updated workflow, added badges

.github/workflows/python-package.yml

@@ -1,7 +1,7 @@
 # This workflow will install Python dependencies, lint, and run tests with a variety of Python versions
 # For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
 
-name: Python package
+name: Test and Lint
 
 on:
   push:
@@ -31,6 +31,11 @@ jobs:
     - name: Analyzing the code with pylint
       run: |
         pylint $(git ls-files '*.py')
+    - name: Analyzing the code with flake8
+      uses: py-actions/flake8@v2
+      with:
+        max-line-length: "88"
+        plugins: "flake8-bugbear==24.4.26"
     - name: Test with pytest
       run: |
         pytest

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
 ci:
-    skip: [pylint]
+    skip: [pylint,flake8]
 exclude: EPS_OUTCAR
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
@@ -40,3 +40,12 @@ repos:
           [
             pytest,
           ]
+-   repo: https://github.com/pycqa/flake8
+    rev: '7.1.0'  # pick a git hash / tag to point to
+    hooks:
+    -   id: flake8
+        args: [--max-line-length=88]
+        additional_dependencies:
+          [
+            flake8-bugbear
+          ]

README.md

@@ -0,0 +1,8 @@
+ramannoodle
+===========
+[![python](https://img.shields.io/badge/Python-3.12-3776AB.svg?style=flat&logo=python&logoColor=white)](https://www.python.org) [![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) [![Checked with mypy](http://www.mypy-lang.org/static/mypy_badge.svg)](http://mypy-lang.org/) [![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/license/mit)
+
+![Tests](reports/tests-badge.svg)
+
+
+`ramannoodle` helps you calculate Raman spectra quickly and efficiency based on VASP calculations. **This software is currently being completely overhauled.** Check out the `legacy` branch for the old (and functional!) version.

ramannoodle/__init__.py

@@ -1,48 +0,0 @@
-"""
-Sample includes:
-
-from dynamics import Phonons
-from dynamics import MDTrajectory
-
-from spectrum import RamanSpectrum
-from spectrum import VibrationalSpectrum
-
-from spectrometer import RamanSpectrometer
-from spectrometer import VibrationalSpectrometer
-
-from spectrum.phonons import PhononRamanSpectrum
-from spectrum.md import MDRamanSpectrum
-
-from polarizability import PolarizabilityModel
-
-from polarizability.taylor import LinearPolarizabilityModel
-
-
-Workflow:
-
-1. Create a Dynamics object from your simulations.
-
-2. Create an InterpolationPolarizabilityModel from your simulations.
-- Set up a Symmetry object from an OUTCAR
-- Set up a model for that symmetry
-- Insert DOF, a set of displacements and polarizabilities (e.g. +,-,
-polarizability_plus,polarizability_minus)
-    - Check that displacements given are colinear.
-    - That that the new displacements are orthogonal to all existing displacements
-    - If checks are successful:
-        - Generate all symmetry equivalent displacements.
-        - Do sanity check to ensure we're still totally orthogonal
-        - add interpolation and normalized dof displacements
-
-Run a virtual experiment
-- Specify RamanSettings (angle, polycrystalline)
-- dynamics.get_spectrum(PolarizabilityModel, SpectrometerSettings) -> RamanSpectrum
-
-Extract Relevant information from RamanSpectrum
-- Spectrum.get_intensities(temperature, correction factors, smearing, etc.)
-- Spectrum.get_wavenumbers()
--
-
-For now, I will not implement SpectrometerSettings. This can wait.
-
-"""

ramannoodle/io/vasp/__init__.py

@@ -1,15 +1,13 @@
 """Utilities for VASP."""
 
 from pathlib import Path
-from typing import TextIO
 import numpy as np
 from numpy.typing import NDArray
 
 from ...dynamics import Phonons
 from ...symmetry import StructuralSymmetry
 from ...globals import ATOMIC_WEIGHTS, ATOMIC_NUMBERS
 from .vasp_utils import (
-    _get_atomic_symbol_from_potcar_line,
     _read_atomic_symbols_from_outcar,
     _read_eigenvector_from_outcar,
     _read_cartesian_positions_from_outcar,

ramannoodle/io/vasp/vasp_utils.py

@@ -104,7 +104,7 @@ def _read_polarizability_from_outcar(outcar_file: TextIO) -> NDArray[np.float64]
 
 
 def _get_lattice_vector_from_outcar_line(line: str) -> NDArray[np.float64]:
-    """e.g.  "11.823066970  0.000000000  0.000000000     0.084580423  0.000000000  0.000000000" """
+    """Extracts lattice vector from an appropriate line from an outcar"""
     return np.array([float(item) for item in line.split()[0:3]])
 
 

ramannoodle/polarizability/__init__.py

@@ -5,12 +5,10 @@
 import numpy as np
 from numpy.typing import NDArray
 from scipy.interpolate import make_interp_spline, BSpline
-import spglib
 
 from . import polarizability_utils
 from ..symmetry.symmetry_utils import is_orthogonal_to_all
 from ..symmetry import StructuralSymmetry
-from ..exceptions import InvalidDOFException, SymmetryException
 
 
 class PolarizabilityModel(ABC):  # pylint: disable=too-few-public-methods

ramannoodle/spectrum/__init__.py

@@ -1,7 +1,5 @@
 """Spectra."""
 
-from abc import ABC, abstractmethod
-
 import numpy as np
 from numpy.typing import NDArray
 

ramannoodle/symmetry/__init__.py

@@ -2,11 +2,10 @@
 
 import numpy as np
 from numpy.typing import NDArray
-from scipy.interpolate import make_interp_spline, BSpline
 import spglib
 
 from . import symmetry_utils
-from ..exceptions import InvalidDOFException, SymmetryException
+from ..exceptions import SymmetryException
 
 
 class StructuralSymmetry:

ramannoodle/symmetry/symmetry_utils.py

@@ -89,7 +89,7 @@ def get_fractional_positions_permutation_matrix(
 def transform_fractional_positions(
     positions: NDArray[np.float64],
     rotation: NDArray[np.float64],
-    translation: NDArray[np.float64] = np.array([0.0, 0.0, 0.0]),
+    translation: NDArray[np.float64],
 ) -> NDArray[np.float64]:
     """Transforms fractional coordinates and applies periodic boundary
     conditions."""

reports/junit/junit.xml

@@ -0,0 +1 @@
+<?xml version="1.0" encoding="utf-8"?><testsuites><testsuite name="pytest" errors="0" failures="0" skipped="0" tests="23" time="49.055" timestamp="2024-07-28T20:57:27.535556-07:00" hostname="edna.local"><testcase classname="test.tests.test_polarizability" name="test_are_collinear[vector_10-vector_20-False]" time="0.001" /><testcase classname="test.tests.test_polarizability" name="test_are_collinear[vector_11-vector_21-False]" time="0.000" /><testcase classname="test.tests.test_polarizability" name="test_are_collinear[vector_12-vector_22-True]" time="0.000" /><testcase classname="test.tests.test_polarizability" name="test_are_collinear[vector_13-vector_23-False]" time="0.000" /><testcase classname="test.tests.test_polarizability" name="test_check_orthogonal[vector_10-vectors0-2]" time="0.000" /><testcase classname="test.tests.test_polarizability" name="test_check_orthogonal[vector_11-vectors1--1]" time="0.000" /><testcase classname="test.tests.test_polarizability" name="test_structural_symmetry[test/data/TiO2_OUTCAR-2-36-known_displacements_shape0]" time="20.316" /><testcase classname="test.tests.test_polarizability" name="test_structural_symmetry[test/data/STO_RATTLED_OUTCAR-135-1-known_displacements_shape1]" time="0.112" /><testcase classname="test.tests.test_polarizability" name="test_structural_symmetry[test/data/LLZO_OUTCAR-9-32-known_displacements_shape2]" time="7.008" /><testcase classname="test.tests.test_polarizability" name="test_get_fractional_positions_permutation_matrix[reference0-permuted0-known0]" time="0.000" /><testcase classname="test.tests.test_polarizability" name="test_find_duplicates[vectors0-None]" time="0.000" /><testcase classname="test.tests.test_polarizability" name="test_find_duplicates[vectors1--0.05]" time="0.000" /><testcase classname="test.tests.test_polarizability" name="test_add_dof[test/data/STO_RATTLED_OUTCAR-0-magnitudes0-1]" time="0.114" /><testcase classname="test.tests.test_polarizability" name="test_add_dof[test/data/TiO2_OUTCAR-0-magnitudes1-72]" time="20.385" /><testcase classname="test.tests.test_vasp" name="test_load_phonons_from_outcar[test/data/TiO2_OUTCAR-108-known_wavenumbers0-known_first_displacement0-known_last_displacement0]" time="0.037" /><testcase classname="test.tests.test_vasp" name="test_get_atomic_symbol_from_potcar_line[ POTCAR:    PAW_PBE Ti_pv 07Sep2000\n-Ti]" time="0.000" /><testcase classname="test.tests.test_vasp" name="test_get_atomic_symbol_from_potcar_line[ POTCAR:    PAW_PBE O 08Apr2002  \n-O]" time="0.000" /><testcase classname="test.tests.test_vasp" name="test_read_atomic_symbols_from_outcar[test/data/TiO2_OUTCAR-known0]" time="0.000" /><testcase classname="test.tests.test_vasp" name="test_read_cartesian_positions_from_outcar[test/data/EPS_OUTCAR-known_first_position0-known_last_position0]" time="0.001" /><testcase classname="test.tests.test_vasp" name="test_read_fractional_positions_from_outcar[test/data/EPS_OUTCAR-known_first_position0-known_last_position0]" time="0.000" /><testcase classname="test.tests.test_vasp" name="test_read_polarizability_from_outcar[test/data/EPS_OUTCAR-known_polarizability0]" time="0.001" /><testcase classname="test.tests.test_vasp" name="test_read_lattice_from_outcar[test/data/TiO2_OUTCAR-known_lattice0]" time="0.000" /><testcase classname="test.tests.test_vasp" name="test_read_lattice_from_outcar[test/data/EPS_OUTCAR-known_lattice1]" time="0.000" /></testsuite></testsuites>

requirements.txt

@@ -1,3 +1,4 @@
+flake8
 numpy
 pre-commit
 pylint

test/tests/test_vasp.py

@@ -15,6 +15,8 @@
 
 from .. import EPS_OUTCAR_NUM_ATOMS, PHONONS_OUTCAR_NUM_ATOMS
 
+# pylint: disable=protected-access
+
 
 @pytest.mark.parametrize(
     "outcar_path_fixture, known_num_atoms, known_wavenumbers,"
@@ -64,9 +66,7 @@ def test_load_phonons_from_outcar(
 )
 def test_get_atomic_symbol_from_potcar_line(potcar_line: str, known: str) -> None:
     """test"""
-    result = vasp_utils._get_atomic_symbol_from_potcar_line(  # pylint: disable=protected-access
-        potcar_line
-    )
+    result = vasp_utils._get_atomic_symbol_from_potcar_line(potcar_line)
     assert result == known
 
 
@@ -80,11 +80,7 @@ def test_read_atomic_symbols_from_outcar(
     known: list[str],
 ) -> None:
     """test"""
-    atomic_symbols = (
-        vasp_utils._read_atomic_symbols_from_outcar(  # pylint: disable=protected-access
-            outcar_file_fixture
-        )
-    )
+    atomic_symbols = vasp_utils._read_atomic_symbols_from_outcar(outcar_file_fixture)
     assert atomic_symbols == known
 
 
@@ -105,7 +101,7 @@ def test_read_cartesian_positions_from_outcar(
     known_last_position: NDArray[np.float64],
 ) -> None:
     """test"""
-    cartesian_positions = vasp_utils._read_cartesian_positions_from_outcar(  # pylint: disable=protected-access
+    cartesian_positions = vasp_utils._read_cartesian_positions_from_outcar(
         outcar_file_fixture, EPS_OUTCAR_NUM_ATOMS
     )
 
@@ -131,7 +127,7 @@ def test_read_fractional_positions_from_outcar(
     known_last_position: NDArray[np.float64],
 ) -> None:
     """test"""
-    fractional_positions = vasp_utils._read_fractional_positions_from_outcar(  # pylint: disable=protected-access
+    fractional_positions = vasp_utils._read_fractional_positions_from_outcar(
         outcar_file_fixture, EPS_OUTCAR_NUM_ATOMS
     )
 
@@ -162,11 +158,7 @@ def test_read_polarizability_from_outcar(
 ) -> None:
     """test"""
 
-    polarizability = (
-        vasp_utils._read_polarizability_from_outcar(  # pylint: disable=protected-access
-            outcar_file_fixture
-        )
-    )
+    polarizability = vasp_utils._read_polarizability_from_outcar(outcar_file_fixture)
 
     assert np.isclose(polarizability, known_polarizability).all()
 
@@ -201,7 +193,5 @@ def test_read_lattice_from_outcar(
     outcar_file_fixture: TextIO, known_lattice: NDArray[np.float64]
 ) -> None:
     """test"""
-    result = vasp_utils._read_lattice_from_outcar(  # pylint: disable=protected-access
-        outcar_file_fixture
-    )
+    result = vasp_utils._read_lattice_from_outcar(outcar_file_fixture)
     assert np.isclose(result, known_lattice).all()