Merge pull request #1 from ecrl/dev

0.1.3

.github/workflows/publish_to_pypi.yml

@@ -0,0 +1,30 @@
+name: Upload new alvaDescPy 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 }}

README.md

@@ -21,7 +21,7 @@ Installation via cloned repository:
 ```
 $ git clone https://github.com/ecrl/alvadescpy
 $ cd alvadescpy
-$ python setup.py install
+$ pip install .
 ```
 
 There are currently no additional dependencies for alvaDescPy, however it requires a valid, licensed installation of [alvaDesc](https://www.alvascience.com/alvadesc/).

alvadescpy/__init__.py

@@ -1,4 +1,5 @@
 from alvadescpy.wrapper import alvadesc
 from alvadescpy.functions import smiles_to_descriptors
 from alvadescpy.wrapper import CONFIG
-__version__ = '0.1.2'
+import pkg_resources
+__version__ = pkg_resources.get_distribution('alvadescpy')

alvadescpy/functions.py

@@ -15,12 +15,13 @@
 from alvadescpy import alvadesc
 
 # custom argument and return variables
-_DESC = TypeVar('_DESC', str, list)
-_RET_VAL = TypeVar('_RET_VAL', dict, list)
+str_or_list = TypeVar('str_or_list', str, list)
+list_or_dict = TypeVar('list_or_dict', dict, list)
 
 
-def smiles_to_descriptors(smiles: str, descriptors: _DESC='ALL',
-                          labels: bool=True) -> _RET_VAL:
+def smiles_to_descriptors(smiles: str_or_list,
+                          descriptors: str_or_list = 'ALL',
+                          labels: bool = True) -> list_or_dict:
     ''' smiles_to_descriptors: returns molecular descriptors for a given
     molecule (represented by its SMILES string)
 
@@ -37,6 +38,8 @@ def smiles_to_descriptors(smiles: str, descriptors: _DESC='ALL',
     '''
 
     if type(smiles) == list:
-        return [alvadesc(ismiles=smi, descriptors=descriptors, labels=labels)[0]
-                for smi in smiles]
+        return [
+            alvadesc(ismiles=smi, descriptors=descriptors, labels=labels)[0]
+            for smi in smiles
+        ]
     return alvadesc(ismiles=smiles, descriptors=descriptors, labels=labels)[0]

alvadescpy/wrapper.py

@@ -9,28 +9,28 @@
 #
 
 # stdlib. imports
-from subprocess import check_output, PIPE, Popen, call
-from csv import writer, QUOTE_ALL
+from subprocess import PIPE, Popen
 from typing import TypeVar
 import platform
-from os.path import realpath
 
 # path to alvaDesc command line interface executable
 CONFIG = {
     'alvadesc_path': None
 }
 plt = platform.system()
 if plt == 'Windows':
-    CONFIG['alvadesc_path'] = 'C:\\Program Files\\Alvascience\\alvaDesc\\alvaDescCLI.exe'
+    CONFIG['alvadesc_path'] = 'C:\\Program Files\\Alvascience\\alvaDesc\\\
+alvaDescCLI.exe'
 elif plt == 'Darwin':
-    CONFIG['alvadesc_path'] = '/Applications/alvaDesc.app/Contents/MacOS/alvaDescCLI'
+    CONFIG['alvadesc_path'] = '/Applications/alvaDesc.app/Contents/MacOS/\
+alvaDescCLI'
 elif plt == 'Linux':
     CONFIG['alvadesc_path'] = '/usr/bin/alvaDescCLI'
 else:
     raise RuntimeError('Unknown/unsupported operating system: {}'.format(plt))
 
 # custom argument variable (either str or list)
-_DESC = TypeVar('_DESC', str, list)
+str_or_list = TypeVar('str_or_list', str, list)
 
 
 def _sub_call(command: str) -> list:
@@ -54,12 +54,15 @@ def _sub_call(command: str) -> list:
     return p.communicate()[0].decode('utf-8')
 
 
-def alvadesc(script: str=None, ismiles: str=None, input_file: str=None,
-             inputtype: str=None, descriptors: _DESC=None, labels: bool=False,
-             ecfp: bool=False, pfp: bool=False, fpsize: int=1024, fpmin: int=0,
-             fpmax: int=2, count: bool=True, bits: int=2, fpoptions: str=None,
-             maccsfp: bool=False, output: str=None, threads: int=None) -> list:
-    ''' alvadesc: calls alvaDesc's command line interface; supports all arguments
+def alvadesc(script: str = None, ismiles: str = None, input_file: str = None,
+             inputtype: str = None, descriptors: str_or_list = None,
+             labels: bool = False, ecfp: bool = False, pfp: bool = False,
+             fpsize: int = 1024, fpmin: int = 0, fpmax: int = 2,
+             count: bool = True, bits: int = 2, fpoptions: str = None,
+             maccsfp: bool = False, output: str = None,
+             threads: int = None) -> list:
+    ''' alvadesc: calls alvaDesc's command line interface; supports all
+    arguments
 
     Args:
         script (str): path to script file containing all available options; if

pyproject.toml

@@ -0,0 +1,22 @@
+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "alvadescpy"
+version = "0.1.3"
+authors = [
+    { name="Travis Kessler", email="[email protected]" },
+]
+description = "Python wrapper for alvaDesc 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/alvadescpy"
+"Bug Tracker" = "https://github.com/ecrl/alvadescpy/issues"