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Merge pull request #308 from OpenBioSim/release_2024.2.0
Release 2024.2.0
2 parents 800e00f + 66b5bc6 commit 25c62e4

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‎.github/workflows/Sandpit_exs.yml‎

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strategy:
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fail-fast: false
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matrix:
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os: ["ubuntu-latest", "macOS-latest",]
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os: ["ubuntu-latest", ]
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python-version: ["3.10",]
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steps:
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python-version: ${{ matrix.python-version }}
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activate-environment: bss_build
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miniforge-version: latest
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miniforge-variant: Mambaforge
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use-mamba: true
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- name: Install dependency
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run: |
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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
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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
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python -m pip install git+https://github.com/Exscientia/MDRestraintsGenerator.git
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# For the testing of BSS.FreeEnergy.AlchemicalFreeEnergy.analysis
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python -m pip install https://github.com/alchemistry/alchemtest/archive/master.zip

‎.github/workflows/devel.yaml‎

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

‎.github/workflows/main.yaml‎

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

‎.github/workflows/pr.yaml‎

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

‎SECURITY.md‎

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

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within the biomolecular simulation community. Our software is hosted via the `OpenBioSim`
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`GitHub <https://github.com/OpenBioSim/biosimspace>`__ organisation.
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`2024.2.0 <https://github.com/openbiosim/biosimspace/compare/2024.1.0...2024.2.0>`_ - Jul 09 2024
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-------------------------------------------------------------------------------------------------
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* Fixed incorect use of ``self`` in :func:`Trajectory.getFrame <BioSimSpace.Trajectory.getFrame>` function (`#281 <https://github.com/OpenBioSim/biosimspace/pull/281>`__).
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* Use SDF as an intermediate for ``antechamber`` if the original molecule was loaded from that format (`#287 <https://github.com/OpenBioSim/biosimspace/pull/287>`__).
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* Detect dummy atoms by checking ``element`` *and* ``ambertype`` properties when creating ``SOMD`` pert files (`#289 <https://github.com/OpenBioSim/biosimspace/pull/289>`__).
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* Add missing ``match_water`` kwarg to ``prepareFEP`` node (`#292 <https://github.com/OpenBioSim/biosimspace/pull/292>`__).
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* Add protein free-energy perturbation functionality (`@akalpokas <https://github.com/akalpokas (`#294 <https://github.com/OpenBioSim/biosimspace/pull/294>`__).
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* Ensure that the LJ sigma parameter for perturbed atoms is non-zero (`#295 <https://github.com/OpenBioSim/biosimspace/pull/295>`__).
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* Fixed return type docstrings for functions in the :mod:`BioSimSpace.Parameters` module (`#298 <https://github.com/OpenBioSim/biosimspace/pull/298>`__).
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* 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>`__).
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* Expose ``SOMD`` torsion modification kwargs (`#302 <https://github.com/OpenBioSim/biosimspace/pull/302>`__).
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`2024.1.0 <https://github.com/openbiosim/biosimspace/compare/2023.5.1...2024.1.0>`_ - Apr 15 2024
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-------------------------------------------------------------------------------------------------
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‎doc/source/tutorials/images/aldose_reductase_mutation_mapping.png‎

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‎doc/source/tutorials/images/pfep_thermodynamic_cycle.png‎

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‎doc/source/tutorials/images/ubiquitin_mutation_mapping.png‎

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‎doc/source/tutorials/index.rst‎

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crystal_water
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hydration_freenrg
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metadynamics
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protein_mutations

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