update install instructions, cleanup pixi.toml to avoid duplicate inf…

…o, fix doc building in nix

.github/workflows/dev_envs.yml

@@ -3,6 +3,9 @@ on:
   pull_request:
   push:
     branches: [latest]
+concurrency:
+  group: ${{ github.ref }}
+  cancel-in-progress: ${{ github.ref != 'refs/heads/latest' }}
 jobs:
   nix:
     runs-on: ${{ matrix.os }}
@@ -23,8 +26,31 @@ jobs:
 
     - run: nix develop --command bash -c "tox -e py310"
 
+  pixi:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-14]
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+
+    - name: set up pixi
+      uses: prefix-dev/[email protected]
+      with:
+        pixi-version: v0.13.0
+        cache: true
+
+    - name: run tests for 3.10
+      shell: pixi run bash {0}
+      run: tox -e py310
+
   mamba:
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-14]
     steps:
     - uses: actions/checkout@v4
       with:
@@ -34,28 +60,18 @@ jobs:
       uses: actions/cache@v4
       env:
         CACHE_NUMBER: 0
-      with:
         path: ~/conda_pkgs_dir
         key:
           ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
 
     - name: setup conda
       uses: conda-incubator/setup-miniconda@392cf345b1784333caa1a1185081c71e6ffd61bc
       with:
-        auto-update-conda: true
         python-version: "3.10"
-        channels: conda-forge,bioconda
-        miniforge-variant: Mambaforge
         miniforge-version: latest
-        use-mamba: true
-        mamba-version: "*"
+        environment-file: dev.yml
         activate-environment: sourmash_dev
         auto-activate-base: false
-        use-only-tar-bz2: true
-
-    - name: install dependencies
-      shell: bash -l {0}
-      run: mamba install 'tox>=3.27,<4' tox-conda rust git compilers pandoc libstdcxx-ng
 
     - name: run tests for 3.10
       shell: bash -l {0}

.gitignore

@@ -37,3 +37,6 @@ wasm-pack.log
 # nix
 .direnv/
 result
+
+# pixi
+.pixi/

dev.yml

@@ -0,0 +1,12 @@
+name: sourmash_dev
+channels:
+  - conda-forge
+dependencies:
+  - clangdev = ">=16.0.6,<17.1"
+  - cxx-compiler = ">=1.7.0,<1.8"
+  - git = "2.41.0.*"
+  - libclang = ">=16.0.6,<17.1"
+  - pandoc = "3.1.3.*"
+  - python = "3.10.*"
+  - rust = ">=1.76.0,<1.77"
+  - tox = ">=4.11.0,<5"

doc/conf.py

@@ -41,6 +41,7 @@
     "nbsphinx",
     "IPython.sphinxext.ipython_console_highlighting",
     "myst_parser",
+    "sphinx_design",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -314,3 +315,7 @@
 
 autodoc_mock_imports = ["sourmash.minhash"]
 myst_heading_anchors = 3
+myst_enable_extensions = [
+    "html_admonition",
+    "colon_fence",
+]

doc/developer.md

@@ -12,33 +12,52 @@ git clone https://github.com/sourmash-bio/sourmash.git
 ```
 sourmash runs under Python 3.10 and later.
 
-We recommend using `conda` or `Nix` for setting up an environment for developing
+We recommend using `conda` for setting up an environment for developing
 new features, running tests and code quality checks.
-Here are some suggestions on how to set them up (note: you only need one =])
+Here are some suggestions on how to set them up
 
-### Using mamba (conda alternative)
+:::{note}
+You only need one of these, no need to install them all!
+:::
+
+::::{tab-set}
+
+:::{tab-item} conda
 
 Follow the [installation instructions](https://github.com/conda-forge/miniforge#install) for
-installing `mambaforge` (a conda distribution that uses
-[`mamba`](https://github.com/TheSnakePit/mamba)
-and the [`conda-forge`](https://conda-forge.org/) channel by default).
+installing `Miniforge3` (a conda distribution that uses
+the [`conda-forge`](https://conda-forge.org/) channel by default).
 
-Once `mamba` is installed, run
+Once `conda` is installed, run
 ```
-mamba create -n sourmash_dev 'tox>=3.27,<4' tox-conda rust git compilers pandoc libstdcxx-ng
+conda env create -n sourmash_dev --file dev.yml
 ```
 to create an environment called `sourmash_dev` containing the programs needed
 for development.
 
-To activate the new environment, run
+Once the environment is created, you can activate it for development with
 ```
 conda activate sourmash_dev
 ```
+
+:::
+
+:::{tab-item} pixi
+
+Follow the [installation instructions](https://github.com/prefix-dev/pixi) for
+installing `pixi`.
+
+To activate the new environment, run
+```
+pixi shell
+```
 and proceed to the ["Running tests and checks"](#running-tests-and-checks) section.
 
-### Using Nix
+:::
+
+:::{tab-item} nix
 
-Follow the [installation instructions](https://nixos.org/manual/nix/stable/#chap-installation)
+Follow the [installation instructions](https://zero-to-nix.com/start/install)
 for setting up Nix in your system (Linux or macOS).
 
 Once Nix is installed, run
@@ -47,18 +66,22 @@ nix develop
 ```
 to start an environment ready for [running tests and checks](#running-tests-and-checks).
 
-### General instructions
+:::
+
+:::{tab-item} General instructions
 
 As long as you have `tox` and a Rust compiler available,
-you can skip `mamba` or `Nix`.
+you can skip `pixi` or `Nix`.
 
 For Rust, we suggest using `rustup` to install the Rust environment:
 ```
 curl https://sh.rustup.rs -sSf | sh
 ```
-And for `tox` you can run
+
+And for `tox` you can use [pipx](https://pipx.pypa.io/latest/installation/) for
+installing it without interfering with other Python environments:
 ```
-python -m pip install tox
+pipx install tox
 ```
 
 We suggest working on sourmash in a virtualenv; e.g. from within the
@@ -74,12 +97,15 @@ pip install -r requirements.txt
 ```
 (but they are already installed in the virtualenv created with `tox -e dev`).
 
-## Updating your developer environment
-
 To update rust to the latest version, use `rustup update`.
 
 To update your Python dependencies to the latest required for sourmash, you can run `pip install -r requirements.txt`.
 
+:::
+
+::::
+
+
 ## Running tests and checks
 
 We use [`tox`](https://tox.readthedocs.io) for managing dependencies and

flake.nix

@@ -130,6 +130,8 @@
             cargo-deny
             #cargo-semver-checks
             nixpkgs-fmt
+
+            pixi
           ];
 
           shellHook = ''