Merge pull request #117 from avmarchenko/master

Updated documentation for some widgets and pcf functions/classes.

Author: tjduigna

.travis.yml

@@ -40,12 +40,14 @@ install:
     - conda install -c conda-forge pandoc pypandoc nbsphinx ipython
     - conda install -q -c conda-forge python-coveralls coverage pytest pytest-cov
     - conda install -q -c conda-forge numexpr nodejs ipywidgets
+#   - conda install -q -c exaanalytics exa
+    - pip install exa
     - pip install travis-sphinx codacy-coverage
-    - git clone https://github.com/exa-analytics/exa.git
-    - cd exa
-    - pip install .
-    - cd ../
-    - pip install -e .
+#   - git clone https://github.com/exa-analytics/exa.git
+#   - cd exa
+#   - pip install .
+#   - cd ../
+#   - pip install -e .
 
 script:
     - export PYTHONDONTWRITEBYTECODE=1

RELEASE.md

@@ -26,9 +26,8 @@ rm -r dist/*
 Publish to `TestPyPI`_ (~/.pypirc required).
 This requires `wheel` and `twine` to be installed.
 ```bash
-python setup.py sdist
-python setup.py bdist_wheel
-twine upload --repository [which] dist/*
+python setup.py sdist    #python setup.py bdist_wheel
+twine upload dist/*
 ```
 The variable `which` refers to the alias for the testing or production
 repository listed in ~/.pypirc.
@@ -47,13 +46,13 @@ npm publish
 Publish to the `exa-analytics`_ channel on  `Anaconda Cloud`.
 This requires that the package hase been released on `PyPI`.
 This requires the anaconda package `conda-build` and `anaconda-client` (run `anaconda login`).
-It is convenient to use a `.condarc` file to add the `conda-forge` channel
-since some auxiliary packages come from there.
+It is convenient to use a `.condarc` file to add the `conda-forge` and 
+`exaanalytics` channels since some auxiliary packages come from there.
 Note that to test a build, set uploading to false (anaconda_upload: false in .condarc) and
 in the meta.yaml source change the url to `git_url: ./`.
 ```bash
 conda build .    # conda build . --output to see location
 # For other python version, conda build --python x.x
 conda convert -f --platform all /path/to/conda-bld/pltfrm/exa-...tar.bz2 -o /path/to/outputdir/
-conda upload /path/to/build/build.tar.bz2    # For each build
+anaconda upload /path/to/build/build.tar.bz2    # For each build
 ```

exatomic/_version.py

@@ -11,5 +11,5 @@
     exa.version_info
     exa.__verion__
 """
-version_info = (0, 3, 11)
+version_info = (0, 4, 0)
 __version__ = ".".join(map(str, version_info))

exatomic/algorithms/pcf.py

@@ -68,6 +68,11 @@ def radial_pair_correlation(universe, a, b, dr=0.05, start=1.0, stop=13.0,
         the volume sampled during computation of two body properties divided by
         the number of properties used in the histogram (the triple summation
         above, divided by the normalization for the radial distance outward).
+
+    Warning:
+        Using a start and stop length different from 0 and simple cubic cell dimension
+        will cause the y axis magnitudes to be inaccurate. This can be remedied by
+        rescaling values appropriately.
     """
     bins = np.arange(start, stop, dr)                     # Discrete values of r for histogram
     if isinstance(a, str):

exatomic/core/universe.py

@@ -275,7 +275,7 @@ def add_molecular_orbitals(self, field_params=None, mocoefs=None,
             uni.field.field_values                        # The generated scalar fields
 
         Args:
-            field_params (dict, pd.Series): see :meth:`exatomic.algorithms.orbital_util.make_fps`
+            field_params (dict, pd.Series): see :func:`exatomic.algorithms.orbital_util.make_fps`
             mocoefs (str): column in :class:`~exatomic.core.orbital.MOMatrix`
             vector (iter): indices of orbitals to evaluate (0-based)
             frame (int): frame of atomic positions for the orbitals

exatomic/widgets/widget.py

@@ -324,7 +324,22 @@ def __init__(self, *scenes, **kwargs):
 
 @register
 class UniverseWidget(ExatomicBox):
-    """:class:`~exatomic.container.Universe` viewing widget."""
+    """
+    Visualize a :class:`~exatomic.core.universe.Universe`.
+
+    .. code-block:: python
+
+        u = exatomic.Universe.load(exatomic.base.resource("adf-lu-valid.hdf5"))
+        scenekwargs = dict(atomcolors=dict(Lu="black"))
+        exatomic.UniverseWidget(u, scenekwargs=scenekwargs)    # In Jupyter notebook
+
+        scenekwargs = dict(atomcolors=dict(Lu="#f442f1"), atomradii=dict(Lu=1.0))
+        exatomic.UniverseWidget(u, scenekwargs=scenekwargs)    # In Jupyter notebook
+
+    Args:
+        uni: The Universe object
+        scenekwargs (dict): Keyword args to be passed to :class:`~exatomic.widgets.widget_base.ExatomicScene`
+    """
     def _frame_folder(self, nframes):
         playable = bool(nframes <= 1)
         flims = dict(min=0, max=nframes-1, step=1, value=0)

exatomic/widgets/widget_base.py

@@ -28,8 +28,14 @@
 
 @register
 class ExatomicScene(DOMWidget):
-    """A three.js sandbox for 3D visualization."""
-
+    """
+    A custom scene (three.js scene) used for visualization
+    of an atomic universe.
+
+    Custom parameters can be inspected using ``vars``. Parameters
+    include field dimensions, the universe itself, field colors,
+    widths, heights for the widget, etc.
+    """
     _model_module_version = Unicode(__js_version__).tag(sync=True)
     _view_module_version = Unicode(__js_version__).tag(sync=True)
     _view_module = Unicode('exatomic').tag(sync=True)
@@ -69,7 +75,6 @@ class ExatomicScene(DOMWidget):
 
     def _handle_custom_msg(self, msg, callback):
         """Custom message handler."""
-
         if msg['type'] == 'image':
             self._save_image(msg['content'])
         elif msg['type'] == 'camera':

meta.yaml

@@ -1,36 +1,26 @@
 {% set name = "exatomic" %}
-{% set version = "0.3.11" %}
+{% set version = "0.4.0" %}
 
 package:
   name: {{ name }}
   version: {{ version }}
 
 source:
-  fn: {{ name }}-{{ version }}.tar.gz
-  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
+  url: https://github.com/exa-analytics/{{ name }}/archive/v{{ version }}.tar.gz
 
 requirements:
   build:
     - python
     - setuptools
 
   run:
-    - python
     - numpy
-    - scipy
-    - matplotlib
-    - seaborn
-    - networkx
     - pandas
-    - notebook
-    - nose
     - numba
-    - six
-    - pytables
-    - sphinx
-    - sphinx_rtd_theme
-    - pandoc
-    - nbsphinx
+    - seaborn
+    - ipywidgets
+    - sympy
+    - numexpr
     - exa
     - sympy
     - symengine
@@ -43,4 +33,4 @@ about:
     home: https://exa-analytics.github.io/{{ name }}
     license: Apache-2.0
     license_file: LICENSE
-    summary: A unified platform for theoretical and computational chemists.
+    summary: A unified platform for theoretical and computational chemists

setup.py

@@ -140,14 +140,14 @@ def run(self):
     },
     'zip_safe': False,
     'license': "Apache License Version 2.0",
-    'author': "Thomas J. Duignan and Alex Marchenko",
+    'author': "Thomas J. Duignan, Alex Marchenko and contributors",
     'author_email': "exa.data.analytics@gmail.com",
     'maintainer_email': "exa.data.analytics@gmail.com",
     'url': "https://exa-analytics.github.io/" + name,
-    'download_url': "https://github.com/exa-analytics/{}/archive/{}.tar.gz".format(name, version),
-    'keywords': ["quantum", "chemistry", "hpc", "jupyter", "notebook", "visualization"],
+    'download_url': "https://github.com/exa-analytics/{}/archive/v{}.tar.gz".format(name, version),
+    'keywords': ["quantum chemistry", "jupyter notebook", "visualization"],
     'classifiers': [
-        "Development Status :: 3 - Alpha",
+        "Development Status :: 4 - Beta",
         "Environment :: Web Environment",
         "Intended Audience :: Developers",
         "Intended Audience :: Science/Research",