Merge pull request #4 from mrc-ide/epic-poc

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

@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main, master, epic-poc]
   pull_request:
-    branches: [main, master]
+    branches: [main, master, epic-poc]
 
 name: R-CMD-check
 

.github/workflows/pkgdown.yaml

@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main, master, epic-poc]
   pull_request:
-    branches: [main, master]
+    branches: [main, master, epic-poc]
   release:
     types: [published]
   workflow_dispatch:

.github/workflows/test-coverage.yaml

@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main, master, epic-poc]
   pull_request:
-    branches: [main, master]
+    branches: [main, master, epic-poc]
 
 name: test-coverage
 

DESCRIPTION

@@ -11,15 +11,20 @@ Description: Reimplementation of orderly based on outpack.
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.1
+RoxygenNote: 7.2.3
 URL: https://github.com/mrc-ide/orderly3
 BugReports: https://github.com/mrc-ide/orderly3/issues
 Imports:
     fs,
+    jsonlite,
     orderly,
-    outpack,
+    outpack (>= 0.2.4),
+    withr,
     yaml
 Suggests:
+    jsonvalidate,
+    mockery,
+    pkgload,
     testthat (>= 3.0.0)
 Config/testthat/edition: 3
 Remotes: mrc-ide/outpack

NAMESPACE

@@ -1 +1,11 @@
 # Generated by roxygen2: do not edit by hand
+
+export(orderly_artefact)
+export(orderly_dependency)
+export(orderly_global_resource)
+export(orderly_parameters)
+export(orderly_plugin_add_metadata)
+export(orderly_plugin_context)
+export(orderly_plugin_register)
+export(orderly_resource)
+export(orderly_run)

R/config.R

@@ -17,13 +17,12 @@ orderly_config_yml_read <- function(path) {
     assert_named(raw)
   }
 
-  ## This has a structure that makes using plugins later easier
   check <- list(
+    plugins = orderly_config_validate_plugins,
     global_resources = orderly_config_validate_global_resources)
 
   required <- character()
-  optional <- c(setdiff(names(check), required))
-
+  optional <- setdiff(names(check), required)
   check_fields(raw, filename, required, optional)
 
   dat <- list()
@@ -42,3 +41,19 @@ orderly_config_validate_global_resources <- function(global_resources,
     global_resources
   }
 }
+
+
+orderly_config_validate_plugins <- function(plugins, filename) {
+  if (is.null(plugins)) {
+    return(NULL)
+  }
+  assert_named(plugins, unique = TRUE, name = sprintf("%s:plugins", filename))
+
+  ret <- list()
+  for (nm in names(plugins)) {
+    dat <- load_orderly_plugin(nm)
+    dat$config <- dat$config(plugins[[nm]], filename)
+    ret[[nm]] <- dat
+  }
+  ret
+}

R/context.R

@@ -0,0 +1,59 @@
+orderly_context <- function() {
+  p <- get_active_packet()
+  is_active <- !is.null(p)
+  if (is_active) {
+    path <- p$path
+    root <- p$root$path
+    config <- p$orderly3$config
+    env <- p$orderly3$envir
+    src <- p$orderly3$src
+    parameters <- p$parameters
+  } else {
+    path <- getwd()
+    root <- detect_orderly_interactive_path(path)$path
+    config <- orderly_root(root, FALSE)$config
+    env <- orderly_environment("orderly3")
+    src <- path
+    parameters <- current_orderly_parameters(src, env)
+  }
+  list(is_active = is_active, path = path, config = config, env = env,
+       root = root, src = src, parameters = parameters,
+       packet = p)
+}
+
+
+## This is a real trick, and is only used in the case where the report
+## is being run interactively, and in that case the correct thing is
+## *almost certainly* the global environment, as the user has to do
+## some tricks to stop that being the case; for example running
+##
+##   source("orderly.R", local = TRUE)
+##
+## We want to find the environment that corresponds to the top level
+## environment for orderly; that will be the one that called the
+## plugin function. So we'll have a stack of frames (corresponding to
+## the environments on the call stack) with *parents* that look like
+## this, outermost first:
+##
+## - (anything else)
+## - (calling environment) <-- this is what we're looking for
+## - (plugin)
+## - (orderly3; orderly_plugin_context)
+## - (orderly3; from orderly_context)
+## - (orderly3; from orderly_environment)
+##
+## so we loop down the stack looking for the first call to a function
+## in the plugin package, then take the frame *above* that.
+##
+## When we want this for a non-plugin case (i.e., the caller is in
+## orderly3) then we just need to pass name = "orderly3" here
+orderly_environment <- function(name) {
+  frames <- sys.frames()
+  for (i in seq_along(frames)[-1]) {
+    if (environmentName(parent.env(frames[[i]])) == name) {
+      return(frames[[i - 1]])
+    }
+  }
+  ## This error should never surface if the plugin is configured correctly
+  stop("Could not determine calling environment safely - please report")
+}

R/interactive.R

@@ -0,0 +1,16 @@
+## This is something that we might improve over time - it will likely
+## be useful to have some sort of "register interactive" function
+## which we could then just look up.
+##
+## I am not sure if we also want to allow working interactively from a
+## draft directory too.
+detect_orderly_interactive_path <- function(path = getwd()) {
+  path_split <- fs::path_split(path)[[1]]
+  is_plausible <- length(path_split) > 2 &&
+    path_split[[length(path_split) - 1]] == "src" &&
+    file.exists(file.path(path, "../..", "orderly_config.yml"))
+  if (!is_plausible) {
+    stop(sprintf("Failed to detect orderly path at '%s'", path))
+  }
+  orderly_root(file.path(path, "../.."), FALSE)
+}