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Use standalone file assertion utilities from reside.utils #176

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Sep 10, 2024
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Exclude generated files from linting
  • Loading branch information
richfitz committed Sep 10, 2024
commit fcd37e91e9651740ec308702df322f4b161542bc
2 changes: 1 addition & 1 deletion .lintr
Original file line number Diff line number Diff line change
Expand Up @@ -4,4 +4,4 @@ linters: linters_with_defaults(
object_usage_linter = NULL,
cyclocomp_linter = NULL
)
exclusions: list("tests/testthat.R", "R/cpp11.R")
exclusions: list("tests/testthat.R", "R/cpp11.R", "R/import-standalone-utils-assert.R", "R/import-standalone-utils-assert-path.R")
15 changes: 7 additions & 8 deletions vignettes/collaboration.Rmd
Original file line number Diff line number Diff line change
Expand Up @@ -233,7 +233,7 @@ This multi-step process means that we avoid copying data that is already known a

It is important that the `.outpack` directory is *not* shared via git; we warn about this now, and you can use `orderly2::ordery_gitignore_update()` to automatically create a suitable `.gitignore` file that will prevent it being accidentally committed.

However,
However,

If Alice and Bob were starting on a new machine they would:

Expand All @@ -253,20 +253,20 @@ One of the simplest ways to share packets with a collaborator is through a share
1. Initialise an orderly location on the shared file system
```{r as="alice"}
orderly2::orderly_init(
root = path_sharepoint_alice,
path_archive = NULL,
use_file_store = TRUE,
root = path_sharepoint_alice,
path_archive = NULL,
use_file_store = TRUE,
require_complete_tree = TRUE
)
```

Create an orderly store with a file store and a complete tree. See `orderly2::orderly_init()` for more details.
1. Add this as a location
```{r, as="alice", inwd = path_alice}
orderly2::orderly_location_add(
"sharepoint", "path", list(path = path_sharepoint_alice))
```

1. Push any packets you want to share
```{r, as="alice", inwd = path_alice}
orderly2::orderly_location_push(id, "sharepoint")
Expand All @@ -280,11 +280,10 @@ Then these will be available for your collaborator to pull. Note that the data i
orderly2::orderly_location_add(
"alices_orderly", "path", list(path = path_sharepoint_bob))
```

1. Pull the metadata and use the packets as desired
```{r, as="bob", inwd = path_bob}
orderly2::orderly_location_pull_metadata(
"alices_orderly"
)
```

3 changes: 2 additions & 1 deletion vignettes/introduction.Rmd
Original file line number Diff line number Diff line change
Expand Up @@ -187,7 +187,8 @@ In addition, there is also a function `orderly::orderly_run_info()` that can be
Let's add some additional annotations to the previous reports:

```{r, include = FALSE}
code_data <- readLines(file.path(path, "src", "incoming_data", "incoming_data.R"))
code_data <- readLines(
file.path(path, "src", "incoming_data", "incoming_data.R"))
writeLines(c(
"orderly2::orderly_strict_mode()",
'orderly2::orderly_resource("data.csv")',
Expand Down