introducing rstudio addin for dso repro stage #19

DSchreyer · 2024-10-25T09:14:32Z

v0.5.1

New Features

Introduced the rstudio addin to dso repro the current stage

DSchreyer · 2024-10-25T09:24:42Z

local testing required

tschwarzl · 2024-10-25T09:36:23Z

R/addin.R

+    dvc_yaml_path <- file.path(stage_path, "dvc.yaml")
+
+    tryCatch({
+      message(glue::glue("Reproducing the current stage"))


Add to "#' @importFrom glue glue" for roxygen to resolve import dependencies

tschwarzl · 2024-10-25T09:37:03Z

R/addin.R

+      message(glue::glue("Report generated: {report_file}"))
+      message(glue::glue("Displaying report file: {report_file}"))
+      # Check the file extension and display in the viewer
+          rstudioapi::viewer(report_file)


import / importFrom with rstudioapi

technically not necessary when using ::.
Afaik the pre-commit checks also ensure that one does not forget to add it to DESCRIPTION

tschwarzl

Very nice.

I would like to like discuss an option to add
"dso repro stage" - with dependencies
"dso repro stage -s" - only single stage
"dso repro stage -f" - force.

grst · 2024-10-25T11:52:36Z

R/addin.R

+      message(glue::glue("Report generated: {report_file}"))
+      message(glue::glue("Displaying report file: {report_file}"))
+      # Check the file extension and display in the viewer
+          rstudioapi::viewer(report_file)


technically not necessary when using ::.
Afaik the pre-commit checks also ensure that one does not forget to add it to DESCRIPTION

CHANGELOG.md

grst · 2024-10-25T11:55:56Z

R/addin.R

+      result <- system2(DSO_EXEC,
+                        c("repro -s", shQuote(dvc_yaml_path)))
+      if (result != 0) {
+        stop("System command failed with status: {result}")


glue seems to be missing here

…im/dso-r into rstudio_addin

DSchreyer · 2024-11-05T12:08:45Z

This hooks will take care of running consistency checks and automatically 
syncing dvc.
Do you want to install the pre-commit hooks now? [y/n]: Aborted.```

pre commit hooks lead to error which is not identified and can not be resolved within rstudio and the current addin

grst · 2024-11-06T07:30:25Z

So do I get this right that not the actual hooks are the problem, but dso asking whether to install the hooks?

DSchreyer · 2024-11-06T10:16:11Z

So do I get this right that not the actual hooks are the problem, but dso asking whether to install the hooks?

correct. DSO asks to installl but the addin is not interactive and therefore it results in an error. When the hooks are installed or dso doesnt ask then it works normally

grst · 2024-11-06T10:25:31Z

ok, then I propose adding an ENV var or command line flag to the dso CLI to not ask that can be used from R

…im/dso-r into rstudio_addin

DSchreyer · 2024-11-07T09:13:19Z

[11/07/24 10:10:47] INFO Compiling a total of 29 config files.
[11/07/24 10:10:49] INFO Configuration compiled successfully.
INFO Running dvc repro -s <stagename>/dvc.yaml/dvc.yaml

Another issue arose: recursive dvc.yaml addition to path

DSchreyer · 2024-11-07T10:28:48Z

Fixed the issue named above and removed the show report function. The show report function froze the session when it was too large. Report can be opened manually inside Rstudio

grst

just two nitpicky things left; LGTM

grst · 2024-11-11T08:57:41Z

CHANGELOG.md

+
+### Fixes
+
+-   Removed ... in reload function


Suggested change

- Removed ... in reload function

- Removed `...` in reload function

grst · 2024-11-11T08:58:15Z

R/addin.R

+#' }
+dso_repro_stage_addin <- function() {
+  check_stage_here()
+  dvc_yaml_path <- stage_here("dvc.yaml")


dvc_yaml_path doesn't seem to be used?

introducing rstudio addin for dso repro stage

b9a2571

DSchreyer requested review from grst and tschwarzl October 25, 2024 09:14

changed docu based on warnings

266b803

tschwarzl reviewed Oct 25, 2024

View reviewed changes

updated stage addin; removed reload ... param

20be58c

grst reviewed Oct 25, 2024

View reviewed changes

DSchreyer and others added 4 commits November 4, 2024 10:48

included dso repro stage with dependencies

941bc91

pre-commit autofixes

8fc0020

styler

da67e1a

Merge branch 'rstudio_addin' of https://github.com/Boehringer-Ingelhe…

e472b57

…im/dso-r into rstudio_addin

updated addin functions for better usage

9171db1

pre-commit autofixes

813dc1b

DSchreyer and others added 3 commits November 6, 2024 12:01

updated addin; included repro function

f942af1

Merge branch 'rstudio_addin' of https://github.com/Boehringer-Ingelhe…

8a7f2c0

…im/dso-r into rstudio_addin

pre-commit autofixes

3a91971

grst mentioned this pull request Nov 6, 2024

ENV var or command line flag to skip pre-commit checks Boehringer-Ingelheim/dso#50

Closed

grst approved these changes Nov 6, 2024

View reviewed changes

fixed dvc.yaml error, removed show report

981881e

removed test_stage

0e0a0ad

DSchreyer requested a review from tschwarzl November 7, 2024 12:09

DSchreyer requested a review from grst November 7, 2024 12:09

DSchreyer and others added 2 commits November 8, 2024 08:02

Merge branch 'main' into rstudio_addin

fabf1c5

pre-commit autofixes

6290307

grst approved these changes Nov 11, 2024

View reviewed changes

changelog fix and dvc_yaml_path removal

8705472

DSchreyer merged commit 550d921 into main Nov 11, 2024
4 of 5 checks passed

DSchreyer deleted the rstudio_addin branch November 11, 2024 13:18

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introducing rstudio addin for dso repro stage #19

introducing rstudio addin for dso repro stage #19

DSchreyer commented Oct 25, 2024

DSchreyer commented Oct 25, 2024

tschwarzl Oct 25, 2024

tschwarzl Oct 25, 2024

grst Oct 25, 2024

tschwarzl left a comment

grst Oct 25, 2024

grst Oct 25, 2024

DSchreyer commented Nov 5, 2024

grst commented Nov 6, 2024

DSchreyer commented Nov 6, 2024

grst commented Nov 6, 2024

DSchreyer commented Nov 7, 2024

DSchreyer commented Nov 7, 2024

grst left a comment

grst Nov 11, 2024

grst Nov 11, 2024 •

edited

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	- Removed ... in reload function
	- Removed `...` in reload function

introducing rstudio addin for dso repro stage #19

introducing rstudio addin for dso repro stage #19

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DSchreyer commented Oct 25, 2024

v0.5.1

New Features

DSchreyer commented Oct 25, 2024

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DSchreyer commented Nov 5, 2024

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