Azure pipelines

azure-pipelines.yml

@@ -1,6 +1,9 @@
 
 trigger:
-- master
+  branches:
+    include:
+      - master
+      - azure-pipelines
 
 pr:
   autoCancel: true
@@ -40,6 +43,12 @@ jobs:
     - bash: echo "##vso[task.prependpath]$CONDA/bin"
       displayName: Add Conda to path
 
+    # On Hosted macOS, the agent user doesn't have ownership of Miniconda's installation directory/
+    # We need to take ownership if we want to update conda or install packages globally
+    - bash: sudo chown -R $USER $CONDA
+      displayName: Take ownership of conda installation
+      condition: eq( variables['Agent.OS'], 'Darwin' )
+
     - bash : echo "##vso[task.prependpath]$(Build.SourcesDirectory)/Cassandra-1.3.1/bin"
       displayName: Add Cassandra to path
 
@@ -111,18 +120,18 @@ jobs:
 - job: StandardMoSDeF
   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)
@@ -158,5 +167,4 @@ jobs:
         source activate test-environment
         python -m pip install --user pytest-azurepipelines
         python -m pytest mosdef_cassandra/tests -v
-      displayName: Run Tests
-
+      displayName: Run Tests

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/__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

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)
@@ -32,15 +32,17 @@ def run_nvt(**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):
@@ -32,6 +33,30 @@ 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 = {

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])
 
@@ -605,6 +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.")
     def test_add_multiple_restricted_insertions(self, methane_oplsaa):
         moveset = mc.MoveSet("gcmc", [methane_oplsaa])
         moveset.add_restricted_insertions(