Fix out-of-dateness propagation

Out-of-dateness was not being propagated correctly for deviant pipeline

Also:
* Replace installed files with temp files
* Update README
* Increment version number

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: makepipe
 Title: Pipeline Tools Inspired by 'GNU Make'
-Version: 0.0.4
+Version: 0.0.5
 Authors@R: 
     person(given = "Kinto",
            family = "Behr",

NEWS.md

@@ -1,3 +1,8 @@
+# makepipe 0.0.5
+
+* Fixed minor bug having to do with the propagation of out-of-dateness in
+Pipeline visualizations.
+
 # makepipe 0.0.4
 
 * Renamed package from `piper` to `makepipe` (#11).

R/Pipeline.R

@@ -196,6 +196,7 @@ Pipeline <- R6::R6Class(classname = "Pipeline", list(
 
     # Propagate out-of-dateness
     for (i in seq_along(edges$to)) {
+      if (edges$.source[i]) next
       edges$out_of_date[i] <- propagate_outofdateness(edges$to[i], edges)
     }
 
@@ -376,7 +377,7 @@ propagate_outofdateness <- function(initial_node, edges, next_node = NULL) {
 
   inputs <- edges[edges$to == next_node, ]
   for (i in seq_along(inputs$from)) {
-    outdated <- inputs$from_mtime[i] > target_mtime
+    outdated <- inputs$out_of_date[i] | inputs$from_mtime[i] > target_mtime
     next_node <- inputs$from[i]
 
     # Base case

README.Rmd

@@ -29,12 +29,21 @@ of data science workflows.
 
 ## Installation
 
-You can install the development version from [GitHub](https://github.com/) with:
+You can install the released version of `makepipe` from 
+[CRAN](https://CRAN.R-project.org) with:
+
+``` r
+install.packages("makepipe")
+```
+
+And the development version from [GitHub](https://github.com/) with:
 
 ``` r
 # install.packages("devtools")
 devtools::install_github("kinto-b/makepipe")
 ```
+
+
 ## Building a pipeline
 
 To construct a pipeline, one simply needs to chain together a number of 
@@ -50,8 +59,8 @@ visualisation of the pipeline. For example:
 library(makepipe)
 make_with_source(
   dependencies = c("data/0_raw_data.csv", "lookup/concordance.csv"),
-  source = c("1 data_prep.R"),
-  targets = c("data/1_data.Rds")
+  source = "1 data_prep.R",
+  targets = "data/1_data.Rds"
 )
 make_with_recipe(
     dependencies = c("data/1_data.Rds", "data/0_pop.Rds"),

README.md

@@ -20,8 +20,14 @@ easy-going, being adaptable to a wide range of data science workflows.
 
 ## Installation
 
-You can install the development version from
-[GitHub](https://github.com/) with:
+You can install the released version of `makepipe` from
+[CRAN](https://CRAN.R-project.org) with:
+
+``` r
+install.packages("makepipe")
+```
+
+And the development version from [GitHub](https://github.com/) with:
 
 ``` r
 # install.packages("devtools")
@@ -44,8 +50,8 @@ For example:
 library(makepipe)
 make_with_source(
   dependencies = c("data/0_raw_data.csv", "lookup/concordance.csv"),
-  source = c("1 data_prep.R"),
-  targets = c("data/1_data.Rds")
+  source = "1 data_prep.R",
+  targets = "data/1_data.Rds"
 )
 make_with_recipe(
     dependencies = c("data/1_data.Rds", "data/0_pop.Rds"),

cran-comments.md

@@ -1,8 +1,8 @@
 ## Resubmission
-This is a resubmission (thank you for taking the time to read my last
-submission). In this version I have:
+This is a re-submission. In this version I have:
 
-* Removed package name and all backticks from Description text. 
+* Replaced installed test files with tempfiles so that the tests only write to
+the temporary directory
 
 ## Test environments
 * local R installation, R 4.1.0

inst/tests/source1.R

@@ -0,0 +1 @@
+makepipe::make_register(5, 'five')

inst/tests/source2.R

@@ -0,0 +1 @@
+2+2

tests/testthat/test-Pipeline.R

@@ -1,9 +1,19 @@
 # Test files -------------------------------------------------------------------
-dependency <- system.file("tests", "mtcars_src.csv", package = "makepipe")
-source1 <- system.file("tests", "mtcars1.R", package = "makepipe")
-source2 <- system.file("tests", "mtcars2.R", package = "makepipe")
-target1 <- system.file("tests", "mtcars.csv", package = "makepipe")
-target2 <- system.file("tests", "mtcars.txt", package = "makepipe")
+dependency <- tempfile(fileext=".csv")
+write.csv(mtcars, dependency)
+
+target1 <- tempfile(fileext=".csv")
+write.csv(mtcars, target1)
+
+target2 <- tempfile(fileext=".txt")
+write.table(mtcars, target2)
+
+source1 <- tempfile(fileext=".R")
+file.copy(system.file("tests", "source1.R", package = "makepipe"), source1)
+
+source2 <- tempfile(fileext=".R")
+file.copy(system.file("tests", "source2.R", package = "makepipe"), source2)
+
 
 # Functions --------------------------------------------------------------------
 order_filetimes <- function(...) {
@@ -166,3 +176,6 @@ test_that("annotations cannot must be character", {
 })
 
 
+# Unlink ------------------------------------------------------------------
+
+unlink(c("dependency", "target1", "target2", "source1", "source2"))

tests/testthat/test-make.R

@@ -1,9 +1,18 @@
 # Test files -------------------------------------------------------------------
-dependency <- system.file("tests", "mtcars_src.csv", package = "makepipe")
-source1 <- system.file("tests", "mtcars1.R", package = "makepipe")
-source2 <- system.file("tests", "mtcars2.R", package = "makepipe")
-target1 <- system.file("tests", "mtcars.csv", package = "makepipe")
-target2 <- system.file("tests", "mtcars.txt", package = "makepipe")
+dependency <- tempfile(fileext=".csv")
+write.csv(mtcars, dependency)
+
+target1 <- tempfile(fileext=".csv")
+write.csv(mtcars, target1)
+
+target2 <- tempfile(fileext=".txt")
+write.table(mtcars, target2)
+
+source1 <- tempfile(fileext=".R")
+file.copy(system.file("tests", "source1.R", package = "makepipe"), source1)
+
+source2 <- tempfile(fileext=".R")
+file.copy(system.file("tests", "source2.R", package = "makepipe"), source2)
 
 # Functions --------------------------------------------------------------------
 order_filetimes <- function(...) {
@@ -240,6 +249,8 @@ test_that("make_with_source returns what's registered", {
   expect_equal(res$result$five, 5)
 })
 
+
+# Printing ---------------------------------------------------------------------
 test_that("make_with_recipe result prints nicely", {
   order_filetimes(target1, dependency)
   x <- make_with_recipe({
@@ -249,8 +260,8 @@ test_that("make_with_recipe result prints nicely", {
 
   expect_output(print(x), regexp = "# makepipe segment")
   expect_output(print(x), regexp = "* Recipe: ")
-  expect_output(print(x), regexp = "* Targets: '.*/mtcars.csv'")
-  expect_output(print(x), regexp = "* File dependencies: '.*/mtcars_src.csv'")
+  expect_output(print(x), regexp = "* Targets: '.*'")
+  expect_output(print(x), regexp = "* File dependencies: '.*'")
   expect_output(print(x), regexp = "* Executed: TRUE")
   expect_output(print(x), regexp = "* Result: 1 object")
   expect_output(print(x), regexp = "* Environment: ")
@@ -270,17 +281,21 @@ test_that("make_with_source result prints nicely", {
   x <- make_with_source(source1, target1, dependency, quiet = TRUE)
 
   expect_output(print(x), regexp = "# makepipe segment")
-  expect_output(print(x), regexp = "* Source: '.*/mtcars1.R'")
-  expect_output(print(x), regexp = "* Targets: '.*/mtcars.csv'")
-  expect_output(print(x), regexp = "* File dependencies: '.*/mtcars_src.csv'")
+  expect_output(print(x), regexp = "* Source: '.*'")
+  expect_output(print(x), regexp = "* Targets: '.*'")
+  expect_output(print(x), regexp = "* File dependencies: '.*'")
   expect_output(print(x), regexp = "* Executed: TRUE")
   expect_output(print(x), regexp = "* Result: 1 object")
   expect_output(print(x), regexp = "* Environment: ")
 
+  order_filetimes(dependency, source1, target1)
   x <- make_with_source(source1, target1, dependency, quiet = TRUE)
   expect_output(print(x), regexp = "* Executed: FALSE")
 })
 
 
+# Unlink ------------------------------------------------------------------
+
+unlink(c("dependency", "target1", "target2", "source1", "source2"))