documentation pass

README.md

@@ -1,6 +1,6 @@
 <div align="center">
-  <img width="300" src="docs/logo_dark.png#gh-dark-mode-only">
-  <img width="300" src="docs/logo.png#gh-light-mode-only">
+  <img width="300" src="docs/source/_static/logo_dark.png#gh-dark-mode-only">
+  <img width="300" src="docs/source/_static/logo.png#gh-light-mode-only">
 </div>
 
 -------

cspell.json

@@ -11,7 +11,9 @@
         "argmax",
         "automodule",
         "AVOGADROS",
+        "docstrings",
         "dtype",
+        "EAFP",
         "EATF",
         "equil",
         "fft",
@@ -23,6 +25,7 @@
         "Grumet",
         "ifft",
         "interp",
+        "LBYL",
         "lexsort",
         "linalg",
         "linewidth",
@@ -35,6 +38,7 @@
         "ndim",
         "newaxis",
         "NIONS",
+        "numpy",
         "outcar",
         "outcars",
         "pathify",
@@ -44,6 +48,7 @@
         "POTCAR",
         "pylint",
         "pytest",
+        "quickstart",
         "Raman",
         "ramannoodle",
         "repr",
@@ -53,6 +58,7 @@
         "timestep",
         "timesteps",
         "toctree",
+        "undoc",
         "VASP",
         "vasprun",
         "VRHFIN",

docs/source/conf.py

@@ -49,5 +49,10 @@
 
 html_theme = 'furo'
 html_static_path = ['_static']
+html_theme_options = {
+    "light_logo": "logo.png",
+    "dark_logo": "logo_dark.png",
+    "sidebar_hide_name": True,
+}
 
 sys.path.insert(0, os.path.abspath('../../'))

docs/source/dev guide.rst

@@ -45,12 +45,12 @@ In no particular order, here are some guidelines that are followed throughout ra
 
 * All public-facing functions should raise descriptive TypeError and ValueError exceptions when invalid arguments are provided. These sorts of exceptions should not be documented in the docstring.
 
-* All array arguments should be numpy arrays. This should be enforced, when appropriate, through exceptions.
+* All array arguments containing floats should be numpy arrays. This should be enforced, when appropriate, through exceptions.
 
 * Docstring descriptions for array arguments should provide a dimension and shape. Uppercase letters can be used for cases where shape is variable. For example, "4D array with shape (M,N,3) where M is ... and N is ...".
 
-* Unless otherwise noted, fractional coordinates are always used. Variables for cartesian coordinates always have "cartesian\_" appended.
+* Unless otherwise noted, fractional coordinates are always used. Variables that are in Cartesian coordinates always have "cartesian\_" appended.
 
 * Use classes widely. Sometimes, a regular function is all that is needed!
 
-* With IO functions, ramannoodle attempts to strike a balance between simplicity and flexibility. `import ramannoodle.io` provides access to generic file readers and writers for a variety of file formats. However, these generic routines do not offer much customization but do offer simplicity. Additional options can be accessed in the code-specific packages, such as `import ramannoodle.io.vasp.poscar`. Use of these is preferred.
+* With IO functions, ramannoodle attempts to strike a balance between simplicity and flexibility. ``import ramannoodle.io.generic`` provides access to generic file readers and writers for a variety of file formats. These generic routines are rather inflexible but are necessary for certain functionality. Users are strongly encouraged to use functions contained in the code-specific IO packages, such as ``import ramannoodle.io.vasp.poscar``.

docs/source/generated/ramannoodle.dynamics.rst

@@ -1,10 +1,26 @@
 ramannoodle.dynamics package
 ============================
 
-Module contents
----------------
-
 .. automodule:: ramannoodle.dynamics
    :members:
    :undoc-members:
    :show-inheritance:
+
+Submodules
+----------
+
+ramannoodle.dynamics.abstract module
+------------------------------------
+
+.. automodule:: ramannoodle.dynamics.abstract
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+ramannoodle.dynamics.phonon module
+----------------------------------
+
+.. automodule:: ramannoodle.dynamics.phonon
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/generated/ramannoodle.io.rst

@@ -1,6 +1,11 @@
 ramannoodle.io package
 ======================
 
+.. automodule:: ramannoodle.io
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 Subpackages
 -----------
 
@@ -12,18 +17,18 @@ Subpackages
 Submodules
 ----------
 
-ramannoodle.io.io\_utils module
--------------------------------
+ramannoodle.io.generic module
+-----------------------------
 
-.. automodule:: ramannoodle.io.io_utils
+.. automodule:: ramannoodle.io.generic
    :members:
    :undoc-members:
    :show-inheritance:
 
-Module contents
----------------
+ramannoodle.io.io\_utils module
+-------------------------------
 
-.. automodule:: ramannoodle.io
+.. automodule:: ramannoodle.io.io_utils
    :members:
    :undoc-members:
    :show-inheritance:

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

@@ -1,21 +1,26 @@
 ramannoodle.io.vasp package
 ===========================
 
+.. automodule:: ramannoodle.io.vasp
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 Submodules
 ----------
 
-ramannoodle.io.vasp.vasp\_utils module
---------------------------------------
+ramannoodle.io.vasp.outcar module
+---------------------------------
 
-.. automodule:: ramannoodle.io.vasp.vasp_utils
+.. automodule:: ramannoodle.io.vasp.outcar
    :members:
    :undoc-members:
    :show-inheritance:
 
-Module contents
----------------
+ramannoodle.io.vasp.poscar module
+---------------------------------
 
-.. automodule:: ramannoodle.io.vasp
+.. automodule:: ramannoodle.io.vasp.poscar
    :members:
    :undoc-members:
    :show-inheritance:

docs/source/generated/ramannoodle.polarizability.rst

@@ -1,37 +1,34 @@
 ramannoodle.polarizability package
 ==================================
 
-Submodules
-----------
-
-ramannoodle.polarizability.art module
--------------------------------------
-
-.. automodule:: ramannoodle.polarizability.art
+.. automodule:: ramannoodle.polarizability
    :members:
    :undoc-members:
    :show-inheritance:
 
-ramannoodle.polarizability.interpolation module
------------------------------------------------
+Submodules
+----------
 
-.. automodule:: ramannoodle.polarizability.interpolation
+ramannoodle.polarizability.abstract module
+------------------------------------------
+
+.. automodule:: ramannoodle.polarizability.abstract
    :members:
    :undoc-members:
    :show-inheritance:
 
-ramannoodle.polarizability.polarizability\_utils module
--------------------------------------------------------
+ramannoodle.polarizability.art module
+-------------------------------------
 
-.. automodule:: ramannoodle.polarizability.polarizability_utils
+.. automodule:: ramannoodle.polarizability.art
    :members:
    :undoc-members:
    :show-inheritance:
 
-Module contents
----------------
+ramannoodle.polarizability.interpolation module
+-----------------------------------------------
 
-.. automodule:: ramannoodle.polarizability
+.. automodule:: ramannoodle.polarizability.interpolation
    :members:
    :undoc-members:
    :show-inheritance:

docs/source/generated/ramannoodle.rst

@@ -1,6 +1,11 @@
 ramannoodle package
 ===================
 
+.. automodule:: ramannoodle
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 Subpackages
 -----------
 
@@ -31,11 +36,3 @@ ramannoodle.globals module
    :members:
    :undoc-members:
    :show-inheritance:
-
-Module contents
----------------
-
-.. automodule:: ramannoodle
-   :members:
-   :undoc-members:
-   :show-inheritance:

docs/source/generated/ramannoodle.spectrum.rst

@@ -1,21 +1,26 @@
 ramannoodle.spectrum package
 ============================
 
+.. automodule:: ramannoodle.spectrum
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 Submodules
 ----------
 
-ramannoodle.spectrum.spectrum\_utils module
--------------------------------------------
+ramannoodle.spectrum.raman module
+---------------------------------
 
-.. automodule:: ramannoodle.spectrum.spectrum_utils
+.. automodule:: ramannoodle.spectrum.raman
    :members:
    :undoc-members:
    :show-inheritance:
 
-Module contents
----------------
+ramannoodle.spectrum.spectrum\_utils module
+-------------------------------------------
 
-.. automodule:: ramannoodle.spectrum
+.. automodule:: ramannoodle.spectrum.spectrum_utils
    :members:
    :undoc-members:
    :show-inheritance:

docs/source/generated/ramannoodle.symmetry.rst

@@ -1,21 +1,26 @@
 ramannoodle.symmetry package
 ============================
 
+.. automodule:: ramannoodle.symmetry
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 Submodules
 ----------
 
-ramannoodle.symmetry.symmetry\_utils module
--------------------------------------------
+ramannoodle.symmetry.structural module
+--------------------------------------
 
-.. automodule:: ramannoodle.symmetry.symmetry_utils
+.. automodule:: ramannoodle.symmetry.structural
    :members:
    :undoc-members:
    :show-inheritance:
 
-Module contents
----------------
+ramannoodle.symmetry.structural\_utils module
+---------------------------------------------
 
-.. automodule:: ramannoodle.symmetry
+.. automodule:: ramannoodle.symmetry.structural_utils
    :members:
    :undoc-members:
    :show-inheritance:

docs/source/index.rst

@@ -6,11 +6,11 @@
 ramannoodle documentation
 =========================
 
-**ramannoodle** is a Python API for calculating Raman spectra from first principles calculations in an efficient, flexible, and transparent way.
+**Ramannoodle** is a Python API for calculating Raman spectra from first principles calculations in an efficient, flexible, and transparent way.
 
 .. note::
 
-   ramannoodle is currently in alpha.
+   Ramannoodle is currently in alpha.
 
 Contents
 --------
@@ -21,5 +21,5 @@ Contents
 
    introduction
    tutorials
-   generated/api
+   API <generated/ramannoodle>
    dev guide