Merge branch 'cleanup'

Author: aradi

.appveyor.yml

@@ -0,0 +1,22 @@
+name: CI
+on: [push, pull_request]
+
+jobs:
+  test-new:
+
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v2
+
+    - uses: actions/setup-python@v1
+      with:
+        python-version: '3.x'
+
+    - name: Install requirements (PIP)
+      run: pip3 install pytest sphinx
+
+    - name: Run test pytest
+      run: python3 -m pytest
+
+    - name: Run doctest
+      run: cd docs; make doctest

.github/workflows/ci.yml

@@ -0,0 +1,14 @@
+==========
+Change Log
+==========
+
+
+Unreleased
+==========
+
+Added
+-----
+
+* Basic functionality to manipulate HSD-data in Python.
+
+* Pip installation

CHANGELOG.rst

@@ -1,4 +1,4 @@
-Copyright (c) 2011-2020  DFTB+ developers group
+Copyright (c) 2011-2021  DFTB+ developers group
 
 All rights reserved.
 

LICENSE

@@ -1,33 +1,43 @@
-************************************
-HSD — Human-friendly Structured Data
-************************************
+**********************************************
+HSD — Make your structured data human friendly
+**********************************************
 
-This Python package contains utilities to read and write files in
-the Human-friendly Structured Data (HSD) format.
+This package contains utilities to read and write files in the Human-friendly
+Structured Data (HSD) format.
 
-It is licensed under the *BSD 2-clause license*.
+The HSD-format is very similar to both JSON and YAML, but tries to minimize the
+effort for **humans** to read and write it. It ommits special characters as much
+as possible (in contrast to JSON) and is not indentation dependent (in contrast
+to YAML). It was developed originally as the input format for the scientific
+simulation tool (`DFTB+ <https://github.com/dftbplus/dftbplus>`_), but is
+of general purpose. Data stored in HSD can be easily mapped to a subset of JSON
+or XML and vica versa.
+
+Detailed `documentation <https://hsd-python.readthedocs.io/>`_ can be found on
+`Read the Docs <https://hsd-python.readthedocs.io/>`_.
 
 
 Installation
 ============
 
-To install the python package in development mode use
+The package can be installed via conda-forge::
 
-.. code::
+  conda install hsd-python
 
-   pip install -e src
+Alternatively, the package can be downloaded and installed via pip into the
+active Python interpreter (preferably using a virtual python environment) by ::
 
+  pip install hsd
+
+or into the user space issueing ::
+
+  pip install --user hsd
 
-The HSD format
-==============
 
-The HSD-format is very similar to both JSON and XML, but tries to minimize the
-effort for humans to read and write it. It ommits special characters as much as
-possible but (in contrast to YAML for example) is not indentation dependent.
+Quick tutorial
+==============
 
-It was developed originally as the input format for a scientific simulation tool
-(`DFTB+ <https://github.com/dftbplus/dftbplus>`_), but is absolutely general. A
-typical input written in HSD looks like ::
+A typical, self-explaining input written in HSD looks like ::
 
   driver {
     conjugate_gradients {
@@ -45,11 +55,13 @@ typical input written in HSD looks like ::
       }
       filling {
         fermi {
-          temperature [kelvin] = 1e-8
+          # This is comment which will be ignored
+          # Note the attribute (unit) of the field below
+          temperature [kelvin] = 100
         }
       }
       k_points_and_weights {
-        supercell_folding = {
+        supercell_folding {
           2   0   0
           0   2   0
           0   0   2
@@ -59,13 +71,56 @@ typical input written in HSD looks like ::
     }
   }
 
-Content in HSD format can be represented as JSON. Content in JSON format can
-similarly be represented as HSD, provided it satisfies one restriction for
-arrays: Either all elements of an array must be objects or none of them. (This
-allows for a clear separation of structure and data and allows for the very
-simple input format.)
+The above input can be parsed into a Python dictionary with::
+
+  import hsd
+  hsdinput = hsd.load("test.hsd")
+
+The dictionary ``hsdinput`` will then look as::
+
+  {
+      "driver": {
+          "conjugate_gradients" {
+              "moved_atoms": [1, 2, "7:19"],
+              "max_steps": 100
+          }
+      },
+      "hamiltonian": {
+          "dftb": {
+              "scc": True,
+              "scc_tolerance": 1e-10,
+              "mixer": {
+                  "broyden": {}
+              },
+              "filling": {
+                  "fermi": {
+                      "temperature": 100,
+                      "temperature.attrib": "kelvin"
+                  }
+              }
+              "k_points_and_weights": {
+                  "supercell_folding": [
+                      [2, 0, 0],
+                      [0, 2, 0],
+                      [0, 0, 2],
+                      [0.5, 0.5, 0.5]
+                  ]
+              }
+          }
+      }
+  }
+
+Being a simple Python dictionary, it can be easily queried and manipulated in
+Python ::
+
+  hsdinput["driver"]["conjugate_gradients"]["max_steps"] = 200
+
+and then stored again in HSD format ::
+
+    hsd.dump(hsdinput, "test2.hsd")
+
+
+License
+========
 
-Content in HSD format can be represented as XML (DOM-tree). Likewise content in
-XML can be converted to HSD, provided it satisfies the restriction that every
-child has either data (text) or further children, but never both of
-them. (Again, this ensures the simplicity of the input format.)
+The hsd-python package is licensed under the `BSD 2-clause license <LICENSE>`_.

README.rst

@@ -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/Makefile

@@ -0,0 +1,33 @@
+*****************
+API documentation
+*****************
+
+.. testsetup::
+
+    import hsd
+
+
+High level routines
+===================
+
+.. autofunction:: hsd.load_string
+
+.. autofunction:: hsd.load
+
+.. autofunction:: hsd.dump_string
+
+.. autofunction:: hsd.dump
+
+
+
+Lower level building blocks
+===========================
+
+.. autoclass:: hsd.HsdParser
+    :members:
+
+.. autoclass:: hsd.HsdEventHandler
+    :members:
+
+.. autoclass:: hsd.HsdDictBuilder
+    :members:

docs/api.rst

@@ -0,0 +1,60 @@
+# 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('../src'))
+
+# -- Project information -----------------------------------------------------
+
+project = 'hsd-python'
+copyright = '2021, DFTB+ developers group'
+author = 'DFTB+ developers group'
+
+# 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.doctest',
+    'sphinx.ext.napoleon'
+]
+
+autodoc_member_order = 'bysource'
+
+# 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 = 'alabaster'
+html_theme = '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']

docs/conf.py

@@ -0,0 +1,14 @@
+.. hsd-python documentation master file, created by
+   sphinx-quickstart on Mon Sep 13 11:38:29 2021.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+########################
+HSD-python documentation
+########################
+
+.. toctree::
+   :maxdepth: 2
+
+   introduction
+   api