Revamp CI setup.

jtilly · Sep 19, 2024 · 32770b6 · 32770b6
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -1,12 +1,32 @@
-name: Test Package
+name: CI
 on: [push]
+
+# Automatically stop old builds on the same branch/PR
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash -el {0}
+
 jobs:
-  build-linux:
-    name: CI
+  pre-commit-checks:
+    name: Pre-commit checks
+    timeout-minutes: 30
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout branch
+        uses: actions/checkout@v4
+      - name: Run pre-commit-conda
+        uses: quantco/pre-commit-conda@v1
+
+  tests:
+    name: Tests
     runs-on: "ubuntu-latest"
     steps:
       - uses: actions/checkout@v3
-      - uses: conda-incubator/setup-miniconda@v2.2.0
+      - uses: conda-incubator/setup-miniconda@v3.0.4
         with:
           miniforge-version: latest
           miniforge-variant: Mambaforge

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,21 @@
+repos:
+  - repo: https://github.com/Quantco/pre-commit-mirrors-prettier
+    rev: 3.2.5
+    hooks:
+      - id: prettier-conda
+        files: \.(md|yml|yaml)$
+  - repo: https://github.com/Quantco/pre-commit-mirrors-pre-commit-hooks
+    rev: 4.6.0
+    hooks:
+      - id: trailing-whitespace-conda
+      - id: end-of-file-fixer-conda
+      - id: check-merge-conflict-conda
+        args: ["--assume-in-merge"]
+  - repo: https://github.com/Quantco/pre-commit-mirrors-typos
+    rev: 1.24.5
+    hooks:
+      - id: typos-conda
+  - repo: https://github.com/Quantco/pre-commit-mirrors-clang-format
+    rev: 18.1.8
+    hooks:
+      - id: clang-format-conda
diff --git a/NEWS.md b/NEWS.md
@@ -1,69 +1,68 @@
 # matchingR 1.3.3
 
- * Fixed unit test for validate functions that caused a CRAN check to fail.
+- Fixed unit test for validate functions that caused a CRAN check to fail.
 
 # matchingR 1.3.2
 
- * Fix vignette index.
+- Fix vignette index.
 
 # matchingR 1.3.1
 
- * Add dummy roommate when number of roommates is odd [#37](https://github.com/jtilly/matchingR/issues/37)
- * Run code base through `styler` and `lintr`
+- Add dummy roommate when number of roommates is odd [#37](https://github.com/jtilly/matchingR/issues/37)
+- Run code base through `styler` and `lintr`
 
 # matchingR 1.3.0
 
- * Allow colleges to have different numbers of slots [#31](https://github.com/jtilly/matchingR/issues/31)
- * Change row names in vignette [#34](https://github.com/jtilly/matchingR/issues/34)
- * Remove need for microbenchmark package [#35](https://github.com/jtilly/matchingR/issues/35)
- * Registration of entry points in compiled code 
+- Allow colleges to have different numbers of slots [#31](https://github.com/jtilly/matchingR/issues/31)
+- Change row names in vignette [#34](https://github.com/jtilly/matchingR/issues/34)
+- Remove need for microbenchmark package [#35](https://github.com/jtilly/matchingR/issues/35)
+- Registration of entry points in compiled code
 
 # matchingR 1.2.2
 
-This is a minor update. 
+This is a minor update.
 
- * Colleges may have different numbers of slots in the college admissions problem ([#30](https://github.com/jtilly/matchingR/issues/30))
+- Colleges may have different numbers of slots in the college admissions problem ([#30](https://github.com/jtilly/matchingR/issues/30))
 
 # matchingR 1.2.1
 
-This is a minor update. 
+This is a minor update.
 
- * Fixed bug in galeShapley.checkStability that resulted in UBSAN throwing an error
+- Fixed bug in galeShapley.checkStability that resulted in UBSAN throwing an error
 
 # matchingR 1.2
 
- * Fixed a bug in the stable roommate matching algorithm that caused
-   problems on Mac OS X / clang
- * Changed function names throughout the package (deprecated old function names)
- * Updated documentation
- * Added tests
- * Removed option to define preferences in row major order
+- Fixed a bug in the stable roommate matching algorithm that caused
+  problems on Mac OS X / clang
+- Changed function names throughout the package (deprecated old function names)
+- Updated documentation
+- Added tests
+- Removed option to define preferences in row major order
 
 # matchingR 1.1.1
 
-This is a minor update. 
-
- * It fixes a memory leak warning in the stable roommate algorithm.
- * It includes minor edits of the vignettes and documentation.
- * We have substantially shortened the computational performance vignette 
-   so that the package can be built and checked faster
+This is a minor update.
 
+- It fixes a memory leak warning in the stable roommate algorithm.
+- It includes minor edits of the vignettes and documentation.
+- We have substantially shortened the computational performance vignette
+  so that the package can be built and checked faster
 
 # matchingR 1.1
 
 This is a major update that added additional algorithms to the package.
 
- * Added algorithm to compute a solution to the stable roommate problem 
-   (`roommate`)
- * Added top trading cycle algorithm (`toptrading`)
- * Switched the layout of preference matrices from row order to column order 
-   to make the code faster
- * Added two vignettes: An introductory vignette to the package in general 
-   and a computational performance vignette
+- Added algorithm to compute a solution to the stable roommate problem
+  (`roommate`)
+- Added top trading cycle algorithm (`toptrading`)
+- Switched the layout of preference matrices from row order to column order
+  to make the code faster
+- Added two vignettes: An introductory vignette to the package in general
+  and a computational performance vignette
 
 # matchingR 1.0.1
 
 Initial release that computes two versions of the Gale-Shapley algorithm:
-    
- * Stable Marriage Problem
- * College Admissions Problem  
+
+- Stable Marriage Problem
+- College Admissions Problem
diff --git a/R/RcppExports.R b/R/RcppExports.R
@@ -74,7 +74,7 @@ cpp_wrapper_galeshapley_check_stability <- function(proposerUtils, reviewerUtils
 #' This is the C++ wrapper for the stable roommate problem. Users should not
 #' call this function directly, but instead use
 #' \code{\link{roommate}}.
-#' 
+#'
 #' @param pref is a matrix with the preference order of each individual in the
 #'   market. If there are \code{n} individuals, then this matrix will be of
 #'   dimension \code{n-1} by \code{n}. The \code{i,j}th element refers to
@@ -115,7 +115,7 @@ cpp_wrapper_irving_check_stability <- function(pref, matchings) {
 }
 
 #' Computes the top trading cycle algorithm
-#' 
+#'
 #' This is the C++ wrapper for the top trading cycle algorithm. Users should not
 #' call this function directly, but instead use
 #' \code{\link{toptrading}}.
@@ -195,4 +195,3 @@ sortIndexOneSided <- function(u) {
 rankIndex <- function(sortedIdx) {
     .Call('_matchingR_rankIndex', PACKAGE = 'matchingR', sortedIdx)
 }
-
diff --git a/README.md b/README.md
@@ -1,36 +1,36 @@
-Matching Algorithms in R and C++
-===============
+# Matching Algorithms in R and C++
+
 [![GitHub Actions](https://github.com/jtilly/matchingR/workflows/Test%20Package/badge.svg)](https://github.com/jtilly/matchingR/actions)
 [![Coverage Status](https://coveralls.io/repos/jtilly/matchingR/badge.svg?branch=master)](https://coveralls.io/github/jtilly/matchingR)
 [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/matchingR)](https://cran.r-project.org/package=matchingR)
 [![CRAN_Downloads](https://cranlogs.r-pkg.org/badges/grand-total/matchingR?color=brightgreen)](https://cran.r-project.org/package=matchingR)
 
-
 [!["You know that I'll never leave you. Not as long as she's with someone."](https://imgs.xkcd.com/comics/all_the_girls.png)](https://xkcd.com/770/ "You know that I'll never leave you. Not as long as she's with someone.")
 
-
 `matchingR` is an R package which quickly computes the [Gale-Shapley algorithm](https://www.jstor.org/stable/2312726), [Irving's algorithm for the stable roommate problem](https://www.sciencedirect.com/science/article/pii/0196677485900331/), and the [top trading cycle algorithm](https://www.sciencedirect.com/science/article/abs/pii/0304406874900330/) for large matching markets. The package provides functions to compute the solutions to the
-  [stable marriage problem](https://en.wikipedia.org/wiki/Stable_matching), the
-  [college admission problem](https://en.wikipedia.org/wiki/Hospital_resident), the
-  [stable roommates problem](https://en.wikipedia.org/wiki/Stable_roommates_problem), and the
-  [house allocation problem](https://web.stanford.edu/~niederle/HouseAllocation.pdf).
+[stable marriage problem](https://en.wikipedia.org/wiki/Stable_matching), the
+[college admission problem](https://en.wikipedia.org/wiki/Hospital_resident), the
+[stable roommates problem](https://en.wikipedia.org/wiki/Stable_roommates_problem), and the
+[house allocation problem](https://web.stanford.edu/~niederle/HouseAllocation.pdf).
 
 The package may be useful when the number of market participants is large or when many matchings need to be computed (e.g., for simulation or estimation purposes). It has been used in practice to compute the Gale-Shapley stable matching with 30,000 participants on each side of the market.
 
 Matching markets are common in practice and widely studied by economists. Popular examples include
 
- * the [National Resident Matching Program](https://www.nrmp.org/) which matches graduates from medical school to residency programs at teaching hospitals throughout the United States
- * the matching of students to schools including the [New York City High School Match](https://www.jstor.org/stable/4132848) or the [Boston Public School Match](https://www.jstor.org/stable/4132849) (and many more)
- * the matching of kidney donors to recipients in [kidney exchanges](https://www.jstor.org/stable/4132851).
+- the [National Resident Matching Program](https://www.nrmp.org/) which matches graduates from medical school to residency programs at teaching hospitals throughout the United States
+- the matching of students to schools including the [New York City High School Match](https://www.jstor.org/stable/4132848) or the [Boston Public School Match](https://www.jstor.org/stable/4132849) (and many more)
+- the matching of kidney donors to recipients in [kidney exchanges](https://www.jstor.org/stable/4132851).
 
-Installation
-------------
+## Installation
 
 `matchingR` may be installed from [CRAN](https://cran.r-project.org/package=matchingR):
+
 ```r
 install.packages("matchingR")
 ```
+
 The latest development release is available from GitHub:
+
 ```r
 devtools::install_github("jtilly/matchingR")
 ```
@@ -40,6 +40,7 @@ devtools::install_github("jtilly/matchingR")
 ### Gale-Shapley Algorithm for Two-Sided Markets
 
 **Stable Marriage Problem**
+
 ```r
 library(matchingR)
 
@@ -63,6 +64,7 @@ galeShapley.checkStability(uM, uW, matching$proposals, matching$engagements)
 ```
 
 **College Admissions Problem**
+
 ```r
 library(matchingR)
 
@@ -100,6 +102,7 @@ galeShapley.checkStability(uStudents, uColleges, matching$matched.students, matc
 ```
 
 ### Irving's Algorithm for the Stable Roommate Problem
+
 ```r
 library(matchingR)
 
@@ -123,6 +126,7 @@ results
 ```
 
 ### Top-Trading Cycle Algorithm
+
 ```r
 library(matchingR)
 
@@ -146,5 +150,6 @@ results
 ```
 
 ## Documentation
-* [Reference Manual](https://jtilly.io/matchingR/matchingR.pdf "Matching Algorithms in R and C++: Reference Manual")
-* [Vignette: Matching Algorithms in R and C++: An Introduction to matchingR](https://jtilly.io/matchingR/vignettes/matchingR-intro.html "Matching Algorithms in R and C++: An Introduction to matchingR")
+
+- [Reference Manual](https://jtilly.io/matchingR/matchingR.pdf "Matching Algorithms in R and C++: Reference Manual")
+- [Vignette: Matching Algorithms in R and C++: An Introduction to matchingR](https://jtilly.io/matchingR/vignettes/matchingR-intro.html "Matching Algorithms in R and C++: An Introduction to matchingR")
diff --git a/environment.yml b/environment.yml
@@ -2,7 +2,7 @@ name: matchingR
 channels:
   - conda-forge
 dependencies:
-  - r-base=4.2
+  - r-base>=4.4
   - r-rcpp
   - r-rcpparmadillo
   - r-testthat

diff --git a/man/matchingR-deprecated.Rd b/man/matchingR-deprecated.Rd
diff --git a/src/Makevars b/src/Makevars
@@ -1,4 +1,4 @@
 CXX_STD = CXX11
 PKG_CPPFLAGS = -I../inst/include
 PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
-PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
+PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)