Merge pull request #676 from gregcaporaso/215-rc1

2.1.5 release candidate 1

ChangeLog.md

@@ -1,24 +1,36 @@
 BIOM-Format ChangeLog
 =====================
 
-biom 2.1.4-dev
---------------
+biom 2.1.5
+----------
+
+New features and bug fixes, released on 21 October 2015.
 
 Changes:
 
-* Codebase is now Python 3 compatible.
+* Codebase is now Python 2/3 compatible. It is currently tested with Python
+  versions 2.7, 3.4 and 3.5.
+* `biom-serve` and the accompanying html interface has been removed.
 
 New Features:
 
 * `Table.head` has been added to retrieve the first few rows and or columns
-    from a table, see issue #639.
+  from a table. This can be accessed through the new ``biom head`` command.
+  See [issue #639](https://github.com/biocore/biom-format/issues/639).
+* ``biom.parse.from_uc`` has been added to support creation of ``biom.Table``
+  objects from vsearch/uclust/usearch ``.uc`` files. This can be accessed
+  through the new ``biom from-uc`` command. See
+  [issue #648](https://github.com/biocore/biom-format/issues/648).
 * Codebase now uses [click](http://click.pocoo.org) instead of
-  [pyqi](https://github.com/biocore/pyqi) to create interfaces
-* `biom-serve` and the accompanying html interface has been removed
+  [pyqi](https://github.com/biocore/pyqi) for its command line interface.
+  See [issue #631](https://github.com/biocore/biom-format/issues/631).
 
 Bug fixes:
 
-* `Table.update_ids` strict check was too aggressive. See #633
+* `Table.update_ids` strict check was too aggressive. See
+ [issue #633](https://github.com/biocore/biom-format/issues/633).
+* `biom --version` now prints the software version (previously the individual
+  commands did this, but not the base command).
 
 biom 2.1.4
 ----------

README.md

@@ -12,5 +12,4 @@ Further details can be found at http://biom-format.org.
 Getting help
 ------------
 
-To get help with biom, you should use the [biom](http://stackoverflow.com/questions/tagged/biom) tag on StackOverflow (SO). Before posting a question, check out SO's guide on how to [ask a question](http://stackoverflow.com/questions/how-to-ask). The biom-format developers regularly monitor the `biom` SO tag.
-
+To get help with biom, you should use the [biom](http://stackoverflow.com/questions/tagged/biom) tag on StackOverflow (SO), or post the the [QIIME Forum](http://forum.qiime.org). Before posting a question, check out SO's guide on how to [ask a question](http://stackoverflow.com/questions/how-to-ask). The biom-format developers regularly monitor the `biom` SO tag.

biom/util.py

@@ -47,7 +47,7 @@
 __maintainer__ = "Daniel McDonald"
 __email__ = "daniel.mcdonald@colorado.edu"
 __format_version__ = (2, 1)
-__version__ = "2.1.4-dev"
+__version__ = "2.1.5"
 
 
 def generate_subsamples(table, n, axis='sample', by_id=False):

doc/conf.py

@@ -66,8 +66,8 @@
 # built documents.
 #
 # The full version, including alpha/beta/rc tags.
-version = "2.1.4-dev"
-release = "2.1.4-dev"
+version = "2.1.5"
+release = "2.1.5"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/index.rst

@@ -59,10 +59,6 @@ To work with BIOM 2.0+ files::
 
     pip install h5py
 
-Equivalently, you can use the ``conda`` package manager available in `Anaconda <http://continuum.io/downloads>`_ or `miniconda <http://conda.pydata.org/miniconda.html>`_ to install ``biom-format`` and its dependencies without having to compile them::
-
-    conda install biom-format
-
 To see a list of all ``biom`` commands, run::
 
     biom

setup.py

@@ -35,7 +35,7 @@
 __credits__ = ["Greg Caporaso", "Daniel McDonald", "Jose Clemente",
                "Jai Ram Rideout", "Jorge Cañardo Alastuey", "Michael Hall"]
 __license__ = "BSD"
-__version__ = "2.1.4-dev"
+__version__ = "2.1.5"
 __maintainer__ = "Daniel McDonald"
 __email__ = "mcdonadt@colorado.edu"