ioNERDSS 2.2__tar.gz → 2.2.2__tar.gz

{ionerdss-2.2/ioNERDSS.egg-info → ionerdss-2.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ioNERDSS
-Version: 2.2
+Version: 2.2.2
 Summary: Package for preparing NERDSS inputs and analysing outputs.
 Author-email: Yue Moon Ying <yying7@jh.edu>, Mankun Sang <msang2@jhu.edu>, Samuel L Foley <sfoley13@jh.edu>, "Zixiu (Hugh) Liu" <zliu140@jhu.edu>, Sikao Guo <sikaoguo@gmail.com>
 License: GPL-3.0
@@ -53,6 +53,7 @@ Requires-Dist: ipywidgets; extra == "jupyter"
 Provides-Extra: simularium
 Requires-Dist: simulariumio; extra == "simularium"
 Requires-Dist: MDAnalysis; extra == "simularium"
+Requires-Dist: pandas<3; extra == "simularium"
 Provides-Extra: docs
 Requires-Dist: mkdocs>=1.6; extra == "docs"
 Provides-Extra: all

{ionerdss-2.2/tests → ionerdss-2.2.2/developer_tests}/unit/analysis/test_io.py

@@ -63,10 +63,65 @@ class TestIOParser(unittest.TestCase):
         if Path(self.temp_dir).exists():
             shutil.rmtree(self.temp_dir)
 
-    @unittest.skip("Skipping transition matrix tests as requested")
+    def _write_transition_file(self, name: str, header: str) -> Path:
+        """Writes a two-time-point transition file using the given matrix header."""
+        path = self.temp_path / name
+        with open(path, 'w') as f:
+            f.write("time: 0\n")
+            f.write(f"{header}\n")
+            f.write("A\n")
+            f.write(" 0 0\n")
+            f.write(" 0 0\n")
+            f.write("lifetime for each mol type:\n")
+            f.write("A\n")
+            f.write("size of the cluster:1\n")
+            f.write("\n")
+            f.write("time: 0.005\n")
+            f.write(f"{header}\n")
+            f.write("A\n")
+            f.write(" 4 2\n")
+            f.write(" 1 3\n")
+            f.write("lifetime for each mol type:\n")
+            f.write("A\n")
+            f.write("size of the cluster:1\n")
+            f.write(" 0.5 0.25\n")
+            f.write("\n")
+        return path
+
     def test_parse_transition_file(self):
         """Test transition file parsing."""
-        pass
+        path = self._write_transition_file(
+            "transition_ok.dat", "transition matrix for each mol type:"
+        )
+        transitions, lifetimes = parser.parse_transition_file(path)
+
+        # The all-zero block at time 0 still counts: the header was found.
+        self.assertEqual(len(transitions), 2)
+        self.assertEqual(transitions[1]["time"], 0.005)
+        np.testing.assert_array_equal(
+            transitions[1]["matrix"], np.array([[4, 2], [1, 3]])
+        )
+
+        self.assertEqual(len(lifetimes), 1)
+        self.assertEqual(lifetimes[0]["lifetimes"][1], [0.5, 0.25])
+
+    def test_parse_transition_file_legacy_typo_header(self):
+        """Pre-fix NERDSS builds write 'transion matrix ...'; both must parse."""
+        typo_path = self._write_transition_file(
+            "transition_typo.dat", "transion matrix for each mol type:"
+        )
+        ok_path = self._write_transition_file(
+            "transition_ok2.dat", "transition matrix for each mol type:"
+        )
+
+        typo_transitions, typo_lifetimes = parser.parse_transition_file(typo_path)
+        ok_transitions, ok_lifetimes = parser.parse_transition_file(ok_path)
+
+        self.assertEqual(len(typo_transitions), len(ok_transitions))
+        for typo, ok in zip(typo_transitions, ok_transitions):
+            self.assertEqual(typo["time"], ok["time"])
+            np.testing.assert_array_equal(typo["matrix"], ok["matrix"])
+        self.assertEqual(typo_lifetimes, ok_lifetimes)
         
     def test_parse_copy_numbers(self):
         """Test copy numbers file parsing."""

{ionerdss-2.2 → ionerdss-2.2.2/ioNERDSS.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ioNERDSS
-Version: 2.2
+Version: 2.2.2
 Summary: Package for preparing NERDSS inputs and analysing outputs.
 Author-email: Yue Moon Ying <yying7@jh.edu>, Mankun Sang <msang2@jhu.edu>, Samuel L Foley <sfoley13@jh.edu>, "Zixiu (Hugh) Liu" <zliu140@jhu.edu>, Sikao Guo <sikaoguo@gmail.com>
 License: GPL-3.0
@@ -53,6 +53,7 @@ Requires-Dist: ipywidgets; extra == "jupyter"
 Provides-Extra: simularium
 Requires-Dist: simulariumio; extra == "simularium"
 Requires-Dist: MDAnalysis; extra == "simularium"
+Requires-Dist: pandas<3; extra == "simularium"
 Provides-Extra: docs
 Requires-Dist: mkdocs>=1.6; extra == "docs"
 Provides-Extra: all

{ionerdss-2.2 → ionerdss-2.2.2}/ioNERDSS.egg-info/SOURCES.txt

@@ -6,6 +6,38 @@ setup.py
 benchmark/benchmark_subcomplexes.py
 benchmark/build_pdbs.py
 benchmark/run_validation_benchmark.py
+developer_tests/graph_based/test_reactions_generation_pipeline.py
+developer_tests/graph_based/test_subcomplexes_extraction.py
+developer_tests/graph_based/test_symmetry_group_identification.py
+developer_tests/integration/__init__.py
+developer_tests/unit/analysis/test_api.py
+developer_tests/unit/analysis/test_io.py
+developer_tests/unit/analysis/test_processing.py
+developer_tests/unit/model/test_platonic_solids.py
+developer_tests/unit/model/components/test_instances.py
+developer_tests/unit/model/components/test_reactions.py
+developer_tests/unit/model/components/test_reference_coordinates.py
+developer_tests/unit/model/components/test_registry.py
+developer_tests/unit/model/components/test_types.py
+developer_tests/unit/model/components/test_units.py
+developer_tests/unit/model/pdb/test_chain_grouping.py
+developer_tests/unit/model/pdb/test_coarse_graining.py
+developer_tests/unit/model/pdb/test_file_manager.py
+developer_tests/unit/model/pdb/test_hyperparameters.py
+developer_tests/unit/model/pdb/test_nerdss_exporter.py
+developer_tests/unit/model/pdb/test_parser.py
+developer_tests/unit/model/pdb/test_ring_regularizer.py
+developer_tests/unit/model/pdb/test_template_builder.py
+developer_tests/unit/model/pdb/test_visualizer.py
+developer_tests/unit/ode_solver/test_ode_solver.py
+developer_tests/unit/utils/test_bond_geometry.py
+developer_tests/unit/utils/test_coords.py
+developer_tests/unit/utils/test_diffusion_constants.py
+developer_tests/unit/utils/test_inertia_tensors.py
+developer_tests/unit/utils/test_rigid_transform.py
+developer_tests/unit/utils/test_rotations.py
+developer_tests/unit/utils/test_steric_clash.py
+developer_tests/unit/utils/test_string_similarity.py
 ioNERDSS.egg-info/PKG-INFO
 ioNERDSS.egg-info/SOURCES.txt
 ioNERDSS.egg-info/dependency_links.txt
@@ -125,38 +157,4 @@ ionerdss/utils/rigid_transform.py
 ionerdss/utils/rotations.py
 ionerdss/utils/steric_clash.py
 ionerdss/utils/string_similarity.py
-ionerdss/utils/vectors.py
-tests/graph_based/test_reactions_generation_pipeline.py
-tests/graph_based/test_subcomplexes_extraction.py
-tests/graph_based/test_symmetry_group_identification.py
-tests/integration/__init__.py
-tests/unit/analysis/test_api.py
-tests/unit/analysis/test_io.py
-tests/unit/analysis/test_processing.py
-tests/unit/gillespie_simulation/test_simple_gillespie.py
-tests/unit/model/test_platonic_solids.py
-tests/unit/model/components/test_instances.py
-tests/unit/model/components/test_reactions.py
-tests/unit/model/components/test_reference_coordinates.py
-tests/unit/model/components/test_registry.py
-tests/unit/model/components/test_types.py
-tests/unit/model/components/test_units.py
-tests/unit/model/pdb/test_chain_grouping.py
-tests/unit/model/pdb/test_coarse_graining.py
-tests/unit/model/pdb/test_file_manager.py
-tests/unit/model/pdb/test_hyperparameters.py
-tests/unit/model/pdb/test_nerdss_exporter.py
-tests/unit/model/pdb/test_parser.py
-tests/unit/model/pdb/test_ring_regularizer.py
-tests/unit/model/pdb/test_template_builder.py
-tests/unit/model/pdb/test_visualizer.py
-tests/unit/ode_solver/test_ode_solver.py
-tests/unit/utils/test_angles.py
-tests/unit/utils/test_bond_geometry.py
-tests/unit/utils/test_coords.py
-tests/unit/utils/test_diffusion_constants.py
-tests/unit/utils/test_inertia_tensors.py
-tests/unit/utils/test_rigid_transform.py
-tests/unit/utils/test_rotations.py
-tests/unit/utils/test_steric_clash.py
-tests/unit/utils/test_string_similarity.py
+ionerdss/utils/vectors.py

{ionerdss-2.2 → ionerdss-2.2.2}/ioNERDSS.egg-info/requires.txt

@@ -55,6 +55,7 @@ accelerate>=0.26
 [simularium]
 simulariumio
 MDAnalysis
+pandas<3
 
 [test]
 pytest

{ionerdss-2.2 → ionerdss-2.2.2}/ioNERDSS.egg-info/top_level.txt

@@ -1,10 +1,10 @@
 benchmark
 data
+deprecated
+developer_tests
 dist
 docs
 env
-examples
 ionerdss
-tests
 tutorials
 website

{ionerdss-2.2 → ionerdss-2.2.2}/ionerdss/analysis/io/parser.py

@@ -21,8 +21,9 @@ logger = logging.getLogger(__name__)
 # Compiled regex patterns for performance
 # Matches: "time: 0.123" or "Time (s): 0.123"
 TIME_PATTERN = re.compile(r"(?:time|Time\s*\(s\)):\s*([-+]?\d*\.?\d+(?:[eE][-+]?\d+)?)")
-# Matches: "transition matrix for each mol type:"
-TRANSITION_HEADER_PATTERN = re.compile(r"transition\s+matrix\s+for\s+each\s+mol\s+type:", re.IGNORECASE)
+# Matches: "transition matrix for each mol type:", and the "transion" misspelling
+# written by NERDSS builds predating the fix in write_transition.cpp
+TRANSITION_HEADER_PATTERN = re.compile(r"transi(?:ti)?on\s+matrix\s+for\s+each\s+mol\s+type:", re.IGNORECASE)
 # Matches: "lifetime for each mol type:"
 LIFETIME_HEADER_PATTERN = re.compile(r"lifetime\s+for\s+each\s+mol\s+type:", re.IGNORECASE)
 # Matches: "size of the cluster: 5"
@@ -62,6 +63,7 @@ def parse_transition_file(file_path: Path) -> Tuple[List[TransitionData], List[L
     
     transitions: List[TransitionData] = []
     lifetimes_list: List[LifetimeData] = []
+    blocks_without_matrix = 0
 
     # Iterate in pairs of (time, block)
     for i in range(1, len(parts), 2):
@@ -74,6 +76,8 @@ def parse_transition_file(file_path: Path) -> Tuple[List[TransitionData], List[L
             # Only add if we have valid data
             if matrix.size > 0:
                 transitions.append({"time": time_val, "matrix": matrix})
+            else:
+                blocks_without_matrix += 1
             
             if lifetime_dict:
                 lifetimes_list.append({"time": time_val, "lifetimes": lifetime_dict})
@@ -82,6 +86,13 @@ def parse_transition_file(file_path: Path) -> Tuple[List[TransitionData], List[L
             logger.debug(f"Skipping malformed block at index {i}: {e}")
             continue
 
+    if blocks_without_matrix and not transitions:
+        logger.warning(
+            f"No transition matrix parsed from {file_path}: "
+            f"{blocks_without_matrix} time block(s) contained no matrix. "
+            f"Check that the file has a 'transition matrix for each mol type:' header."
+        )
+
     return transitions, lifetimes_list
 
 

{ionerdss-2.2 → ionerdss-2.2.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "ioNERDSS"
-version = "2.2"
+version = "2.2.2"
 description = "Package for preparing NERDSS inputs and analysing outputs."
 readme = "README.md"
 license = { text = "GPL-3.0" }
@@ -63,7 +63,12 @@ jupyter = ["jupyter", "jupyterlab", "ipykernel", "ipywidgets"]
 
 simularium = [
     "simulariumio",
-    "MDAnalysis"     # for simulariumio reading NERDSS PDB files
+    "MDAnalysis",    # for simulariumio reading NERDSS PDB files
+    # simulariumio 1.13.0 (latest on PyPI) writes in place into an array that
+    # pandas 3.0+ returns read-only, so its NERDSS converter raises
+    # "ValueError: assignment destination is read-only". The fix is on
+    # simulariumio's GitHub main branch but is not yet released to PyPI.
+    "pandas<3"
 ]
 
 docs = [
@@ -91,4 +96,4 @@ include-package-data = true
 where = ["."]
 
 [tool.pytest.ini_options]
-testpaths = ["tests"]
+testpaths = ["developer_tests"]

ionerdss-2.2/tests/unit/gillespie_simulation/test_simple_gillespie.py

@@ -1,106 +0,0 @@
-"""
-test_simple_gillespie.py
-
-Unit tests for `SimpleGillespieSimulator` in the `ionerdss` package.
-
-Tested Components
------------------
-- `convert_to_microscopic_rate_constants`:
-    Converts macroscopic rate constants to molecule-based (microscopic) rates
-    based on Avogadro's number and reaction order.
-
-- `calculate_propensity`:
-    Calculates the reaction propensities for a set of discrete molecular species.
-
-- `gillespie_simulation`:
-    Runs the full stochastic simulation algorithm (SSA) using the Gillespie direct method.
-
-Test Model
-----------
-The test reactions represent the following system:
-    R1: A + B → C        with macroscopic rate k1 = 1.0e6
-    R2: 2C   → A + 2B    with macroscopic rate k2 = 5.0
-
-Initial species concentrations:
-    y = [A, B, C] = [10, 5, 3]
-Simulation volume:
-    1e-18 L
-
-Author: yying7@jh.edu
--------
-Part of the ioNERDSS modeling framework.
-"""
-
-import unittest
-import numpy as np
-from ionerdss.gillespie_simulation import simple_gillespie as SimpleGillespie
-from ionerdss.gillespie_simulation import adaptive_rates as AdaptiveRates
-
-class TestReactionGillespie(unittest.TestCase):
-
-    def setUp(self):
-        # Example parameters for testing
-        self.macroscopic_rate_constants = np.array([1.0e6, 5.0])
-        self.reactant_matrix = np.array([[1, 1, 0], [0, 0, 2]])
-        self.product_matrix = np.array([[0, 0, 1], [1, 2, 1]])
-        self.volume = 1.0e-18 # Litre!
-        self.y = np.array([10, 5, 3])
-        self.sgs = SimpleGillespie
-
-    def test_convert_to_microscopic_rate_constants(self):
-        microscopic_rate_constants = self.sgs.convert_to_microscopic_rate_constants(
-            self.macroscopic_rate_constants, self.reactant_matrix, self.volume
-        )
-        expected_result = np.array([1.66053928e+00, 1.66053928e-05])
-        np.testing.assert_allclose(microscopic_rate_constants, expected_result)
-
-    def test_calculate_propensity(self):
-        microscopic_rate_constants = np.array([0.1 * 90, 0.05 * 5])
-        propensities = self.sgs.calculate_propensity(self.y, self.reactant_matrix, microscopic_rate_constants)
-        expected_result = np.array([450, 0.75])
-        np.testing.assert_allclose(propensities, expected_result)
-
-    def test_gillespie_simulation(self):
-        max_time = 10.0
-        y_init = np.array([10, 5, 3])
-        
-        record_interval = 10
-        full_update_scheme = True
-
-        y_record, t_record = self.sgs.gillespie_simulation(
-            max_time, y_init, self.reactant_matrix, self.product_matrix,
-            self.macroscopic_rate_constants, record_interval, full_update_scheme
-        )
-
-    def test_gillespie_simulation_1D_adaptive_rate(self):
-
-        ratelist = np.array([10, 0.2])
-        y_init = np.array([10, 3])
-        reactant_matrix = np.array([[2, 0], [0, 1]])
-        product_matrix = np.array([[0, 1], [2, 0]])
-        Length = 50
-        diffusion_constants = np.array([0.1, 0.05])
-        sigmalist = np.array([1, 0])
-        reverse_reaction_pairs = {0:1}
-
-        max_time = 10.0
-        record_interval = 0.01
-        full_update_scheme = True
-
-        rate_update_rule = AdaptiveRates.get_rule(
-            AdaptiveRates.adaptive_bimolecular_rate_1D,
-            Length, diffusion_constants, sigmalist, reverse_reaction_pairs
-        )
-
-        y_record, t_record = self.sgs.run_Gillespie(
-            max_time, y_init, reactant_matrix, product_matrix,
-            ratelist, Length, macroscopic=True, 
-            rate_update_rules=rate_update_rule,
-            record_interval=record_interval, 
-            full_update_scheme=full_update_scheme
-        )
-
-        # You can add more assertions based on the expected behavior of your simulation
-
-if __name__ == '__main__':
-    unittest.main()

ionerdss-2.2/tests/unit/utils/test_angles.py

@@ -1,163 +0,0 @@
-import unittest
-import numpy as np
-from numpy.testing import assert_allclose
-
-
-from ionerdss.utils.angles import (
-    absolute_error_to_angle,
-    angles_between_vector_and_vectors,
-    angles_from_points,
-    dihedrals_from_points,
-    )
-
-class TestAngles(unittest.TestCase):
-
-    def test_absolute_error_to_angle_basic(self):
-        points = np.array([[1, 0, 0], [0, 2, 0], [0, 0, 4]])
-        error = 0.1
-        expected = np.array([0.1 / 1, 0.1 / 2, 0.1 / 4])
-        result = absolute_error_to_angle(error, points)
-        np.testing.assert_allclose(result, expected, rtol=1e-6)
-
-    def test_absolute_error_to_angle_with_small_radius(self):
-        points = np.array([[0, 0, 0], [1e-12, 0, 0]])
-        error = 0.1
-        result = absolute_error_to_angle(error, points, tol=1e-8)
-        self.assertTrue(np.all(result >= 0))
-        self.assertAlmostEqual(result[0], 0.1 / 1e-8)
-        self.assertAlmostEqual(result[1], 0.1 / 1e-8)
-
-    def test_angles_between_vector_and_vectors_basic(self):
-        ref = np.array([1, 0, 0])
-        angle_deg = 47.3
-        angle_rad = np.deg2rad(angle_deg)
-        target_47_3 = np.array([np.cos(angle_rad), np.sin(angle_rad), 0])
-
-        targets = np.array([
-            [1, 0, 0],       # 0 degrees
-            [0, 1, 0],       # 90 degrees
-            [-1, 0, 0],      # 180 degrees
-            [1, 1, 0],       # ~45 degrees
-            target_47_3,     # 47.3 degrees
-        ])
-
-        result = angles_between_vector_and_vectors(ref, targets)
-        expected = np.array([
-            0.0,
-            np.pi / 2,
-            np.pi,
-            np.pi / 4,
-            angle_rad,
-        ])
-        np.testing.assert_allclose(result, expected, rtol=1e-6)
-
-    def test_angles_between_vector_and_zero_vector(self):
-        ref = np.array([1, 0, 0])
-        targets = np.array([
-            [0, 0, 0],  # zero norm
-            [0, 0, 0],  # zero norm
-        ])
-        result = angles_between_vector_and_vectors(ref, targets)
-        expected = np.array([0.0, 0.0])
-        np.testing.assert_array_equal(result, expected)
-
-    def test_angles_between_vector_and_vectors_with_tolerance(self):
-        ref = np.array([1e-12, 0, 0])
-        targets = np.array([[1, 0, 0]])
-        result = angles_between_vector_and_vectors(ref, targets, tol=1e-8)
-        expected = np.array([0.0])  # Denominator too small, treated as 0
-        np.testing.assert_array_equal(result, expected)
-
-    def test_angles_from_points(self):
-
-        # initialize list
-        p1 = []
-        p2 = []
-        p3 = []
-
-        # 90 degrees at vertex (1, 0, 0]
-        p1.append([1, 1, 0])
-        p2.append([1, 0, 0])
-        p3.append([2, 0, 0])
-
-        # 180 degrees at center
-        p1.append([0, 0, 0])
-        p2.append([1, 0, 0])
-        p3.append([2, 0, 0])
-
-        # 60 degrees at any vertex of equilateral triangle
-        p1.append([0, 0, 0])
-        p2.append([1, 0, 0])
-        p3.append([0.5, np.sqrt(3)/2, 0])
-
-        # colinear inward (0 deg)
-        p1.append([2, 0, 0])
-        p2.append([0, 0, 0])
-        p3.append([1, 0, 0])
-
-        # tetrahedron vertices
-        # Approx 70.53° angle between two bonds in tetrahedral geometry
-        p1.append([1, 1, 1])
-        p2.append([0, 0, 0])
-        p3.append([1, -1, -1])
-
-        # test numerical stability
-        p1.append([-1, 0, 0])
-        p2.append([0, 0, 0])
-        p3.append([1, 1e-7, 0])
-
-        # test
-        angle = angles_from_points(p1, p2, p3)
-        np.testing.assert_allclose(angle, np.array([np.pi/2.0,
-                                                0.0,
-                                                2 * np.pi/3.0,
-                                                np.pi,
-                                                np.pi-1.910633236249,
-                                                9.884312e-08]))
-
-class TestDihedralsFromPoints(unittest.TestCase):
-    def test_known_dihedral(self):
-        """
-        Test known values of dihedrals: planar and 90° configurations.
-        """
-        # Dihedral angle 0 degrees
-        p1 = np.array([[1.0, 0.0, 0.0]])
-        p2 = np.array([[0.0, 0.0, 0.0]])
-        p3 = np.array([[0.0, 1.0, 0.0]])
-        p4 = np.array([[1.0, 1.0, 0.0]])
-        dihedrals = dihedrals_from_points(p1, p2, p3, p4)
-        assert_allclose(dihedrals, [np.pi], atol=1e-6)
-
-        # Dihedral angle 90 degrees
-        p4 = np.array([[0.0, 1.0, 1.0]])
-        dihedrals = dihedrals_from_points(p1, p2, p3, p4)
-        assert_allclose(dihedrals, [np.pi/2], atol=1e-6)
-
-        # Dihedral angle -90 degrees
-        p4 = np.array([[0.0, 1.0, -1.0]])
-        dihedrals = dihedrals_from_points(p1, p2, p3, p4)
-        assert_allclose(dihedrals, [-np.pi/2], atol=1e-6)
-
-    def test_batch_dihedrals(self):
-        """
-        Test multiple dihedrals in a single call.
-        """
-        p1 = np.array([[1.0, 0.0, 0.0],
-                       [1.0, 0.0, 0.0]])
-        p2 = np.array([[0.0, 0.0, 0.0],
-                       [0.0, 0.0, 0.0]])
-        p3 = np.array([[0.0, 1.0, 0.0],
-                       [0.0, 1.0, 0.0]])
-        p4 = np.array([[1.0, 1.0, 0.0],
-                       [0.0, 1.0, 1.0]])
-
-        dihedrals = dihedrals_from_points(p1, p2, p3, p4)
-        expected = np.array([np.pi, np.pi/2])
-        assert_allclose(dihedrals, expected, atol=1e-6)
-
-if __name__ == "__main__":
-    unittest.main()
-
-
-if __name__ == "__main__":
-    unittest.main()