Merge pull request #1 from rscherrer/develop

Develop

.Rbuildignore

@@ -1,3 +1,4 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 extra
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

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

@@ -0,0 +1,85 @@
+# 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
+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: windows-latest, r: 'release'}
+          - {os: macOS-latest, r: 'release'}
+          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04,   r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest", http-user-agent: "R/4.1.0 (ubuntu-20.04) R (4.1.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v1
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Restore R package cache
+        uses: actions/cache@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"))')
+
+      - name: Install dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
+
+      - name: Check
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+        run: |
+          options(crayon.enabled = TRUE)
+          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@main
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: speciomer
 Type: Package
 Title: Import Speciome Data into R
-Version: 1.0
+Version: 2.0
 Author: Raphael Scherrer
 Maintainer: Raphael Scherrer <r.scherrer@rug.nl>
 Description: Read binary speciome simulation data into R. Converts them into tibbles. Also a few extra utilities.
@@ -12,21 +12,15 @@ RoxygenNote: 7.1.1
 Suggests: 
     knitr,
     rmarkdown,
-    testthat (>= 3.0.0)
+    testthat (>= 3.0.0),
+    forcats,
+    ggplot2
 VignetteBuilder: knitr
 Imports: 
     magrittr,
     dplyr,
-    forcats,
-    gganimate,
-    ggplot2,
-    ggraph,
-    igraph,
     purrr,
-    rlang,
     stringr,
     tibble,
-    tidygraph,
-    tidyr,
-    tidyselect
+    tidyr
 Config/testthat/edition: 3

NAMESPACE

@@ -1,61 +1,17 @@
 # Generated by roxygen2: do not edit by hand
 
 export("%>%")
-export(add_chromosomes)
 export(as_tibble_speciome)
-export(collect_param)
-export(combine_data)
-export(fetch_dirs)
-export(find_edge)
-export(find_extant)
-export(find_partners)
-export(get_chromosomes)
-export(get_degrees)
-export(give_edges_coordinates)
-export(guess_nedges)
-export(guess_nloci)
-export(guess_nrows)
 export(interpret_variable_names)
-export(is_complete)
-export(is_extant)
-export(is_extinct)
-export(is_missing)
-export(pivot_data)
-export(plot_genome_distributions)
-export(plot_genome_heatmap)
-export(plot_genome_network)
-export(plot_genome_scan)
-export(plot_genome_scatter)
-export(plot_genome_trajectories)
-export(plot_trait_values)
-export(read_arch)
-export(read_arch_file)
-export(read_arch_genome)
-export(read_arch_network)
 export(read_architecture)
 export(read_binary)
 export(read_bitset)
-export(read_data)
 export(read_edges)
-export(read_genome)
-export(read_indiv_loci)
 export(read_individual_genomes)
 export(read_individuals)
 export(read_loci)
-export(read_network)
-export(read_param)
-export(read_param_file)
 export(read_parameters)
-export(read_pedigree)
-export(read_pop)
 export(read_population)
-export(read_sim)
-export(read_slurm_status)
 export(read_speciome)
-export(read_this)
-export(rename_str)
 export(rm_plural_colnames)
-export(set_param_file)
-export(smoothen_data)
-export(trait_colors)
 importFrom(magrittr,"%>%")