Merge pull request #4 from MesoscienceLab/update_1pt6pt1

MesoHOPS 1.6.1

Author: digbennett

pyproject.toml

@@ -6,7 +6,8 @@ dependencies = [
   "scipy",
   "numba",
   "pytest",
-  "pytest-level"
+  "pytest-level",
+  "pytest-cov"
 ]
 requires-python = ">=3.12"
 authors = [

pytest.ini

@@ -1,13 +1,15 @@
-[tool:pytest]
+[pytest]
 testpaths = tests
 python_files = test_*.py
 python_classes = Test*
 python_functions = test_*
+markers =
+    order: enforce execution order of tests
 addopts =
     --verbose
+    --level=1
     --cov=mesohops
     --cov-report=term-missing
     --cov-report=html
     --cov-report=xml
     --cov-fail-under=70
-

src/mesohops/basis/hops_aux.py

@@ -31,7 +31,6 @@ class AuxiliaryVector(Mapping):
         '_index',          # Current index
         '__id_string',     # Unique identifier string
         '__mode_digits',   # Number of digits per mode
-        '__kmax',          # Maximum hierarchy depth
 
         # --- Cached values ---
         '_sum',            # Cached sum of vector elements

src/mesohops/basis/hops_basis.py

@@ -935,7 +935,7 @@ def get_Z2_noise_sparse(self, z_step):
         if self.off_diagonal_couplings:
             # Get the noise associated with system-bath projection operators that
             # couple states in the current basis to a different state.
-            noise_t = (np.conj(z_step[0]) - 2j * np.real(z_step[1]))[
+            noise_t = (np.conj(z_step[0]) - 1j * z_step[1])[
                 self.mode.list_rel_ind_off_diag_L2]
             # Get the noise memory drift associated with system-bath projection
             # operators that couple states in the current basis to a different state.

src/mesohops/basis/hops_fluxfilters.py

@@ -332,6 +332,9 @@ def construct_filter_markov_up(self):
                        filtered out) while False indicates otherwise
                        (positioning is (mode, aux)).
         """
+        if len(self.mode.list_absindex_mode) == 0:
+            return True
+
         M2_mark_filtered_modes = np.array(
             [
                 np.array([param[m] for m in self.mode.list_absindex_mode])
@@ -389,6 +392,9 @@ def construct_filter_triangular_up(self):
                        filtered out) while False indicates otherwise
                        (positioning is (mode, aux)).
         """
+        if len(self.mode.list_absindex_mode) == 0:
+            return True
+
         M2_tri_filtered_modes = np.array(
             [
                 np.array([param[0][m] for m in self.mode.list_absindex_mode])
@@ -442,6 +448,9 @@ def construct_filter_longedge_up(self):
                        filtered out) while False indicates otherwise
                        (positioning is (mode, aux)).
         """
+        if len(self.mode.list_absindex_mode) == 0:
+            return True
+
         M2_le_filtered_modes = np.array(
             [
                 np.array([param[0][m] for m in self.mode.list_absindex_mode])