Merge pull request #12 from dwhswenson/0.1.2

0.1.2

MANIFEST.in

@@ -1 +1,2 @@
 include contact_map/tests/trajectory.pdb
+include LICENSE

README.md

@@ -4,6 +4,7 @@
 [![codebeat badge](https://codebeat.co/badges/c7fb604a-35a8-4ccf-afea-18d6bd494726)](https://codebeat.co/projects/github-com-dwhswenson-contact_map-master)
 [![Codacy Badge](https://api.codacy.com/project/badge/Grade/f7f3cf53698e4655ac8895f13fa5dea6)](https://www.codacy.com/app/dwhswenson/contact_map?utm_source=github.com&utm_medium=referral&utm_content=dwhswenson/contact_map&utm_campaign=Badge_Grade)
 [![Code Climate](https://codeclimate.com/github/dwhswenson/contact_map/badges/gpa.svg)](https://codeclimate.com/github/dwhswenson/contact_map)
+[![PyPI](https://img.shields.io/pypi/v/contact-map.svg)](https://pypi.python.org/pypi/contact-map/)
 
 # Contact Maps
 
@@ -13,8 +14,9 @@ builds on the excellent tools provided by [MDTraj](http://mdtraj.org).
 
 ## Installation
 
-TODO: Neither of these installs actually work until we have a release! Use
-developer build until then.
+> TODO: So far only the `pip`-based install works. The `conda` install is
+> still in development as of 0.1.1. Both approaches will work before 0.2.0.
+> Both approaches work for getting requirements in a developer install.
 
 The easiest way to install is with `conda`. Conda is a powerful package and
 environment management system; if you do not already have a highly
@@ -29,8 +31,8 @@ conda install -c conda-forge contact_map
 
 The second-easiest install, which will work on any Python setup (conda or
 not) is to install via `pip`. Because of some weirdness in how `pip` handles
-packages (like MDTraj) that depend on Numpy, you should install Cython and
-Numpy separately, so the whole install is:
+packages (such as MDTraj) that depend on Numpy, you should install Cython
+and Numpy separately, so the whole install is:
 
 ```bash
 pip install cython
@@ -39,17 +41,25 @@ pip install contact_map
 ```
 
 If you already have Numpy installed, you may need to re-install it with `pip
-install -U --force-reinstall numpy`.
+install -U --force-reinstall numpy`. Note that some systems may require you
+to preface `pip install` commands with `sudo` (depending on where Python
+keeps its packages).
 
 
-### Installing a developer build
+### Developer installation
 
 If you plan to work with the source, or if you want to stay on the bleeding
 edge, you can install a version so that your downloaded/cloned version of
-this git repository 
+this git repository is the live code your Python interpreter sees. We call
+that a "developer installation."
 
 #### 1. Download or clone the respository
 
+If you plan to contribute changes back to the repository, please fork it on
+GitHub and then clone your fork. Otherwise, you can download or clone the
+main repository following [GitHub's
+instructions](https://help.github.com/articles/cloning-a-repository/).
+
 #### 2. Install the requirements
 
 There are two ways to install the requirements. You can either use `conda`
@@ -69,18 +79,23 @@ conda install -y --file requirements.txt
 Or install using `pip`:
 
 ```bash
+pip install cython
+pip install numpy
 pip install -r requirements.txt
 ```
 
-Note that MDTraj can be a bit particular about the numpy that it uses. If,
-in the first step of the `pip` install, MDTraj complains, try running the
-following commands:
+In some cases, you may need to add `-U --force-reinstall` to the Numpy step.
+
+#### 3. Install the package
+
+Change into the package directory (which you got when you cloned/downloaded
+the repository in step 1). This should be the directory with the `setup.py`
+from `contact_map`. Run the command:
 
 ```bash
-pip install cython
-pip install --upgrade --force-reinstall numpy
+pip install -e .
 ```
 
-#### 3. Install the package
-
-##
+The `-e` means that the installation is "editable" (developer version; the
+stuff in this directory will be the live code your Python interpreted uses)
+and the `.` tells it to find `setup.py` in the current directory.

ci/conda-recipe/meta.yaml

@@ -1,6 +1,7 @@
 package:
   name: contact_map
-  version: "0.1.1"
+  # add ".dev" for unreleased versions
+  version: "0.1.2"
 
 source:
   path: ../../
@@ -14,10 +15,6 @@ requirements:
   build:
     - python
     - setuptools
-    - mdtraj
-    - numpy
-    - scipy
-    - pandas
 
   run:
     - python
@@ -35,9 +32,6 @@ test:
   source_files:
     - contact_map/tests/*
 
-  #files:
-    #- contact_map/tests/*pdb
-
   imports:
     - contact_map
 

setup.py

@@ -1,17 +1,15 @@
 """
-Modified from the OPSPiggybacker setup.py
+setup.py for contact_map
 """
-#from distutils.sysconfig import get_config_var
-# from distutils.core import setup, Extension
 from setuptools import setup
-# import numpy
-# import glob
 import os
 import subprocess
 
 ##########################
-VERSION = "0.1.1"
+VERSION = "0.1.2"
 ISRELEASED = True
+if not ISRELEASED:
+    VERSION += ".dev"
 __version__ = VERSION
 PACKAGE_VERSION = VERSION
 REQUIREMENTS=['future', 'numpy', 'mdtraj', 'scipy', 'pandas']
@@ -77,7 +75,7 @@ def write_version_py(filename='contact_map/version.py'):
         GIT_REVISION = 'Unknown'
 
     if not ISRELEASED:
-        FULLVERSION += '.dev-' + GIT_REVISION[:7]
+        FULLVERSION += '-' + GIT_REVISION[:7]
 
     a = open(filename, 'w')
     try:
@@ -109,6 +107,7 @@ def write_version_py(filename='contact_map/version.py'):
     package_data={'contact_map': ['tests/*pdb']},
     ext_modules=[],
     scripts=[],
+    description="Contact maps based on MDTraj",
     long_description=DESCRIPTION,
     platforms=['Linux', 'Mac OS X', 'Unix', 'Windows'],
     install_requires=REQUIREMENTS,