update documentation

.github/workflows/build-wheels.yaml

@@ -0,0 +1,76 @@
+name: Build and upload to PyPI
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - main
+  release:
+    types:
+      - published
+
+jobs:
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, ubuntu-24.04-arm, windows-latest, windows-11-arm, macos-15-intel, macos-latest]
+
+    steps:
+      - uses: actions/checkout@v5
+        with:
+          submodules: recursive  # Critical: fetch packmol submodule
+
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v3.3.0
+        env:
+          # Set macOS deployment target dynamically based on runner
+          CIBW_ENVIRONMENT_MACOS: MACOSX_DEPLOYMENT_TARGET=15.0
+
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
+          path: ./wheelhouse/*.whl
+
+  build_sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+        with:
+          fetch-depth: 0
+          submodules: true
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+
+      - name: Build SDist
+        run: uv build --sdist
+
+      - name: Upload SDist
+        uses: actions/upload-artifact@v4
+        with:
+          name: cibw-sdist
+          path: dist/*.tar.gz
+
+  upload_pypi:
+    needs: [build_wheels, build_sdist]
+    environment: pypi
+    permissions:
+      id-token: write
+    runs-on: ubuntu-latest
+    if: github.event_name == 'release' && github.event.action == 'published'
+    steps:
+      - name: Download all artifacts
+        uses: actions/download-artifact@v5
+        with:
+          pattern: cibw-*
+          path: dist
+          merge-multiple: true
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/pages.yaml

@@ -26,9 +26,9 @@ jobs:
       url: ${{ steps.deployment.outputs.page_url }}
 
     steps:
-      - uses: actions/checkout@v2
-
-      - uses: julia-actions/setup-julia@v2
+      - uses: actions/checkout@v5
+        with:
+          submodules: recursive
 
       - name: Install uv and set the python version
         uses: astral-sh/setup-uv@v5
@@ -38,9 +38,6 @@ jobs:
       - name: Install the project
         run: uv sync --all-extras --dev --all-groups
 
-      - name: Install packmol.jl
-        run: julia -e 'import Pkg; Pkg.add("Packmol")'
-
       - name: Install pandoc
         run: |
           sudo apt update

.github/workflows/pytest.yaml

@@ -21,34 +21,21 @@ jobs:
           - "3.12"
           - "3.11"
           - "3.10"
-        os:
-          - ubuntu-latest
-        packmol-version:
-          - "20.15.1"
+        os: [ubuntu-latest, ubuntu-24.04-arm, windows-latest, macos-15-intel, macos-latest]
+        # windows-11-arm -> rdkit support missing
 
     steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@v2
+      - uses: actions/checkout@v5
+        with:
+          submodules: recursive
       - name: Install uv and set the python version
         uses: astral-sh/setup-uv@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install the project
         run: uv sync --all-extras --dev
-      - name: Install packmol
-        run: |
-          wget https://github.com/m3g/packmol/archive/refs/tags/v${{ matrix.packmol-version}}.tar.gz
-          tar -xvf v${{ matrix.packmol-version}}.tar.gz
-          cd packmol-${{ matrix.packmol-version}}
-          make
-      - name: Install packmol.jl
-        run: |
-          julia -e 'import Pkg; Pkg.add("Packmol")'
       - name: Pytest
         run: |
-          # add packmol to path
-          export PATH=$PATH:$(pwd)/packmol-${{ matrix.packmol-version}}
-
           uv run python --version
           uv run pytest --cov --junitxml=junit.xml -o junit_family=legacy
       - name: Upload coverage to Codecov

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "external/packmol"]
+	path = external/packmol
+	url = https://github.com/m3g/packmol.git

README.md

@@ -41,8 +41,9 @@ print(atoms)
 Given the molecular units, you can build periodic boxes with a given density
 using the `molify.pack` function.
 
-If you have [packmol](https://github.com/m3g/packmol) (at least `v20.15.0`) you
-can use the molify interface as follows:
+The `molify` package ships with an installation of
+[packmol](https://github.com/m3g/packmol). If you like packmol, give it a star
+on GitHub!
 
 ```py
 from molify import pack, smiles2conformers