Use uv more. (#680)

Author: tobiasraabe

.github/workflows/main.yml

@@ -22,13 +22,11 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
+      - uses: astral-sh/setup-uv@v5
         with:
-          python-version-file: .python-version
-          allow-prereleases: true
-          cache: pip
-      - run: pip install tox-uv
-      - run: tox -e typing
+          enable-cache: true
+      - run: uv run --no-dev --group typing mypy
+      - run: uv run --no-dev --group typing nbqa mypy --ignore-missing-imports .
 
   run-tests:
 
@@ -43,12 +41,10 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
+      - uses: astral-sh/setup-uv@v5
         with:
           python-version: ${{ matrix.python-version }}
-          cache: pip
-          allow-prereleases: true
-      - run: pip install tox-uv
+          enable-cache: true
 
       - if: matrix.os == 'ubuntu-latest'
         run: |
@@ -59,7 +55,7 @@ jobs:
 
       - name: Run unit tests and doctests.
         shell: bash -l {0}
-        run: tox -e test -- -m "unit or (not integration and not end_to_end)" --cov=src --cov=tests --cov-report=xml -n auto
+        run: uv run --group test pytest --nbmake -m "unit or (not integration and not end_to_end)" --cov=src --cov=tests --cov-report=xml -n auto
 
       - name: Upload unit test coverage reports to Codecov with GitHub Action
         uses: codecov/codecov-action@v5
@@ -68,7 +64,7 @@ jobs:
 
       - name: Run integration tests.
         shell: bash -l {0}
-        run: tox -e test -- -m integration --cov=src --cov=tests --cov-report=xml -n auto
+        run: uv run --group test pytest --nbmake -m integration --cov=src --cov=tests --cov-report=xml -n auto
 
       - name: Upload integration test coverage reports to Codecov with GitHub Action
         uses: codecov/codecov-action@v5
@@ -77,7 +73,7 @@ jobs:
 
       - name: Run end-to-end tests.
         shell: bash -l {0}
-        run: tox -e test -- -m end_to_end --cov=src --cov=tests --cov-report=xml -n auto
+        run: uv run --group test pytest --nbmake -m end_to_end --cov=src --cov=tests --cov-report=xml -n auto
 
       - name: Upload end_to_end test coverage reports to Codecov with GitHub Action
         uses: codecov/codecov-action@v5

.gitignore

@@ -27,4 +27,3 @@ tests/test_jupyter/*.txt
 .ruff_cache
 .venv
 docs/jupyter_execute
-uv.lock

.readthedocs.yaml

@@ -1,17 +1,18 @@
 version: 2
 
 build:
-  os: ubuntu-22.04
+  os: ubuntu-24.04
   tools:
     python: "3.12"
+  jobs:
+    create_environment:
+      - asdf plugin add uv
+      - asdf install uv latest
+      - asdf global uv latest
+      - UV_PROJECT_ENVIRONMENT=$READTHEDOCS_VIRTUALENV_PATH uv sync --group docs
+    install:
+      - "true"
 
 sphinx:
   configuration: docs/source/conf.py
   fail_on_warning: true
-
-python:
-  install:
-  - method: pip
-    path: .
-    extra_requirements:
-     - docs

pyproject.toml

@@ -46,10 +46,11 @@ text = "MIT"
 name = "Tobias Raabe"
 email = "raabe@posteo.de"
 
-[project.optional-dependencies]
+[dependency-groups]
+dev = ["pygraphviz>=1.11;platform_system=='Linux'"]
 docs = [
     "furo",
-    "ipython",
+    "ipython>=8.13.2",
     "matplotlib",
     "myst-parser",
     "myst-nb",
@@ -85,9 +86,6 @@ Tracker = "https://github.com/pytask-dev/pytask/issues"
 [project.scripts]
 pytask = "pytask:cli"
 
-[tool.uv]
-dev-dependencies = ["tox-uv>=1.7.0", "pygraphviz;platform_system=='Linux'"]
-
 [build-system]
 requires = ["hatchling", "hatch_vcs"]
 build-backend = "hatchling.build"

src/_pytask/build.py

@@ -275,7 +275,7 @@ def build(  # noqa: C901, PLR0912, PLR0913
             session.exit_code = ExitCode.FAILED
 
         except Exception:  # noqa: BLE001
-            console.print(Traceback(sys.exc_info()))
+            console.print(Traceback(sys.exc_info(), show_locals=True))
             session.exit_code = ExitCode.FAILED
 
         session.hook.pytask_unconfigure(session=session)

tests/conftest.py

@@ -123,11 +123,20 @@ class Result(NamedTuple):
 
 def run_in_subprocess(cmd: tuple[str, ...], cwd: Path | None = None) -> Result:
     """Run a command in a subprocess and return the output."""
-    result = subprocess.run(cmd, cwd=cwd, check=False, capture_output=True)
+    kwargs = (
+        {
+            "env": os.environ | {"PYTHONIOENCODING": "utf-8", "TERM": "unknown"},
+            "encoding": "utf-8",
+        }
+        if sys.platform == "win32"
+        else {}
+    )
+
+    result = subprocess.run(
+        cmd, cwd=cwd, check=False, capture_output=True, text=True, **kwargs
+    )
     return Result(
-        exit_code=result.returncode,
-        stdout=result.stdout.decode("utf-8", "replace").replace("\r\n", "\n"),
-        stderr=result.stderr.decode("utf-8", "replace").replace("\r\n", "\n"),
+        exit_code=result.returncode, stdout=result.stdout, stderr=result.stderr
     )
 
 

tests/test_capture.py

@@ -769,6 +769,11 @@ def test_many(self, capfd):  # noqa: ARG002
 
 @pytest.mark.unit
 class TestStdCaptureFDinvalidFD:
+    @pytest.mark.skipif(
+        sys.platform == "darwin" and sys.version_info[:2] == (3, 9),
+        reason="Causes following tests to fail and kills the pytest session with exit "
+        "code 137.",
+    )
     def test_stdcapture_fd_invalid_fd(self, tmp_path, runner):
         source = """
         import os

tests/test_clean.py

@@ -8,31 +8,20 @@
 from _pytask.git import init_repo
 from pytask import ExitCode
 from pytask import cli
-from pytask import storage
 from tests.conftest import enter_directory
 
-_PROJECT_TASK = """
-import pytask
-from pathlib import Path
 
-def task_write_text(path = Path("in.txt"), produces = Path("out.txt")):
-    produces.write_text("a")
-"""
-
-
-_PROJECT_TASK_NEW_INTERFACE = """
-import pytask
-from pathlib import Path
-
-def task_write_text(path=Path("in.txt"), produces=Path("out.txt")):
-    produces.write_text("a")
-"""
-
-
-@pytest.fixture(params=[_PROJECT_TASK, _PROJECT_TASK_NEW_INTERFACE])
-def project(request, tmp_path):
+@pytest.fixture
+def project(tmp_path):
     """Create a sample project to be cleaned."""
-    tmp_path.joinpath("task_module.py").write_text(textwrap.dedent(request.param))
+    content = """
+    import pytask
+    from pathlib import Path
+
+    def task_write_text(path=Path("in.txt"), produces=Path("out.txt")):
+        produces.write_text("a")
+    """
+    tmp_path.joinpath("task_module.py").write_text(textwrap.dedent(content))
     tmp_path.joinpath("in.txt").touch()
 
     tmp_path.joinpath("to_be_deleted_file_1.txt").touch()
@@ -42,28 +31,17 @@ def project(request, tmp_path):
     return tmp_path
 
 
-_GIT_PROJECT_TASK = """
-import pytask
-from pathlib import Path
-
-def task_write_text(path = Path("in_tracked.txt"), produces = Path("out.txt")):
-    produces.write_text("a")
-"""
-
-
-_GIT_PROJECT_TASK_NEW_INTERFACE = """
-import pytask
-from pathlib import Path
-
-def task_write_text(path=Path("in_tracked.txt"), produces=Path("out.txt")):
-    produces.write_text("a")
-"""
-
-
-@pytest.fixture(params=[_GIT_PROJECT_TASK, _GIT_PROJECT_TASK_NEW_INTERFACE])
-def git_project(request, tmp_path):
+@pytest.fixture
+def git_project(tmp_path):
     """Create a sample project to be cleaned."""
-    tmp_path.joinpath("task_module.py").write_text(textwrap.dedent(request.param))
+    content = """
+    import pytask
+    from pathlib import Path
+
+    def task_write_text(path=Path("in_tracked.txt"), produces=Path("out.txt")):
+        produces.write_text("a")
+    """
+    tmp_path.joinpath("task_module.py").write_text(textwrap.dedent(content))
     tmp_path.joinpath("in_tracked.txt").touch()
     tmp_path.joinpath("tracked.txt").touch()
 
@@ -83,11 +61,9 @@ def test_clean_database_ignored(project, runner):
     with enter_directory(project):
         result = runner.invoke(cli, ["build"])
         assert result.exit_code == ExitCode.OK
-        storage.create()
         result = runner.invoke(cli, ["clean"])
         assert result.exit_code == ExitCode.OK
 
-    assert result.exit_code == ExitCode.OK
     text_without_linebreaks = result.output.replace("\n", "")
     assert "to_be_deleted_file_1.txt" in text_without_linebreaks
     assert "to_be_deleted_file_2.txt" in text_without_linebreaks

tests/test_config.py

@@ -120,7 +120,7 @@ def test_paths_are_relative_to_configuration_file(tmp_path):
     session = build(paths=[Path("src")])
     """
     tmp_path.joinpath("script.py").write_text(textwrap.dedent(source))
-    result = run_in_subprocess(("python", "script.py"), cwd=tmp_path)
+    result = run_in_subprocess(("uv", "run", "python", "script.py"), cwd=tmp_path)
     assert result.exit_code == ExitCode.OK
     assert "1  Succeeded" in result.stdout
 

tests/test_execute.py

@@ -20,13 +20,16 @@
 from pytask import build
 from pytask import cli
 from tests.conftest import enter_directory
+from tests.conftest import run_in_subprocess
 
 
-@pytest.mark.xfail(sys.platform == "win32", reason="See #293.")
 @pytest.mark.end_to_end
 def test_python_m_pytask(tmp_path):
     tmp_path.joinpath("task_module.py").write_text("def task_example(): pass")
-    subprocess.run(["python", "-m", "pytask", tmp_path.as_posix()], check=False)
+    result = run_in_subprocess(
+        ("uv", "run", "python", "-m", "pytask", tmp_path.as_posix())
+    )
+    assert result.exit_code == ExitCode.OK
 
 
 @pytest.mark.end_to_end
@@ -657,10 +660,10 @@ def task2() -> None: pass
         sys.exit(session2.exit_code)
     """
     tmp_path.joinpath("task_module.py").write_text(textwrap.dedent(source))
-    result = subprocess.run(
-        ("python", tmp_path.joinpath("task_module.py").as_posix()), check=False
+    result = run_in_subprocess(
+        ("uv", "run", "python", tmp_path.joinpath("task_module.py").as_posix())
     )
-    assert result.returncode == ExitCode.OK
+    assert result.exit_code == ExitCode.OK
 
 
 @pytest.mark.end_to_end
@@ -765,14 +768,14 @@ def task_example() -> Annotated[str, Path("file.txt")]:
     """
     tmp_path.joinpath("task_example.py").write_text(textwrap.dedent(source))
 
-    result = subprocess.run(("pytask"), cwd=tmp_path)  # noqa: PLW1510
-    assert result.returncode == ExitCode.OK
+    result = run_in_subprocess(("pytask",), cwd=tmp_path)
+    assert result.exit_code == ExitCode.OK
 
     hashes = json.loads(tmp_path.joinpath(".pytask", "file_hashes.json").read_text())
     assert len(hashes) == 2
 
-    result = subprocess.run(("pytask"), cwd=tmp_path)  # noqa: PLW1510
-    assert result.returncode == ExitCode.OK
+    result = run_in_subprocess(("pytask",), cwd=tmp_path)
+    assert result.exit_code == ExitCode.OK
 
     hashes_ = json.loads(tmp_path.joinpath(".pytask", "file_hashes.json").read_text())
     assert hashes == hashes_