Merge pull request #308 from OpenBioSim/release_2024.2.0

Release 2024.2.0

.github/workflows/Sandpit_exs.yml

@@ -18,7 +18,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: ["ubuntu-latest", "macOS-latest",]
+        os: ["ubuntu-latest", ]
         python-version: ["3.10",]
 
     steps:
@@ -30,12 +30,10 @@ jobs:
           python-version: ${{ matrix.python-version }}
           activate-environment: bss_build
           miniforge-version: latest
-          miniforge-variant: Mambaforge
-          use-mamba: true
 
       - name: Install dependency
         run: |
-          mamba install -c conda-forge -c openbiosim/label/main biosimspace python=3.10 ambertools gromacs "sire=2023.5" "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=3.10 ambertools gromacs "sire=2024.1.0" "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

.github/workflows/devel.yaml

@@ -43,23 +43,21 @@ jobs:
           python-version: ${{ matrix.python-version }}
           activate-environment: bss_build
           miniforge-version: latest
-          miniforge-variant: Mambaforge
-          use-mamba: true
 #
       - name: Clone the devel branch
         run: git clone -b devel https://github.com/openbiosim/biosimspace
 #
       - name: Setup Conda
-        run: mamba install -y -c conda-forge boa anaconda-client packaging pip-requirements-parser
+        run: conda install -y -c conda-forge boa anaconda-client packaging pip-requirements-parser
 #
       - name: Update Conda recipe
         run: python ${{ github.workspace }}/biosimspace/actions/update_recipe.py
 #
       - name: Prepare build location
         run: mkdir ${{ github.workspace }}/build
 #
-      - name: Build Conda package using mamba build
-        run: conda mambabuild -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/biosimspace/recipes/biosimspace
+      - name: Build Conda package using conda build
+        run: conda build -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/biosimspace/recipes/biosimspace
 #
       - name: Upload Conda package
         run: python ${{ github.workspace }}/biosimspace/actions/upload_package.py

.github/workflows/main.yaml

@@ -40,23 +40,21 @@ jobs:
           python-version: ${{ matrix.python-version }}
           activate-environment: bss_build
           miniforge-version: latest
-          miniforge-variant: Mambaforge
-          use-mamba: true
 #
       - name: Clone the main branch
         run: git clone -b main https://github.com/openbiosim/biosimspace
 #
       - name: Setup Conda
-        run: mamba install -y -c conda-forge boa anaconda-client packaging pip-requirements-parser
+        run: conda install -y -c conda-forge boa anaconda-client packaging pip-requirements-parser
 #
       - name: Update Conda recipe
         run: python ${{ github.workspace }}/biosimspace/actions/update_recipe.py
 #
       - name: Prepare build location
         run: mkdir ${{ github.workspace }}/build
 #
-      - name: Build Conda package using mamba build
-        run: conda mambabuild -c conda-forge -c openbiosim/label/main ${{ github.workspace }}/biosimspace/recipes/biosimspace
+      - name: Build Conda package using conda build
+        run: conda build -c conda-forge -c openbiosim/label/main ${{ github.workspace }}/biosimspace/recipes/biosimspace
 #
       - name: Upload Conda package
         run: python ${{ github.workspace }}/biosimspace/actions/upload_package.py

.github/workflows/pr.yaml

@@ -46,25 +46,23 @@ jobs:
           python-version: ${{ matrix.python-version }}
           activate-environment: bss_build
           miniforge-version: latest
-          miniforge-variant: Mambaforge
-          use-mamba: true
 #
       - name: Clone the feature branch
         run: git clone -b ${{ github.head_ref }} --single-branch https://github.com/${{ env.REPO }} biosimspace
 #
       - name: Setup Conda
-        run: mamba install -y -c conda-forge boa anaconda-client packaging pip-requirements-parser
+        run: conda install -y -c conda-forge boa anaconda-client packaging pip-requirements-parser
 #
       - name: Update Conda recipe
         run: python ${{ github.workspace }}/biosimspace/actions/update_recipe.py
 #
       - name: Prepare build location
         run: mkdir ${{ github.workspace }}/build
 #
-      - name: Build Conda package using mamba build using main channel
+      - name: Build Conda package using conda build using main channel
         if: ${{ github.base_ref == 'main' }}
-        run: conda mambabuild -c conda-forge -c openbiosim/label/main ${{ github.workspace }}/biosimspace/recipes/biosimspace
+        run: conda build -c conda-forge -c openbiosim/label/main ${{ github.workspace }}/biosimspace/recipes/biosimspace
 #
-      - name: Build Conda package using mamba build using dev channel
+      - name: Build Conda package using conda build using dev channel
         if: ${{ github.base_ref != 'main' }}
-        run: conda mambabuild -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/biosimspace/recipes/biosimspace
+        run: conda build -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/biosimspace/recipes/biosimspace

SECURITY.md

@@ -4,13 +4,13 @@
 
 As we have limited resource, we only support the latest major release
 of BioSimSpace with security updates. For example, if the current version
-is 2023.1.0, then only versions 2023.1.0 to 2023.1.X wil have updates,
-which will be released as 2023.1.X+1.
+is 2024.1.0, then only versions 2024.1.0 to 2024.1.X wil have updates,
+which will be released as 2024.1.X+1.
 
 | Version | Supported          |
 | ------- | ------------------ |
-| 2023.5.x | :white_check_mark: |
-| < 2023.5.x| :x:                |
+| 2024.1.x | :white_check_mark: |
+| < 2024.1.x| :x:                |
 
 ## Reporting a Vulnerability
 

doc/source/changelog.rst

@@ -9,6 +9,19 @@ 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.
 
+`2024.2.0 <https://github.com/openbiosim/biosimspace/compare/2024.1.0...2024.2.0>`_ - Jul 09 2024
+-------------------------------------------------------------------------------------------------
+
+* Fixed incorect use of ``self`` in :func:`Trajectory.getFrame <BioSimSpace.Trajectory.getFrame>` function (`#281 <https://github.com/OpenBioSim/biosimspace/pull/281>`__).
+* Use SDF as an intermediate for ``antechamber`` if the original molecule was loaded from that format (`#287 <https://github.com/OpenBioSim/biosimspace/pull/287>`__).
+* Detect dummy atoms by checking ``element`` *and* ``ambertype`` properties when creating ``SOMD`` pert files (`#289 <https://github.com/OpenBioSim/biosimspace/pull/289>`__).
+* Add missing ``match_water`` kwarg to ``prepareFEP`` node (`#292 <https://github.com/OpenBioSim/biosimspace/pull/292>`__).
+* Add protein free-energy perturbation functionality (`@akalpokas <https://github.com/akalpokas (`#294 <https://github.com/OpenBioSim/biosimspace/pull/294>`__).
+* Ensure that the LJ sigma parameter for perturbed atoms is non-zero (`#295 <https://github.com/OpenBioSim/biosimspace/pull/295>`__).
+* Fixed return type docstrings for functions in the :mod:`BioSimSpace.Parameters` module (`#298 <https://github.com/OpenBioSim/biosimspace/pull/298>`__).
+* Don't use ``sire.legacy.Base.wrap`` with the ``file_format`` property to avoid (incorrect) auto string to unit conversion of ``mol2`` to moles squared (`#300 <https://github.com/OpenBioSim/biosimspace/pull/300>`__).
+* Expose ``SOMD`` torsion modification kwargs (`#302 <https://github.com/OpenBioSim/biosimspace/pull/302>`__).
+
 `2024.1.0 <https://github.com/openbiosim/biosimspace/compare/2023.5.1...2024.1.0>`_ - Apr 15 2024
 -------------------------------------------------------------------------------------------------
 

doc/source/tutorials/index.rst

@@ -23,3 +23,4 @@ please :doc:`ask for support. <../support>`
    crystal_water
    hydration_freenrg
    metadynamics
+   protein_mutations