Add pixi to install R. (#50)

Author: tobiasraabe

.gitattributes

@@ -0,0 +1,2 @@
+# GitHub syntax highlighting
+pixi.lock linguist-language=YAML

.github/workflows/main.yml

@@ -5,9 +5,6 @@ concurrency:
   group: ${{ github.head_ref || github.run_id }}
   cancel-in-progress: true
 
-env:
-  CONDA_EXE: mamba
-
 on:
   push:
     branches:
@@ -31,35 +28,28 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
-      - uses: mamba-org/setup-micromamba@v1
+      - uses: prefix-dev/setup-[email protected]
         with:
-          environment-name: gha-testing
-          condarc: |
-            channels:
-              - nodefaults
-              - conda-forge
-          create-args: >-
-            python=${{ matrix.python-version }}
-            mamba
-            tox-conda
-          cache-environment: true
+          pixi-version: v0.20.1
+          cache: true
+          environments: test
 
       # Unit, integration, and end-to-end tests.
 
       - 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=./ --cov-report=xml -n auto
+        run: pixi run -e test 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 == '3.10'
-        shell: bash -l {0}
-        run: bash <(curl -s https://codecov.io/bash) -F unit -c
+      - name: Upload unit 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
+        run: pixi run -e test 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 == '3.10'
-        shell: bash -l {0}
-        run: bash <(curl -s https://codecov.io/bash) -F end_to_end -c
+      - name: Upload end_to_end test coverage reports to Codecov with GitHub Action
+        uses: codecov/codecov-action@v4
+        with:
+          flags: end_to_end

.gitignore

@@ -17,3 +17,10 @@ __pycache__
 build
 dist
 src/pytask_r/_version.py
+
+.mypy_cache
+.ruff_cache
+.pytest_cache
+# pixi environments
+.pixi
+*.egg-info

CHANGES.md

@@ -5,6 +5,11 @@ 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).
 
+## x.x.x - 2024-xx-xx
+
+- {pull}`50` uses pixi to install R and uses uuid4 to generate more robust file names
+  for serialized arguments.
+
 ## 0.4.1 - 2024-04-20
 
 - {pull}`46` modernizes the package.

README.md

@@ -8,7 +8,7 @@
 [![image](https://img.shields.io/github/actions/workflow/status/pytask-dev/pytask-r/main.yml?branch=main)](https://github.com/pytask-dev/pytask-r/actions?query=branch%3Amain)
 [![image](https://codecov.io/gh/pytask-dev/pytask-r/branch/main/graph/badge.svg)](https://codecov.io/gh/pytask-dev/pytask-r)
 [![pre-commit.ci status](https://results.pre-commit.ci/badge/github/pytask-dev/pytask-r/main.svg)](https://results.pre-commit.ci/latest/github/pytask-dev/pytask-r/main)
-[![image](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 
 ______________________________________________________________________
 
@@ -117,7 +117,7 @@ pytask. After a failed execution, you see the command that executed the R script
 report of the task. It looks roughly like this
 
 ```console
-Rscript <options> script.r <path-to>/.pytask/task_py_task_example.json
+Rscript <options> script.r <path-to>/.pytask/pytask-r/<uuid4>.json
 ```
 
 ### Command Line Arguments
@@ -227,7 +227,7 @@ r_serializer = "json"
 **`r_suffix`**
 
 Use this option to set the default suffix of the file which contains serialized paths to
-dependencies and products and more.
+dependencies, products and more.
 
 ```toml
 [tool.pytask.ini_options]