remove perses atommapper and scorer

docs/installation.rst

@@ -501,13 +501,11 @@ See :ref:`installation:mamba_hpc` for more details.
 Optional dependencies
 ---------------------
 
-Certain functionalities are only available if you also install other,
-optional packages.
+Certain functionalities are only available if you also install optional packages.
 
-* **perses tools**: To use perses, you need to install perses and OpenEye,
-  and you need a valid OpenEye license. To install both packages, use::
+* **OpenEye tools**: To use functionality that uses the OpenEye, you must additionally install OpenEye, and you need a valid OpenEye license. To install, use::
 
-    $ mamba install -c openeye perses openeye-toolkits
+    $ mamba install -c openeye openeye-toolkits
 
 Supported Hardware
 ------------------

docs/reference/api/atom_mappers.rst

@@ -23,7 +23,6 @@ Tools for mapping atoms in one molecule to those in another. Used to generate ef
 
     KartografAtomMapper
     LomapAtomMapper
-    PersesAtomMapper
 
 .. rubric:: Data Types
 
@@ -65,17 +64,3 @@ Scorers implemented by the `LOMAP <https://github.com/OpenFreeEnergy/Lomap>`_ pa
     heterocycles_score
     transmuting_methyl_into_ring_score
     transmuting_ring_sizes_score
-
-
-Perses Scorers
-~~~~~~~~~~~~~~
-
-Scorers implemented by the `Perses <https://github.com/choderalab/perses>`_ package.
-
-.. module:: openfe.setup.atom_mapping.perses_scorers
-
-.. autosummary::
-    :nosignatures:
-    :toctree: generated/
-
-    default_perses_scorer

environment.yml

@@ -24,7 +24,6 @@ dependencies:
   - packaging
   - pandas
   - parmed >=4.3.1  # fix to support numpy >=2.3: https://github.com/ParmEd/ParmEd/pull/1387
-  - perses>=0.10.3
   - plugcli
   - pint>=0.24.0
   - pip

news/remove_perses.rst

@@ -0,0 +1,25 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* Perses atom mapper and scorer functionality is deprecated, slated to be removed in ``openfe v2.0`.
+  This includes ``PersesAtomMapper`` and ``default_perses_scorer`` (`PR #1857 <https://github.com/OpenFreeEnergy/openfe/pull/1857>`_).
+
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

src/openfe/__init__.py

@@ -76,10 +76,8 @@
     LigandAtomMapper,
     LigandNetwork,
     LomapAtomMapper,
-    PersesAtomMapper,
     ligand_network_planning,
     lomap_scorers,
-    perses_scorers,
 )
 
 __version__ = version("openfe")

src/openfe/setup/__init__.py

@@ -7,9 +7,7 @@
     LigandAtomMapper,
     LigandAtomMapping,
     LomapAtomMapper,
-    PersesAtomMapper,
     lomap_scorers,
-    perses_scorers,
 )
 
 # TODO: circular import risk with LigandNetwork

src/openfe/setup/atom_mapping/__init__.py

@@ -1,7 +1,6 @@
 from gufe import LigandAtomMapping
 from kartograf import KartografAtomMapper
 
-from . import lomap_scorers, perses_scorers
+from . import lomap_scorers
 from .ligandatommapper import LigandAtomMapper
 from .lomap_mapper import LomapAtomMapper
-from .perses_mapper import PersesAtomMapper