From 7d2eec9045d19e8f5ec9a80d56ec10491ffd929a Mon Sep 17 00:00:00 2001 From: Anna Krystalli Date: Thu, 1 Aug 2024 17:45:56 +0300 Subject: [PATCH 1/8] Remove zoltr dev dependency --- DESCRIPTION | 1 - 1 file changed, 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 4e4a334..251ebc0 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -48,7 +48,6 @@ Suggests: testthat (>= 3.2.0) Remotes: hubverse-org/hubUtils, - reichlab/zoltr, apache/arrow/r@apache-arrow-15.0.2 Config/Needs/website: hubverse-org/hubStyle Depends: From 52825da30b2dd18a411177faf7ad556e3a1bf999 Mon Sep 17 00:00:00 2001 From: Anna Krystalli Date: Thu, 1 Aug 2024 17:46:26 +0300 Subject: [PATCH 2/8] Fix skip_checks arg documentation formatting --- R/connect_hub.R | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/R/connect_hub.R b/R/connect_hub.R index 2fd79b1..c94e16e 100644 --- a/R/connect_hub.R +++ b/R/connect_hub.R @@ -25,12 +25,14 @@ #' `admin.json` and is ignored by default. #' If supplied, it will override hub configuration setting. Multiple formats can #' be supplied to `connect_hub` but only a single file format can be supplied to `connect_mod_out`. -#' @param skip_checks Logical. If `FALSE` (default), check file_format parameter against the -#' hub's model output files. Also excludes invalid model output files when opening hub datasets. -#' Setting to `TRUE`` will improve performance but will result in an error if the model output -#' directory includes invalid files. Cannot be `TRUE` when there are multiple file formats in -#' the hub's model output directory or when the hub's model output directory contains files that -#' are not model output data (for example, a README). +#' @param skip_checks Logical. If `FALSE` (default), check `file_format` parameter +#' against the hub's model output files. Also excludes invalid model output files +#' when opening hub datasets. +#' Setting to `TRUE` will improve performance but will result in an error if +#' the model output directory includes invalid files. **Cannot be `TRUE`** when +#' there are **multiple file formats** in the hub's model output directory or when +#' the hub's model output directory contains **files that are not model output +#' data** (for example, a README). #' @inheritParams create_hub_schema #' #' @return From d163d73f8926bc8cb0541439d1ee6b35d2f97ea4 Mon Sep 17 00:00:00 2001 From: Anna Krystalli Date: Thu, 1 Aug 2024 17:46:35 +0300 Subject: [PATCH 3/8] document --- man/connect_hub.Rd | 12 ++++++++---- man/model_id_merge.Rd | 3 +++ man/model_id_split.Rd | 3 +++ man/validate_model_out_tbl.Rd | 3 ++- 4 files changed, 16 insertions(+), 5 deletions(-) diff --git a/man/connect_hub.Rd b/man/connect_hub.Rd index ca51a16..0327b25 100644 --- a/man/connect_hub.Rd +++ b/man/connect_hub.Rd @@ -57,10 +57,14 @@ behaviour so use with care.} \item{partitions}{a named list specifying the arrow data types of any partitioning column.} -\item{skip_checks}{Logical. If \code{FALSE} (default), check file_format parameter against the -hub's model output files. Also excludes invalid model output files when opening hub datasets. -Setting to TRUE will improve performance but will result in an error if the model output -directory includes invalid files.} +\item{skip_checks}{Logical. If \code{FALSE} (default), check \code{file_format} parameter +against the hub's model output files. Also excludes invalid model output files +when opening hub datasets. +Setting to \code{TRUE} will improve performance but will result in an error if +the model output directory includes invalid files. \strong{Cannot be \code{TRUE}} when +there are \strong{multiple file formats} in the hub's model output directory or when +the hub's model output directory contains \strong{files that are not model output +data} (for example, a README).} \item{model_output_dir}{Either a character string path to a local directory containing model output data diff --git a/man/model_id_merge.Rd b/man/model_id_merge.Rd index e008cfc..4105e79 100644 --- a/man/model_id_merge.Rd +++ b/man/model_id_merge.Rd @@ -6,6 +6,9 @@ \value{ \code{tbl} with either \code{team_abbr} and \code{model_abbr} merged into a single \code{model_id} column or \code{model_id} split into columns \code{team_abbr} and \code{model_abbr}. + +a \link[tibble:tibble]{tibble} with \code{model_id} column split into separate +\code{team_abbr} and \code{model_abbr} columns } \description{ See \code{\link[hubUtils:model_id_merge]{hubUtils::model_id_merge()}} for details. diff --git a/man/model_id_split.Rd b/man/model_id_split.Rd index a6228c1..f58bd69 100644 --- a/man/model_id_split.Rd +++ b/man/model_id_split.Rd @@ -6,6 +6,9 @@ \value{ \code{tbl} with either \code{team_abbr} and \code{model_abbr} merged into a single \code{model_id} column or \code{model_id} split into columns \code{team_abbr} and \code{model_abbr}. + +a \link[tibble:tibble]{tibble} with \code{model_id} column split into separate +\code{team_abbr} and \code{model_abbr} columns } \description{ See \code{\link[hubUtils:model_id_merge]{hubUtils::model_id_merge()}} for details. diff --git a/man/validate_model_out_tbl.Rd b/man/validate_model_out_tbl.Rd index 27189a6..684b15f 100644 --- a/man/validate_model_out_tbl.Rd +++ b/man/validate_model_out_tbl.Rd @@ -4,7 +4,8 @@ \alias{validate_model_out_tbl} \title{Validate a \code{model_out_tbl} object} \value{ -If valid, returns a \code{tbl}. Otherwise throws an error. +If valid, returns a \code{model_out_tbl} class object. Otherwise, throws an +error. } \description{ See \code{\link[hubUtils:validate_model_out_tbl]{hubUtils::validate_model_out_tbl()}} for details. From c4e58f386dfe03557c4e61240d0df869866bc836 Mon Sep 17 00:00:00 2001 From: Anna Krystalli Date: Thu, 1 Aug 2024 17:52:48 +0300 Subject: [PATCH 4/8] return to original docs until hubUtils v0.1.1 released --- man/model_id_merge.Rd | 3 --- man/model_id_split.Rd | 3 --- man/validate_model_out_tbl.Rd | 3 +-- 3 files changed, 1 insertion(+), 8 deletions(-) diff --git a/man/model_id_merge.Rd b/man/model_id_merge.Rd index 4105e79..e008cfc 100644 --- a/man/model_id_merge.Rd +++ b/man/model_id_merge.Rd @@ -6,9 +6,6 @@ \value{ \code{tbl} with either \code{team_abbr} and \code{model_abbr} merged into a single \code{model_id} column or \code{model_id} split into columns \code{team_abbr} and \code{model_abbr}. - -a \link[tibble:tibble]{tibble} with \code{model_id} column split into separate -\code{team_abbr} and \code{model_abbr} columns } \description{ See \code{\link[hubUtils:model_id_merge]{hubUtils::model_id_merge()}} for details. diff --git a/man/model_id_split.Rd b/man/model_id_split.Rd index f58bd69..a6228c1 100644 --- a/man/model_id_split.Rd +++ b/man/model_id_split.Rd @@ -6,9 +6,6 @@ \value{ \code{tbl} with either \code{team_abbr} and \code{model_abbr} merged into a single \code{model_id} column or \code{model_id} split into columns \code{team_abbr} and \code{model_abbr}. - -a \link[tibble:tibble]{tibble} with \code{model_id} column split into separate -\code{team_abbr} and \code{model_abbr} columns } \description{ See \code{\link[hubUtils:model_id_merge]{hubUtils::model_id_merge()}} for details. diff --git a/man/validate_model_out_tbl.Rd b/man/validate_model_out_tbl.Rd index 684b15f..27189a6 100644 --- a/man/validate_model_out_tbl.Rd +++ b/man/validate_model_out_tbl.Rd @@ -4,8 +4,7 @@ \alias{validate_model_out_tbl} \title{Validate a \code{model_out_tbl} object} \value{ -If valid, returns a \code{model_out_tbl} class object. Otherwise, throws an -error. +If valid, returns a \code{tbl}. Otherwise throws an error. } \description{ See \code{\link[hubUtils:validate_model_out_tbl]{hubUtils::validate_model_out_tbl()}} for details. From f6e801e67fedeeb5339ef3d012b1d21d2cf63938 Mon Sep 17 00:00:00 2001 From: Anna Krystalli Date: Thu, 1 Aug 2024 18:12:22 +0300 Subject: [PATCH 5/8] Bump version --- DESCRIPTION | 2 +- NEWS.md | 4 ++++ 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 251ebc0..3cc500c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: hubData Title: Tools for accessing and working with hubverse data -Version: 1.2.0 +Version: 1.2.1 Authors@R: c(person("Anna", "Krystalli", , "annakrystalli@googlemail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-2378-4915")), diff --git a/NEWS.md b/NEWS.md index 0a4b4ce..7eb64f8 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,7 @@ +# hubData 1.2.1 + +* Removed depedency on development version of `zoltr` package. + # hubData 1.2.0 * Adds a `skip_checks` parameter to the `connect_hub` and `connect_model_output` functions. When `skip_checks` is set to `TRUE`, these functions will bypass the default behavior of scanning the hub's model output directory for invalid files. Omitting these checks results in better performance when connecting to cloud-based hubs but can result in errors when querying the data. This option is only valid when connecting to hubs that meet the following criteria: From caf371ac3f256ba0af81e7cea220431afe96584b Mon Sep 17 00:00:00 2001 From: Anna Krystalli Date: Thu, 1 Aug 2024 18:14:54 +0300 Subject: [PATCH 6/8] Fix error in connect_hub vignette function call --- vignettes/articles/connect_hub.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/vignettes/articles/connect_hub.Rmd b/vignettes/articles/connect_hub.Rmd index 508e338..82f098f 100644 --- a/vignettes/articles/connect_hub.Rmd +++ b/vignettes/articles/connect_hub.Rmd @@ -224,7 +224,7 @@ Like `connect_hub`, `connect_model_output` has an optional `skip_checks` argumen ```{r} mod_out_dir_cloud <- s3_bucket("hubverse/hubutils/testhubs/parquet/model-output/") -mod_out_con_cloud <- connect_hub(mod_out_dir_cloud, file_format = "parquet", skip_checks = TRUE) +mod_out_con_cloud <- connect_model_output(mod_out_dir_cloud, file_format = "parquet", skip_checks = TRUE) mod_out_con_cloud ``` From 9cec8ef6aa460357bb0f258f4db1f2a6540eb4ba Mon Sep 17 00:00:00 2001 From: Anna Krystalli Date: Thu, 1 Aug 2024 18:16:01 +0300 Subject: [PATCH 7/8] add news item --- NEWS.md | 1 + 1 file changed, 1 insertion(+) diff --git a/NEWS.md b/NEWS.md index 7eb64f8..f3ae213 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,6 +1,7 @@ # hubData 1.2.1 * Removed depedency on development version of `zoltr` package. +* Fixed minor error in `connect_hub()` article. # hubData 1.2.0 From 4cf529b9391dbec1c2f6363ad9a6a7c00e044b5b Mon Sep 17 00:00:00 2001 From: Anna Krystalli Date: Thu, 1 Aug 2024 18:16:20 +0300 Subject: [PATCH 8/8] Typo!! --- NEWS.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/NEWS.md b/NEWS.md index f3ae213..58847a6 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,6 +1,6 @@ # hubData 1.2.1 -* Removed depedency on development version of `zoltr` package. +* Removed dependency on development version of `zoltr` package. * Fixed minor error in `connect_hub()` article. # hubData 1.2.0