From d64503a6f348b60ddc619b138d955acc325198fa Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 1 May 2026 19:12:14 +0000
Subject: [PATCH 1/2] ci: fix Apptainer install by dropping Launchpad PPA

Agent-Logs-Url: https://github.com/sequana/ribofinder/sessions/6a6f08a0-f2a7-4844-a37b-aba586ae84c3

Co-authored-by: cokelaer <778821+cokelaer@users.noreply.github.com>
---
 .github/workflows/apptainer.yml | 43 +++++++++++----------------------
 1 file changed, 14 insertions(+), 29 deletions(-)

diff --git a/.github/workflows/apptainer.yml b/.github/workflows/apptainer.yml
index 3542cf2..3c97cd0 100644
--- a/.github/workflows/apptainer.yml
+++ b/.github/workflows/apptainer.yml
@@ -28,41 +28,26 @@ jobs:
         sudo rm -rf /usr/share/dotnet
         sudo rm -rf "$AGENT_TOOLSDIRECTORY"
 
-    # Cache APT .deb packages
-    - name: Cache APT archives
-      uses: actions/cache@v3
-      with:
-        path: /var/cache/apt/archives
-        key: ${{ runner.os }}-apt-cache-v1
-
-    # Cache Apptainer installation
-    - name: Cache Apptainer install
-      id: cache-apptainer
-      uses: actions/cache@v3
-      with:
-        path: |
-          /usr/bin/apptainer
-          /usr/lib/apptainer
-          /etc/apptainer
-        key: ${{ runner.os }}-apptainer-v1
-
-    # Install Apptainer only if not cached
-    - name: Install Apptainer
-      if: steps.cache-apptainer.outputs.cache-hit != 'true'
-      run: |
-        sudo apt-get update
-        sudo apt-get install -y software-properties-common graphviz
-        sudo add-apt-repository -y ppa:apptainer/ppa
-        sudo apt-get update
-        sudo apt-get install -y apptainer
-
     # Cache Apptainer image cache (~/.apptainer/cache)
     - name: Cache Apptainer images
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ~/.apptainer/cache
         key: ${{ runner.os }}-apptainer-images-v1
 
+    # Install Apptainer from GitHub releases (avoids flaky Launchpad PPA)
+    - name: Install Apptainer
+      run: |
+        APPTAINER_VERSION=$(curl -s https://api.github.com/repos/apptainer/apptainer/releases/latest \
+          | grep '"tag_name"' | cut -d'"' -f4 | sed 's/v//')
+        wget -q "https://github.com/apptainer/apptainer/releases/download/v${APPTAINER_VERSION}/apptainer_${APPTAINER_VERSION}_amd64.deb"
+        sudo apt-get install -y "./apptainer_${APPTAINER_VERSION}_amd64.deb"
+        apptainer --version
+
+    # Install graphviz
+    - name: Install graphviz
+      run: sudo apt-get install -y graphviz
+
     # Checkout repository
     - name: Checkout repo
       uses: actions/checkout@v4

From 1efe48e394062e772ef2e7d971953cc770cf4556 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 1 May 2026 19:12:53 +0000
Subject: [PATCH 2/2] ci: add error handling, auth token, and cleanup to
 Apptainer install step

Agent-Logs-Url: https://github.com/sequana/ribofinder/sessions/6a6f08a0-f2a7-4844-a37b-aba586ae84c3

Co-authored-by: cokelaer <778821+cokelaer@users.noreply.github.com>
---
 .github/workflows/apptainer.yml | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/apptainer.yml b/.github/workflows/apptainer.yml
index 3c97cd0..a0aa78e 100644
--- a/.github/workflows/apptainer.yml
+++ b/.github/workflows/apptainer.yml
@@ -37,11 +37,19 @@ jobs:
 
     # Install Apptainer from GitHub releases (avoids flaky Launchpad PPA)
     - name: Install Apptainer
+      env:
+        GH_TOKEN: ${{ github.token }}
       run: |
-        APPTAINER_VERSION=$(curl -s https://api.github.com/repos/apptainer/apptainer/releases/latest \
+        APPTAINER_VERSION=$(curl -s -H "Authorization: Bearer ${GH_TOKEN}" \
+          https://api.github.com/repos/apptainer/apptainer/releases/latest \
           | grep '"tag_name"' | cut -d'"' -f4 | sed 's/v//')
+        if [ -z "${APPTAINER_VERSION}" ]; then
+          echo "ERROR: Could not determine Apptainer version" >&2
+          exit 1
+        fi
         wget -q "https://github.com/apptainer/apptainer/releases/download/v${APPTAINER_VERSION}/apptainer_${APPTAINER_VERSION}_amd64.deb"
         sudo apt-get install -y "./apptainer_${APPTAINER_VERSION}_amd64.deb"
+        rm -f "./apptainer_${APPTAINER_VERSION}_amd64.deb"
         apptainer --version
 
     # Install graphviz