Merge branch 'stage-0.1' into release

Author: aradi

.codecov.yml

@@ -0,0 +1,14 @@
+# Codecov configuration to make it a bit less noisy
+coverage:
+  status:
+    patch: false
+    project:
+      default:
+        threshold: 50%
+comment:
+  layout: "header"
+  require_changes: false
+  branches: null
+  behavior: default
+  flags: null
+  paths: null

.github/workflows/ci.yml

@@ -0,0 +1,36 @@
+name: CI
+on: [push, pull_request]
+
+env:
+  HSD_PYTHON_VERSION: '0.1'
+
+jobs:
+  test:
+
+    runs-on: ubuntu-latest
+
+    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 numpy build
+
+    - name: Setup up root directory
+      run: echo "PACKAGE_ROOT=${PWD}/src" >> $GITHUB_ENV
+
+    - name: Build and install package
+      run: |
+        python -m build
+        pip install dist/hsd_python*.whl
+        python -c "import hsd; assert hsd.__version__ == '${HSD_PYTHON_VERSION}'"
+
+    - name: Run test pytest
+      run: python3 -m pytest
+
+    - name: Run doctest
+      run: cd docs; make doctest

.lgtm.yml

@@ -0,0 +1,12 @@
+# Configure LGTM for this package
+
+extraction:
+  python:  # Configure Python
+    python_setup:  # Configure the setup
+      version: 3  # Specify Version 3
+path_classifiers:
+  library:
+    - src/versioneer.py  # Set Versioneer.py to an external "library" (3rd party code)
+    - devtools/*
+  generated:
+    - src/hsd/_version.py

.travis.yml

@@ -0,0 +1,48 @@
+language: python
+
+# Run jobs on container-based infrastructure, can be overridden per job
+
+matrix:
+  include:
+    # Extra includes for OSX since python language is not available by default on OSX
+    - os: osx
+      language: generic
+      env: PYTHON_VER=3.6
+    - os: osx
+      language: generic
+      env: PYTHON_VER=3.7
+
+
+    # Pip can use Travis build-in Python
+    - os: linux
+      python: 3.6
+    - os: linux
+      dist: xenial  # Travis Trusty image does not have Python 3.7, Xenial does
+      python: 3.7
+
+
+before_install:
+    # Additional info about the build
+  - uname -a
+  - df -h
+  - ulimit -a
+
+    # Install the Python environment
+  - source devtools/travis-ci/before_install.sh
+  - python -V
+
+install:
+
+    # Install the package locally
+  - pip install -U pytest pytest-cov codecov
+  - pip install -e src/
+
+
+script:
+  - pytest -v --cov=hsd test/
+
+notifications:
+    email: false
+
+after_success:
+  - codecov

CHANGELOG.rst

@@ -0,0 +1,14 @@
+==========
+Change Log
+==========
+
+
+0.1
+===
+
+Added
+-----
+
+* Basic functionality to manipulate HSD-data in Python.
+
+* Pip installation

LICENSE

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

README.rst

@@ -1,23 +1,43 @@
-************************************
-HSD — Human-friendly Structured Data
-************************************
+**********************************************
+HSD — Make your structured data human friendly
+**********************************************
 
-This Python package contains utilities to write (and soon also to read) files in
-the Human-friendly Structured Data (HSD) format.
+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/>`_.
 
-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.
+Installation
+============
+
+The package can be installed via conda-forge::
+
+  conda install --channel "conda-forge" hsd-python
+
+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 ::
 
-It was developed originally developed as the input format for a scientific
-simulation tool (DFTB+), but is absolutely general. A typical input written in
-HSD would look like ::
+  pip install --user hsd
+
+
+Quick tutorial
+==============
+
+A typical, self-explaining input written in HSD looks like ::
 
   driver {
     conjugate_gradients {
@@ -35,11 +55,13 @@ HSD would look 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
@@ -49,12 +71,56 @@ HSD would look like ::
     }
   }
 
-Content in HSD format can be represented as JSON. Content in JSON format can be
-represented as HSD, provided it satisfies a 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). 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>`_.

devtools/set_version

@@ -0,0 +1,93 @@
+#!/usr/bin/env python3
+
+"""Sets a version number in all relevant project files"""
+
+import sys
+import re
+import os
+
+# The pattern the version number must satisfy
+VERSION_PATTERN = r'\d+\.\d+(?:\.\d+)?(?:-\w+)?'
+
+# List of (file name, search pattern, replacement pattern) tuples for all
+# the occurancies to be replaced.
+FILES_PATTERNS = [('src/hsd/__init__.py',
+                   r'^__version__\s*=\s*([\'"]){}\1'.format(VERSION_PATTERN),
+                   "__version__ = '{version}'"),
+                  ('docs/introduction.rst',
+                   r'hsd-python version[ ]*{}.'.format(VERSION_PATTERN),
+                   'hsd-python version {shortversion}.'),
+                  ('setup.cfg',
+                   r'version\s*=\s*{}'.format(VERSION_PATTERN),
+                   "version = {version}"),
+                  ('docs/conf.py',
+                   r'release\s*=\s*([\'"]){}\1'.format(VERSION_PATTERN),
+                   "release = '{version}'"),
+                  ('.github/workflows/ci.yml',
+                   r'HSD_PYTHON_VERSION:\s*([\'"]){}\1'.format(VERSION_PATTERN),
+                   "HSD_PYTHON_VERSION: '{version}'"),
+                 ]
+
+
+def main():
+    """Main script."""
+
+    if len(sys.argv) < 2:
+        sys.stderr.write("Missing version string\n")
+        sys.exit(1)
+
+    version, shortversion = _get_version_strings(sys.argv[1])
+    rootdir = os.path.join(os.path.dirname(sys.argv[0]), '..')
+    _replace_version_in_files(FILES_PATTERNS, rootdir, version, shortversion)
+    _replace_version_in_changelog(rootdir, version)
+
+
+def _get_version_strings(version):
+    """Returns version and the short version as string"""
+
+    match = re.match(VERSION_PATTERN, version)
+    if match is None:
+        print("Invalid version string")
+        sys.exit(1)
+
+    shortversion = '.'.join(version.split('.')[0:2])
+    return version, shortversion
+
+
+def _replace_version_in_files(files_patterns, rootdir, version, shortversion):
+    """Replaces version number in given files with given search/replacement patterns"""
+
+    for fname, regexp, repl in files_patterns:
+        fname = os.path.join(rootdir, fname)
+        print("Replacments in '{}': ".format(os.path.relpath(fname, rootdir)), end='')
+        fp = open(fname, 'r')
+        txt = fp.read()
+        fp.close()
+        replacement = repl.format(version=version, shortversion=shortversion)
+        newtxt, nsub = re.subn(regexp, replacement, txt, flags=re.MULTILINE)
+        print(nsub)
+        fp = open(fname, 'w')
+        fp.write(newtxt)
+        fp.close()
+
+
+def _replace_version_in_changelog(rootdir, version):
+    """Replaces the unreleased section in CHANGELOG.rst"""
+
+    fname = os.path.join(rootdir, 'CHANGELOG.rst')
+    print("Replacments in '{}': ".format(os.path.relpath(fname, rootdir)), end='')
+    fp = open(fname, 'r')
+    txt = fp.read()
+    fp.close()
+    decoration = '=' * len(version)
+    newtxt, nsub = re.subn(
+        r'^Unreleased\s*\n=+', version + r'\n' + decoration, txt,
+        count=1, flags=re.MULTILINE)
+    print(nsub)
+    fp = open(fname, 'w')
+    fp.write(newtxt)
+    fp.close()
+
+
+if __name__ == '__main__':
+    main()

devtools/travis-ci/before_install.sh

@@ -0,0 +1,21 @@
+# Temporarily change directory to $HOME to install software
+pushd .
+cd $HOME
+# Make sure some level of pip is installed
+python -m ensurepip
+
+if [ "$TRAVIS_OS_NAME" == "osx" ]; then
+    HOMEBREW_NO_AUTO_UPDATE=1 brew upgrade pyenv
+    # Pyenv requires minor revision, get the latest
+    PYENV_VERSION=$(pyenv install --list |grep $PYTHON_VER | sed -n "s/^[ \t]*\(${PYTHON_VER}\.*[0-9]*\).*/\1/p" | tail -n 1)
+    # Install version
+    pyenv install $PYENV_VERSION
+    # Use version for this
+    pyenv global $PYENV_VERSION
+    # Setup up path shims
+    eval "$(pyenv init -)"
+fi
+pip install --upgrade pip setuptools
+
+# Restore original directory
+popd