From cf31cc4cf5c1b4fed5f8be9557b5ba96c8650b51 Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Thu, 5 Feb 2026 10:22:29 +0000
Subject: [PATCH 01/24] Switch to pixi and rattler build.

---
 .github/workflows/devel.yaml          | 59 ++++++++++--------
 .github/workflows/main.yaml           | 57 ++++++++++-------
 .github/workflows/pr.yaml             | 56 +++++++++--------
 README.md                             | 55 ++++++++++++----
 actions/update_recipe.py              | 90 +++++++++++++++------------
 actions/upload_package.py             | 60 ++++++++----------
 environment.yaml                      | 15 -----
 environment_macos.yaml                | 13 ----
 pixi.toml                             | 25 ++++++++
 recipes/somd2/conda_build_config.yaml |  3 -
 recipes/somd2/recipe.yaml             | 68 ++++++++++++++++++++
 recipes/somd2/template.yaml           | 80 ------------------------
 12 files changed, 306 insertions(+), 275 deletions(-)
 delete mode 100644 environment.yaml
 delete mode 100644 environment_macos.yaml
 create mode 100644 pixi.toml
 delete mode 100644 recipes/somd2/conda_build_config.yaml
 create mode 100644 recipes/somd2/recipe.yaml
 delete mode 100644 recipes/somd2/template.yaml

diff --git a/.github/workflows/devel.yaml b/.github/workflows/devel.yaml
index d25fb76..48b6203 100644
--- a/.github/workflows/devel.yaml
+++ b/.github/workflows/devel.yaml
@@ -3,7 +3,7 @@ name: Release Devel
 on:
   workflow_dispatch:
   push:
-    branches: [ devel ]
+    branches: [devel]
 
 jobs:
   build:
@@ -18,11 +18,9 @@ jobs:
           - { 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
           - platform:
               { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
-            python-version: "3.12"  # MacOS can't run 3.12 yet... We want 3.10 and 3.11
+            python-version: "3.12"  # MacOS can't run 3.12 yet... We want 3.10 and 3.11
     environment:
       name: somd2-build
     defaults:
@@ -32,30 +30,37 @@ jobs:
       SIRE_DONT_PHONEHOME: 1
       SIRE_SILENT_PHONEHOME: 1
     steps:
-      - uses: conda-incubator/setup-miniconda@v3
+      #
+      - uses: actions/checkout@v4
         with:
-          auto-update-conda: true
-          python-version: ${{ matrix.python-version }}
-          activate-environment: somd2_build
-          miniforge-version: latest
-#
-      - name: Clone the devel branch
-        run: git clone -b devel https://github.com/openbiosim/somd2
-#
-      - name: Setup Conda
-        run: conda install -y -c conda-forge boa anaconda-client packaging
-#
-      - name: Update Conda recipe
-        run: python ${{ github.workspace }}/somd2/actions/update_recipe.py
-#
-      - name: Prepare build location
-        run: mkdir ${{ github.workspace }}/build
-#
-      - name: Build Conda package using conda build
-        run: conda build -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/somd2/recipes/somd2
-#
-      - name: Upload Conda package
-        run: python ${{ github.workspace }}/somd2/actions/upload_package.py
+          fetch-depth: 0
+      #
+      - name: Compute version info
+        run: python ${{ github.workspace }}/actions/update_recipe.py
+      #
+      - name: Create sdist
+        run: pip install build && python -m build --sdist && mv dist/*.tar.gz somd2-source.tar.gz
+        working-directory: ${{ github.workspace }}
+      #
+      - name: Install rattler-build
+        uses: prefix-dev/rattler-build-action@v0.2.34
+        with:
+          tool-version: latest
+          build-args: --help
+      #
+      - name: Write Python variant config
+        shell: bash
+        run: printf 'python:\n  - "${{ matrix.python-version }}"\n' > "${{ github.workspace }}/python_variant.yaml"
+      #
+      - name: Build package using rattler-build
+        shell: bash
+        run: rattler-build build --recipe "${{ github.workspace }}/recipes/somd2" -c conda-forge -c openbiosim/label/dev --variant-config "${{ github.workspace }}/python_variant.yaml"
+      #
+      - name: Install anaconda-client
+        run: python -m pip install anaconda-client
+      #
+      - name: Upload package
+        run: python ${{ github.workspace }}/actions/upload_package.py
         env:
           ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
           ANACONDA_LABEL: dev
diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml
index 088186e..3ad8384 100644
--- a/.github/workflows/main.yaml
+++ b/.github/workflows/main.yaml
@@ -23,7 +23,7 @@ jobs:
         exclude:
           - platform:
               { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
-            python-version: "3.12"  # MacOS can't run 3.12 yet...
+            python-version: "3.12"  # MacOS can't run 3.12 yet...
     environment:
       name: somd2-build
     defaults:
@@ -33,30 +33,39 @@ jobs:
       SIRE_DONT_PHONEHOME: 1
       SIRE_SILENT_PHONEHOME: 1
     steps:
-      - uses: conda-incubator/setup-miniconda@v3
+      #
+      - uses: actions/checkout@v4
         with:
-          auto-update-conda: true
-          python-version: ${{ matrix.python-version }}
-          activate-environment: somd2_build
-          miniforge-version: latest
-#
-      - name: Clone the main branch
-        run: git clone -b main https://github.com/openbiosim/somd2
-#
-      - name: Setup Conda
-        run: conda install -y -c conda-forge boa anaconda-client packaging
-#
-      - name: Update Conda recipe
-        run: python ${{ github.workspace }}/somd2/actions/update_recipe.py
-#
-      - name: Prepare build location
-        run: mkdir ${{ github.workspace }}/build
-#
-      - name: Build Conda package using conda build
-        run: conda build -c conda-forge -c openbiosim/label/main ${{ github.workspace }}/somd2/recipes/somd2
-#
-      - name: Upload Conda package
-        run: python ${{ github.workspace }}/somd2/actions/upload_package.py
+          ref: main
+          fetch-depth: 0
+      #
+      - name: Compute version info
+        run: python ${{ github.workspace }}/actions/update_recipe.py
+      #
+      - name: Create sdist
+        run: pip install build && python -m build --sdist && mv dist/*.tar.gz somd2-source.tar.gz
+        working-directory: ${{ github.workspace }}
+      #
+      - name: Install rattler-build
+        uses: prefix-dev/rattler-build-action@v0.2.34
+        with:
+          tool-version: latest
+          build-args: --help
+      #
+      - name: Write Python variant config
+        shell: bash
+        run: printf 'python:\n  - "${{ matrix.python-version }}"\n' > "${{ github.workspace }}/python_variant.yaml"
+      #
+      - name: Build package using rattler-build
+        shell: bash
+        run: rattler-build build --recipe "${{ github.workspace }}/recipes/somd2" -c conda-forge -c openbiosim/label/main --variant-config "${{ github.workspace }}/python_variant.yaml"
+      #
+      - name: Install anaconda-client
+        run: python -m pip install anaconda-client
+        if: github.event.inputs.upload_packages == 'true'
+      #
+      - name: Upload package
+        run: python ${{ github.workspace }}/actions/upload_package.py
         env:
           ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
           ANACONDA_LABEL: main
diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index 6191ca5..b6ed02e 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -17,14 +17,12 @@ jobs:
           - { name: "linux", os: "ubuntu-latest", shell: "bash -l {0}" }
           - { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
         exclude:
-          # Exclude all but the latest Python from all
-          # but Linux
           - platform:
               { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
             python-version: "3.10"
           - platform:
               { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
-            python-version: "3.12"  # MacOS can't run 3.12 yet...
+            python-version: "3.12"  # MacOS can't run 3.12 yet...
     environment:
       name: somd2-build
     defaults:
@@ -33,31 +31,35 @@ jobs:
     env:
       SIRE_DONT_PHONEHOME: 1
       SIRE_SILENT_PHONEHOME: 1
-      REPO: "${{ github.event.pull_request.head.repo.full_name || github.repository }}"
     steps:
-      - uses: conda-incubator/setup-miniconda@v3
+      #
+      - uses: actions/checkout@v4
         with:
-          auto-update-conda: true
-          python-version: ${{ matrix.python-version }}
-          activate-environment: somd2_build
-          miniforge-version: latest
-#
-      - name: Clone the feature branch
-        run: git clone -b ${{ github.head_ref }} --single-branch https://github.com/${{ env.REPO }} somd2
-#
-      - name: Setup Conda
-        run: conda install -y -c conda-forge boa anaconda-client packaging
-#
-      - name: Update Conda recipe
-        run: python ${{ github.workspace }}/somd2/actions/update_recipe.py
-#
-      - name: Prepare build location
-        run: mkdir ${{ github.workspace }}/build
-#
-      - name: Build Conda package using conda build using main channel
+          fetch-depth: 0
+      #
+      - name: Compute version info
+        run: python ${{ github.workspace }}/actions/update_recipe.py
+      #
+      - name: Create sdist
+        run: pip install build && python -m build --sdist && mv dist/*.tar.gz somd2-source.tar.gz
+        working-directory: ${{ github.workspace }}
+      #
+      - name: Install rattler-build
+        uses: prefix-dev/rattler-build-action@v0.2.34
+        with:
+          tool-version: latest
+          build-args: --help
+      #
+      - name: Write Python variant config
+        shell: bash
+        run: printf 'python:\n  - "${{ matrix.python-version }}"\n' > "${{ github.workspace }}/python_variant.yaml"
+      #
+      - name: Build package using rattler-build (main channel)
         if: ${{ github.base_ref == 'main' }}
-        run: conda build -c conda-forge -c openbiosim/label/main ${{ github.workspace }}/somd2/recipes/somd2
-#
-      - name: Build Conda package using conda build using dev channel
+        shell: bash
+        run: rattler-build build --recipe "${{ github.workspace }}/recipes/somd2" -c conda-forge -c openbiosim/label/main --variant-config "${{ github.workspace }}/python_variant.yaml"
+      #
+      - name: Build package using rattler-build (dev channel)
         if: ${{ github.base_ref != 'main' }}
-        run: conda build -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/somd2/recipes/somd2
+        shell: bash
+        run: rattler-build build --recipe "${{ github.workspace }}/recipes/somd2" -c conda-forge -c openbiosim/label/dev --variant-config "${{ github.workspace }}/python_variant.yaml"
diff --git a/README.md b/README.md
index f8174c8..3493b61 100644
--- a/README.md
+++ b/README.md
@@ -9,35 +9,66 @@ simulations. Built on top of [Sire](https://github.com/OpenBioSim/sire) and [Ope
 
 ## Installation
 
-First create a conda environment using the provided environment file:
+### Conda package
+
+Install `somd2` directly from the `openbiosim` channel:
 
 ```
-conda env create -f environment.yaml
+conda install -c conda-forge -c openbiosim somd2
 ```
 
-(We recommend using [Miniforge](https://github.com/conda-forge/miniforge).)
+Or, for the development version:
 
-> [!NOTE]
-> On macOS, you will need to use the `environment_macos.yaml` file instead.
+```
+conda install -c conda-forge -c openbiosim/label/dev somd2
+```
 
-Now install `somd2` into the environment:
+### Installing from source (standalone)
+
+To install from source using [pixi](https://pixi.sh), which will
+automatically create an environment with all required dependencies
+(including pre-built [Sire](https://github.com/OpenBioSim/sire),
+[BioSimSpace](https://github.com/OpenBioSim/biosimspace),
+[Ghostly](https://github.com/OpenBioSim/ghostly), and
+[Loch](https://github.com/OpenBioSim/loch)):
 
 ```
-conda activate somd2
-pip install --editable .
+git clone https://github.com/openbiosim/somd2
+cd somd2
+pixi install
+pixi shell
+pip install -e .
 ```
 
-Alternatively, to install into an existing conda environment:
+### Installing from source (full OpenBioSim development)
+
+If you are developing across the full OpenBioSim stack, first install
+[Sire](https://github.com/OpenBioSim/sire) from source by following the
+instructions [here](https://github.com/OpenBioSim/sire#installation), then
+activate its pixi environment:
 
 ```
-conda install -c conda-forge -c openbiosim somd2
+pixi shell --manifest-path /path/to/sire/pixi.toml -e dev
 ```
 
-Or, for the development version:
+You may also need to install other packages from source, e.g.
+[BioSimSpace](https://github.com/OpenBioSim/biosimspace),
+[Ghostly](https://github.com/OpenBioSim/ghostly), and
+[Loch](https://github.com/OpenBioSim/loch):
 
 ```
-conda install -c conda-forge -c openbiosim/label/dev somd2
+pip install -e /path/to/biosimspace/python
+pip install -e /path/to/ghostly
+pip install -e /path/to/loch
+```
+
+Then install `somd2` into the environment:
+
 ```
+pip install -e .
+```
+
+### Testing
 
 You should now have a `somd2` executable in your path. To test, run:
 
diff --git a/actions/update_recipe.py b/actions/update_recipe.py
index ac3ff96..629369a 100644
--- a/actions/update_recipe.py
+++ b/actions/update_recipe.py
@@ -1,50 +1,58 @@
-import sys
+"""Compute git version info for rattler-build.
+
+This script computes GIT_DESCRIBE_TAG and GIT_DESCRIBE_NUMBER from the
+git history and outputs them in GitHub Actions format for setting
+environment variables.
+
+It also writes a _version.py file so that versioningit has a fallback
+when .git is not available (e.g., when rattler-build excludes it).
+"""
+
 import os
 import subprocess
+import sys
 
-# Get the name of the script.
 script = os.path.abspath(sys.argv[0])
-
-# we want to import the 'get_requirements' package from this directory
-sys.path.insert(0, os.path.dirname(script))
-
-# go up one directories to get the source directory
-# (this script is in BioSimSpace/actions/)
 srcdir = os.path.dirname(os.path.dirname(script))
-
-condadir = os.path.join(srcdir, "recipes", "somd2")
-
-print(f"conda recipe in {condadir}")
-
-# Store the name of the recipe and template YAML files.
-recipe = os.path.join(condadir, "meta.yaml")
-template = os.path.join(condadir, "template.yaml")
-
 gitdir = os.path.join(srcdir, ".git")
 
 
 def run_cmd(cmd):
-    p = subprocess.Popen(cmd.split(), stdout=subprocess.PIPE)
-    return str(p.stdout.read().decode("utf-8")).lstrip().rstrip()
-
-
-# Get the remote.
-remote = run_cmd(
-    f"git --git-dir={gitdir} --work-tree={srcdir} config --get remote.origin.url"
-)
-print(remote)
-
-# Get the branch.
-branch = run_cmd(
-    f"git --git-dir={gitdir} --work-tree={srcdir} rev-parse --abbrev-ref HEAD"
-)
-print(branch)
-
-lines = open(template, "r").readlines()
-
-with open(recipe, "w") as FILE:
-    for line in lines:
-        line = line.replace("SOMD2_REMOTE", remote)
-        line = line.replace("SOMD2_BRANCH", branch)
-
-        FILE.write(line)
+    p = subprocess.Popen(cmd.split(), stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+    stdout, _ = p.communicate()
+    return stdout.decode("utf-8").strip()
+
+
+# Get the full git describe output (e.g., "2024.1.0-5-gabcdef" or "2024.1.0")
+describe = run_cmd(f"git --git-dir={gitdir} --work-tree={srcdir} describe --tags")
+
+if "-" in describe:
+    # Format: tag-number-hash (e.g., "2024.1.0-5-gabcdef")
+    parts = describe.rsplit("-", 2)
+    tag = parts[0]
+    number = parts[1]
+    rev = parts[2]  # e.g., "gabcdef"
+    version = f"{tag}+{number}.{rev}"
+else:
+    # Exactly on a tag
+    tag = describe
+    number = "0"
+    version = tag
+
+print(f"GIT_DESCRIBE_TAG={tag}")
+print(f"GIT_DESCRIBE_NUMBER={number}")
+print(f"Version={version}")
+
+# Write to GITHUB_ENV if running in GitHub Actions
+github_env = os.environ.get("GITHUB_ENV")
+if github_env:
+    with open(github_env, "a") as f:
+        f.write(f"GIT_DESCRIBE_TAG={tag}\n")
+        f.write(f"GIT_DESCRIBE_NUMBER={number}\n")
+    print("Exported to GITHUB_ENV")
+
+# Write _version.py for versioningit fallback
+version_file = os.path.join(srcdir, "src", "somd2", "_version.py")
+with open(version_file, "w") as f:
+    f.write(f'__version__ = "{version}"\n')
+print(f"Wrote {version_file}")
diff --git a/actions/upload_package.py b/actions/upload_package.py
index 799638c..22547ad 100644
--- a/actions/upload_package.py
+++ b/actions/upload_package.py
@@ -1,16 +1,18 @@
+"""Upload built packages to the openbiosim Anaconda Cloud channel."""
+
 import os
 import sys
 import glob
+import subprocess
 
 script = os.path.abspath(sys.argv[0])
 
-# go up one directories to get the source directory
-# (this script is in somd2/actions/)
+# Go up one directory to get the source directory.
 srcdir = os.path.dirname(os.path.dirname(script))
 
 print(f"SOMD2 source is in {srcdir}\n")
 
-# Get the anaconda token to authorise uploads
+# Get the anaconda token to authorise uploads.
 if "ANACONDA_TOKEN" in os.environ:
     conda_token = os.environ["ANACONDA_TOKEN"]
 else:
@@ -22,42 +24,30 @@
 else:
     conda_label = "dev"
 
-# get the root conda directory
-conda = os.environ["CONDA"]
-
-# Set the path to the conda-bld directory.
-conda_bld = os.path.join(conda, "envs", "somd2_build", "conda-bld")
-
-print(f"conda_bld = {conda_bld}")
+# Search for rattler-build output first.
+packages = glob.glob(os.path.join("output", "**", "*.conda"), recursive=True)
 
-# Find the packages to upload
-somd2_pkg = glob.glob(os.path.join(conda_bld, "*-*", "somd2-*.tar.bz2"))
+# Fall back to conda-bld output.
+if not packages:
+    if "CONDA" in os.environ:
+        conda = os.environ["CONDA"]
+        conda_bld = os.path.join(conda, "envs", "somd2_build", "conda-bld")
+        packages = glob.glob(
+            os.path.join(conda_bld, "**", "somd2-*.tar.bz2"), recursive=True
+        )
 
-if len(somd2_pkg) == 0:
+if not packages:
     print("No somd2 packages to upload?")
     sys.exit(-1)
 
-packages = somd2_pkg
-
-print(f"Uploading packages:")
-print(" * ", "\n *  ".join(packages))
-
-packages = " ".join(packages)
-
-
-def run_cmd(cmd):
-    import subprocess
-
-    p = subprocess.Popen(cmd.split(), stdout=subprocess.PIPE)
-    return str(p.stdout.read().decode("utf-8")).lstrip().rstrip()
+print("Uploading packages:")
+for pkg in packages:
+    print(f"  * {pkg}")
 
-
-gitdir = os.path.join(srcdir, ".git")
-
-tag = run_cmd(f"git --git-dir={gitdir} --work-tree={srcdir} tag --contains")
+packages_str = " ".join(packages)
 
 # Upload the packages to the openbiosim channel on Anaconda Cloud.
-cmd = f"anaconda --token {conda_token} upload --user openbiosim --label {conda_label} --force {packages}"
+cmd = f"anaconda --token {conda_token} upload --user openbiosim --label {conda_label} --force {packages_str}"
 
 print(f"\nUpload command:\n\n{cmd}\n")
 
@@ -65,8 +55,12 @@ def run_cmd(cmd):
     print("Not uploading as the ANACONDA_TOKEN is not set!")
     sys.exit(-1)
 
-output = run_cmd(cmd)
 
-print(output)
+def run_cmd(cmd):
+    p = subprocess.Popen(cmd.split(), stdout=subprocess.PIPE)
+    return str(p.stdout.read().decode("utf-8")).lstrip().rstrip()
+
 
+output = run_cmd(cmd)
+print(output)
 print("Package uploaded!")
diff --git a/environment.yaml b/environment.yaml
deleted file mode 100644
index e509e02..0000000
--- a/environment.yaml
+++ /dev/null
@@ -1,15 +0,0 @@
-name: somd2
-
-channels:
-  - conda-forge
-  - openbiosim/label/dev
-
-dependencies:
-  - biosimspace
-  - ghostly
-  - filelock
-  - loch
-  - loguru
-  - numba
-  - nvidia-ml-py
-  - versioningit
diff --git a/environment_macos.yaml b/environment_macos.yaml
deleted file mode 100644
index 19083a3..0000000
--- a/environment_macos.yaml
+++ /dev/null
@@ -1,13 +0,0 @@
-name: somd2
-
-channels:
-  - conda-forge
-  - openbiosim/label/dev
-
-dependencies:
-  - biosimspace
-  - ghostly
-  - filelock
-  - loguru
-  - numba
-  - versioningit
diff --git a/pixi.toml b/pixi.toml
new file mode 100644
index 0000000..6058f49
--- /dev/null
+++ b/pixi.toml
@@ -0,0 +1,25 @@
+[workspace]
+name = "somd2"
+channels = ["conda-forge", "openbiosim/label/dev"]
+# No Windows - depends on loch which requires pycuda/pyopencl
+platforms = ["linux-64", "osx-arm64"]
+
+[dependencies]
+python = ">=3.10"
+biosimspace = "*"
+ghostly = "*"
+loch = "*"
+loguru = "*"
+numba = "*"
+
+[target.linux-64.dependencies]
+nvidia-ml-py = "*"
+
+[feature.test.dependencies]
+pytest = "*"
+black = "*"
+
+[environments]
+default = []
+test = ["test"]
+dev = ["test"]
diff --git a/recipes/somd2/conda_build_config.yaml b/recipes/somd2/conda_build_config.yaml
deleted file mode 100644
index 3e8e203..0000000
--- a/recipes/somd2/conda_build_config.yaml
+++ /dev/null
@@ -1,3 +0,0 @@
-pin_run_as_build:
-  sire:
-    max_pin: x.x
diff --git a/recipes/somd2/recipe.yaml b/recipes/somd2/recipe.yaml
new file mode 100644
index 0000000..34bfd3f
--- /dev/null
+++ b/recipes/somd2/recipe.yaml
@@ -0,0 +1,68 @@
+context:
+  name: somd2
+
+package:
+  name: ${{ name }}
+  version: ${{ env.get('GIT_DESCRIBE_TAG', default='PR') }}
+
+source:
+  path: ../../somd2-source.tar.gz
+
+build:
+  number: ${{ env.get('GIT_DESCRIBE_NUMBER', default='0') }}
+  script: python -m pip install . --no-deps --ignore-installed -vv
+
+requirements:
+  host:
+    - pip
+    - python
+    - setuptools
+    - versioningit
+  run:
+    - biosimspace
+    - ghostly
+    - loch
+    - loguru
+    - numba
+    - numpy <2.3  # Remove when nglview >=4.1 is released
+    - python
+    - if: linux
+      then:
+        - nvidia-ml-py
+
+tests:
+  - python:
+      imports:
+        - if: linux
+          then:
+            - somd2
+  - script:
+      - if: linux and x86_64
+        then:
+          - pytest -vvv --color=yes --black src/somd2
+      - if: linux
+        then:
+          - pytest -vvv --color=yes --import-mode=importlib ./tests
+    files:
+      source:
+        - src/somd2/
+        - tests/
+    requirements:
+      run:
+        - pytest
+        - if: linux and x86_64
+          then:
+            - black ==25
+            - pytest-black
+
+about:
+  homepage: https://github.com/openbiosim/somd2
+  license: GPL-3.0-or-later
+  license_file: LICENSE
+  summary: "GPU accelerated free-energy perturbation simulation engine."
+  repository: https://github.com/openbiosim/somd2
+  documentation: https://github.com/openbiosim/somd2
+
+extra:
+  recipe-maintainers:
+    - lohedges
diff --git a/recipes/somd2/template.yaml b/recipes/somd2/template.yaml
deleted file mode 100644
index 27c3f78..0000000
--- a/recipes/somd2/template.yaml
+++ /dev/null
@@ -1,80 +0,0 @@
-{% set name = "somd2" %}
-
-package:
-  name: {{ name }}
-  version: {{ environ.get('GIT_DESCRIBE_TAG', 'PR') }}
-
-source:
-  git_url: SOMD2_REMOTE
-  git_tag: SOMD2_BRANCH
-
-build:
-  number: {{ environ.get('GIT_DESCRIBE_NUMBER', 0) }}
-  script: {{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv
-
-requirements:
-  host:
-    - biosimspace
-    - ghostly
-    - loch
-    - loguru
-    - pip
-    - python
-    - numba
-    - nvidia-ml-py  # [linux]
-    - setuptools
-    - sire
-    - versioningit
-  run:
-    - biosimspace
-    - ghostly
-    - loch
-    - loguru
-    - numba
-    - nvidia-ml-py  # [linux]
-    - python
-    - sire
-
-test:
-  script_env:
-    - SIRE_DONT_PHONEHOME
-    - SIRE_SILENT_PHONEHOME
-  requires:
-    - black == 25   # [linux and x86_64 and py==311]
-    - pytest
-    - pytest-black  # [linux and x86_64 and py==311]
-  imports:
-    - somd2         # [linux]
-  source_files:
-    - src/somd2
-    - tests
-  commands:
-    - pytest -vvv --color=yes --black src/somd2             # [linux and x86_64 and py==311]
-    - pytest -vvv --color=yes --import-mode=importlib tests # [linux]
-
-about:
-  home: https://github.com/openbiosim/somd2
-  license: GPL-3.0-or-later
-  license_file: '{{ environ["RECIPE_DIR"] }}/LICENSE'
-  summary: "GPU accelerated free-energy pertubation simulation engine"
-  dev_url: https://github.com/openbiosim/somd2
-  doc_url: https://github.com/openbiosim/somd2
-  description: |
-                somd2 is an open-source GPU accelerated molecular dynamics engine for
-                alchemical free-energy calculations. Built on top of Sire, BioSimSpace,
-                and OpenMM.
-
-                `conda install -c conda-forge -c openbiosim somd2`
-
-                To install the development version:
-
-                `conda install -c conda-forge -c openbiosim/label/dev somd2`
-
-                When updating the development version it is generally advised to
-                update Sire at the same time:
-
-                `conda install -c conda-forge -c openbiosim/label/dev somd2 sire`
-
-extra:
-  recipe-maintainers:
-    - lohedges

From ec644dbb4e73d7e5ad2ba2d52411e9dbcd9e683e Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Fri, 6 Feb 2026 14:10:26 +0000
Subject: [PATCH 02/24] Add auto-generated version file to gitignore.

---
 .gitignore | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.gitignore b/.gitignore
index e1a8d07..dd1d570 100644
--- a/.gitignore
+++ b/.gitignore
@@ -37,3 +37,6 @@ output.yaml
 
 # Conda recipe (it is auto-generated)
 recipes/somd2/meta.yaml
+
+# Auto-generated version file
+src/somd2/_version.py

From 814cd4720b9acfe23ed5ffda3416663bd238a265 Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Fri, 6 Feb 2026 20:09:18 +0000
Subject: [PATCH 03/24] Save the perturbed system to the output directory.

---
 src/somd2/runner/_base.py | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/src/somd2/runner/_base.py b/src/somd2/runner/_base.py
index 14912eb..0c9db05 100644
--- a/src/somd2/runner/_base.py
+++ b/src/somd2/runner/_base.py
@@ -528,7 +528,17 @@ def __init__(self, system, config):
             self._is_restart = False
             self._cleanup()
 
-        # Save config whenever 'configure' is called to keep it up to date.
+        if self._config.replica_exchange and self._config.perturbed_system is not None:
+            # Check whether the perturbed system was loaded from file. If not
+            # we need to save to the output directory and update the config to
+            # point to the new file.
+            if self._config._perturbed_system_file is None:
+                filename = _Path(self._config.output_directory) / "perturbed_system.s3"
+                _sr.stream.save(perturbed_system, perturbed_system_file)
+                self._config._perturbed_system_file = str(filename)
+                _logger.info(f"Saving perturbed system to {perturbed_system_file}")
+
+        # Write YAML configuration file to the output directory.
         if self._config.write_config:
             _dict_to_yaml(
                 self._config.as_dict(),

From de4a6a32e0a62de73e54789bdad59274b71e05e4 Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Fri, 6 Feb 2026 20:09:53 +0000
Subject: [PATCH 04/24] Only convert if a filename has been set.

---
 src/somd2/config/_config.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/somd2/config/_config.py b/src/somd2/config/_config.py
index 52babac..fed794c 100644
--- a/src/somd2/config/_config.py
+++ b/src/somd2/config/_config.py
@@ -655,7 +655,10 @@ def as_dict(self, sire_compatible=False):
 
         # Use the path for the perturbed_system option, since the system
         # isn't serializable.
-        if self.perturbed_system is not None:
+        if (
+            self.perturbed_system is not None
+            and self._perturbed_system_file is not None
+        ):
             d["perturbed_system"] = str(self._perturbed_system_file)
             d.pop("perturbed_system_file", None)
 

From 2ac817034b686166b1abbf185e68409a828e32b3 Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Mon, 9 Feb 2026 09:13:04 +0000
Subject: [PATCH 05/24] Fix install path.

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 3493b61..3bd2805 100644
--- a/README.md
+++ b/README.md
@@ -57,7 +57,7 @@ You may also need to install other packages from source, e.g.
 [Loch](https://github.com/OpenBioSim/loch):
 
 ```
-pip install -e /path/to/biosimspace/python
+pip install -e /path/to/biosimspace
 pip install -e /path/to/ghostly
 pip install -e /path/to/loch
 ```

From b34748f73a84c5bb7b371efcc4cd0a971bdef827 Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Mon, 9 Feb 2026 09:43:27 +0000
Subject: [PATCH 06/24] Remove numpy pin.

---
 recipes/somd2/recipe.yaml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/recipes/somd2/recipe.yaml b/recipes/somd2/recipe.yaml
index 34bfd3f..b57509b 100644
--- a/recipes/somd2/recipe.yaml
+++ b/recipes/somd2/recipe.yaml
@@ -24,7 +24,6 @@ requirements:
     - loch
     - loguru
     - numba
-    - numpy <2.3  # Remove when nglview >=4.1 is released
     - python
     - if: linux
       then:

From 08f08796dde6ca1c102cd15b2ce015b489b6475d Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Mon, 9 Feb 2026 12:57:14 +0000
Subject: [PATCH 07/24] Fix shell quoting.

---
 .github/workflows/devel.yaml | 7 +++++--
 .github/workflows/main.yaml  | 7 +++++--
 .github/workflows/pr.yaml    | 3 ++-
 3 files changed, 12 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/devel.yaml b/.github/workflows/devel.yaml
index 48b6203..c936033 100644
--- a/.github/workflows/devel.yaml
+++ b/.github/workflows/devel.yaml
@@ -36,7 +36,8 @@ jobs:
           fetch-depth: 0
       #
       - name: Compute version info
-        run: python ${{ github.workspace }}/actions/update_recipe.py
+        shell: bash
+        run: python "${{ github.workspace }}/actions/update_recipe.py"
       #
       - name: Create sdist
         run: pip install build && python -m build --sdist && mv dist/*.tar.gz somd2-source.tar.gz
@@ -57,10 +58,12 @@ jobs:
         run: rattler-build build --recipe "${{ github.workspace }}/recipes/somd2" -c conda-forge -c openbiosim/label/dev --variant-config "${{ github.workspace }}/python_variant.yaml"
       #
       - name: Install anaconda-client
+        shell: bash
         run: python -m pip install anaconda-client
       #
       - name: Upload package
-        run: python ${{ github.workspace }}/actions/upload_package.py
+        shell: bash
+        run: python "${{ github.workspace }}/actions/upload_package.py"
         env:
           ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
           ANACONDA_LABEL: dev
diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml
index 3ad8384..5cdcc46 100644
--- a/.github/workflows/main.yaml
+++ b/.github/workflows/main.yaml
@@ -40,7 +40,8 @@ jobs:
           fetch-depth: 0
       #
       - name: Compute version info
-        run: python ${{ github.workspace }}/actions/update_recipe.py
+        shell: bash
+        run: python "${{ github.workspace }}/actions/update_recipe.py"
       #
       - name: Create sdist
         run: pip install build && python -m build --sdist && mv dist/*.tar.gz somd2-source.tar.gz
@@ -61,11 +62,13 @@ jobs:
         run: rattler-build build --recipe "${{ github.workspace }}/recipes/somd2" -c conda-forge -c openbiosim/label/main --variant-config "${{ github.workspace }}/python_variant.yaml"
       #
       - name: Install anaconda-client
+        shell: bash
         run: python -m pip install anaconda-client
         if: github.event.inputs.upload_packages == 'true'
       #
       - name: Upload package
-        run: python ${{ github.workspace }}/actions/upload_package.py
+        shell: bash
+        run: python "${{ github.workspace }}/actions/upload_package.py"
         env:
           ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
           ANACONDA_LABEL: main
diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index b6ed02e..0cab3e2 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -38,7 +38,8 @@ jobs:
           fetch-depth: 0
       #
       - name: Compute version info
-        run: python ${{ github.workspace }}/actions/update_recipe.py
+        shell: bash
+        run: python "${{ github.workspace }}/actions/update_recipe.py"
       #
       - name: Create sdist
         run: pip install build && python -m build --sdist && mv dist/*.tar.gz somd2-source.tar.gz

From 749f31b6ffe7c008afa3a96f4e1fdee02e55df39 Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Mon, 9 Feb 2026 13:03:27 +0000
Subject: [PATCH 08/24] Use relative paths to avoid path mangling.

---
 .github/workflows/devel.yaml | 4 ++--
 .github/workflows/main.yaml  | 4 ++--
 .github/workflows/pr.yaml    | 2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/devel.yaml b/.github/workflows/devel.yaml
index c936033..5248fd1 100644
--- a/.github/workflows/devel.yaml
+++ b/.github/workflows/devel.yaml
@@ -37,7 +37,7 @@ jobs:
       #
       - name: Compute version info
         shell: bash
-        run: python "${{ github.workspace }}/actions/update_recipe.py"
+        run: python actions/update_recipe.py
       #
       - name: Create sdist
         run: pip install build && python -m build --sdist && mv dist/*.tar.gz somd2-source.tar.gz
@@ -63,7 +63,7 @@ jobs:
       #
       - name: Upload package
         shell: bash
-        run: python "${{ github.workspace }}/actions/upload_package.py"
+        run: python actions/upload_package.py
         env:
           ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
           ANACONDA_LABEL: dev
diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml
index 5cdcc46..685826e 100644
--- a/.github/workflows/main.yaml
+++ b/.github/workflows/main.yaml
@@ -41,7 +41,7 @@ jobs:
       #
       - name: Compute version info
         shell: bash
-        run: python "${{ github.workspace }}/actions/update_recipe.py"
+        run: python actions/update_recipe.py
       #
       - name: Create sdist
         run: pip install build && python -m build --sdist && mv dist/*.tar.gz somd2-source.tar.gz
@@ -68,7 +68,7 @@ jobs:
       #
       - name: Upload package
         shell: bash
-        run: python "${{ github.workspace }}/actions/upload_package.py"
+        run: python actions/upload_package.py
         env:
           ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
           ANACONDA_LABEL: main
diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index 0cab3e2..d5a7531 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -39,7 +39,7 @@ jobs:
       #
       - name: Compute version info
         shell: bash
-        run: python "${{ github.workspace }}/actions/update_recipe.py"
+        run: python actions/update_recipe.py
       #
       - name: Create sdist
         run: pip install build && python -m build --sdist && mv dist/*.tar.gz somd2-source.tar.gz

From d375246d40f562210684c3a2742fca0602fcffc6 Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Wed, 11 Feb 2026 09:26:45 +0000
Subject: [PATCH 09/24] Add linting tools to dev environment.

---
 pixi.toml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/pixi.toml b/pixi.toml
index 6058f49..ccc4f00 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -19,7 +19,11 @@ nvidia-ml-py = "*"
 pytest = "*"
 black = "*"
 
+[feature.lint.dependencies]
+pre-commit = "*"
+ruff = "*"
+
 [environments]
 default = []
 test = ["test"]
-dev = ["test"]
+dev = ["test", "lint"]

From eef379073c616c360ab27d32703e743a0b33eb74 Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Wed, 11 Feb 2026 11:00:09 +0000
Subject: [PATCH 10/24] Add pre-commit.

---
 .pre-commit-config.yaml | 23 +++++++++++++++++++++++
 README.md               | 18 ++++++++++++++++++
 pyproject.toml          |  7 +++++++
 3 files changed, 48 insertions(+)
 create mode 100644 .pre-commit-config.yaml

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 0000000..0043ca4
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,23 @@
+files: ^(src|tests)/
+exclude: ^tests/(input|output)/
+
+repos:
+  # General file quality checks
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-added-large-files
+        args: [--maxkb=1000]  # Prevent files larger than 1MB
+      - id: check-merge-conflict
+
+  # Python formatting and linting
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.8.4
+    hooks:
+      # Run the formatter
+      - id: ruff-format
+      # Run the linter (optional - remove if too strict)
+      - id: ruff
+        args: [--fix, --exit-zero]  # Auto-fix but don't block commits
diff --git a/README.md b/README.md
index 3bd2805..d5ababc 100644
--- a/README.md
+++ b/README.md
@@ -76,6 +76,24 @@ You should now have a `somd2` executable in your path. To test, run:
 somd2 --help
 ```
 
+## Development
+
+Pre-commit hooks are used to ensure consistent code formatting and linting.
+To set up pre-commit in your development environment:
+
+```
+pixi shell -e dev
+pre-commit install
+```
+
+This will run [ruff](https://docs.astral.sh/ruff/) formatting and linting
+checks automatically on each commit. To run the checks manually against all
+files:
+
+```
+pre-commit run --all-files
+```
+
 ## Usage
 
 In order to run an alchemical free-energy simulation you will need to
diff --git a/pyproject.toml b/pyproject.toml
index fd326a6..10a39fc 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -35,3 +35,10 @@ distance-dirty = "{base_version}+{distance}.{vcs}{rev}.dirty"
 
 [tool.versioningit.write]
 file = "src/somd2/_version.py"
+
+[tool.ruff.lint]
+ignore = ["E402"]
+
+[tool.ruff.lint.per-file-ignores]
+"tests/**" = ["F841"]
+

From a57d00f02aee308f00f902c1e702258e4ca0a767 Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Wed, 11 Feb 2026 11:08:28 +0000
Subject: [PATCH 11/24] Autoformat and lint with ruff.

---
 src/somd2/_utils/_somd1.py         | 3 +--
 src/somd2/config/_config.py        | 1 -
 src/somd2/runner/_base.py          | 5 ++---
 src/somd2/runner/_repex.py         | 7 ++-----
 src/somd2/runner/_runner.py        | 1 -
 tests/runner/test_config.py        | 1 -
 tests/runner/test_lambda_values.py | 2 --
 tests/runner/test_repex.py         | 3 ---
 8 files changed, 5 insertions(+), 18 deletions(-)

diff --git a/src/somd2/_utils/_somd1.py b/src/somd2/_utils/_somd1.py
index aa379f7..d25b795 100644
--- a/src/somd2/_utils/_somd1.py
+++ b/src/somd2/_utils/_somd1.py
@@ -548,7 +548,7 @@ def make_compatible(system, fix_perturbable_zero_sigmas=False):
             for idx0 in impropers0_idx.keys():
                 if idx1.equivalent(idx0):
                     # Don't store duplicates.
-                    if not idx0 in impropers_shared_idx.keys():
+                    if idx0 not in impropers_shared_idx.keys():
                         impropers_shared_idx[idx1] = (
                             impropers0_idx[idx0],
                             impropers1_idx[idx1],
@@ -659,7 +659,6 @@ def reconstruct_system(system):
 
     # Loop over all perturbable molecules.
     for mol in pert_mols:
-
         # Delete any AmberParams properties.
         try:
             cursor = mol.cursor()
diff --git a/src/somd2/config/_config.py b/src/somd2/config/_config.py
index fed794c..f8c2986 100644
--- a/src/somd2/config/_config.py
+++ b/src/somd2/config/_config.py
@@ -1459,7 +1459,6 @@ def platform(self):
     @platform.setter
     def platform(self, platform):
         import os as _os
-        import sys as _sys
 
         if not isinstance(platform, str):
             raise TypeError("'platform' must be of type 'str'")
diff --git a/src/somd2/runner/_base.py b/src/somd2/runner/_base.py
index 0c9db05..91febaa 100644
--- a/src/somd2/runner/_base.py
+++ b/src/somd2/runner/_base.py
@@ -402,8 +402,8 @@ def __init__(self, system, config):
                 if len(self._config.rest2_scale) != len(self._lambda_energy):
                     msg = f"Length of 'rest2_scale' must match the number of {_lam_sym} values."
                     if is_missing:
-                        msg += f"If you have omitted some 'lambda_values` from `lambda_energy`, please "
-                        f"add them to `lambda_energy`, along with the corresponding `rest2_scale` values."
+                        msg += "If you have omitted some 'lambda_values` from `lambda_energy`, please "
+                        "add them to `lambda_energy`, along with the corresponding `rest2_scale` values."
                     _logger.error(msg)
                     raise ValueError(msg)
                 # Make sure the end states are close to 1.0.
@@ -429,7 +429,6 @@ def __init__(self, system, config):
 
         # Make sure the REST2 selection is valid.
         if self._config.rest2_selection is not None:
-
             try:
                 atoms = _sr.mol.selection_to_atoms(
                     self._system, self._config.rest2_selection
diff --git a/src/somd2/runner/_repex.py b/src/somd2/runner/_repex.py
index fb42401..cdc1851 100644
--- a/src/somd2/runner/_repex.py
+++ b/src/somd2/runner/_repex.py
@@ -461,7 +461,6 @@ def save_openmm_state(self, index):
         index: int
             The index of the replica.
         """
-        from openmm.unit import angstrom
 
         # Get the current OpenMM state.
         state = (
@@ -1039,8 +1038,7 @@ def run(self):
                     for j in range(num_checkpoint_batches):
                         # Get the indices of the replicas in this batch.
                         replicas = replica_list[
-                            j
-                            * num_checkpoint_workers : (j + 1)
+                            j * num_checkpoint_workers : (j + 1)
                             * num_checkpoint_workers
                         ]
                         with ThreadPoolExecutor(max_workers=num_workers) as executor:
@@ -1063,8 +1061,7 @@ def run(self):
                     for j in range(num_checkpoint_batches):
                         # Get the indices of the replicas in this batch.
                         replicas = replica_list[
-                            j
-                            * num_checkpoint_workers : (j + 1)
+                            j * num_checkpoint_workers : (j + 1)
                             * num_checkpoint_workers
                         ]
                         with ThreadPoolExecutor(max_workers=num_workers) as executor:
diff --git a/src/somd2/runner/_runner.py b/src/somd2/runner/_runner.py
index 12a637c..561bc13 100644
--- a/src/somd2/runner/_runner.py
+++ b/src/somd2/runner/_runner.py
@@ -658,7 +658,6 @@ def generate_lam_vals(lambda_base, increment=0.001):
 
         # Run the simulation, checkpointing in blocks.
         if checkpoint_frequency.value() > 0.0:
-
             # Calculate the number of blocks and the remainder time.
             frac = (time / checkpoint_frequency).value()
 
diff --git a/tests/runner/test_config.py b/tests/runner/test_config.py
index cfb14be..05a2f0b 100644
--- a/tests/runner/test_config.py
+++ b/tests/runner/test_config.py
@@ -1,4 +1,3 @@
-import pytest
 import tempfile
 
 import sire as sr
diff --git a/tests/runner/test_lambda_values.py b/tests/runner/test_lambda_values.py
index ec6267f..ca63d7a 100644
--- a/tests/runner/test_lambda_values.py
+++ b/tests/runner/test_lambda_values.py
@@ -1,9 +1,7 @@
 from pathlib import Path
 
 import tempfile
-import pytest
 
-import sire as sr
 
 from somd2.runner import Runner
 from somd2.config import Config
diff --git a/tests/runner/test_repex.py b/tests/runner/test_repex.py
index a21eb9d..9336053 100644
--- a/tests/runner/test_repex.py
+++ b/tests/runner/test_repex.py
@@ -17,7 +17,6 @@ def test_repex_output(ethane_methanol):
     Validate that repex specific simulation output is generated.
     """
     with tempfile.TemporaryDirectory() as tmpdir:
-
         config = {
             "runtime": "12fs",
             "restart": False,
@@ -92,7 +91,6 @@ def test_rest2_scale(ethane_methanol, rest2_scale, is_valid):
     """Validate the REST2 scale factor handling."""
 
     with tempfile.TemporaryDirectory() as tmpdir:
-
         config = {
             "runtime": "12fs",
             "restart": False,
@@ -130,7 +128,6 @@ def test_rest2_selection(ethane_methanol, rest2_selection, is_valid):
     """Validate the REST2 selection handling."""
 
     with tempfile.TemporaryDirectory() as tmpdir:
-
         config = {
             "runtime": "12fs",
             "restart": False,

From 71f22e28fb2730ce2d8c375cff9e571419c6011c Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Wed, 11 Feb 2026 11:40:07 +0000
Subject: [PATCH 12/24] Remove redundant sections of recipe.

---
 recipes/somd2/recipe.yaml | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/recipes/somd2/recipe.yaml b/recipes/somd2/recipe.yaml
index b57509b..d485c89 100644
--- a/recipes/somd2/recipe.yaml
+++ b/recipes/somd2/recipe.yaml
@@ -44,15 +44,10 @@ tests:
           - pytest -vvv --color=yes --import-mode=importlib ./tests
     files:
       source:
-        - src/somd2/
         - tests/
     requirements:
       run:
         - pytest
-        - if: linux and x86_64
-          then:
-            - black ==25
-            - pytest-black
 
 about:
   homepage: https://github.com/openbiosim/somd2

From 8d289706f2c77b1c76f02624dc561b7f84e11e30 Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Wed, 11 Feb 2026 12:06:18 +0000
Subject: [PATCH 13/24] Update gitignore.

---
 .gitignore | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/.gitignore b/.gitignore
index dd1d570..0084085 100644
--- a/.gitignore
+++ b/.gitignore
@@ -20,7 +20,6 @@ setup.err
 dist/
 build/
 somd2.egg-info
-src/somd2/_version.py
 
 # Test output.
 output.yaml
@@ -35,8 +34,5 @@ output.yaml
 # VSCode config
 .vscode/
 
-# Conda recipe (it is auto-generated)
-recipes/somd2/meta.yaml
-
 # Auto-generated version file
 src/somd2/_version.py

From e117d0ec36567adf3bc5f440c7591878943525a1 Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Wed, 11 Feb 2026 14:04:38 +0000
Subject: [PATCH 14/24] Add rattler-build to development environment.

---
 pixi.toml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pixi.toml b/pixi.toml
index ccc4f00..9559a6e 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -21,6 +21,7 @@ black = "*"
 
 [feature.lint.dependencies]
 pre-commit = "*"
+rattler-build = "*"
 ruff = "*"
 
 [environments]

From 45789e490ed05a4195253f1ed27588b0ec99f787 Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Wed, 11 Feb 2026 15:07:14 +0000
Subject: [PATCH 15/24] Use pixi install of rattler-build.

---
 .github/workflows/devel.yaml | 11 +++++++----
 .github/workflows/main.yaml  | 11 +++++++----
 .github/workflows/pr.yaml    | 11 +++++++----
 3 files changed, 21 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/devel.yaml b/.github/workflows/devel.yaml
index 5248fd1..e45d9e1 100644
--- a/.github/workflows/devel.yaml
+++ b/.github/workflows/devel.yaml
@@ -43,11 +43,14 @@ jobs:
         run: pip install build && python -m build --sdist && mv dist/*.tar.gz somd2-source.tar.gz
         working-directory: ${{ github.workspace }}
       #
-      - name: Install rattler-build
-        uses: prefix-dev/rattler-build-action@v0.2.34
+      - name: Install pixi
+        uses: prefix-dev/setup-pixi@v0.9.4
         with:
-          tool-version: latest
-          build-args: --help
+          run-install: false
+      #
+      - name: Install rattler-build
+        shell: bash
+        run: pixi global install rattler-build
       #
       - name: Write Python variant config
         shell: bash
diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml
index 685826e..354264e 100644
--- a/.github/workflows/main.yaml
+++ b/.github/workflows/main.yaml
@@ -47,11 +47,14 @@ jobs:
         run: pip install build && python -m build --sdist && mv dist/*.tar.gz somd2-source.tar.gz
         working-directory: ${{ github.workspace }}
       #
-      - name: Install rattler-build
-        uses: prefix-dev/rattler-build-action@v0.2.34
+      - name: Install pixi
+        uses: prefix-dev/setup-pixi@v0.9.4
         with:
-          tool-version: latest
-          build-args: --help
+          run-install: false
+      #
+      - name: Install rattler-build
+        shell: bash
+        run: pixi global install rattler-build
       #
       - name: Write Python variant config
         shell: bash
diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index d5a7531..1069e0a 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -45,11 +45,14 @@ jobs:
         run: pip install build && python -m build --sdist && mv dist/*.tar.gz somd2-source.tar.gz
         working-directory: ${{ github.workspace }}
       #
-      - name: Install rattler-build
-        uses: prefix-dev/rattler-build-action@v0.2.34
+      - name: Install pixi
+        uses: prefix-dev/setup-pixi@v0.9.4
         with:
-          tool-version: latest
-          build-args: --help
+          run-install: false
+      #
+      - name: Install rattler-build
+        shell: bash
+        run: pixi global install rattler-build
       #
       - name: Write Python variant config
         shell: bash

From 6b254d7a398c0b048f2cd749a79a39e9ad2a733f Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Thu, 12 Feb 2026 09:08:44 +0000
Subject: [PATCH 16/24] Remove redundant setup.py file.

---
 setup.py | 3 ---
 1 file changed, 3 deletions(-)
 delete mode 100644 setup.py

diff --git a/setup.py b/setup.py
deleted file mode 100644
index 6068493..0000000
--- a/setup.py
+++ /dev/null
@@ -1,3 +0,0 @@
-from setuptools import setup
-
-setup()

From 47d80e4ee91b08b3c9bd4458ecd59cc26efbd516 Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Thu, 12 Feb 2026 12:48:04 +0000
Subject: [PATCH 17/24] Add YAML serialisation for custom lambda schedules and
 restraints.

---
 src/somd2/config/_config.py  | 97 ++++++++++++++++++++++++++++++++++--
 src/somd2/runner/_base.py    | 70 ++++++++++++++++++++++++--
 src/somd2/runner/_runner.py  |  2 +-
 tests/runner/test_restart.py | 47 +++++++++++++++++
 4 files changed, 207 insertions(+), 9 deletions(-)

diff --git a/src/somd2/config/_config.py b/src/somd2/config/_config.py
index f8c2986..49ce7a0 100644
--- a/src/somd2/config/_config.py
+++ b/src/somd2/config/_config.py
@@ -652,6 +652,14 @@ def as_dict(self, sire_compatible=False):
             self._charge_scale_factor
         ):
             d["lambda_schedule"] = "charge_scaled_morph"
+        else:
+            d["lambda_schedule"] = self._serialise_object(self.lambda_schedule)
+
+        # Serialise restraints.
+        if self.restraints is not None:
+            d["restraints"] = [
+                self._serialise_object(restraint) for restraint in self.restraints
+            ]
 
         # Use the path for the perturbed_system option, since the system
         # isn't serializable.
@@ -984,14 +992,21 @@ def lambda_schedule(self, lambda_schedule):
             if isinstance(lambda_schedule, str):
                 # Strip whitespace and convert to lower case.
                 lambda_schedule = lambda_schedule.strip().lower()
-                if lambda_schedule not in self._choices["lambda_schedule"]:
-                    raise ValueError(
-                        f"Lambda schedule not recognised. Valid lambda schedules are: {self._choices['lambda_schedule']}"
-                    )
                 if lambda_schedule == "standard_morph":
                     self._lambda_schedule = _LambdaSchedule.standard_morph()
                 elif lambda_schedule == "charge_scaled_morph":
                     self._lambda_schedule = _LambdaSchedule.charge_scaled_morph(0.2)
+                else:
+                    try:
+                        self._lambda_schedule = self._deserialise_object(
+                            lambda_schedule
+                        )
+                    except Exception:
+                        raise ValueError(
+                            "Unable to deserialise 'lambda_schedule'. Ensure that this is a "
+                            "hex string representation of a valid LambdaSchedule object, or "
+                            f"one of the following strings: {', '.join(self._choices['lambda_schedule'])}"
+                        )
             else:
                 self._lambda_schedule = lambda_schedule
         else:
@@ -1094,12 +1109,27 @@ def restraints(self, restraints):
                 restraints = [restraints]
 
             # Check that all restraints are of the correct type.
+            deserialised_restraints = []
             for restraint in restraints:
-                if not isinstance(restraint, _sr.mm._MM.Restraints):
+                if isinstance(restraint, _sr.mm._MM.Restraints):
+                    continue
+                elif isinstance(restraint, str):
+                    try:
+                        restraint = self._deserialise_object(restraint)
+                    except Exception:
+                        raise ValueError(
+                            "Unable to deserialise restraint. Ensure that this "
+                            "is a hex string representation of a valid sire.mm._MM.Restraints object."
+                        )
+                    deserialised_restraints.append(restraint)
+                else:
                     raise ValueError(
                         "'restraints' must be a sire.mm._MM.Restraints object, or a list of these objects."
                     )
 
+            if len(deserialised_restraints) > 0:
+                restraints = deserialised_restraints
+
         self._restraints = restraints
 
     @property
@@ -2082,6 +2112,63 @@ def overwrite(self, overwrite):
             raise ValueError("'overwrite' must be of type 'bool'")
         self._overwrite = overwrite
 
+    @staticmethod
+    def _serialise_object(obj):
+        """
+        Internal method to serialise a Sire object to a hex string representation
+        for storage in the YAML config file.
+
+        Parameters
+        ----------
+
+        obj: object
+            The Sire object to serialise.
+
+        Returns
+        --------
+
+        hex:
+            The hex string representation of the Sire object.
+        """
+
+        from sire.stream import save
+        from sire.legacy.Qt import QByteArray
+
+        try:
+            hex = QByteArray(save(obj)).to_hex().data()
+        except Exception as e:
+            raise ValueError(f"Unable to serialise object: {e}")
+
+        return hex
+
+    @staticmethod
+    def _deserialise_object(hex):
+        """
+        Internal method to deserialise a Sire object from a hex string representation.
+
+        Parameters
+        ----------
+
+        hex: str
+            The hex string representation of the Sire object.
+
+        Returns
+        -------
+
+        obj:
+            The deserialised Sire object.
+        """
+        from sire.stream import load
+        from sire.legacy.Qt import QByteArray
+
+        try:
+            hex_byte_arrary = QByteArray.from_raw_data(hex, len(hex))
+            obj = load(QByteArray.from_hex(hex_byte_arrary))
+        except Exception as e:
+            raise ValueError(f"Unable to deserialise object: {e}")
+
+        return obj
+
     @classmethod
     def _create_parser(cls):
         """
diff --git a/src/somd2/runner/_base.py b/src/somd2/runner/_base.py
index 91febaa..b6b8c89 100644
--- a/src/somd2/runner/_base.py
+++ b/src/somd2/runner/_base.py
@@ -1354,6 +1354,70 @@ def _compare_configs(config1, config2):
                 v1 = config1[key]
                 v2 = config2[key]
 
+                # None config options stored as a Sire property are converted
+                # to False, so None and Fasle are equivalent for the purposes of
+                # comparison.
+                if v1 is None and not v2:
+                    continue
+                if v2 is None and not v1:
+                    continue
+
+                # Early exit equivalence check.
+                if v1 == v2:
+                    continue
+
+                # Custom lambda schedules are stored as a hexademical string of
+                # serialised object. We need to deserialise them before comparison.
+                if key == "lambda_schedule":
+                    # Standard schedules are stored as strings, so we can compare these directly.
+                    if v1 == v2:
+                        continue
+                    else:
+                        try:
+                            v1 = _Config._deserialise_object(v1)
+                        except Exception as e:
+                            raise ValueError(
+                                f"Unable to deserialise lambda schedule from config1: {str(e)}"
+                            )
+                        try:
+                            v2 = _Config._deserialise_object(v2)
+                        except Exception as e:
+                            raise ValueError(
+                                f"Unable to deserialise lambda schedule from config2: {str(e)}"
+                            )
+                        if v1 != v2:
+                            raise ValueError(
+                                f"{key} has changed since the last run. This is not "
+                                "allowed when using the restart option."
+                            )
+                        else:
+                            continue
+
+                # Restraints are stored as a list of hexadecimal strings of serialised objects.
+                # We need to deserialise them before comparison.
+                elif key == "restraints":
+                    if v1 and v2:
+                        for r1, r2 in zip(v1, v2):
+                            try:
+                                r1 = _Config._deserialise_object(r1)
+                            except Exception as e:
+                                raise ValueError(
+                                    f"Unable to deserialise restraint from config1: {str(e)}"
+                                )
+                            try:
+                                r2 = _Config._deserialise_object(r2)
+                            except Exception as e:
+                                raise ValueError(
+                                    f"Unable to deserialise restraint from config2: {str(e)}"
+                                )
+                            if r1 != r2:
+                                raise ValueError(
+                                    f"{key} has changed since the last run. This is not "
+                                    "allowed when using the restart option."
+                                )
+                            else:
+                                continue
+
                 # Convert GeneralUnits to strings for comparison.
                 if isinstance(v1, _GeneralUnit):
                     v1 = str(v1)
@@ -1363,14 +1427,14 @@ def _compare_configs(config1, config2):
                 # Convert Sire containers to lists for comparison.
                 try:
                     v1 = v1.to_list()
-                except:
+                except Exception:
                     pass
                 try:
                     v2 = v2.to_list()
-                except:
+                except Exception:
                     pass
 
-                if (v1 == None and v2 == False) or (v2 == None and v1 == False):
+                if (v1 is None and v2 == False) or (v2 is None and v1 == False):
                     continue
                 # The GCMC frequency will be automaticall set if None.
                 elif key == "gcmc_frequency" and v1 is None:
diff --git a/src/somd2/runner/_runner.py b/src/somd2/runner/_runner.py
index 561bc13..931b534 100644
--- a/src/somd2/runner/_runner.py
+++ b/src/somd2/runner/_runner.py
@@ -155,7 +155,7 @@ def _initialise_gpu_devices(num_devices, oversubscription_factor=1):
         Returns
         -------
 
-        devices : [(str, int)]
+        devices: [(str, int)]
             List of available device numbers with oversubscription factor.
         """
         devices = []
diff --git a/tests/runner/test_restart.py b/tests/runner/test_restart.py
index 5f9639d..bfb5fd0 100644
--- a/tests/runner/test_restart.py
+++ b/tests/runner/test_restart.py
@@ -228,3 +228,50 @@ def test_restart(mols, request):
         # Load the new checkpoint file and make sure the restart fails
         with pytest.raises(ValueError):
             runner_badconfig = Runner(mols, Config(**config_new))
+
+
+def test_restart_custom_schedule(ethane_methanol):
+    """
+    Test that a restart works when using a non-standard lambda schedule.
+    """
+    mols = ethane_methanol.clone()
+    schedule = sr.cas.LambdaSchedule.standard_decouple()
+
+    with tempfile.TemporaryDirectory() as tmpdir:
+        config = {
+            "runtime": "12fs",
+            "restart": False,
+            "output_directory": tmpdir,
+            "energy_frequency": "4fs",
+            "checkpoint_frequency": "4fs",
+            "frame_frequency": "4fs",
+            "lambda_schedule": schedule,
+            "platform": "CPU",
+            "max_threads": 1,
+            "num_lambda": 2,
+        }
+
+        # Instantiate a runner using the config defined above.
+        runner = Runner(mols, Config(**config))
+
+        del runner
+
+        config_new = {
+            "runtime": "24fs",
+            "restart": True,
+            "output_directory": tmpdir,
+            "energy_frequency": "4fs",
+            "checkpoint_frequency": "4fs",
+            "frame_frequency": "4fs",
+            "lambda_schedule": schedule,
+            "platform": "CPU",
+            "max_threads": 1,
+            "num_lambda": 2,
+            "overwrite": True,
+            "log_level": "DEBUG",
+        }
+
+        runner2 = Runner(mols, Config(**config_new))
+
+        # Run the simulation.
+        runner2.run()

From 5c768502a375c4d95fb697b1f6a2893e35a055ff Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Thu, 12 Feb 2026 15:34:02 +0000
Subject: [PATCH 18/24] Fix handling of different perturbed_system formats.

---
 src/somd2/runner/_base.py | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/src/somd2/runner/_base.py b/src/somd2/runner/_base.py
index b6b8c89..7d3469b 100644
--- a/src/somd2/runner/_base.py
+++ b/src/somd2/runner/_base.py
@@ -532,10 +532,12 @@ def __init__(self, system, config):
             # we need to save to the output directory and update the config to
             # point to the new file.
             if self._config._perturbed_system_file is None:
-                filename = _Path(self._config.output_directory) / "perturbed_system.s3"
-                _sr.stream.save(perturbed_system, perturbed_system_file)
-                self._config._perturbed_system_file = str(filename)
-                _logger.info(f"Saving perturbed system to {perturbed_system_file}")
+                filename = str(
+                    _Path(self._config.output_directory) / "perturbed_system.s3"
+                )
+                _sr.stream.save(self._config.perturbed_system, filename)
+                self._config._perturbed_system_file = filename
+                _logger.info(f"Saving perturbed system to {filename}")
 
         # Write YAML configuration file to the output directory.
         if self._config.write_config:

From d92fa7d3109240a35eb0b2b7dde1440095a11185 Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Thu, 12 Feb 2026 15:50:36 +0000
Subject: [PATCH 19/24] nvidia-ml-py is noarch.

---
 pixi.toml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/pixi.toml b/pixi.toml
index 9559a6e..7a3ffa4 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -11,8 +11,6 @@ ghostly = "*"
 loch = "*"
 loguru = "*"
 numba = "*"
-
-[target.linux-64.dependencies]
 nvidia-ml-py = "*"
 
 [feature.test.dependencies]

From 21085824be79d7ccd3586b53e5cfeea96c991f8b Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Thu, 12 Feb 2026 15:51:14 +0000
Subject: [PATCH 20/24] Fix recipe.

---
 recipes/somd2/recipe.yaml | 15 +++------------
 1 file changed, 3 insertions(+), 12 deletions(-)

diff --git a/recipes/somd2/recipe.yaml b/recipes/somd2/recipe.yaml
index d485c89..ed01f17 100644
--- a/recipes/somd2/recipe.yaml
+++ b/recipes/somd2/recipe.yaml
@@ -24,24 +24,15 @@ requirements:
     - loch
     - loguru
     - numba
+    - nvidia-ml-py
     - python
-    - if: linux
-      then:
-        - nvidia-ml-py
 
 tests:
   - python:
       imports:
-        - if: linux
-          then:
-            - somd2
+        - somd2
   - script:
-      - if: linux and x86_64
-        then:
-          - pytest -vvv --color=yes --black src/somd2
-      - if: linux
-        then:
-          - pytest -vvv --color=yes --import-mode=importlib ./tests
+      - pytest -vvv --color=yes --import-mode=importlib ./tests
     files:
       source:
         - tests/

From 00416d37b0bfd340677ff0a76e7f574af73e3342 Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Thu, 12 Feb 2026 16:02:00 +0000
Subject: [PATCH 21/24] Skip tests on macOS.

---
 recipes/somd2/recipe.yaml | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/recipes/somd2/recipe.yaml b/recipes/somd2/recipe.yaml
index ed01f17..f97ceb6 100644
--- a/recipes/somd2/recipe.yaml
+++ b/recipes/somd2/recipe.yaml
@@ -30,9 +30,13 @@ requirements:
 tests:
   - python:
       imports:
-        - somd2
+        - if: linux
+          then:
+            - somd2
   - script:
-      - pytest -vvv --color=yes --import-mode=importlib ./tests
+      - if: linux
+        then:
+          - pytest -vvv --color=yes --import-mode=importlib ./tests
     files:
       source:
         - tests/

From f571d026befa43dce3ac7bcf24842205be96d311 Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Thu, 12 Feb 2026 16:08:07 +0000
Subject: [PATCH 22/24] Add MANIFEST for tests files and refactor recipe.

---
 MANIFEST.in               | 1 +
 recipes/somd2/recipe.yaml | 6 +++---
 2 files changed, 4 insertions(+), 3 deletions(-)
 create mode 100644 MANIFEST.in

diff --git a/MANIFEST.in b/MANIFEST.in
new file mode 100644
index 0000000..96737d3
--- /dev/null
+++ b/MANIFEST.in
@@ -0,0 +1 @@
+graft tests
diff --git a/recipes/somd2/recipe.yaml b/recipes/somd2/recipe.yaml
index f97ceb6..2f66f79 100644
--- a/recipes/somd2/recipe.yaml
+++ b/recipes/somd2/recipe.yaml
@@ -29,9 +29,9 @@ requirements:
 
 tests:
   - python:
-      imports:
-        - if: linux
-          then:
+      - if: linux
+        then:
+          imports:
             - somd2
   - script:
       - if: linux

From cc4c0c6e60ef638821598e12f9303624587dd535 Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Thu, 12 Feb 2026 16:09:49 +0000
Subject: [PATCH 23/24] Remove import tests since they don't work with
 conditionals.

---
 recipes/somd2/recipe.yaml | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/recipes/somd2/recipe.yaml b/recipes/somd2/recipe.yaml
index 2f66f79..ac9c510 100644
--- a/recipes/somd2/recipe.yaml
+++ b/recipes/somd2/recipe.yaml
@@ -28,11 +28,6 @@ requirements:
     - python
 
 tests:
-  - python:
-      - if: linux
-        then:
-          imports:
-            - somd2
   - script:
       - if: linux
         then:

From 48c5df95034f61db3a5519b353eed8e2b248b57e Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Thu, 12 Feb 2026 16:16:00 +0000
Subject: [PATCH 24/24] Fix recipe conditional formatting.

---
 recipes/somd2/recipe.yaml | 23 +++++++++++++----------
 1 file changed, 13 insertions(+), 10 deletions(-)

diff --git a/recipes/somd2/recipe.yaml b/recipes/somd2/recipe.yaml
index ac9c510..0217074 100644
--- a/recipes/somd2/recipe.yaml
+++ b/recipes/somd2/recipe.yaml
@@ -28,16 +28,19 @@ requirements:
     - python
 
 tests:
-  - script:
-      - if: linux
-        then:
-          - pytest -vvv --color=yes --import-mode=importlib ./tests
-    files:
-      source:
-        - tests/
-    requirements:
-      run:
-        - pytest
+  - if: linux
+    then:
+      - python:
+          imports:
+            - somd2
+      - script:
+          - PYTHONPATH=. pytest -vvv --color=yes --import-mode=importlib ./tests
+        files:
+          source:
+            - tests/
+        requirements:
+          run:
+            - pytest
 
 about:
   homepage: https://github.com/openbiosim/somd2