From b5f1e470d712b9b645cef1f0522eed3ef131302e Mon Sep 17 00:00:00 2001
From: "Matthew J. Milner" <matterhorn103@proton.me>
Date: Tue, 12 Nov 2024 18:56:51 +0100
Subject: [PATCH] Build manually in normal fashion rather than using pre-made
 action

Signed-off-by: Matthew J. Milner <matterhorn103@proton.me>
---
 .github/workflows/flatpak.yml            | 43 +++++++++++++-----------
 flatpak/org.openchemistry.Avogadro2.yaml |  6 ++--
 2 files changed, 27 insertions(+), 22 deletions(-)

diff --git a/.github/workflows/flatpak.yml b/.github/workflows/flatpak.yml
index cc8d7ba9..93d3e58f 100644
--- a/.github/workflows/flatpak.yml
+++ b/.github/workflows/flatpak.yml
@@ -6,58 +6,61 @@ jobs:
   flatpak:
     name: "Flatpak"
     runs-on: ubuntu-latest
-    container:
-      image: bilelmoussaoui/flatpak-github-actions:kde-6.7
-      options: --privileged
 
     steps:
+    - name: Install dependencies
+      run: sudo apt update -qq && sudo apt install -y -qq flatpak flatpak-builder
+    
+    - name: Configure flatpak
+      run: flatpak remote-add --if-not-exists --user flathub https://dl.flathub.org/repo/flathub.flatpakrepo
+
     - name: Checkout openchemistry
       uses: actions/checkout@v4
       with:
         repository: openchemistry/openchemistry
         submodules: false
-        path: src
+        path: openchemistry
         
     - name: Checkout avogadroapp
       uses: actions/checkout@v4
       with:
-        path: src/avogadroapp
+        path: openchemistry/avogadroapp
         
     - name: Checkout avogadrolibs
       uses: actions/checkout@v4
       with:
         repository: openchemistry/avogadrolibs
-        path: src/avogadrolibs
+        path: openchemistry/avogadrolibs
 
     - name: Checkout i18n
       uses: actions/checkout@v4
       with:
         repository: openchemistry/avogadro-i18n
-        path: src/avogadro-i18n
+        path: openchemistry/avogadro-i18n
     
     - name: Checkout avogadrogenerators
       uses: actions/checkout@v4
       with:
         repository: openchemistry/avogenerators
-        path: src/avogadrogenerators
+        path: openchemistry/avogadrogenerators
 
     - name: Checkout crystals
       uses: actions/checkout@v4
       with:
         repository: openchemistry/crystals
-        path: src/crystals
+        path: openchemistry/crystals
 
     - name: Checkout fragments
       uses: actions/checkout@v4
       with:
         repository: openchemistry/fragments
-        path: src/fragments
+        path: openchemistry/fragments
 
     - name: Checkout molecules
       uses: actions/checkout@v4
       with:
         repository: openchemistry/molecules
-        path: src/molecules
+        path: openchemistry/molecules
 
     - name: Checkout Flathub shared-modules
       uses: actions/checkout@v4
@@ -65,21 +68,23 @@ jobs:
         repository: flathub/shared-modules
         path: shared-modules
 
-    - name: Setup tmate session
+    - name: Set up tmate session
       if: failure()
       uses: mxschmitt/action-tmate@v3
 
     - name: Move manifest
-      run: mv src/avogadroapp/flatpak/org.openchemistry.Avogadro2.yaml ./
+      run: mv openchemistry/avogadroapp/flatpak/org.openchemistry.Avogadro2.yaml ./
 
     - name: Build with flatpak-builder
-      uses: flatpak/flatpak-github-actions/flatpak-builder@v6
+      run: flatpak-builder --force-clean --user --install-deps-from=flathub --arch=x86_64 --default-branch=test --repo=repo builddir org.openchemistry.Avogadro2.yaml
+
+    - name: Create bundle
+      run: flatpak build-bundle repo Avogadro2.flatpak org.openchemistry.Avogadro2
+
+    - name: Upload bundle
+      uses: actions/upload-artifact@v4
       with:
-        bundle: avogadro2.flatpak
-        branch: nightly
-        manifest-path: org.openchemistry.Avogadro2.yaml
-        cache: false
-        cache-key: flatpak-builder-${{ github.sha }}
+        path: Avogadro2.flatpak
     
     - name: Cleanup
       if: ${{ always() }} # To ensure this step runs even when earlier steps fail
diff --git a/flatpak/org.openchemistry.Avogadro2.yaml b/flatpak/org.openchemistry.Avogadro2.yaml
index 1d9ed9d4..ef1ee5d8 100644
--- a/flatpak/org.openchemistry.Avogadro2.yaml
+++ b/flatpak/org.openchemistry.Avogadro2.yaml
@@ -1,5 +1,4 @@
 app-id: org.openchemistry.Avogadro2
-default-branch: nightly
 runtime: org.kde.Platform
 sdk: org.kde.Sdk
 runtime-version: "6.7"
@@ -48,9 +47,10 @@ modules:
     sources:
       # Avogadro stuff all already collected together as part of GitHub Actions
       # This means that if using this to build the Flatpak locally, the openchemistry repo and
-      # its submodules must be cloned into ./src in advance of running flatpak-builder with this manifest
+      # its submodules must be cloned into ./openchemistry in advance of running flatpak-builder
+      # with this manifest
       - type: dir
-        path: src
+        path: openchemistry
 
       # Now fetch third-party stuff where the source is expected in `openchemistry/thirdparty`
       # VTK