Switch pytask-r from pixi to uv (#75)

Author: tobiasraabe

.github/workflows/main.yml

@@ -23,46 +23,39 @@ jobs:
 
     steps:
       - uses: actions/checkout@v5
-      - uses: prefix-dev/setup-pixi@v0.9.2
+      - uses: astral-sh/setup-uv@v7
         with:
-          cache: true
-          environments: typing
-      - run: pixi run typing
+          enable-cache: true
+      - name: Install just
+        uses: extractions/setup-just@v3
+      - name: Run type checking
+        run: just typing
 
   run-tests:
 
-    name: Run tests for ${{ matrix.os }} on ${{ matrix.environment }}
+    name: Run tests for ${{ matrix.os }} on ${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
 
     strategy:
       fail-fast: false
       matrix:
         os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
-        environment: ['py310', 'py311', 'py312', 'py313', 'py314']
+        python-version: ['3.10', '3.11', '3.12', '3.13', '3.14']
 
     steps:
       - uses: actions/checkout@v5
-      - uses: prefix-dev/setup-pixi@v0.9.2
+      - uses: r-lib/actions/setup-r@v2
+      - name: Install R packages
+        run: Rscript -e 'install.packages(c("jsonlite", "yaml"), repos="https://cloud.r-project.org")'
+      - uses: astral-sh/setup-uv@v7
         with:
-          cache: true
-          environments: ${{ matrix.environment }}
+          python-version: ${{ matrix.python-version }}
+          enable-cache: true
+      - name: Install just
+        uses: extractions/setup-just@v3
 
-      # Unit, integration, and end-to-end tests.
+      - name: Run tests
+        run: just test-cov
 
-      - name: Run unit tests and doctests.
-        shell: bash -l {0}
-        run: pixi run -e ${{ matrix.environment }} test -m "unit or (not integration and not end_to_end)" --cov-report=xml -n auto
-
-      - name: Upload unit test coverage reports to Codecov with GitHub Action
-        uses: codecov/codecov-action@v5
-        with:
-          flags: unit
-
-      - name: Run end-to-end tests.
-        shell: bash -l {0}
-        run: pixi run -e ${{ matrix.environment }} test -m end_to_end --cov-report=xml -n auto
-
-      - name: Upload end_to_end test coverage reports to Codecov with GitHub Action
+      - name: Upload test coverage reports to Codecov with GitHub Action
         uses: codecov/codecov-action@v5
-        with:
-          flags: end_to_end

.gitignore

@@ -21,6 +21,4 @@ src/pytask_r/_version.py
 .mypy_cache
 .ruff_cache
 .pytest_cache
-# pixi environments
-.pixi
 *.egg-info

.pre-commit-config.yaml

@@ -4,6 +4,7 @@ repos:
     hooks:
     -   id: check-added-large-files
         args: ['--maxkb=25']
+        exclude: ^uv\.lock$
     -   id: check-case-conflict
     -   id: check-merge-conflict
     -   id: check-vcs-permalinks

CHANGES.md

@@ -7,6 +7,7 @@ releases are available on [PyPI](https://pypi.org/project/pytask-r) and
 
 ## 0.4.2 - 2024-xx-xx
 
+- {pull}`75` switches CI and development tooling from pixi to uv.
 - {pull}`50` uses pixi to install R and uses uuid4 to generate more robust file names
   for serialized arguments.
 - {pull}`51` reenables testing with different Python versions.

justfile

@@ -0,0 +1,22 @@
+# Install all dependencies
+install:
+    uv sync --all-groups
+
+# Run tests
+test *FLAGS:
+    uv run --group test pytest {{FLAGS}}
+
+# Run tests with coverage
+test-cov *FLAGS:
+    uv run --group test pytest --cov=src --cov=tests --cov-report=xml -n auto {{FLAGS}}
+
+# Run type checking
+typing:
+    uv run --group typing --group test ty check src/ tests/
+
+# Run linting
+lint:
+    uvx prek run -a
+
+# Run all checks (format, lint, typing, test)
+check: lint typing test

pixi.lock

@@ -34,7 +34,7 @@ Tracker = "https://github.com/pytask-dev/pytask-r/issues"
 [project.entry-points.pytask]
 pytask_r = "pytask_r.plugin"
 
-[project.optional-dependencies]
+[dependency-groups]
 test = ["pytask-parallel", "pytest", "pytest-cov", "pytest-xdist", "pyyaml"]
 typing = ["ty>=0.0.7"]
 
@@ -60,7 +60,6 @@ source = "vcs"
 allow-direct-references = true
 
 [tool.ruff]
-target-version = "py310"
 fix = true
 unsafe-fixes = true
 
@@ -105,57 +104,5 @@ unused-ignore-comment = "ignore"
 [tool.pytest.ini_options]
 testpaths = ["tests"]
 markers = [
-    "wip: Tests that are work-in-progress.",
-    "unit: Flag for unit tests which target mainly a single function.",
-    "integration: Flag for integration tests which may comprise of multiple unit tests.",
-    "end_to_end: Flag for tests that cover the whole program.",
 ]
 norecursedirs = [".idea", ".tox"]
-
-[tool.pixi.workspace]
-channels = ["conda-forge"]
-platforms = ["win-64", "linux-64", "osx-64", "osx-arm64"]
-
-[tool.pixi.target.osx-64.dependencies]
-libgfortran5 = ">=14.2.0"
-
-[tool.pixi.target.osx-arm64.dependencies]
-libgfortran5 = ">=14.2.0"
-
-[tool.pixi.pypi-dependencies]
-pytask_r = { path = ".", editable = true }
-
-[tool.pixi.environments]
-default = { solve-group = "default" }
-test = { features = ["test"], solve-group = "default" }
-typing = { features = ["test", "typing"], solve-group = "default" }
-py310 = { features = ["py310", "test"]}
-py311 = { features = ["py311", "test"]}
-py312 = { features = ["py312", "test"]}
-py313 = { features = ["py313", "test"]}
-py314 = { features = ["py314", "test"]}
-
-[tool.pixi.feature.py310.dependencies]
-python = "3.10.*"
-[tool.pixi.feature.py311.dependencies]
-python = "3.11.*"
-[tool.pixi.feature.py312.dependencies]
-python = "3.12.*"
-[tool.pixi.feature.py313.dependencies]
-python = "3.13.*"
-[tool.pixi.feature.py314.dependencies]
-python = "3.14.*"
-
-[tool.pixi.feature.test.dependencies]
-r-base = ">=4.0.0"
-r-jsonlite = "*"
-r-yaml = "*"
-
-[tool.pixi.feature.test.tasks]
-test = "pytest --cov src --cov tests"
-
-[tool.pixi.feature.typing.dependencies]
-ty = ">=0.0.7"
-
-[tool.pixi.feature.typing.tasks]
-typing = "ty check src/ tests/"

pyproject.toml

@@ -10,7 +10,6 @@
 from pytask_r.serialization import SERIALIZERS
 
 
-@pytest.mark.unit
 @pytest.mark.parametrize(
     ("args", "kwargs", "expectation", "expected"),
     [
@@ -44,7 +43,6 @@ def test_r(args, kwargs, expectation, expected):
         assert result == expected
 
 
-@pytest.mark.unit
 @pytest.mark.parametrize(
     (
         "mark",

tests/test_collect.py

@@ -1,10 +1,8 @@
 from __future__ import annotations
 
-import pytest
 from pytask import build
 
 
-@pytest.mark.end_to_end
 def test_marker_is_configured(tmp_path):
     session = build(paths=tmp_path)
     assert "r" in session.config["markers"]

tests/test_config.py

@@ -15,7 +15,6 @@
 from tests.conftest import parametrize_parse_code_serializer_suffix
 
 
-@pytest.mark.unit
 def test_pytask_execute_task_setup(monkeypatch):
     """Make sure that the task setup raises errors."""
     # Act like r is installed since we do not test this.
@@ -33,7 +32,6 @@ def test_pytask_execute_task_setup(monkeypatch):
 
 
 @needs_rscript
-@pytest.mark.end_to_end
 @parametrize_parse_code_serializer_suffix
 @pytest.mark.parametrize(
     "depends_on",
@@ -75,7 +73,6 @@ def task_run_r_script(
 
 
 @needs_rscript
-@pytest.mark.end_to_end
 @parametrize_parse_code_serializer_suffix
 def test_run_r_script_w_task_decorator(
     runner, tmp_path, parse_config_code, serializer, suffix
@@ -105,7 +102,6 @@ def run_r_script(produces=Path("out.txt")): ...
 
 
 @needs_rscript
-@pytest.mark.end_to_end
 @parametrize_parse_code_serializer_suffix
 def test_raise_error_if_rscript_is_not_found(
     tmp_path, monkeypatch, parse_config_code, serializer, suffix
@@ -139,7 +135,6 @@ def task_run_r_script(produces=Path("out.txt")): ...
 
 
 @needs_rscript
-@pytest.mark.end_to_end
 @parametrize_parse_code_serializer_suffix
 def test_run_r_script_w_saving_workspace(
     runner, tmp_path, parse_config_code, serializer, suffix
@@ -174,7 +169,6 @@ def task_run_r_script(produces=Path("out.txt")): ...
 
 
 @needs_rscript
-@pytest.mark.end_to_end
 @parametrize_parse_code_serializer_suffix
 def test_run_r_script_w_wrong_cmd_option(
     runner, tmp_path, parse_config_code, serializer, suffix
@@ -209,7 +203,6 @@ def task_run_r_script(produces=Path("out.txt")): ...
 
 
 @needs_rscript
-@pytest.mark.end_to_end
 def test_run_r_script_w_custom_serializer(runner, tmp_path):
     task_source = """
     import pytask
@@ -239,7 +232,6 @@ def task_run_r_script(produces=Path("out.txt")): ...
 
 
 @needs_rscript
-@pytest.mark.end_to_end
 def test_run_r_script_fails_w_multiple_markers(runner, tmp_path):
     task_source = """
     import pytask
@@ -259,7 +251,6 @@ def task_run_r_script(produces=Path("out.txt")): ...
 
 
 @needs_rscript
-@pytest.mark.end_to_end
 def test_run_r_script_with_capital_extension(runner, tmp_path):
     task_source = """
     import pytask
@@ -287,7 +278,6 @@ def task_run_r_script(produces=Path("out.txt")): ...
 
 
 @needs_rscript
-@pytest.mark.end_to_end
 @parametrize_parse_code_serializer_suffix
 def test_run_r_script_w_nested_inputs(
     runner, tmp_path, parse_config_code, serializer, suffix