Black

mosdef_cassandra/analysis/thermo.py

@@ -25,7 +25,7 @@ def __init__(self, filename):
         # Read headers
         prp_headers = []
         with open(self.filename) as f:
-            for (idx, line) in enumerate(f):
+            for idx, line in enumerate(f):
                 if idx == 1 or idx == 2:
                     prp_headers.append(line)
                 if idx > 2:

mosdef_cassandra/core/moveset.py

@@ -43,11 +43,16 @@ def __init__(self, ensemble, species_topologies):
                 "species_topologies should be a " "list of species"
             )
 
-        if not (all(isinstance(top, gmso.Topology) for top in species_topologies) or all(
-            isinstance(top, parmed.Structure) for top in species_topologies)):
+        if not (
+            all(isinstance(top, gmso.Topology) for top in species_topologies)
+            or all(
+                isinstance(top, parmed.Structure) for top in species_topologies
+            )
+        ):
 
             raise TypeError(
-                "Each species should be a " "parmed.Structure or gmso.Topology"
+                "Each species should be a "
+                "parmed.Structure or gmso.Topology"
                 "and must be of the same type"
             )
 
@@ -745,46 +750,46 @@ def print(self):
             contents += "========     ".format(idx=idx + 1)
         contents += "\n"
         contents += "    Max translate (Ang):     "
-        for (box, max_translate_box) in enumerate(self.max_translate):
+        for box, max_translate_box in enumerate(self.max_translate):
             if box > 0:
                 contents += "                             "
-            for (idx, max_translate) in enumerate(max_translate_box):
+            for idx, max_translate in enumerate(max_translate_box):
                 contents += "{max_trans:4.2f}          ".format(
                     max_trans=max_translate
                 )
             contents += "(Box {box})".format(box=box + 1)
             contents += "\n"
         contents += "    Max rotate (deg):        "
-        for (box, max_rotate_box) in enumerate(self.max_rotate):
+        for box, max_rotate_box in enumerate(self.max_rotate):
             if box > 0:
                 contents += "                             "
-            for (idx, max_rotate) in enumerate(max_rotate_box):
+            for idx, max_rotate in enumerate(max_rotate_box):
                 contents += "{max_rot:4.2f}         ".format(
                     max_rot=max_rotate
                 )
             contents += "(Box {box})".format(box=box + 1)
             contents += "\n"
         contents += "    Insertable:              "
-        for (idx, insert) in enumerate(self.insertable):
+        for idx, insert in enumerate(self.insertable):
             contents += "{insert}          ".format(insert=insert)
         contents += "\n"
         contents += "    Max dihedral:            "
-        for (idx, max_dih) in enumerate(self.max_dihedral):
+        for idx, max_dih in enumerate(self.max_dihedral):
             contents += "{max_dih:4.2f}          ".format(max_dih=max_dih)
         contents += "\n"
         contents += "    Prob swap:               "
-        for (idx, prob_swap) in enumerate(self.prob_swap_species):
+        for idx, prob_swap in enumerate(self.prob_swap_species):
             contents += "{prob_swap:4.2f}          ".format(
                 prob_swap=prob_swap
             )
         contents += "\n"
         contents += "    Prob regrow:             "
-        for (idx, prob_regrow) in enumerate(self.prob_regrow_species):
+        for idx, prob_regrow in enumerate(self.prob_regrow_species):
             contents += "{regrow:4.2f}          ".format(regrow=prob_regrow)
         contents += "\n"
 
         contents += "\n\nMax volume (Ang^3):\n"
-        for (box, max_vol) in enumerate(self.max_volume):
+        for box, max_vol in enumerate(self.max_volume):
             contents += "    Box {box}: {max_vol}\n".format(
                 box=box + 1, max_vol=max_vol
             )

mosdef_cassandra/core/system.py

@@ -134,11 +134,20 @@ def species_topologies(self, species_topologies):
                     "See help(mosdef_Cassandra.System) for details."
                 )
 
-            if not (all(isinstance(top, gmso.Topology) for top in species_topologies) or all(
-                isinstance(top, parmed.Structure) for top in species_topologies)):
+            if not (
+                all(
+                    isinstance(top, gmso.Topology)
+                    for top in species_topologies
+                )
+                or all(
+                    isinstance(top, parmed.Structure)
+                    for top in species_topologies
+                )
+            ):
 
                 raise TypeError(
-                    "Each species should be a " "parmed.Structure or gmso.Topology"
+                    "Each species should be a "
+                    "parmed.Structure or gmso.Topology"
                     "and must be of the same type"
                 )
 
@@ -149,14 +158,18 @@ def species_topologies(self, species_topologies):
                 subtops = []
                 if isinstance(top, gmso.Topology):
                     for molecule in top.unique_site_labels(name_only=True):
-                        subtops.append(top.create_subtop("molecule", (molecule, 1)))
+                        subtops.append(
+                            top.create_subtop("molecule", (molecule, 1))
+                        )
 
                     if len(subtops) > 1:
-                        raise ValueError("GMSO Topology must contain only one molecule type. For example, "
-                                         "if you have a box of water, you must have a single water molecule "
-                                         "type in the topology. If you have a box of water and methane, you "
-                                         "must have two separate single molecule topologies, one for water "
-                                          " and one for methane.")
+                        raise ValueError(
+                            "GMSO Topology must contain only one molecule type. For example, "
+                            "if you have a box of water, you must have a single water molecule "
+                            "type in the topology. If you have a box of water and methane, you "
+                            "must have two separate single molecule topologies, one for water "
+                            " and one for methane."
+                        )
                     subtops[0].box = top.box
                     top = to_parmed(subtops[0])
                     # top = to_parmed(top)
@@ -357,9 +370,9 @@ def fix_bonds(self):
                 if constrain is None:
                     start_idx = idx_offset
                     end_idx = idx_offset + n_mols * n_atoms
-                    constrained_coordinates[
-                        start_idx:end_idx
-                    ] = unconstrained_coordinates[start_idx:end_idx]
+                    constrained_coordinates[start_idx:end_idx] = (
+                        unconstrained_coordinates[start_idx:end_idx]
+                    )
                 # Else we apply the constraints one molecule
                 # at a time
                 else:

mosdef_cassandra/examples/nvt_gmso.py

@@ -32,15 +32,17 @@ def run_nvt_gmso(**custom_args):
 
     # Run a simulation at 300 K for 10000 MC moves
     mc.run(
-       system=system,
-       moveset=moveset,
-       run_type="equilibration",
-       run_length=10000,
-       temperature=300.0 * u.K,
-       seeds=[12345, 12345],
-       run_name="nvt_gmso",
-       **custom_args,
+        system=system,
+        moveset=moveset,
+        run_type="equilibration",
+        run_length=10000,
+        temperature=300.0 * u.K,
+        seeds=[12345, 12345],
+        run_name="nvt_gmso",
+        **custom_args,
     )
+
+
 #
 
 if __name__ == "__main__":

mosdef_cassandra/runners/__init__.py

@@ -1,2 +1 @@
 
-

mosdef_cassandra/tests/__init__.py

@@ -1,2 +1 @@
 
-

mosdef_cassandra/tests/test_examples.py

@@ -7,6 +7,7 @@
 from mosdef_cassandra.utils.exceptions import *
 from mosdef_cassandra.tests.base_test import BaseTest
 
+
 @pytest.mark.long
 class TestExamples(BaseTest):
     def test_run_nvt(self):

mosdef_cassandra/tests/test_moveset.py

@@ -21,8 +21,10 @@ def test_invalid_species_list(self, methane_oplsaa):
 
     def test_invalid_species_type(self):
         with pytest.raises(
-            TypeError, match=r"Each species should be a " "parmed.Structure or gmso.Topology"
-                "and must be of the same type"
+            TypeError,
+            match=r"Each species should be a "
+            "parmed.Structure or gmso.Topology"
+            "and must be of the same type",
         ):
             moveset = mc.MoveSet("nvt", [1])
 
@@ -605,7 +607,7 @@ def test_invalid_restricted_type_and_species(self, methane_oplsaa):
                 [methane_oplsaa], [["slitpore", None]], [[1, None]]
             )
 
-    @pytest.mark.skip(reason="The purpose of this test is not clear.")    
+    @pytest.mark.skip(reason="The purpose of this test is not clear.")
     def test_add_multiple_restricted_insertions(self, methane_oplsaa):
         moveset = mc.MoveSet("gcmc", [methane_oplsaa])
         moveset.add_restricted_insertions(

mosdef_cassandra/tests/test_writers.py

@@ -22,24 +22,29 @@ def check_start_type_header(inp_contents):
             if "# Start_Type" in line:
                 return idx
         raise AssertionError("Missing '# Start_Type' header")
-    
+
     @staticmethod
     def check_checkpoint_line(inp_contents, start_idx):
         """Helper function to check the checkpoint line format."""
         checkpoint_line = inp_contents[start_idx + 1].strip()
         parts = checkpoint_line.split()
-        assert len(parts) == 2, "The line following '# Start_Type' should have exactly two entries"
-        assert parts[0] == "checkpoint", "The first entry should be 'checkpoint'"
+        assert (
+            len(parts) == 2
+        ), "The line following '# Start_Type' should have exactly two entries"
+        assert (
+            parts[0] == "checkpoint"
+        ), "The first entry should be 'checkpoint'"
 
     @staticmethod
     def check_only_comments_or_whitespace(inp_contents, start_idx):
         """Helper function to check for only comments or whitespace until the next header."""
-        for line in inp_contents[start_idx + 2:]:
+        for line in inp_contents[start_idx + 2 :]:
             line = line.strip()
             if line.startswith("#"):
                 break
-            assert line == "" or line.startswith("!"), \
-                "Only spaces or comments are allowed between the checkpoint line and the next header"
+            assert line == "" or line.startswith(
+                "!"
+            ), "Only spaces or comments are allowed between the checkpoint line and the next header"
 
     @pytest.fixture
     def onecomp_system(self, methane_oplsaa, box):
@@ -1848,17 +1853,17 @@ def test_rst_multiple_rst(self, request, system_fixture, base_name):
         of an automatic equilibration detection loop, in which a simulation needs to
         be restarted if its not equilibrated.
 
-        This test evaluates systems with one or two boxes. Two boxes might be 
+        This test evaluates systems with one or two boxes. Two boxes might be
         problematic because some start types require two lines in the # Start_Type
         section.
-        
+
         This test ensures that the input files generated at each restart step:
         1. Contain a valid # Start_Type header.
         2. Follow the correct checkpoint line format (two entries, starting with "checkpoint").
         3. Include only comments or whitespace between the checkpoint line and the next # header.
 
         Parameters:
-        - system_fixture: The fixture name of the system setup, allowing tests with 
+        - system_fixture: The fixture name of the system setup, allowing tests with
                           both one-component and two-box systems.
         - base_name: The base name used for the generated files (e.g., "nvt" or "gemc").
         """
@@ -1900,4 +1905,6 @@ def test_rst_multiple_rst(self, request, system_fixture, base_name):
                         self.check_checkpoint_line(inp_contents, start_idx)
 
                         # Step 3: Ensure only comments or whitespace are present until the next '#' header
-                        self.check_only_comments_or_whitespace(inp_contents, start_idx)
+                        self.check_only_comments_or_whitespace(
+                            inp_contents, start_idx
+                        )

mosdef_cassandra/writers/writers.py

@@ -54,14 +54,18 @@ def write_mcfs(system, angle_style="harmonic"):
 
         mcf_name = "species{}.mcf".format(species_count + 1)
 
-        if all(isinstance(top, parmed.Structure) for top in system.original_tops):
+        if all(
+            isinstance(top, parmed.Structure) for top in system.original_tops
+        ):
             write_mcf(
                 species,
                 mcf_name,
                 angle_style=angle_style[species_count],
                 dihedral_style=dihedral_style,
             )
-        elif all(isinstance(top, gmso.Topology) for top in system.original_tops):
+        elif all(
+            isinstance(top, gmso.Topology) for top in system.original_tops
+        ):
             gmso_write_mcf(system.original_tops[species_count], mcf_name)
 
 
@@ -139,9 +143,13 @@ def _generate_restart_inp(restart_from, run_name, run_type, run_length):
         if "# Start_Type" in line:
             inp_contents[idx + 1] = "checkpoint " + restart_from + ".out.chk"
             i = idx + 2
-            while i < len(inp_contents) and not inp_contents[i].strip().startswith("#"):
+            while i < len(inp_contents) and not inp_contents[
+                i
+            ].strip().startswith("#"):
                 if not inp_contents[i].strip().startswith("!"):
-                    inp_contents[i] = ""  # Replace non-comment lines with an empty string
+                    inp_contents[i] = (
+                        ""  # Replace non-comment lines with an empty string
+                    )
                 i += 1
         if run_type is not None:
             if "# Run_Type" in line: