mirror of
https://github.com/OpenFreeEnergy/openfe.git
synced 2026-06-04 06:08:09 +08:00
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
This commit is contained in:
Alyssa Travitz
GitHub
@@ -3,16 +3,16 @@ Checklist for releasing a new version of openfe.
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-->
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Make the PR:
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* [ ] 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/).
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* [ ] 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/).
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* [ ] 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`
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* [ ] 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/`.
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* [ ] Verify that`docs/CHANGELOG.rst` looks correct.
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* [ ] Verify that`docs/CHANGELOG.rst` looks correct and that it renders as expected in the docs preview.
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* [ ] 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`.
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* [ ] Make the PR and verify that CI/CD passes.
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* [ ] (feedstock packaging tests)[https://github.com/OpenFreeEnergy/openfe/actions/workflows/release-prep-feedstock.yaml]
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* [ ] (example notebooks)[https://github.com/OpenFreeEnergy/openfe/actions/workflows/release-prep-examplenotebooks.yaml]
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* [ ] (GPU tests)[https://github.com/OpenFreeEnergy/openfe/actions/workflows/aws-gpu-integration-tests.yaml]
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* [ ] [feedstock packaging tests](https://github.com/OpenFreeEnergy/openfe/actions/workflows/release-prep-feedstock.yaml)
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* [ ] [example notebooks](https://github.com/OpenFreeEnergy/openfe/actions/workflows/release-prep-examplenotebooks.yaml)
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* [ ] [GPU tests](https://github.com/OpenFreeEnergy/openfe/actions/workflows/aws-gpu-integration-tests.yaml)
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* [ ] Merge the PR into `main`.
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* [ ] 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`
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After Merging the PR [follow this guide](https://github.com/OpenFreeEnergy/openfe/wiki/How-to-create-a-new-release)
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@@ -4,6 +4,43 @@ Changelog
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.. current developments
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v1.11.0
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====================
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**Added:**
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* Added support for systems with membranes to the following protocols:
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PlainMDProtocol, RelativeHybridTopologyProtocol, SepTopProtocol, and AbsoluteBindingProtocol (`PR #1561 <https://github.com/OpenFreeEnergy/openfe/pull/1561>`_).
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* Added support for membrane systems to ``openfe plan-rbfe-network``.
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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>`_).
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* Added API support for resuming the PlainMDProtocol (`PR #1884 <https://github.com/OpenFreeEnergy/openfe/pull/1884>`_).
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* Added API support for resuming the SepTopProtocol. (`PR #1949 <https://github.com/OpenFreeEnergy/openfe/pull/1949>`_).
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* The ``validate`` method for the SepTopProtocol has been implemented.
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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>`_).
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**Changed:**
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* The SepTopProtocol now has a dedicated Analysis unit.
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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.
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The SepTopProtocolResult now solely uses the Analysis units (`PR #1937 <https://github.com/OpenFreeEnergy/openfe/pull/1937>`_).
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* 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>`_).
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* The default value for the Hybrid TopologyProtocol setting ``turn_off_core_unique_exceptions`` has been changed to ``True``.
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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>`_).
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**Deprecated:**
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* Perses atom mapper and scorer functionality is deprecated, now slated to be removed in ``openfe v1.12``.
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This includes ``PersesAtomMapper`` and ``default_perses_scorer`` (`PR #1857 <https://github.com/OpenFreeEnergy/openfe/pull/1857>`_).
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**Fixed:**
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* 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>`_).
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* System equality checks on resuming no longer expect complete equality in the force parameters.
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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>`_).
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v1.10.0
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====================
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@@ -19,7 +56,7 @@ See the `quickrun documentation <https://docs.openfree.energy/en/v1.10.0/guide/e
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**Deprecated:**
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* Perses atom mapper and scorer functionality is deprecated, slated to be removed in ``openfe v2.0``.
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* Perses atom mapper and scorer functionality is deprecated, slated to be removed in ``openfe v2.0``.
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This includes ``PersesAtomMapper`` and ``default_perses_scorer`` (`PR #1857 <https://github.com/OpenFreeEnergy/openfe/pull/1857>`_).
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**Fixed:**
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@@ -90,7 +127,7 @@ v1.8.0
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**Added:**
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* The ``HybridTopologyFactory`` supports building hybrid OpenMM systems which contain ``CMAPTorsionForces`` on non-alchemical atoms.
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* The ``HybridTopologyFactory`` supports building hybrid OpenMM systems which contain ``CMAPTorsionForces`` on non-alchemical atoms.
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This should allow for simulations using Amber ff19SB (`PR #1695 <https://github.com/OpenFreeEnergy/openfe/pull/1695>`_).
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* 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.
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* 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>`_).
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@@ -193,7 +193,7 @@ try:
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else:
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repo = git.Repo.clone_from(
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"https://github.com/OpenFreeEnergy/ExampleNotebooks.git",
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branch="main", # TODO: update this after making ExampleNotebooks release
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branch="2026.04.28",
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to_path=example_notebooks_path,
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)
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except Exception as e:
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@@ -19,7 +19,7 @@ dependencies:
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- openff-toolkit-base >=0.16.2
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- openff-units==0.3.1 # https://github.com/OpenFreeEnergy/openfe/pull/1374
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- openmm ~=8.4.0 # omit 8.3.0 and 8.3.1 due to https://github.com/openmm/openmm/pull/5069
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- openmmforcefields >=0.15.1 # min needed for https://github.com/OpenFreeEnergy/openfe/pull/414
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- openmmforcefields >=0.15.1 # min needed for https://github.com/openmm/openmmforcefields/pull/414
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- openmmtools >=0.26 # fix to support membrane barostat: https://github.com/choderalab/openmmtools/pull/798
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- packaging
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- pandas
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@@ -1,27 +0,0 @@
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**Added:**
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* <news item>
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**Changed:**
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* The SepTopProtocol now has a dedicated Analysis unit.
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At the top level API, this does not change behaviour, but
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if you are directly interfacing with the ProtocolUnits, you
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will have to account for this change. The SepTopProtocolResult now
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solely uses the Analysis units. PR #1937
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**Deprecated:**
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* <news item>
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**Removed:**
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* <news item>
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**Fixed:**
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**Security:**
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@@ -1,24 +0,0 @@
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**Added:**
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* <news item>
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**Changed:**
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* <news item>
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**Deprecated:**
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* Perses atom mapper and scorer functionality is deprecated, now slated to be removed in ``openfe v1.12``.
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This includes ``PersesAtomMapper`` and ``default_perses_scorer`` (`PR #1857 <https://github.com/OpenFreeEnergy/openfe/pull/1857>`_).
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**Removed:**
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* <news item>
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**Fixed:**
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* <news item>
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**Security:**
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**Added:**
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* <news item>
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**Changed:**
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**Deprecated:**
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* <news item>
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**Removed:**
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* <news item>
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**Fixed:**
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* Fix erroneous logging information message which would mention
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setting up the alchemical system when running simulation or
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analysis units with the hybrid topology, AHFE or ABFE Protocols (PR #1915).
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**Security:**
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* <news item>
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@@ -1,23 +0,0 @@
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**Added:**
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* <news item>
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**Changed:**
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* 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.
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**Deprecated:**
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* <news item>
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**Removed:**
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* <news item>
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**Fixed:**
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**Security:**
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**Added:**
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* <news item>
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**Changed:**
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* <news item>
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**Deprecated:**
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* <news item>
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**Removed:**
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* <news item>
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**Fixed:**
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* System equality checks on resuming no longer expect complete equality
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in the force parameters. This fixes a scenario where small changes
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in precision due to running on different machines would prevent users from
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restarting their simulations (Issue #1913, PR #1914).
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**Security:**
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* <news item>
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@@ -1,24 +0,0 @@
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**Added:**
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* Added support for systems with membranes to the following protocols:
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PlainMDProtocol, RelativeHybridTopologyProtocol, SepTopProtocol, and AbsoluteBindingProtocol.
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**Changed:**
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* <news item>
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**Deprecated:**
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* <news item>
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**Removed:**
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* <news item>
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**Fixed:**
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* <news item>
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**Security:**
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* <news item>
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@@ -1,24 +0,0 @@
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**Added:**
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* Added support for membrane systems to ``openfe plan-rbfe-network``.
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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>`_).
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**Changed:**
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* <news item>
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**Deprecated:**
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* <news item>
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**Removed:**
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* <news item>
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**Fixed:**
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* <news item>
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**Security:**
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* <news item>
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@@ -1,24 +0,0 @@
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**Added:**
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* * Added API support for resuming the PlainMDProtocol.
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PR #1884.
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**Changed:**
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* <news item>
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**Deprecated:**
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* <news item>
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**Removed:**
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**Fixed:**
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* <news item>
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**Security:**
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* <news item>
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@@ -1,24 +0,0 @@
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**Added:**
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* Added API support for resuming the SepTopProtocol.
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PR #1949.
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**Changed:**
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* <news item>
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**Deprecated:**
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* <news item>
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**Removed:**
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**Fixed:**
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**Security:**
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**Added:**
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* <news item>
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**Changed:**
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* Updated the chemical systems user guide and the defining protocols user guide to reflect recent protocol updates, including adding membrane support.
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**Deprecated:**
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* <news item>
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**Removed:**
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* <news item>
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**Fixed:**
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* <news item>
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**Security:**
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* <news item>
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@@ -1,26 +0,0 @@
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**Added:**
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* The `validate` method for the SepTopProtocol has been implemented.
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This means that settings and system validation can mostly be done prior
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to Protocol execuation by calling
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`SepTopProtocol.validate(stateA, stateB, mapping=None)`.
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**Changed:**
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* <news item>
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**Deprecated:**
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* <news item>
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**Removed:**
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**Fixed:**
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**Security:**
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* <news item>
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Reference in New Issue
Block a user