Make slow pytest tests opt-in by default

.github/workflows/ci.yaml

@@ -224,7 +224,7 @@ jobs:
       - name: Run pytest
         run: |
           echo '::add-matcher::.github/problem-matchers/pytest.json'
-          check/pytest -n auto -m "not slow"
+          check/pytest -n auto
 
   pytest-extra:
     if: needs.changes.outputs.python == 'true'
@@ -259,7 +259,7 @@ jobs:
       - name: Run pytest
         run: |
           echo '::add-matcher::.github/problem-matchers/pytest.json'
-          check/pytest -n auto -m "not slow" src/openfermion/resource_estimates
+          check/pytest -n auto src/openfermion/resource_estimates
 
   pytest-compat:
     if: needs.changes.outputs.python == 'true'
@@ -288,7 +288,7 @@ jobs:
       - name: Run pytest
         run: |
           echo '::add-matcher::.github/problem-matchers/pytest.json'
-          check/pytest -n auto -m "not slow"
+          check/pytest -n auto
 
   coverage:
     if: needs.changes.outputs.python == 'true'

.github/workflows/nightly-pytest.yaml

@@ -95,7 +95,7 @@ jobs:
         run: echo '::add-matcher::.github/problem-matchers/pytest.json'
 
       - name: Run Pytest
-        run: check/pytest
+        run: check/pytest --run-slow
 
       - name: Print debugging info upon job failure
         if: failure()

CONTRIBUTING.md

@@ -292,12 +292,14 @@ tests, follow these general principles:
 We use [pytest](https://docs.pytest.org) to run our tests and
 [pytest-cov](https://pytest-cov.readthedocs.io) to compute coverage.
 
-*   While developing, periodically check that changes do not break anything. For fast checks, use
-    `pytest -m "not slow" PATH`, where `PATH` is a directory or pytest file to test.
+*   While developing, periodically check that changes do not break anything. By default, pytest
+    skips tests marked `slow`; use `pytest PATH`, where `PATH` is a directory or pytest file to
+    test.
 
-*   After finishing a task, run `check/pytest` to test all of the OpenFermion code. If your system
-    has multiple processor cores, you can add the option `-n auto` to make pytest use multiple
-    parallel processes for a speed increase. (Beware, though, that this is resource-intensive.)
+*   After finishing a task, run `check/pytest --run-slow` to test all of the OpenFermion code. If
+    your system has multiple processor cores, you can add the option `-n auto` to make pytest use
+    multiple parallel processes for a speed increase. (Beware, though, that this is
+    resource-intensive.)
 
 We don't require 100% coverage, but coverage should be very high, and any uncovered code must be
 annotated with `# pragma: no cover`. To ignore coverage of a single line, place `# pragma: no cover`
@@ -311,7 +313,7 @@ After a task is finished, run each of the following to make sure everything pass
 *   `check/format-incremental` (and `check/format-incremental --apply` to auto-fix format problems)
 *   `check/pylint -j 0`
 *   `check/mypy`
-*   `check/pytest -n auto`
+*   `check/pytest -n auto --run-slow`
 *   `check/pytest-and-incremental-coverage`
 
 ### Pull requests and code reviews

check/pytest

@@ -23,7 +23,7 @@
 #
 # You may specify pytest flags and specific files to test. The file paths
 # must be relative to the repository root. If no files are specified, everything
-# is tested.
+# except tests marked slow is tested. Pass --run-slow to include slow tests.
 ################################################################################
 
 # Get the working directory to the repo root.

check/pytest-and-incremental-coverage

@@ -70,6 +70,7 @@ fi
 check/pytest . \
     -n auto \
     --actually-quiet \
+    --run-slow \
     --cov \
     --cov-report=annotate
 pytest_result=$?

conftest.py

@@ -0,0 +1,40 @@
+# Copyright 2025 Google LLC
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     https://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import re
+from typing import Any
+
+_SLOW_MARKER_RE = re.compile(r"(?<![\w:])slow(?![\w:])")
+
+
+def pytest_addoption(parser: Any) -> None:
+    parser.addoption("--run-slow", action="store_true", default=False, help="run tests marked slow")
+
+
+def pytest_collection_modifyitems(config: Any, items: list[Any]) -> None:
+    markexpr = config.getoption("-m", default="")
+    if config.getoption("--run-slow") or _SLOW_MARKER_RE.search(markexpr):
+        return
+
+    selected = []
+    deselected = []
+    for item in items:
+        if "slow" in item.keywords:
+            deselected.append(item)
+        else:
+            selected.append(item)
+
+    if deselected:
+        config.hook.pytest_deselected(items=deselected)
+        items[:] = selected

pyproject.toml

@@ -25,7 +25,7 @@ disable_warnings = ["no-sysmon"]
 
 [tool.pytest.ini_options]
 markers = [
-    """slow: marks tests as slow (deselect with '-m "not slow"')""",
+    """slow: marks tests as slow (run with '--run-slow' or '-m slow')""",
 ]
 filterwarnings = [
     "ignore:Skipped assert_qasm_is_consistent_with_unitary because qiskit.*:UserWarning",

src/openfermion/testing/pytest_config_test.py

@@ -0,0 +1,105 @@
+# Copyright 2025 Google LLC
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     https://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import importlib.util
+import pathlib
+from typing import Any
+
+_CONFTEST_PATH = pathlib.Path(__file__).parents[3] / "conftest.py"
+_CONFTEST_SPEC = importlib.util.spec_from_file_location("openfermion_pytest_config", _CONFTEST_PATH)
+assert _CONFTEST_SPEC is not None
+assert _CONFTEST_SPEC.loader is not None
+conftest = importlib.util.module_from_spec(_CONFTEST_SPEC)
+_CONFTEST_SPEC.loader.exec_module(conftest)
+
+
+class _FakeHook:
+    def __init__(self) -> None:
+        self.deselected: list[Any] = []
+
+    def pytest_deselected(self, items: list[Any]) -> None:
+        self.deselected = list(items)
+
+
+class _FakeConfig:
+    def __init__(self, *, run_slow: bool = False, markexpr: str = "") -> None:
+        self._run_slow = run_slow
+        self._markexpr = markexpr
+        self.hook = _FakeHook()
+
+    def getoption(self, name: str, default: Any = None) -> Any:
+        if name == "--run-slow":
+            return self._run_slow
+        if name == "-m":
+            return self._markexpr
+        return default
+
+
+class _FakeItem:
+    def __init__(self, *, slow: bool = False) -> None:
+        self.keywords = {"slow": True} if slow else {}
+
+
+def test_fake_config_returns_default_for_unknown_options() -> None:
+    config = _FakeConfig()
+
+    assert config.getoption("--unknown", default="fallback") == "fallback"
+
+
+def test_default_collection_skips_slow_tests() -> None:
+    config = _FakeConfig()
+    slow_item = _FakeItem(slow=True)
+    fast_item = _FakeItem()
+    items = [slow_item, fast_item]
+
+    conftest.pytest_collection_modifyitems(config, items)
+
+    assert items == [fast_item]
+    assert config.hook.deselected == [slow_item]
+
+
+def test_run_slow_keeps_slow_tests() -> None:
+    config = _FakeConfig(run_slow=True)
+    slow_item = _FakeItem(slow=True)
+    fast_item = _FakeItem()
+    items = [slow_item, fast_item]
+
+    conftest.pytest_collection_modifyitems(config, items)
+
+    assert items == [slow_item, fast_item]
+    assert config.hook.deselected == []
+
+
+def test_explicit_slow_mark_expression_keeps_slow_tests() -> None:
+    config = _FakeConfig(markexpr="slow")
+    slow_item = _FakeItem(slow=True)
+    fast_item = _FakeItem()
+    items = [slow_item, fast_item]
+
+    conftest.pytest_collection_modifyitems(config, items)
+
+    assert items == [slow_item, fast_item]
+    assert config.hook.deselected == []
+
+
+def test_unrelated_mark_expression_keeps_default_slow_filter() -> None:
+    config = _FakeConfig(markexpr="not slowpoke")
+    slow_item = _FakeItem(slow=True)
+    fast_item = _FakeItem()
+    items = [slow_item, fast_item]
+
+    conftest.pytest_collection_modifyitems(config, items)
+
+    assert items == [fast_item]
+    assert config.hook.deselected == [slow_item]