Merge pull request #1297 from dib-lab/doc/final-2.0

refresh for 2.0

ChangeLog

@@ -1,3 +1,9 @@
+2015-09-07  Michael R. Crusoe  <[email protected]>
+
+   * doc/roadmap.rst: Updated for 2.0 release.
+   * README.rst: drop unstable badges; fix links
+   * doc/index.rst: point at getting help guide
+
 2015-09-05  Michael R. Crusoe  <[email protected]>
 
    * tests/test_scripts.py: make the script version test more specific; double

README.rst

@@ -41,25 +41,7 @@ khmer
 
 Welcome to khmer: k-mer counting, filtering and graph traversal FTW!
 
-.. image:: https://readthedocs.org/projects/khmer/badge
-    :target: https://readthedocs.org/projects/khmer/
-    :alt: Documentation Status
-.. image:: https://badge.fury.io/py/khmer.svg
-    :target: http://badge.fury.io/py/khmer
-    :alt: PyPI Package
-.. image:: https://pypip.in/d/khmer/badge.svg
-    :target: https://crate.io/packages/khmer
-    :alt: Downloads Counter
-.. image:: https://pypip.in/license/khmer/badge.svg
-    :target: https://pypi.python.org/pypi/khmer/
-    :alt: License
-.. image:: http://ci.ged.msu.edu/job/khmer-master/badge/icon
-    :target: http://ci.ged.msu.edu/job/khmer-master/
-.. image:: https://scan.coverity.com/projects/621/badge.svg
-    :target: https://scan.coverity.com/projects/621
-    :alt: Coverity Scan Build Status
-
-The official repository is at
+The official source code repository is at
 
 https://github.com/dib-lab/khmer
 
@@ -78,27 +60,29 @@ them, please visit the following URLs:
 We chat at https://gitter.im/dib-lab/khmer and the maintainers can be
 contacted at [email protected].
 
-For getting help with please see this guide: http://khmer.readthedocs.org/user/getting-help.html
+For getting help please see this guide: http://khmer.readthedocs.org/en/stable/user/getting-help.html
 
 IMPORTANT NOTE: CITE US!
 ------------------------
 
 khmer is *research software*, so you should cite us when you use it
-in scientific publications!  Please see the CITATION file for
+in scientific publications!  Please see the `CITATION
+<http://khmer.readthedocs.org/en/stable/citations.html>`__ file for
 citation information.
 
 INSTALL INSTRUCTIONS:
 ---------------------
 
-khmer requires a 64-bit operating system and Python 2.7.x. Linux users will need
-the Python development libraries and gcc. OS X users may need XCode installed.
+khmer requires a 64-bit operating system and Python version 2.7.x, 3.3.x, or
+3.4.x. Linux users will need the Python development libraries and gcc. OS X
+users may need XCode installed to build from source.
 
 In short:
 
 ``pip install khmer`` to download, build, and install the latest stable
 version.
 
-For more details see `doc/install.txt <https://khmer.readthedocs.org/en/latest/user/install.html>`_
+For more details see `doc/install.rst <https://khmer.readthedocs.org/en/stable/user/install.html>`_
 
 The use of a virtualenv is recommended, see
 https://virtualenv.readthedocs.org/en/latest/installation.html
@@ -107,7 +91,4 @@ khmer is under the BSD license; see doc/LICENSE.txt. Distribution,
 modification and redistribution, incorporation into other software, and
 pretty much everything else is allowed.
 
-MRC 2014-05-14
-
-.. vim: set filetype=rst
-
+MRC 2015-09-07

doc/index.rst

@@ -66,9 +66,7 @@ common research tasks <https://khmer-recipes.readthedocs.org/>`__.
 You might also be interested in :doc:`papers using or citing khmer
 <user/biblio>`.
 
-**To get help**, please ask questions on `the khmer mailing list
-<http://lists.idyll.org/listinfo/khmer>`__ or `post an issue on
-GitHub <https://github.com/dib-lab/khmer/issues/new>`__.
+**To get help**, :doc:`please follow this guide <user/getting-help>`.
 
 We welcome contributions to the khmer project!  We are friendly and
 supportive of new contributors, and have a :doc:`code of conduct

doc/roadmap.rst

@@ -37,63 +37,67 @@
    Contact: [email protected]
 
 ***************************
-Roadmap to v2.0, v3.0, v4.0
+Roadmap to v3.0, v4.0, v5.0
 ***************************
 
 Background
 ==========
 
 To make the khmer project easier to use and easier to build upon several
 fundamental changes need to happen. This document outlines our plan to do so
-while minimizing the impact of these changes on our existing users.
+while minimizing the impact of these changes on our existing users. The
+version numbers are approximate; there may be additional major number
+releases to support needed changes to the API along the way. This document has
+been updated for v2.0 onwards from the `original roadmap
+<http://khmer.readthedocs.org/en/v1.2/roadmap.html>`__.
 
 The discussion that lead to this document can be read at
 https://github.com/dib-lab/khmer/issues/389
 
-Remainder of v1.x series
+Remainder of v2.x series
 ========================
 
-Start of transition to a single entrypoint named `oxli`. This will be exempt
-from the project's semantic versioning and will be advertised as experimental
-and unstable.
+Continue transition to a single entrypoint named `oxli
+<https://github.com/dib-lab/khmer/blob/master/oxli/__init__.py#L38>`__ . This
+will be exempt from the project's semantic versioning and will not be
+advertised as it is experimental and unstable. (For the 2.0 version we removed
+the ``oxli`` script just prior to release and restored it afterwards to the
+development tree.)
 
-Migration of Python script functionality to a Python module named `oxli`. As
-the code moves over there will be no change to external script functionality or
-their command line interfaces.
+The Python script functionality will continue to migrate to a Python module
+named `oxli <https://github.com/dib-lab/khmer/tree/master/oxli>`__. As the code
+moves over there will be no change to external script functionality or their
+command line interfaces (except for new features).
 
-v2.x series
+v3.x series
 ===========
 
-`oxli` command is now under semantic versioning. Scripts are still the
+The ``oxli`` command is now under semantic versioning. Scripts are still the
 advertised and preferred entry point for users. Developers and workflow systems
-can start to trial `oxli` but need not switch until 3.0. New functionality is
-added to both the scripts and the `oxli` command.
+can start to trial ``oxli`` but need not switch until 4.0. New functionality is
+added to both the scripts and the ``oxli`` command.
 
-v3.0 and project renaming
+v4.0 and project renaming
 =========================
 
 Project renamed to 'oxli'; all references to 'khmer' removed from the code and
 documentation except for a single note in the docs. All scripts dropped as
-their functionality has been moved to the `oxli` command. Websites that we
+their functionality has been moved to the ``oxli`` command. Websites that we
 maintain that have 'khmer' in the URL will have redirects installed.
 
 Refinement of the Python API continues, however it is not part of the semantic
 versioning of the project.
 
-v4.0
+v5.0
 ====
 
 The semantic versioning now extends to the Python API.
 
 Python API wishlist
 ===================
 
-Python 3.0 support
-
 API for multiple container types and implementation of the same.
 
 Cleanup of Python/C++ class hierarchy to cut down on boilerplate glue code.
 
 Switch to new-style Python objects (see LabelHash & Hashbits)
-
-