added github workflows

ropensci · Mar 30, 2024 · 87de4bb · 87de4bb
1 parent 5ac0780
commit 87de4bb
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Showing 23 changed files with 15,050 additions and 14,938 deletions.
diff --git a/.Rhistory b/.Rhistory
@@ -1 +1,4 @@
 roxygen2::roxygenise()
+install.packages("codemetar")
+codemetar::write_codemeta()
+codemetar::give_opinions('C:\\Users\\abiga\\Documents\\WSG\\eDNAjoint')
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -0,0 +1,49 @@
+# 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]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        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
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - 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-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
diff --git a/.github/workflows/test-coverage.yaml b/.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, master]
+  pull_request:
+    branches: [main, master]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package
diff --git a/src/Makevars.win b/src/Makevars.win
@@ -0,0 +1,10 @@
+# Generated by rstantools.  Do not edit by hand.
+
+STANHEADERS_SRC = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "message()" -e "cat(system.file('include', 'src', package = 'StanHeaders', mustWork = TRUE))" -e "message()" | grep "StanHeaders")
+
+STANC_FLAGS = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "cat(ifelse(utils::packageVersion('rstan') >= '2.26', '-DUSE_STANC3',''))")
+PKG_CPPFLAGS = -I"../inst/include" -I"$(STANHEADERS_SRC)" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DRCPP_PARALLEL_USE_TBB=1 $(STANC_FLAGS) -D_HAS_AUTO_PTR_ETC=0
+PKG_CXXFLAGS = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "RcppParallel::CxxFlags()") $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "StanHeaders:::CxxFlags()")
+PKG_LIBS = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "RcppParallel::RcppParallelLibs()") $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "StanHeaders:::LdFlags()")
+
+CXX_STD = CXX17
diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
@@ -1,59 +1,59 @@
-// Generated by using Rcpp::compileAttributes() -> do not edit by hand
-// Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
-
-#include <RcppEigen.h>
-#include <Rcpp.h>
-
-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
-
-
-RcppExport SEXP _rcpp_module_boot_stan_fit4joint_binary_catchability_gamma_mod();
-RcppExport SEXP _rcpp_module_boot_stan_fit4joint_binary_catchability_negbin_mod();
-RcppExport SEXP _rcpp_module_boot_stan_fit4joint_binary_catchability_pois_mod();
-RcppExport SEXP _rcpp_module_boot_stan_fit4joint_binary_cov_catchability_gamma_mod();
-RcppExport SEXP _rcpp_module_boot_stan_fit4joint_binary_cov_catchability_negbin_mod();
-RcppExport SEXP _rcpp_module_boot_stan_fit4joint_binary_cov_catchability_pois_mod();
-RcppExport SEXP _rcpp_module_boot_stan_fit4joint_binary_cov_gamma_mod();
-RcppExport SEXP _rcpp_module_boot_stan_fit4joint_binary_cov_negbin_mod();
-RcppExport SEXP _rcpp_module_boot_stan_fit4joint_binary_cov_pois_mod();
-RcppExport SEXP _rcpp_module_boot_stan_fit4joint_binary_gamma_mod();
-RcppExport SEXP _rcpp_module_boot_stan_fit4joint_binary_negbin_mod();
-RcppExport SEXP _rcpp_module_boot_stan_fit4joint_binary_pois_mod();
-RcppExport SEXP _rcpp_module_boot_stan_fit4traditional_catchability_gamma_mod();
-RcppExport SEXP _rcpp_module_boot_stan_fit4traditional_catchability_negbin_mod();
-RcppExport SEXP _rcpp_module_boot_stan_fit4traditional_catchability_pois_mod();
-RcppExport SEXP _rcpp_module_boot_stan_fit4traditional_gamma_mod();
-RcppExport SEXP _rcpp_module_boot_stan_fit4traditional_negbin_mod();
-RcppExport SEXP _rcpp_module_boot_stan_fit4traditional_pois_mod();
-
-static const R_CallMethodDef CallEntries[] = {
-    {"_rcpp_module_boot_stan_fit4joint_binary_catchability_gamma_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4joint_binary_catchability_gamma_mod, 0},
-    {"_rcpp_module_boot_stan_fit4joint_binary_catchability_negbin_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4joint_binary_catchability_negbin_mod, 0},
-    {"_rcpp_module_boot_stan_fit4joint_binary_catchability_pois_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4joint_binary_catchability_pois_mod, 0},
-    {"_rcpp_module_boot_stan_fit4joint_binary_cov_catchability_gamma_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4joint_binary_cov_catchability_gamma_mod, 0},
-    {"_rcpp_module_boot_stan_fit4joint_binary_cov_catchability_negbin_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4joint_binary_cov_catchability_negbin_mod, 0},
-    {"_rcpp_module_boot_stan_fit4joint_binary_cov_catchability_pois_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4joint_binary_cov_catchability_pois_mod, 0},
-    {"_rcpp_module_boot_stan_fit4joint_binary_cov_gamma_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4joint_binary_cov_gamma_mod, 0},
-    {"_rcpp_module_boot_stan_fit4joint_binary_cov_negbin_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4joint_binary_cov_negbin_mod, 0},
-    {"_rcpp_module_boot_stan_fit4joint_binary_cov_pois_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4joint_binary_cov_pois_mod, 0},
-    {"_rcpp_module_boot_stan_fit4joint_binary_gamma_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4joint_binary_gamma_mod, 0},
-    {"_rcpp_module_boot_stan_fit4joint_binary_negbin_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4joint_binary_negbin_mod, 0},
-    {"_rcpp_module_boot_stan_fit4joint_binary_pois_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4joint_binary_pois_mod, 0},
-    {"_rcpp_module_boot_stan_fit4traditional_catchability_gamma_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4traditional_catchability_gamma_mod, 0},
-    {"_rcpp_module_boot_stan_fit4traditional_catchability_negbin_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4traditional_catchability_negbin_mod, 0},
-    {"_rcpp_module_boot_stan_fit4traditional_catchability_pois_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4traditional_catchability_pois_mod, 0},
-    {"_rcpp_module_boot_stan_fit4traditional_gamma_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4traditional_gamma_mod, 0},
-    {"_rcpp_module_boot_stan_fit4traditional_negbin_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4traditional_negbin_mod, 0},
-    {"_rcpp_module_boot_stan_fit4traditional_pois_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4traditional_pois_mod, 0},
-    {NULL, NULL, 0}
-};
-
-RcppExport void R_init_eDNAjoint(DllInfo *dll) {
-    R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
-    R_useDynamicSymbols(dll, FALSE);
-}
+// Generated by using Rcpp::compileAttributes() -> do not edit by hand
+// Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
+
+#include <RcppEigen.h>
+#include <Rcpp.h>
+
+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
+
+
+RcppExport SEXP _rcpp_module_boot_stan_fit4joint_binary_catchability_gamma_mod();
+RcppExport SEXP _rcpp_module_boot_stan_fit4joint_binary_catchability_negbin_mod();
+RcppExport SEXP _rcpp_module_boot_stan_fit4joint_binary_catchability_pois_mod();
+RcppExport SEXP _rcpp_module_boot_stan_fit4joint_binary_cov_catchability_gamma_mod();
+RcppExport SEXP _rcpp_module_boot_stan_fit4joint_binary_cov_catchability_negbin_mod();
+RcppExport SEXP _rcpp_module_boot_stan_fit4joint_binary_cov_catchability_pois_mod();
+RcppExport SEXP _rcpp_module_boot_stan_fit4joint_binary_cov_gamma_mod();
+RcppExport SEXP _rcpp_module_boot_stan_fit4joint_binary_cov_negbin_mod();
+RcppExport SEXP _rcpp_module_boot_stan_fit4joint_binary_cov_pois_mod();
+RcppExport SEXP _rcpp_module_boot_stan_fit4joint_binary_gamma_mod();
+RcppExport SEXP _rcpp_module_boot_stan_fit4joint_binary_negbin_mod();
+RcppExport SEXP _rcpp_module_boot_stan_fit4joint_binary_pois_mod();
+RcppExport SEXP _rcpp_module_boot_stan_fit4traditional_catchability_gamma_mod();
+RcppExport SEXP _rcpp_module_boot_stan_fit4traditional_catchability_negbin_mod();
+RcppExport SEXP _rcpp_module_boot_stan_fit4traditional_catchability_pois_mod();
+RcppExport SEXP _rcpp_module_boot_stan_fit4traditional_gamma_mod();
+RcppExport SEXP _rcpp_module_boot_stan_fit4traditional_negbin_mod();
+RcppExport SEXP _rcpp_module_boot_stan_fit4traditional_pois_mod();
+
+static const R_CallMethodDef CallEntries[] = {
+    {"_rcpp_module_boot_stan_fit4joint_binary_catchability_gamma_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4joint_binary_catchability_gamma_mod, 0},
+    {"_rcpp_module_boot_stan_fit4joint_binary_catchability_negbin_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4joint_binary_catchability_negbin_mod, 0},
+    {"_rcpp_module_boot_stan_fit4joint_binary_catchability_pois_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4joint_binary_catchability_pois_mod, 0},
+    {"_rcpp_module_boot_stan_fit4joint_binary_cov_catchability_gamma_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4joint_binary_cov_catchability_gamma_mod, 0},
+    {"_rcpp_module_boot_stan_fit4joint_binary_cov_catchability_negbin_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4joint_binary_cov_catchability_negbin_mod, 0},
+    {"_rcpp_module_boot_stan_fit4joint_binary_cov_catchability_pois_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4joint_binary_cov_catchability_pois_mod, 0},
+    {"_rcpp_module_boot_stan_fit4joint_binary_cov_gamma_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4joint_binary_cov_gamma_mod, 0},
+    {"_rcpp_module_boot_stan_fit4joint_binary_cov_negbin_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4joint_binary_cov_negbin_mod, 0},
+    {"_rcpp_module_boot_stan_fit4joint_binary_cov_pois_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4joint_binary_cov_pois_mod, 0},
+    {"_rcpp_module_boot_stan_fit4joint_binary_gamma_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4joint_binary_gamma_mod, 0},
+    {"_rcpp_module_boot_stan_fit4joint_binary_negbin_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4joint_binary_negbin_mod, 0},
+    {"_rcpp_module_boot_stan_fit4joint_binary_pois_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4joint_binary_pois_mod, 0},
+    {"_rcpp_module_boot_stan_fit4traditional_catchability_gamma_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4traditional_catchability_gamma_mod, 0},
+    {"_rcpp_module_boot_stan_fit4traditional_catchability_negbin_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4traditional_catchability_negbin_mod, 0},
+    {"_rcpp_module_boot_stan_fit4traditional_catchability_pois_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4traditional_catchability_pois_mod, 0},
+    {"_rcpp_module_boot_stan_fit4traditional_gamma_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4traditional_gamma_mod, 0},
+    {"_rcpp_module_boot_stan_fit4traditional_negbin_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4traditional_negbin_mod, 0},
+    {"_rcpp_module_boot_stan_fit4traditional_pois_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4traditional_pois_mod, 0},
+    {NULL, NULL, 0}
+};
+
+RcppExport void R_init_eDNAjoint(DllInfo *dll) {
+    R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
+    R_useDynamicSymbols(dll, FALSE);
+}