Update README before creating release (#69)

* update docs before pinning a version

* update version numbers, add lgtm to readme

* add last example to the appropriate README

* make Alpha version clear

README.md

@@ -1,4 +1,4 @@
-[![Build Status](https://travis-ci.org/MobleyLab/chemper.svg?branch=master)](https://travis-ci.org/MobleyLab/chemper) [![codecov](https://codecov.io/gh/MobleyLab/chemper/branch/master/graph/badge.svg)](https://codecov.io/gh/MobleyLab/chemper) [![Documentation Status](https://readthedocs.org/projects/chemper/badge/?version=latest)](http://chemper.readthedocs.io/en/latest/?badge=latest)
+[![Build Status](https://travis-ci.org/MobleyLab/chemper.svg?branch=master)](https://travis-ci.org/MobleyLab/chemper) [![codecov](https://codecov.io/gh/MobleyLab/chemper/branch/master/graph/badge.svg)](https://codecov.io/gh/MobleyLab/chemper) [![Documentation Status](https://readthedocs.org/projects/chemper/badge/?version=latest)](http://chemper.readthedocs.io/en/latest/?badge=latest) [![Total alerts](https://img.shields.io/lgtm/alerts/g/MobleyLab/chemper.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/MobleyLab/chemper/alerts/)
 
 # chemper
 
@@ -28,6 +28,9 @@ For example, if you know you want to assign certain group of angles (sets of thr
 the same equilibrium bond angle and force constant,
 then chemper should generate SMIRKS patterns that maintain that clustering.
 
+**Warning**
+This repository is still under active development. While an initial [version](#versions) is available changes are still expected in the API and the underlying code.
+
 ## Prerequisites
 
 We currently test with Python 3.5, though we expect anything 3.5+ should work.
@@ -73,7 +76,18 @@ pip install -e .
 Below are some details on the tools provided in `chemper` see
 [examples](https://github.com/MobleyLab/chemper/tree/master/examples) for more detailed usage examples
 
-### mol_toolkits
+### SMIRKSifier
+
+This is `chempers` main function.
+It takes groups of molecular fragments which should be typed together and generates a heirarchical list
+of SMIRKS patterns which maintains this typing.
+`chemper`'s `SMIRKSifier` takes a list of molecules and groups of atoms based on index and generates
+a hierarchical list of SMIRKS in just a few lines of code.
+In the example, [general_smirks_for_clusters](https://chemper.readthedocs.io/en/latest/examples/general_smirks_for_clusters.html)
+we cluster bonds in a set of simple hydrocarbons based on order. Then `SMIRKSifer` turns these clusters into a list of SMIRKS patterns.
+The following functionalities are used to make the `SMIRKSifier` possible, but may be useful on their own.
+
+### `mol_toolkits`
 
 As noted [above](#installation), we seek to keep `chemper` independent of the cheminformatics toolkit.
 `mol_toolkits` is created to keep all code dependent on the toolkit installed. It can create molecules from
@@ -134,26 +148,17 @@ In pentane (mol2) however atom1 can be a terminal or middle of the chain carbon
 hydrogen atoms (`Hn` decorator) on the carbon, thus there are two possible SMIRKS patterns for atom `:1`
 `#6AH2X4x0r0+0` or (indicated by the "`,`") `#6AH3X4x0r0+0`. But, atom `:2` only has one possibility `#6AH2X4x0r0+0`.
 
+## Versions
 
-# What's coming next?
-
-The ClusterGraph code can accurately create a SMIRKS pattern for a group of clustered molecular subgraphes.
-However as you can see in the [SMIRKS_from_molecules](examples/using_cluster_graph/SMIRKS_from_molecules.ipynb)
-the SMIRKS created by `ClusterGraph` are highly specific.
-Our final goal here is to maintain a given set of clustering, but to generate relatively general SMIRKS patterns
-that can then be used to assign force field parameters. This use of relatively generic SMIRKS patterns is part of what
-we believe makes the SMIRNOFF force field format so powerful.
-
-One option here would be to go back to the MC sampling used in [SMARTY/SMIRKY](https://github.com/openforcefield/smarty).
-Where the information stored in `ClusterGraph` could be used to make more intelligent/efficient moves.
-However, we believe there is a yet more efficient option where the differences and similarities in `ClusterGraph` objects
-could be used to determine the correct SMIRKS patterns. Thus, the next step is to essentially find the similarities
-and differences in `ClusterGraph`s so that the most general SMIRKS can be used to maintain clustering as the user
-inputs, but not specify more information than necessary.
+### 0.1.0 Alpha Release
+This is a first release of the Alpha testing version of `chemper`. As you can follow in the [issue tracker](https://github.com/MobleyLab/chemper/issues) there are still
+on going problems to resolve. This first release will allow for reference to the concepts and algorithms included here
+for automated chemical perception. However, the API is still in flux and nothing should be considered permanent at this time.
 
 ## Contributors
 
-* [Caitlin Bannan (UCI)](https://github.com/bannanc)
+* [Caitlin C. Bannan (UCI)](https://github.com/bannanc)
+* [Jessica Maat (UCI)](https://github.com/jmaat)
 * [David L. Mobley (UCI)](https://github.com/davidlmobley)
 
 ## Acknowledgments

conf.py

@@ -24,9 +24,9 @@
 author = 'Caitlin C. Bannan'
 
 # The short X.Y version
-version = '0.0.0'
+version = '0.1.0'
 # The full version, including alpha/beta/rc tags
-release = '0.0.0'
+release = '0.1.0'
 
 
 # -- General configuration ---------------------------------------------------

docs/intro.rst

@@ -42,7 +42,8 @@ See :doc:`installation`.
 Contributors
 ------------
 
-* `Caitlin Bannan (UCI) <https://github.com/bannanc>`_
+* `Caitlin C. Bannan (UCI) <https://github.com/bannanc>`_
+* `Jessica Maat (UCI) <https://github.com/jmaat>`_
 * `David L. Mobley (UCI) <https://github.com/davidlmobley>`_
 
 Acknowledgments

examples/README.md

@@ -2,13 +2,13 @@
 
 This is directory stores examples for how to use and work with ChemPer
 
-### Single Mol SMIRKS
+### Generating reasonable SMIRKS patterns
 
-`ChemPerGraph`s convert a molecule into a SMIRKS pattern by 
-converting information about the atoms and bonds. 
-The `ChemPerGraph` stores only one molecule. It can convert only certain atoms or
-the *entire* molecule into a SMIRKS pattern. 
-This direction of molecule to SMIRKS string is new as far as the authors know with chemper. 
+`SMIRKSifier` is used to create a hierarchical list of SMIRKS patterns for 
+bonds which are clustered by order. This is done by first grouping the bonds in 
+a small set of molecules based on their order. Then, the `SMIRKSifier` takes those
+molecules and groups of bonds and create SMIRKS patterns that are specific to these molecules.
+Lastly, these SMIRKS patterns are made more general by removing unncessary decorators. 
 
 ### SMIRKS from Molecules 
 
@@ -17,3 +17,10 @@ They can store information about multiple atoms and bonds simultaneously.
 This is a starting example for how to use ChemPer's `ClusterGraph` class 
 to create SMIRKS patterns from clusters of molecular graphs. 
 
+### Single Mol SMIRKS
+
+`ChemPerGraph`s convert a molecule into a SMIRKS pattern by 
+converting information about the atoms and bonds. 
+The `ChemPerGraph` stores only one molecule. It can convert only certain atoms or
+the *entire* molecule into a SMIRKS pattern. 
+This direction of molecule to SMIRKS string is new as far as the authors know with chemper. 

setup.py

@@ -33,7 +33,7 @@ def find_package_data(data_root, package_root):
 if __name__ == "__main__":
     setuptools.setup(
         name='chemper',        # Make sure to change to match your library name
-        version="0.0.0",    # you should keep track of versions
+        version="0.1.0",    # you should keep track of versions
         description='A python package for automatically sampling chemical perception',     # add a description
         long_description=read('README.md'),
         author='Caitlin C. Bannan',          # add your name to author category
@@ -68,7 +68,7 @@ def find_package_data(data_root, package_root):
         ],
 
         classifiers=[
-            'Development Status :: 4 - Beta',
+            'Development Status :: 4 - Alpha',
             'Intended Audience :: Science/Research',
             'Programming Language :: Python :: 3',
         ],

tests/test_mol_toolkits.py

@@ -1,8 +1,7 @@
 """
 This is a test for the molecule, atom, and bond objects.
-Currently chemper only downloads one version of these objects.
-This test runs for which ever mol_toolkit is available and will
-print which one it is using
+First, it checks which toolkits (OpenEye or RDKit) are available
+It will run tests for each object for all toolkits that are available.
 """
 
 from chemper.mol_toolkits import mol_toolkit
@@ -218,4 +217,4 @@ def test_default_toolkit():
     if mol_toolkit.HAS_OE:
         assert tk == 'openeye'
     else:
-        assert tk == 'rdkit'
+        assert tk == 'rdkit'