Move to rv #3

gnoblet · 2025-12-31T09:59:08Z

No description provided.

…flow

… enhance Python setup

Copilot

Pull request overview

This pull request migrates the project's R package management from renv to rv, a newer package manager. The change includes new activation scripts, configuration files, and updates to the GitHub Actions workflow to support the rv-based dependency management system.

Key Changes

Replaced renv with rv package manager for R dependency management
Added rv wrapper functions and activation scripts for seamless integration
Updated CI/CD pipeline to install and configure rv in GitHub Actions
Migrated project configuration from renv.lock to rproject.toml format

Reviewed changes

Copilot reviewed 7 out of 9 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
`rv/scripts/rvr.R`	Wrapper functions providing R interface to rv CLI commands (summary, plan, sync, add)
`rv/scripts/activate.R`	Activation script that configures R library paths and repositories based on rv configuration
`rv/.gitignore`	Ignores the rv library directory from version control
`rv.lock`	Auto-generated lock file containing pinned package versions and dependencies
`rproject.toml`	New rv configuration file defining project dependencies and R version
`_quarto.yml`	Updated to exclude rv directory from Quarto rendering
`.github/workflows/quarto-publish.yml`	Updated workflow to install rv, restore packages, and configure library paths
`.Rprofile`	Replaced renv activation with rv activation scripts

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Copilot · 2026-01-01T15:54:15Z

.github/workflows/quarto-publish.yml

+        echo "R_LIBS_USER=$HOME/rv/library:$HOME/.local/lib/R/site-library" >> $GITHUB_ENV
+        echo "R_LIBS_SITE=$HOME/rv/library:$HOME/.local/lib/R/site-library" >> $GITHUB_ENV


The library path configuration is inconsistent between the step environment variable definition and the later override. Line 24 sets R_LIBS_USER to "$HOME/.rv/library:$HOME/.local/lib/R/site-library", but line 107 sets it to "$HOME/rv/library:$HOME/.local/lib/R/site-library" (missing the dot before "rv"). This inconsistency will cause the R library path to point to different directories, potentially causing package resolution failures.

Suggested change

echo "R_LIBS_USER=$HOME/rv/library:$HOME/.local/lib/R/site-library" >> $GITHUB_ENV

echo "R_LIBS_SITE=$HOME/rv/library:$HOME/.local/lib/R/site-library" >> $GITHUB_ENV

echo "R_LIBS_USER=$HOME/.rv/library:$HOME/.local/lib/R/site-library" >> $GITHUB_ENV

echo "R_LIBS_SITE=$HOME/.rv/library:$HOME/.local/lib/R/site-library" >> $GITHUB_ENV

Copilot · 2026-01-01T15:54:15Z

.github/workflows/quarto-publish.yml

+    # - name: Build Quarto website
      run: |
+        # export R_LIBS_USER="$HOME/.rv/library:$HOME/.local/lib/R/site-library"
+        # export R_LIBS_SITE="$HOME/.rv/library:$HOME/.local/lib/R/site-library"
        quarto render


The "Build Quarto website" step name is commented out but the actual run command is not commented. This creates a step without a name, which will make the GitHub Actions logs less clear and harder to debug. Either uncomment the name or add a new appropriate name for this step.

Copilot · 2026-01-01T15:54:16Z

.github/workflows/quarto-publish.yml

+    # - name: Check R library paths
+    #   run: Rscript -e '.libPaths()'
+
+    # # 3️⃣ Display the R_LIBS_USER variable
+    # - name: Print R_LIBS_USER
+    #   run: |
+    #     echo "R_HOME       = $R_HOME"
+    #     echo "R_LIBS_USER  = $R_LIBS_USER"
+    #     echo "R_LIBS_SITE  = $R_LIBS_SITE"
+
+    # - name: quarto check
+    #   run: |
+    #     quarto check
+
+    # - name: Print repository tree
+    #   run: |
+    #     echo "Repository tree (depth=3):"
+    #     if command -v tree >/dev/null 2>&1; then
+    #       tree -a -L 3
+    #     else
+    #       find . -maxdepth 3 -print
+    #     fi
+


Large blocks of commented-out debugging code should be removed before merging. These commented sections (lines 112-113, 117-139) appear to be temporary debugging steps that are no longer needed. Keeping them reduces code readability and makes the workflow harder to maintain. If these are needed for future debugging, consider documenting the approach in a separate file or issue.

Suggested change

# - name: Check R library paths

# run: Rscript -e '.libPaths()'

# # 3️⃣ Display the R_LIBS_USER variable

# - name: Print R_LIBS_USER

# run: |

# echo "R_HOME = $R_HOME"

# echo "R_LIBS_USER = $R_LIBS_USER"

# echo "R_LIBS_SITE = $R_LIBS_SITE"

# - name: quarto check

# run: |

# quarto check

# - name: Print repository tree

# run: |

# echo "Repository tree (depth=3):"

# if command -v tree >/dev/null 2>&1; then

# tree -a -L 3

# else

# find . -maxdepth 3 -print

# fi

Copilot · 2026-01-01T15:54:16Z

rv/scripts/rvr.R

+  args <- c(command, "-c", .rv$config_path)
+  res <- system2("rv", args, stdout = TRUE)
+  if (!is.null(attr(res, "status"))) {
+    warning(sprintf("failed to run `rv %s`, check your console for messages", paste(args, collapse = " ")))


The error message references an incorrect command format. The warning message shows "rv %s" but the actual command being executed uses "rv" followed by the arguments. The sprintf format should be "rv %s" with paste(command, collapse = " ") to show the actual command that failed, not "rv %s" with paste(args, collapse = " ") which includes the "-c" flag and config path that are added by the wrapper.

Suggested change

warning(sprintf("failed to run `rv %s`, check your console for messages", paste(args, collapse = " ")))

warning(sprintf("failed to run `rv %s`, check your console for messages", paste(command, collapse = " ")))

Copilot · 2026-01-01T15:54:16Z

.github/workflows/quarto-publish.yml

+    # ---- rv: install and restore project library ----
+    - name: Install rv (A2-ai)
+      run: |
+        curl -sSL https://raw.githubusercontent.com/A2-ai/rv/refs/heads/main/scripts/install.sh | bash


The installation script is sourced directly from the main branch without version pinning or checksum validation. This could lead to unexpected breaking changes if the installation script is updated. Consider pinning to a specific commit SHA or version tag for reproducibility and stability in the CI environment.

Suggested change

curl -sSL https://raw.githubusercontent.com/A2-ai/rv/refs/heads/main/scripts/install.sh | bash

curl -sSL https://raw.githubusercontent.com/A2-ai/rv/refs/tags/v0.1.0/scripts/install.sh | bash

Copilot · 2026-01-01T15:54:16Z

rv/scripts/activate.R

+			"WARNING: R version specified in config (%s) does not match session version (%s).
+rv library will not be activated until the issue is resolved. Entering safe mode...
+			",


The warning message uses inconsistent indentation and formatting. The multi-line string on lines 50-52 has irregular whitespace that will appear awkwardly in the console output. The message should use consistent indentation or be reformatted as a single line with proper formatting.

Suggested change

"WARNING: R version specified in config (%s) does not match session version (%s).

rv library will not be activated until the issue is resolved. Entering safe mode...

",

paste0(

"WARNING: R version specified in config (%s) does not match session version (%s).\n",

"rv library will not be activated until the issue is resolved. Entering safe mode...\n"

),

…ixes two-run issues

gnoblet added 5 commits December 31, 2025 10:54

Initiate rv

3817423

Review quarto GA

f992970

ci: bump R to 4.5.2 and configure rv paths/env in quarto-publish work…

78b7815

…flow

set R_LIBS

bea3a14

ci: update quarto-publish workflow to install system dependencies and…

9bbf6d3

… enhance Python setup

Copilot AI review requested due to automatic review settings January 1, 2026 15:50

Copilot started reviewing on behalf of gnoblet January 1, 2026 15:51 View session

Copilot AI reviewed Jan 1, 2026

View reviewed changes

gnoblet added 2 commits January 1, 2026 17:08

fix: enable building Quarto website by uncommenting the build step, f…

eb065b9

…ixes two-run issues

add quarto check

6673a46

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		echo "R_LIBS_USER=$HOME/rv/library:$HOME/.local/lib/R/site-library" >> $GITHUB_ENV
		echo "R_LIBS_SITE=$HOME/rv/library:$HOME/.local/lib/R/site-library" >> $GITHUB_ENV

	warning(sprintf("failed to run `rv %s`, check your console for messages", paste(args, collapse = " ")))
	warning(sprintf("failed to run `rv %s`, check your console for messages", paste(command, collapse = " ")))

	curl -sSL https://raw.githubusercontent.com/A2-ai/rv/refs/heads/main/scripts/install.sh \| bash
	curl -sSL https://raw.githubusercontent.com/A2-ai/rv/refs/tags/v0.1.0/scripts/install.sh \| bash

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gnoblet commented Dec 31, 2025

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Pull request overview

Key Changes

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