[MRG] release notes for v2.0

.travis.yml

@@ -53,7 +53,7 @@ jobs:
         - CIBW_SKIP='*-manylinux1_i686'
       install: skip
       script:
-        - $PIP install cibuildwheel==0.10.0
+        - sudo $PIP install cibuildwheel==0.10.1
         - cibuildwheel --output-dir wheelhouse
       deploy:
         provider: releases
@@ -69,7 +69,7 @@ jobs:
       osx_image: xcode10.1
       language: generic
       before_script:
-        - $PIP install -U pip setuptools
+        - sudo $PIP install -U pip setuptools
       env:
         - PIP=pip2
         - CIBW_ENVIRONMENT_MACOS='MACOSX_DEPLOYMENT_TARGET=10.11'

MANIFEST.in

@@ -6,3 +6,4 @@ recursive-include third-party *.cc *.h
 global-exclude *.orig
 global-exclude *.pyc
 global-exclude *.so
+prune tests/test-data/

doc/release-notes/sourmash-2.0.md

@@ -0,0 +1,40 @@
+# sourmash v2.0 release notes
+
+We are pleased to announce release 2.0 of sourmash!  This release is
+the first full release of sourmash since 1.0, and provides much
+expanded core functionality as well as many more utility functions.
+
+The full documentation for this version is available at
+https://sourmash.readthedocs.io/en/v2.0/. Documentation for the latest
+released version is at http://sourmash.readthedocs.io/en/stable/.
+
+**This release breaks compatibility with sourmash 1.0: the sourmash
+Python API, command-line, and signature file formats have all changed
+substantially.** Please post questions about migrating to sourmash 2.0
+in the
+[sourmash issue tracker](https://github.com/dib-lab/sourmash/issues/new).
+
+## Major new features since 1.0
+
+This is a list of substantial new features and functionality in sourmash 2.0.
+
+* Added Sequence Bloom Tree search to enable similarity and containment queries on very large collections of signatures in low memory; see `sourmash index`, `sourmash search`, and `sourmash gather` in [the command line documentation](../command-line.html).
+* Added "LCA databases" for fast searching of large databases in not-so-low memory; see [`sourmash lca index` in command-line docs](../command-line.html#sourmash-lca-subcommands-for-taxonomic-classification).
+* Created [precomputed databases](../databases.html) for most of GenBank genomes.
+* Added taxonomic reporting functionality in the `sourmash lca` submodule - [see command-line docs](../command-line.html#sourmash-lca-subcommands-for-taxonomic-classification).
+* Added signature manipulation utilities in the `sourmash signature` submodule - [see command-line docs](../command-line.html#sourmash-signature-subcommands-for-signature-manipulation)
+* Introduced new modulo hash or "scaled" signatures for containment analysis; see [Using sourmash: a practical guide](../using-sourmash-a-guide.html#what-resolution-should-my-signatures-be-how-should-i-compute-them) and [more details in the Python API examples](../api-example.html#sourmash-minhash-objects-and-manipulations).
+* Switched to using JSON instead of YAML for signatures.
+* Many performance optimizations!
+* Many more tests!
+* A much cleaner and more robust [Python API](../api-example.html).
+* Installation via bioconda is now recommended (and actively maintained :)
+* Support for building signatures from BAM files.
+
+## Other features of note
+
+* Renamed Python library to `sourmash` from `sourmash_lib`.
+* Signatures now default to a license of CC0.
+* Implemented `sourmash watch` for classifying streams of data (see [blog post](http://ivory.idyll.org/blog/2017-sourmash-sra-microbial-wgs.html)).
+* Implemented `sourmash categorize` for classifying many signatures (see [blog post](http://ivory.idyll.org/blog/2017-sourmash-sra-microbial-wgs.html)).
+* CSV output enabled from most commands.

setup.py

@@ -50,7 +50,7 @@
     "author": "C. Titus Brown",
     "author_email": "titus@idyll.org",
     "license": "BSD 3-clause",
-    "packages": find_packages(),
+    "packages": find_packages(exclude=["tests", "benchmarks"]),
     "entry_points": {'console_scripts': [
         'sourmash = sourmash.__main__:main'
         ]