Merge pull request #458 from OpenBioSim/release_2025.2.0

Release 2025.2.0

Author: lohedges

.github/workflows/Sandpit_exs.yml

@@ -33,7 +33,7 @@ jobs:
 
       - name: Install dependency
         run: |
-          conda install -c conda-forge -c openbiosim/label/main biosimspace python=3.11 ambertools gromacs "sire=2024.3.0" "alchemlyb>=2.1" pytest openff-interchange pint=0.21 rdkit "jaxlib>0.3.7" tqdm
+          conda install -c conda-forge -c openbiosim/label/main biosimspace python=3.11 ambertools gromacs "sire=2025.1.1" "alchemlyb>=2.1" pytest openff-interchange pint=0.21 rdkit "jaxlib>0.3.7" tqdm
           python -m pip install git+https://github.com/Exscientia/MDRestraintsGenerator.git
           # For the testing of BSS.FreeEnergy.AlchemicalFreeEnergy.analysis
           python -m pip install https://github.com/alchemistry/alchemtest/archive/master.zip

actions/update_recipe.py

@@ -19,7 +19,12 @@
 
 # Store the name of the recipe and template YAML files.
 recipe = os.path.join(condadir, "meta.yaml")
-template = os.path.join(condadir, "template.yaml")
+
+# If the BSS_TEMPLATE environment variable is set, use that as the template.
+if "BSS_TEMPLATE" in os.environ:
+    template = os.environ["BSS_TEMPLATE"]
+else:
+    template = os.path.join(condadir, "template.yaml")
 
 # Now parse all of the requirements
 run_reqs = parse_requirements(os.path.join(srcdir, "requirements.txt"))

doc/source/changelog.rst

@@ -9,11 +9,29 @@ company supporting open-source development of fostering academic/industrial coll
 within the biomolecular simulation community. Our software is hosted via the `OpenBioSim`
 `GitHub <https://github.com/OpenBioSim/biosimspace>`__ organisation.
 
+`2025.2.0 <https://github.com/openbiosim/biosimspace/compare/2024.5.0...2025.2.0>`_ - Oct 08 2025
+-------------------------------------------------------------------------------------------------
+
+* Add support for ``SOMD2`` FEP analysis using data frames with different numbers of samples (`#415 <https://github.com/OpenBioSim/biosimspace/pull/415>`__).
+* Add support for the ABCG2 charge method for GAFF parameterisation (`#421 <https://github.com/OpenBioSim/biosimspace/pull/421>`__).
+* Fixed f-string formatting error in FEP analysis exception message (`#423 <https://github.com/OpenBioSim/biosimspace/pull/423>`__).
+* Fixed FEP energy trajectory slicing when intitial sample time is non-zero (`#424 <https://github.com/OpenBioSim/biosimspace/pull/424>`__).
+* Add workaround for incompatibility between ``ParmEd`` and ``NumPy`` 2.3 (`#428 <https://github.com/OpenBioSim/biosimspace/pull/428>`__).
+* Remove ``AnteChamber`` check when using ``OpenFF-NAGL`` (`#428 <https://github.com/OpenBioSim/biosimspace/pull/428>`__).
+* Add missing OPC water solvation function docstring (`#431 <https://github.com/OpenBioSim/biosimspace/pull/431>`__).
+* Use ``NumPy`` native ``array.tolist()`` rather than ``list(array)`` and add missing ATM protocol ``__str__`` methods (`#435 <https://github.com/OpenBioSim/biosimspace/pull/435>`__).
+* Add missing OPC water solvation function docstring (`#431 <https://github.com/OpenBioSim/biosimspace/pull/431>`__).
+* Allow user to skip writing of velocities to output files (`#437 <https://github.com/OpenBioSim/biosimspace/pull/437>`__).
+* Add support for renumbering molecules when copying a system (`#440 <https://github.com/OpenBioSim/biosimspace/pull/440>`__).
+* Added a molecular editing tutorial (`#447 <https://github.com/OpenBioSim/biosimspace/pull/447>`__).
+* Fixed issue with a non-singleton being used in a set within a mapping pruning function (`#454 <https://github.com/OpenBioSim/biosimspace/pull/454>`__).
+* Fix handling of trajectory frame reconstruction when using a perturbable reference system (`#456 <https://github.com/OpenBioSim/biosimspace/pull/456>`__).
+
 `2025.1.0 <https://github.com/openbiosim/biosimspace/compare/2024.4.1...2025.1.0>`_ - Jul 01 2025
 -------------------------------------------------------------------------------------------------
 
 * Improved robustness of formal charge inference when reading molecules from PDB or SDF files (`#393 <https://github.com/OpenBioSim/biosimspace/pull/393>`__).
-* Make sure the system extracted from AMBER trajectory frames during free-energy perturbation simulations are in the original, unsquashed format (`#403 <https://github.com/OpenBioSim/biosimspace/pull/403>`__).
+* Make sure the system extracted from AMBER trajectory frames during free-energy perturbation simulations is in the original, unsquashed format (`#403 <https://github.com/OpenBioSim/biosimspace/pull/403>`__).
 * Add support for the ``ff19SB`` force field and OPC water (`#406 <https://github.com/OpenBioSim/biosimspace/pull/406>`__).
 * Allow creation of ``SOMD`` perturbation files without modification to ghost atom bonded terms (`#407 <https://github.com/OpenBioSim/biosimspace/pull/407>`__).
 * Support analysis of ``SOMD2`` energy trajectories with time varying lambda sampling (`#408 <https://github.com/OpenBioSim/biosimspace/pull/408>`__).

doc/source/tutorials/index.rst

@@ -25,3 +25,4 @@ please :doc:`ask for support. <../support>`
    metadynamics
    protein_mutations
    alchemical_transfer
+   molecular_editing