Remove deprecated formats, update reader and writer backends (#1191)

* remove hoomdxml * remove protobuf * remove hoomd3 force writers * change backend for mol2 and xyz to gmso * remove protobuf from dev environments * add some TODO notes * change behavior of xyz test * comment out test for elements * fix test based on expected behavior for xyz files, remove wrong n atoms tests, that is being tested for in GMSO test_xyz.py * remove lammpsdata and tests * remove duplicate benzene fixture that reads benzene from a mol2 file * update benzene naming to fix failing rigid tests * add hoomd_writer file that has GSD and snapshot writer * fix typo * add else statement * move to_hoomdsnapshot to conversion, add method in Compound class. Delete old snapshot and gsd writers * fix import * remove hoomd writer file, add TODO flags to conversion * add TODO notes, pass in overwrite to Topology.save(), comment out file formats that require typed systems * remove tests for gsd, hoomd, cassandra and par writers, move tests for loading xys into test_compound * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add check for charges back in save method * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add if statement before checking charge is neutral * remove .top from unit test * remove lammps and lammpsdata files from tests and support in conversion.py * Don't use gmso mol2 backend * remove gmso as backend for mol2 saver * remove Hoomd V3 test from CI * remove par writer and xyz reader/write * pin gmso to latest ver in window env file * add has_hoomd back to io.py, handle tests that use hoomd via gmso * fix syntax * remove unused import * update doc strings with new links, correct file types and methods * add saver mapping to compound.save doc strings --------- Co-authored-by: CalCraven <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
mosdef-hub · Oct 26, 2024 · aabbab6 · aabbab6
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commit aabbab6
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diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml
@@ -54,12 +54,6 @@ jobs:
       - name: Test (OS -> ${{ matrix.os }} / Python -> ${{ matrix.python-version }})
         run: python -m pytest -v --cov=mbuild --cov-report=xml --cov-append --cov-config=setup.cfg --color yes --pyargs mbuild
 
-      - name: Tests for HOOMD-blue (V3)
-        run: |
-          micromamba install -c conda-forge "hoomd>3"
-          python -m pytest -v --cov=mbuild --cov-report=xml --cov-append --cov-config=setup.cfg --color yes mbuild/tests/test_hoomd.py
-        if: runner.os == 'Linux'
-
       - name: Upload Coverage Report
         uses: codecov/codecov-action@v4
         with:

diff --git a/environment-dev-win.yml b/environment-dev-win.yml
@@ -6,7 +6,7 @@ dependencies:
   - bump2version
   - codecov
   - ele
-  - gmso>=0.9.0
+  - gmso>=0.12.4
   - foyer>=0.11.0
   - garnett>=0.7.1
   - gsd>=2.9
@@ -20,7 +20,6 @@ dependencies:
   - parmed>=3.4.3
   - pip
   - pre-commit
-  - protobuf
   - py3Dmol
   - pycifrw
   - pytest

diff --git a/environment-dev.yml b/environment-dev.yml
@@ -21,7 +21,6 @@ dependencies:
   - parmed>=3.4.3
   - pip
   - pre-commit
-  - protobuf
   - py3Dmol
   - pycifrw
   - pytest

diff --git a/mbuild/compound.py b/mbuild/compound.py
@@ -2007,7 +2007,6 @@ def _visualize_py3dmol(
             os.path.join(tmp_dir, "tmp.mol2"),
             include_ports=show_ports,
             overwrite=True,
-            parmed_kwargs={"infer_residues": False},
         )
 
         view = py3Dmol.view()
@@ -2979,15 +2978,9 @@ def save(
         self,
         filename,
         include_ports=False,
-        forcefield_name=None,
-        forcefield_files=None,
-        forcefield_debug=False,
         box=None,
         overwrite=False,
         residues=None,
-        combining_rule="lorentz",
-        foyer_kwargs=None,
-        parmed_kwargs=None,
         **kwargs,
     ):
         """Save the Compound to a file.
@@ -2997,22 +2990,11 @@ def save(
         filename : str
             Filesystem path in which to save the trajectory. The extension or
             prefix will be parsed and control the format. Supported extensions:
-            'hoomdxml', 'gsd', 'gro', 'top', 'lammps', 'lmp', 'mcf', 'pdb', 'xyz',
-            'json', 'mol2', 'sdf', 'psf'. See parmed/structure.py for more
-            information on savers.
+            'gsd', 'gro', 'top', 'mcf', 'pdb', 'xyz',
+            'json', 'mol2', 'sdf', 'psf'. See `mbuild.conversion.save()`
+            for more information about writer methods.
         include_ports : bool, optional, default=False
             Save ports contained within the compound.
-        forcefield_files : str, optional, default=None
-            Apply a forcefield to the output file using a forcefield provided
-            by the `foyer` package.
-        forcefield_name : str, optional, default=None
-            Apply a named forcefield to the output file using the `foyer`
-            package, e.g. 'oplsaa'. `Foyer forcefields
-            <https://github.com/mosdef-hub/foyer/tree/master/foyer/forcefields>`_
-        forcefield_debug : bool, optional, default=False
-            Choose verbosity level when applying a forcefield through `foyer`.
-            Specifically, when missing atom types in the forcefield xml file,
-            determine if the warning is condensed or verbose.
         box : mb.Box, optional, default=self.boundingbox (with buffer)
             Box information to be written to the output file. If 'None', a
             bounding box is used with 0.25nm buffers at each face to avoid
@@ -3022,50 +3004,25 @@ def save(
         residues : str of list of str
             Labels of residues in the Compound. Residues are assigned by
             checking against Compound.name.
-        combining_rule : str, optional, default='lorentz'
-            Specify the combining rule for nonbonded interactions. Only relevant
-            when the `foyer` package is used to apply a forcefield. Valid
-            options are 'lorentz' and 'geometric', specifying Lorentz-Berthelot
-            and geometric combining rules respectively.
-        foyer_kwargs : dict, optional, default=None
-            Keyword arguments to provide to `foyer.Forcefield.apply`.
-            Depending on the file extension these will be passed to either
-            `write_gsd`, `write_hoomdxml`, `write_lammpsdata`,
-            `write_mcf`, or `parmed.Structure.save`.
-            See `parmed structure documentation
-            <https://parmed.github.io/ParmEd/html/structobj/parmed.structure.Structure.html#parmed.structure.Structure.save>`_
-        parmed_kwargs : dict, optional, default=None
-            Keyword arguments to provide to :meth:`mbuild.Compound.to_parmed`
         **kwargs
+            See `mbuild.conversion.save()`.
             Depending on the file extension these will be passed to either
-            `write_gsd`, `write_hoomdxml`, `write_lammpsdata`, `write_mcf`, or
-            `parmed.Structure.save`.
+            Parmed or GMSO backend writers
             See https://parmed.github.io/ParmEd/html/structobj/parmed.structure.
-            Structure.html#parmed.structure.Structure.save
+            Structure.html#parmed.structure.Structure.save and
+            https://github.com/mosdef-hub/gmso/tree/main/gmso/formats
 
         Other Parameters
         ----------------
         ref_distance : float, optional, default=1.0
-            Normalization factor used when saving to .gsd and .hoomdxml formats
+            Normalization factor used when saving to the .gsd format
             for converting distance values to reduced units.
         ref_energy : float, optional, default=1.0
-            Normalization factor used when saving to .gsd and .hoomdxml formats
+            Normalization factor used when saving to the .gsd format
             for converting energy values to reduced units.
         ref_mass : float, optional, default=1.0
-            Normalization factor used when saving to .gsd and .hoomdxml formats
+            Normalization factor used when saving to the .gsd format
             for converting mass values to reduced units.
-        atom_style: str, default='full'
-            Defines the style of atoms to be saved in a LAMMPS data file. The
-            following atom styles are currently supported:
-            'full', 'atomic', 'charge', 'molecular'
-            See `LAMMPS atom style documentation
-            <https://lammps.sandia.gov/doc/atom_style.html>`_ for more
-            information.
-        unit_style: str, default='real'
-            Defines to unit style to be save in a LAMMPS data file.  Defaults
-            to 'real' units. Current styles are supported: 'real', 'lj'. See
-            `LAMMPS unit style documentation_
-            <https://lammps.sandia.gov/doc/units.html>`_ for more information.
 
         Notes
         -----
@@ -3074,29 +3031,24 @@ def save(
         * filename
         * include_ports
 
+        The savers used for each supported file type are:
+        GMSO: .gro, .gsd, .data, .xyz, .mcf, .top
+        Parmed: .mol2, .pdb, .prmtop, .cif, .crd
+        PyBel: .sdf
+
         See Also
         --------
-        conversion.save : Main saver logic
-        formats.gsdwrite.write_gsd : Write to GSD format
-        formats.hoomdxml.write_hoomdxml : Write to Hoomd XML format
-        formats.xyzwriter.write_xyz : Write to XYZ format
-        formats.lammpsdata.write_lammpsdata : Write to LAMMPS data format
-        formats.cassandramcf.write_mcf : Write to Cassandra MCF format
-        formats.json_formats.compound_to_json : Write to a json file
+        mbuild.conversion.save : Main saver logic
+        mbuild.formats.cassandramcf.write_mcf : Write to Cassandra MCF format
+        mbuild.formats.json_formats.compound_to_json : Write to a json file
         """
         conversion.save(
-            self,
-            filename,
-            include_ports,
-            forcefield_name,
-            forcefield_files,
-            forcefield_debug,
-            box,
-            overwrite,
-            residues,
-            combining_rule,
-            foyer_kwargs,
-            parmed_kwargs,
+            compound=self,
+            filename=filename,
+            include_ports=include_ports,
+            box=box,
+            overwrite=overwrite,
+            residues=residues,
             **kwargs,
         )
 
@@ -3246,6 +3198,21 @@ def to_gmso(self, **kwargs):
         """
         return conversion.to_gmso(self, **kwargs)
 
+    def to_hoomdsnapshot(self, **kwargs):
+        """Create a HOOMD-Blue snapshot from an mBuild Compound.
+
+        Parameters
+        ----------
+        compound : mb.Compound
+            The mb.Compound to be converted.
+
+        Returns
+        -------
+        snapshot : gsd.hoomd.Frame
+            HOOMD-Blue compatible topology.
+        """
+        return conversion.to_hoomdsnapshot(self, **kwargs)
+
     # Interface to Trajectory for reading/writing .pdb and .mol2 files.
     # -----------------------------------------------------------------
     def from_trajectory(
-Original file line number
+Diff line change
@@ Expand Up / @@ -21,7 +21,6 @@ dependencies: @@
       - parmed>=3.4.3
       - pip
       - pre-commit
-      - protobuf
       - py3Dmol
       - pycifrw
       - pytest
@@ Expand Down @@