Rename package from orderly to orderly1

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

@@ -38,7 +38,7 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
 

.github/workflows/test-coverage.yaml

@@ -21,7 +21,7 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
 
       - uses: r-lib/actions/setup-pandoc@v1
 

DESCRIPTION

@@ -1,6 +1,6 @@
-Package: orderly
+Package: orderly1
 Title: Lightweight Reproducible Reporting
-Version: 1.6.1
+Version: 1.7.0
 Description: Order, create and store reports from R.  By defining a
     lightweight interface around the inputs and outputs of an
     analysis, a lot of the repetitive work for reproducible research

R/batch.R

@@ -3,7 +3,7 @@
 ##' Run one report multiple times with different sets of parameters.
 ##'
 ##' @param name Name of the report to run (see
-##'   [orderly::orderly_list()]).  A leading `src/` will be
+##'   [orderly1::orderly_list()]).  A leading `src/` will be
 ##'   removed if provided, allowing easier use of autocomplete.
 ##'   Alternatively, the default of `NULL` is useful if you have
 ##'   already set the working directory to be the source directory.
@@ -17,18 +17,18 @@
 ##'   during preparation e.g. because of missing parameters this will
 ##'   error and stop all subsequent parameter sets.
 ##'
-##' @param ... Additional args passed to [orderly::orderly_run()]
+##' @param ... Additional args passed to [orderly1::orderly_run()]
 ##'
-##' @seealso [orderly::orderly_run()] for details of report running
+##' @seealso [orderly1::orderly_run()] for details of report running
 ##'
 ##' @export
 ##' @return List of ids of newly created reports
 ##'
 ##' @examples
 ##'
-##' path <- orderly::orderly_example("demo")
+##' path <- orderly1::orderly_example("demo")
 ##' params <- data.frame(nmin = c(0.2, 0.25))
-##' ids <- orderly::orderly_batch("other", params, root = path)
+##' ids <- orderly1::orderly_batch("other", params, root = path)
 orderly_batch <- function(name = NULL, parameters = NULL,
                           continue_on_error = TRUE, ...) {
   if (NROW(parameters) < 1) {

R/bundle.R

@@ -24,7 +24,7 @@
 ##'   `orderly_bundle_pack` or `orderly_bundle_run`)
 ##'
 ##' @param name Name of the report to pack (see
-##'   [orderly::orderly_list()].  A leading `src/` will be removed if
+##'   [orderly1::orderly_list()].  A leading `src/` will be removed if
 ##'   provided, allowing easier use of autocomplete.
 ##'
 ##' @inheritParams orderly_run
@@ -39,35 +39,35 @@
 ##'
 ##' @export
 ##' @examples
-##' path <- orderly::orderly_example("minimal")
+##' path <- orderly1::orderly_example("minimal")
 ##'
 ##' # A working directory to export bundles to:
 ##' workdir <- tempfile()
 ##'
 ##' # Pack up the "example" report to go:
-##' res <- orderly::orderly_bundle_pack(workdir, "example", root = path)
+##' res <- orderly1::orderly_bundle_pack(workdir, "example", root = path)
 ##'
 ##' # The return value is a list with the id and the path to the zip
 ##' # file created:
 ##' res
 ##'
 ##' # A list of reports bundled in this directory and their status
-##' orderly::orderly_bundle_list(workdir)
+##' orderly1::orderly_bundle_list(workdir)
 ##'
 ##' # Run the bundle (this would ordinarily be done on another computer)
-##' zip <- orderly::orderly_bundle_run(res$path, workdir)
+##' zip <- orderly1::orderly_bundle_run(res$path, workdir)
 ##' zip
 ##'
 ##' # The status has now been updated to reflect the status
-##' orderly::orderly_bundle_list(workdir)
+##' orderly1::orderly_bundle_list(workdir)
 ##'
 ##' # We can import this into the orderly tree
-##' orderly::orderly_bundle_import(zip$path, root = path)
+##' orderly1::orderly_bundle_import(zip$path, root = path)
 ##'
 ##' # This has now been included in your orderly archive and the
 ##' # workdir can be safely deleted
 ##' unlink(workdir, recursive = TRUE)
-##' orderly::orderly_list_archive(path)
+##' orderly1::orderly_list_archive(path)
 orderly_bundle_pack <- function(path, name, parameters = NULL,
                               envir = NULL, root = NULL, locate = TRUE,
                               message = NULL, instance = NULL,

R/cleanup.R

@@ -2,7 +2,7 @@
 ##' (possibly just for a set of report names) and then deletes
 ##' dangling data sets that are not pointed to by any draft or
 ##' committed reports.  Running cleanup does not affect any reports
-##' that have been committed with [orderly::orderly_commit()] (i.e.,
+##' that have been committed with [orderly1::orderly_commit()] (i.e.,
 ##' the contents of the `archive/` directory).
 ##'
 ##' @title Orderly cleanup
@@ -15,28 +15,28 @@
 ##'
 ##' @param failed_only Delete only failed reports (those without the
 ##'   end-of-run metadata).  This will also clean up drafts created by
-##'   [orderly::orderly_test_start()]
+##'   [orderly1::orderly_test_start()]
 ##' @inheritParams orderly_list
 ##' @return No return value, this function is called only for its side effects
 ##' @export
 ##' @examples
 ##' # In a new example orderly, run two reports and commit only the
 ##' # second one:
-##' path <- orderly::orderly_example("minimal")
-##' id1 <- orderly::orderly_run("example", root = path)
-##' id2 <- orderly::orderly_run("example", root = path)
-##' orderly::orderly_commit(id2, root = path)
+##' path <- orderly1::orderly_example("minimal")
+##' id1 <- orderly1::orderly_run("example", root = path)
+##' id2 <- orderly1::orderly_run("example", root = path)
+##' orderly1::orderly_commit(id2, root = path)
 ##'
 ##' # We now have one draft and one archive report:
-##' orderly::orderly_list_drafts(root = path)
-##' orderly::orderly_list_archive(root = path)
+##' orderly1::orderly_list_drafts(root = path)
+##' orderly1::orderly_list_archive(root = path)
 ##'
 ##' # To clean up the drafts:
-##' orderly::orderly_cleanup(root = path)
+##' orderly1::orderly_cleanup(root = path)
 ##'
 ##' # We now have no draft and one archive reports:
-##' orderly::orderly_list_drafts(root = path)
-##' orderly::orderly_list_archive(root = path)
+##' orderly1::orderly_list_drafts(root = path)
+##' orderly1::orderly_list_archive(root = path)
 orderly_cleanup <- function(name = NULL, root = NULL, locate = TRUE,
                             draft = TRUE, data = TRUE, failed_only = FALSE) {
   config <- orderly_config(root, locate)

R/config.R

@@ -7,9 +7,9 @@
 ##'
 ##' @examples
 ##' # The orderly demo, with lots of potential reports:
-##' path <- orderly::orderly_example("demo")
+##' path <- orderly1::orderly_example("demo")
 ##'
-##' orderly::orderly_config(path)
+##' orderly1::orderly_config(path)
 orderly_config <- function(root = NULL, locate = TRUE) {
   if (inherits(root, "orderly_config")) {
     root
@@ -86,10 +86,10 @@ orderly_config_ <- R6::R6Class(
       self$raw <- yaml_read(filename)
 
       v <- self$raw$minimum_orderly_version
-      if (!is.null(v) && utils::packageVersion("orderly") < v) {
+      if (!is.null(v) && utils::packageVersion("orderly1") < v) {
         stop(sprintf(
           "Orderly version '%s' is required, but only '%s' installed",
-          v, utils::packageVersion("orderly")))
+          v, utils::packageVersion("orderly1")))
       }
 
       if (validate) {

R/db.R

@@ -38,13 +38,13 @@
 ##' @export
 ##' @examples
 ##' # Create an orderly that has a single commited report:
-##' path <- orderly::orderly_example("minimal")
-##' id <- orderly::orderly_run("example", root = path)
-##' orderly::orderly_commit(id, root = path)
+##' path <- orderly1::orderly_example("minimal")
+##' id <- orderly1::orderly_run("example", root = path)
+##' orderly1::orderly_commit(id, root = path)
 ##'
 ##' # The source database holds the data that might be accessible via
 ##' # the 'data' entry in orderly.yml:
-##' db <- orderly::orderly_db("source", root = path)
+##' db <- orderly1::orderly_db("source", root = path)
 ##' # This is a list, with one connection per database listed in the
 ##' # orderly_config.yml (an empty list if none are specified):
 ##' db
@@ -54,7 +54,7 @@
 ##'
 ##' # The destination database holds information about the archived
 ##' # reports:
-##' db <- orderly::orderly_db("destination", root = path)
+##' db <- orderly1::orderly_db("destination", root = path)
 ##' DBI::dbListTables(db)
 ##'
 ##' # These tables are documented online:
@@ -141,11 +141,11 @@ orderly_db_args <- function(x, config, name) {
 ##' @export
 ##' @return No return value, this function is called only for its side effects
 ##' @examples
-##' path <- orderly::orderly_example("minimal")
-##' id <- orderly::orderly_run("example", root = path)
-##' orderly::orderly_commit(id, root = path)
+##' path <- orderly1::orderly_example("minimal")
+##' id <- orderly1::orderly_run("example", root = path)
+##' orderly1::orderly_commit(id, root = path)
 ##'
-##' con <- orderly::orderly_db("destination", root = path)
+##' con <- orderly1::orderly_db("destination", root = path)
 ##' DBI::dbReadTable(con, "report_version")
 ##' DBI::dbDisconnect(con)
 ##'
@@ -154,15 +154,15 @@ orderly_db_args <- function(x, config, name) {
 ##' # your own fields - only the fields that orderly looks after can
 ##' # be recovered!)
 ##' file.remove(file.path(path, "orderly.sqlite"))
-##' orderly::orderly_rebuild(path)
+##' orderly1::orderly_rebuild(path)
 ##' file.exists(file.path(path, "orderly.sqlite"))
-##' con <- orderly::orderly_db("destination", root = path)
+##' con <- orderly1::orderly_db("destination", root = path)
 ##' DBI::dbReadTable(con, "report_version")
 ##' DBI::dbDisconnect(con)
 ##'
 ##' # It is safe to rebuild a database repeatedly, though this can be
 ##' # slow with larger databases.
-##' orderly::orderly_rebuild(path)
+##' orderly1::orderly_rebuild(path)
 orderly_rebuild <- function(root = NULL, locate = TRUE, verbose = TRUE,
                             if_schema_changed = FALSE) {
   ## We'll skip warnings here - they'll come out as messages rather

R/db2.R

@@ -79,7 +79,7 @@ report_db_schema_read <- function(fields = NULL, dialect = "sqlite") {
     } else if (x$name == "orderly_schema") {
       x$values <- data_frame(
         schema_version = orderly_schema_version,
-        orderly_version = as.character(utils::packageVersion("orderly")),
+        orderly_version = as.character(utils::packageVersion("orderly1")),
         created = Sys.time())
     } else if (x$name == "orderly_schema_tables") {
       x$values <- data_frame(name = names(d))
@@ -151,7 +151,7 @@ report_db_open_existing <- function(con, config) {
   version_db <- DBI::dbReadTable(con, orderly_schema_table)$schema_version
   version_package <- orderly_schema_version
   if (numeric_version(version_db) < numeric_version(version_package)) {
-    stop("orderly db needs rebuilding with orderly::orderly_rebuild()",
+    stop("orderly db needs rebuilding with orderly1::orderly_rebuild()",
          call. = FALSE)
   }
 
@@ -175,15 +175,15 @@ report_db_open_existing <- function(con, config) {
               config$changelog$public %||% logical(0))
   if (!ok) {
     stop(
-      "changelog labels have changed: rebuild with orderly::orderly_rebuild()",
+      "changelog labels have changed: rebuild with orderly1::orderly_rebuild()",
       call. = FALSE)
   }
 
   tag <- DBI::dbReadTable(con, "tag")$id
   ok <- setequal(tag, config$tags)
   if (!ok) {
     stop(
-      "tags have changed: rebuild with orderly::orderly_rebuild()",
+      "tags have changed: rebuild with orderly1::orderly_rebuild()",
       call. = FALSE)
   }
 }

R/deduplicate.R

@@ -44,13 +44,13 @@
 ##' @export
 ##' @examples
 ##'
-##' path <- orderly::orderly_example("demo")
-##' id1 <- orderly::orderly_run("minimal", root = path)
-##' id2 <- orderly::orderly_run("minimal", root = path)
+##' path <- orderly1::orderly_example("demo")
+##' id1 <- orderly1::orderly_run("minimal", root = path)
+##' id2 <- orderly1::orderly_run("minimal", root = path)
 ##' orderly_commit(id1, root = path)
 ##' orderly_commit(id2, root = path)
 ##' tryCatch(
-##'   orderly::orderly_deduplicate(path, dry_run = TRUE),
+##'   orderly1::orderly_deduplicate(path, dry_run = TRUE),
 ##'   error = function(e) NULL)
 orderly_deduplicate <- function(root = NULL, locate = TRUE, dry_run = TRUE,
                                 quiet = FALSE) {

R/dependencies.R

@@ -25,8 +25,8 @@
 ##' @section Remark:
 ##'
 ##' By default the tree is built using data from the local report
-##'   database (see [orderly::orderly_commit],
-##'   [orderly::orderly_db]). This means that it will not find changes
+##'   database (see [orderly1::orderly_commit],
+##'   [orderly1::orderly_db]). This means that it will not find changes
 ##'   from a report that has not be run and committed. That is, if a
 ##'   user changes a report to use or create different artefacts this
 ##'   will not be picked up by the function until the reports are
@@ -77,16 +77,16 @@
 ##'         report.
 ##' @export
 ##' @examples
-##' path <- orderly::orderly_example("demo")
-##'
-##' id <- orderly::orderly_run("other", root = path, parameters=list(nmin=0))
-##' orderly::orderly_commit(id, root = path)
-##' id <- orderly::orderly_run("use_dependency", root = path)
-##' orderly::orderly_commit(id, root = path)
-##' id <- orderly::orderly_run("use_dependency_2", root = path)
-##' orderly::orderly_commit(id, root = path)
-##' orderly::orderly_graph("other", root = path)
-##' orderly::orderly_graph("use_dependency_2", root = path,
+##' path <- orderly1::orderly_example("demo")
+##'
+##' id <- orderly1::orderly_run("other", root = path, parameters=list(nmin=0))
+##' orderly1::orderly_commit(id, root = path)
+##' id <- orderly1::orderly_run("use_dependency", root = path)
+##' orderly1::orderly_commit(id, root = path)
+##' id <- orderly1::orderly_run("use_dependency_2", root = path)
+##' orderly1::orderly_commit(id, root = path)
+##' orderly1::orderly_graph("other", root = path)
+##' orderly1::orderly_graph("use_dependency_2", root = path,
 ##'                                  direction = "upstream")
 orderly_graph <- function(name, id = "latest", root = NULL, locate = TRUE,
                           direction = "downstream", propagate = TRUE,

R/develop.R

@@ -37,7 +37,7 @@
 ##' happen.  When in doubt, restart your R session.
 ##'
 ##' Note that these functions are much more permissive as to the state
-##' of your `orderly.yml` than [orderly::orderly_run()] - in
+##' of your `orderly.yml` than [orderly1::orderly_run()] - in
 ##' particular, they will run, with a message, even if you have not
 ##' yet defined a `script:` or any `artefacts:`.
 ##'
@@ -47,7 +47,7 @@
 ##' @title Develop an orderly report
 ##'
 ##' @param name Name of the report to develop (see
-##'   [orderly::orderly_list()]).  A leading `src/` will be
+##'   [orderly1::orderly_list()]).  A leading `src/` will be
 ##'   removed if provided, allowing easier use of autocomplete.
 ##'   Alternatively, the default of `NULL` is useful if you have
 ##'   already set the working directory to be the source directory.
@@ -59,23 +59,23 @@
 ##'
 ##' @export
 ##' @examples
-##' path <- orderly::orderly_example("demo")
+##' path <- orderly1::orderly_example("demo")
 ##'
 ##' # This report uses a dependency - it requires that the file
 ##' # incoming.csv exists.  This file is created from the report 'other'
-##' orderly::orderly_develop_status("use_dependency", root = path)
+##' orderly1::orderly_develop_status("use_dependency", root = path)
 ##'
 ##' # Copy the required dependencies over, in this case from a draft report
-##' orderly::orderly_run("other", list(nmin = 0), root = path, echo = FALSE)
-##' orderly::orderly_develop_start("use_dependency", root = path,
+##' orderly1::orderly_run("other", list(nmin = 0), root = path, echo = FALSE)
+##' orderly1::orderly_develop_start("use_dependency", root = path,
 ##'                                use_draft = TRUE)
 ##'
 ##' # Files have been copied across into the source directory
-##' orderly::orderly_develop_status("use_dependency", root = path)
+##' orderly1::orderly_develop_status("use_dependency", root = path)
 ##'
 ##' # The report can then be developed as needed, interactively.  After
 ##' # we're happy things can be cleaned up with
-##' orderly::orderly_develop_clean("use_dependency", root = path)
+##' orderly1::orderly_develop_clean("use_dependency", root = path)
 ##'
 orderly_develop_start <- function(name = NULL, parameters = NULL,
                                   envir = parent.frame(),