Merge pull request #51 from ecrl/dev

Update build/install method, add GitHub workflows, unittest -> pytest

.github/workflows/publish_to_pypi.yml

@@ -0,0 +1,30 @@
+name: Upload new ECNet version to PyPI
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v3
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.11'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+    - name: Build package
+      run: python -m build
+    - name: Publish package to PyPI
+      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/run_tests.yml

@@ -0,0 +1,26 @@
+name: Run ECNet tests
+
+on: [push]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v3
+        with:
+          python-version: '3.11'
+      - name: Install dependencies
+        run: |
+            python -m pip install --upgrade pip
+            pip install build
+            pip install pytest pytest-md
+      - name: Install package
+        run: python -m pip install .
+      - name: Run tests
+        uses: pavelzw/pytest-action@v2
+        with:
+          emoji: false
+          report-title: 'ECNet test report'

README.md

@@ -7,7 +7,6 @@
 [![status](http://joss.theoj.org/papers/f556afbc97e18e1c1294d98e0f7ff99f/status.svg)](http://joss.theoj.org/papers/f556afbc97e18e1c1294d98e0f7ff99f)
 [![GitHub license](https://img.shields.io/badge/license-MIT-blue.svg)](https://raw.githubusercontent.com/ECRL/ECNet/master/LICENSE.txt)
 [![Documentation Status](https://readthedocs.org/projects/ecnet/badge/?version=latest)](https://ecnet.readthedocs.io/en/latest/?badge=latest)
-[![Build Status](https://dev.azure.com/uml-ecrl/package-management/_apis/build/status/ECRL.ECNet?branchName=master)](https://dev.azure.com/uml-ecrl/package-management/_build/latest?definitionId=1&branchName=master)
 
 **ECNet** is an open source Python package for creating machine learning models to predict fuel properties. ECNet comes bundled with a variety of fuel property datasets, including cetane number, yield sooting index, and research/motor octane number. ECNet was built using the [PyTorch](https://pytorch.org/) library, allowing easy implementation of our models in your existing ML pipelines.
 

docs/api_blends.md

@@ -1,16 +1,26 @@
 # ecnet.blends
 
+## ecnet.blends.cetane_number
+
 ::: ecnet.blends.cetane_number
     handler: python
 
+## ecnet.blends.yield_sooting_index
+
 ::: ecnet.blends.yield_sooting_index
     handler: python
 
+## ecnet.blends.kinematic_viscosity
+
 ::: ecnet.blends.kinematic_viscosity
     handler: python
 
+## ecnet.blends.cloud_point
+
 ::: ecnet.blends.cloud_point
     handler: python
 
+## ecnet.blends.lower_heating_value
+
 ::: ecnet.blends.lower_heating_value
     handler: python

docs/api_callbacks.md

@@ -1,13 +1,21 @@
 # ecnet.callbacks
 
+## ecnet.callbacks.CallbackOperator
+
 ::: ecnet.callbacks.CallbackOperator
     handler: python
 
+## ecnet.callbacks.Callback
+
 ::: ecnet.callbacks.Callback
     handler: python
 
+## ecnet.callbacks.LRDecayLinear
+
 ::: ecnet.callbacks.LRDecayLinear
     handler: python
 
+## ecnet.callbacks.Validator
+
 ::: ecnet.callbacks.Validator
     handler: python

docs/api_datasets.md

@@ -1,40 +1,66 @@
 # ecnet.datasets
 
+## ecnet.datasets.QSPRDataset
+
 ::: ecnet.datasets.QSPRDataset
     handler: python
 
+## ecnet.datasets.QSPRDatasetFromFile
+
 ::: ecnet.datasets.QSPRDatasetFromFile
     handler: python
 
+## ecnet.datasets.QSPRDatasetFromValues
+
 ::: ecnet.datasets.QSPRDatasetFromValues
     handler: python
 
+## ecnet.datasets.load_bp
+
 ::: ecnet.datasets.load_bp
     handler: python
 
+## ecnet.datasets.load_cn
+
 ::: ecnet.datasets.load_cn
     handler: python
 
+## ecnet.datasets.load_cp
+
 ::: ecnet.datasets.load_cp
     handler: python
 
+## ecnet.datasets.load_kv
+
 ::: ecnet.datasets.load_kv
     handler: python
 
+## ecnet.datasets.load_lhv
+
 ::: ecnet.datasets.load_lhv
     handler: python
 
+## ecnet.datasets.load_mon
+
 ::: ecnet.datasets.load_mon
     handler: python
 
+## ecnet.datasets.load_pp
+
 ::: ecnet.datasets.load_pp
     handler: python
 
+## ecnet.datasets.load_ron
+
 ::: ecnet.datasets.load_ron
     handler: python
 
+## ecnet.datasets.load_ysi
+
 ::: ecnet.datasets.load_ysi
     handler: python
 
+## ecnet.datasets.load_mp
+
 ::: ecnet.datasets.load_mp
     handler: python

docs/api_tasks.md

@@ -1,13 +1,21 @@
 # ecnet.tasks
 
+## ecnet.tasks.select_rfr
+
 ::: ecnet.tasks.select_rfr
     handler: python
 
+## ecnet.tasks.tune_batch_size
+
 ::: ecnet.tasks.tune_batch_size
     handler: python
 
+## ecnet.tasks.tune_model_architecture
+
 ::: ecnet.tasks.tune_model_architecture
     handler: python
 
+## ecnet.tasks.tune_training_parameters
+
 ::: ecnet.tasks.tune_training_parameters
     handler: python

docs/index.md

@@ -7,7 +7,6 @@
 [![status](http://joss.theoj.org/papers/f556afbc97e18e1c1294d98e0f7ff99f/status.svg)](http://joss.theoj.org/papers/f556afbc97e18e1c1294d98e0f7ff99f)
 [![GitHub license](https://img.shields.io/badge/license-MIT-blue.svg)](https://raw.githubusercontent.com/ECRL/ECNet/master/LICENSE.txt)
 [![Documentation Status](https://readthedocs.org/projects/ecnet/badge/?version=latest)](https://ecnet.readthedocs.io/en/latest/?badge=latest)
-[![Build Status](https://dev.azure.com/uml-ecrl/package-management/_apis/build/status/ECRL.ECNet?branchName=master)](https://dev.azure.com/uml-ecrl/package-management/_build/latest?definitionId=1&branchName=master)
 
 ## Installation
 
@@ -27,4 +26,4 @@ Additional dependencies (torch, sklearn, padelpy, alvadescpy, ecabc) will be ins
 
     git clone https://github.com/ecrl/ecnet
     cd ecnet
-    python setup.py install
+    pip install .

ecnet/__init__.py

@@ -1,2 +1,4 @@
+import pkg_resources
 from .model import ECNet
-__version__ = '4.1.1'
+
+__version__ = pkg_resources.get_distribution("ecnet").version

pyproject.toml

@@ -0,0 +1,43 @@
+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.packages.find]
+exclude = ["databases*", "paper*"]
+
+[tool.setuptools.package-data]
+"*" = ["*.smiles", "*.target"]
+
+[tool.pytest.ini_options]
+filterwarnings = [
+    "ignore::DeprecationWarning",
+]
+
+[project]
+name = "ecnet"
+version = "4.1.2"
+authors = [
+    { name="Travis Kessler", email="travis.j.kessler@gmail.com" },
+]
+description = "Fuel property prediction using QSPR descriptors"
+readme = "README.md"
+requires-python = ">=3.11"
+dependencies = [
+    "torch==2.0.0",
+    "scikit-learn==1.2.2",
+    "padelpy==0.1.15",
+    "alvadescpy==0.1.2",
+    "ecabc==3.0.0"
+]
+classifiers = [
+    "Programming Language :: Python :: 3.11",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+]
+
+[project.urls]
+"Homepage" = "https://github.com/ecrl/ecnet"
+"Bug Tracker" = "https://github.com/ecrl/ecnet/issues"