Merge pull request #48 from ecrl/update-install

Update install method, update unit tests

.github/workflows/publish_to_pypi.yml

@@ -0,0 +1,30 @@
+name: Upload new PaDELPy 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 PaDELPy 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: 'PaDELPy test report'

README.md

@@ -22,7 +22,7 @@ Installation via cloned repository:
 ```
 $ git clone https://github.com/ecrl/padelpy
 $ cd padelpy
-$ python setup.py install
+$ pip install .
 ```
 
 PaDEL-Descriptor is bundled into PaDELPy, therefore an external installation/download of PaDEL-Descriptor is not necessary. There are currently no additional Python dependencies for PaDELPy, however it requires an installation of the [Java JRE](https://www.oracle.com/technetwork/java/javase/downloads/jre8-downloads-2133155.html) version 6+.

padelpy/__init__.py

@@ -1,3 +1,2 @@
 from .wrapper import padeldescriptor
 from .functions import from_mdl, from_smiles, from_sdf
-__version__ = '0.1.13'

padelpy/version.py

@@ -1,4 +1,3 @@
-VERSION = (0, 1, 14, "")
+import pkg_resources
 
-__version__ = ".".join(map(str, VERSION[:-1]))
-__release__ = ".".join(map(str, VERSION))
+__version__ = pkg_resources.get_distribution("padelpy").version

pyproject.toml

@@ -0,0 +1,30 @@
+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools]
+include-package-data = true
+
+[project]
+name = "padelpy"
+version = "0.1.15"
+authors = [
+    { name="Travis Kessler", email="travis.j.kessler@gmail.com" },
+]
+description = "A Python wrapper for PaDEL-Descriptor software"
+readme = "README.md"
+requires-python = ">=3.11"
+classifiers = [
+    "Programming Language :: Python :: 3.11",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+]
+
+[project.urls]
+"Homepage" = "https://github.com/ecrl/padelpy"
+"Bug Tracker" = "https://github.com/ecrl/padelpy/issues"
+
+[tool.pytest.ini_options]
+filterwarnings = [
+    "ignore::DeprecationWarning",
+]

tests/test_all.py

@@ -0,0 +1,34 @@
+import pytest
+
+from padelpy import from_sdf, from_smiles
+
+
+def test_from_smiles():
+    descriptors = from_smiles('CCC')
+    assert len(descriptors) == 1875
+    assert float(descriptors['MW']) == pytest.approx(44.0626, 1e-4)
+    assert int(descriptors['nC']) == 3
+
+
+def test_multiple_smiles():
+    smiles = ['CCC', 'CCCC']
+    descriptors = from_smiles(smiles)
+    assert len(descriptors) == 2
+    assert len(descriptors[0]) == 1875
+
+
+def test_errors():
+    bad_smiles = 'SJLDFGSJ'
+    with pytest.raises(RuntimeError):
+        _ = from_smiles(bad_smiles)
+    bad_smiles = ['SJLDFGSJ', 'CCC']
+    with pytest.raises(RuntimeError):
+        _ = from_smiles(bad_smiles)
+
+
+def test_from_sdf():
+    descriptors = from_sdf('tests/aspirin_3d.sdf')[0]
+    assert len(descriptors) == 1875
+    assert float(descriptors['MW']) == pytest.approx(180.04225, 1e-4)
+    assert float(descriptors['SsCH3']) == pytest.approx(1.2209, 1e-4)
+    assert int(descriptors['nC']) == 9