Merged in fix/consolidate-docs (pull request #65)

Fix/consolidate docs

* Updated logo to latest on docs.

* Remove tutorial and reference documentation.

    Superseded by framework-wide documentation.

* Update API docs.

* Remove acknowledgment page and add support and development page.

Approved-by: Carl Simon Adorf <csadorf@umich.edu>
Approved-by: Vyas Ramasubramani <vramasub@umich.edu>
Approved-by: Bradley Dice <bdice@bradleydice.com>

doc/api.rst

@@ -0,0 +1,165 @@
+.. _api:
+
+=============
+API Reference
+=============
+
+This is the API for the **signac** (core) application.
+
+Command Line Interface
+======================
+
+Some core **signac** functions are---in addition to the Python interface---accessible
+directly via the ``$ signac`` command.
+
+For more information, please see ``$ signac --help``.
+
+.. literalinclude:: cli-help.txt
+
+
+The Project
+===========
+
+.. _python-api-project:
+
+.. currentmodule:: signac
+
+.. autoclass:: Project
+
+.. rubric:: Attributes
+
+.. autosummary::
+
+    Project.build_job_search_index
+    Project.build_job_statepoint_index
+    Project.check
+    Project.clone
+    Project.config
+    Project.create_access_module
+    Project.create_linked_view
+    Project.detect_schema
+    Project.doc
+    Project.document
+    Project.dump_statepoints
+    Project.export_to
+    Project.find_job_documents
+    Project.find_job_ids
+    Project.find_jobs
+    Project.find_statepoints
+    Project.fn
+    Project.get_id
+    Project.get_statepoint
+    Project.groupby
+    Project.groupbydoc
+    Project.import_from
+    Project.index
+    Project.isfile
+    Project.min_len_unique_id
+    Project.num_jobs
+    Project.open_job
+    Project.read_statepoints
+    Project.repair
+    Project.reset_statepoint
+    Project.root_directory
+    Project.sync
+    Project.update_cache
+    Project.update_statepoint
+    Project.workspace
+    Project.write_statepoints
+
+.. autoclass:: Project
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :exclude-members: Job
+
+The Job class
+=============
+
+.. _python-api-job:
+
+.. currentmodule:: signac.contrib.job
+
+.. autoclass:: Job
+
+.. rubric:: Attributes
+
+.. autosummary::
+
+    Job.clear
+    Job.close
+    Job.doc
+    Job.document
+    Job.fn
+    Job.get_id
+    Job.init
+    Job.isfile
+    Job.move
+    Job.open
+    Job.remove
+    Job.reset
+    Job.reset_statepoint
+    Job.sp
+    Job.statepoint
+    Job.sync
+    Job.update_statepoint
+    Job.workspace
+    Job.ws
+
+.. autoclass:: Job
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+The Collection
+==============
+
+.. currentmodule:: signac.contrib.collection
+
+.. autoclass:: Collection
+   :members:
+
+Top-level functions
+===================
+
+.. automodule:: signac
+    :members:
+    :show-inheritance:
+    :exclude-members: Project,Collection,RegexFileCrawler,MasterCrawler,SignacProjectCrawler
+
+
+Submodules
+==========
+
+signac.cite module
+------------------
+
+.. automodule:: signac.cite
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+signac.sync module
+------------------
+
+.. automodule:: signac.sync
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+signac.warnings module
+----------------------
+
+.. automodule:: signac.warnings
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+signac.errors module
+--------------------
+
+.. automodule:: signac.errors
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/cli-help.txt

@@ -0,0 +1,17 @@
+usage: signac [-h] [--debug] [--version] [-v] [-y]
+              {init,project,job,statepoint,document,rm,move,clone,index,find,view,schema,shell,sync,import,export,update-cache,config}
+              ...
+
+signac aids in the management, access and analysis of large-scale
+computational investigations.
+
+positional arguments:
+  {init,project,job,statepoint,document,rm,move,clone,index,find,view,schema,shell,sync,import,export,update-cache,config}
+
+optional arguments:
+  -h, --help            show this help message and exit
+  --debug               Show traceback on error for debugging.
+  --version             Display the version number and exit.
+  -v, --verbosity       Set level of verbosity.
+  -y, --yes             Answer all questions with yes. Useful for scripted
+                        interaction.