Merge branch 'main' of github.com:bjmorgan/vasppy

.github/workflows/build.yml

@@ -10,7 +10,7 @@ jobs:
       timeout-minutes: 30
       strategy:
         matrix:
-          python-version: [3.7, 3.8, 3.9]
+          python-version: ['3.9', '3.10', '3.11']
       steps:
         - uses: actions/checkout@v2
         - name: Set up Python ${{matrix.python-version}}
@@ -26,16 +26,21 @@ jobs:
             pip install types-PyYAML
             pip install pytest
             pip install pytest-cov
+            pip install pylint
             pip install .
             pip list
         - name: Run tests
           run: |
-            pytest --cov-config=.coveragerc --cov=vasppy --cov-report xml
-        - name: Publish code coverage
-          env:
-            CC_TEST_REPORTER_ID: ${{ secrets.CODECLIMATE_REPO_TOKEN }}
-          uses: paambaati/codeclimate-action@v2.7.5
+            pytest --cov-config=.coveragerc --cov=vasppy --cov-report lcov
+        - name: Coveralls GitHub Action
+          uses: coverallsapp/github-action@1.1.3
+          with:
+            path-to-lcov: ./coverage.lcov
+            github-token: ${{ secrets.GITHUB_TOKEN }}
         - name: Static type checking
           run: |
             mypy vasppy
+        - name: PyLint
+          run: |
+              pylint --errors-only vasppy
 

.github/workflows/ruff.yml

@@ -0,0 +1,8 @@
+name: Ruff
+on: [push, pull_request]
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: chartboost/ruff-action@v1

.readthedocs.yaml

@@ -0,0 +1,27 @@
+# Read the Docs configuration file for Sphinx projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+   configuration: docs/source/conf.py
+
+# Optionally build your docs in additional formats such as PDF and ePub
+# formats:
+#    - pdf
+#    - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+   install:
+   - requirements: docs/requirements.txt

.ruff.toml

@@ -0,0 +1,41 @@
+# Enable pycodestyle (`E`) and Pyflakes (`F`) codes by default.
+select = ["E", "F", "B"]
+ignore = ["E501", "E741", "B905"] # B905 valid for 3.10 onwards
+
+# Allow autofix for all enabled rules (when `--fix`) is provided.
+fixable = ["A", "B", "C", "D", "E", "F", "G", "I", "N", "Q", "S", "T", "W", "ANN", "ARG", "BLE", "COM", "DJ", "DTZ", "EM", "ERA", "EXE", "FBT", "ICN", "INP", "ISC", "NPY", "PD", "PGH", "PIE", "PL", "PT", "PTH", "PYI", "RET", "RSE", "RUF", "SIM", "SLF", "TCH", "TID", "TRY", "UP", "YTT"]
+unfixable = []
+
+# Exclude a variety of commonly ignored directories.
+exclude = [
+    ".bzr",
+    ".direnv",
+    ".eggs",
+    ".git",
+    ".git-rewrite",
+    ".hg",
+    ".mypy_cache",
+    ".nox",
+    ".pants.d",
+    ".pytype",
+    ".ruff_cache",
+    ".svn",
+    ".tox",
+    ".venv",
+    "__pypackages__",
+    "_build",
+    "buck-out",
+    "build",
+    "dist",
+    "node_modules",
+    "venv",
+]
+
+# Same as Black.
+line-length = 88
+
+# Allow unused variables when underscore-prefixed.
+dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
+
+# Assume Python 3.9.
+target-version = "py39"

README.md

@@ -2,15 +2,15 @@
 
 [![DOI](https://zenodo.org/badge/17946870.svg)](https://zenodo.org/badge/latestdoi/17946870)
 [![PyPI version](https://badge.fury.io/py/vasppy.svg)](https://badge.fury.io/py/vasppy)
-[![Build Status](https://travis-ci.org/bjmorgan/vasppy.svg?branch=master)](https://travis-ci.org/bjmorgan/vasppy)
-[![Test Coverage](https://codeclimate.com/github/bjmorgan/vasppy/badges/coverage.svg)](https://codeclimate.com/github/bjmorgan/vasppy/coverage)
+[![Build Status](https://github.com/bjmorgan/vasppy/actions/workflows/build.yml/badge.svg)](https://github.com/bjmorgan/vasppy/actions/workflows/build.yml)
+[![Coverage Status](https://coveralls.io/repos/github/bjmorgan/vasppy/badge.svg?branch=main)](https://coveralls.io/github/bjmorgan/vasppy?branch=main)
 [![Documentation Status](https://readthedocs.org/projects/vasppy/badge/?version=latest)](http://vasppy.readthedocs.io/en/latest/?badge=latest)
 
 `vasppy` is a suite of Python tools and scripts written in Python for manipulating and processing [VASP](https://www.vasp.at/) input and output files.
 
 ## Tests
 
-Automated testing of the latest build happens [here](https://travis-ci.org/bjmorgan/vasppy).
+Automated testing of the latest build happens [here](https://github.com/bjmorgan/vasppy/actions/workflows/build.yml)
 
 Manual tests can be run using
 ```

docs/requirements.txt

@@ -1,4 +1,5 @@
-Sphinx>=1.6.3
+Sphinx~=6.2.1
 nbsphinx
 jupyter
+git+https://github.com/bjmorgan/figure_formatting.git
 -r ../requirements.txt

requirements.txt

@@ -1,7 +1,7 @@
-numpy>=1.16.2
+numpy>=1.20
 monty
 pandas
-pymatgen
+pymatgen>=2023.6.28
 PyYAML 
 fortranformat
 scipy>=1.4.1

setup.py

@@ -10,6 +10,7 @@
 
 scripts = ['check_species',
            'checkforce',
+           'convergence_testing',
            'murnfit', 
            'vasp_summary', 
            'poscar_to_cif', 
@@ -18,7 +19,6 @@
            'fat_bands',
            'pimaim_to_poscar',
            'pimaim_to_xtl',
-           'poscar_sort',
            'poscar_to_pimaim',
            'poscar_to_xtl',
            'proc_poscar',
@@ -46,15 +46,13 @@
                       '{} = vasppy.scripts.{}:main'.format(s, s) for s in scripts]},
     license='MIT',
     install_requires=['monty',
-                      'numpy>=1.16.2',
+                      'numpy>=1.20',
                       'pandas',
-                      'pymatgen>=2022.0.0',
+                      'pymatgen>=2023.6.28',
                       'PyYAML', 
-                      'coverage==4.3.4',
-                      'codeclimate-test-reporter',
                       'fortranformat',
                       'scipy>=1.4.1', 
                       'tqdm',
                       'lxml'],
-    python_requires='>=3.7'
+    python_requires='>=3.9'
     )

tests/test_atom.py

@@ -3,14 +3,15 @@
 
 from vasppy.atom import Atom
 
-class AtomTestCase( unittest.TestCase ):
 
-    def test_init_atom( self ):
-        label = 'A'
-        r = np.array( [ 0.1, 0.2, 0.3 ] )
-        atom = Atom( label=label, r=r )
-        self.assertEqual( atom.label, label )
-        np.testing.assert_array_equal( atom.r, r )
+class AtomTestCase(unittest.TestCase):
+    def test_init_atom(self):
+        label = "A"
+        r = np.array([0.1, 0.2, 0.3])
+        atom = Atom(label=label, r=r)
+        self.assertEqual(atom.label, label)
+        np.testing.assert_array_equal(atom.r, r)
 
-if __name__ == '__main__':
+
+if __name__ == "__main__":
     unittest.main()

tests/test_band.py

@@ -4,41 +4,45 @@
 
 from vasppy.band import Band, handle_occupancy
 
-class BandTestCase( unittest.TestCase ):
+
+class BandTestCase(unittest.TestCase):
     """Tests for procar.Band class"""
 
-    def test_band_is_initialised( self ):
+    def test_band_is_initialised(self):
         """Test Band object is initialised"""
         index = 2
         energy = 1.0
         occupancy = 0.5
-        with patch( 'vasppy.band.handle_occupancy' ) as mock_handle_occupancy:
+        with patch("vasppy.band.handle_occupancy") as mock_handle_occupancy:
             mock_handle_occupancy.return_value = 0.5
-            band = Band( index=index, energy=energy, occupancy=occupancy )
-        self.assertEqual( index, band.index )
-        self.assertEqual( energy, band.energy )
-        self.assertEqual( occupancy, band.occupancy )
-        mock_handle_occupancy.assert_has_calls( [call(0.5, negative_occupancies='warn')] )
+            band = Band(index=index, energy=energy, occupancy=occupancy)
+        self.assertEqual(index, band.index)
+        self.assertEqual(energy, band.energy)
+        self.assertEqual(occupancy, band.occupancy)
+        mock_handle_occupancy.assert_has_calls([call(0.5, negative_occupancies="warn")])
+
+    def test_handle_occupancy_raises_valuerror_if_negative_occupancies_is_invalid_keyword(
+        self,
+    ):
+        with self.assertRaises(ValueError):
+            handle_occupancy(0.5, negative_occupancies="foo")
 
-    def test_handle_occupancy_raises_valuerror_if_negative_occupancies_is_invalid_keyword( self ):
-        with self.assertRaises( ValueError ):
-            handle_occupancy( 0.5, negative_occupancies='foo' )
+    def test_handle_occupancy_warns_about_negative_occupancies(self):
+        with warnings.catch_warnings(record=True) as w:
+            handle_occupancy(-0.1, negative_occupancies="warn")
+            self.assertEqual(len(w), 1)
+            self.assertTrue("negative" in str(w[-1].message))
 
-    def test_handle_occupancy_warns_about_negative_occupancies( self ):
-        with warnings.catch_warnings( record=True ) as w:
-            handle_occupancy( -0.1, negative_occupancies='warn' )
-            self.assertEqual( len(w), 1 )
-            self.assertTrue( "negative" in str(w[-1].message) )
+    def test_handle_occupancy_raises_exception_if_negative_occupancies_is_raise(self):
+        with self.assertRaises(ValueError):
+            handle_occupancy(-0.1, negative_occupancies="raise")
 
-    def test_handle_occupancy_raises_exception_if_negative_occupancies_is_raise( self ):
-        with self.assertRaises( ValueError ):
-            handle_occupancy( -0.1, negative_occupancies='raise' )
+    def test_handle_occupancy_if_negative_occupancies_is_ignore(self):
+        self.assertEqual(handle_occupancy(-0.1, negative_occupancies="ignore"), -0.1)
 
-    def test_handle_occupancy_if_negative_occupancies_is_ignore( self ):
-        self.assertEqual( handle_occupancy( -0.1, negative_occupancies='ignore' ), -0.1 )
+    def test_handle_occupancy_zeros_occupancies_if_negative_occupancies_is_zero(self):
+        self.assertEqual(handle_occupancy(-0.1, negative_occupancies="zero"), 0.0)
 
-    def test_handle_occupancy_zeros_occupancies_if_negative_occupancies_is_zero( self ):
-        self.assertEqual( handle_occupancy( -0.1, negative_occupancies='zero' ), 0.0 )
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     unittest.main()