Merge pull request #1702 from dib-lab/pre-release

A few small changes

CHANGELOG.md

@@ -6,7 +6,7 @@ The khmer project's command line scripts adhere to
 [Semantic Versioning](http://semver.org/). The Python and C++ APIs are not yet
 under semantic versioning, but will be in future versions of khmer.
 
-## [2.1] - 2017-05-XX
+## [2.1] - 2017-05-21
 ### Added
 - New `--no-reformat` option for `interleave-reads.py` script disables default
   read name correction behavior.

MANIFEST.in

@@ -1,6 +1,6 @@
 include ChangeLog ez_setup.py IDEAS Makefile README.md setup.cfg
 include versioneer.py MANIFEST.in CITATION CONTRIBUTING.md Doxyfile.in
-include LICENSE TODO .ycm_extra_conf.py
+include LICENSE TODO .ycm_extra_conf.py authors.csv
 recursive-include lib *.hh *.cc [Mm]akefile* get_version.py
 recursive-include khmer *.hh
 recursive-include third-party *.cc *.1 *.xsl README* sample* words* *.sh *.c

doc/dev/release.rst

@@ -126,7 +126,7 @@ release makers, following this checklist by MRC.
         mkdir ../not-khmer # make sure py.test executes tests
                            # from the installed khmer module
         # you might want to add 'and not huge' to the test selection
-        pushd ../not-khmer; pytest --pyargs khmer -m 'not known_failing'; popd
+        pushd ../not-khmer; pytest --pyargs khmer.tests -m 'not known_failing'; popd
 
 
         # Secondly we test via pip
@@ -144,7 +144,7 @@ release makers, following this checklist by MRC.
         cd ../.. # no subdir named khmer here, safe for testing installed khmer module
         normalize-by-median.py --version 2>&1 | grep khmer\ ${new_version}-${rc} && \
                 echo 2nd manual version check passed
-        pytest --pyargs khmer -m 'not known_failing'
+        pytest --pyargs khmer.tests -m 'not known_failing'
 
         # Is the distribution in testenv2 complete enough to build another
         # functional distribution?
@@ -160,7 +160,7 @@ release makers, following this checklist by MRC.
         make test
         pip uninstall -y khmer; pip uninstall -y khmer; make install
         mkdir ../not-khmer
-        pushd ../not-khmer ; pytest --pyargs khmer -m 'not known_failing' ; popd
+        pushd ../not-khmer ; pytest --pyargs khmer.tests -m 'not known_failing' ; popd
 
 #. Publish the new release on the testing PyPI server.  You will need
    to change your PyPI credentials as documented here:
@@ -179,7 +179,7 @@ release makers, following this checklist by MRC.
         pip install -U setuptools==3.4.1
         pip install screed pytest
         pip install -i https://testpypi.python.org/pypi --pre --no-clean khmer
-        pytest --pyargs khmer -m 'not known_failing'
+        pytest --pyargs khmer.tests -m 'not known_failing'
         normalize-by-median.py --version 2>&1 | grep khmer\ ${new_version}-${rc} && \
                 echo 3rd manual version check passed
         cd build/khmer

doc/user/known-issues.rst

@@ -4,24 +4,24 @@
    Copyright (C) 2015 The Regents of the University of California.
    It is licensed under the three-clause BSD license; see LICENSE.
    Contact: [email protected]
-   
+
    Redistribution and use in source and binary forms, with or without
    modification, are permitted provided that the following conditions are
    met:
-   
+
     * Redistributions of source code must retain the above copyright
       notice, this list of conditions and the following disclaimer.
-   
+
     * Redistributions in binary form must reproduce the above
       copyright notice, this list of conditions and the following
       disclaimer in the documentation and/or other materials provided
       with the distribution.
-   
+
     * Neither the name of the Michigan State University nor the names
       of its contributors may be used to endorse or promote products
       derived from this software without specific prior written
       permission.
-   
+
    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
    "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
    LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
@@ -33,12 +33,17 @@
    THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
    (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
    OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-   
+
    Contact: [email protected]
 
 Known Issues
 ============
 
-``load-graph.py`` in multithreaded mode will find slightly different number of
-unique kmers. This is being investigated in
-https://github.com/dib-lab/khmer/issues/1248
+- ``load-graph.py`` in multithreaded mode will find slightly different number of
+  unique kmers. This is being investigated in
+  https://github.com/dib-lab/khmer/issues/1248
+
+- Any scripts that consume FASTA or FASTQ data are unresponsive to attempts to
+  terminate the program with ``ctrl-c``. Eventually khmer should handle this
+  properly, but for now it should be possible to halt a script using ``ctrl-\``.
+  This is being tracked in https://github.com/dib-lab/khmer/issues/1618.