Switch to pixi

.gitattributes

@@ -0,0 +1,2 @@
+# GitHub syntax highlighting
+pixi.lock linguist-language=YAML linguist-generated=true

.github/workflows/ci.yml

@@ -3,87 +3,55 @@ on: [push]
 
 jobs:
   pre-commit-checks:
-    name: pre-commit checks
+    name: Linux - pre-commit checks
     timeout-minutes: 30
     runs-on: ubuntu-latest
-    env:
-      PRE_COMMIT_USE_MICROMAMBA: 1
     steps:
       - name: Checkout branch
         uses: actions/checkout@v4
-      - name: Set up micromamba
-        uses: mamba-org/setup-micromamba@f8b8a1e23a26f60a44c853292711bacfd3eac822
-      - name: Add micromamba to GITHUB_PATH
-        run: echo "${HOME}/micromamba-bin" >> "$GITHUB_PATH"
-      - name: Install Python 3.10
-        uses: actions/setup-python@v5
+      - name: Set up pixi
+        uses: prefix-dev/setup-pixi@v0.8.1
         with:
-          python-version: "3.10"
-      - name: Run pre-commit checks
-        uses: pre-commit/action@v3.0.1
+          environments: lint default
+      - name: pre-commit
+        run: pixi run -e lint pre-commit-run --color=always --show-diff-on-failure
 
   unit-tests:
-    name: Tests - ${{ matrix.os }} - Py${{ matrix.python-version }} - ${{ matrix.note }}
+    name: Tests
     runs-on: ${{ matrix.os }}
+    env:
+      CI: True
     strategy:
       fail-fast: true
       matrix:
         include:
-          - { os: ubuntu-latest,  python-version: '3.9',  note: 'Default Builds' }
-          - { os: ubuntu-latest,  python-version: '3.10', note: 'Default Builds' }
-          - { os: ubuntu-latest,  python-version: '3.11', note: 'Default Builds' }
-          - { os: ubuntu-latest,  python-version: '3.12', note: 'Default Builds' }
-          - { os: ubuntu-latest,  python-version: '3.12', note: 'Nightly Builds' }
-          - { os: macos-latest,   python-version: '3.12', note: 'Default Builds' }
-          - { os: windows-latest, python-version: '3.12', note: 'Default Builds' }
+          - { os: ubuntu-latest, environment: 'py310' }
+          - { os: ubuntu-latest, environment: 'py311' }
+          - { os: ubuntu-latest, environment: 'py312' }
+          - { os: windows-latest, environment: 'py312' }
+          - { os: macos-latest, environment: 'py312' }
+          - { os: ubuntu-latest, environment: 'oldies' }
+          - { os: ubuntu-latest, environment: 'nightly' }
     steps:
       - name: Checkout branch
         uses: actions/checkout@v4
-      - name: Set up conda env
-        uses: mamba-org/setup-micromamba@f8b8a1e23a26f60a44c853292711bacfd3eac822
+      - name: Set up pixi
+        uses: prefix-dev/setup-pixi@992a3081e2f87829e0fff9fb29f4fe6a5d1e80a2
         with:
-          environment-file: ${{ matrix.os == 'windows-latest' && 'environment-win.yml' || 'environment.yml' }}
-          init-shell: ${{ matrix.os == 'windows-latest' && 'powershell' || 'bash' }}
-          cache-environment: true
-          create-args: >-
-            python=${{ matrix.python-version }}
+          environments: ${{ matrix.environment }}
       - name: Install nightlies
-        if: matrix.note == 'Nightly Builds'
-        shell: bash -el {0}
-        run: |
-          PRE_WHEELS="https://pypi.anaconda.org/scientific-python-nightly-wheels/simple/"
-          for pkg in numpy pandas scipy; do
-            echo "Installing $pkg nightly"
-            micromamba remove -y --force $pkg
-            pip install --pre --no-deps --only-binary :all: --upgrade --timeout=60 -i $PRE_WHEELS $pkg
-          done
-          micromamba remove -y --force formulaic
-          pip install --no-deps git+https://github.com/matthewwardrop/formulaic
-          micromamba list
-      - name: Install repository (unix)
-        if: matrix.os != 'windows-latest'
-        shell: bash -el {0}
-        run: pip install --no-use-pep517 --no-deps --disable-pip-version-check -e .
-      - name: Install repository (windows)
-        if: matrix.os == 'windows-latest'
-        shell: powershell
-        run: pip install --no-use-pep517 --no-deps --disable-pip-version-check -e .
-      - name: Run pytest (unix)
-        if: matrix.os != 'windows-latest'
-        shell: bash -el {0}
-        run: pytest -nauto tests -m "not high_memory" --doctest-modules src/
-      - name: Run pytest (windows)
-        if: matrix.os == 'windows-latest'
-        shell: powershell
-        run: pytest -nauto tests -m "not high_memory"
+        if: matrix.NOTE == 'Nightly Builds'
+        run: pixi run -e ${{ matrix.environment }} install-nightlies
+      - name: Install repository
+        run: pixi run -e ${{ matrix.environment }} postinstall
+      - name: Run pytest
+        run: pixi run -e ${{ matrix.environment }} test -nauto -m "not high_memory"
       - name: Run doctest
-        if: matrix.os != 'windows-latest'
-        shell: bash -el {0}
         # Check that the readme example will work by running via doctest.
         # We run outside the repo to make the test a bit more similar to
         # a user running after installing with conda.
         run: |
           mkdir ../temp
           cp README.md ../temp
           cd ../temp
-          python -m doctest -v README.md
+          pixi run --manifest-path ../tabmat/pixi.toml -e ${{ matrix.environment }} python -m doctest -v README.md

.github/workflows/daily.yml

@@ -9,41 +9,42 @@ on:
 
 jobs:
   linux-daily-unittests:
-    name: Daily unit tests - Py${{ matrix.python-version }} - ${{ matrix.note }}
+    name: "Linux - daily unit tests - ${{ matrix.NOTE }}"
     runs-on: ubuntu-latest
+    env:
+      CI: True
     strategy:
       fail-fast: false
       matrix:
         include:
-          - { python-version: '3.9',  note: 'Default Builds' }
-          - { python-version: '3.12', note: 'Nightly Builds' }
+          - environment: 'nightly'
+            NOTE: 'Nightly Builds' # run once with nightlies
+          - environment: 'py312'
+            NOTE: 'Python 3.12' # run once with normal dependencies
     steps:
       - name: Checkout branch
         uses: actions/checkout@v4
-      - uses: mamba-org/setup-micromamba@f8b8a1e23a26f60a44c853292711bacfd3eac822
+      - name: Set up pixi
+        uses: prefix-dev/setup-pixi@992a3081e2f87829e0fff9fb29f4fe6a5d1e80a2
         with:
-          environment-file: environment.yml
-          create-args: >-
-            python=${{ matrix.python-version }}
+          environments: ${{ matrix.environment }}
       - name: Install nightlies
-        if: matrix.note == 'Nightly Builds'
-        shell: bash -el {0}
-        run: |
-          PRE_WHEELS="https://pypi.anaconda.org/scientific-python-nightly-wheels/simple/"
-          for pkg in numpy pandas scipy; do
-            echo "Installing $pkg nightly"
-            micromamba remove -y --force $pkg
-            pip install --pre --no-deps --only-binary :all: --upgrade --timeout=60 -i $PRE_WHEELS $pkg
-          done
-          micromamba remove -y --force formulaic
-          pip install --no-deps git+https://github.com/matthewwardrop/formulaic
-          micromamba list
+        if: matrix.NOTE == 'Nightly Builds'
+        run: pixi run -e ${{ matrix.environment }} install-nightlies
       - name: Install repository
-        shell: bash -el {0}
-        run: pip install --no-use-pep517 --no-deps --disable-pip-version-check -e .
+        run: pixi run -e ${{ matrix.environment }} postinstall
       - name: Run pytest
-        shell: bash -el {0}
-        run: pytest -nauto tests -m "not high_memory" --doctest-modules src/
+        run: pixi run -e ${{ matrix.environment }} test -nauto -m "not high_memory"
+      - name: Run doctest
+        # Check that the readme example will work by running via doctest.
+        # We run outside the repo to make the test a bit more similar to
+        # a user running after installing with conda.
+        run: |
+          mkdir ../temp
+          cp README.md ../temp
+          cd ../temp
+          pixi run --manifest-path ../tabmat/pixi.toml -e ${{ matrix.environment }} python -m doctest -v README.md
+
       - name: Issue on failure
         uses: actions/github-script@v7
         if: ${{ failure() }}

.gitignore

@@ -1,5 +1,6 @@
 # Project-specific
 benchmark/*.csv
+benchmark/data/*.csv
 benchmark/data/*.pkl
 
 # Files created by templating
@@ -147,3 +148,6 @@ pkgs/*
 *.c
 *.cpp
 !*tmpl.cpp
+# pixi environments
+.pixi
+*.egg-info

.pre-commit-config.yaml

@@ -1,16 +1,47 @@
+exclude: ^.pixi$
 repos:
-  - repo: https://github.com/Quantco/pre-commit-mirrors-ruff
-    rev: 0.6.2
+  - repo: local
     hooks:
-      - id: ruff-conda
-      - id: ruff-format-conda
-  - repo: https://github.com/Quantco/pre-commit-mirrors-mypy
-    rev: "1.10.1"
-    hooks:
-      - id: mypy-conda
-  - repo: https://github.com/Quantco/pre-commit-mirrors-cython-lint
-    rev: 0.16.2
-    hooks:
-      - id: cython-lint-conda
-        args: [--no-pycodestyle]
-      - id: double-quote-cython-strings-conda
+      # ensure pixi environments are up to date
+      # workaround for https://github.com/prefix-dev/pixi/issues/1482
+      - id: pixi-install
+        name: pixi-install
+        entry: pixi install -e default -e lint
+        language: system
+        always_run: true
+        require_serial: true
+        pass_filenames: false
+      # ruff
+      - id: ruff
+        name: ruff
+        entry: pixi run -e lint ruff check --fix --exit-non-zero-on-fix --force-exclude
+        language: system
+        types_or: [python, pyi]
+        require_serial: true
+      - id: ruff-format
+        name: ruff-format
+        entry: pixi run -e lint ruff format --force-exclude
+        language: system
+        types_or: [python, pyi]
+        require_serial: true
+      # mypy
+      - id: mypy
+        name: mypy
+        entry: pixi run -e default mypy --allow-redefinition
+        exclude: (^tests/)
+        language: system
+        types: [python]
+        require_serial: true
+      # cython-lint
+      - id: cython-lint
+        name: cython-lint
+        entry: pixi run -e lint cython-lint --no-pycodestyle
+        language: system
+        types: [cython]
+        require_serial: true
+      - id: cython-double-quote
+        name: cython-double-quote
+        entry: pixi run -e lint double-quote-cython-strings
+        language: system
+        types: [cython]
+        require_serial: true

.readthedocs.yml

@@ -2,14 +2,12 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: mambaforge-22.9
+    python: mambaforge-4.10
+  commands:
+    - mamba install -c conda-forge -c nodefaults pixi==0.27.0
+    - pixi run -e docs postinstall
+    - pixi run readthedocs
 sphinx:
   configuration: docs/conf.py
-python:
-  install:
-  - method: pip
-    path: .
-conda:
-  environment: environment.yml
 formats:
-- pdf
+- pdf

CONTRIBUTING.md

@@ -28,51 +28,51 @@ Releases
 
 Development installation
 ------------------------
-For development, you should do an editable installation: 
+We use [pixi](https://prefix.dev/) for setting up the project dependencies. [Install it](https://pixi.sh/latest/#installation) first if you do not have it already. The following commands will set up the project for development:
 
 ```bash
-# First, make sure you have conda-forge as your primary conda channel:
-conda config --add channels conda-forge
-# And install pre-commit
-conda install -y pre-commit
-
 git clone git@github.com:Quantco/tabmat.git
 cd tabmat
 
 # Set up our pre-commit hooks for ruff, mypy, and cython-lint.
-pre-commit install
+pixi run pre-commit-install
+
+# Set up a pixi environment with the dependencies and install the package in editable mode.
+pixi run postinstall
+
+# If you want to install the dependencies necessary for benchmarking against other GLM packages:
+pixi run -e benchmark postinstall
 
-# Set up a conda environment with name "tabmat"
-conda env create
+# If you want to work on the documentation:
+pixi run -e docs postinstall
 
-# Install this package in editable mode. 
-conda activate tabmat
-pip install --no-use-pep517 --disable-pip-version-check -e .
+# You can run any command in the pixi environment with `pixi run <command>`. For example:
+pixi run [-e ENVIRONMENT] ipython
+
+# Alternatively, you can create a shell with the pixi environment activated:
+pixi shell
+
+# A number of pixi tasks are available for commonly used commands.
+# You can run them with `pixi run <task>`.
+# To get a list of available tasks, run:
+pixi task list
 ```
 
 Testing and continuous integration
 --------------------------------------------------
-The test suite is in ``tests/`` and can be run using ``pytest``.
+The test suite is in ``tests/`` and can be run using ``pixi run test``.
 
 Developing the documentation
 ----------------------------------------
 
-The documentation is built with Sphinx. To develop the documentation:
-
-::
-
-   cd docs
-   make html
-   python -m http.server --directory _build/html
-
-Then, navigate to `<http://localhost:8000>`_ to view the documentation.
+The documentation is built with Sphinx. To develop the documentation: ``pixi run serve-docs``. Then, navigate to `<http://localhost:8000>`_ to view the documentation.
 
 Alternatively, if you install `entr <http://eradman.com/entrproject/>`_, then you can auto-rebuild the documentation any time a file changes with:
 
-:: 
-
+```bash
    cd docs
    ./dev
+```
 
 Conda-forge packaging
 ---------------------

docs/benchmarks.rst

@@ -1,9 +1,9 @@
 Benchmarks
 ==========
 
-To generate the data to run all the benchmarks: ``python src/tabmat/benchmark/generate_matrices.py``. Then, to run all the benchmarks: ``python src/tabmat/benchmark/main.py``. To produce or update these figures, open ``src/tabmat/benchmark/visualize_benchmarks.py`` as a notebook via ``jupytext``. 
+To generate the data to run all the benchmarks: ``pixi run benchmark-generate-matrices``. Then, to run all the benchmarks with default settings: ``python src/tabmat/benchmark/benchmark-run``. To produce or update these figures, open ``src/tabmat/benchmark/visualize_benchmarks.py`` as a notebook via ``jupytext``. 
 
-For more info on the benchmark CLI: ``python src/tabmat/benchmark/main.py --help``.
+For more info on the benchmark CLI: ``pixi run python src/tabmat/benchmark/main.py --help``.
 
 Performance
 ^^^^^^^^^^^