Switch build system to pixi and rattler-build

.github/workflows/choose_branch.yaml

@@ -2,8 +2,8 @@ name: Release Branch
 
 # Note that push and pull-request builds are automatically
 # now skipped by GitHub if
-# [skip ci], [ci skip], [no ci], [skip actions], or [actions skip]
-# are in the commit message. We don't need to check for this ourselves.
+# [skip ci], [ci skip], [no ci], [skip actions], or [actions skip]
+# are in the commit message. We don't need to check for this ourselves.
 
 on:
   workflow_dispatch:
@@ -35,7 +35,7 @@ jobs:
             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...
           - platform: { name: "windows", os: "windows-latest", shell: "pwsh" }
             python-version: "3.11"
     environment:
@@ -50,31 +50,32 @@ jobs:
       REPO: "${{ 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: sire_build
-          miniforge-version: latest
+          ref: ${{ github.event.inputs.branch }}
       #
-      - name: Clone the desired branch
-        run: git clone https://github.com/${{ env.REPO }} -b ${{ github.event.inputs.branch }} sire
+      - name: Install rattler-build
+        uses: prefix-dev/rattler-build-action@v0.2.34
+        with:
+          tool-version: latest
+          build-args: --help
       #
-      - name: Setup Conda
-        run: conda install -y -c conda-forge conda-build boa anaconda-client packaging pip-requirements-parser
+      - name: Generate recipe
+        run: python ${{ github.workspace }}/actions/generate_recipe.py --features obs emle
       #
-      - name: Update Conda recipe
-        run: python ${{ github.workspace }}/sire/actions/update_recipe.py
+      - name: Write Python variant config
+        shell: bash
+        run: printf 'python:\n  - "${{ matrix.python-version }}"\n' > "${{ github.workspace }}/python_variant.yaml"
       #
-      - name: Prepare build location
-        run: mkdir ${{ github.workspace }}/build
+      - name: Build package using rattler-build
+        shell: bash
+        run: rattler-build build --recipe "${{ github.workspace }}/recipes/sire" -c conda-forge -c openbiosim/label/dev --variant-config "${{ github.workspace }}/python_variant.yaml"
       #
-      - name: Build Conda package using conda build
-        run: conda build -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire
+      - name: Install anaconda-client
+        run: python -m pip install anaconda-client
       #
-      - name: Upload Conda package
-        # Maybe add the logic here that this is a dev package?
-        run: python ${{ github.workspace }}/sire/actions/upload_package.py
+      - name: Upload package
+        run: python ${{ github.workspace }}/actions/upload_package.py
         env:
-          SRC_DIR: ${{ github.workspace }}/sire
+          SRC_DIR: ${{ github.workspace }}
           ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}

.github/workflows/devel.yaml

@@ -2,8 +2,8 @@ name: Release Devel
 
 # Note that push and pull-request builds are automatically
 # now skipped by GitHub if
-# [skip ci], [ci skip], [no ci], [skip actions], or [actions skip]
-# are in the commit message. We don't need to check for this ourselves.
+# [skip ci], [ci skip], [no ci], [skip actions], or [actions skip]
+# are in the commit message. We don't need to check for this ourselves.
 
 on:
   workflow_dispatch:
@@ -28,7 +28,7 @@ jobs:
           # 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
           - platform: { name: "windows", os: "windows-latest", shell: "pwsh" }
             python-version: "3.10"
           - platform: { name: "windows", os: "windows-latest", shell: "pwsh" }
@@ -45,31 +45,30 @@ jobs:
       REPO: "${{ github.repository }}"
     steps:
       #
-      - uses: conda-incubator/setup-miniconda@v3
-        with:
-          auto-update-conda: true
-          python-version: ${{ matrix.python-version }}
-          activate-environment: sire_build
-          miniforge-version: latest
+      - uses: actions/checkout@v4
       #
-      - name: Clone the devel branch (push to devel)
-        run: git clone https://github.com/${{ env.REPO }} sire
+      - name: Install rattler-build
+        uses: prefix-dev/rattler-build-action@v0.2.34
+        with:
+          tool-version: latest
+          build-args: --help
       #
-      - name: Setup Conda
-        run: conda install -y -c conda-forge conda-build boa anaconda-client packaging pip-requirements-parser
+      - name: Generate recipe
+        run: python ${{ github.workspace }}/actions/generate_recipe.py --features obs emle
       #
-      - name: Update Conda recipe
-        run: python ${{ github.workspace }}/sire/actions/update_recipe.py
+      - name: Write Python variant config
+        shell: bash
+        run: printf 'python:\n  - "${{ matrix.python-version }}"\n' > "${{ github.workspace }}/python_variant.yaml"
       #
-      - name: Prepare build location
-        run: mkdir ${{ github.workspace }}/build
+      - name: Build package using rattler-build
+        shell: bash
+        run: rattler-build build --recipe "${{ github.workspace }}/recipes/sire" -c conda-forge -c openbiosim/label/dev --variant-config "${{ github.workspace }}/python_variant.yaml"
       #
-      - name: Build Conda package using conda build
-        run: conda build -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire
+      - name: Install anaconda-client
+        run: python -m pip install anaconda-client
       #
-      - name: Upload Conda package
-        # Maybe add the logic here that this is a dev package?
-        run: python ${{ github.workspace }}/sire/actions/upload_package.py
+      - name: Upload package
+        run: python ${{ github.workspace }}/actions/upload_package.py
         env:
-          SRC_DIR: ${{ github.workspace }}/sire
+          SRC_DIR: ${{ github.workspace }}
           ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}

.github/workflows/main.yaml

@@ -2,8 +2,8 @@ name: Release Main
 
 # Note that push and pull-request builds are automatically
 # now skipped by GitHub if
-# [skip ci], [ci skip], [no ci], [skip actions], or [actions skip]
-# are in the commit message. We don't need to check for this ourselves.
+# [skip ci], [ci skip], [no ci], [skip actions], or [actions skip]
+# are in the commit message. We don't need to check for this ourselves.
 
 # Only allow this action to run on a manual run.
 # We should specify when run whether or not we want
@@ -45,32 +45,35 @@ jobs:
       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: sire_build
-          miniforge-version: latest
+          ref: main
       #
-      - name: Clone the main branch (push to main)
-        run: git clone -b main https://github.com/openbiosim/sire sire
+      - name: Install rattler-build
+        uses: prefix-dev/rattler-build-action@v0.2.34
+        with:
+          tool-version: latest
+          build-args: --help
       #
-      - name: Setup Conda
-        run: conda install -y -c conda-forge conda-build boa anaconda-client packaging pip-requirements-parser
+      - name: Generate recipe
+        run: python ${{ github.workspace }}/actions/generate_recipe.py --features obs emle
       #
-      - name: Update Conda recipe
-        run: python ${{ github.workspace }}/sire/actions/update_recipe.py
+      - name: Write Python variant config
+        shell: bash
+        run: printf 'python:\n  - "${{ matrix.python-version }}"\n' > "${{ github.workspace }}/python_variant.yaml"
       #
-      - name: Prepare build location
-        run: mkdir ${{ github.workspace }}/build
+      - name: Build package using rattler-build
+        shell: bash
+        run: rattler-build build --recipe "${{ github.workspace }}/recipes/sire" -c conda-forge -c openbiosim/label/dev --variant-config "${{ github.workspace }}/python_variant.yaml"
       #
-      - name: Build Conda package using conda build
-        run: conda build -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire
+      - name: Install anaconda-client
+        run: python -m pip install anaconda-client
+        if: github.event.inputs.upload_packages == 'yes'
       #
-      - name: Upload Conda package
+      - name: Upload package
         # upload to the 'test' channel
-        run: python ${{ github.workspace }}/sire/actions/upload_package.py test
+        run: python ${{ github.workspace }}/actions/upload_package.py test
         env:
-          SRC_DIR: ${{ github.workspace }}/sire
+          SRC_DIR: ${{ github.workspace }}
           ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
         if: github.event.inputs.upload_packages == 'yes'

.github/workflows/pr.yaml

@@ -2,8 +2,8 @@ name: Pull-Request
 
 # Note that push and pull-request builds are automatically
 # now skipped by GitHub if
-# [skip ci], [ci skip], [no ci], [skip actions], or [actions skip]
-# are in the commit message. We don't need to check for this ourselves.
+# [skip ci], [ci skip], [no ci], [skip actions], or [actions skip]
+# are in the commit message. We don't need to check for this ourselves.
 
 on:
   pull_request:
@@ -32,7 +32,7 @@ jobs:
             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...
           - platform: { name: "windows", os: "windows-latest", shell: "pwsh" }
             python-version: "3.11"
     environment:
@@ -47,24 +47,21 @@ jobs:
       REPO: "${{ github.event.pull_request.head.repo.full_name || github.repository }}"
     steps:
       #
-      - uses: conda-incubator/setup-miniconda@v3
-        with:
-          auto-update-conda: true
-          python-version: ${{ matrix.python-version }}
-          activate-environment: sire_build
-          miniforge-version: latest
-      #
-      - name: Clone the feature branch (pull request to devel)
-        run: git clone -b ${{ github.head_ref }} --single-branch https://github.com/${{ env.REPO }} sire
+      - uses: actions/checkout@v4
       #
-      - name: Setup Conda
-        run: conda install -y -c conda-forge conda-build boa anaconda-client packaging pip-requirements-parser
+      - name: Install rattler-build
+        uses: prefix-dev/rattler-build-action@v0.2.34
+        with:
+          tool-version: latest
+          build-args: --help
       #
-      - name: Update Conda recipe
-        run: python ${{ github.workspace }}/sire/actions/update_recipe.py
+      - name: Generate recipe
+        run: python ${{ github.workspace }}/actions/generate_recipe.py --features obs emle
       #
-      - name: Prepare build location
-        run: mkdir ${{ github.workspace }}/build
+      - name: Write Python variant config
+        shell: bash
+        run: printf 'python:\n  - "${{ matrix.python-version }}"\n' > "${{ github.workspace }}/python_variant.yaml"
       #
-      - name: Build Conda package using conda build
-        run: conda build -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire
+      - name: Build package using rattler-build
+        shell: bash
+        run: rattler-build build --recipe "${{ github.workspace }}/recipes/sire" -c conda-forge -c openbiosim/label/dev --variant-config "${{ github.workspace }}/python_variant.yaml"

.gitignore

@@ -10,7 +10,7 @@ build/wrapper/*
 build/module/*
 build/downloads/*
 recipes/sire/meta.yaml
-#files for wrapper
+# files for wrappers
 module_info
 active_headers.data
 exposed_decl.pypp.txt
@@ -57,12 +57,15 @@ tests/cache/*
 # Python autogenerated backup wrappers
 *~
 
-#Atom
+# Atom
 .idea
 
-#VS Code
+# VS Code
 .vscode
 
 .DS_Store
 
 .coverage
+
+# Pixi startup file
+pixi.sh

README.rst

@@ -104,59 +104,44 @@ Installation from source
 
 However, as you are here, it is likely you want to download the latest,
 greatest version of the code, which you will need to compile. To compile
-sire,
-you need a git client to download the source, and a working internet connection
-(needed by the sire compilation scripts to download additional dependencies).
+sire, you need a git client to download the source and
+`pixi <https://pixi.sh>`__ to manage the build environment.
 
-First, you need to create and activate a conda environment, e.g.
+First, clone the sire source code and change into the directory:
 
 .. code-block:: bash
 
-    conda create -n openbiosim-dev "python<3.12"
-    conda activate openbiosim-dev
-
-Next, you need to install the Sire build dependencies.
-
-.. code-block:: bash
-
-    conda install cmake pip-requirements-parser
-
-You will also need to install compilers, e.g. on Linux use
-
-.. code-block:: bash
-
-    conda install gcc gxx
+    git clone https://github.com/OpenBioSim/sire
+    cd sire
 
-on MacOS use
+Next, use pixi to create and activate the development environment. This
+will install all required dependencies, including compilers:
 
 .. code-block:: bash
 
-    conda install clang clangxx
+    pixi install -e dev
+    pixi shell -e dev
 
-and on Windows use
+Now compile and install sire:
 
 .. code-block:: bash
 
-    conda install conda-build
-
-Next, you can clone the sire source code and compile and install sire::
-
-    git clone https://github.com/OpenBioSim/sire
-    cd sire
     python setup.py install
 
 A small word of warning, the compilation can easily take over an hour!
 
-The above will compile sire in your existing conda environment.
+Other pixi environments are available depending on your needs:
 
-If you plan to build `BioSimSpace <https://github.com/openbiosim/biosimspace>`__
-on top of sire, then you will need to resolve BioSimSpace's dependencies at
-the time sire is installed to ensure that it is built in a self-consistent way.
-This can be achieved as follows:
-
-.. code-block:: bash
+* ``pixi install -e default`` - core sire dependencies only
+* ``pixi install -e obs`` - include downstream OpenBioSim package dependencies
+* ``pixi install -e emle`` - include `emle-engine <https://github.com/chemle/emle-engine>`__ dependencies
+* ``pixi install -e dev`` - all of the above plus test dependencies
 
-    python setup.py --install-bss-deps install
+Any additional startup commands can be specified in the ``pixi.sh`` file 
+in the root of the sire repository. This file is automatically sourced when
+you activate the pixi environment, so you can add any additional environment
+variables or startup commands here. (Note that you might see a warning if
+you haven't created this file.)
 
 Support and Development
 =======================

actions/collect_failed.py

@@ -1,4 +1,3 @@
-
 # Script that collects as much as it can from a failed conda build so that it can
 # be stored as a GitHub Actions artifact for download and further debugging
 
@@ -29,15 +28,17 @@
 
 print(f"Zipping up {zipdirs} to {output_filename}")
 
+
 def filter_function(tarinfo):
     filename = tarinfo.name
-    #print(filename)
-    if filename.find('.git') != -1:
-        #print("excluded!")
+    # print(filename)
+    if filename.find(".git") != -1:
+        # print("excluded!")
         return None
     else:
         return tarinfo
 
+
 with tarfile.open(output_filename, "w:bz2") as tar:
     for dir in zipdirs:
         tar.add(dir, arcname=os.path.basename(dir), filter=filter_function)