported.
 
@@ -81,31 +89,28 @@ Visualizing the solutions of differential equations is supported by PararealML t
 
 A few examples of plots generated by PararealML can be seen below.
 
-<p float="left">
+<p>
   <img src="https://user-images.githubusercontent.com/12938964/152646803-e044c86c-f631-4cf6-9f6b-d9efdb6ae8df.png" alt="lorenz" width="400"/>
   <img src="https://user-images.githubusercontent.com/12938964/152624090-cab353b4-0fe4-4d19-b9d0-71c9ff9103f5.png" alt="lorenz phase space" width="400"/> 
 </p>
-<p float="left">
+<p>
   <img src="https://user-images.githubusercontent.com/12938964/153720536-b4c22dc8-d112-4331-bcc5-130c22a36199.gif" alt="n-body" width="400"/>
   <img src="https://user-images.githubusercontent.com/12938964/152625732-f177fe9b-9184-404b-8737-79411e9ea7e3.gif" alt="wave 2d surface" width="400"/> 
 </p>
-<p float="left">
+<p>
   <img src="https://user-images.githubusercontent.com/12938964/152646506-1404a822-dbc9-481e-91ec-b1e6b5a49748.gif" alt="cahn hilliard 3d" width="400"/>
   <img src="https://user-images.githubusercontent.com/12938964/152649580-ced02c20-b95f-4ec2-bd81-d3e34b13f9a5.gif" alt="navier stokes stream" width="400"/> 
 </p>
 
 ## Examples
 The [examples](https://git.ecdf.ed.ac.uk/msc-19-20/s1984842/tree/master/code/python/examples) folder contains a range of different examples of using the library for solving various differential equations both in serial and parallel. The scripts also include examples of using machine learning operators.
 
-## Setup
-To use the Parareal operator, an implementation of the MPI standard must be installed and the `mpicc` program must be on the search path as per the [installation guide](https://mpi4py.readthedocs.io/en/stable/install.html#using-pip) of mpi4py. With that set up, the dependencies of the library may be installed by running `make install`.
-
-## Testing
-To perform linting, execute `make lint`.
-
-The library uses type-hints throughout. For type checking, use the command `make type-check`.
-
-To run the unit tests, execute `make test`.
+## Installation
+To install PararealML, an implementation of the MPI standard must be pre-installed and the `mpicc` program must be on the search path as per the [installation guide](https://mpi4py.readthedocs.io/en/stable/install.html#using-pip) of mpi4py. With that set up, the library can be installed by running `pip install pararealml`.
 
-## Running
-To run any of the examples from the [examples](https://git.ecdf.ed.ac.uk/msc-19-20/s1984842/tree/master/code/python/examples) folder using an arbitrary number of MPI processes, run `make run p={number of processes} example={name of example file without extension}` (e.g. `make run p=4 example=lorenz_parareal`).
+## Development
+ * To install the dependencies of the library, run `make install` (this requires an existing MPI installation and `mpicc`).
+ * To perform linting, execute `make lint`.
+ * The library uses type-hints throughout. For type checking, use the command `make type-check`.
+ * To run the unit tests, execute `make test`.
+ * To run any of the examples from the [examples](https://git.ecdf.ed.ac.uk/msc-19-20/s1984842/tree/master/code/python/examples) folder using an arbitrary number of MPI processes, run `make run p={number of processes} example={name of example file without extension}` (e.g. `make run p=4 example=lorenz_parareal`).

setup.cfg

@@ -1,2 +1,3 @@
 [metadata]
-description_file = README.md
+long_description = file: README.md
+long_description_content_type = text/markdown

setup.py

@@ -1,14 +1,45 @@
 from setuptools import setup, find_packages
 
 setup(
-    name='PararealML',
-    version='0.0.1',
-    description='A parallel-in-time differential equation solver framework '
-                'with machine learning acceleration',
+    name='pararealml',
+    version='0.1.0',
+    description='A machine learning boosted parallel-in-time differential '
+                'equation solver framework',
     url='https://github.com/ViktorC/PararealML',
     author='Viktor Csomor',
     author_email='[email protected]',
     license='MIT',
-    packages=find_packages(),
-    include_package_data=True,
-    zip_safe=False)
+    install_requires=[
+        'numpy>=1.21',
+        'scipy>=1.7.0',
+        'matplotlib>=3.5.0',
+        'sympy>=1.6',
+        'mpi4py>=3.0.0',
+        'scikit-learn>=0.24.0',
+        'tensorflow>=2.0.0',
+        'tensorflow-probability>=0.10.0',
+    ],
+    packages=find_packages(exclude=('tests',)),
+    classifiers=[
+        'Development Status :: 3 - Alpha',
+        'Intended Audience :: Science/Research',
+        'License :: OSI Approved :: MIT License',
+        'Programming Language :: Python :: 3',
+        'Programming Language :: Python :: 3.8',
+        'Programming Language :: Python :: 3.9',
+        'Programming Language :: Python :: 3.10',
+        'Topic :: Scientific/Engineering',
+        'Topic :: Scientific/Engineering :: Artificial Intelligence',
+        'Topic :: Scientific/Engineering :: Mathematics',
+    ],
+    keywords=[
+        'differential equations',
+        'finite difference',
+        'parallel-in-time',
+        'parareal',
+        'machine learning',
+        'deep learning',
+        'physics-informed neural networks',
+        'scientific computing',
+    ],
+    include_package_data=True)