Merge branch 'latest' into lirber/rust_1.75beta_lints

.github/workflows/rust.yml

@@ -163,7 +163,7 @@ jobs:
         run: "curl https://rustwasm.github.io/wasm-pack/installer/init.sh -sSf | sh"
 
       - name: Prepare node for running tests
-        uses: actions/setup-node@v3
+        uses: actions/setup-node@v4
         with:
           node-version: 16
           registry-url: https://registry.npmjs.org/

.github/workflows/rust_publish.yml

@@ -24,7 +24,7 @@ jobs:
           wasm-pack build src/core -d ../../pkg
 
       - name: Prepare node for NPM publishing
-        uses: actions/setup-node@v3
+        uses: actions/setup-node@v4
         with:
           node-version: 12
           registry-url: https://registry.npmjs.org/

doc/index.md

@@ -72,6 +72,8 @@ supported by further funding from the NIH and NSF. Please see
 These tutorials are command line tutorials that should work on Mac OS
 X and Linux. They require about 5 GB of disk space and 5 GB of RAM.
 
+* [Installing sourmash with conda](tutorial-install.md)
+
 * [The first sourmash tutorial - making signatures, comparing, and searching](tutorial-basic.md)
 
 * [Using sourmash LCA to do taxonomic classification](tutorials-lca.md)
@@ -82,8 +84,6 @@ X and Linux. They require about 5 GB of disk space and 5 GB of RAM.
 
 ### How-To Guides
 
-* Installing sourmash
-
 * [Classifying genome sketches](classifying-signatures.md)
 
 * [Working with private collections of genome sketches](sourmash-collections.ipynb)

doc/sidebar.md

@@ -3,6 +3,8 @@
 These tutorials are command line tutorials that should work on Mac OS
 X and Linux. They require about 5 GB of disk space and 5 GB of RAM.
 
+* [Installing sourmash with conda](tutorial-install.md)
+
 * [The first sourmash tutorial - making signatures, comparing, and searching](tutorial-basic.md)
 
 * [Using sourmash LCA to do taxonomic classification](tutorials-lca.md)
@@ -13,8 +15,6 @@ X and Linux. They require about 5 GB of disk space and 5 GB of RAM.
 
 ## How-To Guides
 
-* Installing sourmash
-
 * [Classifying genome sketches](classifying-signatures.md)
 
 * [Working with private collections of genome sketches](sourmash-collections.ipynb)

doc/toc.md

@@ -30,6 +30,7 @@ sourmash-internals.md
 sourmash-sketch.md
 storage.md
 support.md
+tutorial-install.md
 tutorial-basic.md
 tutorial-lemonade.md
 tutorial-lin-taxonomy.md

doc/tutorial-basic.md

@@ -1,55 +1,14 @@
 # The first sourmash tutorial - making signatures, comparing, and searching
 
-This tutorial should run without modification on Linux or Mac OS X,
-under [Miniconda](https://docs.conda.io/en/latest/miniconda.html).
-
 You'll need about 5 GB of free disk space, and about 5 GB of RAM to
 search GenBank.  The tutorial should take about 20 minutes total to
 run. In fact, we have successfully tested it on
 [binder.pangeo.io](https://binder.pangeo.io/v2/gh/binder-examples/r-conda/master?urlpath=urlpath%3Drstudio)
 if you want to give it a try!
 
-## Install miniconda
-
-If you don't have the `conda` command installed, you'll need to install
-miniconda for Python 3.x.
-
-On Linux, this should work:
-```
-wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
-bash Miniconda3-latest-Linux-x86_64.sh -b
-echo export PATH="$HOME/miniconda3/bin:$PATH" >> ~/.bash_profile
-source ~/.bash_profile
-```
-otherwise, follow
-[the miniconda install](https://docs.conda.io/en/latest/miniconda.html).
-
-## Enable [bioconda](https://bioconda.github.io/)
-
-```
-conda config --add channels defaults
-conda config --add channels bioconda
-conda config --add channels conda-forge
-```
-
 ## Install sourmash
 
-To install sourmash, create a new environment named `smash` and install sourmash:
-
-```
-conda create -y -n smash sourmash
-```
-
-and then activate:
-```
-conda activate smash
-```
-
-You should now be able to use the `sourmash` command:
-
-```
-sourmash info
-```
+You'll need to [install sourmash](tutorial-install.md) first!
 
 ## Generate a signature for Illumina reads
 

doc/tutorial-install.md

@@ -0,0 +1,55 @@
+# Installing sourmash
+
+This tutorial should run without modification on Linux or Mac OS X,
+under [Miniforge](https://github.com/conda-forge/miniforge).
+
+You'll need about 5 GB of free disk space.
+
+## Install miniforge
+
+If you don't have the `mamba` command installed, you'll need to install
+[miniforge](https://github.com/conda-forge/miniforge#install).
+
+On Linux, this should work:
+```
+curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
+bash Miniforge3-$(uname)-$(uname -m).sh -b
+
+~/miniforge3/bin/mamba init
+
+echo 'source ~/.bashrc' > ~/.bash_profile
+source ~/.bash_profile
+```
+otherwise, follow the instructions [here](https://github.com/conda-forge/miniforge#install).
+
+## Add bioconda
+
+sourmash is installed from the [bioconda software channel](https://bioconda.github.io/), so you'll need to add that to your config:
+
+```
+conda config --add channels defaults
+conda config --add channels bioconda
+conda config --add channels conda-forge
+conda config --set channel_priority strict
+```
+
+## Install sourmash
+
+To install sourmash, create a new environment named `smash` and install sourmash:
+
+```
+mamba create -y -n smash sourmash
+```
+
+and then activate:
+```
+conda activate smash
+```
+
+You should now be able to use the `sourmash` command:
+
+```
+sourmash info
+```
+
+Voila!