Merge branch 'latest' into olgabot/pranthi-fxn-in-fxn

.github/workflows/rust.yml

@@ -136,15 +136,24 @@ jobs:
   lints:
     name: Lints
     runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        build: [beta, stable]
+        include:
+          - build: beta
+            rust: beta
+          - build: stable
+            rust: stable
     steps:
       - name: Checkout sources
         uses: actions/checkout@v1
 
-      - name: Install stable toolchain
+      - name: Install Rust toolchain
         uses: actions-rs/toolchain@v1
         with:
           profile: minimal
-          toolchain: stable
+          toolchain: ${{ matrix.rust }}
           override: true
           components: rustfmt, clippy
 
@@ -171,10 +180,10 @@ jobs:
           toolchain: stable
           target: wasm32-unknown-unknown
 
-      - uses: actions-rs/install@v0.1
+      - uses: actions-rs/cargo@v1
         with:
-          crate: wasm-pack
-          version: latest
+          command: install
+          args: --force wasm-pack --version 0.10.0
 
       - name: Prepare node for running tests
         uses: actions/setup-node@v1
@@ -188,6 +197,14 @@ jobs:
       - name: run wasm-pack build
         run: wasm-pack build src/core -d ../../pkg
 
+      - name: Prepare package for NPM publishing
+        working-directory: pkg
+        run: npm pack
+
+      - uses: actions/upload-artifact@v2
+        with:
+          path: 'pkg/sourmash*.tgz'
+
   wasm32-wasi:
     name: Run tests under wasm32-wasi
     runs-on: ubuntu-latest

.github/workflows/rust_publish.yml

@@ -18,9 +18,10 @@ jobs:
       - uses: actions-rs/cargo@v1
         with:
           command: install
-          args: --force wasm-pack --version 0.8.1
+          args: --force wasm-pack --version 0.10.0
       - name: run wasm-pack
-        run: wasm-pack build src/core -d ../../pkg
+        run: |
+          wasm-pack build src/core -d ../../pkg
 
       - name: Prepare node for NPM publishing
         uses: actions/setup-node@v1
@@ -29,7 +30,8 @@ jobs:
           registry-url: https://registry.npmjs.org/
 
       - name: Publish to NPM
-        run: '(cd pkg && npm publish)'
+        working-directory: pkg
+        run: npm publish
         env:
           NODE_AUTH_TOKEN: ${{ secrets.NPM_TOKEN }}
 

README.md

@@ -3,14 +3,15 @@
 Quickly search, compare, and analyze genomic and metagenomic data sets.
 
 [![Documentation](https://readthedocs.org/projects/sourmash/badge/?version=latest)](http://sourmash.readthedocs.io/en/latest/)
-[![Build Status](/~https://github.com/dib-lab/sourmash/workflows/Python%20tests/badge.svg)](/~https://github.com/dib-lab/sourmash/actions/)
+[![Gitter](https://badges.gitter.im/sourmash-bio/community.svg)](https://gitter.im/sourmash-bio/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge)
+[![Build Status](/~https://github.com/sourmash-bio/sourmash/workflows/Python%20tests/badge.svg)](/~https://github.com/sourmash-bio/sourmash/actions/)
 [![Bioconda install](https://img.shields.io/conda/dn/bioconda/sourmash.svg?style=flag&label=Bioconda)](https://anaconda.org/bioconda/sourmash)
 <a href="https://pypi.org/project/sourmash/"><img alt="PyPI" src="https://badge.fury.io/py/sourmash.svg"></a>
-[![codecov](https://codecov.io/gh/dib-lab/sourmash/branch/latest/graph/badge.svg)](https://codecov.io/gh/dib-lab/sourmash)
+[![codecov](https://codecov.io/gh/sourmash-bio/sourmash/branch/latest/graph/badge.svg)](https://codecov.io/gh/sourmash-bio/sourmash)
 [![DOI](http://joss.theoj.org/papers/10.21105/joss.00027/status.svg)](http://joss.theoj.org/papers/10.21105/joss.00027)
-<a href="/~https://github.com/dib-lab/sourmash/blob/latest/LICENSE"><img alt="License: 3-Clause BSD" src="https://img.shields.io/badge/License-BSD%203--Clause-blue.svg"></a>
+<a href="/~https://github.com/sourmash-bio/sourmash/blob/latest/LICENSE"><img alt="License: 3-Clause BSD" src="https://img.shields.io/badge/License-BSD%203--Clause-blue.svg"></a>
 
-<p align="center"><img src="https://raw.githubusercontent.com/dib-lab/sourmash/latest/doc/_static/logo.png" height="256" /></p>
+<p align="center"><img src="https://raw.githubusercontent.com/sourmash-bio/sourmash/latest/doc/_static/logo.png" height="256" /></p>
 
 Usage:
 
@@ -80,17 +81,16 @@ $ sourmash --help
 ```
 
 which will install
-[the latest released version](/~https://github.com/dib-lab/sourmash/releases).
+[the latest released version](/~https://github.com/sourmash-bio/sourmash/releases).
 
 ## Support
 
-Please ask questions and files issues
-[on Github](/~https://github.com/dib-lab/sourmash/issues).
+For questions, please open an issue [on Github](/~https://github.com/sourmash-bio/sourmash/issues), or ask in our [chat](https://gitter.im/sourmash-bio/community?utm_source=share-link&utm_medium=link&utm_campaign=share-link).
 
 ## Development
 
 Development happens on github at
-[dib-lab/sourmash](/~https://github.com/dib-lab/sourmash).
+[sourmash-bio/sourmash](/~https://github.com/sourmash-bio/sourmash).
 
 sourmash is developed in Python and Rust, and you will need a Rust
 environment to build it; see [the developer notes](doc/developer.md)
@@ -110,6 +110,18 @@ Tests require py.test and can be run with `make test`.
 Please see [the developer notes](doc/developer.md) for more information
 on getting set up with a development environment.
 
+## Research notice
+
+Please note that this repository is participating in a study into sustainability
+ of open source projects. Data will be gathered about this repository for
+ approximately the next 12 months, starting from 2021-06-11.
+
+Data collected will include number of contributors, number of PRs, time taken to
+ close/merge these PRs, and issues closed.
+
+For more information, please visit
+[our informational page](https://sustainable-open-science-and-software.github.io/) or download our [participant information sheet](https://sustainable-open-science-and-software.github.io/assets/PIS_sustainable_software.pdf).
+
 ----
 
 CTB

doc/api-example.md

@@ -395,7 +395,7 @@ True
 
 (Beware, these are confusing techniques for working with hashes that
 are easy to get wrong! We suggest
-[posting questions in the issue tracker](/~https://github.com/dib-lab/sourmash/issues)
+[posting questions in the issue tracker](/~https://github.com/sourmash-bio/sourmash/issues)
 as you go, if you are interested in exploring this area!)
 
 The hashing function used is identical between num and scaled signatures,
@@ -596,8 +596,8 @@ Now, let's load in all of the signatures from the test directory:
 ...    hashes_inserted = db.insert(sig)
 ...    print(f"Inserted {hashes_inserted} hashes into db.")
 Inserted 493 hashes into db.
-Inserted 525 hashes into db.
 Inserted 490 hashes into db.
+Inserted 525 hashes into db.
 
 ```
 

doc/classifying-signatures.md

@@ -139,7 +139,7 @@ Please see Appendix B, below, for some actual numbers and output.
 
 **Buyer beware:** There are substantial challenges in doing this kind
 of analysis on real metagenomic samples, relating to genome representation
-and strain overlap; see [this issue](/~https://github.com/dib-lab/sourmash/issues/461) for a discussion.
+and strain overlap; see [this issue](/~https://github.com/sourmash-bio/sourmash/issues/461) for a discussion.
 
 ### Computing signature similarity with angular similarity.
 
@@ -173,7 +173,7 @@ We suggest the following approach:
 
 * explore the available databases;
 
-* then ask questions [via the issue tracker](/~https://github.com/dib-lab/sourmash/issues) and we will do our best to help you out!
+* then ask questions [via the issue tracker](/~https://github.com/sourmash-bio/sourmash/issues) and we will do our best to help you out!
 
 This helps us figure out what people are actually interested in doing, and
 any help we provide via the issue tracker will eventually be added into the