BLD/DEV/CI: better Pixi setup (#920)

Author: hameerabbasi

.github/workflows/ci.yml

@@ -6,49 +6,37 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: true
 
+name: "CI"
+
 jobs:
   test:
+    name: Test ${{ matrix.os }} (${{ join(matrix.tasks, ' ') }})
     strategy:
       matrix:
-        os: ['ubuntu-latest']
-        python: ['3.11', '3.12', '3.13']
-        pip_opts: ['']
-        numba_boundscheck: [0]
+        os: [macos-latest, windows-latest]
+        tasks: [[test-numba, test-finch, test-mlir]]
+        environments: [[test, finch, mlir]]
         include:
-          - os: macos-latest
-            python: '3.11'
-          - os: windows-latest
-            python: '3.11'
-          - os: ubuntu-latest
-            python: '3.11'
-            numba_boundscheck: 1
           - os: ubuntu-latest
-            python: '3.11'
-            pip_opts: 'numpy<2'
+            tasks: [test-numba, test-finch, test-mlir, test-numba-mindeps, test-finch-mindeps, test-mlir-mindeps]
+            environments: [mindeps, test, finch, mlir]
       fail-fast: false
     runs-on: ${{ matrix.os }}
-    env:
-      PYTHON_VERSION: ${{ matrix.python }}
-      NUMBA_BOUNDSCHECK: ${{ matrix.numba_boundscheck }}
     steps:
       - name: Checkout Repo
         uses: actions/checkout@v4
-      - uses: mamba-org/setup-micromamba@v2
+      - uses: prefix-dev/setup-pixi@v0.9.4
         with:
-          environment-file: ci/environment.yml
-          init-shell: >-
-            bash
-          cache-environment: true
-          cache-downloads: true
-          post-cleanup: 'all'
-          create-args: >-
-            python=${{ matrix.python }}
-            ${{ matrix.pip_opts }}
-      - name: Install package
-        run: |
-          pip install -e '.[tests]'
+          pixi-version: v0.63.2
+          cache: true
+          environments: ${{ join(matrix.environments, ' ') }}
+      - name: hack for setuptools-scm
+        run: pixi build
       - name: Run tests
-        run: ci/test_backends.sh
+        run: |
+          for task in ${{ join(matrix.tasks, ' ') }}; do
+            pixi run "$task"
+          done
       - uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}

.gitignore

@@ -86,5 +86,4 @@ docs/examples_ipynb/
 
 # Envs
 .pixi/
-pixi.lock
 .venv/

ci/environment.yml

@@ -1,60 +1,95 @@
-[project]
+[workspace]
 authors = ["Hameer Abbasi <2190658+hameerabbasi@users.noreply.github.com>"]
-channels = ["conda-forge"]
+channels = ["https://prefix.dev/conda-forge"]
 name = "sparse"
 platforms = ["osx-arm64", "osx-64", "linux-64", "win-64"]
+preview = ["pixi-build"]
 
-[pypi-dependencies]
-sparse = { path = ".", editable = true }
+[environments]
+test = ["test", "extra"]
+doc = ["doc", "extra"]
+mlir = ["test", "mlir"]
+finch = ["test", "finch"]
+matrepr = ["matrepr"]
+notebooks = ["extra", "mlir", "finch", "notebooks"]
+core = { features = ["core"], no-default-feature = true }
+mindeps = ["test", "extra", "mindeps", "numba-boundscheck", "finch", "mlir"]
+
+# sparse package definition #
+
+[package]
+version = "0.1.0" # TODO: fix this
+
+[package.build.backend]
+name = "pixi-build-python"
+version = "*"
+
+[package.host-dependencies]
+python = ">=3.11,<3.14"
+setuptools = "*"
+setuptools-scm = "*"
+
+[package.run-dependencies]
 numba = ">=0.49"
 numpy = ">=1.17"
 
-[dependencies]
-python = ">=3.11,<3.14"
+# default feature definition #
 
-[feature.extra.pypi-dependencies]
-dask = { version = ">=2024", extras = ["array"] }
+[dev]
+sparse.path = "."
+
+# non-default feature definitions #
+
+# extra
+
+[feature.extra.dependencies]
+dask = ">=2024"
 scipy = ">=0.19"
 scikit-learn = "*"
 
-[feature.doc.pypi-dependencies]
+# doc
+
+[feature.doc.dependencies]
 mkdocs-material = "*"
-mkdocstrings = { version = "*", extras = ["python"] }
+mkdocstrings-python = "*"
 mkdocs-gen-files = "*"
 mkdocs-literate-nav = "*"
 mkdocs-section-index = "*"
 mkdocs-jupyter = "*"
 
-[feature.test.tasks]
-test = "ci/test_Numba.sh"
-test-mlir = "ci/test_MLIR.sh"
-test-finch = "ci/test_Finch.sh"
+# test
 
-[feature.test.pypi-dependencies]
+[feature.test.dependencies]
 pytest = ">=3.5"
 pytest-cov = "*"
 pytest-xdist = "*"
 pytest-codspeed = "*"
 
-[feature.notebooks.pypi-dependencies]
+[feature.test.tasks.test]
+cmd = "pytest -n auto -vvv"
+default-environment = "test"
+
+[feature.test.tasks.test-numba]
+cmd = "pytest --pyargs sparse --doctest-modules --cov-report=xml:coverage_Numba.xml -n auto -vvv"
+default-environment = "test"
+
+# notebooks
+
+[feature.notebooks.dependencies]
 ipykernel = "*"
 nbmake = "*"
 matplotlib = "*"
 networkx = "*"
 jupyterlab = "*"
 
-[feature.matrepr.pypi-dependencies]
-matrepr = "*"
-
-[feature.finch.tasks]
-precompile = "python -c 'import finch'"
+# finch
 
 [feature.finch.dependencies]
 python = ">=3.10"
 juliaup = ">=1.17.10"
+scipy = ">=1.13"
 
 [feature.finch.pypi-dependencies]
-scipy = ">=1.13"
 finch-tensor = ">=0.2.13"
 
 [feature.finch.activation.env]
@@ -63,30 +98,59 @@ SPARSE_BACKEND = "Finch"
 [feature.finch.target.osx-arm64.activation.env]
 PYTHONFAULTHANDLER = "${HOME}/faulthandler.log"
 
+[feature.finch.tasks._precompile]
+cmd = "python -c 'import finch'"
+default-environment = "finch"
+
+[feature.finch.tasks.test-finch]
+cmd = "pytest --pyargs sparse/tests --cov-report=xml:coverage_Finch.xml -n auto -vvv"
+depends-on = ["_precompile"]
+default-environment = "finch"
+
+# mlir
+
 [feature.mlir.dependencies]
-python = ">=3.10,<3.14"
+scipy = ">=0.19"
+pyyaml = "*"
 
 [feature.mlir.pypi-dependencies]
-scipy = ">=0.19"
 finch-mlir = ">=0.0.2"
-"PyYAML" = "*"
 
-[feature.barebones.dependencies]
-python = ">=3.10,<3.13"
-pip = ">=24"
+[feature.mlir.activation.env]
+SPARSE_BACKEND = "MLIR"
+
+[feature.mlir.tasks.test-mlir]
+cmd = "pytest --pyargs sparse/mlir_backend --cov-report=xml:coverage_MLIR.xml -n auto -vvv"
+default-environment = "mlir"
+
+# matrepr
+
+[feature.matrepr.dependencies]
+matrepr = "*"
+
+# core
 
-[feature.barebones.tasks]
-setup-env = {cmd = "ci/setup_env.sh" }
+[feature.core.tasks]
+setup-env = { cmd = "ci/setup_env.sh" }
 test-all = { cmd = "ci/test_all.sh", env = { ACTIVATE_VENV = "1" }, depends-on = ["setup-env"] }
-test-finch = "ci/test_Finch.sh"
 
-[feature.mlir.activation.env]
-SPARSE_BACKEND = "MLIR"
+# mindeps
 
-[environments]
-test = ["test", "extra"]
-doc = ["doc", "extra"]
-mlir-dev = {features = ["test", "mlir"], no-default-feature = true}
-finch-dev = {features = ["test", "finch"], no-default-feature = true}
-notebooks = ["extra", "mlir", "finch", "notebooks"]
-barebones = {features = ["barebones"], no-default-feature = true}
+[feature.mindeps.dependencies]
+python = "3.11.*"
+numpy = "1.*"
+
+[feature.mindeps.tasks.test-numba-mindeps]
+cmd = "pytest --pyargs sparse --cov-report=xml:coverage_Numba.xml -n auto -vvv"
+env.SPARSE_BACKEND = "Numba"
+
+[feature.mindeps.tasks.test-finch-mindeps]
+cmd = "pytest --pyargs sparse/tests --cov-report=xml:coverage_Finch.xml -n auto -vvv"
+env.SPARSE_BACKEND = "Finch"
+
+[feature.mindeps.tasks.test-mlir-mindeps]
+cmd = "pytest --pyargs sparse/mlir_backend --cov-report=xml:coverage_MLIR.xml -n auto -vvv"
+env.SPARSE_BACKEND = "MLIR"
+
+[feature.numba-boundscheck.activation.env]
+NUMBA_BOUNDSCHECK = "1"