From 86b0ce084c20a9d8fcb3dbd19d43c080a21344a1 Mon Sep 17 00:00:00 2001
From: Sam Parmar <107635309+parmsam-pfizer@users.noreply.github.com>
Date: Fri, 22 Sep 2023 17:14:49 -0400
Subject: [PATCH 1/2] draft lockfile read vignette

---
 vignettes/generate-lockfile.Rmd | 72 +++++++++++++++++++++++++++++++++
 1 file changed, 72 insertions(+)
 create mode 100644 vignettes/generate-lockfile.Rmd

diff --git a/vignettes/generate-lockfile.Rmd b/vignettes/generate-lockfile.Rmd
new file mode 100644
index 0000000..35f7310
--- /dev/null
+++ b/vignettes/generate-lockfile.Rmd
@@ -0,0 +1,72 @@
+---
+title: "Generate renv lockfile from log file"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{generate-lockfile}
+  %\VignetteEncoding{UTF-8}
+  %\VignetteEngine{knitr::rmarkdown}
+editor_options: 
+  chunk_output_type: console
+---
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+```
+
+```{r setup}
+library(logrx)
+library(stringr)
+library(dplyr)
+library(renv)
+```
+
+
+```{r run-axecute, echo = FALSE}
+scriptPath <- tempfile()
+
+logDir <- tempdir()
+writeLines(
+  c(
+    "print('hello logrx')", 
+    "library(dplyr)",
+    "count(iris, Species)"
+  ),
+  con = scriptPath
+)
+
+filePath <- file.path(logDir, "log_out_parse")
+
+axecute(scriptPath, log_name = "log_out_parse", log_path = logDir)
+
+parsedFile <- read_log_file(filePath)
+```
+
+
+```{r read-previous-logfile}
+# check that the log file can be parsed
+parsedFile$`Used Package and Functions`
+```
+
+```{r lockfile}
+used_pgks <- parsedFile$`Used Package and Functions` %>%
+  transmute(package_name = str_extract(library, "(?<=package\\:).+"))
+
+temp_lockfile <- tempfile(fileext = ".lockfile")
+
+x <- renv::lockfile_create(
+  type = "custom",
+  packages = used_pgks
+)
+
+renv::lockfile_write(
+  lockfile = x,
+  file = temp_lockfile,
+  type = "custom",
+)
+
+readlines(temp_lockfile)
+```
+

From 634e5da8c5a73dfcaf2f2be54acb4d59c0fce510 Mon Sep 17 00:00:00 2001
From: Sam Parmar <107635309+parmsam-pfizer@users.noreply.github.com>
Date: Sun, 24 Sep 2023 20:18:14 -0400
Subject: [PATCH 2/2] update vignette with short sentences

---
 vignettes/generate-lockfile.Rmd | 19 +++++++++----------
 1 file changed, 9 insertions(+), 10 deletions(-)

diff --git a/vignettes/generate-lockfile.Rmd b/vignettes/generate-lockfile.Rmd
index 35f7310..3bdd46e 100644
--- a/vignettes/generate-lockfile.Rmd
+++ b/vignettes/generate-lockfile.Rmd
@@ -23,8 +23,9 @@ library(dplyr)
 library(renv)
 ```
 
+Axecute a script and get the logfile.
 
-```{r run-axecute, echo = FALSE}
+```{r run_axecute, echo = FALSE}
 scriptPath <- tempfile()
 
 logDir <- tempdir()
@@ -40,17 +41,17 @@ writeLines(
 filePath <- file.path(logDir, "log_out_parse")
 
 axecute(scriptPath, log_name = "log_out_parse", log_path = logDir)
-
-parsedFile <- read_log_file(filePath)
 ```
 
+Later on read (and parse) previous log file as list of objects. 
 
-```{r read-previous-logfile}
-# check that the log file can be parsed
-parsedFile$`Used Package and Functions`
+```{r read_logfile}
+parsedFile <- read_log_file(filePath)
 ```
 
-```{r lockfile}
+Create a renv lockfile based on the used packages mentioned in the logfile.
+
+```{r gen_lockfile}
 used_pgks <- parsedFile$`Used Package and Functions` %>%
   transmute(package_name = str_extract(library, "(?<=package\\:).+"))
 
@@ -58,7 +59,7 @@ temp_lockfile <- tempfile(fileext = ".lockfile")
 
 x <- renv::lockfile_create(
   type = "custom",
-  packages = used_pgks
+  packages = used_pgks$package_name
 )
 
 renv::lockfile_write(
@@ -66,7 +67,5 @@ renv::lockfile_write(
   file = temp_lockfile,
   type = "custom",
 )
-
-readlines(temp_lockfile)
 ```