Merge branch with main

Merge branch 'main' into clean_up

# Conflicts:
#	NAMESPACE
#	R/MainFunctions.R

.Rbuildignore

@@ -25,4 +25,6 @@
 ^\.lib$
 ^history$
 ^Report\.html$
-^Report_files/$
+^Report_files/$
+^cran-comments\.md$
+^codecov\.yml$

.github/workflows/check-standard.yaml

@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, develop, OmmitedSrcFiles]
+    branches: [main, develop]
   pull_request:
-    branches: [main, develop, OmmitedSrcFiles]
+    branches: [main, develop]
 
 name: R-CMD-check
 
@@ -20,10 +20,9 @@ jobs:
         config:
           - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
           - {os: ubuntu-latest,   r: 'oldrel-1'}
-
+          
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
@@ -38,12 +37,22 @@ jobs:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
+
+      - name: R dependencies
+        run: |
+          install.packages('remotes')
+          install.packages('knitr')
+          install.packages('testthat')
+        shell: Rscript {0}
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
+          dependencies: '"hard"'
           extra-packages: any::rcmdcheck
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+          error-on: '"error"'
+

.github/workflows/test-coverage.yaml

@@ -0,0 +1,50 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, develop]
+  pull_request:
+    branches: [main, develop]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+          )
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

DESCRIPTION

@@ -1,14 +1,16 @@
 Package: Explore
 Type: Package
-Title: Exhaustive Procedure for LOgic-Rule Extraction
-Version: 0.2.0
+Title: Exhaustive Procedure for LOgic-Rule Extraction (EXPLORE)
+Version: 0.3.0
 Date: 2020-12-14
-Author: Aniek F Markus 
-Maintainer: Aniek F Markus <[email protected]>
-Description: This package includes the implementation of EXPLORE in C++ and connects it to R. 
+Authors@R: c(
+    person("Aniek", "Markus", , "[email protected]", role = c("aut"), comment = c(ORCID = "0000-0001-5779-4794")),
+    person("Cesar", "Barboza", , "[email protected]", role = c("cre", "aut"), comment = c(ORCID = "0009-0002-4453-3071"))
+  )
+Description: This package is the R Implementation of the Exhaustive Procedure for LOgic-Rule Extraction (EXPLORE) in C++. 
 License: GPL (>= 2)
 Depends:
-    R (>= 3.6.1)
+    R (>= 3.6.0)
 Imports: 
     checkmate,
     farff,
@@ -22,8 +24,8 @@ Suggests:
     testthat (>= 3.0.0),
     knitr,
     rmarkdown,
-    withr
+    withr,
+    covr
 VignetteBuilder: knitr
 Config/testthat/edition: 3
-URL: https://cbarbozaerasmus.github.io/Explore/
-SystemRequirements: GNU make
+URL: https://github.com/mi-erasmusmc/Explore

Explore.Rproj

@@ -1,7 +1,7 @@
 Version: 1.0
 
 RestoreWorkspace: Default
-SaveWorkspace: Default
+SaveWorkspace: No
 AlwaysSaveHistory: Default
 
 EnableCodeIndexing: Yes

NEWS.md

@@ -1,3 +1,11 @@
+# Explore 0.3.0
+
+* Package tested on Windows, MacOs and Linux. R-CMD-Check without errors.
+
+* Improved tests.
+
+* Solving issues for CRAN release.
+
 # Explore 0.2.0
 
 * Added a `NEWS.md` file to track changes to the package.

R/MainFunctions.R

@@ -17,8 +17,8 @@
 #' @param PositiveClass 1 or string (?) (should be one of elements of column 'ClassFeature' in data train). Always provided by the user. The string should be enclused in single quotation marks, e.g. 'class'
 #' @param FeatureInclude Empty or string (should be name of one of columns in data train)
 #' @param Maximize One of list with strings, list = "ACCURACY", "SENSITIVITY", "SPECIFICITY", ...
-#' @param Accuracy Float 0-1 -> default = 0 (if 0, make empty = computationally more beneficial)
-#' @param Specificity  float 0-1, default = 0
+#' @param Accuracy Float 0-0.999 -> default = 0 (if 0, make empty = computationally more beneficial)
+#' @param Specificity float 0-0.999, default = 0
 #' @param PrintSettings True or False
 #' @param PrintPerformance True or False
 #' @param Subsumption True or False
@@ -31,7 +31,7 @@
 #' @importFrom RcppParallel RcppParallelLibs
 trainExplore <- function(train_data = NULL,
                          settings_path = NULL,
-                         output_path, 
+                         output_path = tempdir(), 
                          file_name = "train_data",
                          OutputFile = NULL, 
                          StartRulelength = 1,
@@ -49,16 +49,17 @@ trainExplore <- function(train_data = NULL,
                          Subsumption = TRUE,
                          BranchBound = TRUE,
                          Parallel = FALSE) {
-
-
+
+  if (!dir.exists(output_path)) {
+    dir.create(output_path, recursive = TRUE)
+    }
+
   # Create output folder
   if(!endsWith(output_path, "/")) {
     warning("Output path should end with /, add this")
     output_path <- paste0(output_path, "/")
   }
 
-  if (!file.exists(output_path)) {dir.create(output_path, recursive = TRUE)}
-
   # Variable checks
   errorMessage <- makeAssertCollection()
 
@@ -106,6 +107,8 @@ trainExplore <- function(train_data = NULL,
   Subsumption <- ifelse(Subsumption == TRUE, "yes", "no")
   BranchBound <- ifelse(BranchBound == TRUE, "yes", "no")
   Parallel <- ifelse(Parallel == TRUE, "yes", "no")
+  Accuracy <- ifelse(Accuracy == 0, "", Specificity)
+  Specificity <- ifelse(Specificity == 0, "", Specificity)
 
   # Create project setting
   if (is.null(settings_path)) {

README.Rmd

@@ -11,6 +11,12 @@ out.width = "100%"
 )
 ```
 
+  <!-- badges: start -->
+  [![R-CMD-check](https://github.com/mi-erasmusmc/Explore/actions/workflows/check-standard.yaml/badge.svg)](https://github.com/mi-erasmusmc/Explore/actions/workflows/check-standard.yaml)
+  [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
+  [![Codecov test coverage](https://codecov.io/github/mi-erasmusmc/Explore/branch/develop/graph/badge.svg)](https://app.codecov.io/github/mi-erasmusmc/Explore?branch=develop)
+  <!-- badges: end -->
+
 ## Package overview
 Functions to find a short and accurate decision rule in disjunctive normal form using the Exhaustive Procedure for LOgic-Rule Extraction (EXPLORE) algorithm. The application performs and exhaustive search on all Boolean Normal Form decision rules.
 

README.md

@@ -1,4 +1,12 @@
 
+<!-- badges: start -->
+[![R-CMD-check](https://github.com/mi-erasmusmc/Explore/actions/workflows/check-standard.yaml/badge.svg)](https://github.com/mi-erasmusmc/Explore/actions/workflows/check-standard.yaml)
+[![Lifecycle:
+experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
+[![Codecov test
+coverage](https://codecov.io/github/mi-erasmusmc/Explore/branch/develop/graph/badge.svg)](https://app.codecov.io/github/mi-erasmusmc/Explore?branch=develop)
+<!-- badges: end -->
+
 ## Package overview
 
 Functions to find a short and accurate decision rule in disjunctive

_pkgdown.yml

@@ -1,4 +1,4 @@
-url: https://cbarbozaerasmus.github.io/Explore/
+url: https://mi-erasmusmc.github.io/Explore/
 template:
   bootstrap: 5
 

codecov.yml

@@ -0,0 +1,14 @@
+comment: false
+
+coverage:
+  status:
+    project:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true
+    patch:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true

cran-comments.md

@@ -0,0 +1,5 @@
+## R CMD check results
+
+0 errors | 0 warnings | 1 note
+
+* This is a new release.

src/C++/CMExplore/main.h → src/C++/CMExplore/mainforR.h

@@ -14,7 +14,7 @@
 IOExplore      *MyIOExplore;                                              		// Input object
 Explore        *MyExplore;                                                 		// Explore core object
 
-int main(int argc, char* argv[]);
+// int main(int argc, char* argv[]);
 
 int mainforR(int argc, char* argv[]);
 

src/ExploreInterface.cpp

@@ -1,7 +1,7 @@
 
 // [[Rcpp::depends(BH)]]
 #include <Rcpp.h>
-#include "C++/CMExplore/main.h"
+#include "C++/CMExplore/mainforR.h"
 #include "C++/CMExplore/initialise.h"
 #include "../src/C++/Explore/explore.h"
 
@@ -23,7 +23,7 @@ void runExplore(Rcpp::CharacterVector input) {
   int argc = (int)cstrings.size()+1;
   char** argv = cstrings.data();
 
-  int res = main(argc, argv);
+  int res = mainforR(argc, argv);
 }
 
 /*** R
@@ -36,7 +36,7 @@ void runExplore(Rcpp::CharacterVector input) {
 # runExplore(input)
 */
 
-int main(int argc, char* argv[])
+int mainforR(int argc, char* argv[])
 {
   ExploreSettings ProjectSettings;
 

src/Makevars

@@ -1,7 +1,7 @@
 # Makevars
 CXX_STD = CXX11 -mmacosx-version-min=10.15
 
-SOURCES=$(wildcard C++/*.cpp C++/IOExplore/*.cpp C++/Explore/*.cpp C++/CMExplore/*.cpp)
+SOURCES= C++/common.cpp C++/IOExplore/IOExplore.cpp C++/Explore/bin.cpp C++/Explore/candidate.cpp C++/Explore/classdef.cpp C++/Explore/condition.cpp C++/Explore/conjunction.cpp C++/Explore/constraint.cpp C++/Explore/cutoff.cpp C++/Explore/explore.cpp C++/Explore/feature.cpp C++/Explore/mandatory.cpp C++/Explore/observation.cpp C++/Explore/partition.cpp C++/Explore/performance.cpp C++/Explore/population.cpp C++/Explore/roc.cpp C++/Explore/rocpair.cpp C++/Explore/rule.cpp C++/Explore/set.cpp C++/Explore/timing.cpp
 
 OBJECTS = ExploreInterface.o RcppExports.o $(SOURCES:.cpp=.o)
 

src/Makevars.win

@@ -1,13 +1,13 @@
 # Makevars
 CXX_STD = CXX11 # -mmacosx-version-min=10.15
 
-SOURCES=$(wildcard C++/*.cpp C++/IOExplore/*.cpp C++/Explore/*.cpp C++/CMExplore/*.cpp)
+SOURCES= C++/common.cpp C++/IOExplore/IOExplore.cpp C++/Explore/bin.cpp C++/Explore/candidate.cpp C++/Explore/classdef.cpp C++/Explore/condition.cpp C++/Explore/conjunction.cpp C++/Explore/constraint.cpp C++/Explore/cutoff.cpp C++/Explore/explore.cpp C++/Explore/feature.cpp C++/Explore/mandatory.cpp C++/Explore/observation.cpp C++/Explore/partition.cpp C++/Explore/performance.cpp C++/Explore/population.cpp C++/Explore/roc.cpp C++/Explore/rocpair.cpp C++/Explore/rule.cpp C++/Explore/set.cpp C++/Explore/timing.cpp
 
 OBJECTS = ExploreInterface.o RcppExports.o $(SOURCES:.cpp=.o)
 
-PKG_CXXFLAGS += -DRCPP_PARALLEL_USE_TBB=1
+PKG_CXXFLAGS = -DRCPP_PARALLEL_USE_TBB=1
 
-PKG_LIBS += $(shell "${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" -e "RcppParallel::RcppParallelLibs()")
+PKG_LIBS = `"${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" -e "RcppParallel::RcppParallelLibs()"`
 
 all: $(SHLIB)