ci: Add doctests to CI again. (#767)

Co-authored-by: Willow Ahrens <[email protected]>

Author: hameerabbasi

.github/workflows/ci.yml

@@ -50,7 +50,12 @@ jobs:
           pip install -e '.[tests]'
       - name: Run tests
         run: |
-          SPARSE_BACKEND=Numba pytest --pyargs sparse --cov-report=xml:coverage_Numba.xml -n auto -vvv
+          if [ $(python -c 'import numpy as np; print(np.lib.NumpyVersion(np.__version__) >= "2.0.0a1")') = 'True' ]; then
+            pytest --pyargs sparse --doctest-modules --cov-report=xml:coverage_Numba.xml -n auto -vvv
+          else
+            pytest --pyargs sparse --cov-report=xml:coverage_Numba.xml -n auto -vvv
+          fi
+          python -c 'import finch'
           SPARSE_BACKEND=Finch pytest --pyargs sparse/tests --cov-report=xml:coverage_Finch.xml -n auto -vvv
           SPARSE_BACKEND=MLIR pytest --pyargs sparse/mlir_backend --cov-report=xml:coverage_MLIR.xml -n auto -vvv
       - uses: codecov/codecov-action@v5
@@ -126,6 +131,9 @@ jobs:
         SPARSE_BACKEND: ${{ matrix.backend }}
       run: |
         cd ${GITHUB_WORKSPACE}/array-api-tests
+        if [ "${SPARSE_BACKEND}" = "Finch" ]; then
+            python -c 'import finch'
+        fi
         pytest array_api_tests -v -c pytest.ini -n auto --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:

.gitignore

@@ -49,6 +49,7 @@ coverage.xml
 test_results/
 junit/
 .hypothesis/
+coverage_*.xml
 
 # Translations
 *.mo
@@ -85,4 +86,3 @@ docs/examples_ipynb/
 
 # Pixi envs
 .pixi/
-pixi.lock

ci/environment.yml

@@ -5,14 +5,14 @@ channels:
 dependencies:
   - python
   - pip
-  - numpy
-  - numba
-  - scipy
-  - dask
-  - pytest
-  - pytest-cov
-  - pytest-xdist
   - pip:
     - finch-tensor>=0.2.2
     - finch-mlir>=0.0.2
     - pytest-codspeed
+    - numpy
+    - numba
+    - scipy
+    - dask
+    - pytest
+    - pytest-cov
+    - pytest-xdist

conftest.py

@@ -1,3 +1,7 @@
+import pathlib
+
+import sparse
+
 import pytest
 
 
@@ -7,8 +11,18 @@ def add_doctest_modules(doctest_namespace):
 
     import numpy as np
 
-    if sparse._BackendType.Numba != sparse._BACKEND:
-        pass  # TODO: pytest.skip() skips Finch and MLIR tests
-
     doctest_namespace["np"] = np
     doctest_namespace["sparse"] = sparse
+
+
+def pytest_ignore_collect(collection_path: pathlib.Path, config: pytest.Config) -> bool | None:
+    if "numba_backend" in collection_path.parts and sparse._BackendType.Numba != sparse._BACKEND:
+        return True
+
+    if "mlir_backend" in collection_path.parts and sparse._BackendType.MLIR != sparse._BACKEND:
+        return True
+
+    if "finch_backend" in collection_path.parts and sparse._BackendType.Finch != sparse._BACKEND:
+        return True
+
+    return None

pixi.lock

@@ -12,29 +12,28 @@ numpy = ">=1.17"
 [dependencies]
 python = ">=3.10,<3.13"
 
-[feature.extras.pypi-dependencies]
+[feature.extra.pypi-dependencies]
 dask = { version = ">=2024", extras = ["array"] }
 scipy = ">=0.19"
 scikit-learn = "*"
 
-[feature.docs.pypi-dependencies]
+[feature.doc.pypi-dependencies]
 mkdocs-material = "*"
 mkdocstrings = { version = "*", extras = ["python"] }
 mkdocs-gen-files = "*"
 mkdocs-literate-nav = "*"
 mkdocs-section-index = "*"
 mkdocs-jupyter = "*"
 
-[feature.tests.tasks]
-test = "pytest --pyargs sparse -n auto"
-test-mlir = { cmd = "pytest --pyargs sparse.mlir_backend -v" }
+[feature.test.tasks]
+test = "pytest -n auto --doctest-modules"
+test-mlir = "pytest --pyargs sparse.mlir_backend -v"
 test-finch = { cmd = "pytest --pyargs sparse/tests -n auto -v", depends-on = ["precompile"] }
 
-[feature.tests.dependencies]
+[feature.test.pypi-dependencies]
 pytest = ">=3.5"
 pytest-cov = "*"
 pytest-xdist = "*"
-pre-commit = "*"
 pytest-codspeed = "*"
 
 [feature.notebooks.pypi-dependencies]
@@ -51,6 +50,7 @@ matrepr = "*"
 precompile = "python -c 'import finch'"
 
 [feature.finch.dependencies]
+python = ">=3.10"
 juliaup = ">=1.17.10"
 
 [feature.finch.pypi-dependencies]
@@ -63,16 +63,20 @@ SPARSE_BACKEND = "Finch"
 [feature.finch.target.osx-arm64.activation.env]
 PYTHONFAULTHANDLER = "${HOME}/faulthandler.log"
 
+[feature.mlir.dependencies]
+python = ">=3.10"
+
 [feature.mlir.pypi-dependencies]
 scipy = ">=0.19"
 finch-mlir = ">=0.0.2"
+"PyYAML" = "*"
 
 [feature.mlir.activation.env]
 SPARSE_BACKEND = "MLIR"
 
 [environments]
-tests = ["tests", "extras"]
-docs = ["docs", "extras"]
-mlir-dev = {features = ["tests", "mlir"], no-default-feature = true}
-finch-dev = {features = ["tests", "finch"], no-default-feature = true}
-notebooks = ["extras", "mlir", "finch", "notebooks"]
+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"]

pixi.toml

@@ -1,5 +1,5 @@
 [pytest]
-addopts = --cov-report term-missing --cov-report html --cov-report=term:skip-covered --cov sparse --cov-config .coveragerc --junitxml=junit/test-results.xml
+addopts = --cov-report term-missing --cov-report html --cov-report=term:skip-covered --cov sparse --cov-config .coveragerc
 filterwarnings =
     ignore::PendingDeprecationWarning
 testpaths =

pytest.ini

@@ -9,9 +9,6 @@
 import numpy as np
 import scipy.sparse as sps
 
-if sparse._BACKEND != sparse._BackendType.MLIR:
-    pytest.skip("skipping MLIR tests", allow_module_level=True)
-
 parametrize_dtypes = pytest.mark.parametrize(
     "dtype",
     [

sparse/mlir_backend/tests/__init__.py

@@ -1176,13 +1176,13 @@ def _parse_einsum_input(operands):
     Examples
     --------
     The operand list is simplified to reduce printing:
-    >>> np.random.seed(123)
-    >>> a = np.random.rand(4, 4)
-    >>> b = np.random.rand(4, 4, 4)
-    >>> _parse_einsum_input(("...a,...a->...", a, b))
-    ('za,xza', 'xz', [a, b]) # may vary
-    >>> _parse_einsum_input((a, [Ellipsis, 0], b, [Ellipsis, 0]))
-    ('za,xza', 'xz', [a, b]) # may vary
+    >>> rng = np.random.default_rng(42)
+    >>> a = rng.random((4, 4))
+    >>> b = rng.random((4, 4, 4))
+    >>> _parse_einsum_input(("...a,...a->...", a, b))  # doctest: +SKIP
+    ('za,xza', 'xz', [a, b])
+    >>> _parse_einsum_input((a, [Ellipsis, 0], b, [Ellipsis, 0]))  # doctest: +SKIP
+    ('za,xza', 'xz', [a, b])
     """
 
     if len(operands) == 0:
@@ -2061,7 +2061,7 @@ def asarray(obj, /, *, dtype=None, format="coo", copy=False, device=None):
     Examples
     --------
     >>> x = np.eye(8, dtype="i8")
-    >>> sparse.asarray(x, format="COO")
+    >>> sparse.asarray(x, format="coo")
     <COO: shape=(8, 8), dtype=int64, nnz=8, fill_value=0>
     """