switching to mkdocs + cleanup

CHANGELOG

-v 0.0.2
-
-1) added atomic_properites_lda2015 module and also updated periodictable to show heatmaps of atomic features of lda2015
-
-v 1.0.0
-
-1) added atomic_properties_webele module and corresponding methods to periodictable module to show heatmaps of atomic features accessible.
-2) Updated definition methods in atomic_properites_dft, atomic_properites_lda2015, atomic_properites_pymat, atomic_properites_matminer, atomic_properites_webele
-3) Updated html and pdf documentation to match latest version
-
-v 1.0.1
-
-1) updated python setup process
-2) updated package names according to PEP8
-3) got rid of deprecation warnings
-4)

CHANGELOG.md

+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+
+## v1.0.1
+
+- updated python setup process
+- updated package names according to PEP8
+- got rid of deprecation warnings
+
+
+## v1.0.0
+
+- added atomic_properties_webele module and corresponding methods to periodictable module to show heatmaps of atomic features accessible.
+- Updated definition methods in atomic_properites_dft, atomic_properites_lda2015, atomic_properites_pymat, atomic_properites_matminer, atomic_properites_webele
+- Updated html and pdf documentation to match latest version
+
+
+## v0.0.2
+
+- added atomic_properites_lda2015 module and also updated periodictable to show heatmaps of atomic features of lda2015

CONTRIBUTING.md

-Aakash Ashok Naik

LICENSE.txt

-MIT License
-
-Copyright (c) 2021 nomad-lab
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.

README.md

@@ -107,3 +107,39 @@ One can acess individually different properties using element symbol as followin
 To get a list of properties accessible one can just press Tab after typing in `webele.C.`
 
 Use symbol method from atomic_properties_webele module to acess property of interest of elements at once in similar manner as described for atomic_properties_dft module above.
+
+
+
+
+## Setup dev environment
+
+Setup a virtual environment and install the dependencies
+
+```bash
+pyenv local 3.9
+python -m venv .venv
+source .venv/bin/activate
+```
+
+Install the dependencies
+
+```bash
+pip install -r requirements.txt
+```
+```bash
+pip install  -e '.[docs,dev]'
+```
+
+
+### Update the dependencies for the development environment
+
+```bash
+pip-compile pyproject.toml
+pip-sync
+```
+
+## docs
+
+```bash
+mkdocs serve
+```

docs/Makefile

-# 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/atomicfeaturespackage.rst

-atomic-features-package package
-===============================
-
-Subpackages
------------
-
-.. toctree::
-
-   atomicproperties
-   metainfo
-
-

docs/atomicproperties.md

+## atomic_features_package.atomic_properties package
+
+### atomic_features_package.atomic_properties.atomic_properties_dft module
+
+::: atomic_features_package.atomic_properties.atomic_properties_dft
+
+### atomic_features_package.atomic_properties.atomic_properties_lda2015 module
+
+::: atomic_features_package.atomic_properties.atomic_properties_lda2015
+
+### atomic_features_package.atomic_properties.atomic_properties_matminer module
+
+::: atomic_features_package.atomic_properties.atomic_properties_matminer
+
+### atomic_features_package.atomic_properties.atomic_properties_pymat module
+
+::: atomic_features_package.atomic_properties.atomic_properties_pymat
+
+### atomic_features_package.atomic_properties.periodictable module
+
+::: atomic_features_package.atomic_properties.periodictable
+

docs/atomicproperties.rst

-atomic\_features\_package.atomic\_properties package
-====================================================
-
-atomic\_features\_package.atomic\_properties.atomic\_properties\_dft module
----------------------------------------------------------------------------
-
-.. automodule:: atomic_features_package.atomic_properties.atomic_properties_dft
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-atomic\_features\_package.atomic\_properties.atomic\_properties\_lda2015 module
--------------------------------------------------------------------------------
-
-.. automodule:: atomic_features_package.atomic_properties.atomic_properties_lda2015
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-atomic\_features\_package.atomic\_properties.atomic\_properties\_matminer module
---------------------------------------------------------------------------------
-
-.. automodule:: atomic_features_package.atomic_properties.atomic_properties_matminer
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-atomic\_features\_package.atomic\_properties.atomic\_properties\_pymat module
------------------------------------------------------------------------------
-
-.. automodule:: atomic_features_package.atomic_properties.atomic_properties_pymat
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-atomic\_features\_package.atomic\_properties.periodictable module
------------------------------------------------------------------
-
-.. automodule:: atomic_features_package.atomic_properties.periodictable
-   :members:
-   :undoc-members:
-   :show-inheritance:
-

docs/conf.py

-# 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 = 'atomic-features-package'
-copyright = '2021, Aakash Naik'
-author = 'Aakash Naik'
-
-
-# -- 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','recommonmark']
-
-# 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 = 'bizstyle'#haiku'#'sphinx_rtd_theme'
-
-# 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']
-
-latex_elements = {
-  'extraclassoptions': 'openany,oneside'
-}

docs/getting_started.md

+--8<-- "README.md"

docs/index.md

+# Welcome to atomic-features-package
+
+
+## atomic-features-package package
+
+### Subpackages
+
+::: atomic_features_package.atomic_properties
+::: atomic_features_package.metainfo
\ No newline at end of file

docs/index.rst

-.. atomic-features-package documentation master file, created by
-   sphinx-quickstart on Wed Apr  7 09:39:02 2021.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
-
-Welcome to atomic-features-package's documentation!
-===================================================
-
-.. toctree::
-   :maxdepth: 2
-   :caption: Contents:
-
-   atomicfeaturespackage.rst
-
-
-
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`

docs/make.bat

-@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/metainfo.md

+## atomic_features_package.metainfo package
+
+
+### atomic_features_package.metainfo.metainfo module
+
+::: atomic_features_package.metainfo.metainfo
+

docs/metainfo.rst

-atomic\_features\_package.metainfo package
-==========================================
-
-
-atomic\_features\_package.metainfo.metainfo module
---------------------------------------------------
-
-.. automodule:: atomic_features_package.metainfo.metainfo
-   :members:
-

pyproject.toml

 [build-system]
-requires = ["setuptools"]
-build-backend = "setuptools.build_meta"
+requires = ['setuptools']
+build-backend = 'setuptools.build_meta'
 
 [project]
-name = "atomic-features-package"
-version = "1.0.1"
-authors = [{ name = "Aakash Ashok Naik", email = "naik@fhi-berlin.mpg.de" }]
-description = "Unified package to access atomic properites of elements"
-readme = "README.md"
-requires-python = ">=3.6"
-license = { file = "LICENSE.txt" }
+name = 'atomic-features-package'
+version = '2.0'
+authors = [{ name = 'Aakash Ashok Naik', email = 'naik@fhi-berlin.mpg.de' }]
+description = 'Unified package to access atomic properites of elements'
+readme = 'README.md'
+requires-python = '>=3.9'
+license = {text = 'Apache-2.0'}
 classifiers = [
-    "Programming Language :: Python :: 3",
-    "License :: OSI Approved :: MIT License",
-    "Operating System :: OS Independent",
+    'Programming Language :: Python :: 3',
 ]
 dependencies = [
-    # "nomad-lab",
-    "numpy",
-    "pandas",
-    "mendeleev",
-    "bokeh",
-    "ipywidgets",
-    "typing",
-    "urllib3",
+    # 'nomad-lab',
+    'numpy',
+    'pandas',
+    'mendeleev',
+    'bokeh',
+    'ipywidgets',
+    'typing',
+    'urllib3',
 ]
 
-[project.optional-dependencies]
-docs = ["sphinx", "recommonmark"]
 
+[project.optional-dependencies]
+docs = ['mkdocs', 'mkdocs-material', 'mkdocstrings']
+dev = ['mypy']
 
 [project.urls]
-repository = "https://gitlab.mpcdf.mpg.de/nomad-lab/atomic-features-package"
+repository = 'https://gitlab.mpcdf.mpg.de/nomad-lab/atomic-features-package'