Merge branch 'master' into 4.1

statnet · Jun 15, 2024 · d05a619 · d05a619
2 parents 4dff2d0 + a9e65bc
commit d05a619
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -28,6 +28,9 @@
 #   debug: compile package with -DDEBUG and -UNDEBUG
 #
 #   covr: run in covr mode may be used with 'full' but probably not with others.
+#
+#
+# Typical public, private, and release configurations are provided in the variables below.
 
 on: [push, pull_request]
 
@@ -37,19 +40,23 @@ name: R-CMD-check
 env:
   PUBLIC: ''
   PRIVATE: ''
+  PUBLIC_CONFIG: '{"config":[
+            {"os":"windows-latest", "r":"release", "timeout":360, "flags":"binaries"},
+            {"os":"macOS-latest", "r":"release", "timeout":360, "flags":"binaries, ubsan"},
+            {"os":"ubuntu-latest", "r":"release", "timeout":360, "flags":"full, ubsan, debug"},
+            {"os":"ubuntu-latest", "r":"devel", "timeout":360, "flags":"vignettes, remote"},
+            {"os":"ubuntu-latest", "r":"release", "timeout":360, "flags":"full, covr"}]}'
+  RELEASE_CONFIG: '{"config":[
+            {"os":"windows-latest", "r":"release", "timeout":360, "flags":"binaries, vignettes, remote, strict"},
+            {"os":"macOS-latest", "r":"release", "timeout":360, "flags":"binaries, ubsan, vignettes, remote, strict"},
+            {"os":"ubuntu-latest", "r":"release", "timeout":360, "flags":"full, ubsan, debug, strict"},
+            {"os":"ubuntu-latest", "r":"devel", "timeout":360, "flags":"vignettes, remote, strict"},
+            {"os":"ubuntu-latest", "r":"release", "timeout":360, "flags":"full, covr, strict"}]}'
+  PRIVATE_CONFIG: '{"config":[
+            {"os":"ubuntu-latest", "r":"release", "timeout":10, "flags":"none"}
+            ]}'
 
 jobs:
-## Remove-Old-Artifacts:
-##   runs-on: ubuntu-latest
-##   timeout-minutes: 10
-##
-##   steps:
-##   - name: Remove old artifacts
-##     uses: c-hive/[email protected]
-##     with:
-##       age: '1 month'
-##       skip-recent: 8
-
   Set-Matrix-Private:
     runs-on: ubuntu-latest
     outputs:
@@ -87,24 +94,16 @@ jobs:
         run: |
           if [[ "${{ env.IAM }}" == 'public' ]] # Public: full set.
           then
-            config='{"config":[
-            {"os":"windows-latest", "r":"release", "timeout":360, "flags":"remote, vignettes, strict, binaries"},
-            {"os":"macOS-latest", "r":"release", "timeout":360, "flags":"remote, vignettes, strict, binaries, ubsan"},
-            {"os":"ubuntu-20.04", "r":"release", "rspm":"https://packagemanager.rstudio.com/cran/__linux__/focal/latest", "timeout":360, "flags":"strict, full, ubsan, debug"},
-            {"os":"ubuntu-20.04", "r":"devel", "rspm":"https://packagemanager.rstudio.com/cran/__linux__/focal/latest", "timeout":360, "flags":"strict, vignettes, remote"},
-            {"os":"ubuntu-20.04", "r":"release", "rspm":"https://packagemanager.rstudio.com/cran/__linux__/focal/latest", "timeout":360, "flags":"full, covr"}]}'
+            config='${{ env.RELEASE_CONFIG }}'
           elif [[ "${{ env.FOUND_PUBLIC }}" != '0' ]] # Private with no public analogue: reduced set.
           then
-            config='{"config":[
-            {"os":"ubuntu-20.04", "r":"release", "rspm":"https://packagemanager.rstudio.com/cran/__linux__/focal/latest", "timeout":10, "flags":"none"}
-            ]}'
+            config='${{ env.PRIVATE_CONFIG }}'
           else # Private with public analogue: no checking.
             config=''
           fi
-          config="${config//'%'/'%25'}"
-          config="${config//$'\n'/'%0A'}"
-          config="${config//$'\r'/'%0D'}"
-          echo "::set-output name=matrix::$config"
+          config="${config//$'\r'/' '}"
+          config="${config//$'\n'/' '}"
+          echo "matrix=$config" >> $GITHUB_OUTPUT
 
   R-CMD-check:
     needs: Set-Matrix-Private
@@ -122,7 +121,6 @@ jobs:
     env:
       HOMEBREW_NO_INSTALL_CLEANUP: 1
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
 
     steps:
       - name: If available, use the Janitor's key rather than the repository-specific key.
@@ -136,60 +134,40 @@ jobs:
           fi
         shell: bash
 
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
+          use-public-rspm: true
           r-version: ${{ matrix.config.r }}
 
-      - name: Install GhostScript (on Linux if running vignettes)
+      - name: Install tidy (on Linux if running vignettes)
         if: runner.os == 'Linux' && contains(matrix.config.flags, 'vignettes')
         run: |
-          /usr/bin/sudo DEBIAN_FRONTEND=noninteractive apt-get install -y ghostscript
+          /usr/bin/sudo DEBIAN_FRONTEND=noninteractive apt-get install -y tidy
         shell: bash
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - name: Install tinytex (system)
         if: contains(matrix.config.flags, 'vignettes')
-        uses: r-lib/actions/setup-tinytex@v1
+        uses: r-lib/actions/setup-tinytex@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}
-
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        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-
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
-          sudo apt-get install -y libcurl4-openssl-dev
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("pkgbuild"); stopifnot(require("pkgbuild"))
-          remotes::install_cran("rcmdcheck"); stopifnot(require("rcmdcheck"))
-          remotes::install_cran("covr"); stopifnot(require("covr"))
-        shell: Rscript {0}
+          extra-packages: |
+            any::rcmdcheck
+            any::covr
+            any::V8
+            any::xml2
+          needs: |
+            check
+            coverage
 
       - name: Install tinytex (R)
         if: contains(matrix.config.flags, 'vignettes')
         run: |
-          remotes::install_cran("tinytex")
+          if(!requireNamespace("tinytex", quietly = TRUE)) pak::pkg_install("tinytex")
           tinytex:::install_yihui_pkgs()
           tinytex::tlmgr_install("makeindex")
         shell: Rscript {0}
@@ -203,7 +181,7 @@ jobs:
 
       - name: Upload build results
         if: contains(matrix.config.flags, 'binaries') && !failure()
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-binaries
           path: binaries
@@ -239,18 +217,21 @@ jobs:
 
           error_on <- if(Sys.getenv("FAIL_ON_WARN") == "true") "warning" else "error"
 
+          extra_flags <- c()
+
           if(Sys.getenv("USE_UBSAN") == "true"){
-            Sys.setenv(PKG_LIBS=paste(Sys.getenv("PKG_LIBS"), "-fsanitize=undefined"),
-                       PKG_CFLAGS=paste(Sys.getenv("PKG_CFLAGS"), "-fsanitize=undefined"),
-                       PKG_CXXFLAGS=paste(Sys.getenv("PKG_CXXFLAGS"), "-fsanitize=undefined"),
-                       UBSAN_OPTIONS=paste(Sys.getenv("UBSAN_OPTIONS"), "print_stacktrace=1"))
+            extra_flags <- c(extra_flags, "-fsanitize=undefined")
+            Sys.setenv(UBSAN_OPTIONS=paste(Sys.getenv("UBSAN_OPTIONS"), "print_stacktrace=1"))
           }
 
-          if(Sys.getenv("SET_DEBUG") == "true"){
-            Sys.setenv(PKG_LIBS=paste(Sys.getenv("PKG_LIBS"), "-UNDEBUG -DDEBUG"),
-                       PKG_CXXFLAGS=paste(Sys.getenv("PKG_CXXFLAGS"), "-UNDEBUG -DDEBUG"),
-                       PKG_CFLAGS=paste(Sys.getenv("PKG_CFLAGS"), "-UNDEBUG -DDEBUG"))
-          }
+          if(Sys.getenv("SET_DEBUG") == "true") extra_flags <- c(extra_flags, "-UNDEBUG", "-DDEBUG")
+
+          # Before R 4.3.0, R itself was not compliant.
+          if(getRversion() >= "4.3") extra_flags <- c(extra_flags, "-Wstrict-prototypes")
+
+          Sys.setenv(PKG_LIBS=paste(c(Sys.getenv("PKG_LIBS"), extra_flags), collapse=" "),
+                     PKG_CXXFLAGS=paste(c(Sys.getenv("PKG_CXXFLAGS"), extra_flags), collapse=" "),
+                     PKG_CFLAGS=paste(c(Sys.getenv("PKG_CFLAGS"), extra_flags), collapse=" "))
 
           rcmdcheck::rcmdcheck(args = check_args, build_args = build_args, error_on = error_on, check_dir = "check")
         shell: Rscript {0}
@@ -274,24 +255,36 @@ jobs:
 
       - name: Upload check results
         if: contains(matrix.config.flags, 'covr') == false && failure()
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-results
           path: |
             check
             !check/*/00_pkg_src
 
-      - name: Preinstall package to work around an issue in covr # can be removed after covr update
-        if: contains(matrix.config.flags, 'covr')
-        run: R CMD INSTALL .
-        shell: bash
-
       - name: Test coverage
         if: contains(matrix.config.flags, 'covr')
         timeout-minutes: ${{ matrix.config.timeout }}
         env:
           _R_CHECK_CRAN_INCOMING_REMOTE_: false
           _R_CHECK_FORCE_SUGGESTS_: ${{ runner.os != 'macOS' }} # Rmpi is not available on macOS.
           ENABLE_statnet_TESTS: ${{ contains(matrix.config.flags, 'full') }}
-        run: covr::codecov(type=c("tests","examples"))
+        run: |
+          cov <- covr::package_coverage(
+            type=c("tests", "examples"),
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          covr::to_cobertura(cov)
         shell: Rscript {0}
+
+      - name: Upload coverage results
+        if: contains(matrix.config.flags, 'covr')
+        uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,20 +1,22 @@
 Package: ergm.count
-Version: 4.1.1
-Date: 2022-05-24
+Version: 4.1.2
+Date: 2024-06-15
 Title: Fit, Simulate and Diagnose Exponential-Family Models for Networks with Count Edges
 Authors@R: c(
-           person("Pavel N.", "Krivitsky", role=c("aut","cre"), email="[email protected]", comment=c(ORCID="0000-0002-9101-3362")),
-	   person("Mark S.", "Handcock", role=c("ctb"), email="[email protected]"),
-           person("David R.", "Hunter", role=c("ctb"), email="[email protected]"),
+           person(c("Pavel", "N."), "Krivitsky", role=c("aut","cre"), email="[email protected]", comment=c(ORCID="0000-0002-9101-3362")),
+           person(c("Mark", "S."), "Handcock", role=c("ctb"), email="[email protected]"),
+           person(c("David", "R."), "Hunter", role=c("ctb"), email="[email protected]"),
            person("Joyce", "Cheng", role=c("ctb"), email="[email protected]"))
 Depends:
     ergm (>= 4.2.1),
     network (>= 1.15)
 Imports:
-    statnet.common (>= 4.2.0)
+    statnet.common (>= 4.2.0),
+    Rdpack (>= 2.4)
 LinkingTo:
     ergm
-Description: A set of extensions for the 'ergm' package to fit weighted networks whose edge weights are counts. See Krivitsky (2012) <doi:10.1214/12-EJS696> and Krivitsky, Hunter, Morris, and Klumb (2021) <arXiv:2106.04997>.
+RdMacros: Rdpack
+Description: A set of extensions for the 'ergm' package to fit weighted networks whose edge weights are counts. See Krivitsky (2012) <doi:10.1214/12-EJS696> and Krivitsky, Hunter, Morris, and Klumb (2023) <doi:10.18637/jss.v105.i06>.
 License: GPL-3 + file LICENSE
 URL: https://statnet.org
 BugReports: https://github.com/statnet/ergm.count/issues
@@ -24,7 +26,7 @@ Suggests:
     rmarkdown,
     testthat (>= 3.0.0)
 VignetteBuilder: rmarkdown, knitr
-RoxygenNote: 7.2.0
+RoxygenNote: 7.3.1
 Roxygen: list(markdown = TRUE)
 Encoding: UTF-8
 Config/testthat/parallel: true

diff --git a/LICENSE b/LICENSE
@@ -36,4 +36,4 @@ Martina Morris, University of Washington
 
 The 'statnet' development team
 
-Copyright 2008-2022
+Copyright 2008-2024
diff --git a/NAMESPACE b/NAMESPACE
@@ -3,4 +3,5 @@
 import(ergm)
 import(network)
 import(statnet.common)
+importFrom(Rdpack,reprompt)
 useDynLib(ergm.count)
diff --git a/R/InitErgmReference.R b/R/InitErgmReference.R
@@ -5,7 +5,7 @@
 #  open source, and has the attribution requirements (GPL Section 7) at
 #  https://statnet.org/attribution .
 #
-#  Copyright 2008-2022 Statnet Commons
+#  Copyright 2008-2024 Statnet Commons
 ################################################################################
 
 #' @templateVar name Poisson

diff --git a/R/InitWtErgmProposal.R b/R/InitWtErgmProposal.R
@@ -5,7 +5,7 @@
 #  open source, and has the attribution requirements (GPL Section 7) at
 #  https://statnet.org/attribution .
 #
-#  Copyright 2008-2022 Statnet Commons
+#  Copyright 2008-2024 Statnet Commons
 ################################################################################
 
 #' @templateVar name Disc

diff --git a/R/InitWtErgmTerm.R b/R/InitWtErgmTerm.R
@@ -5,7 +5,7 @@
 #  open source, and has the attribution requirements (GPL Section 7) at
 #  https://statnet.org/attribution .
 #
-#  Copyright 2008-2022 Statnet Commons
+#  Copyright 2008-2024 Statnet Commons
 ################################################################################
 
 #' @templateVar name CMP

diff --git a/R/data.R b/R/data.R
@@ -5,7 +5,7 @@
 #  open source, and has the attribution requirements (GPL Section 7) at
 #  https://statnet.org/attribution .
 #
-#  Copyright 2008-2022 Statnet Commons
+#  Copyright 2008-2024 Statnet Commons
 ################################################################################
 #' Karate club social network of Zachary (1977)
 #'