Update the 'refactor/subparsers' branch from #245. (#722)

.coveragerc

@@ -1,3 +1,11 @@
 [run]
-include=sourmash,sourmash_lib/*.py
-omit=setup.py,tests/test__minhash.py,tests/test_sourmash.py,tests/sourmash_tst_utils.py,third-party/smhasher/MurmurHash3.cc
+include=
+    sourmash/*.py
+    sourmash_lib/*.py
+omit =
+    doc/conf.py
+    setup.py
+    tests/*
+    third-party/smhasher/MurmurHash3.cc
+    .tox/*
+    benchmarks/*

.git_archival.txt

@@ -0,0 +1 @@
+ref-names: $Format:%D$

.gitattributes

@@ -0,0 +1 @@
+.git_archival.txt  export-subst

.gitignore

@@ -19,3 +19,8 @@ _minhash.so
 .coverage
 sourmash_lib/_minhash.cpp
 sourmash/_minhash.cpp
+.asv/
+.eggs/
+.pytest_cache
+.python-version
+sourmash/version.py

.travis.yml

@@ -1,48 +1,83 @@
 language: python
-services:
-- redis-server
-- docker
+os: linux
+dist: xenial
+
+cache:
+  directories:
+    - $HOME/.cache/pip
+
 branches:
   only:
   - master
   - "/^v.*$/"
-matrix:
-  fast_finish: true
+
+script: tox
+
+install: pip install tox-travis
+
+jobs:
+  allow_failures:
+    - name: integration (ipfs/redis)
   include:
-  - os: linux
-    python: '2.7'
-    sudo: required
-    dist: xenial
-    env:
-    - TOX_ENV=py27
-  - os: linux
-    python: '3.5'
-    sudo: required
-    dist: xenial
-    env:
-    - TOX_ENV=py35
-  - os: linux
-    python: '3.6'
-    sudo: required
-    dist: xenial
-    env:
-    - TOX_ENV=py36
-install:
-- pip install tox
-- sudo snap install ipfs
-script:
-- "/snap/bin/ipfs daemon --init --offline &"
-- tox -e $TOX_ENV
-before_deploy:
-- git clean -xfd
-- docker run --rm -v `pwd`:/io quay.io/pypa/manylinux1_x86_64 $PRE_CMD /io/.travis/build-wheels.sh
-  $TOX_ENV
-deploy:
-  provider: releases
-  api_key:
-    secure: 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
-  file_glob: true
-  file: dist/sourmash*.whl
-  skip_cleanup: true
-  on:
-    tags: true
+    - &check
+      stage: check # do a pre-screen to make sure this is even worth testing
+      python: 3.7
+
+    - &test
+      stage: test
+      python: 2.7
+    - <<: *test
+      os: osx
+      language: generic
+      env:
+        - TOXENV=py36
+    - <<: *test
+      python: 3.7
+      name: integration (ipfs/redis)
+      before_install:
+        - sudo snap install ipfs
+        - "/snap/bin/ipfs --version"
+        - "/snap/bin/ipfs daemon --init --offline &>/dev/null &"
+      services:
+        - redis-server
+        - docker
+    - <<: *test
+      python: 3.6
+    - <<: *test
+      python: 3.5
+
+    - &wheel
+      stage: build wheel and send to github releases
+      python: 3.7
+      services:
+        - docker
+      env:
+        - PIP=pip
+        - CIBW_SKIP='*-manylinux1_i686'
+      install: skip
+      script:
+        - sudo $PIP install cibuildwheel==0.10.2
+        - cibuildwheel --output-dir wheelhouse
+      deploy:
+        provider: releases
+        api_key:
+          secure: "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"
+        file_glob: true
+        file: wheelhouse/sourmash*.whl
+        skip_cleanup: true
+        on:
+          tags: true
+    - <<: *wheel
+      os: osx
+      osx_image: xcode10.1
+      language: generic
+      before_script:
+        - sudo $PIP install -U pip setuptools
+      env:
+        - PIP=pip2
+        - CIBW_ENVIRONMENT_MACOS='MACOSX_DEPLOYMENT_TARGET=10.11'
+
+stages:
+  - check
+  - test
+  - wheel

.travis/install_cargo.sh

@@ -0,0 +1,4 @@
+#! /bin/sh
+curl https://sh.rustup.rs -sSf | sh -s -- -y --default-toolchain stable
+export PATH="$HOME/.cargo/bin:$PATH"
+rustc -V

CITATION.cff

@@ -0,0 +1,13 @@
+cff-version: 1.0.3
+message: If you use this software, please cite it as below.
+title: sourmash: a library for MinHash sketching of DNA
+version: 2.0.0
+doi: 10.21105/joss.00027
+date-released: 2019-01-10
+authors:
+  - family-names: Brown
+    given-names: C. Titus
+    orcid: https://orcid.org/0000-0001-6001-2677
+  - family-names: Irber Junior
+    given-names: Luiz Carlos
+    orcid: https://orcid.org/0000-0003-4371-9659

Cargo.toml

@@ -0,0 +1,75 @@
+[package]
+name = "sourmash"
+version = "0.3.0"
+authors = ["Luiz Irber <[email protected]>"]
+description = "MinHash sketches for genomic data"
+repository = "https://github.com/luizirber/sourmash-rust"
+keywords = ["minhash", "bioinformatics"]
+categories = ["science", "algorithms", "data-structures"]
+license = "BSD-3-Clause"
+edition = "2018"
+
+[lib]
+name = "sourmash"
+crate-type = ["cdylib", "rlib"]
+bench = false
+
+[profile.release]
+lto=true
+
+[features]
+from-finch = ["finch", "needletail"]
+
+[workspace]
+
+#[build-dependencies]
+#cbindgen = "~0.6.7"
+
+[dependencies]
+byteorder = "^1.2"
+cfg-if = "0.1"
+clap = { version = "~2.32", features = ["yaml"] }
+env_logger = "0.6.0"
+exitfailure = "0.5.1"
+failure = "0.1.3"
+failure_derive = "0.1.3"
+finch = { version = "~0.1.6", optional = true }
+fixedbitset = "^0.1.9"
+human-panic = "1.0.1"
+lazy_static = "1.0.0"
+lazy-init = "0.3.0"
+log = "0.4.0"
+md5 = "0.6.0"
+murmurhash3 = "~0.0.5"
+needletail = { version = "~0.2.1", optional = true }
+serde = "1.0"
+serde_derive = "~1.0.58"
+serde_json = "1.0.2"
+ukhs = "0.3.4"
+bio = { git = "https://github.com/luizirber/rust-bio", branch = "feature/fastx_reader" }
+primal = "0.2.3"
+pdatastructs = "0.5.0"
+itertools = "0.8.0"
+typed-builder = "0.3.0"
+csv = "1.0.7"
+
+[target.'cfg(target_arch = "wasm32")'.dependencies.wasm-bindgen]
+version = "^0.2"
+features = ["serde-serialize"]
+
+[target.'cfg(not(target_arch = "wasm32"))'.dependencies.ocf]
+version = "0.1"
+path = "ocf"
+default-features = false
+features = ["bz2"]
+
+[dev-dependencies]
+proptest = "^0.8"
+criterion = "^0.2"
+rand = "^0.5"
+tempfile = "3"
+assert_matches = "1.2"
+
+[[bench]]
+name = "index"
+harness = false

MANIFEST.in

@@ -9,3 +9,4 @@ global-exclude *.so
 graft tests
 global-exclude *.orig
 global-exclude *.pyc
+prune tests/test-data/

Makefile

@@ -16,7 +16,7 @@ dist: FORCE
 	$(PYTHON) setup.py sdist
 
 test: all
-	pip install '.[test]'
+	pip install -e '.[test]'
 	$(PYTHON) -m pytest
 
 doc: .PHONY
@@ -35,4 +35,7 @@ wheel:
 	docker pull $${DOCKER_IMAGE} ; \
 	docker run --rm -v `pwd`:/io $${DOCKER_IMAGE} /io/travis/build-wheels.sh
 
+last-tag:
+	git fetch -p -q; git tag -l | sort -V | tail -1
+
 FORCE:

README.md

@@ -1,7 +1,7 @@
 # sourmash
 
 [![Documentation](https://readthedocs.org/projects/sourmash/badge/?version=latest)](http://sourmash.readthedocs.io/en/latest/)
-[![Build Status](https://travis-ci.org/dib-lab/sourmash.svg?branch=master)](https://travis-ci.org/dib-lab/sourmash)
+[![Build Status](https://travis-ci.com/dib-lab/sourmash.svg?branch=master)](https://travis-ci.com/dib-lab/sourmash)
 [![codecov](https://codecov.io/gh/dib-lab/sourmash/branch/master/graph/badge.svg)](https://codecov.io/gh/dib-lab/sourmash)
 [![DOI](http://joss.theoj.org/papers/10.21105/joss.00027/status.svg)](http://joss.theoj.org/papers/10.21105/joss.00027)
 
@@ -13,11 +13,7 @@ Usage:
     sourmash compare *.sig -o distances
     sourmash plot distances
 
-We have demo notebooks on binder that you can interact with:
-
-[![Binder](http://mybinder.org/badge.svg)](http://mybinder.org/repo/dib-lab/sourmash)
-
-Sourmash is [published on JOSS](http://dx.doi.org/10.21105/joss.00027).
+Sourmash 1.0 is [published on JOSS](https://doi.org/10.21105/joss.00027); please cite that paper if you use sourmash (`doi: 10.21105/joss.00027`):.
 
 ----
 
@@ -26,18 +22,30 @@ combined with @ctb's love of whiskey.
 ([Sour mash](https://en.wikipedia.org/wiki/Sour_mash) is used in
 making whiskey.)
 
-Authors: [C. Titus Brown](mailto:[email protected]) ([@ctb](http://github.com/ctb)) and [Luiz C. Irber, Jr](mailto:[email protected]) ([@luizirber](http://github.com/luizirber)).
+Primary authors: [C. Titus Brown](mailto:[email protected]) ([@ctb](http://github.com/ctb)) and [Luiz C. Irber, Jr](mailto:[email protected]) ([@luizirber](http://github.com/luizirber)).
 
 sourmash is a product of the
 [Lab for Data-Intensive Biology](http://ivory.idyll.org/lab/) at the
 [UC Davis School of Veterinary Medicine](http://www.vetmed.ucdavis.edu).
 
 ## Installation
 
-We currently recommend installing the 2.0 pre-release series.
-You can use pip to do that like so:
+We recommend using bioconda to install sourmash:
+
+```
+conda install sourmash
+```
+This will install the latest stable version of sourmash 2.
+
+You can also use pip to install sourmash:
+
+```
+pip install sourmash
+```
+
+A quickstart tutorial [is available](https://sourmash.readthedocs.io/en/latest/tutorials.html).
 
-    pip install --pre sourmash
+### Requirements
 
 sourmash runs under both Python 2.7.x and Python 3.5+.  The base
 requirements are screed and ijson, together with a C++ development
@@ -55,7 +63,7 @@ For `search` and `gather` you also need `khmer` version 2.1+.
 Bioconda is a channel for the [conda](http://conda.pydata.org/docs/intro.html) package manager with a focus on bioinformatics software. After installing conda you will need to add the bioconda channel as well as the [other channels](https://bioconda.github.io/index.html#set-up-channels) bioconda depends on. Once you have setup bioconda, you can install sourmash by running:
 
 ```bash
-$ conda create -n sourmash_env sourmash python=3.6.4
+$ conda create -n sourmash_env -c conda-forge -c bioconda sourmash python=3.7
 $ source activate sourmash_env
 $ sourmash compute -h
 ```
@@ -85,4 +93,4 @@ Please see [the developer notes](doc/developer.md) for more information.
 ----
 
 CTB
-June 2018
+Dec 2018