Merge pull request #901 from padix-key/pixi

Replace Conda setup with Pixi setup

Author: padix-key

.gitattributes

@@ -1,3 +1,4 @@
 tests/structure/data/* linguist-vendored
 tests/sequence/data/* linguist-vendored
 src/biotite/sequence/align/matrix_data/* linguist-vendored
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true -diff

.github/workflows/test_and_deploy.yml

@@ -28,8 +28,6 @@ env:
     --ignore={project}//tests//test_doctest.py
     --ignore={project}//tests//test_modname.py
   CIBW_DEPENDENCY_VERSIONS: "pinned"
-  # Configuration for the architecture-agnostic jobs
-  PY_VERSION: "3.12"  # Keep in sync with version in environment.yml
 
 
 jobs:
@@ -38,27 +36,13 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
-    - uses: actions-rs/toolchain@v1
+    - uses: prefix-dev/setup-pixi@v0.9.6
       with:
-        toolchain: 1.95.0
-        override: true
-        components: rustfmt, clippy
-    - uses: actions/setup-python@v5
-      with:
-        python-version: "3.12"
-    - name: Install ruff
-      # Keep in sync with the corresponding versions in pyproject.toml
-      run: pip install ruff==0.9.7 numpydoc==1.8.0
-    - name: Check code formatting
-      run: ruff format --diff
-    - name: Lint code base
-      run: ruff check
-    - name: Check docstring formatting
-      run: numpydoc lint src/biotite/**/*.py
-    - name: Check Rust formatting
-      run: cargo fmt --check
-    - name: Check Rust lints
-      run: cargo clippy -- -Dwarnings
+        environments: lint
+        cache: true
+        cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
+    - name: Check code style and type annotations
+      run: pixi run lint
 
 
   build-internal:
@@ -71,28 +55,14 @@ jobs:
           # so 'switcher.py' works correctly in 'docs' job
           fetch-depth: 0
           fetch-tags: true
-      - uses: actions/setup-python@v5
+      - uses: prefix-dev/setup-pixi@v0.9.6
         with:
-          python-version: ${{ env.PY_VERSION }}
-      - name: Get current CCD for hashing
-        run: wget https://files.wwpdb.org/pub/pdb/data/monomers/components.cif.gz
-      - name: Cache CCD
-        uses: actions/cache@v4
-        id: cache-ccd
-        with:
-          path: ./src/biotite/structure/info/components.bcif
-          key: cache-${{ hashFiles('src/biotite/setup_ccd.py') }}-${{ hashFiles('components.cif.gz') }}
-      - name: Remove CCD used for hashing
-        run: rm components.cif.gz
-      - name: Build internal CCD
-        if: steps.cache-ccd.outputs.cache-hit != 'true'
-        run: |
-          pip install -e .
-          python -m biotite.setup_ccd
-      - name: Install build backend
-        run: pip install build
-      - name: Build distribution
-        run: python -m build --wheel
+          environments: test
+          activate-environment: true
+          cache: true
+          cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
+      - name: Build CCD and wheel
+        run: pixi run build-wheel
       - uses: actions/upload-artifact@v4
         with:
           name: internal-build
@@ -201,27 +171,27 @@ jobs:
     runs-on: ubuntu-latest
     needs:
       - build-internal
-    defaults:
-      run:
-        shell: bash -l {0}
 
     steps:
       - uses: actions/checkout@v4
       - uses: actions/download-artifact@v4
         with:
           name: internal-build
           path: dist
-      - uses: conda-incubator/setup-miniconda@v3
+      - uses: prefix-dev/setup-pixi@v0.9.6
         with:
-          environment-file: environment.yml
-          miniforge-version: latest
-      - name: Install distribution
-        run: pip install ./dist/*.whl
+          environments: test
+          activate-environment: true
+          cache: true
+          cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
+      - name: Install pre-built wheel into the pixi environment
+        # `--no-deps` because conda already provides all runtime dependencies
+        run: pixi run python -m pip install --no-deps ./dist/*.whl
       - name: Run tests
         # Running NCBI BLAST and SRA takes too long
         # The tests on the NCBI Entrez database are not reliable enough
         run: >
-          pytest
+          pixi run pytest
           --durations=50
           --ignore="tests//application//test_blast.py"
           --ignore="tests//application//test_sra.py"
@@ -239,27 +209,23 @@ jobs:
     runs-on: ubuntu-latest
     needs:
       - build-internal
-    defaults:
-      run:
-        shell: bash -l {0}
 
     steps:
       - uses: actions/checkout@v4
       - uses: actions/download-artifact@v4
         with:
           name: internal-build
           path: dist
-      - uses: conda-incubator/setup-miniconda@v3
+      - uses: prefix-dev/setup-pixi@v0.9.6
         with:
-          activate-environment: biotite-dev
-          miniforge-version: latest
-          python-version: ${{ env.PY_VERSION }}
-      - name: Install Muscle 5
-        run: conda install -c bioconda "muscle=5"
-      - name: Install distribution and pytest
-        run: pip install .//dist//*.whl pytest
+          environments: test-muscle5
+          activate-environment: true
+          cache: true
+          cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
+      - name: Install pre-built wheel into the pixi environment
+        run: pixi run python -m pip install --no-deps ./dist/*.whl
       - name: Test Muscle 5 interface
-        run: pytest --durations=50 tests//application//test_msa.py
+        run: pixi run pytest --durations=50 tests//application//test_msa.py
 
 
   docs:
@@ -268,9 +234,6 @@ jobs:
     runs-on: ubuntu-latest
     needs:
       - build-internal
-    defaults:
-      run:
-        shell: bash -l {0}
     env:
       NCBI_API_KEY: ${{ secrets.NCBI_API_KEY }}
 
@@ -280,10 +243,12 @@ jobs:
       with:
         name: internal-build
         path: dist
-    - uses: conda-incubator/setup-miniconda@v3
+    - uses: prefix-dev/setup-pixi@v0.9.6
       with:
-        environment-file: environment.yml
-        miniforge-version: latest
+        environments: doc
+        cache: true
+        activate-environment: true
+        cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
     - name: Restore cached partially build docs from a failed previous build
       id: cache-docs-restore
       uses: actions/cache/restore@v4
@@ -294,18 +259,20 @@ jobs:
           doc/examples/gallery
           build/doc
           build/jupyter_execute
-    - name: Install distribution
-      run: pip install dist/*.whl
+    - name: Install pre-built wheel into the pixi environment
+      run: pixi run python -m pip install --no-deps ./dist/*.whl
+    # Calling `sphinx-build` directly instead of `doc` task
+    # to avoid the time consuming call of the `install` task
     - name: Build base documentation
-      run: sphinx-build -a -D plot_gallery=0 doc build/doc
+      run: pixi run sphinx-build -a -D plot_gallery=0 doc build/doc
     - name: Build tutorial and gallery
       if: >
         (
           github.event_name == 'release' &&
           github.event.action == 'published'
         )
         || github.event_name == 'workflow_dispatch'
-      run: sphinx-build -a doc build/doc
+      run: pixi run sphinx-build -a doc build/doc
     - name: Cache partially built docs from failed build
       id: cache-docs-save
       if: failure()
@@ -340,15 +307,17 @@ jobs:
         with:
           name: internal-build
           path: dist
-      - uses: actions/setup-python@v5
+      - uses: prefix-dev/setup-pixi@v0.9.6
         with:
-          python-version: ${{ env.PY_VERSION }}
-      - name: Install dependencies
-        run: pip install dist//*.whl pytest pytest-codspeed
+          environments: test
+          cache: true
+          cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
+      - name: Install pre-built wheel into the pixi environment
+        run: pixi run -e test python -m pip install --no-deps ./dist/*.whl
       - name: Run benchmarks
         uses: CodSpeedHQ/action@v3
         with:
-          run: pytest --codspeed benchmarks
+          run: pixi run -e test pytest --codspeed benchmarks
 
 
   upload-package:

.gitignore

@@ -56,6 +56,12 @@ htmlcov
 # Ignore potential directory created during install
 biotite.egg-info
 
+# Pixi environments
+.pixi/*
+
+# Marker file used by the `_current-date` pixi task
+/.date
+
 # Ignore IntelliJ IDEA directory and project files
 .idea
 *.iml

doc/contribution/development.rst

@@ -65,7 +65,22 @@ To make code changes ready for a pull request, simply run
    $ ruff format
    $ ruff check --fix
 
-and fix the remaining linter complaints.
+for *Python* code and
+
+.. code-block:: console
+
+   $ cargo fmt
+   $ cargo clippy --fix --allow-dirty
+
+for *Rust* code, and fix the remaining linter complaints.
+
+Equivalently, run
+
+.. code-block:: console
+
+   $ pixi run format
+
+in a *Pixi* setup.
 
 Dependencies
 ------------

doc/contribution/documentation.rst

@@ -15,12 +15,18 @@ Therefore, the documentation is based on *reStructuredText* files.
 The line length of these ``*.rst`` files is also limited to 79 characters
 where reasonable.
 
-To build the documentation, run from the root directory of the repository:
+To build the documentation, run from the root directory of the repository
 
 .. code-block:: console
 
     $ sphinx-build doc build/doc
 
+or in a ``pixi``-managed environment
+
+.. code-block:: console
+
+    $ pixi run doc-full
+
 Documentation structure
 -----------------------
 *Biotite* employs the
@@ -79,6 +85,12 @@ To build the documentation without the gallery and the tutorial, run
 
     $ sphinx-build -D plot_gallery=0 doc build/doc
 
+or, equivalently,
+
+.. code-block:: console
+
+    $ pixi run doc
+
 You may also ask the *Biotite* maintainers to run the example script and check
 the generated page, if building the gallery on your device is not possible.
 

doc/contribution/index.rst

@@ -33,19 +33,37 @@ version of *Biotite*.
 Requirements
 ------------
 
-Development of *Biotite* requires a few packages in addition to the ones
-specified in
-`pyproject.toml <http://raw.githubusercontent.com/biotite-dev/biotite/master/pyproject.toml>`_.
-The full list is provided in
+For development of *Biotite* we recommend using the `Pixi <https://pixi.prefix.dev>`_
+environment specified in the ``pyproject.toml``.
+
+.. code-block:: console
+
+   $ pixi run install
+   $ pixi shell
+
+The most common workflows are exposed as tasks (run ``pixi task list``
+to see all of them), for example:
+
+.. code-block:: console
+
+   $ pixi run test
+   $ pixi run lint
+   $ pixi run format
+   $ pixi run doc
+
+Conda setup
+^^^^^^^^^^^
+
+If ``conda``/``mamba`` is preferred, the required packages are mirrored in the
 `environment.yml <http://raw.githubusercontent.com/biotite-dev/biotite/master/environment.yml>`_.
-If you use the `Conda <https://docs.conda.io>`_ package manager, you can simply
-create a environment with all required dependencies by running
 
 .. code-block:: console
 
    $ conda env create -f environment.yml
    $ conda activate biotite-dev
 
+Note that the `conda` setup is considered deprecated and may be removed in the future.
+
 Contributing examples
 ---------------------
 

doc/contribution/testing.rst

@@ -7,29 +7,17 @@ While developing a new feature or fixing a bug, it is handy to run a test
 script against the code you are working on.
 To ensure that the imported package ``biotite`` points to the code you are
 working on, you may want to install the local repository clone in *editable*
-mode:
+mode via
 
 .. code-block:: console
 
     $ pip install -e .
 
-If you are writing or using an extension module in *Cython*, consider using
-`pyximport <https://cython.readthedocs.io/en/latest/src/userguide/source_files_and_compilation.html#compiling-with-pyximport>`_
-at the beginning of the script you use for testing.
+or
 
-.. code-block:: python
-
-    import numpy as np
-    import pyximport
-    pyximport.install(
-        build_in_temp=False,
-        setup_args={"include_dirs":np.get_include()},
-        language_level=3
-    )
+.. code-block:: console
 
-To enforce the recompilation of the changed *Cython* module, delete the
-respective compiled module (``.dll`` or ``.so``) from the ``src/`` directory,
-if already existing.
+    $ pixi run install
 
 Unit tests
 ----------
@@ -44,6 +32,12 @@ run the tests:
    $ pip install -e ".[test]"
    $ pytest
 
+In a Pixi-managed environment this is equivalent to
+
+.. code-block:: console
+
+   $ pixi run test
+
 Benchmarks
 ----------
 As outlined before, computation speed is one of the project's main goals.

doc/examples/scripts/structure/modeling/docking.py

@@ -66,6 +66,7 @@
 app = autodock.VinaApp(ligand, receptor, ref_ligand_center, [20, 20, 20])
 # For reproducibility
 app.set_seed(0)
+app.set_cpu(1)
 # This is the maximum number:
 # Vina may find less interesting binding modes
 # and thus output less models