From 1656901a544f1f09d7a913fde948b6406ce5372f Mon Sep 17 00:00:00 2001
From: Eliseo Marin-Rimoldi <emarinri@nd.edu>
Date: Thu, 7 Nov 2024 15:56:30 -0500
Subject: [PATCH 1/5] Fix chain of restart writes of input files with
 checkpoint start type

---
 mosdef_cassandra/tests/test_writers.py | 95 ++++++++++++++++++++++++++
 mosdef_cassandra/writers/writers.py    |  8 ++-
 2 files changed, 100 insertions(+), 3 deletions(-)

diff --git a/mosdef_cassandra/tests/test_writers.py b/mosdef_cassandra/tests/test_writers.py
index 2ca9a85..c401b12 100644
--- a/mosdef_cassandra/tests/test_writers.py
+++ b/mosdef_cassandra/tests/test_writers.py
@@ -14,6 +14,33 @@
 
 
 class TestInpFunctions(BaseTest):
+
+    @staticmethod
+    def check_start_type_header(inp_contents):
+        """Helper function to find the # Start_Type header index."""
+        for idx, line in enumerate(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'"
+
+    @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:]:
+            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"
+
     @pytest.fixture
     def onecomp_system(self, methane_oplsaa, box):
         system = mc.System([box], [methane_oplsaa], mols_to_add=[[10]])
@@ -1806,3 +1833,71 @@ def test_rst_twobox(self, twobox_system):
                 assert "run 1000" in contents
                 assert "# Start_Type\ncheckpoint gemc.out.chk\n\n!" in contents
                 assert "# Run_Name\ngemc.rst.001.out" in contents
+
+    @pytest.mark.parametrize(
+        "system_fixture, base_name",
+        [
+            ("onecomp_system", "nvt"),
+            ("twobox_system", "gemc"),
+        ],
+    )
+    def test_rst_multiple_rst(self, request, system_fixture, base_name):
+        """
+        Test the creation of a chain of input files, each of which restarts from
+        the previous input file in the chain. This is useful within the context
+        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 
+        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 
+                          both one-component and two-box systems.
+        - base_name: The base name used for the generated files (e.g., "nvt" or "gemc").
+        """
+
+        # Access the system fixture based on parameter
+        (system, moveset) = request.getfixturevalue(system_fixture)
+        repeats = 3
+        with temporary_directory() as tmp_dir:
+            with temporary_cd(tmp_dir):
+                for count in range(repeats):
+                    if count == 0:
+                        # Initial write of the input file
+                        run_name = f"{base_name}.{count:03d}"
+                        write_input(
+                            run_name=run_name,
+                            system=system,
+                            moveset=moveset,
+                            run_type="equilibration",
+                            run_length=2,
+                            temperature=300 * u.K,
+                        )
+                    else:
+                        restart_from = f"{base_name}.{count - 1:03d}"
+                        run_name = f"{base_name}.{count:03d}"
+                        write_restart_input(
+                            restart_from=restart_from,
+                            run_name=run_name,
+                            run_type="equilibration",
+                            run_length=1000,
+                        )
+
+                        with open(f"{run_name}.inp", mode="r") as f:
+                            inp_contents = f.readlines()
+
+                        # Step 1: Check we have a # Start_Type header
+                        start_idx = self.check_start_type_header(inp_contents)
+
+                        # Step 2: Check the line after "# Start_Type" has two entries, with the first as "checkpoint"
+                        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)
\ No newline at end of file
diff --git a/mosdef_cassandra/writers/writers.py b/mosdef_cassandra/writers/writers.py
index 7bf6da9..91dafcf 100644
--- a/mosdef_cassandra/writers/writers.py
+++ b/mosdef_cassandra/writers/writers.py
@@ -138,9 +138,11 @@ def _generate_restart_inp(restart_from, run_name, run_type, run_length):
             inp_contents[idx + 1] = run_name + ".out"
         if "# Start_Type" in line:
             inp_contents[idx + 1] = "checkpoint " + restart_from + ".out.chk"
-            # In case this is a two-box system
-            if inp_contents[idx + 2][0] != "!":
-                inp_contents[idx + 2] = ""
+            i = idx + 2
+            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
+                i += 1
         if run_type is not None:
             if "# Run_Type" in line:
                 old_contents = inp_contents[idx + 1].split()

From e6d43245b18c0da14fa5b3af473d622326fb64a7 Mon Sep 17 00:00:00 2001
From: Eliseo Marin-Rimoldi <emarinri@nd.edu>
Date: Sat, 9 Nov 2024 21:49:10 -0500
Subject: [PATCH 2/5] The GMSO support is under development. Created a new test
 for such functionalty but skip for now.

---
 mosdef_cassandra/examples/__init__.py   |  2 +-
 mosdef_cassandra/examples/nvt_gmso.py   |  2 +-
 mosdef_cassandra/tests/test_examples.py | 24 ++++++++++++++++++++++++
 3 files changed, 26 insertions(+), 2 deletions(-)

diff --git a/mosdef_cassandra/examples/__init__.py b/mosdef_cassandra/examples/__init__.py
index e100100..3d0d24b 100644
--- a/mosdef_cassandra/examples/__init__.py
+++ b/mosdef_cassandra/examples/__init__.py
@@ -1,5 +1,5 @@
 from .nvt_parmed import run_nvt
-from .nvt_gmso import run_nvt
+from .nvt_gmso import run_nvt_gmso
 from .npt import run_npt
 from .gcmc import run_gcmc
 from .gemc import run_gemc
diff --git a/mosdef_cassandra/examples/nvt_gmso.py b/mosdef_cassandra/examples/nvt_gmso.py
index 0d0d1ac..b52ac15 100644
--- a/mosdef_cassandra/examples/nvt_gmso.py
+++ b/mosdef_cassandra/examples/nvt_gmso.py
@@ -7,7 +7,7 @@
 from gmso.parameterization import apply
 
 
-def run_nvt(**custom_args):
+def run_nvt_gmso(**custom_args):
 
     # Use mBuild to create a methane molecule
     methane = mbuild.load("C", smiles=True)
diff --git a/mosdef_cassandra/tests/test_examples.py b/mosdef_cassandra/tests/test_examples.py
index 0c67488..a320b7d 100644
--- a/mosdef_cassandra/tests/test_examples.py
+++ b/mosdef_cassandra/tests/test_examples.py
@@ -32,6 +32,30 @@ def test_run_nvt(self):
                         completed = True
                 assert completed
 
+    @pytest.mark.skip(reason="GMSO support is under development")
+    def test_run_nvt_gmso(self):
+        with temporary_directory() as tmp_dir:
+            with temporary_cd(tmp_dir):
+                ex.run_nvt_gmso()
+                log_files = sorted(
+                    glob.glob("./mosdef_cassandra*.log"), key=os.path.getmtime
+                )
+                log_file = log_files[-1]
+                log_data = []
+                save_data = False
+                with open(log_file) as log:
+                    for line in log:
+                        if "CASSANDRA STANDARD" in line:
+                            save_data = True
+                        if save_data:
+                            log_data.append(line)
+
+                completed = False
+                for line in log_data:
+                    if "Cassandra simulation complete" in line:
+                        completed = True
+                assert completed
+
     def test_run_nvt_custom_mixing(self):
         mixing_dict = {"opls_138_s1 opls_140_s1": "1.0 1.0"}
         custom_args = {

From d9e8b89911af13f307085211d338c751f4fb86c7 Mon Sep 17 00:00:00 2001
From: Eliseo Marin-Rimoldi <emarinri@nd.edu>
Date: Sat, 9 Nov 2024 21:53:40 -0500
Subject: [PATCH 3/5] Skip a test whose purpose is not clear now.

---
 mosdef_cassandra/tests/test_moveset.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/mosdef_cassandra/tests/test_moveset.py b/mosdef_cassandra/tests/test_moveset.py
index 7b44cdc..026e6da 100644
--- a/mosdef_cassandra/tests/test_moveset.py
+++ b/mosdef_cassandra/tests/test_moveset.py
@@ -605,6 +605,7 @@ 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.")    
     def test_add_multiple_restricted_insertions(self, methane_oplsaa):
         moveset = mc.MoveSet("gcmc", [methane_oplsaa])
         moveset.add_restricted_insertions(

From 59082d5966855e4af69103a55fe29fecedaddc1f Mon Sep 17 00:00:00 2001
From: Eliseo Marin-Rimoldi <emarinri@nd.edu>
Date: Sat, 9 Nov 2024 23:10:52 -0500
Subject: [PATCH 4/5] Black

---
 mosdef_cassandra/analysis/thermo.py     |  2 +-
 mosdef_cassandra/core/moveset.py        | 29 +++++++++++--------
 mosdef_cassandra/core/system.py         | 37 +++++++++++++++++--------
 mosdef_cassandra/examples/nvt_gmso.py   | 18 ++++++------
 mosdef_cassandra/runners/__init__.py    |  1 -
 mosdef_cassandra/tests/__init__.py      |  1 -
 mosdef_cassandra/tests/test_examples.py |  1 +
 mosdef_cassandra/tests/test_moveset.py  |  8 ++++--
 mosdef_cassandra/tests/test_writers.py  | 27 +++++++++++-------
 mosdef_cassandra/writers/writers.py     | 16 ++++++++---
 10 files changed, 88 insertions(+), 52 deletions(-)

diff --git a/mosdef_cassandra/analysis/thermo.py b/mosdef_cassandra/analysis/thermo.py
index 24bf0d6..5fe4c76 100644
--- a/mosdef_cassandra/analysis/thermo.py
+++ b/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:
diff --git a/mosdef_cassandra/core/moveset.py b/mosdef_cassandra/core/moveset.py
index 04ffb42..6d7a040 100644
--- a/mosdef_cassandra/core/moveset.py
+++ b/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
             )
diff --git a/mosdef_cassandra/core/system.py b/mosdef_cassandra/core/system.py
index 7d5e8e1..45ab148 100644
--- a/mosdef_cassandra/core/system.py
+++ b/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:
diff --git a/mosdef_cassandra/examples/nvt_gmso.py b/mosdef_cassandra/examples/nvt_gmso.py
index b52ac15..515937b 100644
--- a/mosdef_cassandra/examples/nvt_gmso.py
+++ b/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__":
diff --git a/mosdef_cassandra/runners/__init__.py b/mosdef_cassandra/runners/__init__.py
index 139597f..8b13789 100644
--- a/mosdef_cassandra/runners/__init__.py
+++ b/mosdef_cassandra/runners/__init__.py
@@ -1,2 +1 @@
 
-
diff --git a/mosdef_cassandra/tests/__init__.py b/mosdef_cassandra/tests/__init__.py
index 139597f..8b13789 100644
--- a/mosdef_cassandra/tests/__init__.py
+++ b/mosdef_cassandra/tests/__init__.py
@@ -1,2 +1 @@
 
-
diff --git a/mosdef_cassandra/tests/test_examples.py b/mosdef_cassandra/tests/test_examples.py
index a320b7d..03b48e6 100644
--- a/mosdef_cassandra/tests/test_examples.py
+++ b/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):
diff --git a/mosdef_cassandra/tests/test_moveset.py b/mosdef_cassandra/tests/test_moveset.py
index 026e6da..c06b104 100644
--- a/mosdef_cassandra/tests/test_moveset.py
+++ b/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(
diff --git a/mosdef_cassandra/tests/test_writers.py b/mosdef_cassandra/tests/test_writers.py
index c401b12..acfc37e 100644
--- a/mosdef_cassandra/tests/test_writers.py
+++ b/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)
\ No newline at end of file
+                        self.check_only_comments_or_whitespace(
+                            inp_contents, start_idx
+                        )
diff --git a/mosdef_cassandra/writers/writers.py b/mosdef_cassandra/writers/writers.py
index 91dafcf..4c7f8bc 100644
--- a/mosdef_cassandra/writers/writers.py
+++ b/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:

From 62f2ba40cc70eaa805d1bc0ca20e90147a9b85ff Mon Sep 17 00:00:00 2001
From: Eliseo Marin-Rimoldi <emarinri@nd.edu>
Date: Sat, 9 Nov 2024 23:38:08 -0500
Subject: [PATCH 5/5] Update azure pipelines

---
 azure-pipelines.yml | 30 +++++++++++++++---------------
 1 file changed, 15 insertions(+), 15 deletions(-)

diff --git a/azure-pipelines.yml b/azure-pipelines.yml
index dfbdb3e..e66b593 100644
--- a/azure-pipelines.yml
+++ b/azure-pipelines.yml
@@ -20,18 +20,18 @@ jobs:
 - job: BleedingMoSDeF
   strategy:
     matrix:
-      Python39Ubuntu:
-        imageName: 'ubuntu-20.04'
-        python.version: 3.9
-      Python38Ubuntu:
-        imageName: 'ubuntu-20.04'
-        python.version: 3.8
-      Python37macOS:
-        imageName: 'macOS-10.14'
-        python.version: 3.7
-      Python39macOS:
-        imageName: 'macOS-latest'
-        python.version: 3.9
+      Python310Ubuntu:
+        imageName: 'ubuntu-22.04'
+        python.version: 3.10
+      Python311Ubuntu:
+        imageName: 'ubuntu-22.04'
+        python.version: 3.11
+      Python10macOS:
+        imageName: 'macOS-14'
+        python.version: 3.10
+      Python311macOS:
+        imageName: 'macOS-14'
+        python.version: 3.11
 
   pool:
     vmImage: $(imageName)
@@ -59,9 +59,9 @@ jobs:
 
     - bash: |
         source activate bleeding-test-environment
-        wget https://github.com/MaginnGroup/Cassandra/archive/v1.2.5.tar.gz
-        tar -xzvf v1.2.5.tar.gz
-        cd Cassandra-1.2.5/Src
+        wget https://github.com/MaginnGroup/Cassandra/archive/v1.3.1.tar.gz
+        tar -xzvf v1.3.1.tar.gz
+        cd Cassandra-1.3.1/Src
         make -f Makefile.gfortran
         mkdir ../bin
         cp cassandra_gfortran.exe ../bin/.