Merge pull request #26 from hubverse-org/to-hubverse

Rename org name
hubverse-org · Jun 18, 2024 · 3774cb4 · 3774cb4
2 parents d53544c + 2ddd783
commit 3774cb4
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diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -18,7 +18,7 @@ Our procedures for contributing bigger changes, code in particular, generally fo
 
 ### Pull request process
 
-*   Fork the package and clone onto your computer. If you haven't done this before, we recommend using `usethis::create_from_github("Infectious-Disease-Modeling-Hubs/hubAdmin", fork = TRUE)`.
+*   Fork the package and clone onto your computer. If you haven't done this before, we recommend using `usethis::create_from_github("hubverse-org/hubAdmin", fork = TRUE)`.
 
 *   Install all development dependencies with `devtools::install_dev_deps()`, and then make sure the package passes R CMD check by running `devtools::check()`. 
     If R CMD check doesn't pass cleanly, it's a good idea to ask for help before continuing. 

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -10,14 +10,14 @@ Authors@R:
       person("Evan L.", "Ray", , "[email protected]", role = "ctb"),
       person(family = "Consortium of Infectious Disease Modeling Hubs",
            role = c("cph")))
-Description: A set of utility functions for administering hubverse Infectious Disease Modeling Hubs.
+Description: A set of utility functions for administering hubverse Hubs.
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.1
 Config/testthat/edition: 3
-URL: https://github.com/Infectious-Disease-Modeling-Hubs/hubAdmin
-BugReports: https://github.com/Infectious-Disease-Modeling-Hubs/hubAdmin/issues
+URL: https://github.com/hubverse-org/hubAdmin
+BugReports: https://github.com/hubverse-org/hubAdmin/issues
 Imports: 
     checkmate,
     cli,
@@ -43,9 +43,9 @@ Suggests:
     rmarkdown,
     testthat (>= 3.2.0)
 Remotes:
-    Infectious-Disease-Modeling-Hubs/hubData@feature/handle-samples,
-    Infectious-Disease-Modeling-Hubs/hubUtils@enhancement/v3-utils
-Config/Needs/website: Infectious-Disease-Modeling-Hubs/hubStyle
+    hubverse-org/hubData@feature/handle-samples,
+    hubverse-org/hubUtils@enhancement/v3-utils
+Config/Needs/website: hubverse-org/hubStyle
 Depends: 
     R (>= 2.10)
 LazyData: true

diff --git a/NEWS.md b/NEWS.md
@@ -12,4 +12,4 @@
 
 # hubAdmin 0.0.1
 
-* Initial package release resulting from split of `hubUtils` package. See [`hubUtils` NEWS.md](https://github.com/Infectious-Disease-Modeling-Hubs/hubUtils/blob/main/NEWS.md) for details including previous release notes.
+* Initial package release resulting from split of `hubUtils` package. See [`hubUtils` NEWS.md](https://github.com/hubverse-org/hubUtils/blob/main/NEWS.md) for details including previous release notes.
diff --git a/R/check_input.R b/R/check_input.R
@@ -130,7 +130,7 @@ check_input <- function(input, property, parent_schema, # nolint: cyclocomp_lint
           "!" = "Cannot determine appropriate type for argument
         {.arg {property_name}}, type validation skipped.
          Schema may be invalid. Consult relevant schema and consider opening an issue at
-        {.url https://github.com/Infectious-Disease-Modeling-Hubs/schemas/issues}"
+        {.url https://github.com/hubverse-org/schemas/issues}"
         ),
         call = call
       )

diff --git a/R/config-schema-utils.R b/R/config-schema-utils.R
@@ -42,16 +42,16 @@ check_config_schema_version <- function(schema_version, config = c("tasks", "adm
   }
 
   check_prefix <- grepl(
-    "https://raw.githubusercontent.com/Infectious-Disease-Modeling-Hubs/schemas/main/",
+    "https://raw.githubusercontent.com/(hubverse-org|Infectious-Disease-Modeling-Hubs)/schemas/main/",
     schema_version,
-    fixed = TRUE
+    fixed = FALSE
   )
 
   if (!check_prefix) {
     cli::cli_abort(c(
       "x" = "Invalid {.code schema_version} property.",
       "i" = "Valid {.code schema_version} properties should start with
-                         {.val https://raw.githubusercontent.com/Infectious-Disease-Modeling-Hubs/schemas/main/}
+                         {.val https://raw.githubusercontent.com/hubverse-org/schemas/main/}
                          and resolve to the schema file's raw contents on GitHub."
     ))
   }
@@ -89,9 +89,9 @@ validate_schema_version_property <- function(validation, config = c("tasks", "ad
     )
   }
 
-  check_prefix <- grepl("https://raw.githubusercontent.com/Infectious-Disease-Modeling-Hubs/schemas/main/",
+  check_prefix <- grepl("https://raw.githubusercontent.com/(hubverse-org|Infectious-Disease-Modeling-Hubs)/schemas/main/",
     schema_version,
-    fixed = TRUE
+    fixed = FALSE
   )
 
   if (!check_prefix) {
@@ -103,7 +103,7 @@ validate_schema_version_property <- function(validation, config = c("tasks", "ad
         keyword = "schema_version prefix",
         message = paste(
           "Invalid 'schema_version' property. Should start with",
-          "'https://raw.githubusercontent.com/Infectious-Disease-Modeling-Hubs/schemas/main/'"
+          "'https://raw.githubusercontent.com/hubverse-org/schemas/main/'"
         ),
         schema = "",
         data = schema_version

diff --git a/R/create_task_id.R b/R/create_task_id.R
@@ -13,8 +13,8 @@
 #'   values are required.
 #' @param schema_version Character string specifying the json schema version to
 #'   be used for validation. The default value `"latest"` will use the latest version
-#'   available in the Infectious Disease Modeling Hubs
-#'   [schemas repository](https://github.com/Infectious-Disease-Modeling-Hubs/schemas).
+#'   available in the hubverse
+#'   [schemas repository](https://github.com/hubverse-org/schemas).
 #'   Alternatively, a specific version of a schema (e.g. `"v0.0.1"`)  can be
 #'   specified.
 #' @details `required` and `optional` vectors for standard task_ids defined in a Hub schema

diff --git a/R/validate_config.R b/R/validate_config.R
@@ -20,13 +20,12 @@
 #' @param schema_version Character string specifying the json schema version to
 #'   be used for validation. The default value `"from_config"` will use the
 #'   version specified in the `schema_version` property of the config file.
-#'   `"latest"` will use the latest version available in the Infectious Disease
-#'   Modeling Hubs
-#'   [schemas repository](https://github.com/Infectious-Disease-Modeling-Hubs/schemas).
+#'   `"latest"` will use the latest version available in the hubverse
+#'   [schemas repository](https://github.com/hubverse-org/schemas).
 #'   Alternatively, a specific version of a schema (e.g. `"v0.0.1"`)  can be
 #'  specified.
-#' @param branch The branch of the Infectious Disease Modeling Hubs
-#'   [schemas repository](https://github.com/Infectious-Disease-Modeling-Hubs/schemas)
+#' @param branch The branch of the hubverse
+#'   [schemas repository](https://github.com/hubverse-org/schemas)
 #'   from which to fetch schema. Defaults to `"main"`.
 #' @return Returns the result of validation. If validation is successful, will
 #'   return `TRUE`. If any validation errors are detected, returns `FALSE` with

diff --git a/R/validate_hub_config.R b/R/validate_hub_config.R
@@ -119,8 +119,8 @@ validate_hub_config <- function(hub_path = ".", schema_version = "from_config",
   attr(validations, "config_dir") <- fs::path(hub_path, "hub-config")
   attr(validations, "schema_version") <- schema_version
   attr(validations, "schema_url") <- gsub(
-    "https://raw.githubusercontent.com/Infectious-Disease-Modeling-Hubs/schemas/",
-    "https://github.com/Infectious-Disease-Modeling-Hubs/schemas/tree/",
+    "https://raw.githubusercontent.com/hubverse-org/schemas/",
+    "https://github.com/hubverse-org/schemas/tree/",
     unique(schema_url_dirnames),
     fixed = TRUE
   )

diff --git a/README.Rmd b/README.Rmd
@@ -14,15 +14,15 @@ knitr::opts_chunk$set(
 ```
 
 
-# hubAdmin <a href="https://Infectious-Disease-Modeling-Hubs.github.io/hubAdmin/"><img src="man/figures/logo.png" align="right" height="131" alt="hubAdmin website" /></a>
+# hubAdmin <a href="https://hubverse-org.github.io/hubAdmin/"><img src="man/figures/logo.png" align="right" height="131" alt="hubAdmin website" /></a>
 
 <!-- badges: start -->
 [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
 [![CRAN status](https://www.r-pkg.org/badges/version/hubAdmin)](https://CRAN.R-project.org/package=hubAdmin)
-[![R-CMD-check](https://github.com/Infectious-Disease-Modeling-Hubs/hubAdmin/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/Infectious-Disease-Modeling-Hubs/hubAdmin/actions/workflows/R-CMD-check.yaml)
+[![R-CMD-check](https://github.com/hubverse-org/hubAdmin/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/hubverse-org/hubAdmin/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
-The goal of hubAdmin is to provide a set of utility functions for administering hubverse Infectious Disease Modeling Hubs. 
+The goal of hubAdmin is to provide a set of utility functions for administering hubverse Hubs. 
 
 This package is part of the [hubverse](https://hubdocs.readthedocs.io/en/latest/) ecosystem, which aims to provide a set of tools for infectious disease modeling hubs to share and collaborate on their work.
 
@@ -32,7 +32,7 @@ You can install the development version of hubAdmin from [GitHub](https://github
 
 ``` r
 # install.packages("remotes")
-remotes::install_github("Infectious-Disease-Modeling-Hubs/hubAdmin")
+remotes::install_github("hubverse-org/hubAdmin")
 ```
 
 > #####  **Note:**

diff --git a/README.md b/README.md
@@ -1,19 +1,19 @@
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
-# hubAdmin <a href="https://Infectious-Disease-Modeling-Hubs.github.io/hubAdmin/"><img src="man/figures/logo.png" align="right" height="131" alt="hubAdmin website" /></a>
+# hubAdmin <a href="https://hubverse-org.github.io/hubAdmin/"><img src="man/figures/logo.png" align="right" height="131" alt="hubAdmin website" /></a>
 
 <!-- badges: start -->
 
 [![Lifecycle:
 experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
 [![CRAN
 status](https://www.r-pkg.org/badges/version/hubAdmin)](https://CRAN.R-project.org/package=hubAdmin)
-[![R-CMD-check](https://github.com/Infectious-Disease-Modeling-Hubs/hubAdmin/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/Infectious-Disease-Modeling-Hubs/hubAdmin/actions/workflows/R-CMD-check.yaml)
+[![R-CMD-check](https://github.com/hubverse-org/hubAdmin/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/hubverse-org/hubAdmin/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
 The goal of hubAdmin is to provide a set of utility functions for
-administering hubverse Infectious Disease Modeling Hubs.
+administering hubverse Hubs.
 
 This package is part of the
 [hubverse](https://hubdocs.readthedocs.io/en/latest/) ecosystem, which
@@ -27,7 +27,7 @@ You can install the development version of hubAdmin from
 
 ``` r
 # install.packages("remotes")
-remotes::install_github("Infectious-Disease-Modeling-Hubs/hubAdmin")
+remotes::install_github("hubverse-org/hubAdmin")
 ```
 
 > ##### **Note:**

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -1,3 +1,3 @@
-url: https://infectious-disease-modeling-hubs.github.io/hubAdmin/
+url: https://hubverse-org.github.io/hubAdmin/
 template:
   package: hubStyle
diff --git a/man/create_output_type_mean.Rd b/man/create_output_type_mean.Rd
diff --git a/man/create_output_type_quantile.Rd b/man/create_output_type_quantile.Rd
diff --git a/man/create_target_metadata_item.Rd b/man/create_target_metadata_item.Rd
diff --git a/man/create_task_id.Rd b/man/create_task_id.Rd
diff --git a/man/validate_config.Rd b/man/validate_config.Rd
diff --git a/man/validate_hub_config.Rd b/man/validate_hub_config.Rd
diff --git a/tests/_snaps/create_config.md b/tests/_snaps/create_config.md
@@ -4,7 +4,7 @@
       create_config(rounds)
     Output
       $schema_version
-      [1] "https://raw.githubusercontent.com/Infectious-Disease-Modeling-Hubs/schemas/main/v2.0.0/tasks-schema.json"
+      [1] "https://raw.githubusercontent.com/hubverse-org/schemas/main/v2.0.0/tasks-schema.json"
       
       $rounds
       $rounds[[1]]
@@ -105,7 +105,7 @@
       attr(,"class")
       [1] "config" "list"  
       attr(,"schema_id")
-      [1] "https://raw.githubusercontent.com/Infectious-Disease-Modeling-Hubs/schemas/main/v2.0.0/tasks-schema.json"
+      [1] "https://raw.githubusercontent.com/hubverse-org/schemas/main/v2.0.0/tasks-schema.json"
 
 # create_config functions error correctly
 

diff --git a/tests/_snaps/create_model_task.md b/tests/_snaps/create_model_task.md
@@ -85,7 +85,7 @@
       attr(,"class")
       [1] "model_task" "list"      
       attr(,"schema_id")
-      [1] "https://raw.githubusercontent.com/Infectious-Disease-Modeling-Hubs/schemas/main/v2.0.0/tasks-schema.json"
+      [1] "https://raw.githubusercontent.com/hubverse-org/schemas/main/v2.0.0/tasks-schema.json"
 
 ---
 
@@ -249,7 +249,7 @@
       attr(,"class")
       [1] "model_task" "list"      
       attr(,"schema_id")
-      [1] "https://raw.githubusercontent.com/Infectious-Disease-Modeling-Hubs/schemas/main/v2.0.0/tasks-schema.json"
+      [1] "https://raw.githubusercontent.com/hubverse-org/schemas/main/v2.0.0/tasks-schema.json"
 
 # create_output_type_point functions error correctly
 
@@ -308,6 +308,6 @@
       x `schema_id` attributes are not consistent across all arguments.
       Argument `schema_id` attributes:
       * task_ids : invalid_schema_id
-      * output_type : https://raw.githubusercontent.com/Infectious-Disease-Modeling-Hubs/schemas/main/v2.0.0/tasks-schema.json
-      * target_metadata : https://raw.githubusercontent.com/Infectious-Disease-Modeling-Hubs/schemas/main/v2.0.0/tasks-schema.json
+      * output_type : https://raw.githubusercontent.com/hubverse-org/schemas/main/v2.0.0/tasks-schema.json
+      * target_metadata : https://raw.githubusercontent.com/hubverse-org/schemas/main/v2.0.0/tasks-schema.json
 
diff --git a/tests/_snaps/create_model_tasks.md b/tests/_snaps/create_model_tasks.md
@@ -92,7 +92,7 @@
       attr(,"n")
       [1] 1
       attr(,"schema_id")
-      [1] "https://raw.githubusercontent.com/Infectious-Disease-Modeling-Hubs/schemas/main/v2.0.0/tasks-schema.json"
+      [1] "https://raw.githubusercontent.com/hubverse-org/schemas/main/v2.0.0/tasks-schema.json"
 
 ---
 
@@ -361,7 +361,7 @@
       attr(,"n")
       [1] 2
       attr(,"schema_id")
-      [1] "https://raw.githubusercontent.com/Infectious-Disease-Modeling-Hubs/schemas/main/v2.0.0/tasks-schema.json"
+      [1] "https://raw.githubusercontent.com/hubverse-org/schemas/main/v2.0.0/tasks-schema.json"
 
 # create_model_tasks functions error correctly
 
@@ -393,5 +393,5 @@
       x `schema_id` attributes are not consistent across all items.
       Item `schema_id` attributes:
       * Item 1 : invalid_schema_id
-      * Item 2 : https://raw.githubusercontent.com/Infectious-Disease-Modeling-Hubs/schemas/main/v2.0.0/tasks-schema.json
+      * Item 2 : https://raw.githubusercontent.com/hubverse-org/schemas/main/v2.0.0/tasks-schema.json
 
diff --git a/tests/_snaps/create_output_type.md b/tests/_snaps/create_output_type.md
@@ -65,7 +65,7 @@
       attr(,"n")
       [1] 3
       attr(,"schema_id")
-      [1] "https://raw.githubusercontent.com/Infectious-Disease-Modeling-Hubs/schemas/main/v2.0.0/tasks-schema.json"
+      [1] "https://raw.githubusercontent.com/hubverse-org/schemas/main/v2.0.0/tasks-schema.json"
 
 # create_output_type functions error correctly
Original file line number	Diff line number	Diff line change
Expand Up		@@ -12,4 +12,4 @@

		# hubAdmin 0.0.1

		* Initial package release resulting from split of `hubUtils` package. See [`hubUtils` NEWS.md](https://github.com/Infectious-Disease-Modeling-Hubs/hubUtils/blob/main/NEWS.md) for details including previous release notes.
		* Initial package release resulting from split of `hubUtils` package. See [`hubUtils` NEWS.md](https://github.com/hubverse-org/hubUtils/blob/main/NEWS.md) for details including previous release notes.