Merge branch 'main' into pagerank-example

Author: mtsokol

.codecov.yml

@@ -1,28 +1,18 @@
-comment:
-  layout: "header, diff, changes, uncovered"
-
+comment: false
 coverage:
   status:
     project:
       default:
-          # Total project must not drop by more than 3%
-          target: auto
-          threshold: "3%"
+          # Total project must be 95%
+          target: '100%'
+          threshold: '5%'
 
     patch:
       default:
           # Patch coverage must be 92%
-          target: auto
-          threshold: "92%"
+          target: '100%'
+          threshold: '8%'
 
   precision: 2
   round: down
-  range: 70...98
-
-  ignore:
-    - sparse/tests/
-    - sparse/_version.py
-    - ^(?!sparse\/)
-
-codecov:
-  token: 8de77158-fc37-47be-930c-f98739f9e5bf
+  range: 80...98

.github/workflows/ci.yml

@@ -1,12 +1,18 @@
+defaults:
+  run:
+    shell: bash -leo pipefail {0}
+
+concurrency:
+  group: ${{ github.head_ref }}
+  cancel-in-progress: true
+
 jobs:
   test:
-    defaults:
-      run:
-        shell: bash -el {0}
     strategy:
       matrix:
         os: [ubuntu-latest]
         python: ['3.10', '3.11', '3.12']
+        pip_opts: ['']
         numba_boundscheck: [0]
         include:
           - os: macos-latest
@@ -16,6 +22,9 @@ jobs:
           - os: ubuntu-latest
             python: '3.10'
             numba_boundscheck: 1
+          - os: ubuntu-latest
+            python: '3.10'
+            pip_opts: "--pre -U"
       fail-fast: false
     runs-on: ${{ matrix.os }}
     env:
@@ -24,63 +33,33 @@ jobs:
     steps:
       - name: Checkout Repo
         uses: actions/checkout@v4
-      - name: Cache conda
-        uses: actions/cache@v4
-        env:
-          # Increase this value to reset cache if ci/environment.yml has not changed
-          CACHE_NUMBER: 0
-        with:
-          path: ~/conda_pkgs_dir
-          key:
-            test-${{ matrix.os }}-conda-py${{ matrix.python }}-${{ env.CACHE_NUMBER }}-${{
-            hashFiles('ci/environment.yml') }}
-      - uses: julia-actions/setup-julia@v1
+      - name: Set up Python
+        uses: actions/setup-python@v5
         with:
-          version: '1.10.0'
-      - uses: conda-incubator/setup-miniconda@v3
-        with:
-          activate-environment: sparse-dev
-          allow-softlinks: true
-          environment-file: ci/environment.yml
           python-version: ${{ matrix.python }}
-          miniforge-version: latest
+          cache: 'pip'
       - name: Install package
         run: |
           pip install -e .[tests]
+          pip install ${{ matrix.pip_opts }} numpy numba
       - name: Run tests
         run: |
-          pytest --pyargs sparse
+          SPARSE_BACKEND=Numba pytest --pyargs sparse --cov-report=xml:coverage_Numba.xml -n 4 -vvv
+          SPARSE_BACKEND=Finch pytest --pyargs sparse/tests --cov-report=xml:coverage_Finch.xml -n 4 -vvv
       - uses: codecov/codecov-action@v4
         if: always()
-      - name: Publish Test Results
-        uses: EnricoMi/publish-unit-test-result-action/composite@v2
-        if: always()
         with:
-          files: "**/test-*.xml"
+          files: ./**/coverage*.xml
   docs:
-    defaults:
-      run:
-        shell: bash -el {0}
     runs-on: ubuntu-latest
     steps:
       - name: Checkout Repo
         uses: actions/checkout@v4
-      - name: Cache conda
-        uses: actions/cache@v4
-        env:
-          # Increase this value to reset cache if ci/environment.yml has not changed
-          CACHE_NUMBER: 0
+      - name: Set up Python
+        uses: actions/setup-python@v5
         with:
-          path: ~/conda_pkgs_dir
-          key:
-            docs-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('ci/environment.yml') }}
-      - uses: conda-incubator/setup-miniconda@v3
-        with:
-          activate-environment: sparse-dev
-          allow-softlinks: true
-          environment-file: ci/environment.yml
           python-version: '3.10'
-          miniforge-version: latest
+          cache: 'pip'
       - name: Install package
         run: |
           pip install -e .[docs]
@@ -92,29 +71,15 @@ jobs:
           name: Documentation
           path: _build/html
   benchmarks:
-    defaults:
-      run:
-        shell: bash -el {0}
     runs-on: ubuntu-latest
     steps:
       - name: Checkout Repo
         uses: actions/checkout@v4
-      - name: Cache conda
-        uses: actions/cache@v4
-        env:
-          # Increase this value to reset cache if ci/environment.yml has not changed
-          CACHE_NUMBER: 0
-        with:
-          path: ~/conda_pkgs_dir
-          key:
-            benchmarks-${{ env.CACHE_NUMBER }}-${{ hashFiles('ci/environment.yml') }}
-      - uses: conda-incubator/setup-miniconda@v3
+      - name: Set up Python
+        uses: actions/setup-python@v5
         with:
-          activate-environment: sparse-dev
-          allow-softlinks: true
-          environment-file: ci/environment.yml
           python-version: '3.10'
-          miniforge-version: latest
+          cache: 'pip'
       - name: Install asv
         run: |
           pip install asv
@@ -128,16 +93,22 @@ jobs:
     - name: Checkout Repo
       uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v5.1.0
+      uses: actions/setup-python@v5
       with:
         python-version: '3.11'
+        cache: 'pip'
     - name: Build and install Sparse
       run: |
+        pip install -U setuptools wheel
         python -m pip install '.[finch]' scipy
     - name: Run examples
       run: |
         source ci/test_examples.sh
   array_api_tests:
+    strategy:
+      matrix:
+        backend: ['Numba', 'Finch']
+      fail-fast: false
     runs-on: ubuntu-latest
     steps:
     - name: Checkout Repo
@@ -146,26 +117,27 @@ jobs:
       uses: actions/checkout@v4
       with:
         repository: data-apis/array-api-tests
-        ref: '3cf8ef654c456d9fd1633d64e67b4470465940e9'  # Latest commit as of 2024-04-09
+        ref: '33f2d2ea2f3dd2b3ceeeb4519d55e08096184149'  # Latest commit as of 2024-05-29
         submodules: 'true'
         path: 'array-api-tests'
     - name: Set up Python
-      uses: actions/setup-python@v5.1.0
+      uses: actions/setup-python@v5
       with:
         python-version: '3.11'
+        cache: 'pip'
     - name: Install build and test dependencies from PyPI
       run: |
-        python -m pip install -r array-api-tests/requirements.txt
+        python -m pip install pytest-xdist -r array-api-tests/requirements.txt
     - name: Build and install Sparse
       run: |
         python -m pip install '.[finch]'
     - name: Run the test suite
       env:
         ARRAY_API_TESTS_MODULE: sparse
-        SPARSE_BACKEND: Finch
+        SPARSE_BACKEND: ${{ matrix.backend }}
       run: |
         cd ${GITHUB_WORKSPACE}/array-api-tests
-        pytest array_api_tests/test_signatures.py -v -c pytest.ini --ci --max-examples=2 --derandomize --disable-deadline -o xfail_strict=True --xfails-file ${GITHUB_WORKSPACE}/ci/array-api-skips.txt
+        pytest array_api_tests -v -c pytest.ini -n 4 --max-examples=2 --derandomize --disable-deadline -o xfail_strict=True --xfails-file ${GITHUB_WORKSPACE}/ci/${{ matrix.backend }}-array-api-xfails.txt --skips-file ${GITHUB_WORKSPACE}/ci/${{ matrix.backend }}-array-api-skips.txt
 on:
   # Trigger the workflow on push or pull request,
   # but only for the main branch

.gitignore

@@ -80,3 +80,6 @@ sandbox.py
 
 # Version file
 sparse/_version.py
+
+# Benchmark Results
+results/

.pre-commit-config.yaml

@@ -17,7 +17,7 @@ repos:
       args: ["--autofix", "--no-ensure-ascii"]
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.4.4
+  rev: v0.4.8
   hooks:
     - id: ruff
       args: ["--fix"]

asv.conf.json

@@ -4,40 +4,17 @@
   ],
   "build_command": [],
   "environment_type": "virtualenv",
-  "exclude": [
-    {
-      "env": {
-        "SPARSE_BACKEND": "Finch"
-      },
-      "req": {
-        "finch-tensor": null
-      }
-    },
-    {
-      "env": {
-        "SPARSE_BACKEND": "Numba"
-      },
-      "req": {
-        "finch-tensor": ""
-      }
-    }
-  ],
   "install_command": [
     "pip install --no-deps ."
   ],
   "matrix": {
     "env": {
       "SPARSE_BACKEND": [
-        "Finch",
         "Numba"
       ]
     },
     "env_nobuild": {},
     "req": {
-      "finch-tensor": [
-        "",
-        null
-      ],
       "numba": [
         ""
       ],