merge and fix conflicts. Pin hoomd<5

.github/ISSUE_TEMPLATE/BUG_REPORT.md

@@ -0,0 +1,26 @@
+---
+name: Bug report
+about: Report a bug in GMSO
+
+---
+
+**Bug summary**
+
+What were you trying to do and what happened instead? Please copy and paste the stack output
+
+
+**Code to reproduce the behavior**
+
+Please include a code snippet that can be used to reproduce this bug.
+
+```python
+# Paste your code here
+#
+#
+```
+
+**Software versions**
+
+- Which version of GMSO are you using? (`python -c "import gmso; print(gmso.__version__)"`)
+- Which version of Python (`python --version`)?
+- Which operating system?

.github/ISSUE_TEMPLATE/FEATURE_REQUEST.md

@@ -0,0 +1,17 @@
+---
+name: Feature request
+about: Suggest an improvement to GMSO
+
+---
+
+**Describe the behavior you would like added to GMSO**
+A clear and concise description of what the proposed idea is.
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/ISSUE_TEMPLATE/QUESTION.md

@@ -0,0 +1,7 @@
+---
+name: Questions/discussions
+about: For usage questions, important notes, and other discussions.
+
+---
+
+**A summary of the question or discussion topic.**

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,8 @@
+### PR Summary:
+
+### PR Checklist
+------------
+ - [ ] Includes appropriate unit test(s)
+ - [ ] Appropriate docstring(s) are added/updated
+ - [ ] Code is (approximately) PEP8 compliant
+ - [ ] Issue(s) raised/addressed?

.pre-commit-config.yaml

@@ -10,7 +10,7 @@ ci:
 repos:
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.7.0
+  rev: v0.9.2
   hooks:
     # Run the linter.
     - id: ruff

codecov.yml

@@ -4,3 +4,5 @@ ignore:
   - "gmso/paper"
   - "gmso/formats/networkx.py"
   - "gmso/external/convert_foyer_xml.py"
+  - "gmso/.github/ISSUE_TEMPLATE"
+  - "gmso/.github/PULL_REQUEST_TEMPLATE.md"

environment-dev.yml

@@ -12,7 +12,7 @@ dependencies:
   - pydantic>=2
   - networkx
   - pytest
-  - mbuild>=0.17.0
+  - mbuild>=1.1
   - openbabel>=3.0.0
   - foyer>=0.11.3
   - forcefield-utilities>=0.2.1
@@ -28,5 +28,5 @@ dependencies:
   - pandas
   - symengine
   - python-symengine
-  - hoomd
+  - hoomd>=4.0,<5.0
   - importlib_resources

gmso/abc/abstract_potential.py

@@ -135,7 +135,7 @@ def add_tag(self, tag: str, value: Any, overwrite=True) -> None:
         """Add metadata for a particular tag"""
         if self.tags.get(tag) and not overwrite:
             raise ValueError(
-                f"Tag {tag} already exists. " f"Please use overwrite=True to overwrite"
+                f"Tag {tag} already exists. Please use overwrite=True to overwrite"
             )
         self.tags[tag] = value
 

gmso/core/box.py

@@ -46,7 +46,7 @@ def _validate_lengths(lengths):
     ):
         if lengths[0] > 0 and lengths[1] > 0:
             warnings.warn(
-                "A c value of 0 was passed. This will be " "interpreted as a 2-D box."
+                "A c value of 0 was passed. This will be interpreted as a 2-D box."
             )
         else:
             raise ValueError(

gmso/core/parametric_potential.py

@@ -252,7 +252,7 @@ def etree(self, units=None):
                     f"Please specify member_classes or member_types attribute."
                 )
             for idx, value in enumerate(iterating_attribute):
-                attrib[f"{prefix}{idx+1}"] = str(value)
+                attrib[f"{prefix}{idx + 1}"] = str(value)
         xml_element = etree.Element(self.__class__.__name__, attrib=attrib)
         params = etree.SubElement(xml_element, "Parameters")
 
@@ -340,7 +340,6 @@ def member_types(x):
 
         desc = desc.replace(
             ">",
-            f", \n parameters: {self.parameters},\n"
-            f"member types: {member_types(self)}>",
+            f", \n parameters: {self.parameters},\nmember types: {member_types(self)}>",
         )
         return desc

gmso/core/topology.py

@@ -793,8 +793,7 @@ def _set_scaling_factor(self, value, molecule_id, interaction, name, index):
 
         if any(np.isnan(value)):
             raise ValueError(
-                f"Cannot assign a nan/NoneType to `{name}`. "
-                f"Provided value: {org_value}"
+                f"Cannot assign a nan/NoneType to `{name}`. Provided value: {org_value}"
             )
 
         if value.shape != (1,) and value.shape != (3,):
@@ -1788,7 +1787,7 @@ def _parse_parameter_expression(self, df, parameter, unyts_bool):
             getattr(getattr(self, parameter)[0], parameter[:-1] + "_type").parameters
         ):
             df[
-                f"Parameter {i} ({param}) {getattr(getattr(self, parameter)[0], parameter[:-1]+'_type').parameters[param].units}"
+                f"Parameter {i} ({param}) {getattr(getattr(self, parameter)[0], parameter[:-1] + '_type').parameters[param].units}"
             ] = list(
                 _return_float_for_unyt(
                     getattr(connection, parameter[:-1] + "_type").parameters[param],

gmso/external/convert_foyer_xml.py

@@ -270,7 +270,7 @@ def _write_nbforces(forcefield, ff_kwargs):
             nonBondedAtomTypes,
             "AtomType",
             attrib_dict={
-                "name": atom_type.get("name", f"AtomType-{j+1}"),
+                "name": atom_type.get("name", f"AtomType-{j + 1}"),
                 "atomclass": atom_type.get("class", ""),
                 "element": atom_type.get("element", ""),
                 "charge": atom_type.get("charge", "0.0"),

gmso/external/convert_hoomd.py

@@ -811,7 +811,7 @@ def _parse_nonbonded_forces(
         if i == 0:
             exclusions.append("bond")
         else:
-            exclusions.append(f"1-{i+2}")
+            exclusions.append(f"1-{i + 2}")
     nlist = hoomd.md.nlist.Cell(exclusions=exclusions, buffer=nlist_buffer)
 
     nbonded_forces = list()

gmso/formats/lammpsdata.py

@@ -647,7 +647,9 @@ def _validate_unit_compatibility(top, base_unyts):
                 float(base_unyts.convert_parameter(parameter, n_decimals=6, name=name)),
                 parameter.value,
                 atol=1e-3,
-            ), f"Units System {base_unyts.usystem} is not compatible with {atype} with value {parameter}"
+            ), (
+                f"Units System {base_unyts.usystem} is not compatible with {atype} with value {parameter}"
+            )
 
 
 def _write_header(out_file, top, atom_style, dihedral_parser):
@@ -1171,7 +1173,7 @@ def _write_conn_data(out_file, top, connStr, sorted_typesList):
             if sort_by_types(ele) == ctype_members
         ]
         for index in indexList:
-            typeStr = f"{i+1:<6d}\t{index+1:<6d}\t"
+            typeStr = f"{i + 1:<6d}\t{index + 1:<6d}\t"
             sorted_membersList = sort_connection_members(conn, sort_by="index", top=top)
             indexStr = "\t".join(
                 [

gmso/formats/mcf.py

@@ -315,7 +315,7 @@ def _write_atom_information(mcf, top, in_ring):
     mcf.write("{:d}\n".format(len(top.sites)))
     for idx, site in enumerate(top.sites):
         mcf.write(
-            "{:<4d}  " "{:<6s}  " "{:<2s}  " "{:8.4f}  " "{:12.8f}  ".format(
+            "{:<4d}  {:<6s}  {:<2s}  {:8.4f}  {:12.8f}  ".format(
                 idx + 1,
                 atypes_list[idx],
                 names[idx],
@@ -325,15 +325,15 @@ def _write_atom_information(mcf, top, in_ring):
         )
         if vdw_style == "LJ":
             mcf.write(
-                "{:3s}  " "{:10.5f}  " "{:10.5f}".format(
+                "{:3s}  {:10.5f}  {:10.5f}".format(
                     vdw_style,
                     (site.atom_type.parameters["epsilon"] / u.kb).in_units("K").value,
                     site.atom_type.parameters["sigma"].in_units("Angstrom").value,
                 )
             )
         elif vdw_style == "Mie":
             mcf.write(
-                "{:3s}  " "{:10.5f}  " "{:10.5f}  " "{:8.3f}  " "{:8.3f}".format(
+                "{:3s}  {:10.5f}  {:10.5f}  {:8.3f}  {:8.3f}".format(
                     vdw_style,
                     (site.atom_type.parameters["epsilon"] / u.kb).in_units("K").value,
                     site.atom_type.parameters["sigma"].in_units("Angstrom").value,
@@ -363,7 +363,7 @@ def _write_bond_information(mcf, top):
     mcf.write("{:d}\n".format(len(top.bonds)))
     for idx, bond in enumerate(top.bonds):
         mcf.write(
-            "{:<4d}  " "{:<4d}  " "{:<4d}  " "{:s}  " "{:10.5f}\n".format(
+            "{:<4d}  {:<4d}  {:<4d}  {:s}  {:10.5f}\n".format(
                 idx + 1,
                 top.get_index(bond.connection_members[0]) + 1,
                 top.get_index(bond.connection_members[1]) + 1,
@@ -403,7 +403,7 @@ def _write_angle_information(mcf, top):
         angle_style = _get_angle_style(angle)
         if angle_style == "fixed":
             mcf.write(
-                "{:s}  " "{:10.5f}\n".format(
+                "{:s}  {:10.5f}\n".format(
                     angle_style,
                     angle.connection_type.parameters["theta_eq"]
                     .in_units(u.degree)
@@ -412,7 +412,7 @@ def _write_angle_information(mcf, top):
             )
         elif angle_style == "harmonic":
             mcf.write(
-                "{:s}  " "{:10.5f} " "{:10.5f}\n".format(
+                "{:s}  {:10.5f} {:10.5f}\n".format(
                     angle_style,
                     (0.5 * angle.connection_type.parameters["k"] / u.kb)
                     .in_units("K/rad**2")
@@ -452,7 +452,7 @@ def _write_dihedral_information(mcf, top):
     mcf.write("{:d}\n".format(len(top.dihedrals)))
     for idx, dihedral in enumerate(top.dihedrals):
         mcf.write(
-            "{:<4d}  " "{:<4d}  " "{:<4d}  " "{:<4d}  " "{:<4d}  ".format(
+            "{:<4d}  {:<4d}  {:<4d}  {:<4d}  {:<4d}  ".format(
                 idx + 1,
                 top.get_index(dihedral.connection_members[0]) + 1,
                 top.get_index(dihedral.connection_members[1]) + 1,
@@ -488,7 +488,7 @@ def _write_dihedral_information(mcf, top):
             # So we need to exclude the last term in the GMSO topology.
             dihedral_style = "OPLS"
             mcf.write(
-                "{:s}  " "{:10.5f}  " "{:10.5f}  " "{:10.5f}  " "{:10.5f}\n".format(
+                "{:s}  {:10.5f}  {:10.5f}  {:10.5f}  {:10.5f}\n".format(
                     dihedral_style,
                     0.5
                     * dihedral.connection_type.parameters["k0"]
@@ -510,7 +510,7 @@ def _write_dihedral_information(mcf, top):
             )
         elif dihedral_style == "CHARMM":
             mcf.write(
-                "{:s}  " "{:10.5f}  " "{:10.5f}  " "{:10.5f}\n".format(
+                "{:s}  {:10.5f}  {:10.5f}  {:10.5f}\n".format(
                     dihedral_style,
                     dihedral.connection_type.parameters["k"].in_units("kJ/mol").value,
                     dihedral.connection_type.parameters["n"],
@@ -521,7 +521,7 @@ def _write_dihedral_information(mcf, top):
             )
         elif dihedral_style == "HARMONIC":
             mcf.write(
-                "{:s}  " "{:10.5f}  " "{:10.5f}\n".format(
+                "{:s}  {:10.5f}  {:10.5f}\n".format(
                     dihedral_style.lower(),
                     0.5
                     * dihedral.connection_type.parameters["k"].in_units("kJ/mol").value,
@@ -558,8 +558,7 @@ def _write_improper_information(mcf, top):
     improper_style = "harmonic"
     for i, improper in enumerate(top.impropers):
         mcf.write(
-            "{:<4d}  {:<4d}  {:<4d}  {:<4d}  {:<4d}"
-            "  {:s}  {:10.5f}  {:10.5f}\n".format(
+            "{:<4d}  {:<4d}  {:<4d}  {:<4d}  {:<4d}  {:s}  {:10.5f}  {:10.5f}\n".format(
                 i + 1,
                 top.get_index(improper.connection_members[0]) + 1,
                 top.get_index(improper.connection_members[1]) + 1,

gmso/formats/top.py

@@ -58,15 +58,10 @@ def write_top(top, filename, top_vars=None):
             )
         )
         out_file.write(
-            "[ defaults ]\n"
-            "; nbfunc\t"
-            "comb-rule\t"
-            "gen-pairs\t"
-            "fudgeLJ\t\t"
-            "fudgeQQ\n"
+            "[ defaults ]\n; nbfunc\tcomb-rule\tgen-pairs\tfudgeLJ\t\tfudgeQQ\n"
         )
         out_file.write(
-            "{0}\t\t" "{1}\t\t" "{2}\t\t" "{3}\t\t" "{4}\n\n".format(
+            "{0}\t\t{1}\t\t{2}\t\t{3}\t\t{4}\n\n".format(
                 top_vars["nbfunc"],
                 top_vars["comb-rule"],
                 top_vars["gen-pairs"],
@@ -76,25 +71,12 @@ def write_top(top, filename, top_vars=None):
         )
 
         out_file.write(
-            "[ atomtypes ]\n"
-            "; name\t"
-            "at.num\t\t"
-            "mass\t"
-            "charge\t\t"
-            "ptype\t"
-            "sigma\t"
-            "epsilon\n"
+            "[ atomtypes ]\n; name\tat.num\t\tmass\tcharge\t\tptype\tsigma\tepsilon\n"
         )
 
         for atom_type in top.atom_types(PotentialFilters.UNIQUE_NAME_CLASS):
             out_file.write(
-                "{0:12s}"
-                "{1:4s}"
-                "{2:12.5f}"
-                "{3:12.5f}\t"
-                "{4:4s}"
-                "{5:12.5f}"
-                "{6:12.5f}\n".format(
+                "{0:12s}{1:4s}{2:12.5f}{3:12.5f}\t{4:4s}{5:12.5f}{6:12.5f}\n".format(
                     atom_type.name,
                     str(_lookup_atomic_number(atom_type)),
                     atom_type.mass.in_units(u.amu).value,
@@ -115,7 +97,7 @@ def write_top(top, filename, top_vars=None):
             "bond_restraints": "\n[ bonds ] ;Harmonic potential restraint\n"
             "; ai\taj\tfunct\tb0\t\tkb\n",
             "pairs": "\n[ pairs ]\n; ai\taj\tfunct\n",
-            "angles": "\n[ angles ]\n" "; ai\taj\tak\tfunct\tphi_0\t\tk0\n",
+            "angles": "\n[ angles ]\n; ai\taj\tak\tfunct\tphi_0\t\tk0\n",
             "angle_restraints": (
                 "\n[ angle_restraints ]\n"
                 "; ai\taj\tai\tak\tfunct\ttheta_eq\tk\tmultiplicity\n"
@@ -132,14 +114,14 @@ def write_top(top, filename, top_vars=None):
         }
         for tag in unique_molecules:
             """Write out nrexcl for each unique molecule."""
-            out_file.write("\n[ moleculetype ]\n" "; name\tnrexcl\n")
+            out_file.write("\n[ moleculetype ]\n; name\tnrexcl\n")
 
             # TODO: Lookup and join nrexcl from each molecule object
-            out_file.write("{0}\t" "{1}\n\n".format(tag, top_vars["nrexcl"]))
+            out_file.write("{0}\t{1}\n\n".format(tag, top_vars["nrexcl"]))
 
             """Write out atoms for each unique molecule."""
             out_file.write(
-                "[ atoms ]\n" "; nr\ttype\tresnr\tresidue\t\tatom\tcgnr\tcharge\tmass\n"
+                "[ atoms ]\n; nr\ttype\tresnr\tresidue\t\tatom\tcgnr\tcharge\tmass\n"
             )
             # Each unique molecule need to be reindexed (restarting from 0)
             # The shifted_idx_map is needed to make sure all the atom index used in
@@ -148,14 +130,7 @@ def write_top(top, filename, top_vars=None):
             for idx, site in enumerate(unique_molecules[tag]["sites"]):
                 shifted_idx_map[top.get_index(site)] = idx
                 out_file.write(
-                    "{0:8s}"
-                    "{1:12s}"
-                    "{2:8s}"
-                    "{3:12s}"
-                    "{4:8s}"
-                    "{5:4s}"
-                    "{6:12.5f}"
-                    "{7:12.5f}\n".format(
+                    "{0:8s}{1:12s}{2:8s}{3:12s}{4:8s}{5:4s}{6:12.5f}{7:12.5f}\n".format(
                         str(idx + 1),
                         site.atom_type.name,
                         str(site.molecule.number + 1 if site.molecule else 1),
@@ -302,9 +277,9 @@ def write_top(top, filename, top_vars=None):
                                 )
                             )
 
-        out_file.write("\n[ system ]\n" "; name\n" "{0}\n\n".format(top.name))
+        out_file.write("\n[ system ]\n; name\n{0}\n\n".format(top.name))
 
-        out_file.write("[ molecules ]\n" "; molecule\tnmols\n")
+        out_file.write("[ molecules ]\n; molecule\tnmols\n")
         for tag in unique_molecules:
             out_file.write(
                 "{0}\t{1}\n".format(tag, len(unique_molecules[tag]["subtags"]))