[MRG] update various descriptions to talk about k-mers, not just DNA

.github/workflows/metadata.yml

@@ -16,4 +16,4 @@ jobs:
 
       - name: Trigger new archival in software heritage on new tags
         if: startsWith(github.ref, 'refs/tags/')
-        run: curl https://archive.softwareheritage.org/api/1/origin/save/git/url/https://github.com/dib-lab/sourmash.git/
+        run: curl https://archive.softwareheritage.org/api/1/origin/save/git/url/https://github.com/sourmash-bio/sourmash.git/

asv.conf.json

@@ -1,7 +1,7 @@
 {
     "version": 1,
     "project": "sourmash",
-    "project_url": "https://github.com/dib-lab/sourmash",
+    "project_url": "https://github.com/sourmash-bio/sourmash",
     "repo": ".",
     "branches": ["latest"],
     "dvcs": "git",

codemeta.json

@@ -5,7 +5,7 @@
 
   ],
   "identifier": "",
-  "codeRepository": "https://github.com/dib-lab/sourmash",
+  "codeRepository": "https://github.com/sourmash-bio/sourmash",
   "datePublished": "2016-06-07",
   "dateModified": "2016-06-07",
   "dateCreated": "2016-06-07",
@@ -14,4 +14,4 @@
   "license": "BSD 3-clause",
   "title": "sourmash",
   "version": "v1.0.0"
-}
+}

doc/api-example.md

@@ -241,7 +241,7 @@ ValueError: invalid DNA character in input k-mer: NTGCGAGTGTTGAAGTTCGGCGGTACATCA
 For protein sequences, sourmash does not currently do any invalid
 character detection; k-mers are hashed as they are, and can only be
 matched by an identical k-mer (with the same invalid character).
-(Please [file an issue](https://github.com/dib-lab/sourmash/issues) if
+(Please [file an issue](https://github.com/sourmash-bio/sourmash/issues) if
 you'd like us to change this!)
 ```
 >>> K = 7

pyproject.toml

@@ -10,7 +10,7 @@ build-backend = 'setuptools.build_meta'
 
 [project]
 name = "sourmash"
-description = "tools for comparing DNA sequences with MinHash sketches"
+description = "tools for comparing biological sequences with k-mer sketches"
 readme = "README.md"
 
 authors = [
@@ -91,9 +91,9 @@ license = { text = "BSD 3-Clause License" }
 [project.urls]
 "Homepage" = "https://sourmash.bio/"
 "Documentation" = "https://sourmash.readthedocs.io"
-"CI" = "https://github.com/dib-lab/sourmash/actions"
-"Source" = "https://github.com/dib-lab/sourmash"
-"Tracker" = "https://github.com/dib-lab/sourmash/issues"
+"CI" = "https://github.com/sourmash-bio/sourmash/actions"
+"Source" = "https://github.com/sourmash-bio/sourmash"
+"Tracker" = "https://github.com/sourmash-bio/sourmash/issues"
 
 [project.scripts]
 "sourmash" = "sourmash.__main__:main"
@@ -120,7 +120,7 @@ doc = [
   "sphinxcontrib-napoleon",
   "nbsphinx",
   "ipython",
-  "docutils>=0.17.1,<0.19.0",
+  "docutils>=0.17.1,<0.18",
 ]
 storage = [
   "ipfshttpclient>=0.4.13",

src/core/Cargo.toml

@@ -3,7 +3,7 @@ name = "sourmash"
 version = "0.11.0"
 authors = ["Luiz Irber <[email protected]>"]
 description = "MinHash sketches for genomic data"
-repository = "https://github.com/dib-lab/sourmash"
+repository = "https://github.com/sourmash-bio/sourmash"
 keywords = ["minhash", "bioinformatics"]
 categories = ["science", "algorithms", "data-structures"]
 license = "BSD-3-Clause"

src/core/README.md

@@ -6,11 +6,11 @@
 [![](http://meritbadge.herokuapp.com/sourmash)](https://crates.io/crates/sourmash)
 [![Rust API Documentation on docs.rs](https://docs.rs/sourmash/badge.svg)](https://docs.rs/sourmash)
 [![build-status]][github-actions]
-[![codecov](https://codecov.io/gh/dib-lab/sourmash/branch/latest/graph/badge.svg)](https://codecov.io/gh/dib-lab/sourmash)
-<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>
+[![codecov](https://codecov.io/gh/sourmash-bio/sourmash/branch/latest/graph/badge.svg)](https://codecov.io/gh/sourmash-bio/sourmash)
+<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>
 
-[build-status]: https://github.com/dib-lab/sourmash/workflows/Rust%20checks/badge.svg
-[github-actions]: https://github.com/dib-lab/sourmash/actions?query=workflow%3A%22Rust+checks%22
+[build-status]: https://github.com/sourmash-bio/sourmash/workflows/Rust%20checks/badge.svg
+[github-actions]: https://github.com/sourmash-bio/sourmash/actions?query=workflow%3A%22Rust+checks%22
 
 ----
 
@@ -29,12 +29,12 @@ sourmash is a product of the
 ## Support
 
 Please ask questions and files issues
-[on Github](https://github.com/dib-lab/sourmash/issues).
+[on Github](https://github.com/sourmash-bio/sourmash/issues).
 
 ## Development
 
 Development happens on github at
-[dib-lab/sourmash](https://github.com/dib-lab/sourmash).
+[sourmash-bio/sourmash](https://github.com/sourmash-bio/sourmash).
 
 ## Minimum supported Rust version
 

src/sourmash/__init__.py

@@ -1,5 +1,5 @@
-"""A library for computing hash sketches from DNA sequences, comparing
-them to each other, and plotting the results.
+"""A library for creating k-mer sketches from biological sequences, comparing
+them to each other, and working with the results.
 
 Public API:
 
@@ -12,7 +12,7 @@ class MinHash - hash sketch class
 
 Please see https://sourmash.readthedocs.io/en/latest/api.html for API docs.
 
-The sourmash code is available at github.com/dib-lab/sourmash/ under the
+The sourmash code is available at github.com/sourmash-bio/sourmash/ under the
 BSD 3-Clause license.
 """
 from deprecation import deprecated

src/sourmash/cli/__init__.py

@@ -123,7 +123,7 @@ def get_parser():
         if dirpath in alias:
             usage += '        sourmash {gd:s} --help\n'.format(gd=alias[dirpath])
 
-    desc = 'Compute, compare, manipulate, and analyze MinHash sketches of DNA sequences.\n\nUsage instructions:\n' + usage
+    desc = 'Create, compare, and manipulate k-mer sketches of biological sequences.\n\nUsage instructions:\n' + usage
     parser = SourmashParser(prog='sourmash', description=desc, formatter_class=RawDescriptionHelpFormatter, usage=SUPPRESS)
     parser._optionals.title = 'Options'
     parser.add_argument('-v', '--version', action='version', version='sourmash '+ sourmash.VERSION)