Troubleshoot RTD import errors

docs/install.rst

@@ -1,23 +1,23 @@
 Install pAPRika
 ==========================
 
-We recommend installing pAPRika in a fresh `conda` environment if possible. There are three ways to install this package:
+We recommend installing pAPRika in a fresh ``conda`` environment if possible. There are three ways to install this package:
 
-1. The latest release on `conda-forge`:
-    a. `conda install -c conda-forge paprika`
+1. The latest release on ``conda-forge``:
+    a. ``conda install -c conda-forge paprika``
     b. To use all features of pAPRika, you must either have [AmberTools](http://ambermd.org/AmberTools.php) in your `$PATH` or separately install AmberTools with `conda install -c http://ambermd.org/downloads/ambertools/conda/ ambertools=18`.
-    c. To use OpenMM features: `conda install -c omnia openmm`.
+    c. To use OpenMM features: ``conda install -c omnia openmm``.
 
 2. The master branch on GitHub:
-    a. Clone this `git` repository, then inside the `paprika` directory:
-    b. Change the `name` field in `devtools/conda-envs/test_env.yaml` to be `paprika`.
-    c. Create the environment: `conda env create -f devtools/conda-envs/test_env.yaml`.
-    d. Activate the environment: `conda activate paprika`
-    e. Install `paprika` in the environment: `pip install .`
+    a. Clone this ``git`` repository, then inside the ``paprika`` directory:
+    b. Change the ``name`` field in ``devtools/conda-envs/test_env.yaml`` to be ``paprika``.
+    c. Create the environment: ``conda env create -f devtools/conda-envs/test_env.yaml``.
+    d. Activate the environment: ``conda activate paprika``
+    e. Install ``paprika`` in the environment: ``pip install .``
 
 3. The latest release on GitHub:
-    a. Download [the latest release](https://github.com/slochower/pAPRika/releases), extract it, and change to the `paprika` directory:
-    b. Change the `name` field in `devtools/conda-envs/test_env.yaml` to be `paprika`.
-    c. Create the environment: `conda env create -f devtools/conda-envs/test_env.yaml`.
-    d. Activate the environment: `conda activate paprika`
-    e. Install `paprika` in the environment: `pip install .`
+    a. Download [the latest release](https://github.com/slochower/pAPRika/releases), extract it, and change to the ``paprika`` directory:
+    b. Change the ``name`` field in ``devtools/conda-envs/test_env.yaml`` to be ``paprika``.
+    c. Create the environment: ``conda env create -f devtools/conda-envs/test_env.yaml``.
+    d. Activate the environment: ``conda activate paprika``
+    e. Install ``paprika`` in the environment: ``pip install .``

setup.py

@@ -2,15 +2,15 @@
 pAPRika
 Advanced toolkit for binding free energy calculations
 """
-from setuptools import setup
+from setuptools import setup, find_packages
 import versioneer
 
 short_description = __doc__.split("\n")
 
 try:
     with open("README.md", "r") as handle:
         long_description = handle.read()
-except:
+except IOError:
     long_description = "\n".join(short_description[2:]),
 
 
@@ -27,13 +27,14 @@
     license='BSD-3-Clause',
 
     # Which Python importable modules should be included when your package is installed
-    packages=['paprika', "paprika.tests"],
+    packages=find_packages(),
 
     # Optional include package data to ship with your package
     # Comment out this line to prevent the files from being packaged with your software
     # Extend/modify the list to include/exclude other items as need be
     package_data={'paprika': ["data/*.dat"]
                   },
+    include_package_data=True,
 
     # Additional entries you may want simply uncomment the lines you want and fill in the data
     # author_email='me@place.org',      # Author email