dynutils v1.0.6

.Rbuildignore

@@ -10,3 +10,4 @@
 ^vignettes/.*\.md$
 ^vignettes/.*/.*\.png$
 ^LICENSE\.md$
+^\.github$

.github/.gitignore

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

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

@@ -0,0 +1,83 @@
+on:
+  push:
+    branches:
+      - master
+      - devel
+  pull_request:
+    branches:
+      - master
+  schedule:
+    - cron: "0 0 * * 1"
+
+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-16.04, r: '3.6', rspm: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}
+          - {os: ubuntu-16.04, r: 'release', rspm: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@master
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-pandoc@master
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        uses: actions/cache@v1
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-r-${{ matrix.config.r }}-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-
+
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        env:
+          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
+        run: |
+          Rscript -e "remotes::install_github('r-hub/sysreqs')"
+          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
+          sudo -s eval "$sysreqs"
+
+      - 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: 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@master
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check
+

.github/workflows/test_coverage.yml

@@ -0,0 +1,54 @@
+on:
+  push:
+    branches:
+      - master
+      - devel
+  pull_request:
+    branches:
+      - master
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@master
+
+      - uses: r-lib/actions/setup-pandoc@master
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), "depends.Rds", version = 2)
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        uses: actions/cache@v1
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ubuntu-r-release-${{ hashFiles('depends.Rds') }}
+          restore-keys: ubuntu-r-release-
+
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        env:
+          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
+        run: |
+          Rscript -e "remotes::install_github('rcannood/sysreqs')"
+          sysreqs=$(Rscript -e "pkgs <- unique(c(sysreqs:::get_cran_sysreqs(sysreqs:::get_cran_deps('covr')), sysreqs::sysreqs('DESCRIPTION'))); cat(sysreqs:::sysreq_commands_pkgs(pkgs))")
+          sudo -s eval "$sysreqs"
+
+      - name: Install dependencies
+        run: |
+          install.packages(c("remotes"))
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("covr")
+        shell: Rscript {0}
+
+      - name: Test coverage
+        run: covr::codecov()
+        shell: Rscript {0}
+

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: dynutils
 Type: Package
 Title: Common Functionality for the 'dynverse' Packages
-Version: 1.0.5
+Version: 1.0.6
 Authors@R: c(
     person(
       "Robrecht", 
@@ -26,7 +26,7 @@ License: MIT + file LICENSE
 URL: https://github.com/dynverse/dynutils
 BugReports: https://github.com/dynverse/dynutils/issues
 LazyData: TRUE
-RoxygenNote: 7.0.2
+RoxygenNote: 7.1.1
 Depends:
   R (>= 3.0.0)
 Imports: 

NAMESPACE

@@ -62,6 +62,7 @@ importFrom(assertthat,assert_that)
 importFrom(crayon,bold)
 importFrom(crayon,green)
 importFrom(crayon,red)
+importFrom(desc,desc)
 importFrom(dplyr,enquo)
 importFrom(dplyr,n)
 importFrom(dplyr,slice)

NEWS.md

@@ -1,4 +1,10 @@
-# dynutils 1.0.5
+# dynutils 1.0.6
+
+* MINOR CHANGE `calculate_distance()`: Allow for many more distance measures.
+
+* BUG FIX: Import `desc::desc()` where needed.
+
+# dynutils 1.0.5 (2020-02-21)
 
  * BUG FIX `install_packages()`: will not try to install packages when the session is not interactive.
 

R/calculate_distance.R

@@ -25,7 +25,8 @@
 calculate_distance <- function(
   x,
   y = NULL,
-  method = c("pearson", "spearman", "cosine", "euclidean", "manhattan"),
+  method = c("pearson", "spearman", "cosine", "euclidean", "chisquared",
+             "hamming", "kullback", "manhattan", "maximum", "canberra", "minkowski"),
   margin = 1
 ) {
   method <- match.arg(method)
@@ -149,11 +150,13 @@ list_similarity_methods <- function() eval(formals(calculate_similarity)$method)
 #' @export
 #' @rdname deprecated
 euclidean_distance <- function(x, y = NULL) {
+  .Deprecated("calculate_distance")
   as.matrix(calculate_distance(x, y, method = "euclidean"))
 }
 
 #' @export
 #' @rdname deprecated
 correlation_distance <- function(x, y = NULL) {
+  .Deprecated("calculate_distance")
   as.matrix(calculate_distance(x, y, method = "spearman"))
 }

R/development.R

@@ -37,6 +37,7 @@ switch_devel <- function(file = "DESCRIPTION", desc = desc::desc(file = file)) {
 #' @export
 #' @rdname switch_devel
 #' @importFrom stringr str_replace_all str_subset str_detect
+#' @importFrom desc desc
 switch_master <- function(file = "DESCRIPTION", desc = desc::desc(file = file)) {
   # set version to 9000
   version <- as.character(desc$get_version())

README.md

@@ -21,27 +21,21 @@ check out [dynverse.org](https://dynverse.org).
 ## Latest changes
 
 Check out `news(package = "dynutils")` or [NEWS.md](NEWS.md) for a full
-list of
-changes.
+list of changes.
 
 <!-- This section gets automatically generated from inst/NEWS.md, and also generates inst/NEWS -->
 
-### Recent changes in dynutils 1.0.5
+### Recent changes in dynutils 1.0.6
 
-  - BUG FIX `install_packages()`: will not try to install packages when
-    the session is not interactive.
-
-  - LICENSE: Change to MIT.
+-   MINOR CHANGE `calculate_distance()`: Allow for many more distance
+    measures.
 
-### Recent changes in dynutils 1.0.4 (2019-10-03)
+### Recent changes in dynutils 1.0.5 (2020-02-21)
 
-  - BUG FIX `recent_news()`: do not prepend subsections.
-
-  - BUG FIX `switch_cran()`: add missing version variable.
+-   BUG FIX `install_packages()`: will not try to install packages when
+    the session is not interactive.
 
-  - REMOVAL `update_news()` remove this function as R 3.6 natively
-    supports markdown news
-format.
+-   LICENSE: Change to MIT.
 
 ## Dynverse dependencies
 

cran-comments.md

@@ -1,8 +1,8 @@
-# dynutils 1.0.5
+# dynutils 1.0.6
 
- * BUG FIX `install_packages()`: will not try to install packages when the session is not interactive.
- 
- * LICENSE: Change to MIT.
+* MINOR CHANGE `calculate_distance()`: Allow for many more distance measures.
+
+* BUG FIX: Import `desc::desc()` where needed.
 
 ## Test environments
 * local Fedora 31 installation, R 3.6.2
@@ -26,21 +26,24 @@ A reverse dependency check was run on all downstream dependencies.
 (Summary at [revdep/README.md](revdep/README.md)). No new problems were found.
 
 ```
-> revdepcheck::revdep_check(timeout = as.difftime(60, units = "mins"), num_workers = 8)
-── INSTALL ─────────────────────────────────────────────────────── 2 versions ──
+> revdepcheck::revdep_check(timeout = as.difftime(600, units = "mins"), num_workers = 30)
+── INIT ────────────────────────────────────────────────────────────────────────
+── INSTALL ─────────────────────────────────────────────────────────────────────
 Installing CRAN version of dynutils
+also installing the dependencies ‘cli’, ‘utf8’, ‘R6’, ‘rprojroot’, ‘ellipsis’, ‘generics’, ‘lifecycle’, ‘rlang’, ‘tidyselect’, ‘vctrs’, ‘RcppParallel’, ‘RcppArmadillo’, ‘fansi’, ‘pillar’, ‘pkgconfig’, ‘assertthat’, ‘crayon’, ‘desc’, ‘dplyr’, ‘proxyC’, ‘purrr’, ‘Rcpp’, ‘remotes’, ‘tibble’
+
 Installing DEV version of dynutils
-Installing 30 packages: assertthat, crayon, desc, dplyr, magrittr, proxyC, purrr, Rcpp, remotes, stringr, tibble, backports, rlang, cli, fansi, pillar, pkgconfig, glue, utf8, vctrs, ellipsis, digest, R6, rprojroot, tidyselect, BH, plogr, RcppParallel, RcppArmadillo, stringi
-── CHECK ───────────────────────────────────────────────────────── 6 packages ──
-✔ babelwhale 1.0.1                       ── E: 1     | W: 0     | N: 0          
-✔ lmds 0.1.0                             ── E: 0     | W: 0     | N: 1          
-✔ GillespieSSA2 0.2.5                    ── E: 0     | W: 0     | N: 1          
-✔ dynparam 1.0.0                         ── E: 0     | W: 0     | N: 1          
-I SCORPIUS 1.0.5                         ── E: 1     | W: 0     | N: 0          
-✔ dynwrap 1.1.4                          ── E: 1     | W: 0     | N: 0          
+Installing 26 packages: digest, assertthat, vctrs, utf8, rlang, lifecycle, fansi, ellipsis, crayon, cli, Rcpp, magrittr, purrr, pkgconfig, pillar, RcppArmadillo, RcppParallel, tidyselect, tibble, R6, generics, rprojroot, remotes, proxyC, dplyr, desc
+── CHECK ───────────────────────────────────────────────────────────────────────
+✓ babelwhale 1.0.1                       ── E: 1     | W: 0     | N: 0                                                                                                                                                                   
+✓ lmds 0.1.0                             ── E: 0     | W: 0     | N: 1                                                                                                                                                                   
+✓ dynparam 1.0.2                         ── E: 0     | W: 0     | N: 0                                                                                                                                                                   
+✓ dynwrap 1.2.1                          ── E: 1     | W: 0     | N: 2                                                                                                                                                                   
+✓ GillespieSSA2 0.2.7                    ── E: 0     | W: 0     | N: 1                                                                                                                                                                   
+✓ SCORPIUS 1.0.7                         ── E: 0     | W: 0     | N: 0                                                                                                                                                                   
 OK: 6                                                                         
 BROKEN: 0
-Total time: 27 min
+Total time: 6 min
 ── REPORT ──────────────────────────────────────────────────────────────────────
 Writing summary to 'revdep/README.md'
 Writing problems to 'revdep/problems.md'