Merge pull request #73 from Infectious-Disease-Modeling-Hubs/enhancem…

…ent/hubstyle

Upgrade to hubStyle template. Fix linting issues

.Rbuildignore

@@ -11,3 +11,9 @@
 ^attic$
 ^data-raw$
 ^vignettes/articles$
+^\.DS_Store$
+^\.Rhistory$
+^\.Rdata$
+^\.httr-oauth$
+^\.secrets$
+^\.lintr$

.github/CODE_OF_CONDUCT.md

@@ -38,80 +38,18 @@ Examples of unacceptable behavior include:
 
 ## Enforcement Responsibilities
 
-Community leaders are responsible for clarifying and enforcing our standards of
-acceptable behavior and will take appropriate and fair corrective action in
-response to any behavior that they deem inappropriate, threatening, offensive,
-or harmful.
+Community leaders are responsible for clarifying our standards of acceptable behavior. Enforcement is the responsibility of the [Code of Conduct Committee](https://hubdocs.readthedocs.io/en/latest/coc/committee.html), who will take appropriate and fair corrective action in response to any behavior that they deem inappropriate, threatening, offensive, or harmful. 
 
-Community leaders have the right and responsibility to remove, edit, or reject
-comments, commits, code, wiki edits, issues, and other contributions that are
-not aligned to this Code of Conduct, and will communicate reasons for moderation
-decisions when appropriate.
+Instances of abusive, harassing, or otherwise unacceptable behavior [may be reported to any member of the Code of Conduct Committee](https://hubdocs.readthedocs.io/en/latest/coc/committee.html). All complaints will be reviewed and investigated promptly and fairly. 
 
-## Scope
-
-This Code of Conduct applies within all community spaces, and also applies when
-an individual is officially representing the community in public spaces.
-Examples of representing our community include using an official e-mail address,
-posting via an official social media account, or acting as an appointed
-representative at an online or offline event.
-
-## Enforcement
-
-Instances of abusive, harassing, or otherwise unacceptable behavior may be
-reported to any of the following community leaders responsible for enforcement: Lucie Contamin ([email protected]),
-  Emily Howerton ([email protected]) or
-  Seb Funk ([email protected]). 
-All complaints will be reviewed and investigated promptly and fairly.
-
-All community leaders are obligated to respect the privacy and security of the
-reporter of any incident.
-
-## Enforcement Guidelines
-
-Community leaders will follow these Community Impact Guidelines in determining
-the consequences for any action they deem in violation of this Code of Conduct:
-
-### 1. Correction
+The Code of Conduct Committee will use the [Enforcement Manual](https://hubdocs.readthedocs.io/en/latest/coc/enforcement-manual.html) in determining the consequences for any action they deem in violation of this Code of Conduct. All community leaders and Code of Conduct Committee members are obligated to respect the privacy and security of the reporter of any incident.
 
-**Community Impact**: Use of inappropriate language or other behavior deemed
-unprofessional or unwelcome in the community.
 
-**Consequence**: A private, written warning from community leaders, providing
-clarity around the nature of the violation and an explanation of why the
-behavior was inappropriate. A public apology may be requested.
-
-### 2. Warning
-
-**Community Impact**: A violation through a single incident or series of
-actions.
-
-**Consequence**: A warning with consequences for continued behavior. No
-interaction with the people involved, including unsolicited interaction with
-those enforcing the Code of Conduct, for a specified period of time. This
-includes avoiding interactions in community spaces as well as external channels
-like social media. Violating these terms may lead to a temporary or permanent
-ban.
-
-### 3. Temporary Ban
-
-**Community Impact**: A serious violation of community standards, including
-sustained inappropriate behavior.
-
-**Consequence**: A temporary ban from any sort of interaction or public
-communication with the community for a specified period of time. No public or
-private interaction with the people involved, including unsolicited interaction
-with those enforcing the Code of Conduct, is allowed during this period.
-Violating these terms may lead to a permanent ban.
-
-### 4. Permanent Ban
+## Scope
 
-**Community Impact**: Demonstrating a pattern of violation of community
-standards, including sustained inappropriate behavior, harassment of an
-individual, or aggression toward or disparagement of classes of individuals.
+This Code of Conduct applies within all community spaces, and also applies when an individual is officially representing the community in public spaces. 
+Examples of representing our community include using an official e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event.
 
-**Consequence**: A permanent ban from any sort of public interaction within the
-community.
 
 ## Attribution
 

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

@@ -1,9 +1,5 @@
 # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
-#
-# NOTE: This workflow is overkill for most R packages and
-# check-standard.yaml is likely a better choice.
-# usethis::use_github_action("check-standard") will install it.
 on:
   push:
     branches: [main, master]
@@ -23,11 +19,7 @@ jobs:
       matrix:
         config:
           - {os: macos-latest,   r: 'release'}
-
           - {os: windows-latest, r: 'release'}
-          # use 4.1 to check with rtools40's older compiler
-          - {os: windows-latest, r: '4.1'}
-
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
           - {os: ubuntu-latest,   r: 'oldrel-1'}
@@ -37,7 +29,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 

.github/workflows/lint.yaml

@@ -0,0 +1,32 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: lint
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::lintr, local::.
+          needs: lint
+
+      - name: Lint
+        run: lintr::lint_package()
+        shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: true

.github/workflows/pkgdown-netlify-preview.yaml

@@ -1,4 +1,4 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# # Workflow derived from https://github.com/r-lib/pkgdown/blob/main/.github/workflows/pkgdown.yaml
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:

.github/workflows/test-coverage.yaml

@@ -15,7 +15,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -31,7 +31,7 @@ jobs:
           covr::codecov(
             quiet = FALSE,
             clean = FALSE,
-            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
         shell: Rscript {0}
 
@@ -44,7 +44,7 @@ jobs:
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package

.gitignore

@@ -5,3 +5,4 @@
 .DS_Store
 docs
 attic
+.secrets

.lintr

@@ -0,0 +1,5 @@
+linters: linters_with_defaults(
+    line_length_linter = line_length_linter(120L),
+    commented_code_linter = NULL,
+    object_length_linter = object_length_linter(length = 50L)
+  )

R/capture_exec_error.R

@@ -13,7 +13,7 @@ capture_exec_error <- function(file_path, msg, call = NULL) {
   if (is.null(call)) {
     call <- rlang::caller_call()
     if (!is.null(call)) {
-        call <- rlang::call_name(call)
+      call <- rlang::call_name(call)
     }
   }
 
@@ -37,18 +37,18 @@ capture_exec_error <- function(file_path, msg, call = NULL) {
 #' inherits from subclass `<hub_check>`.
 #' @export
 capture_exec_warning <- function(file_path, msg, call = NULL) {
-    if (is.null(call)) {
-        call <- rlang::caller_call()
-    }
-    if (!is.null(call)) {
-        call <- rlang::call_name(call)
-    }
+  if (is.null(call)) {
+    call <- rlang::caller_call()
+  }
+  if (!is.null(call)) {
+    call <- rlang::call_name(call)
+  }
 
-    rlang::warning_cnd(
-        c("check_exec_warn", "hub_check"),
-        where = file_path,
-        call = call,
-        message = msg,
-        use_cli_format = TRUE
-    )
+  rlang::warning_cnd(
+    c("check_exec_warn", "hub_check"),
+    where = file_path,
+    call = call,
+    message = msg,
+    use_cli_format = TRUE
+  )
 }

R/check_config_hub_valid.R

@@ -7,8 +7,8 @@
 #' @export
 check_config_hub_valid <- function(hub_path) {
   valid_config <- hubUtils::validate_hub_config(hub_path) %>%
-      suppressMessages() %>%
-      suppressWarnings()
+    suppressMessages() %>%
+    suppressWarnings()
 
   check <- all(unlist(valid_config))
 

R/check_file_exists.R

@@ -1,22 +1,25 @@
 #' Check file exists at the file path specified
-#' 
+#'
 #' @param subdir subdirectory within the hub
 #' @inheritParams check_valid_round_id
 #' @inherit check_valid_round_id return
 #'
 #' @export
 check_file_exists <- function(file_path, hub_path = ".",
-                              subdir = c("model-output", "model-metadata",
-                                         "hub-config")) {
-    abs_path <- abs_file_path(file_path, hub_path, subdir)
-    rel_path <- rel_file_path(file_path, hub_path, subdir)
-    check <- fs::file_exists(abs_path)
+                              subdir = c(
+                                "model-output", "model-metadata",
+                                "hub-config"
+                              )) {
+  abs_path <- abs_file_path(file_path, hub_path, subdir)
+  rel_path <- rel_file_path(file_path, hub_path, subdir) # nolint: object_usage_linter
+  check <- fs::file_exists(abs_path)
 
-    capture_check_cnd(
-        check = check,
-        file_path = file_path,
-        msg_subject = "File",
-        msg_attribute = cli::format_inline("at path {.path {rel_path}}."),
-        msg_verbs = c("exists", "does not exist"),
-        error = TRUE)
+  capture_check_cnd(
+    check = check,
+    file_path = file_path,
+    msg_subject = "File",
+    msg_attribute = cli::format_inline("at path {.path {rel_path}}."),
+    msg_verbs = c("exists", "does not exist"),
+    error = TRUE
+  )
 }

R/check_file_format.R

@@ -5,23 +5,24 @@
 #'
 #' @export
 check_file_format <- function(file_path, hub_path, round_id) {
-    file_format <- fs::path_ext(file_path)
-    file_formats <- get_hub_file_formats(hub_path, round_id)
+  file_format <- fs::path_ext(file_path)
+  file_formats <- get_hub_file_formats(hub_path, round_id)
 
-    check <- file_format %in% file_formats
+  check <- file_format %in% file_formats
 
-    if (check) {
-        details <- NULL
-    } else {
-        details <- cli::format_inline("Must be one of {.val {file_formats}}
+  if (check) {
+    details <- NULL
+  } else {
+    details <- cli::format_inline("Must be one of {.val {file_formats}}
                                       not {.val {file_format}}")
-    }
+  }
 
-    capture_check_cnd(
-        check = check,
-        file_path = file_path,
-        msg_subject = "File",
-        msg_attribute = "accepted hub format.",
-        error = TRUE,
-        details = details)
+  capture_check_cnd(
+    check = check,
+    file_path = file_path,
+    msg_subject = "File",
+    msg_attribute = "accepted hub format.",
+    error = TRUE,
+    details = details
+  )
 }

R/check_file_location.R

@@ -7,26 +7,26 @@
 #'
 #' @export
 check_file_location <- function(file_path) {
+  dir_name <- dirname(file_path)
+  model_id <- parse_file_name(file_path)$model_id
+  check <- model_id == dir_name
 
-    dir_name <- dirname(file_path)
-    model_id <- parse_file_name(file_path)$model_id
-    check <- model_id == dir_name
-
-    if (check) {
-        details <- NULL
-    } else {
-        details <- cli::format_inline(
-            "File should be submitted to directory
+  if (check) {
+    details <- NULL
+  } else {
+    details <- cli::format_inline(
+      "File should be submitted to directory
             {.val {model_id}} not {.val {dir_name}}"
-            )
-    }
+    )
+  }
 
-    capture_check_cnd(
-        check = check,
-        file_path = file_path,
-        msg_subject = "File directory name",
-        msg_attribute = cli::format_inline("{.var model_id}
+  capture_check_cnd(
+    check = check,
+    file_path = file_path,
+    msg_subject = "File directory name",
+    msg_attribute = cli::format_inline("{.var model_id}
                                            metadata in file name."),
-        msg_verbs = c("matches", "must match"),
-        details = details)
+    msg_verbs = c("matches", "must match"),
+    details = details
+  )
 }

R/check_file_name.R

@@ -9,9 +9,9 @@ check_file_name <- function(file_path) {
     "try-error"
   )
   if (check) {
-      details <- NULL
+    details <- NULL
   } else {
-      details <- "Could not correctly parse submission metadata."
+    details <- "Could not correctly parse submission metadata."
   }
   capture_check_cnd(
     check = check,