Add all downstream OpenBioSim dependencies.

Author: lohedges

.github/workflows/choose_branch.yaml

@@ -61,7 +61,7 @@ jobs:
           build-args: --help
       #
       - name: Generate recipe
-        run: python ${{ github.workspace }}/actions/generate_recipe.py --features bss emle
+        run: python ${{ github.workspace }}/actions/generate_recipe.py --features obs emle
       #
       - name: Write Python variant config
         shell: bash

.github/workflows/devel.yaml

@@ -54,7 +54,7 @@ jobs:
           build-args: --help
       #
       - name: Generate recipe
-        run: python ${{ github.workspace }}/actions/generate_recipe.py --features bss emle
+        run: python ${{ github.workspace }}/actions/generate_recipe.py --features obs emle
       #
       - name: Write Python variant config
         shell: bash

.github/workflows/main.yaml

@@ -56,7 +56,7 @@ jobs:
           build-args: --help
       #
       - name: Generate recipe
-        run: python ${{ github.workspace }}/actions/generate_recipe.py --features bss emle
+        run: python ${{ github.workspace }}/actions/generate_recipe.py --features obs emle
       #
       - name: Write Python variant config
         shell: bash

.github/workflows/pr.yaml

@@ -56,7 +56,7 @@ jobs:
           build-args: --help
       #
       - name: Generate recipe
-        run: python ${{ github.workspace }}/actions/generate_recipe.py --features bss emle
+        run: python ${{ github.workspace }}/actions/generate_recipe.py --features obs emle
       #
       - name: Write Python variant config
         shell: bash

README.rst

@@ -133,7 +133,7 @@ A small word of warning, the compilation can easily take over an hour!
 Other pixi environments are available depending on your needs:
 
 * ``pixi install -e default`` - core sire dependencies only
-* ``pixi install -e bss`` - include BioSimSpace compatibility dependencies
+* ``pixi install -e obs`` - include downstream OpenBioSim package dependencies
 * ``pixi install -e emle`` - include EMLE engine dependencies
 * ``pixi install -e dev`` - all of the above plus test dependencies
 

actions/generate_recipe.py

@@ -5,7 +5,7 @@
 appropriate if/then conditional blocks for platform-specific dependencies.
 
 Usage:
-    python actions/generate_recipe.py [--features bss emle]
+    python actions/generate_recipe.py [--features obs emle]
 
 The --features flag controls which optional dependency groups are
 included in the host section of the recipe.
@@ -66,7 +66,7 @@ def parse_args():
         "--features",
         nargs="*",
         default=[],
-        help="Optional feature groups to include (e.g. bss emle)",
+        help="Optional feature groups to include (e.g. obs emle)",
     )
     parser.add_argument(
         "--pixi-toml",

doc/source/install.rst

@@ -317,13 +317,13 @@ install all required dependencies, including compilers:
 Several environments are available depending on your needs:
 
 * ``default`` - core sire dependencies only
-* ``bss`` - include `BioSimSpace <https://biosimspace.org>`__ compatibility dependencies
+* ``obs`` - include downstream OpenBioSim package dependencies (e.g. BioSimSpace)
 * ``emle`` - include EMLE engine dependencies
-* ``full`` - include both BSS and EMLE dependencies
+* ``full`` - include both OBS and EMLE dependencies
 * ``dev`` - all of the above plus test dependencies
 
 If you plan to install `BioSimSpace <https://biosimspace.org>`__ on
-top of :mod:`sire`, use at least the ``bss`` or ``dev`` environment.
+top of :mod:`sire`, use at least the ``obs`` or ``dev`` environment.
 This ensures that incompatible versions of shared dependencies are not
 accidentally installed.
 
@@ -404,7 +404,7 @@ definitions:
 
 .. code-block:: bash
 
-   $ python actions/generate_recipe.py --features bss emle
+   $ python actions/generate_recipe.py --features obs emle
 
 This creates ``recipes/sire/recipe.yaml``. The ``--features`` flag controls
 which optional dependency groups are included. Omit features to build a
@@ -413,7 +413,7 @@ lighter package:
 .. code-block:: bash
 
    $ python actions/generate_recipe.py              # core only
-   $ python actions/generate_recipe.py --features bss   # core + BioSimSpace
+   $ python actions/generate_recipe.py --features obs   # core + BioSimSpace
 
 You can edit the generated ``recipe.yaml`` to further customise the
 dependency pins if needed.

pixi.toml

@@ -52,17 +52,18 @@ kartograf = ">=1.0.0"
 pybind11 = "==2.11.1"
 
 # =============================================================================
-# BSS (BioSimSpace) feature
-# These aren't needed by Sire, but allow it to be built in a self-consistent
-# way so that BioSimSpace can be installed on top of it.
+# OBS (OpenBioSim) feature
+# Dependencies for downstream OpenBioSim packages (biosimspace, ghostly, loch, somd2).
 # =============================================================================
-[feature.bss.dependencies]
+[feature.obs.dependencies]
 openmmtools = ">=0.21.5"
 configargparse = "*"
 ipywidgets = "*"
 kcombu_bss = "*"
+loguru = "*"
 lomap2 = "*"
 nglview = "*"
+numba = "*"
 openff-interchange-base = "*"
 openff-toolkit-base = "*"
 parmed = "*"
@@ -71,26 +72,30 @@ pydot = "*"
 pygtail = "*"
 pyyaml = "*"
 
-[feature.bss.target.linux-64.dependencies]
+[feature.obs.target.linux-64.dependencies]
 ambertools = ">=22"
 gromacs = "*"
 alchemlyb = "*"
 mdtraj = "*"
 mdanalysis = "*"
+# loch/somd2 deps (pycuda/pyopencl only available on linux-64)
+pyopencl = "*"
+pycuda = "*"
+nvidia-ml-py = "*"
 
-[feature.bss.target.linux-aarch64.dependencies]
+[feature.obs.target.linux-aarch64.dependencies]
 ambertools = ">=22"
 gromacs = "*"
 # alchemlyb, mdtraj, mdanalysis not available on linux-aarch64
 
-[feature.bss.target.osx-arm64.dependencies]
+[feature.obs.target.osx-arm64.dependencies]
 ambertools = ">=22"
 # gromacs not available on osx-arm64
 alchemlyb = "*"
 mdtraj = "*"
 mdanalysis = "*"
 
-[feature.bss.target.win-64.dependencies]
+[feature.obs.target.win-64.dependencies]
 # ambertools and gromacs not available on Windows
 alchemlyb = "*"
 mdtraj = "*"
@@ -150,8 +155,8 @@ kartograf = ">=1.0.0"
 # =============================================================================
 [environments]
 default = []
-bss = ["bss"]
+obs = ["obs"]
 emle = ["emle"]
-full = ["bss", "emle"]
+full = ["obs", "emle"]
 test = ["test"]
-dev = ["bss", "emle", "test"]
+dev = ["obs", "emle", "test"]