Docclean (#161)

* add contributor to docs

* move info to contribs

* try to do install reqs

* appease stickler

* now print correctly

* add pdf to gitignore

* fill in references

.gitignore

@@ -4,6 +4,7 @@
 *csv
 *xlsx
 *png
+*pdf
 
 # Apple file system
 *.DS_STORE

CONTRIBUTING.rst

@@ -1,14 +1,21 @@
-Contributor Guidelines
-======================
+
+Have a question? Get in touch!
+------------------------------
+
+- Report bugs, suggest features or view the source code `on GitHub`_.
+- For less well defined questions or ideas, use the `mailing list`_.
+
+.. _mailing list: https://groups.google.com/forum/#!forum/pyam
+.. _on GitHub: http://github.com/IAMconsortium/pyam
+
+
+Interested in Contributing? Welcome to the team!
+------------------------------------------------
 
 The pyam package has been developed with the explicit aim to facilitate
 open and collaborative analysis of integrated assessment and climate models.
 We appreciate contributions to the code base and development of new features.
 
-The community mailing list for questions and discussions on new features is
-hosted by Googlegroups. Please join at `groups.google.com/d/forum/pyam`_
-and use <[email protected]> to send an email to the *pyam* community.
-
 Please use the GitHub *Issues* feature to raise questions concerning potential
 bugs or to propose new features, but search and read resolved/closed topics on
 similar subjects before raising a new issue.
@@ -23,6 +30,4 @@ believe that when posting ideas or submitting code to an open-source project,
 it should be obvious and self-evident that any such contributions
 are made in the spirit of open collaborative development.
 
-.. _`groups.google.com/d/forum/pyam` : https://groups.google.com/d/forum/pyam
-
 .. _`pep8`: https://www.python.org/dev/peps/pep-0008/

doc/source/conf.py

@@ -43,6 +43,7 @@
     'sphinxcontrib.programoutput',
     'sphinx.ext.mathbase',
     'sphinx_gallery.gen_gallery',
+    'sphinxcontrib.bibtex',
 ]
 
 sphinx_gallery_conf = {

doc/source/index.rst

@@ -34,10 +34,6 @@ Release v\ |version|.
 The **pyam** Python package provides a range of diagnostic tools and functions
 for analyzing and visualizing data from your favorite assessment model(s).
 
-The *community mailing* list for questions and discussions on new features is
-hosted by Googlegroups. Please join at `groups.google.com/d/forum/pyam`_
-and use <[email protected]> to send an email to the *pyam* community.
-
 The source code for **pyam** is available on `Github`_.
 
 .. _`Github`:
@@ -79,20 +75,11 @@ Documentation
    examples/index
    api
 
-
-Get in touch
-------------
-
-- Report bugs, suggest features or view the source code `on GitHub`_.
-- For less well defined questions or ideas, use the `mailing list`_.
-
-.. _mailing list: https://groups.google.com/forum/#!forum/pyam
-.. _on GitHub: http://github.com/IAMconsortium/pyam
+.. include:: ../../CONTRIBUTING.rst
 
 License
 -------
 
 :code:`pyam` is available under the open source `Apache License`_.
 
-.. _Apache LIcense: http://www.apache.org/licenses/LICENSE-2.0.html
-
+.. _Apache License: http://www.apache.org/licenses/LICENSE-2.0.html

doc/source/install.rst

@@ -27,6 +27,15 @@ From Source
 Depedencies
 ~~~~~~~~~~~
 
+Like any software project, we stand on the shoulders of giants. Our particular
+giants include :code:`numpy` :cite:`numpy`, :code:`matplotlib`
+:cite:`matplotlib`, and :code:`pandas` :cite:`pandas`. Explicit requirements are
+fully enumerated below.
+
+The required depedencies for :code:`pyam` are:
+
+  .. program-output:: python -c 'import sys; sys.path.append("../.."); import requirements; requirements.display()'
+
 The optional depedencies for :code:`pyam` are:
 
   .. include:: ../../requirements.txt
@@ -38,3 +47,10 @@ The depedencies for building this documentation are:
   .. include:: ../requirements.txt
 	  :start-line: 0
 	  :literal:
+
+References
+**********
+
+.. bibliography:: refs.bib
+   :style: plain 
+   :all:

doc/source/refs.bib

@@ -0,0 +1,33 @@
+
+@Misc{numpy,
+author =    {Travis Oliphant},
+title =     {{NumPy}: A guide to {NumPy}},
+year =      {2006--},
+howpublished = {USA: Trelgol Publishing},
+url = "http://www.numpy.org/"
+}
+
+@Article{matplotlib,
+Author    = {Hunter, J. D.},
+Title     = {Matplotlib: A 2D graphics environment},
+Journal   = {Computing In Science \& Engineering},
+Volume    = {9},
+Number    = {3},
+Pages     = {90--95},
+abstract  = {Matplotlib is a 2D graphics package used for Python
+for application development, interactive scripting, and
+publication-quality image generation across user
+interfaces and operating systems.},
+publisher = {IEEE COMPUTER SOC},
+doi       = {10.1109/MCSE.2007.55},
+year      = 2007
+}
+
+@InProceedings{pandas,
+  author    = {Wes McKinney},
+  title     = {Data Structures for Statistical Computing in Python},
+  booktitle = {Proceedings of the 9th Python in Science Conference},
+  pages     = {51 - 56},
+  year      = {2010},
+  editor    = {Stefan van der Walt and Jarrod Millman}
+}

requirements.py

@@ -0,0 +1,17 @@
+install_requirements = [
+    "argparse",
+    "numpy",
+    "requests",
+    "pandas >=0.21.0",
+    "PyYAML",
+    "xlrd",
+    "xlsxwriter",
+    "matplotlib",
+    "seaborn",
+    "six",
+]
+
+
+def display():
+    for x in install_requirements:
+        print(x)

setup.py

@@ -9,6 +9,8 @@
 from setuptools import setup, Command
 from subprocess import call
 
+import requirements
+
 # Thanks to http://patorjk.com/software/taag/
 logo = r"""
  ______   __  __     ______     __    __
@@ -64,18 +66,7 @@ def main():
     package_data = {
         'pyam': ['region_mappings/*'],
     }
-    install_requirements = [
-        "argparse",
-        "numpy",
-        "requests",
-        "pandas >=0.21.0",
-        "PyYAML",
-        "xlrd",
-        "xlsxwriter",
-        "matplotlib",
-        "seaborn",
-        "six",
-    ]
+    install_requirements = requirements.install_requirements
     extra_requirements = {
         'tests': ['coverage', 'pytest', 'pytest-cov', 'pytest-mpl'],
         'docs': ['sphinx', 'sphinx_rtd_theme'],