From e6634cf83e7648f04f230122c1e4adf153a02c22 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Thu, 4 Dec 2025 07:48:30 -0800 Subject: [PATCH 1/3] Updated CHANGELOG for 1.8.0 --- docs/CHANGELOG.rst | 20 ++++++++++++++++++++ news/cmap_support.rst | 24 ------------------------ news/gather_abfe_septop.rst | 23 ----------------------- news/gather_by_gufe.rst | 23 ----------------------- news/install_docs.rst | 23 ----------------------- news/jax-warning.rst | 26 -------------------------- 6 files changed, 20 insertions(+), 119 deletions(-) delete mode 100644 news/cmap_support.rst delete mode 100644 news/gather_abfe_septop.rst delete mode 100644 news/gather_by_gufe.rst delete mode 100644 news/install_docs.rst delete mode 100644 news/jax-warning.rst diff --git a/docs/CHANGELOG.rst b/docs/CHANGELOG.rst index 6dbe873ed..cd28b32fc 100644 --- a/docs/CHANGELOG.rst +++ b/docs/CHANGELOG.rst @@ -4,6 +4,26 @@ Changelog .. current developments +v1.8.0 +==================== + +**Added:** + +* The ``HybridTopologyFactory`` supports building hybrid OpenMM systems which contain ``CMAPTorsionForces`` on non-alchemical atoms. This should allow for simulations using + Amber ff19SB. See `PR #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 Toplogies 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 (#1585). + Fixes #1499. + +* Disable JAX acceleration by default, see https://docs.openfree.energy/en/latest/guide/troubleshooting.html#pymbar-disable-jax for more information (#1694). + +**Changed:** + +* ``openfe gather`` is now more rigorous in extracting ligand names and run types. These are now determined directly from component attributes, rather than relying on naming conventions. See `PR #1691 `_ for more details. +* Updated installation docs to recommend ``miniconda`` with ``conda-lock`` as the preferred installation method (PR #1692). + + + v1.7.0 ==================== diff --git a/news/cmap_support.rst b/news/cmap_support.rst deleted file mode 100644 index bd7220025..000000000 --- a/news/cmap_support.rst +++ /dev/null @@ -1,24 +0,0 @@ -**Added:** - -* The ``HybridTopologyFactory`` supports building hybrid OpenMM systems which contain ``CMAPTorsionForces`` on non-alchemical atoms. This should allow for simulations using - Amber ff19SB. See `PR #1695 `_ - -**Changed:** - -* - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* - -**Security:** - -* diff --git a/news/gather_abfe_septop.rst b/news/gather_abfe_septop.rst deleted file mode 100644 index ada1983de..000000000 --- a/news/gather_abfe_septop.rst +++ /dev/null @@ -1,23 +0,0 @@ -**Added:** - -* 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 Toplogies and Absolute Binding Free Energy protocols, respectively. These commands are experimental and are liable to be changed in a future release. - -**Changed:** - -* - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* - -**Security:** - -* diff --git a/news/gather_by_gufe.rst b/news/gather_by_gufe.rst deleted file mode 100644 index 32cc0b3a3..000000000 --- a/news/gather_by_gufe.rst +++ /dev/null @@ -1,23 +0,0 @@ -**Added:** - -* - -**Changed:** - -* ``openfe gather`` is now more rigorous in extracting ligand names and run types. These are now determined directly from component attributes, rather than relying on naming conventions. See `PR #1691 `_ for more details. - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* - -**Security:** - -* diff --git a/news/install_docs.rst b/news/install_docs.rst deleted file mode 100644 index 37637a28e..000000000 --- a/news/install_docs.rst +++ /dev/null @@ -1,23 +0,0 @@ -**Added:** - -* - -**Changed:** - -* Updated installation docs to recommend ``miniconda`` with ``conda-lock`` as the preferred installation method (PR #1692). - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* - -**Security:** - -* diff --git a/news/jax-warning.rst b/news/jax-warning.rst deleted file mode 100644 index 57aebff84..000000000 --- a/news/jax-warning.rst +++ /dev/null @@ -1,26 +0,0 @@ -**Added:** - -* Emit a clarifying log message when a user gets a warning from JAX (#1585). - Fixes #1499. - -* Disable JAX acceleration by default, see https://docs.openfree.energy/en/latest/guide/troubleshooting.html#pymbar-disable-jax for more information (#1694). - -**Changed:** - -* - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* - -**Security:** - -* From 8157c06378c4ad9b484efd3c89244b19ac605dcf Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Mon, 8 Dec 2025 09:20:45 -0800 Subject: [PATCH 2/3] format changelog --- docs/CHANGELOG.rst | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) diff --git a/docs/CHANGELOG.rst b/docs/CHANGELOG.rst index cd28b32fc..dfbf045d7 100644 --- a/docs/CHANGELOG.rst +++ b/docs/CHANGELOG.rst @@ -10,17 +10,15 @@ v1.8.0 **Added:** * The ``HybridTopologyFactory`` supports building hybrid OpenMM systems which contain ``CMAPTorsionForces`` on non-alchemical atoms. This should allow for simulations using - Amber ff19SB. See `PR #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 Toplogies 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 (#1585). - Fixes #1499. - -* Disable JAX acceleration by default, see https://docs.openfree.energy/en/latest/guide/troubleshooting.html#pymbar-disable-jax for more information (#1694). + Amber ff19SB (`PR #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 `_, fixes `Issue #1499 `_). +* Disable JAX acceleration by default, see https://docs.openfree.energy/en/latest/guide/troubleshooting.html#pymbar-disable-jax for more information (`PR #1694 `_). **Changed:** -* ``openfe gather`` is now more rigorous in extracting ligand names and run types. These are now determined directly from component attributes, rather than relying on naming conventions. See `PR #1691 `_ for more details. -* Updated installation docs to recommend ``miniconda`` with ``conda-lock`` as the preferred installation method (PR #1692). +* ``openfe gather`` is now more rigorous in extracting ligand names and run types. These are now determined directly from component attributes, rather than relying on naming conventions. (`PR #1691 `_). +* Updated installation docs to recommend ``miniconda`` with ``conda-lock`` as the preferred installation method (`PR #1692 `_). From f2ed7e382c9eeaebfb0d65a7f361b6f10b707f5e Mon Sep 17 00:00:00 2001 From: Alyssa Travitz <31974495+atravitz@users.noreply.github.com> Date: Mon, 8 Dec 2025 09:32:30 -0800 Subject: [PATCH 3/3] Update docs/CHANGELOG.rst Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com> --- docs/CHANGELOG.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/CHANGELOG.rst b/docs/CHANGELOG.rst index dfbf045d7..7b262e8d0 100644 --- a/docs/CHANGELOG.rst +++ b/docs/CHANGELOG.rst @@ -9,8 +9,8 @@ v1.8.0 **Added:** -* The ``HybridTopologyFactory`` supports building hybrid OpenMM systems which contain ``CMAPTorsionForces`` on non-alchemical atoms. This should allow for simulations using - Amber ff19SB (`PR #1695 `_). +* The ``HybridTopologyFactory`` supports building hybrid OpenMM systems which contain ``CMAPTorsionForces`` on non-alchemical atoms. + This should allow for simulations using Amber ff19SB (`PR #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 `_, fixes `Issue #1499 `_). * Disable JAX acceleration by default, see https://docs.openfree.energy/en/latest/guide/troubleshooting.html#pymbar-disable-jax for more information (`PR #1694 `_).