Upgrade to uv and ty

.github/workflows/main.yml

@@ -22,13 +22,13 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
         with:
-          python-version-file: .python-version
-          allow-prereleases: true
-          cache: pip
-      - run: pip install tox-uv
-      - run: tox -e typing
+          enable-cache: true
+      - name: Install just
+        uses: extractions/setup-just@v2
+      - run: just typing
 
   run-tests:
 
@@ -39,33 +39,30 @@ jobs:
       fail-fast: false
       matrix:
         os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
 
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
         with:
-          python-version: ${{ matrix.python-version }}
-          cache: pip
-          allow-prereleases: true
-      - run: pip install tox-uv
+          enable-cache: true
+      - name: Install just
+        uses: extractions/setup-just@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        run: uv python install ${{ matrix.python-version }}
 
-      # Unit, integration, and end-to-end tests.
-
-      - name: Run unit tests and doctests.
+      - name: Run tests
         shell: bash -l {0}
-        run: tox -e test -- -m "unit or (not integration and not end_to_end)" --cov=./ --cov-report=xml -n auto
+        run: just test
 
-      - name: Upload unit test coverage reports to Codecov with GitHub Action
+      - name: Upload test coverage reports to Codecov with GitHub Action
         uses: codecov/codecov-action@v4
-        with:
-          flags: unit
 
-      - name: Run end-to-end tests.
-        shell: bash -l {0}
-        run: tox -e test -- -m end_to_end --cov=./ --cov-report=xml -n auto
+      - name: Run tests with lowest resolution
+        if: matrix.python-version == '3.9' && matrix.os == 'ubuntu-latest'
+        run: just test-lowest
 
-      - name: Upload end_to_end test coverage reports to Codecov with GitHub Action
-        uses: codecov/codecov-action@v4
-        with:
-          flags: end_to_end
+      - name: Run tests with highest resolution
+        if: matrix.python-version == '3.13' && matrix.os == 'ubuntu-latest'
+        run: just test-highest

.pre-commit-config.yaml

@@ -29,10 +29,10 @@ repos:
     hooks:
     -   id: ruff
     -   id: ruff-format
--   repo: https://github.com/dosisod/refurb
-    rev: v2.1.0
+-   repo: https://github.com/astral-sh/uv-pre-commit
+    rev: 0.8.3
     hooks:
-    -   id: refurb
+    -   id: uv-lock
 -   repo: https://github.com/executablebooks/mdformat
     rev: 0.7.22
     hooks:

CHANGES.md → CHANGELOG.md

@@ -5,10 +5,12 @@ chronological order. Releases follow [semantic versioning](https://semver.org/)
 releases are available on [PyPI](https://pypi.org/project/pytask-stata) and
 [Anaconda.org](https://anaconda.org/conda-forge/pytask-stata).
 
-## 0.4.1 - 2024-xx-xx
+## 0.5.0 - 2025-07-26
 
 - {pull}`37` updates the CI.
-- {pull}`38` updates tests for pytask v0.5.
+- {pull}`38` updates tests for pytask v0.5.0.
+- {pull}`41` use uv, use ty, update tests and CI, raise minimum python version to 3.9
+  and support Python 3.13.
 
 ## 0.4.0 - 2024-03-19
 

justfile

@@ -0,0 +1,26 @@
+# Install all dependencies
+install:
+    uv sync --all-groups
+
+# Run tests
+test:
+    uv run --group test pytest --cov=src --cov=tests --cov-report=xml
+
+# Run type checking
+typing:
+    uv run --group typing --group test ty check
+
+# Run linting and formatting
+lint:
+    uvx --with pre-commit-uv pre-commit run -a
+
+# Run all checks (format, lint, typing, test)
+check: lint typing test
+
+# Run tests with lowest dependency resolution
+test-lowest:
+    uv run --group test --resolution lowest-direct pytest
+
+# Run tests with highest dependency resolution
+test-highest:
+    uv run --group test --resolution highest pytest

pyproject.toml

@@ -14,18 +14,14 @@ classifiers = [
     "Programming Language :: Python :: 3",
     "Programming Language :: Python :: 3 :: Only",
 ]
-requires-python = ">=3.8"
-dependencies = ["click", "pytask>=0.4"]
+requires-python = ">=3.9"
+dependencies = ["click>=8.1.8,!=8.2.0", "pytask>=0.5.2"]
 dynamic = ["version"]
 
 [project.readme]
 file = "README.md"
 content-type = "text/markdown"
 
-[project.optional-dependencies]
-test = ["pytest", "pytest-cov", "pytest-xdist"]
-typing = ["mypy"]
-
 [project.urls]
 Homepage = "https://github.com/pytask-dev/pytask-stata"
 Documentation = "https://github.com/pytask-dev/pytask-stata"
@@ -36,11 +32,13 @@ Changelog = "https://github.com/pytask-dev/pytask-stata/blob/main/CHANGES.md"
 [project.entry-points]
 pytask = { pytask_stata = "pytask_stata.plugin" }
 
-[tool.rye]
-managed = true
-dev-dependencies = [
-    "tox-uv>=1.8.2",
+[dependency-groups]
+test = [
+    "pytest>=8.4.0",
+    "pytest-cov>=5.0.0",
+    "pytest-xdist>=3.6.1",
 ]
+typing = ["pytask-parallel>=0.5.1", "ty"]
 
 [tool.hatch.build.hooks.vcs]
 version-file = "src/pytask_stata/_version.py"
@@ -59,31 +57,13 @@ source = "vcs"
 [tool.hatch.metadata]
 allow-direct-references = true
 
-[tool.mypy]
-files = ["src", "tests"]
-check_untyped_defs = true
-disallow_any_generics = true
-disallow_incomplete_defs = true
-disallow_untyped_defs = true
-no_implicit_optional = true
-warn_redundant_casts = true
-warn_unused_ignores = true
-
-[[tool.mypy.overrides]]
-module = "tests.*"
-disallow_untyped_defs = false
-ignore_errors = true
-
 [tool.ruff]
-target-version = "py38"
 fix = true
 unsafe-fixes = true
 
 [tool.ruff.lint]
 select = ["ALL"]
 ignore = [
-    "ANN101",
-    "ANN102",
     "ANN401", # flake8-annotate typing.Any
     "COM812", # Comply with ruff-format.
     "ISC001", # Comply with ruff-format.
@@ -104,8 +84,5 @@ convention = "numpy"
 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"]

src/pytask_stata/collect.py

@@ -62,8 +62,8 @@ def pytask_collect_task(
             raise ValueError(msg)
 
         mark = _parse_stata_mark(mark=marks[0])
-        script, options = stata(**marks[0].kwargs)
-        obj.pytask_meta.markers.append(mark)
+        script, options = stata(**marks[0].kwargs)  # ty: ignore[missing-argument]
+        obj.pytask_meta.markers.append(mark)  # ty: ignore[possibly-unbound-attribute]
 
         # Collect the nodes in @pytask.mark.julia and validate them.
         path_nodes = Path.cwd() if path is None else path.parent
@@ -141,7 +141,7 @@ def pytask_collect_task(
         dependencies["_executable"] = executable_node
 
         partialed = functools.partial(run_stata_script, _cwd=path.parent)
-        markers = obj.pytask_meta.markers if hasattr(obj, "pytask_meta") else []
+        markers = obj.pytask_meta.markers if hasattr(obj, "pytask_meta") else []  # ty: ignore[unresolved-attribute]
 
         task: PTask
         if path is None:
@@ -187,6 +187,6 @@ def pytask_collect_task(
 
 def _parse_stata_mark(mark: Mark) -> Mark:
     """Parse a Stata mark."""
-    script, options = stata(**mark.kwargs)
+    script, options = stata(**mark.kwargs)  # ty: ignore[missing-argument]
     parsed_kwargs = {"script": script or None, "options": options or []}
     return Mark("stata", (), parsed_kwargs)

src/pytask_stata/execute.py

@@ -40,14 +40,14 @@ def pytask_execute_task_teardown(session: Session, task: PTask) -> None:
     """
     if has_mark(task, "stata"):
         if session.config["platform"] == "win32":
-            log_name = task.depends_on["_log_name"].load()
+            log_name = task.depends_on["_log_name"].load()  # ty: ignore[call-non-callable]
             if isinstance(task, PTaskWithPath):
                 path_to_log = task.path.with_name(log_name).with_suffix(".log")
             else:
-                path_to_log = Path.cwd(log_name).with_name(log_name).with_suffix(".log")
+                path_to_log = Path.cwd() / f"{log_name}.log"
         else:
             node = task.depends_on["_script"]
-            path_to_log = node.path.with_suffix(".log")
+            path_to_log = node.path.with_suffix(".log")  # ty: ignore[call-non-callable,possibly-unbound-attribute]
 
         n_lines = session.config["stata_check_log_lines"]
 

src/pytask_stata/shared.py

@@ -3,10 +3,10 @@
 from __future__ import annotations
 
 import sys
+from collections.abc import Iterable
+from collections.abc import Sequence
 from typing import TYPE_CHECKING
 from typing import Any
-from typing import Iterable
-from typing import Sequence
 
 if TYPE_CHECKING:
     from pathlib import Path

tests/test_collect.py

@@ -9,7 +9,6 @@
 from pytask_stata.collect import stata
 
 
-@pytest.mark.unit
 @pytest.mark.parametrize(
     ("args", "kwargs", "expectation", "expected"),
     [
@@ -29,11 +28,10 @@
 )
 def test_stata(args, kwargs, expectation, expected):
     with expectation:
-        options = stata(*args, **kwargs)
+        options = stata(*args, **kwargs)  # ty: ignore[missing-argument]
         assert options == expected
 
 
-@pytest.mark.unit
 @pytest.mark.parametrize(
     ("mark", "expectation", "expected"),
     [

tests/test_config.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)
 

tests/test_execute.py

@@ -18,7 +18,6 @@
 from tests.conftest import needs_stata
 
 
-@pytest.mark.unit
 @pytest.mark.parametrize(
     ("stata", "expectation"),
     [(executable, does_not_raise()) for executable in STATA_COMMANDS]
@@ -31,7 +30,7 @@ def test_pytask_execute_task_setup_raise_error(stata, platform, expectation):
     task = Task(
         base_name="task_example",
         path=Path(),
-        function=None,
+        function=lambda: None,  # ty: ignore[invalid-argument-type]
         markers=[Mark("stata", (), {})],
     )
 
@@ -42,7 +41,6 @@ def test_pytask_execute_task_setup_raise_error(stata, platform, expectation):
 
 
 @needs_stata
-@pytest.mark.end_to_end
 def test_run_do_file(runner, tmp_path):
     task_source = """
     import pytask
@@ -72,7 +70,6 @@ def task_run_do_file():
 
 
 @needs_stata
-@pytest.mark.end_to_end
 def test_run_do_file_w_task_decorator(runner, tmp_path):
     task_source = """
     import pytask
@@ -102,7 +99,6 @@ def run_do_file():
         assert tmp_path.joinpath("script.log").exists()
 
 
-@pytest.mark.end_to_end
 def test_raise_error_if_stata_is_not_found(tmp_path, monkeypatch):
     task_source = """
     from pytask import mark, task
@@ -124,11 +120,10 @@ def task_run_do_file():
     session = build(paths=tmp_path)
 
     assert session.exit_code == ExitCode.FAILED
-    assert isinstance(session.execution_reports[0].exc_info[1], RuntimeError)
+    assert isinstance(session.execution_reports[0].exc_info[1], RuntimeError)  # ty: ignore[non-subscriptable]
 
 
 @needs_stata
-@pytest.mark.end_to_end
 def test_run_do_file_w_wrong_cmd_option(runner, tmp_path):
     """Apparently, Stata simply discards wrong cmd options."""
     task_source = """
@@ -154,7 +149,6 @@ def task_run_do_file():
 
 
 @needs_stata
-@pytest.mark.end_to_end
 def test_run_do_file_by_passing_path(runner, tmp_path):
     """Replicates example under "Command Line Arguments" in Readme."""
     task_source = """
@@ -180,7 +174,6 @@ def task_run_do_file():
 
 
 @needs_stata
-@pytest.mark.end_to_end
 def test_run_do_file_fails_with_multiple_marks(runner, tmp_path):
     task_source = """
     import pytask
@@ -201,7 +194,6 @@ def task_run_do_file():
 
 
 @needs_stata
-@pytest.mark.end_to_end
 def test_with_task_without_path(runner, tmp_path):
     task_source = """
     import pytask

tests/test_normal_execution_w_plugin.py

@@ -9,7 +9,6 @@
 from pytask import cli
 
 
-@pytest.mark.end_to_end
 @pytest.mark.parametrize(
     "dependencies",
     [(), ("in.txt",), ("in_1.txt", "in_2.txt")],

tests/test_parallel.py

@@ -24,7 +24,6 @@
 
 
 @needs_stata
-@pytest.mark.end_to_end
 def test_parallel_parametrization_over_source_files_w_loop(runner, tmp_path):
     source = """
     import pytask
@@ -56,7 +55,6 @@ def task_execute_do_file():
 
 
 @needs_stata
-@pytest.mark.end_to_end
 def test_parallel_parametrization_over_source_file_w_loop(runner, tmp_path):
     source = """
     import pytask