Migrate to pixi (#12)

* Draft usage of pixi in ci.yml.

* Add names.

* Wrap values in quotes.

* Convert item to list.

* Fix typo.

* Add missing action.

* Move pchs to pixi.

* Fix syntax error.

* Add missing tasks.

* Fix mypy job.

* Bring back mypy pch.

* Bring back mypy pch.

* Remove redundant dependency.

* Adapt readthedocs configuration.

* Create docs environment.

* Fix docs task.

* Update .pre-commit-config.yaml

Co-authored-by: Pavel Zwerschke <[email protected]>

* Update pixi.toml

Co-authored-by: Pavel Zwerschke <[email protected]>

* Update .github/workflows/ci.yml

Co-authored-by: Pavel Zwerschke <[email protected]>

* Update pixi.toml

Co-authored-by: Pavel Zwerschke <[email protected]>

* Update pixi.toml

Co-authored-by: Pavel Zwerschke <[email protected]>

* Update lock.

* Remove redundant mypy step.

* Fix unit test name.

* Also update benchmark action.

* Fix typo.

* Disable Windows tests.

* Remove redundant reference to lint environment.

* Update .pre-commit-config.yaml

Co-authored-by: Pavel Zwerschke <[email protected]>

* Update .github/workflows/ci.yml

Co-authored-by: Pavel Zwerschke <[email protected]>

* Replace license headers.

* Replace double quotes by single quotes.

---------

Co-authored-by: Pavel Zwerschke <[email protected]>

.github/workflows/benchmarks.yml

@@ -13,20 +13,14 @@ jobs:
     name: Run benchmarks
     runs-on: ubuntu-latest
     steps:
-      - name: Checkout
+      - name: Checkout branch
         uses: actions/checkout@v4
-        with:
-          ref: main
-          fetch-depth: 0
-      - name: Setup conda
-        uses: mamba-org/setup-micromamba@v1
-        with:
-          condarc-file: .github/assets/.condarc
-          environment-file: benchmarks/environment.yml
-      - name: Install package
-        run: python -m pip install -e .
-      - name: Run benchmark.py
-        run: python benchmarks/benchmark.py
+      - name: Set up pixi
+        uses: prefix-dev/[email protected]
+      - name: Install repository
+        run: |
+          pixi run -e default postinstall
+          pixi run -e default python benchmarks/benchmark.py
       - name: Update readme.md
         run: |
           line_number=`grep "| T-learner" benchmarks/readme.md -n | cut -f1 -d:`

.github/workflows/ci.yml

@@ -18,68 +18,41 @@ jobs:
     steps:
       - name: Checkout branch
         uses: actions/checkout@v4
+      - name: Set up pixi
+        uses: prefix-dev/[email protected]
         with:
-          ref: ${{ github.head_ref }}
-          # needed for 'pre-commit-mirrors-insert-license'
-          fetch-depth: 0
-      - name: Run pre-commit-conda
-        uses: quantco/pre-commit-conda@v1
-
-  mypy-type-checks:
-    name: Mypy Type Checks
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout branch
-        uses: actions/checkout@v4
-        with:
-          ref: ${{ github.head_ref }}
-          fetch-depth: 0
-      - name: Set up Conda env
-        uses: mamba-org/setup-micromamba@422500192359a097648154e8db4e39bdb6c6eed7
-        with:
-          condarc-file: .github/assets/.condarc
-          environment-file: environment.yml
-          cache-environment: true
-      - name: Install repository
-        run: python -m pip install --no-build-isolation --no-deps --disable-pip-version-check -e .
-      - name: Run mypy
-        run: mypy .
+          environments: default lint
+      - name: pre-commit
+        run: pixi run pre-commit-run --color=always --show-diff-on-failure
 
   unit-tests:
-    name: Unit Tests - ${{ matrix.os == 'ubuntu-latest' && 'Linux' || 'Windows' }} - Python ${{ matrix.python-version }}
+    name: Unit Tests
     timeout-minutes: 30
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest]
-        python-version: ["3.10", "3.11", "3.12"]
+        os: [ubuntu-latest, macos-latest]
+        env: ["py310", "py311", "py312"]
     steps:
       - name: Checkout branch
         uses: actions/checkout@v4
+      - name: Set up pixi
+        uses: prefix-dev/[email protected]
         with:
-          ref: ${{ github.head_ref }}
-          fetch-depth: 0
-      - name: Set up Conda env
-        uses: mamba-org/setup-micromamba@422500192359a097648154e8db4e39bdb6c6eed7
-        with:
-          condarc-file: .github/assets/.condarc
-          environment-file: environment.yml
-          cache-environment: true
-          create-args: >-
-            python=${{ matrix.python-version }}
-            pytest-md
-            pytest-emoji
+          environments: ${{ matrix.env }}
       - name: Install repository
-        run: python -m pip install --no-build-isolation --no-deps --disable-pip-version-check -e .
-      - name: Run unittests
-        uses: quantco/pytest-action@v2
+        run: |
+          pixi run -e ${{ matrix.env }} postinstall
+          pixi run -e ${{ matrix.env }} coverage
+      - name: Generate code coverage report
+        if: matrix.python-version == '3.12'
+        uses: codecov/[email protected]
         with:
-          report-title: Unit Tests - ${{ matrix.os == 'ubuntu-latest' && 'Linux' || 'Windows' }} - Python ${{ matrix.python-version }}
-          custom-arguments: --cov=metalearners --cov-report=xml --cov-report term-missing --color=yes
+          file: ./coverage.xml
       - name: Upload coverage reports to Codecov
-        if: matrix.python-version == '3.12'
-        uses: codecov/codecov-action@125fc84a9a348dbcf27191600683ec096ec9021c
+        if: matrix.env == 'py312'
+        uses: codecov/codecov-action@v3.1.3
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
           file: ./coverage.xml

.pre-commit-config.yaml

@@ -1,45 +1,81 @@
+exclude: ^\.pixi
 repos:
-  - repo: https://github.com/Quantco/pre-commit-mirrors-insert-license
-    rev: 1.3.0
+  - repo: local
     hooks:
+      # 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
       - id: insert-license
+        name: insert-license
+        entry: pixi run -e lint insert-license
         types: [python]
+        language: system
         args:
           - --license-base64
-          - IyBDb3B5cmlnaHQgKGMpIFF1YW50Q28gMjAyNC0yMDI0CiMgU1BEWC1MaWNlbnNlLUlkZW50aWZpZXI6IEJTRC0zLUNsYXVzZQo=
+          - Q29weXJpZ2h0IChjKSBRdWFudENvIDIwMjQtMjAyNApTUERYLUxpY2Vuc2UtSWRlbnRpZmllcjogQlNELTMtQ2xhdXNl
           - --dynamic-years
           - --comment-style
           - "#"
-  - repo: https://github.com/Quantco/pre-commit-mirrors-docformatter
-    rev: 1.7.5
-    hooks:
-      - id: docformatter-conda
-  - repo: https://github.com/Quantco/pre-commit-mirrors-ruff
-    rev: 0.4.7
-    hooks:
-      - id: ruff-conda
-  - repo: https://github.com/Quantco/pre-commit-mirrors-black
-    rev: 24.4.2
-    hooks:
+      - id: docformatter
+        name: docformatter
+        entry: pixi run -e lint docformatter
+        args: [-i]
+        types: [python]
+        language: system
+      - 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: black-conda
-  - repo: https://github.com/Quantco/pre-commit-mirrors-mypy
-    rev: 1.10.0
-    hooks:
-      - id: mypy-conda
-        additional_dependencies: [-c, conda-forge, types-setuptools]
-  - repo: https://github.com/Quantco/pre-commit-mirrors-prettier
-    rev: 3.2.5
-    hooks:
-      - id: prettier-conda
+        name: black-conda
+        entry: pixi run -e lint black
+        language: system
+        require_serial: true
+        types: [python]
+      - id: mypy
+        name: mypy
+        entry: pixi run -e default mypy
+        language: system
+        types: [python]
+        args: ["--ignore-missing-imports", "--scripts-are-modules"]
+        require_serial: true
+      - id: prettier
+        name: prettier
+        entry: pixi run -e lint prettier
+        language: system
         files: \.(md|yml|yaml)$
-  - repo: https://github.com/Quantco/pre-commit-mirrors-pre-commit-hooks
-    rev: 4.6.0
-    hooks:
-      - id: trailing-whitespace-conda
-      - id: end-of-file-fixer-conda
-      - id: check-merge-conflict-conda
+        types: [text]
+        args: ["--write", "--list-different", "--ignore-unknown"]
+      - id: trailing-whitespace
+        name: trim trailing whitespace
+        language: system
+        entry: pixi run -e lint trailing-whitespace-fixer
+        types: [text]
+        stages: [commit, push, manual]
+      - id: end-of-file-fixer
+        name: fix end of files
+        language: system
+        entry: pixi run -e lint end-of-file-fixer
+        types: [text]
+        stages: [commit, push, manual]
+      - id: check-merge-conflict
+        name: check for merge conflicts
+        language: system
+        entry: pixi run -e lint check-merge-conflict
+        types: [text]
         args: ["--assume-in-merge"]
-  - repo: https://github.com/Quantco/pre-commit-mirrors-typos
-    rev: 1.21.0
-    hooks:
-      - id: typos-conda
+      - id: typos
+        name: typos
+        entry: pixi run -e lint typos --force-exclude
+        language: system
+        types: [text]
+        exclude: "\\.csv$"
+        require_serial: true

.readthedocs.yml

@@ -2,17 +2,13 @@ version: 2
 build:
   os: ubuntu-20.04
   tools:
-    python: mambaforge-4.10
+    python: mambaforge-latest
+  commands:
+    - mamba install -c conda-forge -c nodefaults pixi
+    - pixi run -e docs postinstall
+    - pixi run -e docs docs
+    - pixi run -e docs readthedocs
 sphinx:
   configuration: docs/conf.py
-python:
-  install:
-    - method: pip
-      path: .
-      extra_requirements:
-        - doc
-        - test
-conda:
-  environment: environment.yml
 formats:
   - pdf

benchmarks/benchmark.py

@@ -1,5 +1,5 @@
-# # Copyright (c) QuantCo 2024-2024
-# # SPDX-License-Identifier: BSD-3-Clause
+# Copyright (c) QuantCo 2024-2024
+# SPDX-License-Identifier: BSD-3-Clause
 
 import json
 from pathlib import Path

data/download_twins.py

@@ -1,5 +1,5 @@
-# # Copyright (c) QuantCo 2024-2024
-# # SPDX-License-Identifier: BSD-3-Clause
+# Copyright (c) QuantCo 2024-2024
+# SPDX-License-Identifier: BSD-3-Clause
 
 import pandas as pd
 from git_root import git_root

docs/conf.py

@@ -1,5 +1,5 @@
-# # Copyright (c) QuantCo 2024-2024
-# # SPDX-License-Identifier: BSD-3-Clause
+# Copyright (c) QuantCo 2024-2024
+# SPDX-License-Identifier: BSD-3-Clause
 
 # Configuration file for the Sphinx documentation builder.
 #

metalearners/__init__.py

@@ -1,5 +1,5 @@
-# # Copyright (c) QuantCo 2024-2024
-# # SPDX-License-Identifier: BSD-3-Clause
+# Copyright (c) QuantCo 2024-2024
+# SPDX-License-Identifier: BSD-3-Clause
 
 import importlib.metadata
 import warnings

metalearners/_typing.py

@@ -1,5 +1,5 @@
-# # Copyright (c) QuantCo 2024-2024
-# # SPDX-License-Identifier: BSD-3-Clause
+# Copyright (c) QuantCo 2024-2024
+# SPDX-License-Identifier: BSD-3-Clause
 
 from collections.abc import Collection, Mapping
 from typing import Literal, Protocol, Union

metalearners/_utils.py

@@ -1,5 +1,5 @@
-# # Copyright (c) QuantCo 2024-2024
-# # SPDX-License-Identifier: BSD-3-Clause
+# Copyright (c) QuantCo 2024-2024
+# SPDX-License-Identifier: BSD-3-Clause
 
 from collections.abc import Callable
 from inspect import signature

metalearners/cross_fit_estimator.py

@@ -1,5 +1,5 @@
-# # Copyright (c) QuantCo 2024-2024
-# # SPDX-License-Identifier: BSD-3-Clause
+# Copyright (c) QuantCo 2024-2024
+# SPDX-License-Identifier: BSD-3-Clause
 
 import warnings
 from dataclasses import dataclass, field

metalearners/data_generation.py

@@ -1,5 +1,5 @@
-# # Copyright (c) QuantCo 2024-2024
-# # SPDX-License-Identifier: BSD-3-Clause
+# Copyright (c) QuantCo 2024-2024
+# SPDX-License-Identifier: BSD-3-Clause
 
 from typing import Literal
 

metalearners/drlearner.py

@@ -1,5 +1,5 @@
-# # Copyright (c) QuantCo 2024-2024
-# # SPDX-License-Identifier: BSD-3-Clause
+# Copyright (c) QuantCo 2024-2024
+# SPDX-License-Identifier: BSD-3-Clause
 
 import numpy as np
 from joblib import Parallel, delayed

metalearners/explainer.py

@@ -1,5 +1,5 @@
-# # Copyright (c) QuantCo 2024-2024
-# # SPDX-License-Identifier: BSD-3-Clause
+# Copyright (c) QuantCo 2024-2024
+# SPDX-License-Identifier: BSD-3-Clause
 
 from collections.abc import Collection
 

metalearners/metalearner.py

@@ -1,5 +1,5 @@
-# # Copyright (c) QuantCo 2024-2024
-# # SPDX-License-Identifier: BSD-3-Clause
+# Copyright (c) QuantCo 2024-2024
+# SPDX-License-Identifier: BSD-3-Clause
 
 from abc import ABC, abstractmethod
 from collections.abc import Callable, Collection

metalearners/outcome_functions.py

@@ -1,5 +1,5 @@
-# # Copyright (c) QuantCo 2024-2024
-# # SPDX-License-Identifier: BSD-3-Clause
+# Copyright (c) QuantCo 2024-2024
+# SPDX-License-Identifier: BSD-3-Clause
 
 from collections.abc import Callable