From 96d4a66ee080fdb758988c0088001858cb7f9aea Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Mon, 9 Feb 2026 17:23:53 -0800 Subject: [PATCH 1/6] Updated CHANGELOG for 1.9.0 --- docs/CHANGELOG.rst | 26 ++++++++++++++++++++++++++ news/fix_image_crop.rst | 23 ----------------------- news/issue-1120.rst | 25 ------------------------- news/multi-unit-afe.rst | 26 -------------------------- news/validate-rfe.rst | 26 -------------------------- 5 files changed, 26 insertions(+), 100 deletions(-) delete mode 100644 news/fix_image_crop.rst delete mode 100644 news/issue-1120.rst delete mode 100644 news/multi-unit-afe.rst delete mode 100644 news/validate-rfe.rst diff --git a/docs/CHANGELOG.rst b/docs/CHANGELOG.rst index 7d0e99c85..26b1f9fa7 100644 --- a/docs/CHANGELOG.rst +++ b/docs/CHANGELOG.rst @@ -4,6 +4,32 @@ Changelog .. current developments +v1.9.0 +==================== + +**Added:** + +* The `validate` method for the RelativeHybridTopologyProtocol has been + implemented. This means that settings and system validation can mostly + be done prior to Protocol execution by calling + `RelativeHybridTopologyProtocol.validate(stateA, stateB, mapping)`. + +**Changed:** + +* The absolute free energy protocols have been broken into multiple + protocol units, allowing for setup, run, and analysis to happen + separately in the future when relevant changes to protocol execution are + made (PR #1776). + +**Fixed:** + +* Fixed bug in ligand network visualization (such as with ``openfe view-ligand-network``) so that ligand names are no longer cut off by the plot border (`PR 1822 `_). +* Endstates in the RelativeHybridTopologyProtocol are now being created + in a manner that allows for isomorphic molecules that differ between + endstates to have different parameters (Issue #1120). + + + v1.8.1 ==================== diff --git a/news/fix_image_crop.rst b/news/fix_image_crop.rst deleted file mode 100644 index 3d1f1d31c..000000000 --- a/news/fix_image_crop.rst +++ /dev/null @@ -1,23 +0,0 @@ -**Added:** - -* - -**Changed:** - -* - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* Fixed bug in ligand network visualization (such as with ``openfe view-ligand-network``) so that ligand names are no longer cut off by the plot border (`PR 1822 `_). - -**Security:** - -* diff --git a/news/issue-1120.rst b/news/issue-1120.rst deleted file mode 100644 index 55c8286b7..000000000 --- a/news/issue-1120.rst +++ /dev/null @@ -1,25 +0,0 @@ -**Added:** - -* - -**Changed:** - -* - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* Endstates in the RelativeHybridTopologyProtocol are now being created - in a manner that allows for isomorphic molecules that differ between - endstates to have different parameters (Issue #1120). - -**Security:** - -* diff --git a/news/multi-unit-afe.rst b/news/multi-unit-afe.rst deleted file mode 100644 index 6831b07f2..000000000 --- a/news/multi-unit-afe.rst +++ /dev/null @@ -1,26 +0,0 @@ -**Added:** - -* - -**Changed:** - -* The absolute free energy protocols have been broken into multiple - protocol units, allowing for setup, run, and analysis to happen - separately in the future when relevant changes to protocol execution are - made (PR #1776). - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* - -**Security:** - -* diff --git a/news/validate-rfe.rst b/news/validate-rfe.rst deleted file mode 100644 index d7036e8d4..000000000 --- a/news/validate-rfe.rst +++ /dev/null @@ -1,26 +0,0 @@ -**Added:** - -* The `validate` method for the RelativeHybridTopologyProtocol has been - implemented. This means that settings and system validation can mostly - be done prior to Protocol execution by calling - `RelativeHybridTopologyProtocol.validate(stateA, stateB, mapping)`. - -**Changed:** - -* - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* - -**Security:** - -* From 35027dba51a427de0b6f79e221b146715e65dfcd Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Mon, 9 Feb 2026 17:28:57 -0800 Subject: [PATCH 2/6] add links to changelog --- docs/CHANGELOG.rst | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/docs/CHANGELOG.rst b/docs/CHANGELOG.rst index 26b1f9fa7..e45faa87b 100644 --- a/docs/CHANGELOG.rst +++ b/docs/CHANGELOG.rst @@ -9,24 +9,22 @@ v1.9.0 **Added:** -* The `validate` method for the RelativeHybridTopologyProtocol has been - implemented. This means that settings and system validation can mostly - be done prior to Protocol execution by calling - `RelativeHybridTopologyProtocol.validate(stateA, stateB, mapping)`. +* The ``validate`` method for the RelativeHybridTopologyProtocol has been implemented. + This means that settings and system validation can mostly be done prior to Protocol execution by calling ``RelativeHybridTopologyProtocol.validate(stateA, stateB, mapping)`` (`PR 1740 `_). **Changed:** * The absolute free energy protocols have been broken into multiple protocol units, allowing for setup, run, and analysis to happen separately in the future when relevant changes to protocol execution are - made (PR #1776). + made (`PR 1776 `_). **Fixed:** * Fixed bug in ligand network visualization (such as with ``openfe view-ligand-network``) so that ligand names are no longer cut off by the plot border (`PR 1822 `_). * Endstates in the RelativeHybridTopologyProtocol are now being created in a manner that allows for isomorphic molecules that differ between - endstates to have different parameters (Issue #1120). + endstates to have different parameters (`PR 1772 `_). From 90ad45bed7496523f8b7920534c7fde12ebfc535 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Mon, 9 Feb 2026 17:37:04 -0800 Subject: [PATCH 3/6] fix ci path --- .github/workflows/test-feedstock-pkg-build.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test-feedstock-pkg-build.yaml b/.github/workflows/test-feedstock-pkg-build.yaml index b152bcc20..bb4e901bf 100644 --- a/.github/workflows/test-feedstock-pkg-build.yaml +++ b/.github/workflows/test-feedstock-pkg-build.yaml @@ -46,7 +46,7 @@ jobs: # TODO just checkout the repo where we need it? - name: Copy source code to recipe folder - run: cp -r src/openfe openfe-feedstock/recipe/openfe_source + run: cp -r openfe openfe-feedstock/recipe/openfe_source - name: Modify feedstock to use local path run: | From ffa07281cc534a5f8aca6bfd9c856b87cadc401e Mon Sep 17 00:00:00 2001 From: Alyssa Travitz <31974495+atravitz@users.noreply.github.com> Date: Tue, 10 Feb 2026 12:19:05 -0800 Subject: [PATCH 4/6] Apply suggestions from code review Co-authored-by: Irfan Alibay --- docs/CHANGELOG.rst | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/docs/CHANGELOG.rst b/docs/CHANGELOG.rst index e45faa87b..29b2dd762 100644 --- a/docs/CHANGELOG.rst +++ b/docs/CHANGELOG.rst @@ -14,11 +14,13 @@ v1.9.0 **Changed:** -* The absolute free energy protocols have been broken into multiple +* The absolute free energy protocols (AbsoluteBindingProtocol and AbsoluteSolvationProtocol) have been broken into multiple protocol units, allowing for setup, run, and analysis to happen separately in the future when relevant changes to protocol execution are made (`PR 1776 `_). - +* The relative free energy protocol (RelativeHybridTopologyProtocol) has been + broken into multiple protocol units, allowing for the setup, run, analysis to happen + separately (`PR 1773 `_). **Fixed:** * Fixed bug in ligand network visualization (such as with ``openfe view-ligand-network``) so that ligand names are no longer cut off by the plot border (`PR 1822 `_). From f860da9837134073a4165bd3ccf71366a5d8d618 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Wed, 11 Feb 2026 08:48:06 -0800 Subject: [PATCH 5/6] Updated CHANGELOG for 1.9.0 --- docs/CHANGELOG.rst | 9 +++++++++ news/test-download-all.rst | 23 ----------------------- 2 files changed, 9 insertions(+), 23 deletions(-) delete mode 100644 news/test-download-all.rst diff --git a/docs/CHANGELOG.rst b/docs/CHANGELOG.rst index 29b2dd762..a6109949f 100644 --- a/docs/CHANGELOG.rst +++ b/docs/CHANGELOG.rst @@ -4,6 +4,15 @@ Changelog .. current developments +v1.9.0 +==================== + +**Added:** + +* Added ``openfe test --download-only`` flag, which caches all test data stored remotely. + + + v1.9.0 ==================== diff --git a/news/test-download-all.rst b/news/test-download-all.rst deleted file mode 100644 index f0c31b08a..000000000 --- a/news/test-download-all.rst +++ /dev/null @@ -1,23 +0,0 @@ -**Added:** - -* Added ``openfe test --download-only`` flag, which caches all test data stored remotely. - -**Changed:** - -* - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* - -**Security:** - -* From 557db299d444f795a3550459b1ef5be0b22e3f40 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Wed, 11 Feb 2026 08:50:45 -0800 Subject: [PATCH 6/6] update changelog --- docs/CHANGELOG.rst | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/docs/CHANGELOG.rst b/docs/CHANGELOG.rst index a6109949f..acce0fc38 100644 --- a/docs/CHANGELOG.rst +++ b/docs/CHANGELOG.rst @@ -4,12 +4,6 @@ Changelog .. current developments -v1.9.0 -==================== - -**Added:** - -* Added ``openfe test --download-only`` flag, which caches all test data stored remotely. @@ -21,6 +15,8 @@ v1.9.0 * The ``validate`` method for the RelativeHybridTopologyProtocol has been implemented. This means that settings and system validation can mostly be done prior to Protocol execution by calling ``RelativeHybridTopologyProtocol.validate(stateA, stateB, mapping)`` (`PR 1740 `_). +* Added ``openfe test --download-only`` flag, which downloads all test data stored remotely to the local cache (`PR 1814 `_). + **Changed:** * The absolute free energy protocols (AbsoluteBindingProtocol and AbsoluteSolvationProtocol) have been broken into multiple @@ -30,6 +26,7 @@ v1.9.0 * The relative free energy protocol (RelativeHybridTopologyProtocol) has been broken into multiple protocol units, allowing for the setup, run, analysis to happen separately (`PR 1773 `_). + **Fixed:** * Fixed bug in ligand network visualization (such as with ``openfe view-ligand-network``) so that ligand names are no longer cut off by the plot border (`PR 1822 `_).