Cleanup

.Rbuildignore

@@ -1,12 +1,13 @@
-^renv$
-^renv\.lock$
 ^.*\.Rproj$
-^\.Rproj\.user$
 ^LICENSE\.md$
 ^README.Rmd
-^\.travis\.yml$
+^\.Rproj\.user$
 ^\.github$
+^\.travis\.yml$
 ^_pkgdown\.yml$
+^data-raw
 ^docs$
 ^pkgdown$
-^data-raw
+^renv$
+^renv\.lock$
+^codemeta\.json$

.Rprofile

@@ -1,7 +1,7 @@
-if (interactive()) {
-  if (file.exists("~/.Rprofile")) {
-    source("~/.Rprofile")
-  }
+r_profile <- file.path(Sys.getenv("HOME"), ".Rprofile")
+
+if (interactive() && file.exists(r_profile)) {
+    source(r_profile) # nolint: undesirable_function_linter.
 }
 
-source("renv/activate.R")
+source("renv/activate.R") # nolint: undesirable_function_linter.

.github/workflows/pkgdown.yml

@@ -28,7 +28,7 @@ jobs:
         id: install-r
 
       - uses: r-lib/actions/setup-pandoc@v1
-      
+
       - uses: r-lib/actions/setup-tinytex@v1
 
       - name: Install pak and query dependencies

.github/workflows/rworkflows.yml

@@ -0,0 +1,54 @@
+name: rworkflows
+on:
+  workflow_dispatch:
+  push:
+    branches:
+    - master
+    - main
+    - devel
+    - RELEASE_**
+  pull_request:
+    branches:
+    - master
+    - main
+    - devel
+    - RELEASE_**
+jobs:
+  rworkflows:
+    permissions:
+      contents: write
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+    container: ${{ matrix.config.cont }}
+    strategy:
+      fail-fast: ${{ false }}
+      matrix:
+        config:
+        - os: ubuntu-latest
+          bioc: devel
+          r: auto
+          cont: bioconductor/bioconductor_docker:devel
+          rspm: https://packagemanager.rstudio.com/cran/__linux__/latest/release
+        - os: macOS-latest
+          bioc: release
+          r: auto
+        - os: windows-latest
+          bioc: release
+          r: auto
+    steps:
+    - uses: neurogenomics/rworkflows@master
+      with:
+        run_bioccheck: ${{ true }}
+        run_rcmdcheck: ${{ true }}
+        as_cran: ${{ true }}
+        run_vignettes: ${{ true }}
+        has_testthat: ${{ true }}
+        run_covr: ${{ true }}
+        run_pkgdown: ${{ true }}
+        has_runit: ${{ false }}
+        has_latex: ${{ false }}
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run_docker: ${{ false }}
+        DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }}
+        runner_os: ${{ runner.os }}
+        cache_version: cache-v1

.lintr

@@ -0,0 +1,12 @@
+linters: linters_with_tags(
+    tags = c("default", "style", "misc", "potential-bug", "performance", "documentation", "risky", "package_development"),
+    line_length_linter(length = 80L),
+    indentation_linter(indent = 4L, hanging_indent_style = "never"),
+    undesirable_function_linter(modify_defaults(
+        defaults = default_undesirable_functions, library = NULL)),
+    object_usage_linter = NULL,
+    object_name_linter(styles = c("camelCase")))
+encoding: "UTF-8"
+exclusions: list(
+    "renv/activate.R",
+    "doc/")

.pre-commit-config.yaml

@@ -0,0 +1,127 @@
+# All available hooks: https://pre-commit.com/hooks.html
+# R specific hooks: https://github.com/lorenzwalthert/precommit
+exclude: '.*\.(csv|tsv|xls)$'
+repos:
+-   repo: https://github.com/lorenzwalthert/precommit
+    rev: v0.4.2
+    hooks:
+    -   id: use-tidy-description
+    -   id: codemeta-description-updated
+    -   id: spell-check
+        exclude: >
+          (?x)^(
+          .*\.[rR]|
+          .*\.feather|
+          .*\.jpeg|
+          .*\.pdf|
+          .*\.png|
+          .*\.py|
+          .*\.RData|
+          .*\.rd(s|a)|
+          .*\.Rd(s|a)|
+          .*\.RD(S|A)|
+          .*\.Rproj|
+          .*\.sh|
+          (.*/|)\.gitignore|
+          (.*/|)\.gitlab-ci\.yml|
+          (.*/|)\.lintr|
+          (.*/|)\.pre-commit-.*|
+          (.*/|)\.Rbuildignore|
+          (.*/|)\.Renviron|
+          (.*/|)\.Rprofile|
+          (.*/|)\.travis\.yml|
+          (.*/|)appveyor\.yml|
+          (.*/|)NAMESPACE|
+          (.*/|)renv/settings\.dcf|
+          (.*/|)renv\.lock|
+          (.*/|)WORDLIST|
+          \.github/workflows/.*|
+          data/.*|
+          .*\.(gz|xz|bz2)|
+          )$
+    -   id: readme-rmd-rendered
+    -   id: parsable-R
+    -   id: no-browser-statement
+    -   id: no-debug-statement
+    -   id: deps-in-desc
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+    -   id: check-added-large-files
+        args: ['--maxkb=500']
+    -   id: file-contents-sorter
+        files: '^\.Rbuildignore$'
+    -   id: end-of-file-fixer
+        exclude: '\.Rd'
+    -   id: check-json
+    -   id: check-merge-conflict
+    -   id: mixed-line-ending
+        args:
+        -   --fix=no
+    -   id: trailing-whitespace
+    - id: no-commit-to-branch
+      args:
+        - --branch
+        - devel
+        - --branch
+        - RELEASE.*
+-   repo: https://github.com/compilerla/conventional-pre-commit
+    rev: v3.2.0
+    hooks:
+    -   args:
+        -   build
+        -   chore
+        -   ci
+        -   docs
+        -   feat
+        -   fix
+        -   perf
+        -   refactor
+        -   revert
+        -   style
+        -   test
+        -   bump
+        id: conventional-pre-commit
+        stages:
+        -   commit-msg
+-   repo: https://github.com/Lucas-C/pre-commit-hooks
+    rev: v1.5.5
+    hooks:
+    -   id: forbid-crlf
+    -   id: remove-crlf
+    -   id: forbid-tabs
+        exclude: '.*\.[xls|tsv]$'
+    -   id: remove-tabs
+        exclude: '.*\.[xls|tsv]$'
+-   repo: local
+    hooks:
+    -   id: style_files
+        name: Apply bioconductor style
+        entry: >
+            Rscript --vanilla -e "styler::style_pkg(transformers = styler::tidyverse_style(indent_by = 4))"
+        language: system
+    -   id: lint_files
+        name: Apply lintr
+        entry: >
+            Rscript --vanilla -e "lintr::lint_package()"
+        language: system
+    -   id: forbid-to-commit
+        name: Don't commit common R artifacts
+        entry: Cannot commit .Rhistory, .RData, .Rds or .rds.
+        language: fail
+        files: '\.(Rhistory|RData|Rds|rds)$'
+    -   id: codemeta-json-updated
+        name: Update codemeta.json
+        entry: >
+          Rscript --vanilla -e "codemetar::write_codemeta()"
+        language: system
+        files: DESCRIPTION
+        stages: [commit]
+    -   id: bump-version
+        name: Bump version
+        entry: >
+          ./utilities/bump-version.sh
+        language: system
+        always_run: true
+        pass_filenames: false
+        stages: [post-commit]

DESCRIPTION

@@ -1,14 +1,18 @@
 Package: KRSA
-Type: Package
 Title: KRSA: Kinome Random Sampling Analyzer
-Version: 1.0.0.9000
-Author: Khaled Alganem
-Maintainer: Khaled Alganem <[email protected]>
-Description: KRSA: Kinome Random Sampling Analyzer
-    This package aims to pre-process and analyze PamChip array data. From reading bionavigator crosstab view files to generating network models on kinome data.  
+Version: 1.99.0
+Date: 2023-10-10
+Authors@R:
+    c(person(c("Ali", "Sajid"), "Imami", , "[email protected]", role = c("aut", "cre"),
+           comment = c(ORCID = "0000-0003-3684-3539")),
+    person("Khaled", "Alganem", "[email protected]" ,role = "aut", comment = c(ORCID = "0000-0003-4419-3708")))
+Description: The goal of this package is to analyze the PamChip data and identify the changes in the active kinome.
+        The package can preprocess the PamChip data output from BioNavigator and use Random Sampling and Permutation Analysis
+        to identify upstream kinases. Additionally, this package provides a set of useful visualizations for the PamChip data.
 License: MIT + file LICENSE
+URL: https://github.com/CogDisResLab/KRSA
 Encoding: UTF-8
-Imports: 
+Imports:
     magrittr,
     tibble,
     readr,
@@ -27,15 +31,18 @@ Imports:
     ggsignif,
     httr,
     jsonlite
-Depends: 
-    R (>= 3.5.0)
-LazyData: true
-RoxygenNote: 7.2.1
-Suggests: 
+Depends:
+    R (>= 4.3.0)
+Suggests:
     knitr,
     rmarkdown,
     markdown,
     tidyverse,
     gt,
-    furrr
-VignetteBuilder: knitr
+    furrr,
+    biocthis,
+    usethis
+BugReports: https://support.bioconductor.org/tag/KRSA
+biocViews: Software
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.2.3

LICENSE

@@ -1,2 +1,2 @@
-YEAR: 2021
-COPYRIGHT HOLDER: KRSA authors
+YEAR: 2020
+COPYRIGHT HOLDER: Cognitive Disorders Research Lab

LICENSE.md

@@ -1,6 +1,6 @@
 # MIT License
 
-Copyright (c) 2021 KRSA authors
+Copyright (c) 2020 Cognitive Disorders Research Lab
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

R/data.R

@@ -104,6 +104,3 @@
 #' }
 #'
 "ptk_pamchip_86402_mapping"
-
-
-

R/enrichr_lib_call.R

@@ -47,4 +47,3 @@ process_output <- function(x) {
   x
 
 }
-

R/krsa_ce_output_kinases.R

@@ -13,10 +13,8 @@
 #'
 
 krsa_ce_output_kinases <- function(krsa_table, file_name) {
-
-  krsa_table %>%
-    dplyr::select(Kinase, Z) %>%
-    dplyr::rename(Score = Z) %>%
-    readr::write_delim(file=file_name)
-
+    krsa_table %>%
+        dplyr::select(Kinase, Z) %>%
+        dplyr::rename(Score = Z) %>%
+        readr::write_delim(file = file_name)
 }

R/krsa_ce_output_peptides.R

@@ -16,10 +16,8 @@
 #'
 
 krsa_ce_output_peptides <- function(peptide_table, metric, file_name) {
-
-  peptide_table %>%
-    dplyr::select(Peptide, {{ metric }}) %>%
-    dplyr::rename(Score = {{ metric }}) %>%
-    readr::write_delim(file=file_name)
-
+    peptide_table %>%
+        dplyr::select(Peptide, {{ metric }}) %>%
+        dplyr::rename(Score = {{ metric }}) %>%
+        readr::write_delim(file = file_name)
 }

R/krsa_histogram_plot.R

@@ -30,4 +30,3 @@ krsa_histogram_plot <- function(data,data2,kinases) {
     ggplot2::theme_bw() +
     ggplot2::theme(plot.title = ggplot2::element_text(hjust = 0.5))
 }
-

R/krsa_show_peptides.R

@@ -25,5 +25,3 @@ pluckPeptides <- function(x) {
   dplyr::tibble(NumberOfPeptides = length(x)
   )
 }
-
-

R/krsa_top_hits.R

@@ -23,5 +23,3 @@ krsa_top_hits <- function(zTable,z_thr) {
     dplyr::pull(Kinase) %>%
     unique()
 }
-
-