Merge devel into master

.Rbuildignore

@@ -10,3 +10,6 @@
 ^appveyor\.yml$
 ^containers$
 ^README\.Rmd$
+^LICENSE\.md$
+^LICENSE\.md$
+^\.github$

.github/.gitignore

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

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

@@ -0,0 +1,84 @@
+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 }}
+    if: "!contains(github.event.head_commit.message, 'ci skip')"
+    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"}
+          - {os: ubuntu-16.04, r: 'devel', 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 +1,55 @@
+on:
+  push:
+    branches:
+      - master
+      - devel
+  pull_request:
+    branches:
+      - master
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    if: "!contains(github.event.head_commit.message, 'ci skip')"
+    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: dynparam
 Type: Package
 Title: Creating Meta-Information for Parameters
-Version: 1.0.0
+Version: 1.0.2
 Authors@R: c(
     person(
       "Robrecht", 
@@ -24,9 +24,9 @@ Description: Provides tools for describing parameters of algorithms in an abstra
   Description can include an id, a description, a domain (range or list of values),
   and a default value. 'dynparam' can also convert parameter sets to a 'ParamHelpers' format, 
   in order to be able to use 'dynparam' in conjunction with 'mlrMBO'.
-License: GPL-3
+License: MIT + file LICENSE
 LazyData: TRUE
-RoxygenNote: 6.1.1
+RoxygenNote: 7.1.1
 Roxygen: list(markdown = TRUE)
 Encoding: UTF-8
 Depends:
@@ -36,15 +36,12 @@ Imports:
   carrier,
   dplyr,
   dynutils (>= 1.0.2),
-  Hmisc,
   magrittr,
   purrr,
   stringr,
-  testthat,
   tibble,
   tidyr
 Suggests:
+  lhs,
   ParamHelpers,
-  lhs
-Remotes:
-  dynverse/dynutils@master
+  testthat

LICENSE

@@ -0,0 +1,2 @@
+YEAR: 2014-2020
+COPYRIGHT HOLDER: Robrecht Cannoodt, Wouter Saelens

LICENSE.md

@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2014-2020 Robrecht Cannoodt, Wouter Saelens
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

NAMESPACE

@@ -62,7 +62,6 @@ import(dplyr)
 import(dynutils)
 import(purrr)
 import(tidyr)
-importFrom(Hmisc,capitalize)
 importFrom(carrier,crate)
 importFrom(magrittr,"%$%")
 importFrom(magrittr,"%<>%")

NEWS.md

@@ -0,0 +1,11 @@
+# dynparam 1.0.2 (04-01-2021)
+
+* MINOR CHANGES: Set `check.environment` to `FALSE` in unit tests to fix breaking changes in R devel.
+
+# dynparam 1.0.1 (24-06-2020)
+* MINOR CHANGES: Move testthat to Suggests.
+* MINOR CHANGES: Use `expect_equal(., ., tolerance = .)` instead of `expect_lte(abs(. - .), .)` in tests.
+
+# dynparam 1.0.0 (02-04-2019)
+
+* INITIAL RELEASE: dynparam helps describe method parameters.

R/param_super.R

@@ -154,7 +154,6 @@ on_failure(is_parameter) <- function(call, env) {
 #' @param x The parameter
 #' @param sep A separator between different fields
 #'
-#' @importFrom Hmisc capitalize
 #' @importFrom stringr str_replace_all str_replace str_glue_data
 #'
 #' @export
@@ -167,7 +166,7 @@ get_description <- function(
   description <-
     (x$description %||% "") %>%                     # use "" if no description is provided
     str_replace_all("\n", "") %>%                   # remove newlines
-    Hmisc::capitalize() %>%                         # capitalise sentences
+    capitalise() %>%                         # capitalise sentences
     str_replace_all("\\\\link\\[[a-zA-Z0-9_:]*\\]\\{([^\\}]*)\\}", "\\1") %>%  # substitute \link[X](Y) with just Y
     str_replace_all("[ \t\\.]*$", "")               # remove trailing whitespace and punctuation
 
@@ -180,7 +179,7 @@ get_description <- function(
     lis[!names(lis) %in% c("id", "type")] %>%
     as.list() %>%
     stringr::str_glue_data("{names(.)}: {.}") %>%
-    Hmisc::capitalize() %>%
+    capitalise() %>%
     paste0(collapse = sep)
 
   paste0(description, sep, extra_text)
@@ -201,3 +200,11 @@ as_descriptive_tibble.parameter <- function(x) {
     default = collapse_set(x$default)
   )
 }
+
+
+
+capitalise <- function(string) {
+  capped <- grep("^[A-Z]", string, invert = TRUE)
+  substr(string[capped], 1, 1) <- toupper(substr(string[capped], 1, 1))
+  return(string)
+}

README.Rmd

@@ -144,12 +144,11 @@ as_paramhelper(parameters)
 
 ## Latest changes
 
-Check out `news(package = "dynparam")` or [NEWS.md](inst/NEWS.md) for a full list of changes.
+Check out `news(package = "dynparam")` or [NEWS.md](NEWS.md) for a full list of changes.
 
-<!-- This section gets automatically generated from inst/NEWS.md, and also generates inst/NEWS -->
+<!-- This section gets automatically generated from NEWS.md, and also generates inst/NEWS -->
 
 ```{r news, echo=FALSE, results="asis"}
-dynutils::update_news()
 base::cat(dynutils::recent_news())
 ```
 

README.md

@@ -236,13 +236,12 @@ sip(parameters, n = 2)
 ```
 
     ## # A tibble: 2 x 8
-    ##   num_iter delta   method  inverse dimreds  ks      quantiles .object_class
-    ##      <int> <list>  <chr>   <lgl>   <list>   <list>  <list>    <list>       
-    ## 1       90 <dbl [… spearm… TRUE    <chr [3… <dbl [… <dbl [2]> <chr [1]>    
-    ## 2      332 <dbl [… spearm… TRUE    <chr [4… <dbl [… <dbl [2]> <chr [1]>
+    ##   num_iter delta     method  inverse dimreds   ks        quantiles .object_class
+    ##      <int> <list>    <chr>   <lgl>   <list>    <list>    <list>    <list>       
+    ## 1     1823 <dbl [3]> kendall FALSE   <chr [3]> <dbl [2]> <dbl [2]> <chr [1]>    
+    ## 2      125 <dbl [3]> pearson TRUE    <chr [2]> <dbl [2]> <dbl [2]> <chr [1]>
 
-Convert paramhelper
-    object:
+Convert paramhelper object:
 
 ``` r
 as_paramhelper(parameters)
@@ -268,16 +267,21 @@ as_paramhelper(parameters)
 
 ## Latest changes
 
-Check out `news(package = "dynparam")` or [NEWS.md](inst/NEWS.md) for a
-full list of
-changes.
+Check out `news(package = "dynparam")` or [NEWS.md](NEWS.md) for a full
+list of changes.
 
-<!-- This section gets automatically generated from inst/NEWS.md, and also generates inst/NEWS -->
+<!-- This section gets automatically generated from NEWS.md, and also generates inst/NEWS -->
 
-### Recent changes in dynparam 1.0.0 (02-04-2019)
+### Recent changes in dynparam 1.0.2 (04-01-2021)
 
-  - INITIAL RELEASE: dynparam helps describe method
-parameters.
+  - MINOR CHANGES: Set `check.environment` to `FALSE` in unit tests to
+    fix breaking changes in R devel.
+
+### Recent changes in dynparam 1.0.1 (24-06-2020)
+
+  - MINOR CHANGES: Move testthat to Suggests.
+  - MINOR CHANGES: Use `expect_equal(., ., tolerance = .)` instead of
+    `expect_lte(abs(. - .), .)` in tests.
 
 ## Dynverse dependencies
 

cran-comments.md

@@ -1,17 +1,22 @@
-This is a new package for being able to describe parameters in an abstract way.
+# dynparam 1.0.2 (04-01-2021)
+
+* MINOR CHANGES: Set `check.environment` to `FALSE` in unit tests to fix breaking changes in R devel.
 
 ## Test environments
-* local Fedora install, R 3.5.2
-* ubuntu 14.04 (on travis-ci), R 3.5.2
-* win-builder (release and devel)
+* local Fedora install, R 4.0.3
+* ubuntu 16.04 (with Github Actions; R 3.6, release, devel)
+* Mac OS X (with Github Actions; R release)
+* Windows (with Github Actions; R release)
+* win-builder (devel)
 
 ## R CMD check results
 
 ```
-── R CMD check results ───────────────────────────────────── dynparam 1.0.0 ────
-Duration: 36.9s
+── R CMD check results ───────────────────────────────────── dynparam 1.0.2 ────
+Duration: 31.4s
 
-0 errors ✔ | 0 warnings ✔ | 0 notes ✔
+0 errors ✓ | 0 warnings ✓ | 0 notes ✓
 
 R CMD check succeeded
+
 ```