[pre-commit.ci] pre-commit autoupdate (#40)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Tobias Raabe <raabe@posteo.de>

Author: pre-commit-ci[bot]

.github/workflows/main.yml

@@ -27,16 +27,22 @@ jobs:
       fail-fast: false
       matrix:
         os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
-        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.8', '3.9', '3.10', '3.11']
 
     steps:
       - uses: actions/checkout@v4
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: mamba-org/setup-micromamba@v1
         with:
-          auto-update-conda: false
-          python-version: ${{ matrix.python-version }}
-          channels: conda-forge,nodefaults
-          miniforge-variant: Mambaforge
+          environment-name: gha-testing
+          condarc: |
+            channels:
+              - nodefaults
+              - conda-forge
+          create-args: >-
+            python=${{ matrix.python-version }}
+            mamba
+            tox-conda
+          cache-environment: true
 
       - name: Install core dependencies.
         shell: bash -l {0}
@@ -49,7 +55,7 @@ jobs:
         run: tox -e pytest -- -m "unit or (not integration and not end_to_end)" --cov=./ --cov-report=xml -n auto
 
       - name: Upload coverage report for unit tests and doctests.
-        if: runner.os == 'Linux' && matrix.python-version == '3.8'
+        if: runner.os == 'Linux' && matrix.python-version == '3.10'
         shell: bash -l {0}
         run: bash <(curl -s https://codecov.io/bash) -F unit -c
 
@@ -58,6 +64,6 @@ jobs:
         run: tox -e pytest -- -m end_to_end --cov=./ --cov-report=xml -n auto
 
       - name: Upload coverage reports of end-to-end tests.
-        if: runner.os == 'Linux' && matrix.python-version == '3.8'
+        if: runner.os == 'Linux' && matrix.python-version == '3.10'
         shell: bash -l {0}
         run: bash <(curl -s https://codecov.io/bash) -F end_to_end -c

.pre-commit-config.yaml

@@ -17,25 +17,25 @@ repos:
     -   id: python-no-log-warn
     -   id: python-use-type-annotations
     -   id: text-unicode-replacement-char
--   repo: https://github.com/asottile/reorder_python_imports
-    rev: v3.9.0
+-   repo: https://github.com/asottile/reorder-python-imports
+    rev: v3.12.0
     hooks:
     -   id: reorder-python-imports
         args: [--py37-plus, --add-import, 'from __future__ import annotations']
 -   repo: https://github.com/asottile/setup-cfg-fmt
-    rev: v2.2.0
+    rev: v2.5.0
     hooks:
     -   id: setup-cfg-fmt
 -   repo: https://github.com/psf/black
-    rev: 23.3.0
+    rev: 23.9.1
     hooks:
     -   id: black
--   repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.261
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.0.292
     hooks:
       - id: ruff
 -   repo: https://github.com/dosisod/refurb
-    rev: v1.15.0
+    rev: v1.21.0
     hooks:
     -   id: refurb
         args: [--ignore, FURB126]
@@ -45,7 +45,7 @@ repos:
     -   id: interrogate
         args: [-v, --fail-under=40, src, tests]
 -   repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.16
+    rev: 0.7.17
     hooks:
     -   id: mdformat
         additional_dependencies: [
@@ -54,11 +54,11 @@ repos:
         ]
         args: [--wrap, "88"]
 - repo: https://github.com/codespell-project/codespell
-  rev: v2.2.4
+  rev: v2.2.6
   hooks:
     -   id: codespell
 -   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: 'v1.2.0'
+    rev: 'v1.5.1'
     hooks:
     -   id: mypy
         args: [

setup.cfg

@@ -7,7 +7,7 @@ url = https://github.com/pytask-dev/pytask-r
 author = Tobias Raabe
 author_email = raabe@posteo.de
 license = MIT
-license_file = LICENSE
+license_files = LICENSE
 platforms = any
 classifiers =
     Development Status :: 4 - Beta
@@ -28,7 +28,7 @@ install_requires =
     click
     pybaum>=0.1.1
     pytask>=0.3
-python_requires = >=3.7
+python_requires = >=3.8
 include_package_data = True
 package_dir = =src
 zip_safe = False

src/pytask_r/collect.py

@@ -25,7 +25,7 @@ def run_r_script(script: Path, options: list[str], serialized: Path) -> None:
     """Run an R script."""
     cmd = ["Rscript", script.as_posix(), *options, str(serialized)]
     print("Executing " + " ".join(cmd) + ".")  # noqa: T201
-    subprocess.run(cmd, check=True)
+    subprocess.run(cmd, check=True)  # noqa: S603
 
 
 @hookimpl

src/pytask_r/shared.py

@@ -15,12 +15,12 @@ def r(
     *,
     script: str | Path,
     options: str | Iterable[str] | None = None,
-    serializer: str | Callable[..., str] | str | None = None,
+    serializer: str | Callable[..., str] | None = None,
     suffix: str | None = None,
 ) -> tuple[
     str | Path | None,
     str | Iterable[str] | None,
-    str | Callable[..., str] | str | None,
+    str | Callable[..., str] | None,
     str | None,
 ]:
     """Parse input to the ``@pytask.mark.r`` decorator.