From c019d65a8577f1dd4b224ec0ad3df0d7d3ee5e2c Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Thu, 5 Feb 2026 13:19:41 +0000
Subject: [PATCH 01/12] Switch to pixi and rattler build.

---
 .github/workflows/devel.yaml         | 59 +++++++++---------
 .github/workflows/main.yaml          | 58 ++++++++++--------
 .github/workflows/pr.yaml            | 56 ++++++++---------
 README.md                            | 42 ++++++++++---
 actions/update_recipe.py             | 90 +++++++++++++++-------------
 actions/upload_package.py            | 60 +++++++++----------
 environment.yaml                     | 11 ----
 pixi.toml                            | 23 +++++++
 recipes/loch/conda_build_config.yaml |  3 -
 recipes/loch/recipe.yaml             | 41 +++++++++++++
 recipes/loch/template.yaml           | 77 ------------------------
 11 files changed, 269 insertions(+), 251 deletions(-)
 delete mode 100644 environment.yaml
 create mode 100644 pixi.toml
 delete mode 100644 recipes/loch/conda_build_config.yaml
 create mode 100644 recipes/loch/recipe.yaml
 delete mode 100644 recipes/loch/template.yaml

diff --git a/.github/workflows/devel.yaml b/.github/workflows/devel.yaml
index efffc43..7aea1fe 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: loch-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: loch_build
-          miniforge-version: latest
-#
-      - name: Clone the devel branch
-        run: git clone -b devel https://github.com/openbiosim/loch
-#
-      - name: Setup Conda
-        run: conda install -y -c conda-forge boa anaconda-client packaging
-#
-      - name: Update Conda recipe
-        run: python ${{ github.workspace }}/loch/actions/update_recipe.py
-#
-      - name: Prepare build location
-        run: mkdir ${{ github.workspace }}/build
-#
-      - name: Build Conda package using conda build
-        run: conda build --no-test -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/loch/recipes/loch
-#
-      - name: Upload Conda package
-        run: python ${{ github.workspace }}/loch/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 loch-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/loch" -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 efc7634..ab57b66 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... 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: loch-build
     defaults:
@@ -33,30 +33,40 @@ 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: loch_build
-          miniforge-version: latest
-#
-      - name: Clone the main branch
-        run: git clone -b main https://github.com/openbiosim/loch
-#
-      - name: Setup Conda
-        run: conda install -y -c conda-forge boa anaconda-client packaging
-#
-      - name: Update Conda recipe
-        run: python ${{ github.workspace }}/loch/actions/update_recipe.py
-#
-      - name: Prepare build location
-        run: mkdir ${{ github.workspace }}/build
-#
-      - name: Build Conda package using conda build
-        run: conda build --no-test -c conda-forge -c openbiosim/label/main ${{ github.workspace }}/loch/recipes/loch
-#
-      - name: Upload Conda package
-        run: python ${{ github.workspace }}/loch/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 loch-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/loch" -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: ${{ secrets.ANACONDA_TOKEN }}
           ANACONDA_LABEL: main
+        if: github.event.inputs.upload_packages == 'true'
diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index c6d7b35..0df1896 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -17,14 +17,12 @@ jobs:
           - { name: "linux", os: "ubuntu-latest", shell: "bash -l {0}" }
           - { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
         exclude:
-          # Exclude all but the latest Python from all
-          # but Linux
           - platform:
               { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
             python-version: "3.10"
           - platform:
               { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
-            python-version: "3.12"  # MacOS can't run 3.12 yet...
+            python-version: "3.12"  # MacOS can't run 3.12 yet...
     environment:
       name: loch-build
     defaults:
@@ -33,31 +31,35 @@ jobs:
     env:
       SIRE_DONT_PHONEHOME: 1
       SIRE_SILENT_PHONEHOME: 1
-      REPO: "${{ 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: loch_build
-          miniforge-version: latest
-#
-      - name: Clone the feature branch
-        run: git clone -b ${{ github.head_ref }} --single-branch https://github.com/${{ env.REPO }} loch
-#
-      - name: Setup Conda
-        run: conda install -y -c conda-forge boa anaconda-client packaging
-#
-      - name: Update Conda recipe
-        run: python ${{ github.workspace }}/loch/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 loch-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 --no-test -c conda-forge -c openbiosim/label/main ${{ github.workspace }}/loch/recipes/loch
-#
-      - name: Build Conda package using conda build using dev channel
+        shell: bash
+        run: rattler-build build --recipe "${{ github.workspace }}/recipes/loch" -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 --no-test -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/loch/recipes/loch
+        shell: bash
+        run: rattler-build build --recipe "${{ github.workspace }}/recipes/loch" -c conda-forge -c openbiosim/label/dev --variant-config "${{ github.workspace }}/python_variant.yaml"
diff --git a/README.md b/README.md
index 6fc0064..6eb965e 100644
--- a/README.md
+++ b/README.md
@@ -19,31 +19,57 @@ and [PyOpenCL](https://documen.tician.de/pyopencl/).
 
 ## Installation
 
-First, create a conda environment with the required dependencies:
+### Conda package
+
+Install `loch` directly from the `openbiosim` channel:
+
+```
+conda install -c conda-forge -c openbiosim loch
+```
+
+Or, for the development version:
 
 ```
-conda env create -f environment.yaml
-conda activate loch
+conda install -c conda-forge -c openbiosim/label/dev loch
 ```
 
-Next, clone the repository and install the package:
+### 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) and
+[BioSimSpace](https://github.com/OpenBioSim/biosimspace)):
 
 ```
 git clone https://github.com/openbiosim/loch
 cd loch
+pixi install
+pixi shell
 pip install -e .
 ```
 
-Alternatively, to install `loch` 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 openbiosim loch
+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):
 
 ```
-conda install -c conda-forge -c openbiosim/label/dev loch
+pip install -e /path/to/biosimspace/python
+```
+
+Then install `loch` into the environment:
+
+```
+pip install -e .
 ```
 
 ## How does it work?
diff --git a/actions/update_recipe.py b/actions/update_recipe.py
index 9586933..8d82bcb 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", "loch")
-
-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("LOCH_REMOTE", remote)
-        line = line.replace("LOCH_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", "loch", "_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 26c1299..96984fa 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 loch/actions/)
+# Go up one directory to get the source directory.
 srcdir = os.path.dirname(os.path.dirname(script))
 
 print(f"Loch 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", "loch_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
-loch_pkg = glob.glob(os.path.join(conda_bld, "*-*", "loch-*.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", "loch_build", "conda-bld")
+        packages = glob.glob(
+            os.path.join(conda_bld, "**", "loch-*.tar.bz2"), recursive=True
+        )
 
-if len(loch_pkg) == 0:
+if not packages:
     print("No loch packages to upload?")
     sys.exit(-1)
 
-packages = loch_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 be4b621..0000000
--- a/environment.yaml
+++ /dev/null
@@ -1,11 +0,0 @@
-name: loch
-
-channels:
-  - conda-forge
-  - openbiosim/label/dev
-
-dependencies:
-  - biosimspace
-  - loguru
-  - pycuda
-  - pyopencl
diff --git a/pixi.toml b/pixi.toml
new file mode 100644
index 0000000..993d157
--- /dev/null
+++ b/pixi.toml
@@ -0,0 +1,23 @@
+[workspace]
+name = "loch"
+channels = ["conda-forge", "openbiosim/label/dev"]
+# No Windows - pycuda/pyopencl only available on linux-64
+platforms = ["linux-64", "osx-arm64"]
+
+[dependencies]
+python = ">=3.10"
+biosimspace = "*"
+loguru = "*"
+pyopencl = "*"
+
+[target.linux-64.dependencies]
+pycuda = "*"
+
+[feature.test.dependencies]
+pytest = "*"
+black = "*"
+
+[environments]
+default = []
+test = ["test"]
+dev = ["test"]
diff --git a/recipes/loch/conda_build_config.yaml b/recipes/loch/conda_build_config.yaml
deleted file mode 100644
index 3e8e203..0000000
--- a/recipes/loch/conda_build_config.yaml
+++ /dev/null
@@ -1,3 +0,0 @@
-pin_run_as_build:
-  sire:
-    max_pin: x.x
diff --git a/recipes/loch/recipe.yaml b/recipes/loch/recipe.yaml
new file mode 100644
index 0000000..0ccd676
--- /dev/null
+++ b/recipes/loch/recipe.yaml
@@ -0,0 +1,41 @@
+context:
+  name: loch
+
+package:
+  name: ${{ name }}
+  version: ${{ env.get('GIT_DESCRIBE_TAG', default='PR') }}
+
+source:
+  path: ../../loch-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
+    - loguru
+    - numpy <2.3  # Remove when nglview >=4.1 is released
+    - pyopencl
+    - python
+    - if: not osx
+      then:
+        - pycuda
+
+about:
+  homepage: https://github.com/openbiosim/loch
+  license: GPL-3.0-or-later
+  license_file: LICENSE
+  summary: "CUDA accelerated Grand Canonical Monte Carlo (GCMC) water sampling code."
+  repository: https://github.com/openbiosim/loch
+  documentation: https://github.com/openbiosim/loch
+
+extra:
+  recipe-maintainers:
+    - lohedges
diff --git a/recipes/loch/template.yaml b/recipes/loch/template.yaml
deleted file mode 100644
index 39320ee..0000000
--- a/recipes/loch/template.yaml
+++ /dev/null
@@ -1,77 +0,0 @@
-{% set name = "loch" %}
-
-package:
-  name: {{ name }}
-  version: {{ environ.get('GIT_DESCRIBE_TAG', 'PR') }}
-
-source:
-  git_url: LOCH_REMOTE
-  git_tag: LOCH_BRANCH
-
-build:
-  number: {{ environ.get('GIT_DESCRIBE_NUMBER', 0) }}
-  script: {{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv
-
-requirements:
-  host:
-    - biosimspace
-    - loguru
-    - pip
-    - pycuda # [not osx]
-    - pyopencl
-    - python
-    - setuptools
-    - sire
-    - versioningit
-  run:
-    - biosimspace
-    - loguru
-    - pycuda # [not osx]
-    - pyopencl
-    - 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:
-    - loch
-  source_files:
-    - src/loch
-    - tests
-  commands:
-    - pytest -vvv --color=yes --black src/loch # [linux and x86_64 and py==311]
-    - pytest -vvv --color=yes --import-mode=importlib tests
-
-about:
-  home: https://github.com/openbiosim/loch
-  license: GPL-3.0-or-later
-  license_file: '{{ environ["RECIPE_DIR"] }}/LICENSE'
-  summary: "CUDA accelerated Grand Canonical Monte Carlo (GCMC) water sampling code."
-  dev_url: https://github.com/openbiosim/loch
-  doc_url: https://github.com/openbiosim/loch
-  description: |
-                CUDA accelerated Grand Canonical Monte Carlo (GCMC) water sampling code.
-                Built on top of Sire, BioSimSpace, and OpenMM.
-
-                To install:
-
-                `conda install -c conda-forge -c openbiosim loch`
-
-                To install the development version:
-
-                `conda install -c conda-forge -c openbiosim/label/dev loch`
-
-                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 loch sire`
-
-extra:
-  recipe-maintainers:
-    - lohedges

From 938596e47b2434e61d5ff7836876295a76d4e7ed Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Fri, 6 Feb 2026 14:11:07 +0000
Subject: [PATCH 02/12] Add auto-generated version file to gitignore.

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

diff --git a/.gitignore b/.gitignore
index ec886b6..62feb86 100644
--- a/.gitignore
+++ b/.gitignore
@@ -37,3 +37,6 @@ output.yaml
 
 # Conda recipe (it is auto-generated)
 recipes/loch/meta.yaml
+
+# Auto-generated version file.
+src/loch/_version.py

From dd328930552d6ef075d6446d597e21a24ed45fb5 Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Mon, 9 Feb 2026 09:13:43 +0000
Subject: [PATCH 03/12] Fix install path for BioSimSpace.

---
 README.md | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/README.md b/README.md
index 6eb965e..050cad0 100644
--- a/README.md
+++ b/README.md
@@ -63,7 +63,7 @@ You may also need to install other packages from source, e.g.
 [BioSimSpace](https://github.com/OpenBioSim/biosimspace):
 
 ```
-pip install -e /path/to/biosimspace/python
+pip install -e /path/to/biosimspace
 ```
 
 Then install `loch` into the environment:
@@ -97,7 +97,7 @@ import sire as sr
 mols = sr.load_test_files("bpti.prm7", "bpti.rst7")
 ```
 
-2) Create a `GCMCSampler`:
+1) Create a `GCMCSampler`:
 
 ```python
 from loch import GCMCSampler
@@ -131,7 +131,7 @@ The GPU platform is controlled via the `platform` argument, which can be set to
 attempt to use the CUDA platform first, falling back to OpenCL if CUDA is not
 available.
 
-3) Get the GCMC system:
+1) Get the GCMC system:
 
 In order to perform a simulation we need to get back the GCMC system, which
 contains an additional `num_ghost_waters` number of ghost water molecules
@@ -141,7 +141,7 @@ that are used for insertion moves.
 gcmc_system = sampler.system()
 ```
 
-4) Create an OpenMM context:
+1) Create an OpenMM context:
 
 We can directly use the Sire dynamics interface to create an OpenMM context
 for us, e.g.:
@@ -177,7 +177,7 @@ a crash:
 sampler.bind_dynamics(d)
 ```
 
-5) Run dynamics with GCMC sampling:
+1) Run dynamics with GCMC sampling:
 
 ```python
 # Set the cycle frequency for saving ghost residue indices.

From 0847c146e593184fc29827e7ba63c137b9e0f1d6 Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Mon, 9 Feb 2026 09:43:50 +0000
Subject: [PATCH 04/12] Remove numpy pin.

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

diff --git a/recipes/loch/recipe.yaml b/recipes/loch/recipe.yaml
index 0ccd676..96172ee 100644
--- a/recipes/loch/recipe.yaml
+++ b/recipes/loch/recipe.yaml
@@ -21,7 +21,6 @@ requirements:
   run:
     - biosimspace
     - loguru
-    - numpy <2.3  # Remove when nglview >=4.1 is released
     - pyopencl
     - python
     - if: not osx

From 70d19a8282a9534291f9d5cc739fbddee73d391c Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Mon, 9 Feb 2026 12:57:22 +0000
Subject: [PATCH 05/12] 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 7aea1fe..d7eb4dc 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 loch-source.tar.gz
@@ -57,10 +58,12 @@ jobs:
         run: rattler-build build --recipe "${{ github.workspace }}/recipes/loch" -c conda-forge -c openbiosim/label/dev --variant-config "${{ 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 ab57b66..26aaa54 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 loch-source.tar.gz
@@ -61,11 +62,13 @@ jobs:
         run: rattler-build build --recipe "${{ github.workspace }}/recipes/loch" -c conda-forge -c openbiosim/label/main --variant-config "${{ 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 0df1896..535698f 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 loch-source.tar.gz

From b2b30d7c66f70a1132e25cb9039b03e511de5444 Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Mon, 9 Feb 2026 13:04:19 +0000
Subject: [PATCH 06/12] 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 d7eb4dc..7113f4f 100644
--- a/.github/workflows/devel.yaml
+++ b/.github/workflows/devel.yaml
@@ -37,7 +37,7 @@ jobs:
       #
       - name: Compute version info
         shell: bash
-        run: python "${{ github.workspace }}/actions/update_recipe.py"
+        run: python actions/update_recipe.py
       #
       - name: Create sdist
         run: pip install build && python -m build --sdist && mv dist/*.tar.gz loch-source.tar.gz
@@ -63,7 +63,7 @@ jobs:
       #
       - name: Upload package
         shell: bash
-        run: python "${{ github.workspace }}/actions/upload_package.py"
+        run: python actions/upload_package.py
         env:
           ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
           ANACONDA_LABEL: dev
diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml
index 26aaa54..6321b3a 100644
--- a/.github/workflows/main.yaml
+++ b/.github/workflows/main.yaml
@@ -41,7 +41,7 @@ jobs:
       #
       - name: Compute version info
         shell: bash
-        run: python "${{ 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 loch-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: ${{ secrets.ANACONDA_TOKEN }}
           ANACONDA_LABEL: main
diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index 535698f..2597b3f 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -39,7 +39,7 @@ jobs:
       #
       - name: Compute version info
         shell: bash
-        run: python "${{ 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 loch-source.tar.gz

From 540f204220daaaac31578d3ea520275e531d1396 Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Wed, 11 Feb 2026 09:26:58 +0000
Subject: [PATCH 07/12] 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 993d157..611213e 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -17,7 +17,11 @@ pycuda = "*"
 pytest = "*"
 black = "*"
 
+[feature.lint.dependencies]
+pre-commit = "*"
+ruff = "*"
+
 [environments]
 default = []
 test = ["test"]
-dev = ["test"]
+dev = ["test", "lint"]

From 1269989d4ea6b5ab01986a335513816e251a65b2 Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Wed, 11 Feb 2026 11:00:21 +0000
Subject: [PATCH 08/12] Add pre-commit.

---
 .pre-commit-config.yaml | 23 +++++++++++++++++++++++
 README.md               | 18 ++++++++++++++++++
 pyproject.toml          |  6 ++++++
 src/loch/_sampler.py    |  1 -
 4 files changed, 47 insertions(+), 1 deletion(-)
 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 050cad0..ecac423 100644
--- a/README.md
+++ b/README.md
@@ -72,6 +72,24 @@ Then install `loch` into the environment:
 pip install -e .
 ```
 
+## 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
+```
+
 ## How does it work?
 
 Instead of computing the energy change for each trial insertion/deletion with
diff --git a/pyproject.toml b/pyproject.toml
index bf6e2e6..4271342 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -29,3 +29,9 @@ distance-dirty = "{base_version}+{distance}.{vcs}{rev}.dirty"
 
 [tool.versioningit.write]
 file = "src/loch/_version.py"
+
+[tool.ruff.lint]
+ignore = ["E402"]
+
+[tool.ruff.lint.per-file-ignores]
+"tests/**" = ["F841"]
diff --git a/src/loch/_sampler.py b/src/loch/_sampler.py
index d17057c..ba36f95 100644
--- a/src/loch/_sampler.py
+++ b/src/loch/_sampler.py
@@ -2394,7 +2394,6 @@ def _set_water_state(self, context, indices=None, states=None, force=False):
 
         # Loop over the indices and states.
         for idx, state in zip(indices, states):
-
             # Skip if the state is unchanged.
             if not force and self._water_state[idx] == state:
                 continue

From ad6474f1f80eaafbb4684b9315823b84d58b4b2d Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Wed, 11 Feb 2026 12:06:36 +0000
Subject: [PATCH 09/12] Update gitignore.

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

diff --git a/.gitignore b/.gitignore
index 62feb86..e2611c2 100644
--- a/.gitignore
+++ b/.gitignore
@@ -20,7 +20,6 @@ setup.err
 dist/
 build/
 loch.egg-info
-src/loch/_version.py
 
 # Test output.
 output.yaml
@@ -35,8 +34,5 @@ output.yaml
 # VSCode config
 .vscode/
 
-# Conda recipe (it is auto-generated)
-recipes/loch/meta.yaml
-
 # Auto-generated version file.
 src/loch/_version.py

From daf479c4130bb09a13b38bfc79b825ea93518275 Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Wed, 11 Feb 2026 14:04:59 +0000
Subject: [PATCH 10/12] Add rattler-build to development environment.

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

diff --git a/pixi.toml b/pixi.toml
index 611213e..fe72127 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -19,6 +19,7 @@ black = "*"
 
 [feature.lint.dependencies]
 pre-commit = "*"
+rattler-build = "*"
 ruff = "*"
 
 [environments]

From 5148e2dc13aa5c10a5e954a6de5af0785d6cb3c7 Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Wed, 11 Feb 2026 15:06:33 +0000
Subject: [PATCH 11/12] 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 7113f4f..ee0200e 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 loch-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 6321b3a..a80b5c2 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 loch-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 2597b3f..54cef13 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 loch-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 d303506a8e612cf1d130710d962c36bc4e9a1baf Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Thu, 12 Feb 2026 09:09:04 +0000
Subject: [PATCH 12/12] 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()