Merge branch 'neurogenomics:master' into hotfix_quarto

.Rhistory

@@ -1,52 +1,3 @@
-jsn <- jsonlite::read_json(path)
-names(jsn)
-testthat::expect_true(
-all(c("image","features","customizations") %in% names(jsn))
-)
-devtools::check_man()
-file.edit("Rprofile")
-file.edit(".Rprofile")
-BiocManager::repositories()
-devtools::check_man()
-library(rworkflows)
-deparse(BiocManager::repositories())
-cat(deparse(BiocManager::repositories()))
-cont4 <- construct_cont(default_tag = "release",
-default_registry = "ghcr.io",
-run_check_cont = TRUE)
-cont4 <- construct_cont(default_tag = "release",
-default_registry = NULL,
-run_check_cont = TRUE)
-is.null(c("a","b"))
-library(rworkflows)
-cont4 <- construct_cont(default_tag = "release",
-default_registry = NULL,
-run_check_cont = TRUE)
-devoptera::args2vars(construct_cont)
-default_registry
-default_registry=NULL
-default_registry <- check_registry(registry = default_registry)
-#### Remove any trailing : (e.g. when default_tag=NULL) ####
-cont <- lapply(cont, function(x){
-if(is.null(x)) NULL else trimws(x,whitespace = ":")
-})
-#### Run QC ####
-cont2 <- lapply(cont,function(co){
-if(is.null(co)){
-return(NULL)
-} else if(!grepl("/",co) &&
-!is.null(default_cont)){
-messager("Only tag name supplied to 'cont'.",
-"Assuming default=",shQuote(default_cont),v=verbose)
-co <- paste(default_cont,co,sep=":")
-} else if(!grepl(":",co) |
-!grepl(default_cont,co)) {
-return(co)
-}
-splt <- strsplit(co,":")[[1]]
-bioc_version <- rev(splt)[1]
-if(isTRUE(versions_explicit)){
-if(grepl(":",co)){
 info <- bioc_r_versions(bioc_version = bioc_version)
 return(
 paste0(splt[[1]],":RELEASE_",gsub("[.]","_",info$bioc))
@@ -510,3 +461,52 @@ library(rworkflows)
 ?testthat::skip_on_cran()
 testthat::skip_if_offline()
 readLines("https://hub.docker.com/v2/repositories//bioconductor/bioconductor_docker/tags?page_size=1000")
+devtools::check_man()
+devtools::install_dev_deps()
+devtools::install_dev_deps()
+gh::gh_token()
+file.edit("~/.Renviron")
+credentials::set_github_pat()
+gh::gh_token()
+devtools::install_dev_deps()
+credentials::set_github_pat()
+devtools::install_dev_deps()
+devtools::build()
+devtools::check_man()
+version
+version
+install.packages("devtools")
+install.packages("BiocManager")
+install.packages("devtools")
+devtools::install_dev_deps()
+devtools::check_man()
+install.packages("roxygen2")
+devtools::check_man()
+devtools::install_dev_deps()
+packageVersion("roxygen2")
+version
+version
+version()
+version()
+version
+rworkflows::use_workflow()
+rworkflows::use_workflow(force_new = T)
+gh::gh_token()
+credentials::set_github_pat()
+a1 <- construct_authors()
+library()
+library(rworkflows)
+a1 <- construct_authors()
+testthat::expect_equal(as.character(a1), "yourGivenName yourFamilyName <[email protected]> [cre] (yourOrcidId)")
+a2 <- construct_authors(authors = "Test 1, Test1")
+testthat::expect_equal(as.character(a2), "Test 1, Test1")
+testthat::expect_equal(as.character(a1), "yourGivenName yourFamilyName <[email protected]> [cre] (yourOrcidId)")
+testthat::expect_true(as.character(a1) %in%
+c("yourGivenName yourFamilyName <[email protected]> [cre] (ORCID: yourOrcidId)",
+"yourGivenName yourFamilyName <[email protected]> [cre] (yourOrcidId)"))
+installed.packages()
+names(installed.packages())
+rownames(installed.packages())
+"reticulate" %in% rownames(installed.packages())
+credentials::set_github_pat()
+remotes::install_github("r-lib/remotes")

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,104 @@
+name: 🐛 Bug Report
+description: File a bug report
+labels: [bug, no-bot]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for taking the time to fill out this issue! :hugs:
+        
+        However note the following before opening an issue:
+        :warning: **IF YOU DON'T FILL IN THE TEMPLATE, YOUR ISSUE IS LIABLE TO BE CLOSED.** :warning:
+
+  - type: checkboxes
+    id: checklist
+    attributes:
+      label: "Checklist"
+      options:
+        - label: "I am able to reproduce the bug with the latest version"
+          required: true
+        - label: "I checked, but didn't find any duplicates (open OR closed) of this issue in the repo"
+          required: true
+
+  - type: input
+    id: version
+    attributes:
+     label: Affected version
+     description: "What version are you currently using?"
+     placeholder: "x.y.z (check with the `packageVersion()` R function)"
+    validations:
+      required: true
+
+  - type: textarea
+    id: steps-to-reproduce
+    attributes:
+      label: Steps to reproduce the bug
+      description: |
+        Please add **ALL** the code necessary to reproduce the bug here (step-by-step).
+        By 'reproduce', we mean that someone else can copy and paste the exact same code into their R console, execute it, and get the exact same output as you.
+        
+        This means you need to define all variables *within* the example, including data.
+        You can upload a small sample of your data by dragging-and-dropping it into this Issue. 
+        Alternatively, you can include code to create some dummy data that reproduces the error. 
+        If that's not possible, please at least include a screenshot of your data and other relevant details.
+        
+        See [here](https://www.r-bloggers.com/2020/10/how-to-make-a-reprex/) for an intro to making a reproducible example (i.e. reprex) and why they're important! 
+      placeholder: |
+        # For example:
+        df <- data.frame(list(a=rep(2,3), b=rep(1,3)))
+        df["bTYPO"]
+    validations:
+      required: true
+
+  - type: textarea
+    id: actual-behavior
+    attributes:
+      label: Actual behavior
+      description: |
+        Copy and paste the R console output. 
+      placeholder: |
+        # For example:
+        Error in `[.data.frame`(df, "bTYPO") : undefined columns selected
+    validations:
+      required: true
+
+  - type: textarea
+    id: expected-behavior
+    attributes:
+      label: Expected behavior
+      description: |
+        Tell us what you expect to happen.
+      placeholder: |
+        The values of the data.frame column are printed.
+    validations:
+      required: true
+
+  - type: textarea
+    id: session-info
+    validations:
+      required: true
+    attributes:
+      label: Session info
+      description: |
+        Copy and paste the output of the `sessionInfo() R function.
+      placeholder: |
+        R version 4.4.1 (2024-06-14)  
+        Platform: aarch64-apple-darwin20  
+        Running under: macOS 15.0  
+        
+        Matrix products: default  
+        BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib   
+        LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0  
+        
+        locale:  
+        [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8  
+        
+        time zone: Europe/London  
+        tzcode source: internal 
+        
+        attached base packages:  
+        [1] stats     graphics  grDevices utils     datasets  methods   base       
+        ...
+        ...
+        ...
+ 

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1 @@
+blank_issues_enabled: false

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -0,0 +1,40 @@
+name: ⭐ Feature Request
+description: Submit a feature request
+labels: [enhancement, no-bot]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for submitting a feature request! 
+        
+  - type: textarea
+    id: the-feature-request
+    attributes:
+      label: The feature request
+      description:
+        Write a clear and concise description of what the feature or problem is.
+      placeholder: |
+        I think it could be improved by adding [...]
+    validations:
+      required: true
+
+  - type: textarea
+    id: proposed-solution
+    attributes:
+      label: Proposed solution
+      description: Share how this will benefit its users.
+      placeholder: |
+        - One idea would be to add an [...], similar to how this package did [LINK].
+        - An alternative solution might be [...]
+    validations:
+      required: true
+
+  - type: textarea
+    id: additional-context
+    attributes:
+      label: Additional context
+      description:
+        Please include any other context, like screenshots or mockups, if
+        applicable.
+      placeholder: |
+        Our lab studies [...] and thought it would be cool to try [...]

.github/workflows/rworkflows.yml

@@ -25,7 +25,7 @@ jobs:
         - os: ubuntu-latest
           r: auto
           bioc: release
-          cont: ghcr.io/bioconductor/bioconductor_docker:RELEASE_3_18
+          cont: ghcr.io/bioconductor/bioconductor_docker:RELEASE_3_19
           python-version: 3.11
         - os: macOS-latest
           r: latest

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: rworkflows
 Type: Package
 Title: Test, Document, Containerise, and Deploy R Packages
-Version: 1.0.1
+Version: 1.0.3
 Authors@R:
     c(person(given = "Brian",
            family = "Schilder",
@@ -64,4 +64,4 @@ VignetteBuilder: knitr
 License: GPL-3
 Config/testthat/edition: 3
 LazyData: true
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2

NEWS.md

@@ -1,3 +1,27 @@
+# rworkflows 1.0.3
+
+## New features
+
+* New arg `run_telemetry` allows users to disable workflow telemetry.
+
+## Bug fixes
+
+* Add `GITHUB_TOKEN: ${{ inputs.GITHUB_TOKEN }}` to all code check steps.
+
+# rworkflows 1.0.2
+
+## New features
+
+* Update to R 4.4.1 and ensure everything still works.
+* Update *rworkflows.yml* to use new Bioc release, 3.19
+
+## Bug fixes
+
+* Get back up on CRAN after deprecation occurred while I was away.
+* Remove .*Rprofile* (didn't seem to help CRAN and was getting outdated)
+* *test-construct_conda_yml.R*: Add conditional to only run certain steps 
+  if `reticulate` is installed (for `noSuggests` tests in CRAN).
+
 # rworkflows 1.0.1
 
 ## New features

R/use_issue_template.R

@@ -10,8 +10,9 @@
 #' @importFrom here here
 #' @examples 
 #' path <- use_issue_template(save_dir=tempdir())
-use_issue_template <- function(templates=c("bug_report.md",
-                                           "feature_request.md"),
+use_issue_template <- function(templates=c("bug_report.yml",
+                                           "feature_request.yml",
+                                           "config.yml"),
                                save_dir=here::here(".github",
                                                    "ISSUE_TEMPLATE"),
                                path=file.path(save_dir,templates),