Build: replace milksnake with maturin (#2393)

While investigating why the [Python 3.11] PR failed in conda-forge I
found out that there is an error in [milksnake]. Main issue is that
milksnake seems to be abandoned, without recent releases, so submitting
a PR to fix there might be unfruitful.

[Python 3.11]:
conda-forge/sourmash-minimal-feedstock#36
[milksnake]: https://github.com/getsentry/milksnake

[maturin] is a PEP517-compatible backend for building packages and aimed
at Rust packages (pure or mixed with more Python code, like sourmash).
It is actively maintained, and supports the `cffi` bindings case that we
use too.

[maturin]: https://maturin.rs

This PR is based on pyocd/cmsis-pack-manager#195
Closes #1564 (previous try
with `setuptools-rust`)

.github/workflows/build_wheel.yml

@@ -31,7 +31,7 @@ jobs:
           - build: macos-arm64
             os: macos-latest
             arch: arm64
-            macos_target: 'MACOSX_DEPLOYMENT_TARGET=11 CARGO_BUILD_TARGET=aarch64-apple-darwin'
+            macos_target: 'MACOSX_DEPLOYMENT_TARGET=11.0 CARGO_BUILD_TARGET=aarch64-apple-darwin'
       fail-fast: false
 
     steps:

.github/workflows/dev_envs.yml

@@ -11,25 +11,14 @@ jobs:
       with:
         fetch-depth: 0
 
-    - name: Cache nix store
-      id: cache-nix
-      uses: actions/cache@v3
+    - uses: cachix/install-nix-action@v18
       with:
-        path: |
-          ~/.nix-portable/store
-          ~/bin/nix-portable
-        key: nix-${{ hashFiles('shell.nix') }}-${{ hashFiles('nix/**') }}-v009
-
-    - name: Install nix-portable
-      if: steps.cache-nix.outputs.cache-hit != 'true'
-      run: |
-        mkdir ~/bin
-        wget -qO ~/bin/nix-portable https://github.com/DavHau/nix-portable/releases/download/v009/nix-portable
-        chmod +x ~/bin/nix-portable
+        extra_nix_config: |
+          access-tokens = github.com=${{ secrets.GITHUB_TOKEN }}
 
-    - run: ~/bin/nix-portable nix-shell --command "tox -e py39"
+    - run: nix run .# -- --version
 
-    - run: ~/bin/nix-portable nix run . -- --version
+    - run: nix-shell --command "tox -e py39"
 
   mamba:
     runs-on: ubuntu-latest

.github/workflows/python.yml

@@ -1,4 +1,4 @@
-# note: to invalidate caches, adjust the pip-v? and tox-v? numbers below.
+# note: to invalidate caches, adjust the pip-v? number below.
 name: Python tests
 
 on:
@@ -14,7 +14,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-22.04, macos-latest]
-        py: ["3.10", "3.9", "3.8"]
+        py: ["3.11", "3.10", "3.9", "3.8"]
       fail-fast: false
 
     steps:
@@ -36,7 +36,7 @@ jobs:
         uses: actions/cache@v3
         with:
           path: ${{ steps.pip-cache.outputs.dir }}
-          key: ${{ runner.os }}-pip-v4-${{ hashFiles('**/setup.cfg') }}
+          key: ${{ runner.os }}-pip-v4-${{ hashFiles('**/pyproject.toml') }}
           restore-keys: |
             ${{ runner.os }}-pip-v4-
 
@@ -65,7 +65,7 @@ jobs:
         uses: actions/cache@v3
         with:
           path: .tox/
-          key: ${{ runner.os }}-tox-v4-${{ hashFiles('**/setup.cfg') }}
+          key: ${{ runner.os }}-tox-v4-${{ hashFiles('**/pyproject.toml') }}
           restore-keys: |
             ${{ runner.os }}-tox-v4-
 

.github/workflows/rust.yml

@@ -268,26 +268,17 @@ jobs:
 
       - uses: actions-rs/toolchain@v1
         with:
-          toolchain: 1.48.0
+          toolchain: 1.56.1
           override: true
 
       - name: check if README matches MSRV defined here
-        run: grep '1.48.0' src/core/README.md
-
-      - name: Set up Python 3.8
-        uses: actions/setup-python@v4
-        with:
-          python-version: "3.8"
-
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          python -m pip install -e .
+        run: grep '1.56.1' src/core/README.md
 
       - name: Check if it builds properly
         uses: actions-rs/cargo@v1
         with:
           command: build
+          args: --all-features
 
   check_cbindgen:
     name: "Check if cbindgen runs cleanly for generating the C headers"

.gitignore

@@ -26,7 +26,6 @@ src/sourmash/_lowlevel*.py
 Pipfile
 Pipfile.lock
 target/
-Cargo.lock
 .eggs
 .asv
 pkg/

asv.conf.json

@@ -11,8 +11,7 @@
     "html_dir": ".asv/html",
     "build_cache_size": 8,
     "build_command": [
-      "python -m pip install 'setuptools_scm[toml]>=4,<6' milksnake",
-      "python setup.py build",
+      "python -m pip install 'setuptools_scm[toml]>=4,<6' milksnake maturin",
       "PIP_NO_BUILD_ISOLATION=false python -mpip wheel --no-deps --no-index -w {build_cache_dir} {build_dir}"
     ]
 }