Merge pull request #278 from OpenBioSim/release_2024.1.0

Release 2024.1.0

Author: lohedges

.github/workflows/Sandpit_exs.yml

@@ -35,7 +35,7 @@ jobs:
 
       - name: Install dependency
         run: |
-          mamba install -c conda-forge -c openbiosim/label/main biosimspace python=3.10 ambertools gromacs "sire=2023.4" "alchemlyb>=2.1" pytest openff-interchange pint=0.21 rdkit "jaxlib>0.3.7" tqdm
+          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
           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

@@ -13,23 +13,21 @@ jobs:
       max-parallel: 9
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
         platform:
           - { name: "windows", os: "windows-latest", shell: "pwsh" }
           - { name: "linux", os: "ubuntu-latest", shell: "bash -l {0}" }
           - { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
         exclude:
-          # Exclude all but the latest Python from all but Linux
+          # Exclude all but the latest Python from all
+          # but Linux
           - platform:
               { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
-            python-version: "3.9"
+            python-version: "3.12"  # MacOS can't run 3.12 yet... We want 3.10 and 3.11
           - platform: { name: "windows", os: "windows-latest", shell: "pwsh" }
-            python-version: "3.9"
-          - platform:
-              { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
             python-version: "3.10"
           - platform: { name: "windows", os: "windows-latest", shell: "pwsh" }
-            python-version: "3.10"
+            python-version: "3.11"
     environment:
       name: biosimspace-build
     defaults:
@@ -39,7 +37,7 @@ jobs:
       SIRE_DONT_PHONEHOME: 1
       SIRE_SILENT_PHONEHOME: 1
     steps:
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}
@@ -52,7 +50,7 @@ jobs:
         run: git clone -b devel https://github.com/openbiosim/biosimspace
 #
       - name: Setup Conda
-        run: mamba install -y -c conda-forge boa anaconda-client packaging=21 pip-requirements-parser
+        run: mamba 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

.github/workflows/main.yaml

@@ -16,11 +16,15 @@ jobs:
       max-parallel: 9
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
         platform:
           - { name: "windows", os: "windows-latest", shell: "pwsh" }
           - { name: "linux", os: "ubuntu-latest", shell: "bash -l {0}" }
           - { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
+        exclude:
+          - platform:
+              { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
+            python-version: "3.12"  # MacOS can't run 3.12 yet...
     environment:
       name: biosimspace-build
     defaults:
@@ -30,7 +34,7 @@ jobs:
       SIRE_DONT_PHONEHOME: 1
       SIRE_SILENT_PHONEHOME: 1
     steps:
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}
@@ -43,7 +47,7 @@ jobs:
         run: git clone -b main https://github.com/openbiosim/biosimspace
 #
       - name: Setup Conda
-        run: mamba install -y -c conda-forge boa anaconda-client packaging=21 pip-requirements-parser
+        run: mamba 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

.github/workflows/pr.yaml

@@ -12,7 +12,7 @@ jobs:
       max-parallel: 9
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
         platform:
           - { name: "windows", os: "windows-latest", shell: "pwsh" }
           - { name: "linux", os: "ubuntu-latest", shell: "bash -l {0}" }
@@ -22,14 +22,14 @@ jobs:
           # but Linux
           - platform:
               { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
-            python-version: "3.9"
+            python-version: "3.10"
           - platform: { name: "windows", os: "windows-latest", shell: "pwsh" }
-            python-version: "3.9"
+            python-version: "3.10"
           - platform:
               { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
-            python-version: "3.10"
+            python-version: "3.12"  # MacOS can't run 3.12 yet...
           - platform: { name: "windows", os: "windows-latest", shell: "pwsh" }
-            python-version: "3.10"
+            python-version: "3.11"
     environment:
       name: biosimspace-build
     defaults:
@@ -40,7 +40,7 @@ jobs:
       SIRE_SILENT_PHONEHOME: 1
       REPO: "${{ github.event.pull_request.head.repo.full_name || github.repository }}"
     steps:
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}
@@ -53,7 +53,7 @@ jobs:
         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=21 pip-requirements-parser
+        run: mamba 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

README.rst

@@ -63,35 +63,35 @@ Conda package
 The easiest way to install BioSimSpace is using our `conda channel <https://anaconda.org/openbiosim/repo>`__.
 BioSimSpace is built using dependencies from `conda-forge <https://conda-forge.org/>`__,
 so please ensure that the channel takes strict priority. We recommend using
-`Mambaforge <https://github.com/conda-forge/miniforge#mambaforge>`__.
+`Miniforge <https://github.com/conda-forge/miniforge>`__.
 
 To create a new environment:
 
 .. code-block:: bash
 
-    mamba create -n openbiosim -c conda-forge -c openbiosim biosimspace
-    mamba activate openbiosim
+    conda create -n openbiosim -c conda-forge -c openbiosim biosimspace
+    conda activate openbiosim
 
 To install the latest development version you can use:
 
 .. code-block:: bash
 
-    mamba create -n openbiosim-dev -c conda-forge -c openbiosim/label/dev biosimspace
-    mamba activate openbiosim-dev
+    conda create -n openbiosim-dev -c conda-forge -c openbiosim/label/dev biosimspace
+    conda activate openbiosim-dev
 
 When updating the development version it is generally advised to update `Sire <https://github.com/openbiosim/sire>`_
 at the same time:
 
 .. code-block:: bash
 
-    mamba update -c conda-forge -c openbiosim/label/dev biosimspace sire
+    conda update -c conda-forge -c openbiosim/label/dev biosimspace sire
 
 Unless you add the required channels to your Conda configuration, then you'll
 need to add them when updating, e.g., for the development package:
 
 .. code-block:: bash
 
-    mamba update -c conda-forge -c openbiosim/label/dev biosimspace
+    conda update -c conda-forge -c openbiosim/label/dev biosimspace
 
 Installing from source
 ^^^^^^^^^^^^^^^^^^^^^^
@@ -146,8 +146,8 @@ latest development code into that.
 
 .. code-block:: bash
 
-   mamba create -n openbiosim-dev -c conda-forge -c openbiosim/label/dev biosimspace --only-deps
-   mamba activate openbiosim-dev
+   conda create -n openbiosim-dev -c conda-forge -c openbiosim/label/dev biosimspace --only-deps
+   conda activate openbiosim-dev
    git clone https://github.com/openbiosim/biosimspace
    cd biosimspace/python
    BSS_SKIP_DEPENDENCIES=1 python setup.py develop

SECURITY.md

@@ -9,8 +9,8 @@ which will be released as 2023.1.X+1.
 
 | Version | Supported          |
 | ------- | ------------------ |
-| 2023.1.x | :white_check_mark: |
-| < 2023.1.x| :x:                |
+| 2023.5.x | :white_check_mark: |
+| < 2023.5.x| :x:                |
 
 ## Reporting a Vulnerability
 

doc/source/changelog.rst

@@ -9,6 +9,20 @@ 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.
 
+`2024.1.0 <https://github.com/openbiosim/biosimspace/compare/2023.5.1...2024.1.0>`_ - Apr 15 2024
+-------------------------------------------------------------------------------------------------
+
+* Switch to using Langevin integrator for GROMACS free energy simulations (`#264 <https://github.com/OpenBioSim/biosimspace/pull/264>`__).
+* Add support for clearing and disabling the IO file cache (`#266 <https://github.com/OpenBioSim/biosimspace/pull/266>`__).
+* Add support for using ``openff-nagl`` to generate partial charges (`#267 <https://github.com/OpenBioSim/biosimspace/pull/267>`__).
+* Fixed non-reproducible search for backbone restraint atom indices (`#270 <https://github.com/OpenBioSim/biosimspace/pull/270>`__).
+* Add support for AMBER as an alchemical free-energy simulation engine (`#272 <https://github.com/OpenBioSim/biosimspace/pull/272>`__).
+* Switch to using ``os.path.join`` to generate directory file names (`#276 <https://github.com/OpenBioSim/biosimspace/pull/276>`__).
+* Make sure the ``fileformat`` property is preserved when creating single molecule systems (`#276 <https://github.com/OpenBioSim/biosimspace/pull/276>`__).
+* Add a ``getRestraintType`` method to the base protocol that returns ``None`` (`#276 <https://github.com/OpenBioSim/biosimspace/pull/276>`__).
+* Add missing ``themostat_time_constant`` kwarg to the :class:`Metadynamics <BioSimSpace.Protocol.Metdynamics>` protocol (`#276 <https://github.com/OpenBioSim/biosimspace/pull/276>`__).
+
+
 `2023.5.1 <https://github.com/openbiosim/biosimspace/compare/2023.5.0...2023.5.1>`_ - Mar 20 2024
 -------------------------------------------------------------------------------------------------
 

doc/source/conf.py

@@ -43,7 +43,7 @@
 
 # General information about the project.
 project = "biosimspace"
-copyright = "2017-2023"
+copyright = "2017-2024"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the

doc/source/contributing/packaging.rst

@@ -4,12 +4,11 @@
 Development process
 ===================
 
-:mod:`BioSimSpace` uses a ``main``, ``devel`` and ``future`` development process,
+:mod:`BioSimSpace` uses a ``main`` and ``devel`` development process,
 using feature branches for all code development.
 
 * ``main`` - this always contains the latest official release.
 * ``devel`` - this always contains the latest development release, which will become the next official release.
-* ``future`` - this contains pull requests that have been accepted, but which are targetted for a future release (i.e. not the next official release)
 
 Code should be developed on a fork or in a feature branch called ``feature_{feature}``.
 When your feature is ready, please submit a pull request against ``devel``. This
@@ -27,29 +26,8 @@ tests, examples and/or tutorial instructions.
   the tutorials or writing a detailed description for the website.
 
 Assuming the CI completes successfully, then one of the release team will
-conduct a code review. The outcome of the review will be one of the following;
-
-1. This feature is ready, and should be part of the next official release. The pull request
-   will be accepted into ``devel``. This will trigger our CI/CD process, building the new dev
-   package and uploading it to `anaconda.org <https://anaconda.org/openbiosim/biosimspace>`__
-   for everyone to use.
-
-2. This feature is good, but it is not yet ready to be part of the next offical release. This
-   could be because the feature is part of a series, and all of the series need to be finished
-   before release. Or because we are in a feature freeze period. Or because you want more time
-   for people to explore and play with the feature before it is officially released (and would
-   then need to be supported, and backwards compatibility maintained). If this is the case (or
-   it is your request) then the pull request will be redirected into the ``future`` branch.
-   Once it (and features that depend on it) are ready, you can then issue a pull request for
-   all of the features at once into ``devel``. It will be noted that each of the individual
-   parts have already been code reviewed, so the process to accept the combination
-   into ``devel`` should be more straightforward.
-
-3. This feature is good, but more work is needed before it can be accepted. This could be
-   because some of the unit tests haven't passed, or the latest version of ``devel`` hasn't
-   been merged. Or there may be changes that are requested that would make the code easier
-   to maintain or to preserve backwards compatibility. If this is the case, then we
-   will engage in conversation with you and will work together to rectify any issues.
+conduct a code review, with the code being merged into ``devel`` if it is
+approved.
 
 Bug fixes or issue fixes are developed on fix branches, called ``fix_{number}`` (again in
 either the main repository or forks). If no `issue thread <https://github.com/OpenBioSim/biosimspace/issues>`__

doc/source/contributing/roadmap.rst

@@ -76,8 +76,6 @@ You can keep up with what we are working on in several ways;
 * Keep an eye on the various ``feature_X`` branches as they appear in the repository. Feel free to initiate
   a conversation on GitHub with the developer who is working on that branch if you want to learn more, or
   want to make suggestions or offer a helping hand.
-* Clone and build your own copy of the ``future`` branch. This is the bleeding edge, and things may change and break.
-  But it is the earliest way to use the future version of :mod:`BioSimSpace`.
 
 Wishlists / suggestions
 =======================