From b716cd64dd571619c4c1c91aac24dd6561a25180 Mon Sep 17 00:00:00 2001
From: Samuel Wein <sam@samwein.com>
Date: Fri, 10 Nov 2023 16:23:53 +0100
Subject: [PATCH 01/24] Update openms_ci_matrix_full.yml

---
 .github/workflows/openms_ci_matrix_full.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/openms_ci_matrix_full.yml b/.github/workflows/openms_ci_matrix_full.yml
index d92167ab2e3..a22e9576d2e 100644
--- a/.github/workflows/openms_ci_matrix_full.yml
+++ b/.github/workflows/openms_ci_matrix_full.yml
@@ -425,7 +425,7 @@ jobs:
           mkdir -p ~/.ssh/
           echo "$PASS" > ~/.ssh/private.key
           sudo chmod 600 ~/.ssh/private.key
-#          rsync --progress -avz -e "ssh -i ~/.ssh/private.key -o StrictHostKeyChecking=no" $GITHUB_WORKSPACE/* "$USER@$HOST:/OpenMSInstaller/${folder}"
+          rsync --progress -avz -e "ssh -i ~/.ssh/private.key -o StrictHostKeyChecking=no" $GITHUB_WORKSPACE/* "$USER@$HOST:/OpenMSInstaller/${folder}"
 
         # TODO create softlinks to latest nightly
         # TODO create and upload file hashes, at least for release candidate
@@ -613,4 +613,4 @@ jobs:
           mkdir -p ~/.ssh/
           echo "$PASS" > ~/.ssh/private.key
           sudo chmod 600 ~/.ssh/private.key
-#          rsync --progress -avz -e "ssh -i ~/.ssh/private.key -o StrictHostKeyChecking=no" $GITHUB_WORKSPACE/de.openms.update/target/repository/* "$USER@$HOST:/knime-plugin/updateSite/$folder/"
+          rsync --progress -avz -e "ssh -i ~/.ssh/private.key -o StrictHostKeyChecking=no" $GITHUB_WORKSPACE/de.openms.update/target/repository/* "$USER@$HOST:/knime-plugin/updateSite/$folder/"

From dd1c5eab81e4373053ccdda4e1b41d256c6d6405 Mon Sep 17 00:00:00 2001
From: Samuel Wein <sam@samwein.com>
Date: Fri, 10 Nov 2023 18:10:50 +0100
Subject: [PATCH 02/24] Update openms_ci_matrix_full.yml

try to upload documentation
---
 .github/workflows/openms_ci_matrix_full.yml | 41 ++++++++++++++++++++-
 1 file changed, 39 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/openms_ci_matrix_full.yml b/.github/workflows/openms_ci_matrix_full.yml
index a22e9576d2e..5eb98dc4d4c 100644
--- a/.github/workflows/openms_ci_matrix_full.yml
+++ b/.github/workflows/openms_ci_matrix_full.yml
@@ -361,6 +361,15 @@ jobs:
           ${{ github.workspace }}/OpenMS/bld/*.exe
           ${{ github.workspace }}/OpenMS/bld/*.deb
           ${{ github.workspace }}/OpenMS/bld/*.pkg
+
+    - if: steps.set-vars.outputs.pkg_type != 'none' && [[ "${{ matrix.os }}" == ubuntu-* ]] # Only upload docs when we are building the package, use the ubuntu build simply 'cause its fast
+      name: Upload Documentation as artifacts
+      uses: actions/upload-artifact@v3
+      with:
+        name: documentation
+        path: |
+          ${{ github.workspace }}/OpenMS/doc/**
+
         
     - if: steps.set-vars.outputs.pkg_type != 'none' || inputs.knime
       name: Generate KNIME descriptors and payloads
@@ -371,7 +380,6 @@ jobs:
         cmake -DSEARCH_ENGINES_DIRECTORY="$GITHUB_WORKSPACE/_thirdparty" -DENABLE_PREPARE_KNIME_PACKAGE=ON .
         cmake --build . --target prepare_knime_package
         
-
     - if: steps.set-vars.outputs.pkg_type != 'none' || inputs.knime
       name: Upload KNIME payload and descriptors as artifacts
       uses: actions/upload-artifact@v3
@@ -413,7 +421,7 @@ jobs:
         run: |
           echo "Upload"
           if [[ "${{ env.RUN_NAME }}" == "nightly" ]]; then
-            folder=nightly
+            folder=nightlyGHA                                                    # TODO: Change back when we deactivate Jenkins
           elif [[ "${{ env.RUN_NAME }}" == "release/*" ]]; then
             tmpfolder=${{ env.RUN_NAME }}
             folder=${tmpfolder/release/RC_GHA}                                   # TODO: change back to RC after proper release
@@ -427,6 +435,35 @@ jobs:
           sudo chmod 600 ~/.ssh/private.key
           rsync --progress -avz -e "ssh -i ~/.ssh/private.key -o StrictHostKeyChecking=no" $GITHUB_WORKSPACE/* "$USER@$HOST:/OpenMSInstaller/${folder}"
 
+      - name: Download Documentation
+        uses: actions/download-artifact@v3
+        with:
+          name: documentation
+
+      - name: Upload Documentation
+        shell: bash
+        env:
+          PASS: ${{ secrets.ARCHIVE_RRSYNC_SSH }}
+          USER: ${{ secrets.ARCHIVE_RRSYNC_USER }}
+          HOST: ${{ secrets.ARCHIVE_RRSYNC_HOST }}
+        run: |
+          echo "Upload"
+          if [[ "${{ env.RUN_NAME }}" == "nightly" ]]; then
+            folder=nightlyGHA                                                    # TODO: Change back when we deactivate Jenkins
+          elif [[ "${{ env.RUN_NAME }}" == "release/*" ]]; then
+            tmpfolder=${{ env.RUN_NAME }}
+            folder=${tmpfolder/release/RC_GHA}                                   # TODO: change back to RC after proper release
+          else
+            folder=experimental/${{ env.RUN_NAME }}
+          fi
+          echo $folder
+
+          mkdir -p ~/.ssh/
+          echo "$PASS" > ~/.ssh/private.key
+          sudo chmod 600 ~/.ssh/private.key
+
+          # Upload documentation FIXME
+          rsync --progress -avz -e "ssh -i ~/.ssh/private.key -o StrictHostKeyChecking=no" $GITHUB_WORKSPACE/OpenMS/doc "$USER@$HOST:/Documentation/${folder}"
         # TODO create softlinks to latest nightly
         # TODO create and upload file hashes, at least for release candidate
 

From b103f45c60cdb04231a785110fab4250f52ce74a Mon Sep 17 00:00:00 2001
From: Samuel Wein <sam@samwein.com>
Date: Mon, 13 Nov 2023 11:16:52 +0100
Subject: [PATCH 03/24] Update openms_ci_matrix_full.yml

Fixes from suggestions
---
 .github/workflows/openms_ci_matrix_full.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/openms_ci_matrix_full.yml b/.github/workflows/openms_ci_matrix_full.yml
index 5eb98dc4d4c..e13609c3ae6 100644
--- a/.github/workflows/openms_ci_matrix_full.yml
+++ b/.github/workflows/openms_ci_matrix_full.yml
@@ -428,7 +428,7 @@ jobs:
           else
             folder=experimental/${{ env.RUN_NAME }}
           fi
-          echo $folder
+          echo "Uploading installers to: " $folder
 
           mkdir -p ~/.ssh/
           echo "$PASS" > ~/.ssh/private.key
@@ -632,14 +632,14 @@ jobs:
         run: |
           echo "Upload"
           if [[ "${{ env.RUN_NAME }}" == "nightly" ]]; then
-            folder=nightly
+            folder=nightlyGHA
           elif [[ "${{ env.RUN_NAME }}" == "release/*" ]]; then
             tmpfolder=${{ env.RUN_NAME }}
-            folder=${tmpfolder/release/RC}
+            folder=${tmpfolder/release/RC}GHA
           else
             folder=experimental/${{ env.RUN_NAME }}
           fi
-          echo $folder
+          echo "Uploading KNIME site to:" $folder
 
           # correct permissions of files to upload
           chmod -R o+r $GITHUB_WORKSPACE/de.openms.update/target/repository/*

From e4d3d91dc9a41de754ee21579d49ceacb5a4c0ca Mon Sep 17 00:00:00 2001
From: Samuel Wein <sam@samwein.com>
Date: Mon, 13 Nov 2023 12:21:46 +0100
Subject: [PATCH 04/24] Update .github/workflows/openms_ci_matrix_full.yml

Co-authored-by: Julianus Pfeuffer <j.pfeuffer@fu-berlin.de>
---
 .github/workflows/openms_ci_matrix_full.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/openms_ci_matrix_full.yml b/.github/workflows/openms_ci_matrix_full.yml
index a07dc26e17d..344f77c01e7 100644
--- a/.github/workflows/openms_ci_matrix_full.yml
+++ b/.github/workflows/openms_ci_matrix_full.yml
@@ -362,7 +362,8 @@ jobs:
           ${{ github.workspace }}/OpenMS/bld/*.deb
           ${{ github.workspace }}/OpenMS/bld/*.pkg
 
-    - if: steps.set-vars.outputs.pkg_type != 'none' && [[ "${{ matrix.os }}" == ubuntu-* ]] # Only upload docs when we are building the package, use the ubuntu build simply 'cause its fast
+    - if: steps.set-vars.outputs.pkg_type != 'none' && matrix.os == ubuntu-* 
+    # Only upload docs when we are building the package, use the ubuntu build simply 'cause its fast
       name: Upload Documentation as artifacts
       uses: actions/upload-artifact@v3
       with:

From 8e893e06d5e15acb8a1c81d80278238a9df4e216 Mon Sep 17 00:00:00 2001
From: Samuel Wein <sam@samwein.com>
Date: Mon, 13 Nov 2023 12:24:35 +0100
Subject: [PATCH 05/24] Update openms_ci_matrix_full.yml

---
 .github/workflows/openms_ci_matrix_full.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/openms_ci_matrix_full.yml b/.github/workflows/openms_ci_matrix_full.yml
index 344f77c01e7..6fd938fac30 100644
--- a/.github/workflows/openms_ci_matrix_full.yml
+++ b/.github/workflows/openms_ci_matrix_full.yml
@@ -362,7 +362,7 @@ jobs:
           ${{ github.workspace }}/OpenMS/bld/*.deb
           ${{ github.workspace }}/OpenMS/bld/*.pkg
 
-    - if: steps.set-vars.outputs.pkg_type != 'none' && matrix.os == ubuntu-* 
+    - if: steps.set-vars.outputs.pkg_type != 'none' && matrix.os == "ubuntu-*" 
     # Only upload docs when we are building the package, use the ubuntu build simply 'cause its fast
       name: Upload Documentation as artifacts
       uses: actions/upload-artifact@v3

From c09b16cf1a9c76a46cf006fbbc6e87742f6aef15 Mon Sep 17 00:00:00 2001
From: Julianus Pfeuffer <j.pfeuffer@fu-berlin.de>
Date: Mon, 13 Nov 2023 12:25:50 +0100
Subject: [PATCH 06/24] Update .github/workflows/openms_ci_matrix_full.yml

---
 .github/workflows/openms_ci_matrix_full.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/openms_ci_matrix_full.yml b/.github/workflows/openms_ci_matrix_full.yml
index 6fd938fac30..37dcb1703b2 100644
--- a/.github/workflows/openms_ci_matrix_full.yml
+++ b/.github/workflows/openms_ci_matrix_full.yml
@@ -362,7 +362,7 @@ jobs:
           ${{ github.workspace }}/OpenMS/bld/*.deb
           ${{ github.workspace }}/OpenMS/bld/*.pkg
 
-    - if: steps.set-vars.outputs.pkg_type != 'none' && matrix.os == "ubuntu-*" 
+    - if: steps.set-vars.outputs.pkg_type != 'none' && matrix.os == 'ubuntu-*'
     # Only upload docs when we are building the package, use the ubuntu build simply 'cause its fast
       name: Upload Documentation as artifacts
       uses: actions/upload-artifact@v3

From a46fd83b7521e6eb4752123e7062c2d139c4d7db Mon Sep 17 00:00:00 2001
From: Samuel Wein <sam@samwein.com>
Date: Mon, 13 Nov 2023 14:56:46 +0100
Subject: [PATCH 07/24] Update openms_ci_matrix_full.yml

---
 .github/workflows/openms_ci_matrix_full.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/openms_ci_matrix_full.yml b/.github/workflows/openms_ci_matrix_full.yml
index 37dcb1703b2..fd3e2fd4d87 100644
--- a/.github/workflows/openms_ci_matrix_full.yml
+++ b/.github/workflows/openms_ci_matrix_full.yml
@@ -362,7 +362,7 @@ jobs:
           ${{ github.workspace }}/OpenMS/bld/*.deb
           ${{ github.workspace }}/OpenMS/bld/*.pkg
 
-    - if: steps.set-vars.outputs.pkg_type != 'none' && matrix.os == 'ubuntu-*'
+    - if: steps.set-vars.outputs.pkg_type != 'none' && startsWith(matrix.os, 'ubuntu')
     # Only upload docs when we are building the package, use the ubuntu build simply 'cause its fast
       name: Upload Documentation as artifacts
       uses: actions/upload-artifact@v3

From 757fa38914fe69e1a151610bc9f43fae124e4695 Mon Sep 17 00:00:00 2001
From: Samuel Wein <sam@samwein.com>
Date: Mon, 13 Nov 2023 16:29:22 +0100
Subject: [PATCH 08/24] Update openms_ci_matrix_full.yml

---
 .github/workflows/openms_ci_matrix_full.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/openms_ci_matrix_full.yml b/.github/workflows/openms_ci_matrix_full.yml
index fd3e2fd4d87..35e0b245038 100644
--- a/.github/workflows/openms_ci_matrix_full.yml
+++ b/.github/workflows/openms_ci_matrix_full.yml
@@ -464,7 +464,7 @@ jobs:
           sudo chmod 600 ~/.ssh/private.key
 
           # Upload documentation FIXME
-          rsync --progress -avz -e "ssh -i ~/.ssh/private.key -o StrictHostKeyChecking=no" $GITHUB_WORKSPACE/OpenMS/doc "$USER@$HOST:/Documentation/${folder}"
+          rsync --progress -avz -e "ssh -i ~/.ssh/private.key -o StrictHostKeyChecking=no" $GITHUB_WORKSPACE/* "$USER@$HOST:/Documentation/${folder}"
         # TODO create softlinks to latest nightly
         # TODO create and upload file hashes, at least for release candidate
 

From c16a424dda51f9dccf8f278fa8042e697698d744 Mon Sep 17 00:00:00 2001
From: Samuel Wein <sam@samwein.com>
Date: Tue, 14 Nov 2023 09:43:47 +0100
Subject: [PATCH 09/24] Update openms_ci_matrix_full.yml

Enable tutorial building update path to download docs artifiact
---
 .github/workflows/openms_ci_matrix_full.yml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/openms_ci_matrix_full.yml b/.github/workflows/openms_ci_matrix_full.yml
index 35e0b245038..bcac6181973 100644
--- a/.github/workflows/openms_ci_matrix_full.yml
+++ b/.github/workflows/openms_ci_matrix_full.yml
@@ -10,7 +10,7 @@ on:
     inputs:
       package:
         type: boolean
-        description: Build and upload packages/installer?
+        description: Build and upload packages/installer/Documentation?
         default: false
       knime:
         type: boolean
@@ -294,7 +294,7 @@ jobs:
           ENABLE_STYLE_TESTING: "OFF"
           ENABLE_TOPP_TESTING: "ON"
           ENABLE_CLASS_TESTING: "ON"
-          ENABLE_TUTORIALS: "OFF"
+          ENABLE_TUTORIALS: "ON"
           ENABLE_GCC_WERROR: "OFF" # TODO think about that
           SEARCH_ENGINES_DIRECTORY: ${{ github.workspace }}/_thirdparty
           WITH_GUI: "ON"
@@ -440,6 +440,7 @@ jobs:
         uses: actions/download-artifact@v3
         with:
           name: documentation
+          path: $GITHUB_WORKSPACE/docs
 
       - name: Upload Documentation
         shell: bash
@@ -464,7 +465,7 @@ jobs:
           sudo chmod 600 ~/.ssh/private.key
 
           # Upload documentation FIXME
-          rsync --progress -avz -e "ssh -i ~/.ssh/private.key -o StrictHostKeyChecking=no" $GITHUB_WORKSPACE/* "$USER@$HOST:/Documentation/${folder}"
+          rsync --progress -avz -e "ssh -i ~/.ssh/private.key -o StrictHostKeyChecking=no" $GITHUB_WORKSPACE/docs "$USER@$HOST:/Documentation/${folder}"
         # TODO create softlinks to latest nightly
         # TODO create and upload file hashes, at least for release candidate
 

From 9feee9ed147e8a657e53323ecd435ef2ee313096 Mon Sep 17 00:00:00 2001
From: Samuel Wein <sam@samwein.com>
Date: Tue, 14 Nov 2023 10:41:30 +0100
Subject: [PATCH 10/24] Update openms_ci_matrix_full.yml

revert tutorial change
---
 .github/workflows/openms_ci_matrix_full.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/openms_ci_matrix_full.yml b/.github/workflows/openms_ci_matrix_full.yml
index bcac6181973..a46854edb4a 100644
--- a/.github/workflows/openms_ci_matrix_full.yml
+++ b/.github/workflows/openms_ci_matrix_full.yml
@@ -294,7 +294,7 @@ jobs:
           ENABLE_STYLE_TESTING: "OFF"
           ENABLE_TOPP_TESTING: "ON"
           ENABLE_CLASS_TESTING: "ON"
-          ENABLE_TUTORIALS: "ON"
+          ENABLE_TUTORIALS: "OFF"
           ENABLE_GCC_WERROR: "OFF" # TODO think about that
           SEARCH_ENGINES_DIRECTORY: ${{ github.workspace }}/_thirdparty
           WITH_GUI: "ON"

From f537498f9cd4d03ca93f3de632d955d6b091d5c5 Mon Sep 17 00:00:00 2001
From: Julianus Pfeuffer <j.pfeuffer@fu-berlin.de>
Date: Tue, 14 Nov 2023 12:26:01 +0100
Subject: [PATCH 11/24] test doxygen

---
 .github/workflows/openms_ci_matrix_full.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/openms_ci_matrix_full.yml b/.github/workflows/openms_ci_matrix_full.yml
index a46854edb4a..d4c835de54c 100644
--- a/.github/workflows/openms_ci_matrix_full.yml
+++ b/.github/workflows/openms_ci_matrix_full.yml
@@ -10,7 +10,7 @@ on:
     inputs:
       package:
         type: boolean
-        description: Build and upload packages/installer/Documentation?
+        description: Build and upload packages/installer/documentation?
         default: false
       knime:
         type: boolean
@@ -156,6 +156,8 @@ jobs:
           
           if [[ "${{ steps.set-vars.outputs.pkg_type }}" != "none" ]]; then
             sudo apt-get -qq install -y doxygen ghostscript graphviz
+            echo "Testing doxygen"
+            doxygen --version
           fi
         fi
         

From 728679254c63d313aa1c1fe4a99b39dc8f509a78 Mon Sep 17 00:00:00 2001
From: Samuel Wein <sam@samwein.com>
Date: Thu, 16 Nov 2023 11:56:15 +0100
Subject: [PATCH 12/24] Disable building docs on windows and Mac (temporarily)

---
 .github/workflows/openms_ci_matrix_full.yml | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/openms_ci_matrix_full.yml b/.github/workflows/openms_ci_matrix_full.yml
index d4c835de54c..9c05b0f5037 100644
--- a/.github/workflows/openms_ci_matrix_full.yml
+++ b/.github/workflows/openms_ci_matrix_full.yml
@@ -78,14 +78,17 @@ jobs:
           echo "xvfb=xvfb-run -a" >> $GITHUB_OUTPUT
           echo "static_boost=OFF" >> $GITHUB_OUTPUT
           if [ "$DO_PACKAGE" = true ]; then
+            echo "enable_docs=ON" >> $GITHUB_OUTPUT
             echo "pkg_type=deb" >> $GITHUB_OUTPUT
           else
+            echo "enable_docs=OFF" >> $GITHUB_OUTPUT
             echo "pkg_type=none" >> $GITHUB_OUTPUT
           fi
           echo "cxx_compiler=${{ matrix.compiler }}-${{ matrix.compiler_ver }}" >> $GITHUB_OUTPUT
         fi
         
         if [[ "${{ matrix.os }}" == windows-* ]]; then
+          echo "enable_docs=OFF" >> $GITHUB_OUTPUT
           echo "tp_folder=Windows" >> $GITHUB_OUTPUT
           echo "contrib_os=windows" >> $GITHUB_OUTPUT
           echo "contrib_os_ver=" >> $GITHUB_OUTPUT
@@ -101,6 +104,7 @@ jobs:
         fi
 
         if [[ "${{ matrix.os }}" == macos-* ]]; then
+          echo "enable_docs=OFF" >> $GITHUB_OUTPUT
           echo "tp_folder=MacOS" >> $GITHUB_OUTPUT
           echo "contrib_os=macOS" >> $GITHUB_OUTPUT
           echo "contrib_os_ver=10.15.5/" >> $GITHUB_OUTPUT
@@ -170,7 +174,7 @@ jobs:
           echo "C:\Program Files (x86)\GitHub CLI" >> $GITHUB_PATH
 
           if [[ "${{ steps.set-vars.outputs.pkg_type }}" != "none" ]]; then
-            choco install doxygen.portable ghostscript graphviz -y --no-progress
+            # choco install doxygen.portable ghostscript graphviz -y --no-progress
             # uses a custom NSIS, which provides 8-k string support and has UltraModernUI integrated already
             curl --no-progress-meter -L -o NSIS.tar.gz https://github.com/OpenMS/NSIS/raw/main/NSIS.tar.gz
             ## overwrite existing NSIS (which has only 1k-string support)
@@ -183,9 +187,9 @@ jobs:
           echo "cmake_prefix=$Qt5_DIR/lib/cmake;$Qt5_DIR" >> $GITHUB_OUTPUT
           brew install --quiet ccache autoconf automake libtool ninja && brew link --overwrite ccache
 
-          if [[ "${{ steps.set-vars.outputs.pkg_type }}" != "none" ]]; then
-            brew install --quiet doxygen ghostscript graphviz
-          fi
+          #if [[ "${{ steps.set-vars.outputs.pkg_type }}" != "none" ]]; then
+          #  brew install --quiet doxygen ghostscript graphviz
+          #fi
         fi
 
 
@@ -296,7 +300,7 @@ jobs:
           ENABLE_STYLE_TESTING: "OFF"
           ENABLE_TOPP_TESTING: "ON"
           ENABLE_CLASS_TESTING: "ON"
-          ENABLE_TUTORIALS: "OFF"
+          ENABLE_DOCS: ${{ steps.set-vars.outputs.enable_docs }}
           ENABLE_GCC_WERROR: "OFF" # TODO think about that
           SEARCH_ENGINES_DIRECTORY: ${{ github.workspace }}/_thirdparty
           WITH_GUI: "ON"

From 137285afb60abddbf900fc720dcd572b5da8ef89 Mon Sep 17 00:00:00 2001
From: Samuel Wein <sam@samwein.com>
Date: Thu, 16 Nov 2023 14:20:15 +0100
Subject: [PATCH 13/24] Update .github/workflows/openms_ci_matrix_full.yml

Co-authored-by: Julianus Pfeuffer <j.pfeuffer@fu-berlin.de>
---
 .github/workflows/openms_ci_matrix_full.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/openms_ci_matrix_full.yml b/.github/workflows/openms_ci_matrix_full.yml
index 313c37891fb..efa0295e71e 100644
--- a/.github/workflows/openms_ci_matrix_full.yml
+++ b/.github/workflows/openms_ci_matrix_full.yml
@@ -375,7 +375,7 @@ jobs:
       with:
         name: documentation
         path: |
-          ${{ github.workspace }}/OpenMS/doc/**
+          ${{ github.workspace }}/OpenMS/bld/doc/**
 
         
     - if: steps.set-vars.outputs.pkg_type != 'none' || inputs.knime

From d283c5267ead87c5a4b5a24b019bbbe66678192e Mon Sep 17 00:00:00 2001
From: Samuel Wein <sam@samwein.com>
Date: Thu, 16 Nov 2023 14:22:28 +0100
Subject: [PATCH 14/24] Update openms_ci_matrix_full.yml

Reenable docs on windows
---
 .github/workflows/openms_ci_matrix_full.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/openms_ci_matrix_full.yml b/.github/workflows/openms_ci_matrix_full.yml
index efa0295e71e..fc96a047433 100644
--- a/.github/workflows/openms_ci_matrix_full.yml
+++ b/.github/workflows/openms_ci_matrix_full.yml
@@ -88,7 +88,7 @@ jobs:
         fi
         
         if [[ "${{ matrix.os }}" == windows-* ]]; then
-          echo "enable_docs=OFF" >> $GITHUB_OUTPUT
+          echo "enable_docs=ON" >> $GITHUB_OUTPUT
           echo "tp_folder=Windows" >> $GITHUB_OUTPUT
           echo "contrib_os=windows" >> $GITHUB_OUTPUT
           echo "contrib_os_ver=" >> $GITHUB_OUTPUT
@@ -174,7 +174,7 @@ jobs:
           echo "C:\Program Files (x86)\GitHub CLI" >> $GITHUB_PATH
 
           if [[ "${{ steps.set-vars.outputs.pkg_type }}" != "none" ]]; then
-            # choco install doxygen.portable ghostscript graphviz -y --no-progress
+            choco install doxygen.portable ghostscript graphviz -y --no-progress
             # uses a custom NSIS, which provides 8-k string support and has UltraModernUI integrated already
             curl --no-progress-meter -L -o NSIS.tar.gz https://github.com/OpenMS/NSIS/raw/main/NSIS.tar.gz
             ## overwrite existing NSIS (which has only 1k-string support)

From fae1c4db9e0a2ca9fc2752bee7dddee60df2a0f7 Mon Sep 17 00:00:00 2001
From: Samuel Wein <sam@samwein.com>
Date: Thu, 16 Nov 2023 15:04:05 +0100
Subject: [PATCH 15/24] Update openms_ci_matrix_full.yml

Zip documentation before uploading as artifact.
---
 .github/workflows/openms_ci_matrix_full.yml | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/openms_ci_matrix_full.yml b/.github/workflows/openms_ci_matrix_full.yml
index fc96a047433..77ff21f4963 100644
--- a/.github/workflows/openms_ci_matrix_full.yml
+++ b/.github/workflows/openms_ci_matrix_full.yml
@@ -368,6 +368,15 @@ jobs:
           ${{ github.workspace }}/OpenMS/bld/*.deb
           ${{ github.workspace }}/OpenMS/bld/*.pkg
 
+    #Zip the documentation first, since there are :: which make the upload action choke.
+    - if: steps.set-vars.outputs.pkg_type != 'none' && startsWith(matrix.os, 'ubuntu')
+      name: Zip Documentation
+      uses: thedoctor0/zip-release@0.7.6
+      with:
+        type: 'zip'
+        path: ${{ github.workspace }}/OpenMS/bld/doc/**
+        filename: 'documentation.zip'
+
     - if: steps.set-vars.outputs.pkg_type != 'none' && startsWith(matrix.os, 'ubuntu')
     # Only upload docs when we are building the package, use the ubuntu build simply 'cause its fast
       name: Upload Documentation as artifacts
@@ -375,7 +384,7 @@ jobs:
       with:
         name: documentation
         path: |
-          ${{ github.workspace }}/OpenMS/bld/doc/**
+          ${{ github.workspace }}/documentation.zip
 
         
     - if: steps.set-vars.outputs.pkg_type != 'none' || inputs.knime
@@ -455,6 +464,8 @@ jobs:
           USER: ${{ secrets.ARCHIVE_RRSYNC_USER }}
           HOST: ${{ secrets.ARCHIVE_RRSYNC_HOST }}
         run: |
+          unzip $GITHUB_WORKSPACE/docs/documentation.zip -d $GITHUB_WORKSPACE/docs
+          rm $GITHUB_WORKSPACE/docs/documentation.zip
           echo "Upload"
           if [[ "${{ env.RUN_NAME }}" == "nightly" ]]; then
             folder=nightlyGHA                                                    # TODO: Change back when we deactivate Jenkins

From 855c4ea9232ab3fdd6a3589f6cc5ea93ef4bebba Mon Sep 17 00:00:00 2001
From: Samuel Wein <sam@samwein.com>
Date: Thu, 16 Nov 2023 16:23:48 +0100
Subject: [PATCH 16/24] Update openms_ci_matrix_full.yml

---
 .github/workflows/openms_ci_matrix_full.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/openms_ci_matrix_full.yml b/.github/workflows/openms_ci_matrix_full.yml
index 77ff21f4963..eed2bcc3bad 100644
--- a/.github/workflows/openms_ci_matrix_full.yml
+++ b/.github/workflows/openms_ci_matrix_full.yml
@@ -464,7 +464,7 @@ jobs:
           USER: ${{ secrets.ARCHIVE_RRSYNC_USER }}
           HOST: ${{ secrets.ARCHIVE_RRSYNC_HOST }}
         run: |
-          unzip $GITHUB_WORKSPACE/docs/documentation.zip -d $GITHUB_WORKSPACE/docs
+          unzip $GITHUB_WORKSPACE/docs/documentation.zip -d /docs
           rm $GITHUB_WORKSPACE/docs/documentation.zip
           echo "Upload"
           if [[ "${{ env.RUN_NAME }}" == "nightly" ]]; then

From 99aa90a888b74ca7ca6e5938f42851c299538ccc Mon Sep 17 00:00:00 2001
From: Samuel Wein <sam@samwein.com>
Date: Thu, 16 Nov 2023 17:50:50 +0100
Subject: [PATCH 17/24] Update openms_ci_matrix_full.yml

---
 .github/workflows/openms_ci_matrix_full.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/openms_ci_matrix_full.yml b/.github/workflows/openms_ci_matrix_full.yml
index eed2bcc3bad..79686cec66b 100644
--- a/.github/workflows/openms_ci_matrix_full.yml
+++ b/.github/workflows/openms_ci_matrix_full.yml
@@ -455,7 +455,7 @@ jobs:
         uses: actions/download-artifact@v3
         with:
           name: documentation
-          path: $GITHUB_WORKSPACE/docs
+          path: docs
 
       - name: Upload Documentation
         shell: bash
@@ -464,7 +464,7 @@ jobs:
           USER: ${{ secrets.ARCHIVE_RRSYNC_USER }}
           HOST: ${{ secrets.ARCHIVE_RRSYNC_HOST }}
         run: |
-          unzip $GITHUB_WORKSPACE/docs/documentation.zip -d /docs
+          unzip $GITHUB_WORKSPACE/docs/documentation.zip -d $GITHUB_WORKSPACE/docs
           rm $GITHUB_WORKSPACE/docs/documentation.zip
           echo "Upload"
           if [[ "${{ env.RUN_NAME }}" == "nightly" ]]; then

From 2d8bf58a4fdc28cbd947306d12ab8ceb08888d70 Mon Sep 17 00:00:00 2001
From: Samuel Wein <sam@samwein.com>
Date: Fri, 17 Nov 2023 09:29:14 +0100
Subject: [PATCH 18/24] Update openms_ci_matrix_full.yml

use directory instead of path on zip action
---
 .github/workflows/openms_ci_matrix_full.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/openms_ci_matrix_full.yml b/.github/workflows/openms_ci_matrix_full.yml
index 79686cec66b..8ba17ff6749 100644
--- a/.github/workflows/openms_ci_matrix_full.yml
+++ b/.github/workflows/openms_ci_matrix_full.yml
@@ -374,7 +374,7 @@ jobs:
       uses: thedoctor0/zip-release@0.7.6
       with:
         type: 'zip'
-        path: ${{ github.workspace }}/OpenMS/bld/doc/**
+        directory: ${{ github.workspace }}/OpenMS/bld/doc
         filename: 'documentation.zip'
 
     - if: steps.set-vars.outputs.pkg_type != 'none' && startsWith(matrix.os, 'ubuntu')

From dd823180e9af7de33572533f845623f35d90644b Mon Sep 17 00:00:00 2001
From: Samuel Wein <sam@samwein.com>
Date: Fri, 17 Nov 2023 10:13:28 +0100
Subject: [PATCH 19/24] Update openms_ci_matrix_full.yml

Exclude non-html stuff
---
 .github/workflows/openms_ci_matrix_full.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/openms_ci_matrix_full.yml b/.github/workflows/openms_ci_matrix_full.yml
index 8ba17ff6749..1b4d637fcb6 100644
--- a/.github/workflows/openms_ci_matrix_full.yml
+++ b/.github/workflows/openms_ci_matrix_full.yml
@@ -375,6 +375,7 @@ jobs:
       with:
         type: 'zip'
         directory: ${{ github.workspace }}/OpenMS/bld/doc
+        exclusions: '/CMakeFiles/* /doxygen/* /code_examples/*'
         filename: 'documentation.zip'
 
     - if: steps.set-vars.outputs.pkg_type != 'none' && startsWith(matrix.os, 'ubuntu')
@@ -384,7 +385,7 @@ jobs:
       with:
         name: documentation
         path: |
-          ${{ github.workspace }}/documentation.zip
+          ${{ github.workspace }}/OpenMS/bld/doc/documentation.zip
 
         
     - if: steps.set-vars.outputs.pkg_type != 'none' || inputs.knime

From d96686adae346ea98e0a1a839be99e67a5c6549e Mon Sep 17 00:00:00 2001
From: Samuel Wein <sam@samwein.com>
Date: Fri, 17 Nov 2023 11:05:11 +0100
Subject: [PATCH 20/24] Update openms_ci_matrix_full.yml

Fix base directory for Rsync
---
 .github/workflows/openms_ci_matrix_full.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/openms_ci_matrix_full.yml b/.github/workflows/openms_ci_matrix_full.yml
index 1b4d637fcb6..87289c45c7d 100644
--- a/.github/workflows/openms_ci_matrix_full.yml
+++ b/.github/workflows/openms_ci_matrix_full.yml
@@ -450,7 +450,7 @@ jobs:
           mkdir -p ~/.ssh/
           echo "$PASS" > ~/.ssh/private.key
           sudo chmod 600 ~/.ssh/private.key
-          rsync --progress -avz -e "ssh -i ~/.ssh/private.key -o StrictHostKeyChecking=no" $GITHUB_WORKSPACE/* "$USER@$HOST:/OpenMSInstaller/${folder}"
+          rsync --progress -avz -e "ssh -i ~/.ssh/private.key -o StrictHostKeyChecking=no" $GITHUB_WORKSPACE/docs/* "$USER@$HOST:/OpenMSInstaller/${folder}"
 
       - name: Download Documentation
         uses: actions/download-artifact@v3

From 840fe63eed156202bffab420c3c5da53740cdf6a Mon Sep 17 00:00:00 2001
From: Samuel Wein <sam@samwein.com>
Date: Fri, 17 Nov 2023 11:59:56 +0100
Subject: [PATCH 21/24] Update openms_ci_matrix_full.yml

Fix trailing slash
---
 .github/workflows/openms_ci_matrix_full.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/openms_ci_matrix_full.yml b/.github/workflows/openms_ci_matrix_full.yml
index 87289c45c7d..8fc9d9104db 100644
--- a/.github/workflows/openms_ci_matrix_full.yml
+++ b/.github/workflows/openms_ci_matrix_full.yml
@@ -450,7 +450,7 @@ jobs:
           mkdir -p ~/.ssh/
           echo "$PASS" > ~/.ssh/private.key
           sudo chmod 600 ~/.ssh/private.key
-          rsync --progress -avz -e "ssh -i ~/.ssh/private.key -o StrictHostKeyChecking=no" $GITHUB_WORKSPACE/docs/* "$USER@$HOST:/OpenMSInstaller/${folder}"
+          rsync --progress -avz -e "ssh -i ~/.ssh/private.key -o StrictHostKeyChecking=no" $GITHUB_WORKSPACE/* "$USER@$HOST:/OpenMSInstaller/${folder}"
 
       - name: Download Documentation
         uses: actions/download-artifact@v3
@@ -483,7 +483,7 @@ jobs:
           sudo chmod 600 ~/.ssh/private.key
 
           # Upload documentation FIXME
-          rsync --progress -avz -e "ssh -i ~/.ssh/private.key -o StrictHostKeyChecking=no" $GITHUB_WORKSPACE/docs "$USER@$HOST:/Documentation/${folder}"
+          rsync --progress -avz -e "ssh -i ~/.ssh/private.key -o StrictHostKeyChecking=no" $GITHUB_WORKSPACE/docs/ "$USER@$HOST:/Documentation/${folder}"
         # TODO create softlinks to latest nightly
         # TODO create and upload file hashes, at least for release candidate
 

From 8c0838af8a5549c61c1fa070b71779c14608de74 Mon Sep 17 00:00:00 2001
From: Samuel Wein <sam@samwein.com>
Date: Sat, 18 Nov 2023 10:57:09 +0100
Subject: [PATCH 22/24] Update openms_ci_matrix_full.yml

Renable docs for Mac when building package, disable building docs when no package.
---
 .github/workflows/openms_ci_matrix_full.yml | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/openms_ci_matrix_full.yml b/.github/workflows/openms_ci_matrix_full.yml
index 8fc9d9104db..bd3dafe1184 100644
--- a/.github/workflows/openms_ci_matrix_full.yml
+++ b/.github/workflows/openms_ci_matrix_full.yml
@@ -88,7 +88,6 @@ jobs:
         fi
         
         if [[ "${{ matrix.os }}" == windows-* ]]; then
-          echo "enable_docs=ON" >> $GITHUB_OUTPUT
           echo "tp_folder=Windows" >> $GITHUB_OUTPUT
           echo "contrib_os=windows" >> $GITHUB_OUTPUT
           echo "contrib_os_ver=" >> $GITHUB_OUTPUT
@@ -97,24 +96,27 @@ jobs:
           echo "static_boost=ON" >> $GITHUB_OUTPUT
           if [ "$DO_PACKAGE" = true ]; then
             echo "pkg_type=nsis" >> $GITHUB_OUTPUT
+            echo "enable_docs=ON" >> $GITHUB_OUTPUT
           else
-            echo "pkg_type=none" >> $GITHUB_OUTPUT
+            echo "pkg_type=none" >> $GITHUB_OUTPUT           
+            echo "enable_docs=OFF" >> $GITHUB_OUTPUT
           fi
           echo "cxx_compiler=${{ matrix.compiler }}" >> $GITHUB_OUTPUT
         fi
 
         if [[ "${{ matrix.os }}" == macos-* ]]; then
-          echo "enable_docs=OFF" >> $GITHUB_OUTPUT
-          echo "tp_folder=MacOS" >> $GITHUB_OUTPUT
-          echo "contrib_os=macOS" >> $GITHUB_OUTPUT
+          echo "tp_folder=MacOS" >> $GITHUB_OUTPUT          echo "contrib_os=macOS" >> $GITHUB_OUTPUT
           echo "contrib_os_ver=10.15.5/" >> $GITHUB_OUTPUT
           echo "contrib_compiler=appleclang-11.0.0/" >> $GITHUB_OUTPUT
           echo "xvfb=" >> $GITHUB_OUTPUT
           echo "static_boost=ON" >> $GITHUB_OUTPUT
           if [ "$DO_PACKAGE" = true ]; then
             echo "pkg_type=pkg" >> $GITHUB_OUTPUT
+            echo "enable_docs=ON" >> $GITHUB_OUTPUT
           else
             echo "pkg_type=none" >> $GITHUB_OUTPUT
+            echo "enable_docs=OFF" >> $GITHUB_OUTPUT
+
           fi
           if [[ "${{ matrix.compiler }}" == "xcode" ]]; then
             sudo xcode-select -s '/Applications/Xcode_${{ matrix.compiler_ver }}.app/Contents/Developer'

From 4eb649242e9dd219cd9a7225756034eed87914e2 Mon Sep 17 00:00:00 2001
From: Samuel Wein <sam@samwein.com>
Date: Tue, 21 Nov 2023 12:09:10 +0100
Subject: [PATCH 23/24] Fix typo

---
 .github/workflows/openms_ci_matrix_full.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/openms_ci_matrix_full.yml b/.github/workflows/openms_ci_matrix_full.yml
index 5a3ab58f93a..e7325c16c7a 100644
--- a/.github/workflows/openms_ci_matrix_full.yml
+++ b/.github/workflows/openms_ci_matrix_full.yml
@@ -105,7 +105,8 @@ jobs:
         fi
 
         if [[ "${{ matrix.os }}" == macos-* ]]; then
-          echo "tp_folder=MacOS" >> $GITHUB_OUTPUT          echo "contrib_os=macOS" >> $GITHUB_OUTPUT
+          echo "tp_folder=MacOS" >> $GITHUB_OUTPUT
+          echo "contrib_os=macOS" >> $GITHUB_OUTPUT
           echo "contrib_os_ver=10.15.5/" >> $GITHUB_OUTPUT
           echo "contrib_compiler=appleclang-11.0.0/" >> $GITHUB_OUTPUT
           echo "xvfb=" >> $GITHUB_OUTPUT

From 59ee60e0652adf027a9f96de5c7fbac8b0760ce7 Mon Sep 17 00:00:00 2001
From: Julianus Pfeuffer <j.pfeuffer@fu-berlin.de>
Date: Tue, 21 Nov 2023 22:34:56 +0100
Subject: [PATCH 24/24] Fix SpectrumAnnotator small metadata issue (#7216)

---
 src/openms/source/CHEMISTRY/SpectrumAnnotator.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/openms/source/CHEMISTRY/SpectrumAnnotator.cpp b/src/openms/source/CHEMISTRY/SpectrumAnnotator.cpp
index c0b4fdb86f8..61e30f3ffdb 100644
--- a/src/openms/source/CHEMISTRY/SpectrumAnnotator.cpp
+++ b/src/openms/source/CHEMISTRY/SpectrumAnnotator.cpp
@@ -122,7 +122,7 @@ namespace OpenMS
     }
     const Param& sap = sa.getParameters();
     spec.setMetaValue("fragment_mass_tolerance", sap.getValue("tolerance"));
-    spec.setMetaValue("fragment_mass_tolerance_ppm", false);
+    spec.setMetaValue("fragment_mass_tolerance_ppm", sap.getValue("is_relative_tolerance").toBool());
     spec.setStringDataArrays(PeakSpectrum::StringDataArrays(1, type_annotations));
     spec.setFloatDataArrays(PeakSpectrum::FloatDataArrays(1, error_annotations));
   }