diff --git a/doc/other-languages.md b/doc/other-languages.md index 49f64dcd0a..80bc5c8b81 100644 --- a/doc/other-languages.md +++ b/doc/other-languages.md @@ -32,7 +32,7 @@ sourmash_comp_matrix <- as.matrix(sourmash_comp_matrix) ``` -See the output of plotting and clustering this matrix by downloading and opening [this html](https://raw.githubusercontent.com/dib-lab/sourmash/latest/doc/_static/ecoli-cmp.html), produced by [this RMarkdown file](https://raw.githubusercontent.com/dib-lab/sourmash/latest/doc/_static/ecoli-cmp.Rmd). +See the output of plotting and clustering this matrix by downloading and opening [this html](https://raw.githubusercontent.com/sourmash-bio/sourmash/latest/doc/_static/ecoli-cmp.html), produced by [this RMarkdown file](https://raw.githubusercontent.com/sourmash-bio/sourmash/latest/doc/_static/ecoli-cmp.Rmd). -You can download the `ecoli.cmp.csv` file itself [here](https://raw.githubusercontent.com/dib-lab/sourmash/latest/doc/_static/ecoli.cmp.csv). +You can download the `ecoli.cmp.csv` file itself [here](https://raw.githubusercontent.com/sourmash-bio/sourmash/latest/doc/_static/ecoli.cmp.csv). diff --git a/doc/release-notes/releases.md b/doc/release-notes/releases.md index 6a492e1c24..bd7e302c21 100644 --- a/doc/release-notes/releases.md +++ b/doc/release-notes/releases.md @@ -1,7 +1,7 @@ # sourmash release notes Please see the -[github releases page](https://github.com/dib-lab/sourmash/releases) +[github releases page](https://github.com/sourmash-bio/sourmash/releases) for detailed release notes for each version! ```{toctree} diff --git a/doc/release-notes/sourmash-2.0.md b/doc/release-notes/sourmash-2.0.md index f3fd868661..c3b8647dd5 100644 --- a/doc/release-notes/sourmash-2.0.md +++ b/doc/release-notes/sourmash-2.0.md @@ -12,7 +12,7 @@ released version is at http://sourmash.readthedocs.io/en/stable/. 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). +[sourmash issue tracker](https://github.com/sourmash-bio/sourmash/issues/new). ## Major new features since 1.0 diff --git a/doc/release-notes/sourmash-3.0.md b/doc/release-notes/sourmash-3.0.md index f4add5824e..db82b72611 100644 --- a/doc/release-notes/sourmash-3.0.md +++ b/doc/release-notes/sourmash-3.0.md @@ -10,25 +10,25 @@ released version is at http://sourmash.readthedocs.io/en/stable/. Python API, command-line, signature and databases file formats are all the same.** We are releasing 3.0 to indicate the build system and internal implementation changed. Please post questions about migrating to sourmash 3.0 -in the [sourmash issue tracker](https://github.com/dib-lab/sourmash/issues/new). +in the [sourmash issue tracker](https://github.com/sourmash-bio/sourmash/issues/new). ## Highlighted changes since 2.0 -This is a list of substantial new features and functionality since sourmash 2.0. For more details check the [releases page on GitHub](https://github.com/dib-lab/sourmash/releases). +This is a list of substantial new features and functionality since sourmash 2.0. For more details check the [releases page on GitHub](https://github.com/sourmash-bio/sourmash/releases). Features: -- Replacing C++ with Rust ([#424](https://github.com/dib-lab/sourmash/pull/424)) -- Create an `Index` abstract base class ([#556](https://github.com/dib-lab/sourmash/pull/556)) -- Dayhoff and HP encoding for proteins ([#689](https://github.com/dib-lab/sourmash/pull/689)) ([#758](https://github.com/dib-lab/sourmash/pull/758)) -- Add `sourmash signature filter` to do abundance filtering. ([#748](https://github.com/dib-lab/sourmash/pull/748)) -- Parallelized compare function with multiprocessing ([#709](https://github.com/dib-lab/sourmash/pull/709)) -- add compute signatures for 10x bam file ([#713](https://github.com/dib-lab/sourmash/pull/713)) +- Replacing C++ with Rust ([#424](https://github.com/sourmash-bio/sourmash/pull/424)) +- Create an `Index` abstract base class ([#556](https://github.com/sourmash-bio/sourmash/pull/556)) +- Dayhoff and HP encoding for proteins ([#689](https://github.com/sourmash-bio/sourmash/pull/689)) ([#758](https://github.com/sourmash-bio/sourmash/pull/758)) +- Add `sourmash signature filter` to do abundance filtering. ([#748](https://github.com/sourmash-bio/sourmash/pull/748)) +- Parallelized compare function with multiprocessing ([#709](https://github.com/sourmash-bio/sourmash/pull/709)) +- add compute signatures for 10x bam file ([#713](https://github.com/sourmash-bio/sourmash/pull/713)) Improvements: -- improve error handling in `sourmash lca index`. ([#798](https://github.com/dib-lab/sourmash/pull/798)) -- Include more base deps: numpy, scipy and matplotlib ([#770](https://github.com/dib-lab/sourmash/pull/770)) -- use `bam2fasta` package to simplify `sourmash compute` ([#768](https://github.com/dib-lab/sourmash/pull/768)) -- add a `--abundances-from` flag to sourmash signature intersect, to preserve abundances ([#747](https://github.com/dib-lab/sourmash/pull/747)) -- Compare outputs can be saved to an output dir ([#715](https://github.com/dib-lab/sourmash/pull/715)) +- improve error handling in `sourmash lca index`. ([#798](https://github.com/sourmash-bio/sourmash/pull/798)) +- Include more base deps: numpy, scipy and matplotlib ([#770](https://github.com/sourmash-bio/sourmash/pull/770)) +- use `bam2fasta` package to simplify `sourmash compute` ([#768](https://github.com/sourmash-bio/sourmash/pull/768)) +- add a `--abundances-from` flag to sourmash signature intersect, to preserve abundances ([#747](https://github.com/sourmash-bio/sourmash/pull/747)) +- Compare outputs can be saved to an output dir ([#715](https://github.com/sourmash-bio/sourmash/pull/715)) diff --git a/doc/release-notes/sourmash-4.0.md b/doc/release-notes/sourmash-4.0.md index 681233ad16..c8e40d5a19 100644 --- a/doc/release-notes/sourmash-4.0.md +++ b/doc/release-notes/sourmash-4.0.md @@ -12,7 +12,7 @@ Please see [our migration guide](../support.md#migrating-from-sourmash-v3x-to-sourmash-v4x) for guidance on updating to sourmash v4, and post questions about migrating to sourmash 4.0 in the -[sourmash issue tracker](https://github.com/dib-lab/sourmash/issues/new). +[sourmash issue tracker](https://github.com/sourmash-bio/sourmash/issues/new). ## Major changes for 4.0 @@ -23,7 +23,7 @@ release; you should get the same results with v4 as you get with v3, except where command-line parameters need to be adjusted as noted below (see: protein ksize #1277, lca summarize changes #1175, sourmash gather on signatures without abundance #1328). Please -[file an issue](https://github.com/dib-lab/sourmash/issues) if your +[file an issue](https://github.com/sourmash-bio/sourmash/issues) if your results change! ### New or changed behavior diff --git a/doc/tutorial-long.md b/doc/tutorial-long.md index 60d7c1f145..149f377954 100644 --- a/doc/tutorial-long.md +++ b/doc/tutorial-long.md @@ -82,7 +82,7 @@ About two years ago, [Ondov et al. (2016)](https://genomebiology.biomedcentral.c The basic idea behind MinHash is that you pick a small subset of k-mers to look at, and you use those as a proxy for *all* the k-mers. The trick is that you pick the k-mers randomly but consistently: so if a chosen k-mer is present in two data sets of interest, it will be picked in both. This is done using a clever trick that we can try to explain to you in class - but either way, trust us, it works! -We have implemented a MinHash approach in our [sourmash software](https://github.com/dib-lab/sourmash/), which can do some nice things with samples. We'll show you some of these things next! +We have implemented a MinHash approach in our [sourmash software](https://github.com/sourmash-bio/sourmash/), which can do some nice things with samples. We'll show you some of these things next! ## Installing sourmash @@ -357,7 +357,7 @@ Let's grab a sample collection of 50 E. coli genomes and unpack it -- mkdir ecoli_many_sigs cd ecoli_many_sigs -curl -O -L https://github.com/dib-lab/sourmash/raw/master/data/eschericia-sigs.tar.gz +curl -O -L https://github.com/sourmash-bio/sourmash/raw/master/data/eschericia-sigs.tar.gz tar xzf eschericia-sigs.tar.gz rm eschericia-sigs.tar.gz @@ -472,7 +472,7 @@ from the [Shakya et al. 2013 mock metagenome paper](https://www.ncbi.nlm.nih.gov/pubmed/23387867). ``` -wget https://github.com/dib-lab/sourmash/raw/master/doc/_static/shakya-unaligned-contigs.sig +wget https://github.com/sourmash-bio/sourmash/raw/master/doc/_static/shakya-unaligned-contigs.sig sourmash lca gather shakya-unaligned-contigs.sig genbank-k31.lca.json ``` diff --git a/tests/test_minhash.py b/tests/test_minhash.py index 8d095abd77..05802c0bff 100644 --- a/tests/test_minhash.py +++ b/tests/test_minhash.py @@ -1,4 +1,4 @@ -# This file is part of sourmash, https://github.com/dib-lab/sourmash/, and is +# This file is part of sourmash, https://github.com/sourmash-bio/sourmash/, and is # Copyright (C) 2016, The Regents of the University of California. # # Redistribution and use in source and binary forms, with or without