add sample in dataset.rst

MANIFEST.in

@@ -1,4 +1,4 @@
-include README.md
-include CONTRIBUTING.md
-include LICENSE
+include *.rst LICENSE.rst CHANGES.rst requirements*.txt
+recursive-include xenonpy *.py *.json *.yaml
+recursive-exclude tests/*.*
 recursive-include licences *

README.rst

@@ -0,0 +1,56 @@
+.. Copyright 2017 TsumiNa. All rights reserved.
+
+
+What is Xenon.Py project
+========================
+.. image:: https://badges.gitter.im/yoshida-lab/XenonPy.svg
+    :alt: Join the chat at https://gitter.im/yoshida-lab/XenonPy
+    :target: https://gitter.im/yoshida-lab/XenonPy?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge
+
+.. image:: https://travis-ci.org/yoshida-lab/XenonPy.svg?branch=master
+    :alt: Build Status
+    :target: https://travis-ci.org/yoshida-lab/XenonPy
+
+**Xenon.Py** is a Python library focus on the material informatics which be designed for material explore based on machine learning.
+
+The main purpose of this project is to build a complex system to calculate various chem/phys descriptors for machine learning then extend them to explore material space.
+To reach this target, system also provide model training routines and try to re-use pre-trained model by various deep learning methods such as **transfer learning**.
+
+This project has just started and a long way to run. The final goal of this project is to build a all-in-one virtual material development environment include:
+
+* **Dataset and Pre-trained models out-of-box**
+* **Various descriptor calculation methods**
+* **Model training and re-use**
+* **Combined with deep learning methods seamless**
+* **Visualization tools for analysis and publish ready**
+
+Xenon.Py inspired by matminer: https://hackingmaterials.github.io/matminer/.
+
+Xenon.Py is a open source project https://github.com/yoshida-lab/XenonPy.
+
+See our documents for details: http://xenonpy.readthedocs.io 
+
+
+Contribution guidelines
+=======================
+
+* Discussion with others
+* Docstring use `Numpy style`_.
+* Check codes with Pylint
+* Writing tests if possible
+
+
+* With issues_
+* With Gitter_
+
+
+
+Copyright and license
+=====================
+
+Code and documentation © 2017 TsumiNa.
+Released under the BSD-3 license.
+
+.. _issues: https://github.com/yoshida-lab/XenonPy/issues
+.. _Gitter: https://gitter.im/yoshida-lab/XenonPy
+.. _Numpy style: https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt

Untitled.ipynb

@@ -0,0 +1,32 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.5.4"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

docs/source/conf.py

@@ -22,6 +22,8 @@
 
 sys.path.insert(0, os.path.abspath('../../'))
 
+import xenonpy as package
+
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
@@ -58,18 +60,18 @@
 master_doc = 'index'
 
 # General information about the project.
-project = 'XenonPy'
+project = package.__name__
 copyright = '2018, TsumiNa'
-author = 'TsumiNa'
+author = package.__author__
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = '0.1'
+version = package.__version__
 # The full version, including alpha/beta/rc tags.
-release = '0.1.0'
+release = version + package.__release__
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/source/dataset.rst

@@ -15,7 +15,7 @@ The ``elements_completed`` dataset only have 94 elements from `H` to `Pu` with 5
 .. _mendeleev: https://mendeleev.readthedocs.io
 .. _pymatgen: http://pymatgen.org/
 
-.. [1] `Int J Methods Psychiatr Res. 2011 Mar 1; 20(1): 40–49.`__
+.. [1] Int J Methods Psychiatr Res. 2011 Mar 1; 20(1): 40–49.
             doi: `10.1002/mpr.329 <10.1002/mpr.329>`_
 
 The followig data are currently available in ``elements``:
@@ -103,5 +103,5 @@ The followig data are currently available in ``elements``:
 Load dataset
 ============
 
-You can use :class:`~xenonpy.utils.datatools.Loader` to load preset dataset.
-See `loader_saver sample <https://github.com/yoshida-lab/XenonPy/blob/master/samples/data_loader.ipynb>`_ for details.
+You can use :class:`~xenonpy.utils.Loader` to load preset dataset.
+See `loader_saver sample <https://github.com/yoshida-lab/XenonPy/blob/master/samples/load_and_save_data.ipynb>`_ for details.

docs/source/installation.rst

@@ -46,6 +46,10 @@ or, to install Xenon.Py in your user home folder, run the command:
 
     $ pip install xenonpy --user
 
+You also have to install PyTorch_.
+Because the pip installation of ``pytorch`` dependent on your working system and python environment.
+To install ``pytorch``, please follow the `Get Started` section on the PyTorch_ office sit.
+
 To update, simply type ``pip install --upgrade xenonpy``.
 
 
@@ -72,7 +76,7 @@ To update Xenon.Py, enter your cloned folder and type ``git pull`` then ``pip in
 Troubleshooting/Issues
 ----------------------
 
-Having issues installing? Contract us with issues_ and Gitter_.
+Having issues installing? Contract us at issues_ and Gitter_.
 
 When open issues, please describing your problem in full
 (including your system specifications, Python version information, and input/output log).
@@ -85,3 +89,4 @@ When open issues, please describing your problem in full
 .. _Github repository: https://github.com/yoshida-lab/XenonPy
 .. _issues: https://github.com/yoshida-lab/XenonPy/issues
 .. _Gitter: https://gitter.im/yoshida-lab/XenonPy
+.. _PyTorch: http://pytorch.org/

pyinstrument/meta.yaml

@@ -0,0 +1,48 @@
+{% set name = "pyinstrument" %}
+{% set version = "2.0.1" %}
+{% set file_ext = "tar.gz" %}
+{% set hash_type = "sha256" %}
+{% set hash_value = "6856fa6c08a77d23b2772b705dd6c8143e1b1dc4617036822a3f518453743dfd" %}
+
+package:
+  name: '{{ name|lower }}'
+  version: '{{ version }}'
+
+source:
+  fn: '{{ name }}-{{ version }}.{{ file_ext }}'
+  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.{{ file_ext }}
+  '{{ hash_type }}': '{{ hash_value }}'
+
+build:
+  number: 0
+  entry_points:
+    - pyinstrument = pyinstrument.__main__:main
+  script: python setup.py install --single-version-externally-managed --record=record.txt
+
+requirements:
+  build:
+    - python
+    - setuptools
+    - pyinstrument_cext
+  run:
+    - python
+    - pyinstrument_cext
+
+test:
+  imports:
+    - pyinstrument
+  commands:
+    - pyinstrument --help
+
+about:
+  home: https://github.com/joerick/pyinstrument
+  license: BSD License
+  license_family: BSD
+  license_file: ''
+  summary: A call stack profiler for Python. Inspired by Apple's Instruments.app
+  description: ''
+  doc_url: ''
+  dev_url: ''
+
+extra:
+  recipe-maintainers: ''