Merge pull request #57 from pyiron/docs

First version of the documentation

.ci_support/environment-docs.yml

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+channels:
+- conda-forge
+dependencies:
+  - nbsphinx
+  - sphinx
+  - myst-parser
+  - numpy
+  - ase =3.22.1
+  - coverage
+  - numpy =1.26.0
+  - scipy =1.11.3
+  - spglib =2.1.0
+  - phonopy =2.20.0
+  - structuretoolkit =0.0.11
+  - seekpath =2.1.0
+  - lammps =2023.08.02
+  - pandas =2.1.3
+  - pylammpsmpi =0.2.5
+  - jinja2 =3.1.2

.readthedocs.yml

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+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+build:
+  os: "ubuntu-20.04"
+  tools:
+    python: "mambaforge-4.10"
+
+# 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: []
+
+# Install pyiron from conda
+conda:
+  environment: .ci_support/environment-docs.yml
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  install:
+    - method: pip
+      path: .

docs/Makefile

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+# 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     = source
+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/make.bat

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+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%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.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/conf.py

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+# 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
+
+project = 'atomistics'
+copyright = '2023, Jan Janssen'
+author = 'Jan Janssen'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = ["myst_parser", 'sphinx.ext.autodoc', 'sphinx.ext.napoleon']
+
+templates_path = ['_templates']
+exclude_patterns = []
+
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'alabaster'
+html_static_path = ['_static']
+
+
+# -- Generate API documentation ----------------------------------------------
+# https://www.sphinx-doc.org/en/master/man/sphinx-apidoc.html
+
+from sphinx.ext.apidoc import main
+main(['-e', '-o', 'apidoc', '../../atomistics/', '--force'])

docs/source/index.rst

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+====================================================================
+atomistics - Interfaces for atomistic simulation codes and workflows
+====================================================================
+
+:Author:  Jan Janssen
+:Contact: [email protected]
+
+First version of the documentation for the :code:`atomistics` package.
+
+
+Documentation
+-------------
+
+.. toctree::
+   :maxdepth: 2
+
+   installation
+   simulationcodes
+   materialproperties
+
+* :ref:`modindex`

docs/source/installation.md

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+# Installation 
+## pypi-based Installation 
+```
+pip install atomistics
+```
+
+### GPAW
+```
+pip install atomistics[gpaw]
+```
+
+### LAMMPS
+```
+pip install atomistics[lammps]
+```
+
+### Phonopy
+```
+pip install atomistics[phonopy]
+```
+
+## conda-based Installation 
+```
+conda install -c conda-forge atomistics
+```
+
+### Ab-init 
+```
+conda install -c conda-forge abinit
+```
+
+### GPAW 
+```
+conda install -c conda-forge gpaw
+```
+
+### LAMMPS 
+```
+conda install -c conda-forge lammps pylammpsmpi jinja2 pandas
+```
+
+### Quantum Espresso 
+```
+conda install -c conda-forge qe
+```
+
+### Siesta
+```
+conda install -c conda-forge siesta
+```
+
+### Phonopy
+```
+conda install -c phonopy seekpath structuretoolkit
+```