Add documentation for main modules (orest-d#10)

Establish a sphinx compatible documentation of the API of all modules. The goal is to document all functions a user might use not the inner workings of the classes.

.gitignore

@@ -1,3 +1,8 @@
+# autogenerated by dephell
+setup.py
+# autogenerated by poetry2conda
+py4vasp-env.yml
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS ?=
+SPHINXBUILD ?= sphinx-build
+SOURCEDIR = .
+BUILDDIR = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+ @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+ @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/conf.py

@@ -0,0 +1,57 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# 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.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = "py4vasp"
+copyright = "2020, Vasp Software GmbH"
+author = "Vasp Software GmbH"
+
+# The full version, including alpha/beta/rc tags
+release = "0.1"
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = ["sphinx.ext.autodoc", "sphinx.ext.napoleon"]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages. See the documentation for
+# a list of builtin themes.
+#
+html_theme = "nature"
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ["_static"]
+
+# remove common py4vasp prefix from index
+modindex_common_prefix = ["py4vasp."]

docs/data_api.rst

@@ -0,0 +1,6 @@
+Refining the raw data
+=====================
+
+.. automodule:: py4vasp.data
+ :members:
+ :undoc-members:

docs/exceptions_api.rst

@@ -0,0 +1,6 @@
+Exceptions
+==========
+
+.. automodule:: py4vasp.exceptions
+ :members:
+ :undoc-members:

docs/index.rst

@@ -0,0 +1,29 @@
+py4vasp
+=======
+
+*py4vasp* is a python interface to extract data from Vasp calculations. It is
+intended mainly to get a quick look at the data and provide functionality to
+export it into common formats that can be used by other more sophisticated
+postprocessing tools. A second domain of application is for people that want to
+write python scripts based on the data calculated by Vasp. This tool interfaces
+directly with the new HDF5 file format and thereby avoids parsing issues
+associated with the XML or OUTCAR files.
+
+For these two groups of users, we provide a different level of access. The
+simple routines used in the tutorials will read the data from the file directly
+and then generate the requested plot. For script developers, we provide an
+expert interface were the data is lazily loaded as needed with some greater
+flexibility when the data file is opened and closed.
+
+.. toctree::
+ :maxdepth: 2
+ :caption: Contents:
+
+ modules
+
+Indices and tables
+------------------
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+ set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+ echo.
+ echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+ echo.installed, then set the SPHINXBUILD environment variable to point
+ echo.to the full path of the 'sphinx-build' executable. Alternatively you
+ 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/
+ exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/modules.rst

@@ -0,0 +1,10 @@
+API documentation
+=================
+
+.. toctree::
+ :maxdepth: 2
+ :caption: Modules:
+
+ raw_api
+ data_api
+ exceptions_api

docs/raw_api.rst

@@ -0,0 +1,6 @@
+Extracting the raw data
+=======================
+
+.. automodule:: py4vasp.raw
+ :members:
+ :undoc-members: