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Fix update_datasets.yaml: remove incorrect working-directory and add safe.directory for container git#51

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Fix update_datasets.yaml: remove incorrect working-directory and add safe.directory for container git#51
jonthegeek merged 3 commits into
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Copilot AI commented May 5, 2026 •
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Two issues cause fatal: not in a git directory in the container job's "Commit" step.

Issue 1: working-directory: ${{ github.workspace }} evaluates to /github/workspace inside a container job, which is not mounted. This caused git commands to run from a path with no .git directory.

Issue 2 (root cause): actions/checkout writes the safe.directory entry to a temporary HOME (/__w/_temp/<uuid>/.gitconfig), but the container's actual HOME is /github/home. Git inside the container reads from /github/home/.gitconfig, which has no safe.directory entry. Since the repo files are owned by the runner user (uid 1001) while the container may run as a different user, git 2.35.2+ treats the repo as unsafe — surfacing as fatal: not in a git directory. This error existed even before the working-directory lines were added.

Changes

  • .github/workflows/update_datasets.yaml:
    • Remove working-directory: ${{ github.workspace }} from the "Update data" and "🚀 Commit" steps — the container's default workdir (/__w/ttmeta/ttmeta) is already the repo root.
    • Add git config --global --add safe.directory "$(pwd)" at the start of the "🚀 Commit" step, writing the safe.directory entry into the container's actual HOME so git trusts the working directory.

The "Update data" step silently tolerated the wrong directory because the R script uses here::here() to resolve paths; the shell git commands in the Commit step had no such fallback.

Copilot AI linked an issue May 5, 2026 that may be closed by this pull request
Fix update_datasets.yaml #50
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Copilot AI changed the title [WIP] Fix update_datasets.yaml workflow issue Fix update_datasets.yaml: remove incorrect working-directory in container job May 5, 2026
Copilot AI requested a review from jonthegeek May 5, 2026 13:53
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I added those lines on the advice of another agent because I was getting exactly the same error. Removing them will not fix the problem. We may indeed have to remove them, but there has to be something else causing the issue.

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Copilot AI commented May 5, 2026

I added those lines on the advice of another agent because I was getting exactly the same error. Removing them will not fix the problem. We may indeed have to remove them, but there has to be somethin...

You're right — I confirmed this by checking earlier failing runs (e.g., run 25378717920 / commit 12ffd652) which had the same fatal: not in a git directory error without the working-directory lines.

The actual root cause: actions/checkout writes the safe.directory entry to a temporary HOME (/__w/_temp/<uuid>/.gitconfig), but the container's actual HOME is /github/home. Git inside the container reads from /github/home/.gitconfig, which has no safe.directory entry. Since the repo files are owned by the runner user (uid 1001) while the container may run as a different user, git 2.35.2+ treats the repo as unsafe and refuses to use it — surfacing as fatal: not in a git directory.

Fix in commit 4ba932e:

  1. Keep the removal of working-directory: ${{ github.workspace }} (still correct — that expression evaluates to /github/workspace in container context, which isn't the repo path)
  2. Add git config --global --add safe.directory "$(pwd)" at the start of the Commit step to explicitly mark the working directory as trusted within the container's HOME context

Copilot AI changed the title Fix update_datasets.yaml: remove incorrect working-directory in container job Fix update_datasets.yaml: remove incorrect working-directory and add safe.directory for container git May 5, 2026
Copilot AI requested a review from jonthegeek May 5, 2026 14:21
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🌐 PR pkgdown deployed

This report was generated by this GitHub Actions run.

Last updated: 2026-05-05 14:31:19 UTC

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jonthegeek
jonthegeek approved these changes May 10, 2026
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Looks like this should work. We'll see!

@jonthegeek jonthegeek marked this pull request as ready for review May 10, 2026 14:52
@jonthegeek jonthegeek merged commit a2296bd into main May 10, 2026
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@jonthegeek jonthegeek deleted the copilot/fix-update-datasets-yaml branch May 10, 2026 14:52
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Fix update_datasets.yaml

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