Prepared the package for pip and pypi.

MANIFEST.in

@@ -1,5 +1,3 @@
 include README.md
 include LICENSE.txt
-include forward/templates/default.html
-recursive-include forward/templates *
-recursive-include forward/tests/data *
+prune forward/static/js/build/.module-cache

docs/source/report.rst

@@ -85,7 +85,8 @@ the files are in the `forward/static` subdirectory of the repo. If you want
 to extend the report without adding js dependencies, you don't need to take
 care of Bower, because all of the required files are included in the repo. This
 decision was made to make it easier for developers to play with the frond-end
-without tedious configuration.
+without tedious configuration. If you want to update the js dependencies, you
+may edit the ``bower.json`` file and run ``bower update``.
 
 Nonetheless, front-end developers will need to build their javascript. This is
 because `react` code uses `JSX` which needs to be converted to regular

forward/static/bower.json

@@ -1,6 +1,6 @@
 {
   "name": "forwardUI",
-  "version": "0.0.0",
+  "version": "0.1.0",
   "homepage": "https://github.com/legaultmarc/forward",
   "authors": [
     "Marc-André Legault <legaultmarc@gmail.com>"
@@ -13,7 +13,6 @@
   ],
   "dependencies": {
     "react": "0.13.3",
-    "bokehjs": "http://cdn.pydata.org/bokeh/release/bokeh-0.9.1.min.js",
     "jquery": "2.1.4",
     "d3": "3.5.6"
   },

setup.py

@@ -7,6 +7,7 @@
 # python setup.py sdist --format zip
 
 import os
+import functools
 
 from setuptools import setup, find_packages
 
@@ -33,21 +34,54 @@ def write_version_file(fn=None):
         a.close()
 
 
+def get_package_data():
+    base = os.path.join(os.path.dirname(os.path.abspath(__file__)))
+    os.chdir(base)
+    roots = {"templates", "static", os.path.join("tests", "data")}
+
+    excludes = {"forward/static/js/build/.module-cache",
+                "forward/static/js/build/.module-cache/manifest"}
+
+    paths = []
+
+    for root in roots:
+        root = os.path.join("forward", root)
+        for cur, dirs, files in os.walk(root):
+            if cur in excludes:
+                continue
+            join = functools.partial(os.path.join, cur)
+            paths.extend(map(join, files))
+
+    # Remove the leading forward.
+    paths = [i[8:] for i in paths]
+
+    return paths
+
+
 def setup_package():
     # Saving the version into a file
     write_version_file()
 
     setup(
         name="forward",
         version=VERSION,
-        description="Utilities for pheWAS experiments using cohorts.",
-        long_description=("This package facilitates common pheWAS analysis "
-                          "and automates report creation and data archiving."),
+        description="Tool for gene-based phenomic experiments using cohorts.",
+        long_description=("This package facilitates common phenomic analyses "
+                          "and automates report creation and data management."
+                          ""),
         author=u"Marc-André Legault",
         author_email="legaultmarc@gmail.com",
         url="https://github.com/legaultmarc/forward",
         license="CC BY-NC 4.0",
         packages=find_packages(exclude=["tests", ]),
+        package_data={
+            "forward": get_package_data()
+        },
+        entry_points={
+            "console_scripts": [
+                "forward-cli=forward.scripts.forward_cli:parse_args"
+            ],
+        },
         classifiers=["Development Status :: 4 - Beta",
                      "Intended Audience :: Developers",
                      "Intended Audience :: Science/Research",
@@ -56,19 +90,20 @@ def setup_package():
                      "Operating System :: POSIX :: Linux",
                      "Programming Language :: Python",
                      "Programming Language :: Python :: 2.7",
+                     "Programming Language :: Python :: 3",
                      "Topic :: Scientific/Engineering :: Bio-Informatics"],
         test_suite="forward.tests.test_suite",
         keywords="bioinformatics genomics phewas epidemiology cohort",
         install_requires=["numpy >= 1.8.1", "pandas >= 0.15",
                           "gepyto >= 0.9.2", "SQLAlchemy >= 0.9.8",
                           "PyYAML >= 3.11", "scipy >= 0.14.0",
-                          "matplotlib >= 1.4.2", "Jinja2 >= 2.7.3",
-                          "xlrd >= 0.9.3", "seaborn >= 0.5.1",
-                          "six >= 1.9.0"],
+                          "Jinja2 >= 2.7.3", "xlrd >= 0.9.3",
+                          "six >= 1.9.0", "h5py >= 2.5.0", "pyplink >= 1.0.2",
+                          "Pygments >= 2.0.2", "statsmodels >= 0.6.1",
+                          "Flask >= 0.10.0", "patsy >= 0.4.0"],
+        zip_safe=False
     )
 
-    return
-
 
 if __name__ == "__main__":
     setup_package()