Merge branch 'main' into add-pr-text-checker

Author: mhucka

.github/workflows/ci.yaml

@@ -12,8 +12,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-# yamllint disable rule:line-length
-
 name: Scorecard analysis
 run-name: Run Scorecard scanner for security best practices
 
@@ -34,11 +32,6 @@ on:
 
   # Allow manual invocation.
   workflow_dispatch:
-    inputs:
-      debug:
-        description: 'Run with debugging options'
-        type: boolean
-        default: true
 
 concurrency:
   # Cancel any previously-started but still active runs on the same branch.
@@ -50,7 +43,11 @@ permissions: read-all
 
 jobs:
   run-scorecard:
-    if: github.repository_owner == 'quantumlib'
+    # Skip fork PRs to avoid "Analysis configuration not found" errors.
+    if: >-
+      github.repository_owner == 'quantumlib' &&
+      (github.event_name != 'pull_request' ||
+       github.event.pull_request.head.repo.fork == false)
     name: Scorecard analyzer
     runs-on: ubuntu-24.04
     permissions:
@@ -64,33 +61,21 @@ jobs:
           persist-credentials: false
 
       - name: Run Scorecard analysis
+        # yamllint disable rule:line-length
         uses: ossf/scorecard-action@4eaacf0543bb3f2c246792bd56e8cdeffafb205a # v2.4.3
         with:
-          # Save the results
           results_file: scorecard-results.sarif
           results_format: sarif
-          # Only publish results for non-fork PRs or scheduled runs.
-          publish_results: >-
-            ${{github.event_name != 'pull_request'
-              || github.event.pull_request.head.repo.fork == false}}
+          publish_results: true
 
       - name: Upload results to code-scanning dashboard
-        # Skip upload for fork PRs to avoid "Analysis configuration not found" / 404 errors.
-        if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.fork == false
-        uses: github/codeql-action/upload-sarif@c10b8064de6f491fea524254123dbe5e09572f13 # v4.35.1
+        # yamllint disable rule:line-length
+        uses: github/codeql-action/upload-sarif@95e58e9a2cdfd71adc6e0353d5c52f41a045d225 # v4.35.2
         with:
           sarif_file: scorecard-results.sarif
 
-      - if: github.event.inputs.debug == true || runner.debug == true
-        name: Upload results as artifacts to the workflow Summary page
-        uses: actions/upload-artifact@bbbca2ddaa5d8feaa63e36b76fdaad77386f024f # v7.0.0
-        with:
-          name: Scorecard SARIF file
-          path: scorecard-results.sarif
-          retention-days: 5
-
-  # Scorecard currently (ver. 2.4.x) doesn't allow submissions from jobs having
-  # steps that use "run:". To print to the summary, we need to use another job.
+  # Scorecard doesn't allow submissions from jobs having steps that use "run:".
+  # Printing a summary needs to use "run:", so we have to use a separate job.
   write-summary:
     name: Scorecard results
     needs: run-scorecard

.github/workflows/scorecard-scanner.yaml

@@ -285,7 +285,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The BCS hamiltonian evovles spin conserved and number broken wavefunctions."
+    "The BCS hamiltonian evolves spin conserved and number broken wavefunctions."
    ]
   },
   {
@@ -357,7 +357,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Exact evolution of individual n-body anti-Hermitian gnerators"
+    "Exact evolution of individual n-body anti-Hermitian generators"
    ]
   },
   {

docs/fqe/tutorials/hamiltonian_time_evolution_and_expectation_estimation.ipynb

@@ -31,12 +31,6 @@
     + 0.5 * \sum_{p,q,r,s} h[p,q,r,s] a_p^\dagger a_q^\dagger a_r a_s
 """
 
-# Define a compatible basestring for checking between Python 2 and 3
-try:
-    basestring
-except NameError:  # pragma: no cover
-    basestring = str
-
 
 # Define error objects which inherit from Exception.
 class MoleculeNameError(Exception):
@@ -248,7 +242,7 @@ def name_molecule(geometry, basis, multiplicity, charge, description):
     Raises:
         MoleculeNameError: If spin multiplicity is not valid.
     """
-    if not isinstance(geometry, basestring):
+    if not isinstance(geometry, str):
         # Get sorted atom vector.
         atoms = [item[0] for item in geometry]
         atom_charge_info = [(atom, atoms.count(atom)) for atom in set(atoms)]
@@ -501,7 +495,7 @@ def __init__(
 
         # Metadata fields with default values.
         self.charge = charge
-        if not isinstance(description, basestring):
+        if not isinstance(description, str):
             raise TypeError("description must be a string.")
         self.description = description
 
@@ -518,7 +512,7 @@ def __init__(
                 self.filename = data_directory + '/' + self.name
 
         # Attributes generated automatically by class.
-        if not isinstance(geometry, basestring):
+        if not isinstance(geometry, str):
             self.n_atoms = len(geometry)
             self.atoms = sorted(
                 [row[0] for row in geometry], key=lambda atom: periodic_hash_table[atom]
@@ -707,7 +701,7 @@ def save(self):
         with h5py.File("{}.hdf5".format(tmp_name), "w") as f:
             # Save geometry (atoms and positions need to be separate):
             d_geom = f.create_group("geometry")
-            if not isinstance(self.geometry, basestring):
+            if not isinstance(self.geometry, str):
                 atoms = [numpy.bytes_(item[0]) for item in self.geometry]
                 positions = numpy.array([list(item[1]) for item in self.geometry])
             else:
@@ -909,11 +903,10 @@ def load(self):
                         key.tobytes().decode('utf-8'): value
                         for key, value in zip(keys[...], values[...])
                     }
+                else:
+                    self.general_calculations = {}
             else:
-                # TODO: test the no cover
-                # no coverage here because pathway is check on
-                # bad user generated file
-                self.general_calculations = None  # pragma: nocover
+                self.general_calculations = {}
 
     def get_from_file(self, property_name):
         """Helper routine to re-open HDF5 file and pull out single property.

src/openfermion/chem/molecular_data.py

@@ -12,7 +12,10 @@
 """Tests for molecular_data."""
 
 import os
+import tempfile
 import unittest
+from unittest.mock import patch
+import h5py
 import numpy.random
 import scipy.linalg
 import numpy as np
@@ -347,3 +350,32 @@ def test_missing_calcs_for_integrals(self):
             molecule.get_k()
         with self.assertRaises(MissingCalculationError):
             molecule.get_antisym()
+
+    def test_load_no_general_calculations(self):
+        # Make fake molecule.
+        with tempfile.NamedTemporaryFile(suffix='.hdf5') as tmp_file:
+            filename = tmp_file.name
+            geometry = [('H', (0.0, 0.0, 0.0)), ('H', (0.0, 0.0, 0.7414))]
+            basis = '6-31g*'
+            multiplicity = 1
+            molecule = MolecularData(geometry, basis, multiplicity, filename=filename)
+            molecule.save()
+
+            # Manually remove the general_calculations_keys dataset.
+            with h5py.File(filename, 'r+') as f:
+                del f['general_calculations_keys']
+
+            # Load the molecule and check that general_calculations is empty.
+            new_molecule = MolecularData(filename=filename)
+            self.assertEqual(new_molecule.general_calculations, {})
+
+    def test_get_from_file_exceptions(self):
+        with patch('h5py.File') as mock_file:
+            mock_file.return_value.__enter__.return_value.__getitem__.side_effect = KeyError
+            data = self.molecule.get_from_file("nonexistent_property")
+            self.assertIsNone(data)
+
+        with patch('h5py.File') as mock_file:
+            mock_file.side_effect = IOError
+            data = self.molecule.get_from_file("any_property")
+            self.assertIsNone(data)

src/openfermion/chem/molecular_data_test.py

@@ -12,12 +12,12 @@
 
 """Tests for pubchem.py."""
 
-import time
 import unittest
 from unittest.mock import patch
 
 import numpy
 import pytest
+import pubchempy
 
 from openfermion.chem.pubchem import geometry_from_pubchem
 from openfermion.testing.testing_utils import module_importable
@@ -152,7 +152,7 @@ def test_water_2d(self):
         with pytest.raises(ValueError, match='Incorrect value for the argument structure'):
             _ = geometry_from_pubchem('water', structure='foo')
 
-    @pytest.mark.flaky(retries=3, delay=2)
+    @pytest.mark.flaky(retries=3, delay=2, only_on=[pubchempy.ServerBusyError])
     def test_geometry_from_pubchem_live_api(self):
-        water_geometry = geometry_from_pubchem('water')  # pragma: no cover
-        self.assertEqual(len(water_geometry), 3)  # pragma: no cover
+        water_geometry = geometry_from_pubchem('water')
+        self.assertEqual(len(water_geometry), 3)

src/openfermion/chem/pubchem_test.py

@@ -19,8 +19,6 @@
 
 from openfermion.ops.operators import BinaryPolynomial
 
-# import openfermion.ops.operators._binary_polynomial as bp
-
 
 def shift_decoder(decoder, shift_constant):
     """Shifts the indices of a decoder by a constant.

src/openfermion/ops/operators/binary_code.py

@@ -338,17 +338,9 @@ def module_importable(module):
         bool
 
     """
-    import sys
+    from importlib import util
 
-    if sys.version_info >= (3, 4):
-        from importlib import util
-
-        plug_spec = util.find_spec(module)
-    else:
-        # Won't enter unless Python<3.4, so ignore for testing
-        import pkgutil  # pragma: ignore
-
-        plug_spec = pkgutil.find_loader(module)  # pragma: no cover
+    plug_spec = util.find_spec(module)
     if plug_spec is None:
         return False
     else: