documentation pass

.gitignore

@@ -265,3 +265,4 @@ $RECYCLE.BIN/
 
 # End of https://www.toptal.com/developers/gitignore/api/macos,linux,windows,python,visualstudiocode
 session
+test/Testing.ipynb

.pre-commit-config.yaml

@@ -40,6 +40,7 @@ repos:
           [
             pytest,
           ]
+        exclude: "conf.py"
 -   repo: https://github.com/pycqa/flake8
     rev: '7.1.0'  # pick a git hash / tag to point to
     hooks:

cspell.json

@@ -6,10 +6,13 @@
     "dictionaryDefinitions": [],
     "dictionaries": [],
     "words": [
+        "anharmonic",
         "argmax",
+        "automodule",
         "AVOGADROS",
         "dtype",
         "EATF",
+        "equil",
         "fft",
         "fftfreq",
         "fftpack",
@@ -19,7 +22,10 @@
         "ifft",
         "interp",
         "linalg",
+        "linewidth",
         "LLZO",
+        "mathtext",
+        "matplotlib",
         "ndarray",
         "ndim",
         "newaxis",
@@ -42,7 +48,8 @@
         "VASP",
         "VRHFIN",
         "wavenumber",
-        "wavenumbers"
+        "wavenumbers",
+        "wspace"
     ],
     "ignoreWords": [],
     "import": []

docs/Examples - ramannoodle.ipynb

@@ -57,7 +57,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# phononsepseps_OUTCAR contains phonons (duh) as well as the equilibrium TiO2 structure.\n",
+    "# phonons_OUTCAR contains phonons (duh) as well as the equilibrium TiO2 structure.\n",
     "phonon_outcar = \"../test/data/TiO2/phonons_OUTCAR\"\n",
     "\n",
     "# Read the phonons\n",
@@ -287,7 +287,7 @@
     "\n",
     "\n",
     "for axis_i, (i,j) in enumerate([(0,0),(1,1),(2,2),(0,1),(0,2),(1,2)]):\n",
-    "    axis = axes[axis_i]\n",
+    "    axis = axes[axis_i] # type: ignore\n",
     "    for interp,sign,color in zip(target_interps,signs,['pink', 'red', 'orange']):\n",
     "        if sign < 0:\n",
     "            print('negative sign')\n",

docs/make.bat

@@ -10,8 +10,6 @@ if "%SPHINXBUILD%" == "" (
 set SOURCEDIR=source
 set BUILDDIR=build
 
-if "%1" == "" goto help
-
 %SPHINXBUILD% >NUL 2>NUL
 if errorlevel 9009 (
 	echo.
@@ -21,10 +19,12 @@ if errorlevel 9009 (
 	echo.may add the Sphinx directory to PATH.
 	echo.
 	echo.If you don't have Sphinx installed, grab it from
-	echo.http://sphinx-doc.org/
+	echo.https://www.sphinx-doc.org/
 	exit /b 1
 )
 
+if "%1" == "" goto help
+
 %SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
 goto end
 

docs/source/conf.py

@@ -1,26 +1,33 @@
-"""Configuration file for the Sphinx documentation builder."""
+"""Sphinx conf.py."""
+# pylint: skip-file
+# flake-8: noqa
+# cspell: disable
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
 import sys
 import os
 
-# -- Project information
-
 project = 'ramannoodle'
-copyright = "2023-present Willis O'Leary"
+copyright = "2024, Willis O'Leary"
 author = "Willis O'Leary"
+release = 'v.0.1.1-alpha'
 
-release = 'dev'
-version = 'dev'
-
-# -- General configuration
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
 extensions = [
-    'sphinx.ext.duration',
-    'sphinx.ext.doctest',
     'sphinx.ext.autodoc',
     'sphinx.ext.autosummary',
     'sphinx.ext.intersphinx',
     'sphinx.ext.napoleon',
-    'sphinx_rtd_theme',
+    'nbsphinx',
+    'IPython.sphinxext.ipython_console_highlighting'
 ]
 autodoc_typehints = 'description'
 
@@ -33,15 +40,14 @@
 intersphinx_disabled_domains = ['std']
 
 templates_path = ['_templates']
+exclude_patterns = []
 
-# -- Options for HTML output
+language = 'Python'
 
-html_theme = 'sphinx_rtd_theme'
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
-# -- Options for EPUB output
-epub_show_urls = 'footnote'
+html_theme = 'furo'
+html_static_path = ['_static']
 
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
 sys.path.insert(0, os.path.abspath('../../'))

docs/source/generated/api.rst

@@ -0,0 +1,41 @@
+Public API
+===================
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   ramannoodle.dynamics
+   ramannoodle.io
+   ramannoodle.polarizability
+   ramannoodle.spectrum
+   ramannoodle.symmetry
+
+Submodules
+----------
+
+ramannoodle.exceptions module
+-----------------------------
+
+.. automodule:: ramannoodle.exceptions
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+ramannoodle.globals module
+--------------------------
+
+.. automodule:: ramannoodle.globals
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: ramannoodle
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/generated/ramannoodle.dynamics.rst

@@ -1,12 +1,10 @@
-ramannoodle.dynamics
-====================
+ramannoodle.dynamics package
+============================
 
-.. automodule:: ramannoodle.dynamics
-
-
-   .. rubric:: Classes
+Module contents
+---------------
 
-   .. autosummary::
-
-      Dynamics
-      Phonons
+.. automodule:: ramannoodle.dynamics
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/generated/ramannoodle.io.rst

@@ -1,13 +1,29 @@
-ramannoodle.io
-==============
+ramannoodle.io package
+======================
 
-.. automodule:: ramannoodle.io
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   ramannoodle.io.vasp
 
+Submodules
+----------
 
-   .. rubric:: Functions
+ramannoodle.io.io\_utils module
+-------------------------------
 
-   .. autosummary::
+.. automodule:: ramannoodle.io.io_utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
 
-      read_phonons
-      read_positions_and_polarizability
-      read_structural_symmetry
+Module contents
+---------------
+
+.. automodule:: ramannoodle.io
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/generated/ramannoodle.io.vasp.rst

@@ -1,13 +1,21 @@
-ramannoodle.io.vasp
-===================
+ramannoodle.io.vasp package
+===========================
 
-.. automodule:: ramannoodle.io.vasp
+Submodules
+----------
 
+ramannoodle.io.vasp.vasp\_utils module
+--------------------------------------
 
-   .. rubric:: Functions
+.. automodule:: ramannoodle.io.vasp.vasp_utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
 
-   .. autosummary::
+Module contents
+---------------
 
-      read_phonons_from_outcar
-      read_positions_and_polarizability_from_outcar
-      read_structural_symmetry_from_outcar
+.. automodule:: ramannoodle.io.vasp
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/generated/ramannoodle.polarizability.rst

@@ -1,11 +1,29 @@
-ramannoodle.polarizability
-==========================
+ramannoodle.polarizability package
+==================================
 
-.. automodule:: ramannoodle.polarizability
+Submodules
+----------
+
+ramannoodle.polarizability.interpolation module
+-----------------------------------------------
 
+.. automodule:: ramannoodle.polarizability.interpolation
+   :members:
+   :undoc-members:
+   :show-inheritance:
 
-   .. rubric:: Classes
+ramannoodle.polarizability.polarizability\_utils module
+-------------------------------------------------------
 
-   .. autosummary::
+.. automodule:: ramannoodle.polarizability.polarizability_utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
 
-      PolarizabilityModel
+Module contents
+---------------
+
+.. automodule:: ramannoodle.polarizability
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/generated/ramannoodle.spectrum.rst

@@ -1,11 +1,21 @@
-ramannoodle.spectrum
-====================
+ramannoodle.spectrum package
+============================
 
-.. automodule:: ramannoodle.spectrum
+Submodules
+----------
 
+ramannoodle.spectrum.spectrum\_utils module
+-------------------------------------------
 
-   .. rubric:: Classes
+.. automodule:: ramannoodle.spectrum.spectrum_utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
 
-   .. autosummary::
+Module contents
+---------------
 
-      PhononRamanSpectrum
+.. automodule:: ramannoodle.spectrum
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/generated/ramannoodle.symmetry.rst

@@ -1,11 +1,21 @@
-ramannoodle.symmetry
-====================
+ramannoodle.symmetry package
+============================
 
-.. automodule:: ramannoodle.symmetry
+Submodules
+----------
 
+ramannoodle.symmetry.symmetry\_utils module
+-------------------------------------------
 
-   .. rubric:: Classes
+.. automodule:: ramannoodle.symmetry.symmetry_utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
 
-   .. autosummary::
+Module contents
+---------------
 
-      StructuralSymmetry
+.. automodule:: ramannoodle.symmetry
+   :members:
+   :undoc-members:
+   :show-inheritance: