README update and other tidying

.github/workflows/test.yml

@@ -1,4 +1,4 @@
-name: Run tests
+name: Tests
 
 on:
   push:
@@ -13,6 +13,7 @@ concurrency:
 
 jobs:
   test:
+    name: test (py${{ matrix.python-version }}, ${{ matrix.os }})
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false

.vscode/settings.json

@@ -9,7 +9,7 @@
     "files.insertFinalNewline": true,
     "files.trimTrailingWhitespace": true,
     "files.trimFinalNewlines": true,
-    "python.defaultInterpreterPath": "./venv/bin/python",
+    "python.defaultInterpreterPath": "./.venv/bin/python",
     "[python]": {
         "editor.defaultFormatter": "charliermarsh.ruff",
         "editor.rulers": [88]

README.md

@@ -2,19 +2,11 @@
 
 [![PyPI Version](https://img.shields.io/pypi/v/PubChemPy.svg?style=flat)](https://pypi.python.org/pypi/PubChemPy)
 [![License](https://img.shields.io/pypi/l/PubChemPy.svg?style=flat)](https://github.com/mcs07/PubChemPy/blob/main/LICENSE)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.541438.svg)](https://doi.org/10.5281/zenodo.593126)
+[![Tests](https://github.com/mcs07/PubChemPy/actions/workflows/test.yml/badge.svg)](https://github.com/mcs07/PubChemPy/actions/workflows/test.yml)
 
 PubChemPy provides a way to interact with PubChem in Python. It allows chemical searches by name, substructure and similarity, chemical standardization, conversion between chemical file formats, depiction and retrieval of chemical properties.
 
-```pycon
->>> from pubchempy import get_compounds, Compound
->>> comp = Compound.from_cid(1423)
->>> print(comp.smiles)
-CCCCCCCNC1CCCC1CCCCCCC(=O)O
->>> comps = get_compounds('Aspirin', 'name')
->>> print(comps[0].xlogp)
-1.2
-```
-
 ## Installation
 
 Install PubChemPy using:
@@ -25,11 +17,36 @@ pip install pubchempy
 
 Alternatively, try one of the other [installation options](https://docs.pubchempy.org/en/latest/guide/install.html).
 
+## Example usage
+
+Retrieve a compound by its PubChem Compound Identifier (CID) and print its SMILES and IUPAC name:
+
+```pycon
+>>> import pubchempy as pcp
+>>> comp = pcp.Compound.from_cid(1423)
+>>> print(comp.smiles)
+CCCCCCCNC1CCCC1CCCCCCC(=O)O
+>>> print(comp.iupac_name)
+7-[2-(heptylamino)cyclopentyl]heptanoic acid
+```
+
+Search compounds by name and print the SMILES and molecular weight of the first result:
+
+```pycon
+>>> results = pcp.get_compounds("Aspirin", "name")
+>>> print(results[0].smiles)
+CC(=O)OC1=CC=CC=C1C(=O)O
+>>> print(results[0].molecular_weight)
+180.16
+```
+
 ## Documentation
 
 Full documentation is available at https://docs.pubchempy.org.
 
-## Contribute
+This includes a [step-by-step guide on how to use PubChemPy](https://docs.pubchempy.org/en/latest/guide/gettingstarted.html), as well as a [complete API reference](https://docs.pubchempy.org/en/latest/api.html).
+
+## Contributing
 
 - Feature ideas and bug reports are welcome on the [Issue Tracker](https://github.com/mcs07/PubChemPy/issues).
 - Fork the [source code](https://github.com/mcs07/PubChemPy) on GitHub, make changes and file a pull request.

tests/test_download.py

@@ -1,7 +1,6 @@
 """Test downloading."""
 
 import csv
-import os
 
 import pytest