Add pre-commit hooks.

jtilly · Sep 19, 2024 · 7993a74 · 7993a74
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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/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)
diff --git a/src/galeshapley.cpp b/src/galeshapley.cpp
@@ -60,74 +60,74 @@ List cpp_wrapper_galeshapley(const umat& proposerPref, const mat& reviewerUtils)
 
     // number of proposers (men)
     int M = proposerPref.n_cols;
-    
+
     // number of reviewers (women)
     int N = proposerPref.n_rows;
-    
+
     // initialize engagements, proposals
     vec engagements(N), proposals(M);
-    
-    // create an integer queue of bachelors 
+
+    // create an integer queue of bachelors
     // the idea of using queues for this problem is borrowed from
     // http://rosettacode.org/wiki/Stable_marriage_problem#C.2B.2B
     queue<int> bachelors;
-    
+
     // set all proposals to N (aka no proposals)
     proposals.fill(N);
-    
+
     // set all engagements to M (aka no engagements)
     engagements.fill(M);
-    
+
     // every proposer starts out as a bachelor
     for(int iX=M-1; iX >= 0; iX--) {
         bachelors.push(iX);
     }
 
     // loop until there are no more proposals to be made
     while (!bachelors.empty()) {
-        
+
         // get the index of the proposer
         int proposer = bachelors.front();
-        
-        // get the proposer's preferences: we use a raw pointer to the memory 
+
+        // get the proposer's preferences: we use a raw pointer to the memory
         // used by the column `proposer` for performance reasons (this is to avoid
         // making a copy of the proposers vector of preferences)
         const uword * proposerPrefcol = proposerPref.colptr(proposer);
-        
+
         // find the best available match for proposer
         for(int jX=0; jX<N; jX++) {
-        
+
             // get the index of the reviewer that the proposer is interested in
             // by dereferencing the pointer; increment the pointer after use (not its value)
             const uword wX = *proposerPrefcol++;
-        
+
             // check if wX is available (`M` means unmatched)
             if(engagements(wX)==M) {
-        
+
                 // if available, then form a match
                 engagements(wX) = proposer;
                 proposals(proposer) = wX;
-        
+
                 // go to the next proposer
                 break;
             }
-          
+
             // wX is already matched, let's see if wX can be poached
             if(reviewerUtils(proposer, wX) > reviewerUtils(engagements(wX), wX)) {
-          
+
                 // wX's previous partner becomes unmatched (`N` means unmatched)
                 proposals(engagements(wX)) = N;
                 bachelors.push(engagements(wX));
-          
+
                 // proposer and wX form a match
                 engagements(wX) = proposer;
                 proposals(proposer) = wX;
-          
+
                 // go to the next proposer
                 break;
             }
         }
-        
+
         // remove proposer from bachelor queue: proposer will remain unmatched
         bachelors.pop();
     }
@@ -171,13 +171,13 @@ bool cpp_wrapper_galeshapley_check_stability(mat proposerUtils, mat reviewerUtil
 
     // number of workers
     const int M = proposerUtils.n_cols;
-    
+
     // number of firms
     const int N = proposerUtils.n_rows;
-    
+
     // number of slots per firm
     const int slotsReviewers = engagements.n_cols;
-    
+
     // number of slots per worker
     const int slotsProposers = proposals.n_cols;
 
@@ -191,19 +191,19 @@ bool cpp_wrapper_galeshapley_check_stability(mat proposerUtils, mat reviewerUtil
         proposerUtils.insert_rows(N, 1);
         proposerUtils.row(N).fill(-1e10);
     }
-    
+
     // loop over workers
     for(int wX=0; wX<M; wX++) {
-    
+
         // loop over firms
         for(int fX=0; fX<N; fX++) {
-    
+
             // loop over multiple "slots" at the same worker
             for(int swX=0;swX<slotsProposers;swX++) {
-    
+
                 // loop over multiple slots at the same firm
                 for(int sfX=0;sfX<slotsReviewers;sfX++) {
-    
+
                     // check if wX and fX would rather be matched with each other than with their actual matches
                     if(reviewerUtils(wX, fX) > reviewerUtils(engagements(fX, sfX), fX) && proposerUtils(fX, wX) > proposerUtils(proposals(wX, swX), wX)) {
                         ::Rf_warning("matching is not stable; worker %d would rather be matched to firm %d and vice versa.\n", wX, fX);

diff --git a/src/roommate.cpp b/src/roommate.cpp
@@ -24,7 +24,7 @@
 //' 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