Merge branch 'main' into performance-optimization-list-append-15142826470891655336

Author: mhucka

check/mypy

@@ -14,7 +14,7 @@
 # limitations under the License.
 
 ################################################################################
-# Runs mypy on the repository using a preconfigured mypy.ini file.
+# Runs mypy on the repository starting from the root.
 #
 # Usage:
 #     check/mypy [--flags]
@@ -25,7 +25,7 @@ cd "$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" || exit 1
 cd "$(git rev-parse --show-toplevel)" || exit 1
 
 echo -e -n "\033[31m"
-mypy --config-file=dev_tools/conf/mypy.ini "$@" .
+mypy "$@" .
 result=$?
 echo -e -n "\033[0m"
 

check/pytest-and-incremental-coverage

@@ -70,8 +70,7 @@ fi
 check/pytest . \
     --actually-quiet \
     --cov \
-    --cov-report=annotate \
-    --cov-config=dev_tools/conf/.coveragerc
+    --cov-report=annotate
 pytest_result=$?
 
 # Analyze coverage files.

dev_tools/conf/.coveragerc

@@ -14,11 +14,59 @@
 
 [tool.black]
 line-length = 100
-target_version = ['py310', 'py311', 'py312', 'py313']
+target-version = ['py310', 'py311', 'py312', 'py313']
 skip-string-normalization = true
 skip-magic-trailing-comma = true
 
 [tool.coverage.run]
 # Speed up pytest-cov on Python 3.12+ by enabling sys.monitoring if possible.
 core = "sysmon"
 disable_warnings = ["no-sysmon"]
+
+# Omit files outside the current working directory.
+# Note: this means coverage must be run from the openfermion repo root.
+# Failure to do so will result in false positives.
+omit = [
+    "./profiling/performance_benchmarks.py",
+    "./dev_tools/*",
+]
+
+[tool.mypy]
+implicit_optional = true
+
+# TODO: this is temporary for 1.7.0 release. Remove this & fix the errors.
+ignore_errors = true
+
+[[tool.mypy.overrides]]
+module = "__main__"
+follow_imports = "silent"
+ignore_missing_imports = true
+
+[[tool.mypy.overrides]]
+module = [
+    "_pytest.*",
+    "absl",
+    "apiclient.*",
+    "h5py",
+    "numpy.*",
+    "pubchempy",
+    "pybtas",
+    "pyscf.*",
+    "pytest.*",
+    "scipy.*",
+    "tensorflow_docs",
+]
+follow_imports = "silent"
+ignore_missing_imports = true
+
+[[tool.mypy.overrides]]
+module = "sympy.*"
+ignore_missing_imports = true
+
+[[tool.mypy.overrides]]
+module = "tensorflow_docs.*"
+ignore_missing_imports = true
+
+[[tool.mypy.overrides]]
+module = "deprecation"
+follow_untyped_imports = true

dev_tools/conf/mypy.ini

@@ -12,9 +12,11 @@
 
 """Tests for pubchem.py."""
 
+import os
+
 import numpy
-import pytest
 import pubchempy
+import pytest
 
 from openfermion.chem.pubchem import geometry_from_pubchem
 from openfermion.testing.testing_utils import module_importable
@@ -149,7 +151,12 @@ def test_water_2d(self, monkeypatch):
         with pytest.raises(ValueError, match='Incorrect value for the argument structure'):
             _ = geometry_from_pubchem('water', structure='foo')
 
-    @pytest.mark.flaky(retries=3, delay=2, only_on=[pubchempy.ServerBusyError])
+    # Skip if running in a CI environment.
+    @pytest.mark.skipif(
+        'CI' in os.environ,
+        reason='Skipping Pubchem API tests in CI to avoid failures due to busy servers.',
+    )
+    @pytest.mark.flaky(retries=8, delay=30, only_on=[pubchempy.ServerBusyError])
     def test_geometry_from_pubchem_live_api(self):
         water_geometry = geometry_from_pubchem('water')
         assert len(water_geometry) == 3