release prep for v1.11.0 (#1967)

* Updated CHANGELOG for 1.11.0

* add PR links

* update release prep template

* fix code formatting

* Updated CHANGELOG for 1.11.0

* update example notebook tag

* update comment in env

Author: atravitz

.github/PULL_REQUEST_TEMPLATE/release_template.md

@@ -3,16 +3,16 @@ Checklist for releasing a new version of openfe.
 -->
 
 Make the PR:
-* [ ] Create a new release-prep branch corresponding to the version name, e.g. `release-prep-v1.2.0`.  Note: please follow [semantic versioning](https://semver.org/).
+* [ ] Create a new release prep branch corresponding to the version name, e.g. `release/v1.2.0`.  Note: please follow [semantic versioning](https://semver.org/).
 * [ ] Check that all user-relevant updates are included in the `news/` rever `.rst` files. You can backfill any additional items by making a new .rst, e.g. `backfill.rst`
 * [ ] Run [rever](https://regro.github.io/rever-docs/index.html#), e.g. `rever 1.2.0`. This will auto-commit `docs/CHANGELOG.md` and remove the `.rst` files from `news/`. 
-* [ ] Verify that`docs/CHANGELOG.rst` looks correct.
+* [ ] Verify that`docs/CHANGELOG.rst` looks correct and that it renders as expected in the docs preview.
+* [ ] If needed, create a release of the [example notebooks repository](https://github.com/OpenFreeEnergy/ExampleNotebooks) and update the pinned release version in the `openfe/docs/conf.py`.
 * [ ] Make the PR and verify that CI/CD passes. 
-  * [ ] (feedstock packaging tests)[https://github.com/OpenFreeEnergy/openfe/actions/workflows/release-prep-feedstock.yaml]
-  * [ ] (example notebooks)[https://github.com/OpenFreeEnergy/openfe/actions/workflows/release-prep-examplenotebooks.yaml]
-  * [ ] (GPU tests)[https://github.com/OpenFreeEnergy/openfe/actions/workflows/aws-gpu-integration-tests.yaml]
+  * [ ] [feedstock packaging tests](https://github.com/OpenFreeEnergy/openfe/actions/workflows/release-prep-feedstock.yaml)
+  * [ ] [example notebooks](https://github.com/OpenFreeEnergy/openfe/actions/workflows/release-prep-examplenotebooks.yaml)
+  * [ ] [GPU tests](https://github.com/OpenFreeEnergy/openfe/actions/workflows/aws-gpu-integration-tests.yaml)
 * [ ] Merge the PR into `main`.
-* [ ] Make a PR into the [example notebooks repository](https://github.com/OpenFreeEnergy/ExampleNotebooks) to update the version used in `showcase/openfe_showcase.ipynb` and `.binder/environment.yml`
 
 After Merging the PR [follow this guide](https://github.com/OpenFreeEnergy/openfe/wiki/How-to-create-a-new-release)
 

docs/CHANGELOG.rst

@@ -4,6 +4,43 @@ Changelog
 
 .. current developments
 
+
+v1.11.0
+====================
+
+**Added:**
+
+* Added support for systems with membranes to the following protocols:
+  PlainMDProtocol, RelativeHybridTopologyProtocol, SepTopProtocol, and AbsoluteBindingProtocol (`PR #1561 <https://github.com/OpenFreeEnergy/openfe/pull/1561>`_).
+* Added support for membrane systems to ``openfe plan-rbfe-network``.
+  Use ``--protein-membrane`` instead of the ``--protein`` argument, and see the tutorial on preparing membrane systems (`PR #1896 <https://github.com/OpenFreeEnergy/openfe/pull/1896>`_).
+* Added API support for resuming the PlainMDProtocol (`PR #1884 <https://github.com/OpenFreeEnergy/openfe/pull/1884>`_).
+* Added API support for resuming the SepTopProtocol. (`PR #1949 <https://github.com/OpenFreeEnergy/openfe/pull/1949>`_).
+* The ``validate`` method for the SepTopProtocol has been implemented.
+  This means that settings and system validation can mostly be done prior to Protocol execuation by calling ``SepTopProtocol.validate(stateA, stateB, mapping=None)`` (`PR #1946 <https://github.com/OpenFreeEnergy/openfe/pull/1946>`_).
+
+**Changed:**
+
+* The SepTopProtocol now has a dedicated Analysis unit.
+  At the top level API, this does not change behavior, but if you are directly interfacing with th ProtocolUnits, you will have to account for this change.
+  The SepTopProtocolResult now solely uses the Analysis units (`PR #1937 <https://github.com/OpenFreeEnergy/openfe/pull/1937>`_).
+* Updated the chemical systems user guide and the defining protocols user guide to reflect recent protocol updates, including adding membrane support (`PR #1933 <https://github.com/OpenFreeEnergy/openfe/pull/1933>`_).
+* The default value for the Hybrid TopologyProtocol setting ``turn_off_core_unique_exceptions`` has been changed to ``True``.
+  This means 1-4 interactions involving the unique alchemical atoms and core regions will now be interpolated on/off accordingly by default (`PR #1856 <https://github.com/OpenFreeEnergy/openfe/pull/1856>`_).
+
+**Deprecated:**
+
+* Perses atom mapper and scorer functionality is deprecated, now slated to be removed in ``openfe v1.12``.
+  This includes ``PersesAtomMapper`` and ``default_perses_scorer`` (`PR #1857 <https://github.com/OpenFreeEnergy/openfe/pull/1857>`_).
+
+**Fixed:**
+
+* Fix erroneous logging information message which would mention setting up the alchemical system when running simulation or analysis units with the hybrid topology, AHFE or ABFE Protocols (`PR #1915 <https://github.com/OpenFreeEnergy/openfe/pull/1915>`_).
+* System equality checks on resuming no longer expect complete equality in the force parameters.
+  This fixes a scenario where small changes in precision due to running on different machines would prevent users from restarting their simulations (`PR #1914 <https://github.com/OpenFreeEnergy/openfe/pull/1914>`_).
+
+
+
 v1.10.0
 ====================
 
@@ -19,7 +56,7 @@ See the `quickrun documentation <https://docs.openfree.energy/en/v1.10.0/guide/e
 
 **Deprecated:**
 
-* Perses atom mapper and scorer functionality is deprecated, slated to be removed in ``openfe v2.0``. 
+* 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:**
@@ -90,7 +127,7 @@ v1.8.0
 
 **Added:**
 
-* The ``HybridTopologyFactory`` supports building hybrid OpenMM systems which contain ``CMAPTorsionForces`` on non-alchemical atoms. 
+* The ``HybridTopologyFactory`` supports building hybrid OpenMM systems which contain ``CMAPTorsionForces`` on non-alchemical atoms.
   This should allow for simulations using Amber ff19SB (`PR #1695 <https://github.com/OpenFreeEnergy/openfe/pull/1695>`_).
 * Added experimental features ``openfe gather-septop`` and ``openfe gather-abfe``, which are analogous to ``openfe gather`` and allow for gathering results generated by the Separated Topologies and Absolute Binding Free Energy protocols, respectively.  These commands are experimental and are liable to be changed in a future release.
 * Emit a clarifying log message when a user gets a warning from JAX (`PR #1585 <https://github.com/OpenFreeEnergy/openfe/pull/1585>`_, fixes `Issue #1499 <https://github.com/OpenFreeEnergy/openfe/issues/1499>`_).

docs/conf.py

@@ -193,7 +193,7 @@
     else:
         repo = git.Repo.clone_from(
             "https://github.com/OpenFreeEnergy/ExampleNotebooks.git",
-            branch="main",  # TODO: update this after making ExampleNotebooks release
+            branch="2026.04.28",
             to_path=example_notebooks_path,
         )
 except Exception as e:

environment.yml

@@ -19,7 +19,7 @@ dependencies:
   - openff-toolkit-base >=0.16.2
   - openff-units==0.3.1  # https://github.com/OpenFreeEnergy/openfe/pull/1374
   - openmm ~=8.4.0  # omit 8.3.0 and 8.3.1 due to https://github.com/openmm/openmm/pull/5069
-  - openmmforcefields >=0.15.1  # min needed for https://github.com/OpenFreeEnergy/openfe/pull/414
+  - openmmforcefields >=0.15.1  # min needed for https://github.com/openmm/openmmforcefields/pull/414
   - openmmtools >=0.26  # fix to support membrane barostat: https://github.com/choderalab/openmmtools/pull/798
   - packaging
   - pandas