Merge pull request #940 from OpenFreeEnergy/update-zenodo

Update CITATION.cff

.github/workflows/ci.yaml

@@ -73,6 +73,7 @@ jobs:
       - name: "Setup Micromamba"
         uses: mamba-org/setup-micromamba@v1
         with:
+          micromamba-version: '1.5.6-0'
           micromamba-binary-path: ~/.local/bin/micromamba
           environment-file: environment.yml
           environment-name: openfe_env

.github/workflows/conda_cron.yaml

@@ -34,6 +34,7 @@ jobs:
       - name: Setup Micromamba
         uses: mamba-org/setup-micromamba@v1
         with:
+          micromamba-version: '1.5.6-0'
           micromamba-binary-path: ~/.local/bin/micromamba
           environment-name: openfe
           create-args: >-

.github/workflows/gpu-runner.yaml

@@ -55,6 +55,7 @@ jobs:
       - name: "Setup Micromamba"
         uses: mamba-org/setup-micromamba@v1
         with:
+          micromamba-version: '1.5.6-0'
           environment-file: environment.yml
           environment-name: openfe_env
           condarc: |

.github/workflows/installer.yaml

@@ -37,6 +37,7 @@ jobs:
     - name: Install constructor environment with Micromamba
       uses: mamba-org/setup-micromamba@v1
       with:
+        micromamba-version: '1.5.6-0'
         micromamba-binary-path: ~/.local/bin/micromamba
         environment-name: installer
         create-args: >-

.github/workflows/mypy.yaml

@@ -28,6 +28,7 @@ jobs:
       - name: "Setup Micromamba"
         uses: mamba-org/setup-micromamba@v1
         with:
+          micromamba-version: '1.5.6-0'
           environment-file: environment.yml
           environment-name: openfe_env
           cache-environment: true

.github/workflows/package-tests.yaml

@@ -22,6 +22,7 @@ jobs:
       - name: "Setup Micromamba"
         uses: mamba-org/setup-micromamba@v1
         with:
+          micromamba-version: '1.5.6-0'
           environment-file: environment.yml
           environment-name: openfe_env
           cache-environment: true

CITATION.cff

@@ -28,9 +28,15 @@ authors:
 - given-names: "David"
   family-names: "Dotson"
   orcid: "https://orcid.org/0000-0001-5879-2942"
+- given-names: Joshua T.
+  family-names: Horton
+  orcid: 'https://orcid.org/0000-0001-8694-7200'
+- given-names: Matthew
+  family-names: Thompson
+  orcid: 'https://orcid.org/0000-0002-1460-3983'
 title: "The Open Free Energy library"
-version: 1.0
-date-released: 2024-04-19
+version: 1.1.0
+date-released: 2024-09-25
 url: "https://openfree.energy/"
 repository-code: "https://github.com/openfreeEnergy/openfe"
 doi: 10.5281/zenodo.8344247

docs/CHANGELOG.rst

@@ -4,6 +4,41 @@ Changelog
 
 .. current developments
 
+v1.1.0
+====================
+
+**Added:**
+
+* Extended system solvation tooling, including support for; non-cubic boxes,
+  explicitly defining the number of waters added, the box vectors, and box size
+  as supported by `Modeller.addSolvent` in OpenMM 8.0 and above.
+
+**Changed:**
+
+* Improved documentation of the OpenMMSolvationSettings.
+* The `PersesAtomMapper` now uses openff.units inline with the rest of the package.
+* Structural analysis data is no longer written to `structural_analysis.json`
+  but rather a 32bit numpy compressed file named `structural_analysis.npz`
+  (PR #937).
+* Structural analysis array data is no longer directly returned in the
+  RelativeHybridTopologyProtocol result dictionary. Instead it should
+  be accessed from the serialized NPZ file `structural_analysis.npz`.
+  The `structural_analysis` key now contains a path to the NPZ file,
+  if the structural analysis did not fail (the `structural_analysis_error`
+  key will instead be present on failure) (PR #937).
+* Add duecredit citations for pymbar when calling
+  `openfe.protocols.openmm_utils.multistate_analysis`.
+
+**Fixed:**
+
+* 2D RMSD plotting now allows for fewer than 5 states (PR #896).
+* 2D RMSD plotting no longer draws empty axes when
+  the number of states - 1 is not divisible by 4 (PR #896).
+* The RelativeHybridTopologyProtocol result unit is now much smaller,
+  due to the removal of structural analysis data (PR #937).
+
+
+
 v1.0.1
 ====================