Reorganize Tests against R (#906)

* Update project toml with conda-forge available R packages

* Added new pytest marks for r_against_core and r_against_extended

* Updated packages to install for extended R environment

* Added test markers in pytest init and related pixi dev tasks

* Moved the extended mark of a fixture to the relevant function so pytest stops complaining

* Adjusted extended R test scripts to skip over modules not properly installed

* Updated R requirements to correct install issues.

* Added skip summary on tasks that may cover R tests

* Updated the documentation around changes to R tests.

* Added R as dependency to docs as well to avoid need for global install

* UNTESTED: Updated git workflow actions to reflect new R install?

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* pixi lock

* Made changes to make car a core R package

* Added check on mpdata availability

* Fix: forgot to label car tests as core instead of extended

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: Matthew Shapiro <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Alexander Fischer <[email protected]>

Author: 4 people

.github/workflows/ci-tests.yaml

@@ -46,7 +46,7 @@ jobs:
         run: |
           R_LIB_PATH="${{ github.workspace }}/.pixi/envs/dev/lib/R/library"
           mkdir -p $R_LIB_PATH
-          Rscript -e ".libPaths('$R_LIB_PATH'); install.packages(c('fixest', 'broom','did2s', 'wildrwolf', 'ivDiag', 'car'),  lib='/home/runner/work/pyfixest/pyfixest/.pixi/envs/dev/lib/R/library')"
+          Rscript -e ".libPaths('$R_LIB_PATH'); install.packages(c('did2s', 'wildrwolf', 'ivDiag'),  lib='/home/runner/work/pyfixest/pyfixest/.pixi/envs/dev/lib/R/library', repos = c('https://cran.rstudio.com', 'https://s3alfisc.r-universe.dev'))"
           Rscript -e ".libPaths('$R_LIB_PATH'); install.packages('ritest', lib='/home/runner/work/pyfixest/pyfixest/.pixi/envs/dev/lib/R/library', repos = c('https://grantmcdermott.r-universe.dev'))"
       - name: Run 'regular' tests
         run: |
@@ -94,11 +94,12 @@ jobs:
         run: |
           R_LIB_PATH="${{ github.workspace }}/.pixi/envs/dev/lib/R/library"
           mkdir -p $R_LIB_PATH
-          Rscript -e ".libPaths('$R_LIB_PATH'); install.packages(c('fixest', 'broom','did2s', 'wildrwolf', 'ivDiag', 'car'),  lib='/home/runner/work/pyfixest/pyfixest/.pixi/envs/dev/lib/R/library')"
+          Rscript -e ".libPaths('$R_LIB_PATH'); install.packages(c('did2s', 'wildrwolf', 'ivDiag'),  lib='/home/runner/work/pyfixest/pyfixest/.pixi/envs/dev/lib/R/library', repos = c('https://cran.rstudio.com', 'https://s3alfisc.r-universe.dev'))"
           Rscript -e ".libPaths('$R_LIB_PATH'); install.packages('ritest', lib='/home/runner/work/pyfixest/pyfixest/.pixi/envs/dev/lib/R/library', repos = c('https://grantmcdermott.r-universe.dev'))"
       - name: Run tests against r
         run: |
-          pixi run tests-against-r
+          pixi run tests-against-r-core
+          pixi run tests-against-r-extended
 
       - name: Upload coverage to Codecov (partial)
         uses: codecov/codecov-action@v4

.github/workflows/extended_tests.yaml

@@ -44,10 +44,10 @@ jobs:
         run: |
           R_LIB_PATH="${{ github.workspace }}/.pixi/envs/dev/lib/R/library"
           mkdir -p $R_LIB_PATH
-          Rscript -e ".libPaths('$R_LIB_PATH'); install.packages(c('fixest', 'broom','did2s', 'wildrwolf', 'ivDiag', 'car'),  lib='/home/runner/work/pyfixest/pyfixest/.pixi/envs/dev/lib/R/library')"
+          Rscript -e ".libPaths('$R_LIB_PATH'); install.packages(c('did2s', 'wildrwolf', 'ivDiag'),  lib='/home/runner/work/pyfixest/pyfixest/.pixi/envs/dev/lib/R/library', repos = c('https://cran.rstudio.com', 'https://s3alfisc.r-universe.dev'))"
           Rscript -e ".libPaths('$R_LIB_PATH'); install.packages('ritest', lib='/home/runner/work/pyfixest/pyfixest/.pixi/envs/dev/lib/R/library', repos = c('https://grantmcdermott.r-universe.dev'))"
       - name: Run long tests with coverage
-        run: pixi r tests-extended
+        run: pixi run tests-extended
 
       - name: Upload coverage to Codecov (partial)
         uses: codecov/codecov-action@v4

docs/contributing.qmd

@@ -90,14 +90,17 @@ pixi run lint
 
 and you're ready to go! After installation, the task will run all linting rules via `ruff`.
 
-We’ve included other tasks to help install the necessary R packages for running unit tests or to run different sets of tests:
+We’ve included other tasks to help with testing. Almost all the necessary dependencies to run tests are included in the dev environment,
+except for R packages unavailable through conda-forge.
 ```{.bash .code-copy}
-# install all R development dependencies
-pixi run install-r
+# attempt to install non-conda R dependencies
+pixi run install-r-extended
 # run all tests via pytest
 pixi run tests
-# run all tests excluding very computationally demanding tests
+# run all tests excluding very computationally demanding tests or R-based tests
 pixi run tests-regular
+# run all tests that depend on the extra R dependencies
+pixi run tests-against-r-extended
 # rerun failed tests
 pixi run tests-rerun
 ```
@@ -132,26 +135,10 @@ winget install -e --id Python.Python.3.11
 
 ### Installing R
 
-Note that installing R and the R packages listed below is only necessary if you want to test against R in your local installation.
-You can also test against R by using github actions.
+Note that R and R dependencies available through conda-forge are installed by pixi to the local project if you use the dev environment.
+Some extra R dependencies may require additional development tools not included in the environment, for example:
 
-On Mac/Linux:
-```{.bash .code-copy}
-brew install r
-```
-
-Depending on your local set up, you may need to install additional libraries, for
-example:
-
-```{.bash .code-copy}
-sudo apt install gcc-11 cmake
-```
-
-On Windows using [Winget](https://winget.run/pkg/RProject/R):
-
-```{.bash .code-copy}
-winget install -e --id RProject.R
-```
+Depending on your local set up, you may need to install additional libraries to compile those extra dependencies, like a version of `gcc` and `cmake`.
 
 ### Installing Quarto