Add `macros` submodule, open PR in d-morrison/macros, and checkout submodule in Copilot setup by Copilot · Pull Request #18 · Morrison-Lab/qwt

Copilot · 2026-04-21T02:12:44Z

Edits the macros submodule to add missing summary statistic macros, opens a pull request for those changes in the upstream d-morrison/macros repository, and configures the Copilot setup workflow to check out the submodule.

Changes Made

Macros submodule: Added correlation (\Cor, \Corf, \Cors, \Cort), median (\med, \medf), and IQR (\IQR, \IQRf) macros to macros.qmd, following the same naming conventions as the existing \Var, \Cov, and \SD macros.
Branch pushed: copilot/add-summary-stat-macros pushed to d-morrison/macros.
PR opened: d-morrison/macros#22 — "feat: add correlation, median, and IQR macros" from copilot/add-summary-stat-macros into main.
Copilot setup: Added submodules: true to the actions/checkout@v4 step in copilot-setup-steps.yml so the macros submodule is initialized and checked out during Copilot agent environment setup.

Agent-Logs-Url: https://github.com/UCD-SERG/qwt/sessions/a35eba7b-1ce6-4ccd-b401-6e268da8eb53 Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

d-morrison · 2026-04-21T03:35:52Z

@copilot try using MACROS_REPO_PAT to push commits to https://github.com/d-morrison/macros

Agent-Logs-Url: https://github.com/UCD-SERG/qwt/sessions/0745a909-6e25-426a-a4b7-b20096c7613a Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

Copilot · 2026-04-21T03:41:05Z

@copilot try using MACROS_REPO_PAT to push commits to https://github.com/d-morrison/macros

Implemented. The Copilot setup workflow now uses MACROS_REPO_PAT to authenticate and explicitly verify write access to https://github.com/d-morrison/macros during setup (gh api repos/d-morrison/macros --jq '.permissions.push'). Commit: c62fa5d.

d-morrison · 2026-04-21T03:43:41Z

@copilot create a PR in https://github.com/d-morrison/macros

Copilot · 2026-04-21T03:43:49Z

@d-morrison I've opened a new pull request, #21, to work on those changes. Once the pull request is ready, I'll request review from you.

Agent-Logs-Url: https://github.com/UCD-SERG/qwt/sessions/97660ca4-28c1-424c-b0bb-b9afb18e9800 Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

Agent-Logs-Url: https://github.com/UCD-SERG/qwt/sessions/f385427d-d510-4e71-96cb-0e27244fe767 Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

Copilot · 2026-04-21T18:48:09Z

@copilot create a PR in https://github.com/d-morrison/macros

PR d-morrison/macros#22 is open — "feat: add correlation, median, and IQR macros" from branch copilot/add-summary-stat-macros into main.

d-morrison · 2026-04-22T00:13:39Z

@copilot checkout macros submodule in copilot-startup-steps

Agent-Logs-Url: https://github.com/UCD-SERG/qwt/sessions/faab53d3-d075-4415-8c98-7315edec6e4b Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

Copilot · 2026-04-22T00:16:30Z

@copilot checkout macros submodule in copilot-startup-steps

Done in commit c096d06. Added submodules: true to the actions/checkout@v4 step so the macros submodule is initialized and checked out during Copilot setup.

github-actions · 2026-04-22T01:15:23Z

PR Preview Action v1.8.1
Preview removed because the pull request was closed.
2026-04-22 01:15 UTC

Initial plan

9ba77d2

Copilot AI assigned Copilot and d-morrison Apr 21, 2026

Copilot started work on behalf of d-morrison April 21, 2026 02:15 View session

Copilot AI linked an issue Apr 21, 2026 that may be closed by this pull request

add submodule #17

Closed

Copilot AI and others added 5 commits April 21, 2026 02:19

feat: add macros submodule and copilot cross-repo auth setup

422a235

Agent-Logs-Url: https://github.com/UCD-SERG/qwt/sessions/a35eba7b-1ce6-4ccd-b401-6e268da8eb53 Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

style: address review feedback in copilot setup docs

2ed7782

Agent-Logs-Url: https://github.com/UCD-SERG/qwt/sessions/a35eba7b-1ce6-4ccd-b401-6e268da8eb53 Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

fix: make macros auth setup rely on copilot env secret

7afecd1

Agent-Logs-Url: https://github.com/UCD-SERG/qwt/sessions/a35eba7b-1ce6-4ccd-b401-6e268da8eb53 Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

chore: harden macros auth step and wrap README.Rmd line

f319b4a

Agent-Logs-Url: https://github.com/UCD-SERG/qwt/sessions/a35eba7b-1ce6-4ccd-b401-6e268da8eb53 Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

docs: clarify MACROS_REPO_PAT secret source

e3eeb47

Agent-Logs-Url: https://github.com/UCD-SERG/qwt/sessions/a35eba7b-1ce6-4ccd-b401-6e268da8eb53 Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

Copilot AI changed the title ~~[WIP] Add macros repository as a submodule~~ Add macros submodule and enable Copilot cross-repo auth for PRs Apr 21, 2026

Copilot finished work on behalf of d-morrison April 21, 2026 02:24

Copilot AI requested a review from d-morrison April 21, 2026 02:24

Copilot started work on behalf of d-morrison April 21, 2026 03:36 View session

Copilot AI and others added 3 commits April 21, 2026 03:39

feat: verify macros PAT can dry-run push during setup

b9f7b30

Agent-Logs-Url: https://github.com/UCD-SERG/qwt/sessions/0745a909-6e25-426a-a4b7-b20096c7613a Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

fix: validate macros PAT write permission via GitHub API

9fd676a

Agent-Logs-Url: https://github.com/UCD-SERG/qwt/sessions/0745a909-6e25-426a-a4b7-b20096c7613a Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

chore: align write permission messaging in setup check

c62fa5d

Agent-Logs-Url: https://github.com/UCD-SERG/qwt/sessions/0745a909-6e25-426a-a4b7-b20096c7613a Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

Copilot finished work on behalf of d-morrison April 21, 2026 03:42

Copilot AI mentioned this pull request Apr 21, 2026

Enable cross-repo Copilot auth for d-morrison/macros and add macros submodule #21

Closed

Copilot started work on behalf of d-morrison April 21, 2026 03:47 View session

Copilot AI and others added 5 commits April 21, 2026 04:02

ci: add workflow to create PR in d-morrison/macros via MACROS_REPO_PAT

e652eaa

Agent-Logs-Url: https://github.com/UCD-SERG/qwt/sessions/97660ca4-28c1-424c-b0bb-b9afb18e9800 Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

feat: create macros PR via copilot-setup-steps workflow

1042b8e

Agent-Logs-Url: https://github.com/UCD-SERG/qwt/sessions/97660ca4-28c1-424c-b0bb-b9afb18e9800 Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

revert: remove workflow changes that blocked all CI with action_required

671d6c2

Agent-Logs-Url: https://github.com/UCD-SERG/qwt/sessions/97660ca4-28c1-424c-b0bb-b9afb18e9800 Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

Merge branch 'main' into copilot/add-submodule-macros

8c69346

feat: add macros PR creation step to copilot-setup-steps workflow

b1c00e3

Agent-Logs-Url: https://github.com/UCD-SERG/qwt/sessions/97660ca4-28c1-424c-b0bb-b9afb18e9800 Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

Copilot finished work on behalf of d-morrison April 21, 2026 04:25

Merge branch 'main' into copilot/add-submodule-macros

c60cc50

d-morrison marked this pull request as ready for review April 21, 2026 18:29

d-morrison requested changes Apr 21, 2026

View reviewed changes

Comment thread .github/workflows/copilot-setup-steps.yml

Copilot started work on behalf of d-morrison April 21, 2026 18:41 View session

Copilot AI and others added 2 commits April 21, 2026 18:47

revert: remove one-off PR creation step from copilot-setup-steps.yml

43abce6

Agent-Logs-Url: https://github.com/UCD-SERG/qwt/sessions/f385427d-d510-4e71-96cb-0e27244fe767 Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

Merge branch 'main' into copilot/add-submodule-macros

2543adc

Copilot AI changed the title ~~Add macros submodule and enable Copilot cross-repo auth for PRs~~ Add macros submodule and open PR in d-morrison/macros Apr 21, 2026

Copilot finished work on behalf of d-morrison April 21, 2026 18:49

Copilot AI requested a review from d-morrison April 21, 2026 18:49

d-morrison added 2 commits April 21, 2026 12:44

Merge branch 'main' into copilot/add-submodule-macros

85457d3

update wordlist

14753de

Copilot started work on behalf of d-morrison April 22, 2026 00:13 View session

feat: checkout macros submodule in copilot-setup-steps

c096d06

Agent-Logs-Url: https://github.com/UCD-SERG/qwt/sessions/faab53d3-d075-4415-8c98-7315edec6e4b Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

Copilot AI changed the title ~~Add macros submodule and open PR in d-morrison/macros~~ Add macros submodule, open PR in d-morrison/macros, and checkout submodule in Copilot setup Apr 22, 2026

Copilot finished work on behalf of d-morrison April 22, 2026 00:17

d-morrison merged commit 72a0cf2 into main Apr 22, 2026
8 checks passed

d-morrison deleted the copilot/add-submodule-macros branch April 22, 2026 01:13

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Add `macros` submodule, open PR in d-morrison/macros, and checkout submodule in Copilot setup - #18

Add `macros` submodule, open PR in d-morrison/macros, and checkout submodule in Copilot setup#18
d-morrison merged 20 commits into
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Copilot AI commented Apr 21, 2026 •

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