Add a (minimal) test suite

.github/workflows/pylint.yml

@@ -7,7 +7,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9", "3.12"]
+        python-version: ["3.9", "3.11"]
     steps:
     - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
@@ -21,4 +21,4 @@ jobs:
         pip install .
     - name: Analysing the code with pylint
       run: |
-        pylint $(git ls-files '*.py')
+        pylint $(git ls-files 'mctools/*.py')

.github/workflows/pytest.yml

@@ -0,0 +1,27 @@
+name: Pytest
+
+on: [push]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.11"]
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install pytest flake8 flake8-pytest-style
+        pip install .
+    - name: Lint the test files with flake8-pytest-style
+      run: |
+        flake8 tests/
+    - name: Test with pytest
+      run: |
+        pytest

README.md

@@ -6,22 +6,15 @@ and developed further while at [Scanlon Materials Theory Group](https://github.c
 
 The recommended way of installing is to clone the repository and make a local installation using pip:
 
-``` shell
+```bash
 git clone https://github.com/ajjackson/mctools.git
 cd mctools
 pip install --user -e .
 ```
 
-ase-convert (Convert structure files)
--------------------------------------
-Use ASE to read a crystal structure file and write out to target format. Call with `-h` flag for usage information. ASE can also get this information from some output file formats, which is useful.
-
-```
-# EXAMPLE: read relaxed structure from aims output and write VASP input
-bash> ase_convert.py aims.out POSCAR
-
-# EXAMPLE: Convert between files with non-standard names
-bash> ase_convert.py -f vasp MY_SUPER_POSCAR -t cif MY_SUPER_CIF
+To run unit tests, install pytest and run with
+```bash
+python -m pytest
 ```
 
 get-spacegroup (Spacegroup tolerances)

mctools/generic/get_energy.py

@@ -1,23 +1,6 @@
-#! /usr/bin/env python
-
-###############################################################################
-# Copyright 2017 Adam Jackson
-###############################################################################
-#    This program is free software: you can redistribute it and/or modify
-#    it under the terms of the GNU General Public License as published by
-#    the Free Software Foundation, either version 3 of the License, or
-#    (at your option) any later version.
-#
-#    This program is distributed in the hope that it will be useful,
-#    but WITHOUT ANY WARRANTY; without even the implied warranty of
-#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-#    GNU General Public License for more details.
-#
-#    You should have received a copy of the GNU General Public License
-#    along with this program.  If not, see <http://www.gnu.org/licenses/>.
-###############################################################################
-
 from argparse import ArgumentParser
+from typing import List, Optional
+
 import ase.io
 
 
@@ -27,15 +10,18 @@ def get_energy(filename):
     return atoms.get_total_energy()
 
 
-def main():
+def main(params: Optional[List[str]] = None):
     """Get calculated energy from output file using ASE"""
 
     parser = ArgumentParser(description="Read energy from output")
     parser.add_argument("filename", type=str, nargs='?',
                         default="vasprun.xml",
                         help="Path to ab initio output file")
 
-    args = parser.parse_args()
+    if params:
+        args = parser.parse_args(params)
+    else:
+        args = parser.parse_args()
 
     energy = get_energy(args.filename)
     print(energy)

tests/test_get_energy.py

@@ -0,0 +1,31 @@
+import ase.build
+from ase.calculators.singlepoint import SinglePointCalculator
+import ase.io
+import pytest
+
+from mctools.generic.get_energy import get_energy, main
+
+
+ENERGY = 3.141
+FILENAME = "methane.extxyz"
+
+
+@pytest.fixture
+def methane_with_energy() -> ase.Atoms:
+    atoms = ase.build.molecule("CH4")
+    atoms.calc = SinglePointCalculator(atoms, energy=ENERGY)
+    return atoms
+
+
+def test_get_energy(methane_with_energy, tmp_path) -> None:
+    ase.io.write(tmp_path / FILENAME, methane_with_energy)
+
+    assert get_energy(tmp_path / FILENAME) == pytest.approx(ENERGY)
+
+
+def test_main(methane_with_energy, tmp_path, capsys) -> None:
+    ase.io.write(tmp_path / FILENAME, methane_with_energy)
+
+    main([str(tmp_path / FILENAME)])
+    captured = capsys.readouterr()
+    assert float(captured.out) == pytest.approx(ENERGY)