Merge remote-tracking branch 'origin/main' into test/pymbar-with-numba

Author: mikemhenry

.github/pull_request_template.md

@@ -14,7 +14,7 @@ see https://regro.github.io/rever-docs/news.html for details on how to add news
 Checklist
 * [ ] All new code is appropriately documented (user-facing code _must_ have complete docstrings).
 * [ ] Added a ``news`` entry, or the changes are not user-facing.
-* [ ] Ran pre-commit by making a comment with `pre-commit.ci autofix` before requesting review.
+* [ ] Ran pre-commit: you can run [pre-commit](https://pre-commit.com) locally or comment on this PR with `pre-commit.ci autofix`.
 
 Manual Tests: these are slow so don't need to be run every commit, only before merging and when relevant changes are made (generally at reviewer-discretion). 
 * [ ] [GPU integration tests](https://github.com/OpenFreeEnergy/openfe/actions/workflows/gpu-integration-tests.yaml)

.github/workflows/ci.yaml

@@ -35,7 +35,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: ["ubuntu-latest", "macos-latest"]
+        os: ["ubuntu-latest"]
         openeye: ["no"]
         python-version:
           - "3.11"
@@ -45,6 +45,9 @@ jobs:
           - os: "ubuntu-latest"
             python-version: "3.13"
             openeye: "yes"
+          - os: "macos-latest"
+            python-version: "3.12"
+            openeye: "no"
 
     env:
       OE_LICENSE: ${{ github.workspace }}/oe_license.txt

.github/workflows/conda_cron.yaml

@@ -20,11 +20,15 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: ['ubuntu-latest', 'macos-latest']
+        os: ['ubuntu-latest']
         python-version:
           - "3.11"
           - "3.12"
           - "3.13"
+        include:
+        - os: "macos-latest"
+          python-version: "3.12"
+          openeye: "no"
     steps:
       - name: Checkout Code
         uses: actions/checkout@v4

.github/workflows/cpu-long-tests.yaml

@@ -92,7 +92,7 @@ jobs:
           DUECREDIT_ENABLE: 'yes'
           OFE_INTEGRATION_TESTS: FALSE
         run: |
-          pytest -n logical -vv --durations=10 --runslow openfecli/tests/ openfe/tests/
+          pytest -n logical -vv --durations=10 --runslow src/openfecli/tests/ src/openfe/tests/
 
   stop-aws-runner:
     runs-on: ubuntu-latest

.github/workflows/gpu-integration-tests.yaml

@@ -96,7 +96,7 @@ jobs:
           OFE_INTEGRATION_TESTS: TRUE
         run: |
           # The -m flag will only run tests with @pytest.mark.integration
-          pytest -n logical -vv --durations=10 -m integration openfecli/tests/ openfe/tests/
+          pytest -n logical -vv --durations=10 -m integration src/openfecli/tests/ src/openfe/tests/
 
   stop-aws-runner:
     runs-on: ubuntu-latest

.github/workflows/test-example-notebooks.yaml

@@ -12,7 +12,7 @@ defaults:
     shell: bash -leo pipefail {0}
 
 jobs:
-  test-conda-build:
+  test-example-notebooks:
     runs-on: ubuntu-latest
 
     steps:

.pre-commit-config.yaml

@@ -10,6 +10,7 @@ repos:
   rev: v6.0.0
   hooks:
   - id: check-added-large-files
+    args: ["--maxkb=900"]
   - id: check-case-conflict
   - id: check-executables-have-shebangs
   - id: check-symlinks
@@ -19,12 +20,12 @@ repos:
   - id: debug-statements
 
 - repo: https://github.com/tox-dev/pyproject-fmt
-  rev: "v2.8.0"
+  rev: "v2.11.1"
   hooks:
     - id: pyproject-fmt
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.13.3
+  rev: v0.14.10
   hooks:
     # Run the linter.
     - id: ruff

MANIFEST.in

@@ -1,18 +1,18 @@
-recursive-include openfe/tests/data/ *.sdf
-recursive-include openfe/tests/data/ *.bz2
-recursive-include openfe/tests/data/ *.csv
-recursive-include openfe/tests/data/ *.pdb
-recursive-include openfe/tests/data/ *.mol2
-recursive-include openfe/tests/data/ *.xml
-recursive-include openfe/tests/data/ *.graphml
-recursive-include openfe/tests/data/ *.edge
-recursive-include openfe/tests/data/ *.dat
-recursive-include openfe/tests/data/ *.txt
-recursive-include openfe/tests/data/ *.gz
-recursive-include openfe/tests/data/ *json_results.gz
-include openfecli/tests/data/*.json
-include openfecli/tests/data/*.tar.gz
-include openfecli/tests/commands/test_gather/*.tsv
-recursive-include openfecli/tests/ *.sdf
-recursive-include openfecli/tests/ *.pdb
-include openfe/tests/data/openmm_rfe/vacuum_nocoord.nc
+recursive-include src/openfe/tests/data/ *.sdf
+recursive-include src/openfe/tests/data/ *.bz2
+recursive-include src/openfe/tests/data/ *.csv
+recursive-include src/openfe/tests/data/ *.pdb
+recursive-include src/openfe/tests/data/ *.mol2
+recursive-include src/openfe/tests/data/ *.xml
+recursive-include src/openfe/tests/data/ *.graphml
+recursive-include src/openfe/tests/data/ *.edge
+recursive-include src/openfe/tests/data/ *.dat
+recursive-include src/openfe/tests/data/ *.txt
+recursive-include src/openfe/tests/data/ *.gz
+recursive-include src/openfe/tests/data/ *json_results.gz
+include src/openfecli/tests/data/*.json
+include src/openfecli/tests/data/*.tar.gz
+include src/openfecli/tests/commands/test_gather/*.tsv
+recursive-include src/openfecli/tests/ *.sdf
+recursive-include src/openfecli/tests/ *.pdb
+include src/openfe/tests/data/openmm_rfe/vacuum_nocoord.nc

docs/CHANGELOG.rst

@@ -4,6 +4,55 @@ 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 <https://github.com/OpenFreeEnergy/openfe/pull/1740>`_).
+
+* Added ``openfe test --download-only`` flag, which downloads all test data stored remotely to the local cache (`PR 1814 <https://github.com/OpenFreeEnergy/openfe/pull/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 <https://github.com/OpenFreeEnergy/openfe/pull/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 <https://github.com/OpenFreeEnergy/openfe/pull/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 <https://github.com/OpenFreeEnergy/openfe/pull/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 <https://github.com/OpenFreeEnergy/openfe/pull/1772>`_).
+
+
+
+v1.8.1
+====================
+
+**Added:**
+
+* Added a progress bar for ``openfe gather`` JSON loading (`PR #1786 <https://github.com/OpenFreeEnergy/openfe/pull/1786>`_).
+
+**Fixed:**
+
+* Due to issues with OpenFF's handling of toolkit registries
+  with NAGL, the use of NAGL models (e.g. AshGC) when OpenEye
+  is installed but not requested as the charge backend has been
+  disabled (Issue #1760, `PR #1762 <https://github.com/OpenFreeEnergy/openfe/pull/1762>`_).
+* 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 <https://github.com/OpenFreeEnergy/openfe/pull/1822>`_).
+
+
+
 v1.8.0
 ====================
 
@@ -14,6 +63,7 @@ v1.8.0
 * 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 <https://github.com/OpenFreeEnergy/openfe/pull/1585>`_, fixes `Issue #1499 <https://github.com/OpenFreeEnergy/openfe/issues/1499>`_).
 * Disable JAX acceleration by default, see https://docs.openfree.energy/en/latest/guide/troubleshooting.html#pymbar-disable-jax for more information (`PR #1694 <https://github.com/OpenFreeEnergy/openfe/pull/1692>`_).
+* New options have been added to the ``AlchemicalSettings`` of the ``SepTopProtocol``, ``AbsoluteSolvationProtocol`` and ``AbsoluteBindingProtocol``. Notably, these options allow users to control the softcore parameters as well as the use of long range dispersion corrections (`PR #1742 <https://github.com/OpenFreeEnergy/openfe/pull/1742>`_).
 
 **Changed:**
 

docs/conf.py

@@ -103,6 +103,7 @@
 
 autodoc_mock_imports = [
     "cinnabar",
+    "dill",
     "MDAnalysis",
     "matplotlib",
     "mdtraj",
@@ -192,7 +193,7 @@
     else:
         repo = git.Repo.clone_from(
             "https://github.com/OpenFreeEnergy/ExampleNotebooks.git",
-            branch="2025.12.04",
+            branch="2026.01.26",
             to_path=example_notebooks_path,
         )
 except Exception as e: