add documentation (#748)

* initial docs

* add rtd info

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.readthedocs.yaml

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+version: 2
+
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.12"
+  jobs:
+    post_create_environment:
+      # Install poetry
+      # https://python-poetry.org/docs/#installing-manually
+      - pip install poetry
+    post_install:
+      # Install dependencies with 'docs' dependency group
+      # https://python-poetry.org/docs/managing-dependencies/#dependency-groups
+      # VIRTUAL_ENV needs to be set manually for now.
+      # See https://github.com/readthedocs/readthedocs.org/pull/11152/
+      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install --with docs
+
+sphinx:
+  configuration: docs/source/conf.py

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
+
+import zndraw
+
+project = "ZnDraw"
+copyright = "2024, Fabian Zills"
+author = "Fabian Zills"
+release = zndraw.__version__
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = []
+
+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 = "furo"
+html_static_path = ["_static"]

docs/source/index.rst

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+ZnDraw documentation
+====================
+
+A python-first visualisation and editing tool for atomic structures.
+
+Installation
+------------
+
+ZnDraw can be installed via pip:
+
+.. code:: console
+
+   $ pip install zndraw
+
+Usage
+-----
+You can use the command line interface to visualise atomic structures.
+ZnDraw uses a local web server to display the visualisation and runs in your default web browser.
+You can use port forwarding to access the visualisation from a remote machine.
+
+.. code:: console
+
+      $ zndraw file.xyz
+
+
+.. toctree::
+   :maxdepth: 2
+   :hidden:
+
+   python-api

docs/source/python-api.rst

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+Python interface
+================
+
+The ``zndraw`` package provides a Python interface to interact with the visualisation tool.
+To use this API, you need to have a running instance of the ZnDraw web server.
+
+.. note::
+
+    You can run a local webserver by using the command line interface.
+
+    .. code:: console
+
+        $ zndraw file.xyz --port 1234
+
+
+.. code:: python
+
+    from zndraw import ZnDraw
+
+    vis = ZnDraw(url="http://localhost:1234", token="c91bb84f")
+
+
+.. note::
+
+    In ZnDraw each visualisation is associated with a unique token.
+    You find this token in the URL of the visualisation.
+    This token can be used to interact with the visualisation using the Python API.
+    Additionally, you can use the token to share the visualisation with others or view
+    the visualisation from different angles in different browser tabs.
+
+
+The ``vis`` object provides a Python interface to interact with the visualisation.
+Most basically, it behaves like a Python list of `ase.Atoms <https://wiki.fysik.dtu.dk/ase/ase/atoms.html>`_ objects.
+Modifying the list will update the visualisation in real-time.
+
+.. code:: python
+
+    import ase.io as aio
+
+    frames = aio.read("file.xyz", index=":")
+    vis.extend(frames)