update makefile and exports

.github/workflows/R-CMD-check.yaml

@@ -1,18 +1,10 @@
-# NOTE: This workflow is overkill for most R packages
-# check-standard.yaml is likely a better choice
-# usethis::use_github_action("check-standard") will install it.
-#
-# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
-# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+# 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
-      - master
+    branches: [master, dev]
   pull_request:
-    branches:
-      - main
-      - master
+    branches: [master, dev]
 
 name: R-CMD-check
 
@@ -26,86 +18,31 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: windows-latest, r: '3.6', rspm: "https://packagemanager.rstudio.com/cran/latest"}
-          - {os: ubuntu-18.04,   r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest", http-user-agent: "R/4.0.0 (ubuntu-18.04) R (4.0.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
-          - {os: ubuntu-18.04,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
-          - {os: ubuntu-18.04,   r: 'oldrel',  rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
-          - {os: ubuntu-18.04,   r: '3.6',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
-          - {os: ubuntu-18.04,   r: '3.5',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
 
     env:
-      RSPM: ${{ matrix.config.rspm }}
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-r@v1
-        id: install-r
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
 
-      - uses: r-lib/actions/setup-pandoc@v1
-
-      - name: Install pak and query dependencies
-        run: |
-          install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/")
-          saveRDS(pak::pkg_deps("local::.", dependencies = TRUE), ".github/r-depends.rds")
-        shell: Rscript {0}
-
-      - name: Restore R package cache
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: |
-            ${{ env.R_LIBS_USER }}/*
-            !${{ env.R_LIBS_USER }}/pak
-          key: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-${{ hashFiles('.github/r-depends.rds') }}
-          restore-keys: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          pak::local_system_requirements(execute = TRUE)
-          pak::pkg_system_requirements("rcmdcheck", execute = TRUE)
-        shell: Rscript {0}
-
-      - name: Install dependencies
-        run: |
-          pak::local_install_dev_deps(upgrade = TRUE)
-          pak::pkg_install("rcmdcheck")
-        shell: Rscript {0}
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - name: Session info
-        run: |
-          options(width = 100)
-          pkgs <- installed.packages()[, "Package"]
-          sessioninfo::session_info(pkgs, include_base = TRUE)
-        shell: Rscript {0}
-
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_: false
-        run: |
-          options(crayon.enabled = TRUE)
-          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
-
-      - name: Show testthat output
-        if: always()
-        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
-        shell: bash
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ matrix.config.os }}-r${{ matrix.config.r }}-results
-          path: check
-
-      - name: Don't use tar from old Rtools to store the cache
-        if: ${{ runner.os == 'Windows' && startsWith(steps.install-r.outputs.installed-r-version, '3.6' ) }}
-        shell: bash
-        run: echo "C:/Program Files/Git/usr/bin" >> $GITHUB_PATH
+          upload-snapshots: false

.github/workflows/test-coverage.yaml

@@ -1,48 +1,47 @@
+# 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
-      - master
+    branches: [main, master]
   pull_request:
-    branches:
-      - main
-      - master
+    branches: [main, master]
 
 name: test-coverage
 
+permissions: read-all
+
 jobs:
   test-coverage:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
-
-      - uses: r-lib/actions/setup-r@v1
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
 
-      - name: Restore R package cache
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+          extra-packages: any::covr, any::xml2
+          needs: coverage
 
-      - name: Install dependencies
+      - name: Test coverage
         run: |
-          install.packages(c("remotes"))
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("covr")
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          covr::to_cobertura(cov)
         shell: Rscript {0}
 
-      - name: Test coverage
-        run: covr::codecov()
-        shell: Rscript {0}
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash

DESCRIPTION

@@ -2,7 +2,7 @@ Package: sitsfeats
 Type: Package
 Title: Satellite Image Time Series Features
 Version: 0.0.1
-Date: 2021-06-02
+Date: 2024-05-10
 Authors@R: 
     c(person(given = "Felipe",
              family = "Carvalho", 
@@ -31,7 +31,6 @@ Imports:
     sf,
     sfheaders,
     geos,
-    libgeos,
     ggplot2,
     cowplot
 Suggests: 
@@ -41,4 +40,4 @@ Suggests:
     wk,
     covr
 LinkingTo: Rcpp, RcppArmadillo
-RoxygenNote: 7.1.1
+RoxygenNote: 7.3.1

README.Rmd

@@ -58,10 +58,10 @@ library(tibble)
 # loading example time series
 data("timeseries")
 
-polar_metrics <- tibble::tibble(area_q1 = sitsfeats::area_q1(timeseries),
-                                area_q2 = sitsfeats::area_q2(timeseries),
-                                area_q3 = sitsfeats::area_q3(timeseries),
-                                area_q4 = sitsfeats::area_q3(timeseries))
+polar_metrics <- tibble::tibble(area_q1 = area_q1(timeseries),
+                                area_q2 = area_q2(timeseries),
+                                area_q3 = area_q3(timeseries),
+                                area_q4 = area_q3(timeseries))
 
 polar_metrics
 ```
@@ -73,8 +73,9 @@ polar_metrics
 one_instance <- timeseries[1,]
 
 # plot first time series example
-sitsfeats::polar_plot(one_instance)
+polar_plot(one_instance)
 ```
 
 ## Getting help
+
 Feel free to create issues if you have any questions.

README.md

@@ -19,8 +19,8 @@ The goal of the sitsfeats package is to extract temporal metrics from
 satellite images time series. The metrics implemented in this version
 are:
 
-  - **basics**: statistics metrics
-  - **polar**: polar metrics
+- **basics**: statistics metrics
+- **polar**: polar metrics
 
 The implementations of this package are based on the
 [stmetrics](https://github.com/brazil-data-cube/stmetrics) library in
@@ -54,13 +54,13 @@ library(tibble)
 # loading example time series
 data("timeseries")
 
-polar_metrics <- tibble::tibble(area_q1 = sitsfeats::area_q1(timeseries),
-                                area_q2 = sitsfeats::area_q2(timeseries),
-                                area_q3 = sitsfeats::area_q3(timeseries),
-                                area_q4 = sitsfeats::area_q3(timeseries))
+polar_metrics <- tibble::tibble(area_q1 = area_q1(timeseries),
+                                area_q2 = area_q2(timeseries),
+                                area_q3 = area_q3(timeseries),
+                                area_q4 = area_q3(timeseries))
 
 polar_metrics
-#> # A tibble: 5 x 4
+#> # A tibble: 5 × 4
 #>   area_q1[,1] area_q2[,1] area_q3[,1] area_q4[,1]
 #>         <dbl>       <dbl>       <dbl>       <dbl>
 #> 1   29443841.   14207184.   30180681.   30180681.
@@ -77,7 +77,7 @@ polar_metrics
 one_instance <- timeseries[1,]
 
 # plot first time series example
-sitsfeats::polar_plot(one_instance)
+polar_plot(one_instance)
 ```
 
 <img src="man/figures/README-unnamed-chunk-3-1.png" width="100%" style="display: block; margin: auto;" />

src/Makevars

@@ -1,14 +1,5 @@
 
-## With R 3.1.0 or later, you can uncomment the following line to tell R to
-## enable compilation with C++11 (where available)
-##
-## Also, OpenMP support in Armadillo prefers C++11 support. However, for wider
-## availability of the package we do not yet enforce this here.  It is however
-## recommended for client packages to set it.
-##
-## And with R 3.4.0, and RcppArmadillo 0.7.960.*, we turn C++11 on as OpenMP
-## support within Armadillo prefers / requires it
-CXX_STD = CXX11
-
+## Armadillo requires it
+# CXX_STD = CXX11
 PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
 PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

src/Makevars.win

@@ -1,14 +1,4 @@
 
-## With R 3.1.0 or later, you can uncomment the following line to tell R to 
-## enable compilation with C++11 (where available)
-##
-## Also, OpenMP support in Armadillo prefers C++11 support. However, for wider
-## availability of the package we do not yet enforce this here.  It is however
-## recommended for client packages to set it.
-##
-## And with R 3.4.0, and RcppArmadillo 0.7.960.*, we turn C++11 on as OpenMP
-## support within Armadillo prefers / requires it
-CXX_STD = CXX11
-
-PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS) 
+# CXX_STD = CXX11
+PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
 PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

src/RcppExports.cpp

@@ -6,6 +6,11 @@
 
 using namespace Rcpp;
 
+#ifdef RCPP_USE_GLOBAL_ROSTREAM
+Rcpp::Rostream<true>&  Rcpp::Rcout = Rcpp::Rcpp_cout_get();
+Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
+#endif
+
 // max_calc
 arma::vec max_calc(const arma::mat& mtx);
 RcppExport SEXP _sitsfeats_max_calc(SEXP mtxSEXP) {