From 42d25184c85aa8deff9ac606adf8db01dd7f58f3 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 1 May 2026 18:43:14 +0000
Subject: [PATCH 1/2] ci: fix Apptainer install by dropping Launchpad PPA

Agent-Logs-Url: https://github.com/sequana/bioconvert/sessions/ca1c9a8e-e545-4209-8096-b3f648cb6682

Co-authored-by: cokelaer <778821+cokelaer@users.noreply.github.com>
---
 .github/workflows/apptainer.yml | 39 +++++++++------------------------
 1 file changed, 10 insertions(+), 29 deletions(-)

diff --git a/.github/workflows/apptainer.yml b/.github/workflows/apptainer.yml
index 4999d4c..3c521b4 100644
--- a/.github/workflows/apptainer.yml
+++ b/.github/workflows/apptainer.yml
@@ -28,41 +28,22 @@ 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
-        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
+
     # Checkout repository
     - name: Checkout repo
       uses: actions/checkout@v4

From 1ac31eea20087346255bb400d76c455bc322e09a Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 1 May 2026 18:43:42 +0000
Subject: [PATCH 2/2] ci: add fallback version and remove silent wget for
 Apptainer install

Agent-Logs-Url: https://github.com/sequana/bioconvert/sessions/ca1c9a8e-e545-4209-8096-b3f648cb6682

Co-authored-by: cokelaer <778821+cokelaer@users.noreply.github.com>
---
 .github/workflows/apptainer.yml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/apptainer.yml b/.github/workflows/apptainer.yml
index 3c521b4..3d19c76 100644
--- a/.github/workflows/apptainer.yml
+++ b/.github/workflows/apptainer.yml
@@ -40,7 +40,11 @@ jobs:
       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_${APPTAINER_VERSION}_amd64.deb"
+        if [ -z "${APPTAINER_VERSION}" ]; then
+          echo "Failed to detect Apptainer version from GitHub API; falling back to 1.3.6"
+          APPTAINER_VERSION="1.3.6"
+        fi
+        wget "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