From 9588d0f560d0985a68f016ee74e5c53e99b2ee3a Mon Sep 17 00:00:00 2001
From: Nik <192305627+ntoulemonde@users.noreply.github.com>
Date: Wed, 17 Jun 2026 17:22:53 +0200
Subject: [PATCH 01/20] update checkout version
---
.github/workflows/preview.yaml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/.github/workflows/preview.yaml b/.github/workflows/preview.yaml
index 3f8cfd7a..8eeaffcf 100644
--- a/.github/workflows/preview.yaml
+++ b/.github/workflows/preview.yaml
@@ -12,7 +12,7 @@ jobs:
pull-requests: write
steps:
- name: Check out repository
- uses: actions/checkout@v4
+ uses: actions/checkout@v6
- name: Install R
uses: r-lib/actions/setup-r@v2
From 020c9e85e5f85f61e091853c3f4fcce762771edc Mon Sep 17 00:00:00 2001
From: Nik <192305627+ntoulemonde@users.noreply.github.com>
Date: Wed, 17 Jun 2026 17:38:29 +0200
Subject: [PATCH 02/20] no CNAME
---
.github/workflows/preview.yaml | 4 ++++
1 file changed, 4 insertions(+)
diff --git a/.github/workflows/preview.yaml b/.github/workflows/preview.yaml
index 8eeaffcf..27d8cc78 100644
--- a/.github/workflows/preview.yaml
+++ b/.github/workflows/preview.yaml
@@ -27,6 +27,10 @@ jobs:
source ~/.bashrc
rv sync
+ - name: Don't publish CNAME for preview
+ run: |
+ rm CNAME
+
- name: Set up Quarto environment
uses: quarto-dev/quarto-actions/setup@v2
From dfa1e7062c6dbbc944a9e70e3b776c81f9a475c8 Mon Sep 17 00:00:00 2001
From: Nik <192305627+ntoulemonde@users.noreply.github.com>
Date: Wed, 17 Jun 2026 17:56:22 +0200
Subject: [PATCH 03/20] with docker
---
.github/workflows/preview.yaml | 12 ++++++++----
1 file changed, 8 insertions(+), 4 deletions(-)
diff --git a/.github/workflows/preview.yaml b/.github/workflows/preview.yaml
index 27d8cc78..0c2e2bab 100644
--- a/.github/workflows/preview.yaml
+++ b/.github/workflows/preview.yaml
@@ -10,14 +10,18 @@ jobs:
permissions:
contents: read
pull-requests: write
+ container:
+ image: inseefrlab/onyxia-r-minimal:4.6.0
+ volumes:
+ - /tmp/data:/data
steps:
- name: Check out repository
uses: actions/checkout@v6
- - name: Install R
- uses: r-lib/actions/setup-r@v2
- with:
- r-version: '4.6'
+ # - name: Install R
+ # uses: r-lib/actions/setup-r@v2
+ # with:
+ # r-version: '4.6'
- name: Install dependencies
run: |
From 78e275e41a324e16b90d44d2c661f4eaa8c5b165 Mon Sep 17 00:00:00 2001
From: Nik <192305627+ntoulemonde@users.noreply.github.com>
Date: Wed, 17 Jun 2026 17:57:26 +0200
Subject: [PATCH 04/20] typo tag container
---
.github/workflows/preview.yaml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/.github/workflows/preview.yaml b/.github/workflows/preview.yaml
index 0c2e2bab..b5e0f665 100644
--- a/.github/workflows/preview.yaml
+++ b/.github/workflows/preview.yaml
@@ -11,7 +11,7 @@ jobs:
contents: read
pull-requests: write
container:
- image: inseefrlab/onyxia-r-minimal:4.6.0
+ image: inseefrlab/onyxia-r-minimal:r4.6.0
volumes:
- /tmp/data:/data
steps:
From 5cf395d0ada35313c1af786eaa239292208dc6c6 Mon Sep 17 00:00:00 2001
From: Nik <192305627+ntoulemonde@users.noreply.github.com>
Date: Wed, 17 Jun 2026 18:03:40 +0200
Subject: [PATCH 05/20] with admin for container
---
.github/workflows/preview.yaml | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/.github/workflows/preview.yaml b/.github/workflows/preview.yaml
index b5e0f665..4c0a6885 100644
--- a/.github/workflows/preview.yaml
+++ b/.github/workflows/preview.yaml
@@ -12,8 +12,7 @@ jobs:
pull-requests: write
container:
image: inseefrlab/onyxia-r-minimal:r4.6.0
- volumes:
- - /tmp/data:/data
+ options: --user root # Force root user
steps:
- name: Check out repository
uses: actions/checkout@v6
From eff90059ca8253922e795e4dadd85e64b4a2dc1c Mon Sep 17 00:00:00 2001
From: Nik <192305627+ntoulemonde@users.noreply.github.com>
Date: Wed, 17 Jun 2026 20:18:27 +0200
Subject: [PATCH 06/20] no source
---
.github/workflows/preview.yaml | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/.github/workflows/preview.yaml b/.github/workflows/preview.yaml
index 4c0a6885..cf49aafe 100644
--- a/.github/workflows/preview.yaml
+++ b/.github/workflows/preview.yaml
@@ -26,8 +26,8 @@ jobs:
run: |
sudo ./docker/dependencies.sh
curl -sSL https://raw.githubusercontent.com/A2-ai/rv/refs/heads/main/scripts/install.sh | bash
- export PATH="~/.local/bin:$PATH"
- source ~/.bashrc
+ export PATH="$HOME/.local/bin:$PATH" # Use $HOME instead of ~ for reliability
+ . ~/.bashrc
rv sync
- name: Don't publish CNAME for preview
From 310889488b4b7c15cce8ab4afc697b34e6638d62 Mon Sep 17 00:00:00 2001
From: Nik <192305627+ntoulemonde@users.noreply.github.com>
Date: Wed, 17 Jun 2026 21:02:14 +0200
Subject: [PATCH 07/20] fix permissions bot
---
.github/workflows/preview.yaml | 7 +------
1 file changed, 1 insertion(+), 6 deletions(-)
diff --git a/.github/workflows/preview.yaml b/.github/workflows/preview.yaml
index cf49aafe..17edeeba 100644
--- a/.github/workflows/preview.yaml
+++ b/.github/workflows/preview.yaml
@@ -8,7 +8,7 @@ jobs:
build-preview:
runs-on: ubuntu-latest
permissions:
- contents: read
+ contents: write
pull-requests: write
container:
image: inseefrlab/onyxia-r-minimal:r4.6.0
@@ -17,11 +17,6 @@ jobs:
- name: Check out repository
uses: actions/checkout@v6
- # - name: Install R
- # uses: r-lib/actions/setup-r@v2
- # with:
- # r-version: '4.6'
-
- name: Install dependencies
run: |
sudo ./docker/dependencies.sh
From 2a207d3db6584fd6351f6cf56dbeda0f31b09355 Mon Sep 17 00:00:00 2001
From: Nik <192305627+ntoulemonde@users.noreply.github.com>
Date: Wed, 17 Jun 2026 22:04:53 +0200
Subject: [PATCH 08/20] with concurrency
---
.github/workflows/preview.yaml | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/.github/workflows/preview.yaml b/.github/workflows/preview.yaml
index 17edeeba..30eb7539 100644
--- a/.github/workflows/preview.yaml
+++ b/.github/workflows/preview.yaml
@@ -4,12 +4,14 @@ on:
name: Quarto Preview
+concurrency:
+ group: ${{ github.workflow }}-${{ github.ref }}
+
jobs:
build-preview:
runs-on: ubuntu-latest
permissions:
contents: write
- pull-requests: write
container:
image: inseefrlab/onyxia-r-minimal:r4.6.0
options: --user root # Force root user
From c52adad974608ae59102dfcfb64ca46e8e338f23 Mon Sep 17 00:00:00 2001
From: Nik <192305627+ntoulemonde@users.noreply.github.com>
Date: Wed, 17 Jun 2026 22:08:07 +0200
Subject: [PATCH 09/20] update render site
---
.github/workflows/preview.yaml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/.github/workflows/preview.yaml b/.github/workflows/preview.yaml
index 30eb7539..ca6cc22b 100644
--- a/.github/workflows/preview.yaml
+++ b/.github/workflows/preview.yaml
@@ -41,7 +41,7 @@ jobs:
uses: peaceiris/actions-gh-pages@v3
with:
github_token: ${{ secrets.GITHUB_TOKEN }}
- publish_dir: ./_site
+ publish_dir: ./_public
destination_dir: previews/pr-${{ github.event.pull_request.number }}
keep_files: true
From d091de6ded25b087d4611b939ef215f4d21e9b6a Mon Sep 17 00:00:00 2001
From: Nik <192305627+ntoulemonde@users.noreply.github.com>
Date: Wed, 17 Jun 2026 22:16:11 +0200
Subject: [PATCH 10/20] update concurrency
---
.github/workflows/preview.yaml | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/.github/workflows/preview.yaml b/.github/workflows/preview.yaml
index ca6cc22b..c6f7ca32 100644
--- a/.github/workflows/preview.yaml
+++ b/.github/workflows/preview.yaml
@@ -5,7 +5,8 @@ on:
name: Quarto Preview
concurrency:
- group: ${{ github.workflow }}-${{ github.ref }}
+ group: ${{ github.workflow }}-pr-${{ github.event.pull_request.number }} # Unique Quarto Preview per PR
+ cancel-in-progress: true
jobs:
build-preview:
From d4453bf1ce067c803120eaa4256770b9de2c8673 Mon Sep 17 00:00:00 2001
From: Nik <192305627+ntoulemonde@users.noreply.github.com>
Date: Wed, 17 Jun 2026 22:23:03 +0200
Subject: [PATCH 11/20] update permissions to write comment
---
.github/workflows/preview.yaml | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/.github/workflows/preview.yaml b/.github/workflows/preview.yaml
index c6f7ca32..355fbaa6 100644
--- a/.github/workflows/preview.yaml
+++ b/.github/workflows/preview.yaml
@@ -12,7 +12,8 @@ jobs:
build-preview:
runs-on: ubuntu-latest
permissions:
- contents: write
+ contents: write # For pushing to gh-pages branch
+ pull-requests: write # For permissions to write comments on PRs
container:
image: inseefrlab/onyxia-r-minimal:r4.6.0
options: --user root # Force root user
From 952860a680b10c0b6f58c9e418ab0d5d112d7bda Mon Sep 17 00:00:00 2001
From: Nik <192305627+ntoulemonde@users.noreply.github.com>
Date: Wed, 17 Jun 2026 22:25:59 +0200
Subject: [PATCH 12/20] with delete preview when closed
---
.github/workflows/preview.yaml | 28 ++++++++++++++++++++++++++++
1 file changed, 28 insertions(+)
diff --git a/.github/workflows/preview.yaml b/.github/workflows/preview.yaml
index 355fbaa6..47dae5fe 100644
--- a/.github/workflows/preview.yaml
+++ b/.github/workflows/preview.yaml
@@ -10,6 +10,7 @@ concurrency:
jobs:
build-preview:
+ if: github.event.action != 'closed' # If closing the PR, no publishing
runs-on: ubuntu-latest
permissions:
contents: write # For pushing to gh-pages branch
@@ -59,3 +60,30 @@ jobs:
repo: context.repo.repo,
body: `🔍 Preview deployed! View it here: [PR #${pr_number} Preview](${preview_url})`
});
+
+# For this workflow only
+ delete-preview:
+ if: github.event.action == 'closed' # Only run when PR is closed
+ runs-on: ubuntu-latest
+ steps:
+ - name: Check out repository
+ uses: actions/checkout@v6
+ with:
+ fetch-depth: 0 # To enable full access to Git repo
+ ref: ${{ github.event.pull_request.head.ref }} # Reference of the commit to checkout to. To ensure it's the one of the PR
+ repository: ${{github.event.pull_request.head.repo.full_name}} # Reference to the branch to checkout to. Useful with PR from forks
+
+ - name: Remove preview
+ id: remove-preview
+ uses: rossjrw/pr-preview-action@v1.8.1
+ with:
+ action: remove
+ token: ${{ secrets.DEPLOY_GH_PAGES_TOKEN }} # Uses a token to allow preview from forks
+
+ - name: Comment PR that preview was removed
+ uses: marocchino/sticky-pull-request-comment@v3
+ with:
+ header: pr-preview
+ message: |
+ Preview removed because the pull request was closed.
+ ${{ steps.remove-preview.outputs.action-start-time }}
\ No newline at end of file
From 5805076b01176b5174f9c08a369f230aba7cf121 Mon Sep 17 00:00:00 2001
From: Nik <192305627+ntoulemonde@users.noreply.github.com>
Date: Wed, 17 Jun 2026 22:49:08 +0200
Subject: [PATCH 13/20] triggered when PR is closed
---
.github/workflows/preview.yaml | 5 +++++
1 file changed, 5 insertions(+)
diff --git a/.github/workflows/preview.yaml b/.github/workflows/preview.yaml
index 47dae5fe..517d7a69 100644
--- a/.github/workflows/preview.yaml
+++ b/.github/workflows/preview.yaml
@@ -1,5 +1,10 @@
on:
pull_request:
+ types:
+ - opened
+ - reopened
+ - synchronize # When the ref of the branch is updated (= commit to the branch to merge)
+ - closed # Including closed to remove preview when PR is closed.
branches: main
name: Quarto Preview
From c69ee03cca77545a60958ae508a9cee6ff93014b Mon Sep 17 00:00:00 2001
From: Nik <192305627+ntoulemonde@users.noreply.github.com>
Date: Wed, 17 Jun 2026 22:51:51 +0200
Subject: [PATCH 14/20] update comment to sticky comment - to avoid multiple
comment
---
.github/workflows/preview.yaml | 18 +++++++-----------
1 file changed, 7 insertions(+), 11 deletions(-)
diff --git a/.github/workflows/preview.yaml b/.github/workflows/preview.yaml
index 517d7a69..5c7aa9f3 100644
--- a/.github/workflows/preview.yaml
+++ b/.github/workflows/preview.yaml
@@ -53,18 +53,14 @@ jobs:
destination_dir: previews/pr-${{ github.event.pull_request.number }}
keep_files: true
- - name: Comment PR with preview link
- uses: actions/github-script@v7
+ - name: Comment PR (custom)
+ uses: marocchino/sticky-pull-request-comment@v3
with:
- script: |
- const pr_number = context.issue.number;
- const preview_url = `https://${{ github.repository_owner }}.github.io/utilitR/previews/pr-${pr_number}/`;
- github.rest.issues.createComment({
- issue_number: context.issue.number,
- owner: context.repo.owner,
- repo: context.repo.repo,
- body: `🔍 Preview deployed! View it here: [PR #${pr_number} Preview](${preview_url})`
- });
+ header: pr-preview
+ message: |
+ :rocket: View preview at
${{ steps.deploy-preview.outputs.preview-url }}
+ Built to branch gh-pages at ${{ steps.deploy-preview.outputs.action-start-time }}.
Preview will be ready when the GitHub Pages deployment is complete.
+
# For this workflow only
delete-preview:
From 31f64deefc4711abbb6e41e56b7aa2f72c3eeeb2 Mon Sep 17 00:00:00 2001
From: Nik <192305627+ntoulemonde@users.noreply.github.com>
Date: Wed, 17 Jun 2026 22:55:33 +0200
Subject: [PATCH 15/20] no mc and lib dependancies
---
.github/workflows/preview.yaml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/.github/workflows/preview.yaml b/.github/workflows/preview.yaml
index 5c7aa9f3..d23ea808 100644
--- a/.github/workflows/preview.yaml
+++ b/.github/workflows/preview.yaml
@@ -29,7 +29,7 @@ jobs:
- name: Install dependencies
run: |
- sudo ./docker/dependencies.sh
+ # sudo ./docker/dependencies.sh
curl -sSL https://raw.githubusercontent.com/A2-ai/rv/refs/heads/main/scripts/install.sh | bash
export PATH="$HOME/.local/bin:$PATH" # Use $HOME instead of ~ for reliability
. ~/.bashrc
From 91dc9c5886e9568e6b23f61fe380e96923a66120 Mon Sep 17 00:00:00 2001
From: Nik <192305627+ntoulemonde@users.noreply.github.com>
Date: Thu, 18 Jun 2026 09:54:00 +0200
Subject: [PATCH 16/20] update token permissions and rm checkout
---
.github/workflows/preview.yaml | 23 ++++++++++++-----------
1 file changed, 12 insertions(+), 11 deletions(-)
diff --git a/.github/workflows/preview.yaml b/.github/workflows/preview.yaml
index d23ea808..ac589db4 100644
--- a/.github/workflows/preview.yaml
+++ b/.github/workflows/preview.yaml
@@ -32,7 +32,7 @@ jobs:
# sudo ./docker/dependencies.sh
curl -sSL https://raw.githubusercontent.com/A2-ai/rv/refs/heads/main/scripts/install.sh | bash
export PATH="$HOME/.local/bin:$PATH" # Use $HOME instead of ~ for reliability
- . ~/.bashrc
+ . ~/.bashrc # no source command for this container, so use . instead
rv sync
- name: Don't publish CNAME for preview
@@ -64,22 +64,23 @@ jobs:
# For this workflow only
delete-preview:
- if: github.event.action == 'closed' # Only run when PR is closed
+ if: github.event.action == 'closed'
runs-on: ubuntu-latest
+ permissions:
+ contents: write # Required for gh-pages pushes
steps:
- - name: Check out repository
- uses: actions/checkout@v6
- with:
- fetch-depth: 0 # To enable full access to Git repo
- ref: ${{ github.event.pull_request.head.ref }} # Reference of the commit to checkout to. To ensure it's the one of the PR
- repository: ${{github.event.pull_request.head.repo.full_name}} # Reference to the branch to checkout to. Useful with PR from forks
-
- name: Remove preview
- id: remove-preview
uses: rossjrw/pr-preview-action@v1.8.1
with:
action: remove
- token: ${{ secrets.DEPLOY_GH_PAGES_TOKEN }} # Uses a token to allow preview from forks
+ token: ${{ secrets.GITHUB_TOKEN }}
+ deploy-repository: ${{ github.repository }}
+ preview-branch: gh-pages
+ umbrella-dir: previews # Match your deploy dir (e.g., "previews/pr-1")
+ env:
+ DEPLOY_REPO: ${{ github.repository }}
+ DEPLOY_BRANCH: gh-pages
+ DEPLOY_TOKEN: ${{ secrets.GITHUB_TOKEN }}
- name: Comment PR that preview was removed
uses: marocchino/sticky-pull-request-comment@v3
From 71d587a191ab04d90c1e604eccc8315158e00935 Mon Sep 17 00:00:00 2001
From: Nik <192305627+ntoulemonde@users.noreply.github.com>
Date: Thu, 18 Jun 2026 09:57:57 +0200
Subject: [PATCH 17/20] fix
---
.github/workflows/preview.yaml | 19 ++++++++++---------
1 file changed, 10 insertions(+), 9 deletions(-)
diff --git a/.github/workflows/preview.yaml b/.github/workflows/preview.yaml
index ac589db4..c87642a6 100644
--- a/.github/workflows/preview.yaml
+++ b/.github/workflows/preview.yaml
@@ -64,23 +64,24 @@ jobs:
# For this workflow only
delete-preview:
- if: github.event.action == 'closed'
+ if: github.event.action == 'closed' # Only run when PR is closed
runs-on: ubuntu-latest
permissions:
contents: write # Required for gh-pages pushes
steps:
+ - name: Check out repository
+ uses: actions/checkout@v6
+ with:
+ fetch-depth: 0 # To enable full access to Git repo
+ ref: ${{ github.event.pull_request.head.ref }} # Reference of the commit to checkout to. To ensure it's the one of the PR
+ repository: ${{github.event.pull_request.head.repo.full_name}} # Reference to the branch to checkout to. Useful with PR from forks
+
- name: Remove preview
+ id: remove-preview
uses: rossjrw/pr-preview-action@v1.8.1
with:
action: remove
- token: ${{ secrets.GITHUB_TOKEN }}
- deploy-repository: ${{ github.repository }}
- preview-branch: gh-pages
- umbrella-dir: previews # Match your deploy dir (e.g., "previews/pr-1")
- env:
- DEPLOY_REPO: ${{ github.repository }}
- DEPLOY_BRANCH: gh-pages
- DEPLOY_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+ token: ${{ secrets.GITHUB_TOKEN }}
- name: Comment PR that preview was removed
uses: marocchino/sticky-pull-request-comment@v3
From 4c5ba7e4e0debee8cdeb49950ee7f1a5aa75851b Mon Sep 17 00:00:00 2001
From: Nik <192305627+ntoulemonde@users.noreply.github.com>
Date: Thu, 18 Jun 2026 10:01:44 +0200
Subject: [PATCH 18/20] fix sticky comment
---
.github/workflows/preview.yaml | 1 +
1 file changed, 1 insertion(+)
diff --git a/.github/workflows/preview.yaml b/.github/workflows/preview.yaml
index c87642a6..650543bc 100644
--- a/.github/workflows/preview.yaml
+++ b/.github/workflows/preview.yaml
@@ -68,6 +68,7 @@ jobs:
runs-on: ubuntu-latest
permissions:
contents: write # Required for gh-pages pushes
+ pull-requests: write # Required to comment PR
steps:
- name: Check out repository
uses: actions/checkout@v6
From 68601c07d9b8d775add6644010f6769cd0db758a Mon Sep 17 00:00:00 2001
From: Nik <192305627+ntoulemonde@users.noreply.github.com>
Date: Thu, 18 Jun 2026 10:16:27 +0200
Subject: [PATCH 19/20] with correct dir to delete previews
---
.github/workflows/preview.yaml | 1 +
1 file changed, 1 insertion(+)
diff --git a/.github/workflows/preview.yaml b/.github/workflows/preview.yaml
index 650543bc..9647bb6a 100644
--- a/.github/workflows/preview.yaml
+++ b/.github/workflows/preview.yaml
@@ -82,6 +82,7 @@ jobs:
uses: rossjrw/pr-preview-action@v1.8.1
with:
action: remove
+ umbrella-dir: previews # <-- Match your deploy directory
token: ${{ secrets.GITHUB_TOKEN }}
- name: Comment PR that preview was removed
From 81f62ab81adf7a4658bf989448bd21189bb767c6 Mon Sep 17 00:00:00 2001
From: Nik <192305627+ntoulemonde@users.noreply.github.com>
Date: Thu, 18 Jun 2026 10:23:00 +0200
Subject: [PATCH 20/20] typos comment previews
---
.github/workflows/preview.yaml | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/.github/workflows/preview.yaml b/.github/workflows/preview.yaml
index 9647bb6a..3b2075af 100644
--- a/.github/workflows/preview.yaml
+++ b/.github/workflows/preview.yaml
@@ -29,7 +29,6 @@ jobs:
- name: Install dependencies
run: |
- # sudo ./docker/dependencies.sh
curl -sSL https://raw.githubusercontent.com/A2-ai/rv/refs/heads/main/scripts/install.sh | bash
export PATH="$HOME/.local/bin:$PATH" # Use $HOME instead of ~ for reliability
. ~/.bashrc # no source command for this container, so use . instead
@@ -82,7 +81,7 @@ jobs:
uses: rossjrw/pr-preview-action@v1.8.1
with:
action: remove
- umbrella-dir: previews # <-- Match your deploy directory
+ umbrella-dir: previews
token: ${{ secrets.GITHUB_TOKEN }}
- name: Comment PR that preview was removed