Merge branch 'refactor/polishing'

BioGenies · Jan 21, 2021 · 57272d4 · 57272d4
2 parents 32d2074 + f668496
commit 57272d4
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Showing 19 changed files with 27 additions and 49 deletions.
diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
@@ -63,9 +63,6 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      ## to avoid conversion of configure.ac
-      - name: Configure git
-        run: git config --global core.autocrlf false
 
       ## Set the R library to the directory matching the
       ## R packages cache step further below when running on Docker (Linux).
@@ -76,7 +73,7 @@ jobs:
           echo ".libPaths('/__w/_temp/Library')" > ~/.Rprofile
 
       ## Most of these steps are the same as the ones in
-      ## https://github.com/r-lib/actions/blob/master/examples/check -standard.yaml
+      ## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml
       ## If they update their steps, we will also need to update ours.
       - name: Checkout Repository
         uses: actions/checkout@v2
@@ -125,10 +122,6 @@ jobs:
       - name: Install macOS system dependencies
         if: matrix.config.os == 'macOS-latest'
         run: |
-          mkdir ~/.R
-          touch ~/.R/Makevars
-          echo "CXX_STD = CXX17" > ~/.R/Makevars
-        
           ## Enable installing XML from source if needed
           brew install libxml2
           echo "XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV
@@ -140,8 +133,8 @@ jobs:
           ## For textshaping, required by ragg, and required by pkgdown
           brew install harfbuzz fribidi
 
-          ## Helps compile RCurl from source; added forced ignoring deps
-          brew uninstall --ignore-dependencies curl
+          ## For installing usethis's dependency gert
+          brew install libgit2
 
       - name: Install Windows system dependencies
         if: runner.os == 'Windows'
@@ -160,7 +153,7 @@ jobs:
           BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE)
         shell: Rscript {0}
 
-      - name: Install dependencies
+      - name: Install dependencies pass 1
         run: |
           ## Try installing the package dependencies in steps. First the local
           ## dependencies, then any remaining dependencies to avoid the
@@ -169,19 +162,18 @@ jobs:
           ## https://github.com/r-lib/remotes/issues/296
           ## Ideally, all dependencies should get installed in the first pass.
 
-          ## Temporary for now due to https://github.com/ropensci/RefManageR/issues/79
-          remotes::install_github("ropensci/bibtex")
-          remotes::install_github("ropensci/RefManageR")
-          remotes::install_github("cboettig/knitcitations")
-
           ## Pass #1 at installing dependencies
           message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
           remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE)
+        continue-on-error: true
+        shell: Rscript {0}
 
+      - name: Install dependencies pass 2
+        run: |
           ## Pass #2 at installing dependencies
           message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****'))
           remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE)
-
+          
           ## For running the checks
           message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
           remotes::install_cran("rcmdcheck")

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: tidysq
 Type: Package
 Title: Tidy processing and analysis of biological sequences
-Version: 0.9.0
+Version: 1.0.0
 Date: 2020-12-10
 Authors@R: c(person("Dominik", "Rafacz", 
            email = "[email protected]",
@@ -60,7 +60,8 @@ Suggests:
     spelling,
     testthat (>= 2.1.0),
     withr (>= 2.2.0),
-    knitr
+    knitr,
+    purrr
 License: GPL (>= 2)
 URL: https://github.com/michbur/tidysq
 BugReports: https://github.com/michbur/tidysq/issues

diff --git a/R/doc-tidysq.R b/R/doc-tidysq.R
@@ -2,7 +2,7 @@
 #'
 #' @description The \code{tidysq} package is a toolbox for the analysis of 
 #' biological sequences in a tidy way.
-#' @author Michal Burdukiewicz, Dominik Rafacz, Leon Eyrich Jessen
+#' @author Michal Burdukiewicz, Dominik Rafacz, Mateusz Bąkała, Leon Eyrich Jessen
 #' @docType package
 #' @importFrom stats na.omit rnorm setNames
 #' @importFrom utils download.file installed.packages

diff --git a/R/export_sq.R b/R/export_sq.R
@@ -9,7 +9,7 @@
 #'
 #' @template x
 #' @param export_format [\code{character(1)}]\cr
-#'  A string indicating desired class (with specified package for disambiguity).
+#'  A string indicating desired class (with specified package for clarity).
 #' @template name
 #' @template three-dots
 #'

diff --git a/R/substitute_letters.R b/R/substitute_letters.R
@@ -1,6 +1,6 @@
 #' Substitute letters in a sequence
 #' 
-#' @description Replaces all occurrfuences of a letter with another.
+#' @description Replaces all occurrences of a letter with another.
 #' 
 #' @template x
 #' @param encoding [\code{character} || \code{numeric}]\cr

diff --git a/R/util-checkmate-functions.R b/R/util-checkmate-functions.R
@@ -1,3 +1,5 @@
+globalVariables("x")
+
 check_sq_type <- function(type, null.ok = FALSE, unt.ok = FALSE, atp.ok = FALSE) {
   check_choice(type,
                choices = c("dna_bsc", "dna_ext", "rna_bsc",

diff --git a/R/write_fasta.R b/R/write_fasta.R
@@ -15,7 +15,7 @@
 #'
 #' @details
 #' Whenever a name has more letters than \code{width} parameter, nothing
-#' happens, as only sequences are splited to fit within designated space.
+#' happens, as only sequences are split to fit within designated space.
 #'
 #' @examples
 #' \dontrun{

diff --git a/inst/WORDLIST b/inst/WORDLIST
@@ -25,6 +25,7 @@ atp
 Available’
 Avbelj
 Bae
+Bąkała
 Bastolla
 bata
 Beghin
@@ -292,6 +293,7 @@ Venanzi
 VFF
 Vihinen
 von
+vectorized
 Waals
 Warme
 wat

diff --git a/inst/include/tidysq/constants/WarningLevel.h b/inst/include/tidysq/constants/WarningLevel.h
@@ -1,5 +1,3 @@
-#pragma clang diagnostic push
-#pragma ide diagnostic ignored "cert-err58-cpp"
 #pragma once
 
 #include <unordered_map>
@@ -22,4 +20,3 @@ namespace tidysq::constants {
             {"error", LVL_ERROR}
     };
 }
-#pragma clang diagnostic pop
diff --git a/inst/include/tidysq/constants/ambiguous_maps.h b/inst/include/tidysq/constants/ambiguous_maps.h
@@ -1,5 +1,3 @@
-#pragma clang diagnostic push
-#pragma ide diagnostic ignored "cert-err58-cpp"
 #pragma once
 
 #include <map>
@@ -44,5 +42,3 @@ namespace tidysq::constants {
             {"N", {"A", "C", "G", "U", "W", "S", "M", "K", "R", "Y", "B", "D", "H", "V", "N"}}
     };
 }
-
-#pragma clang diagnostic pop
diff --git a/inst/include/tidysq/constants/complement_tables.h b/inst/include/tidysq/constants/complement_tables.h
@@ -1,5 +1,3 @@
-#pragma clang diagnostic push
-#pragma ide diagnostic ignored "cert-err58-cpp"
 #pragma once
 
 #include "tidysq/tidysq-typedefs.h"
@@ -16,5 +14,3 @@ namespace tidysq::constants {
             {14u, 14u}
     };
 }
-
-#pragma clang diagnostic pop
diff --git a/inst/include/tidysq/constants/standard_letters.h b/inst/include/tidysq/constants/standard_letters.h
@@ -1,5 +1,3 @@
-#pragma clang diagnostic push
-#pragma ide diagnostic ignored "cert-err58-cpp"
 #pragma once
 
 #include <unordered_map>
@@ -21,5 +19,3 @@ namespace tidysq::constants {
                               "S", "T", "U", "V", "W", "X", "Y", "Z", "-", "*"}}
     };
 }
-
-#pragma clang diagnostic pop
diff --git a/inst/include/tidysq/constants/translate_tables.h b/inst/include/tidysq/constants/translate_tables.h
@@ -1,5 +1,3 @@
-#pragma clang diagnostic push
-#pragma ide diagnostic ignored "cert-err58-cpp"
 #pragma once
 
 #include "tidysq/tidysq-typedefs.h"
@@ -210,5 +208,3 @@ namespace tidysq::constants {
                  }}
     };
 }
-
-#pragma clang diagnostic pop
diff --git a/man/export_sq.Rd b/man/export_sq.Rd
diff --git a/man/substitute_letters.Rd b/man/substitute_letters.Rd
diff --git a/man/tidysq-package.Rd b/man/tidysq-package.Rd
diff --git a/man/write_fasta.Rd b/man/write_fasta.Rd
diff --git a/vignettes/advanced-alphabet.Rmd b/vignettes/advanced-alphabet.Rmd
@@ -25,11 +25,11 @@ sq_dna <- sq(c("CTGAATGCAGT", "ATGCCGT", "CAGACCATT"))
 alphabet(sq_dna)
 ```
 
-It is strongly discouraged to manually assign different alphabet, as it may result in undesirable behaviour.
+It is strongly discouraged to manually assign different alphabet, as it may result in undesirable behavior.
 
 ## Standard alphabets
 
-Alphabets can be divided into standard and non-standard types. Both these groups have similar behaviour, but standard alphabets have additional functionalities available due to their biological interpretation.
+Alphabets can be divided into standard and non-standard types. Both these groups have similar behavior, but standard alphabets have additional functionalities available due to their biological interpretation.
 
 Standard alphabets can be subdivided into basic and extended alphabets, both groups closely linked. For every standard alphabet there exists a type such that if an `sq` object has this type, then its `alphabet` attribute has this alphabet as value.
 

diff --git a/vignettes/quick-start.Rmd b/vignettes/quick-start.Rmd
@@ -36,7 +36,7 @@ sq_dna
 
 There are several thing to note. First, each sequence is an element of `sq` object. Many operations are vectorized --- they are applied to all sequences of a vector --- and `sq` objects are no different in this regard. Second, the first line of output says: `basic DNA sequences list`. This means that all sequences of this object are of DNA type and do not use ambiguous letters (more about that in "Advanced alphabet techniques" vignette).
 
-## Subsequencing
+## Subsetting sequences
 
 Manipulating sequence objects is an integral part of `tidysq`. `sq` objects can be easily subsetted using usual R syntax: