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: | diff --git a/docs/CHANGELOG.rst b/docs/CHANGELOG.rst index 7d0e99c85..acce0fc38 100644 --- a/docs/CHANGELOG.rst +++ b/docs/CHANGELOG.rst @@ -4,6 +4,38 @@ 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)`` (`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 + 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 `_). +* Endstates in the RelativeHybridTopologyProtocol are now being created + in a manner that allows for isomorphic molecules that differ between + endstates to have different parameters (`PR 1772 `_). + + + 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/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:** - -* 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:** - -*