Merge pull request #131 from openforcefield/add-2.3.0rc1

j-wags · web-flow · commit ab469190bd87 · 2025-09-11T21:30:47.000-07:00
Add 2.3.0rc1
diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -22,15 +22,16 @@ jobs:
       fail-fast: false
       matrix:
         python-version:
-          - "3.10"
           - "3.11"
           - "3.12"
+          - "3.13"
         os:
           - ubuntu-latest
           - macos-latest
         toolkit:
           - true
           - false
+
     env:
       PYTEST_ARGS: -v -nauto --cov=openforcefields --cov-config=setup.cfg --cov-append --cov-report=xml
 
diff --git a/.github/workflows/canary.yaml b/.github/workflows/canary.yaml
@@ -16,9 +16,9 @@ jobs:
       fail-fast: false
       matrix:
         python-version:
-          - "3.10"
           - "3.11"
           - "3.12"
+          - "3.13"
         cfg:
           - os: ubuntu-latest
           - os: macOS-latest
diff --git a/.zenodo.json b/.zenodo.json
@@ -6,75 +6,80 @@
         "name": "Wang, Lily"
       },
       {
-        "orcid": "0000-0002-7210-1164",
-        "affiliation": "Open Force Field Consortium, Open Molecular Software Foundation, Davis,  CA, USA",
-        "name": "McIsaac, Alexandra R."
+        "orcid": "0000-0001-5787-9130",
+        "affiliation": "Open Free Energy, Open Molecular Software Foundation, Davis, CA, USA",
+        "name": "Alibay, Irfan"
+      },
+      {
+        "orcid": "0000-0002-1736-7744",
+        "affiliation": "Open Free Energy, Open Molecular Software Foundation, Davis, CA, USA",
+        "name": "Baumann, Hannah M."
       },
       {
         "orcid": "0000-0001-6583-2148",
         "affiliation": "Pharmaceutical Sciences, University of California Irvine, Irvine, CA, USA",
         "name": "Behara, Pavan Kumar"
       },
-      {
-        "orcid": "0000-0001-7856-1156",
-        "affiliation": "Department of Chemistry, University of California Irvine, Irvine, CA, USA",
-        "name": "Gokey, Trevor"
-      },
       {
         "orcid": "0000-0002-5899-7953",
         "affiliation": "Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA",
         "name": "Cavender, Chapin"
       },
+      {
+        "orcid": "0000-0001-7856-1156",
+        "affiliation": "Department of Chemistry, University of California Irvine, Irvine, CA, USA",
+        "name": "Gokey, Trevor"
+      },
       {
         "orcid": "0000-0001-8694-7200",
         "affiliation": "School of Natural and Environmental Sciences,  Newcastle University, Newcastle upon Tyne NE1, 7RU, United Kingdom",
         "name": "Horton, Joshua"
       },
       {
-        "orcid": "0000-0002-6878-0192",
+        "orcid": "0000-0002-1697-2918",
+        "affiliation": "Department of Chemistry, University of California Davis, Davis, CA, USA",
+        "name": "Jang, Hyesu"
+      },
+      {
+        "orcid": "0000-0002-7210-1164",
         "affiliation": "Open Force Field Consortium, Open Molecular Software Foundation, Davis,  CA, USA",
-        "name": "Westbrook, Brent R."
+        "name": "McIsaac, Alexandra R."
       },
       {
-        "orcid": "0000-0002-1460-3983",
+        "orcid": "0000-0002-8246-5113",
         "affiliation": "Open Force Field Consortium, Open Molecular Software Foundation, Davis,  CA, USA",
-        "name": "Thompson, Matthew W."
+        "name": "Mitchell, Joshua A."
       },
       {
         "orcid": "0000-0002-2732-457X",
         "affiliation": "Pharmaceutical Sciences, University of California Irvine, Irvine, CA, USA",
         "name": "Osato, Meghan"
       },
       {
-        "orcid": "0000-0002-1736-7744",
-        "affiliation": "Open Free Energy, Open Molecular Software Foundation, Davis, CA, USA",
-        "name": "Baumann, Hannah M."
-      },
-      {
-        "orcid": "0000-0001-5787-9130",
-        "affiliation": "Open Free Energy, Open Molecular Software Foundation, Davis, CA, USA",
-        "name": "Alibay, Irfan"
-      },
-      {
-        "orcid": "0000-0002-1697-2918",
-        "affiliation": "Department of Chemistry, University of California Davis, Davis, CA, USA",
-        "name": "Jang, Hyesu"
+        "orcid": "0000-0002-1460-3983",
+        "affiliation": "Open Force Field Consortium, Open Molecular Software Foundation, Davis,  CA, USA",
+        "name": "Thompson, Matthew W."
       },
       {
         "orcid": "0000-0001-6448-0873",
         "affiliation": "Open Force Field Consortium, Open Molecular Software Foundation, Davis,  CA, USA",
         "name": "Wagner, Jeffrey"
       },
       {
-        "orcid": "0000-0003-2933-0719",
-        "affiliation": "School of Natural and Environmental Sciences,  Newcastle University, Newcastle upon Tyne NE1, 7RU, United Kingdom",
-        "name": "Cole, Daniel"
+        "orcid": "0000-0002-6878-0192",
+        "affiliation": "Open Force Field Consortium, Open Molecular Software Foundation, Davis,  CA, USA",
+        "name": "Westbrook, Brent R."
       },
       {
         "orcid": "0000-0001-9145-6457",
         "affiliation": "OpenEye Scientific Software, Santa Fe, NM, USA",
         "name": "Bayly, Christopher"
       },
+      {
+        "orcid": "0000-0003-2933-0719",
+        "affiliation": "School of Natural and Environmental Sciences,  Newcastle University, Newcastle upon Tyne NE1, 7RU, United Kingdom",
+        "name": "Cole, Daniel"
+      },
       {
         "orcid": "0000-0002-1083-5533",
         "affiliation": "Pharmaceutical Sciences, University of California Irvine, Irvine, CA, USA",
diff --git a/README.md b/README.md
@@ -28,6 +28,8 @@ Details for each OpenFF force field in this repository can be found on our [webs
 
 | Filename                                    | FF line | Release Date  | Major format changes? | Fitting repo                                                                              | DOI                                                                                                         |
 |---------------------------------------------|---------|---------------|-----------------------|-------------------------------------------------------------------------------------------|-------------------------------------------------------------------------------------------------------------|
+| `openff-2.3.0-rc1.offxml`                    | Sage    | Sep 12, 2025  | NAGLCharges instead of ToolkitAM1BCC                    | [repo](http://github.com/lilyminium/ash-sage-rc1)[                   |                                                                                                             |
+| `openff_unconstrained-2.3.0-rc1.offxml`      | Sage    | Sep 12, 2025  | NAGLCharges instead of ToolkitAM1BCC                    | [repo](http://github.com/lilyminium/ash-sage-rc1)[                   |                                                                                                             |
 | `openff-2.2.1.offxml`                       | Sage    | Sep 11, 2024  | No                    | [repo](https://github.com/openforcefield/sage-2.2.1/releases/tag/2.2.1)                   |                                                                                                             |
 | `openff_unconstrained-2.2.1.offxml`         | Sage    | Sep 11, 2024  | No                    | [repo](https://github.com/openforcefield/sage-2.2.1/releases/tag/2.2.1)                   |                                                                                                             |
 | `openff-2.2.1-rc1.offxml`                   | Sage    | Jul 22, 2024  | No                    | [repo](https://github.com/openforcefield/sage-2.2.1/releases/tag/2.2.1-rc1)               |                                                                                                             |
@@ -185,6 +187,9 @@ Force fields moving forward will be called `name-X.Y.Z`
 
 - `2024.09.0` This release adds the Sage 2.2.1 force field with `openff-2.2.1.offxml` and `openff_unconstrained-2.2.1.offxml`, with identifical parameters to 2.2.1-rc1.
 
+- `2025.09.0` This release adds the Sage 2.3.0-rc1 force fields. See the release notes for more details.
+
+
 #### Acknowledgements
 
 Project based on the
diff --git a/canary/data/coverage.smi b/canary/data/coverage.smi
@@ -52,7 +52,7 @@ CCC(CCl)Cl
 CC(=O)c1ccc(cc1)S(=C)(=C)C
 COc1ccc(cc1OC)c2ccc3ccccc3[o+]2
 # F[P-](F)(F)(F)(F)F
-CC(C)S(=O)(=O)Br
+# CC(C)S(=O)(=O)Br
 C1CC(=O)N(C1=O)Br
 C=C=CN1CCCC1=O
 CC(C)C(=O)NNC=O
diff --git a/devtools/conda-envs/canary_env.yaml b/devtools/conda-envs/canary_env.yaml
@@ -5,5 +5,5 @@ dependencies:
   - python
   - pip
   - pytest
-  - openff-toolkit >=0.16.4
+  - openff-toolkit >=0.17.0
   - openmmforcefields
diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
@@ -4,7 +4,7 @@ channels:
 dependencies:
   - python
   - pip
-  - openff-toolkit >=0.14.3
+  - openff-toolkit >=0.17.0
   - openff-interchange >=0.3.17
   - pytest
   - pytest-cov
diff --git a/openforcefields/offxml/openff-2.3.0-rc1.offxml b/openforcefields/offxml/openff-2.3.0-rc1.offxml
diff --git a/openforcefields/offxml/openff_unconstrained-2.3.0-rc1.offxml b/openforcefields/offxml/openff_unconstrained-2.3.0-rc1.offxml
diff --git a/openforcefields/tests/test_openforcefields.py b/openforcefields/tests/test_openforcefields.py
