Modernize package. (#46)

Author: tobiasraabe

.github/workflows/main.yml

@@ -27,7 +27,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
 
     steps:
       - uses: actions/checkout@v4
@@ -44,10 +44,6 @@ jobs:
             tox-conda
           cache-environment: true
 
-      - name: Install core dependencies.
-        shell: bash -l {0}
-        run: mamba install -c conda-forge tox-conda coverage mamba
-
       # Unit, integration, and end-to-end tests.
 
       - name: Run unit tests and doctests.

.pre-commit-config.yaml

@@ -17,10 +17,6 @@ repos:
     -   id: python-no-log-warn
     -   id: python-use-type-annotations
     -   id: text-unicode-replacement-char
--   repo: https://github.com/asottile/setup-cfg-fmt
-    rev: v2.5.0
-    hooks:
-    -   id: setup-cfg-fmt
 -   repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.3.7
     hooks:
@@ -55,12 +51,6 @@ repos:
             types-setuptools
         ]
         pass_filenames: false
--   repo: https://github.com/mgedmin/check-manifest
-    rev: "0.49"
-    hooks:
-    -   id: check-manifest
-        args: [--no-build-isolation]
-        additional_dependencies: [setuptools-scm, wheel, toml]
 -   repo: meta
     hooks:
     -   id: check-hooks-apply

CHANGES.md

@@ -5,6 +5,10 @@ chronological order. Releases follow [semantic versioning](https://semver.org/)
 releases are available on [PyPI](https://pypi.org/project/pytask-r) and
 [Anaconda.org](https://anaconda.org/conda-forge/pytask-r).
 
+## 0.4.1 - 2024-xx-xx
+
+- {pull}`46` modernizes the package.
+
 ## 0.4.0 - 2023-10-08
 
 - {pull}`42` makes the package compatible with pytask v0.4.0.

pyproject.toml

@@ -1,9 +1,65 @@
+[project]
+name = "pytask_r"
+description = "Run R scripts with pytask."
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: R",
+]
+requires-python = ">=3.8"
+dependencies = ["click", "pluggy>=1.0.0", "pytask>=0.4.0"]
+dynamic = ["version"]
+
+[[project.authors]]
+name = "Tobias Raabe"
+email = "[email protected]"
+
+[project.readme]
+file = "README.md"
+content-type = "text/markdown"
+
+[project.license]
+text = "MIT"
+
+[project.urls]
+Homepage = "https://github.com/pytask-dev/pytask-r"
+Changelog = "https://github.com/pytask-dev/pytask-r/blob/main/CHANGES.md"
+Documentation = "https://github.com/pytask-dev/pytask-r"
+Github = "https://github.com/pytask-dev/pytask-r"
+Tracker = "https://github.com/pytask-dev/pytask-r/issues"
+
+[project.entry-points.pytask]
+pytask_r = "pytask_r.plugin"
+
+[project.optional-dependencies]
+test = ["pytask-parallel", "pytest", "pytest-cov", "pytest-xdist", "pyyaml"]
+
+[tool.rye]
+managed = true
+
 [build-system]
-requires = ["setuptools>=45", "wheel", "setuptools_scm[toml]>=6.0"]
-build-backend = "setuptools.build_meta"
+requires = ["hatchling", "hatch-vcs"]
+build-backend = "hatchling.build"
+
+[tool.hatch.build.hooks.vcs]
+version-file = "src/pytask_r/_version.py"
+
+[tool.hatch.build.targets.sdist]
+exclude = ["tests"]
+only-packages = true
+
+[tool.hatch.build.targets.wheel]
+exclude = ["tests"]
+only-packages = true
+
+[tool.hatch.version]
+source = "vcs"
 
-[tool.setuptools_scm]
-write_to = "src/pytask_r/_version.py"
+[tool.hatch.metadata]
+allow-direct-references = true
 
 [tool.mypy]
 files = ["src", "tests"]
@@ -27,21 +83,16 @@ unsafe-fixes = true
 
 [tool.ruff.lint]
 extend-ignore = [
-    "S101",  # raise errors for asserts.
-    "B905",  # strict parameter for zip that was implemented in py310.
-    "ANN101",  # type annotating self
-    "ANN102",  # type annotating cls
-    "FBT",  # flake8-boolean-trap
-    "EM",  # flake8-errmsg
-    "ANN401",  # flake8-annotate typing.Any
-    "PD",  # pandas-vet
-    "COM812",  # Comply with ruff-format
-    "ISC001",  # Comply with ruff-format
+    "ANN101", # type annotating self
+    "ANN102", # type annotating cls
+    "ANN401",
+    "COM812", # Comply with ruff-format
+    "ISC001", # Comply with ruff-format
 ]
 select = ["ALL"]
 
 [tool.ruff.lint.per-file-ignores]
-"tests/*" = ["D", "ANN"]
+"tests/*" = ["D", "ANN", "S101"]
 
 [tool.ruff.lint.pydocstyle]
 convention = "numpy"

setup.cfg

@@ -27,11 +27,11 @@ def pytask_execute_task_setup(task: PTask) -> None:
             )
             raise RuntimeError(msg)
 
-        assert len(marks) == 1
+        if len(marks) > 1:
+            msg = "Only one R marker is allowed per task."
+            raise ValueError(msg)
 
-        _, _, serializer, suffix = r(**marks[0].kwargs)
-        assert serializer
-        assert suffix
+        _, _, serializer, _ = r(**marks[0].kwargs)
 
         serialized_node: PythonNode = task.depends_on["_serialized"]  # type: ignore[assignment]
         serialized_node.value.parent.mkdir(parents=True, exist_ok=True)  # type: ignore[union-attr]

src/pytask_r/execute.py

@@ -2,26 +2,17 @@
 envlist = pytest
 
 [testenv]
+# Cannot use package = editable, because tox-conda does not support tox v4.
 usedevelop = true
 
-[testenv:pytest]
+[testenv:test]
+extras = test
 conda_channels =
     conda-forge
-    conda-forge/label/pytask_rc
-    conda-forge/label/pytask_parallel_rc
     nodefaults
 conda_deps =
-    pytask >=0.4.0
-    pytask-parallel >=0.4.0
-
-    # Optional dependencies.
-    pyyaml
     r-base >=4
     r-jsonlite
     r-yaml
-
-    pytest
-    pytest-cov
-    pytest-xdist
 commands =
     pytest {posargs}