avogadro 1.102.0__tar.gz

avogadro-1.102.0/.clang-format

@@ -0,0 +1,92 @@
+---
+# This was based on the Mozilla style from clang-format 3.8.
+# Effectively creating a snapshot to produce more consistent results with later
+# versions of clang-format.
+Language:        Cpp
+AccessModifierOffset: -2
+AlignAfterOpenBracket: Align
+AlignConsecutiveAssignments: false
+AlignConsecutiveDeclarations: false
+AlignEscapedNewlinesLeft: false
+AlignOperands:   true
+AlignTrailingComments: true
+AllowAllParametersOfDeclarationOnNextLine: false
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+AllowShortLoopsOnASingleLine: false
+AlwaysBreakAfterDefinitionReturnType: None
+AlwaysBreakAfterReturnType: None
+AlwaysBreakBeforeMultilineStrings: false
+AlwaysBreakTemplateDeclarations: true
+BinPackArguments: true
+BinPackParameters: true
+BraceWrapping:
+  AfterClass:      true
+  AfterControlStatement: false
+  AfterEnum:       true
+  AfterFunction:   true
+  AfterNamespace:  false
+  AfterObjCDeclaration: false
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+  AfterUnion:      true
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+  IndentBraces:    false
+BreakBeforeBinaryOperators: None
+BreakBeforeBraces: Mozilla
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+BreakConstructorInitializersBeforeComma: false
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+CommentPragmas:  '^ IWYU pragma:'
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+ConstructorInitializerIndentWidth: 2
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+Cpp11BracedListStyle: false
+DerivePointerAlignment: false
+DisableFormat:   false
+ExperimentalAutoDetectBinPacking: false
+ForEachMacros:   [ foreach, Q_FOREACH, BOOST_FOREACH ]
+IncludeCategories:
+  - Regex:           '^"(llvm|llvm-c|clang|clang-c)/'
+    Priority:        2
+  - Regex:           '^(<|"(gtest|isl|json)/)'
+    Priority:        3
+  - Regex:           '.*'
+    Priority:        1
+IndentCaseLabels: true
+IndentWidth:     2
+IndentWrappedFunctionNames: false
+KeepEmptyLinesAtTheStartOfBlocks: true
+MacroBlockBegin: ''
+MacroBlockEnd:   ''
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+ObjCBlockIndentWidth: 2
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+Standard:        Cpp11
+TabWidth:        8
+UseTab:          Never
+...
+

avogadro-1.102.0/.clang-tidy

@@ -0,0 +1,30 @@
+Checks: 'bugprone*,
+        clang-analyzer*,
+        cppcoreguidelines*,
+        misc-uniqueptr-reset-release,
+        misc-unused*,
+        misc-redundant-expression,
+        modernize-avoid-bind,modernize-concat-nested-namespaces,
+        modernize-loop-convert,modernize-macro-to-enum,modernize-use-bool-literals,
+        modernize-use-auto,modernize-use-nullptr,modernize-use-override,
+        modernize-raw-string-literal,modernize-use-emplace,modernize-pass-by-value,
+        modernize-use-using,
+        performance-avoid-endl,
+        performance-faster*,
+        performance-for-range-copy,
+        performance-inefficient*,performance-type-promotion*,
+        performance-unnecessary-copy-initialization,
+        performance-move-const-arg,
+        readability-const-return-type,
+        readability-container*,
+        readability-duplicate-include,
+        readability-delete-null-pointer,
+        readability-qualified-auto,
+        readability-redundant*,
+        readability-simplify*,
+        -cppcoreguidelines-avoid-magic-numbers,
+        -cppcoreguidelines-owning-memory,
+        -readability-else-after-return,
+        -portability-restrict-system-includes,
+        -modernize-use-trailing-return-type'
+FormatStyle:     file

avogadro-1.102.0/.clang-tidy-ignore

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+thirdparty/*
+core/graph.cpp
+

avogadro-1.102.0/.codacy.yaml

@@ -0,0 +1,6 @@
+---
+engines:
+  cppcheck:
+    language: c++
+exclude_paths:
+  - "thirdparty/**"

avogadro-1.102.0/.github/FUNDING.yml

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+# These are supported funding model platforms
+
+open_collective: avogadro # Replace with a single Open Collective username

avogadro-1.102.0/.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve
+
+---
+
+**Avogadro version: (please complete the following information from the About box):**
+ - Avogadrolibs: (e.g. 1.90.0-316-g6d14770)
+ - Qt: (e.g., 5.9.5)
+
+**Desktop version: (please complete the following information):**
+ - OS: [e.g. MacOS]
+ - Version [e.g. 10.12.4]
+ - Compiler (if you built from source)
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Additional context**
+Add any other context about the problem here. **Please consider uploading or linking test files.**

avogadro-1.102.0/.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest an idea for this project
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I wish Avogadro calculated XYQ moments to render with ..
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen. Please be detailed. How might this feature work (e.g., first a window would open and you'd click to …)
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.
+
+Please consider opening a topic on https://discuss.avogadro.cc/ to allow further public discussion

avogadro-1.102.0/.github/PULL_REQUEST_TEMPLATE

@@ -0,0 +1,37 @@
+Developer Certificate of Origin
+Version 1.1
+
+Copyright (C) 2004, 2006 The Linux Foundation and its contributors.
+1 Letterman Drive
+Suite D4700
+San Francisco, CA, 94129
+
+Everyone is permitted to copy and distribute verbatim copies of this
+license document, but changing it is not allowed.
+
+
+Developer's Certificate of Origin 1.1
+
+By making a contribution to this project, I certify that:
+
+(a) The contribution was created in whole or in part by me and I
+    have the right to submit it under the open source license
+    indicated in the file; or
+
+(b) The contribution is based upon previous work that, to the best
+    of my knowledge, is covered under an appropriate open source
+    license and I have the right under that license to submit that
+    work with modifications, whether created in whole or in part
+    by me, under the same open source license (unless I am
+    permitted to submit under a different license), as indicated
+    in the file; or
+
+(c) The contribution was provided directly to me by some other
+    person who certified (a), (b) or (c) and I have not modified
+    it.
+
+(d) I understand and agree that this project and the contribution
+    are public and that a record of the contribution (including all
+    personal information I submit with it, including my sign-off) is
+    maintained indefinitely and may be redistributed consistent with
+    this project or the open source license(s) involved.

avogadro-1.102.0/.github/codeql-config.yml

@@ -0,0 +1,8 @@
+query-filters:
+  - exclude:
+      id: cpp/integer-multiplication-cast-to-long
+paths-ignore:
+  - '**/moc_*.*'
+  - '**/ui_*.h'
+  - 'thirdparty/**/*.*'
+  - 'utilities/**/*.*'

avogadro-1.102.0/.github/config.yml

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+# Configuration for welcome - https://github.com/behaviorbot/welcome
+
+# Configuration for new-issue-welcome - https://github.com/behaviorbot/new-issue-welcome
+
+# Comment to be posted to on first time issues
+newIssueWelcomeComment: >
+  Thanks for opening your first issue here! Please try to include example files and screenshots if possible.
+  If you're looking for support, please post on our forum: https://discuss.avogadro.cc/
+# Configuration for new-pr-welcome - https://github.com/behaviorbot/new-pr-welcome
+
+# Comment to be posted to on PRs from first time contributors in your repository
+newPRWelcomeComment: >
+  Thanks for opening this pull request! Please check out our contributing guidelines and check for the automated tests.
+# Configuration for first-pr-merge - https://github.com/behaviorbot/first-pr-merge
+
+# Comment to be posted to on pull requests merged by a first time user
+firstPRMergeComment: >
+  Congrats on merging your first pull request! 🎉 Thanks for making Avogadro better for everyone!

avogadro-1.102.0/.github/dependabot.yml

@@ -0,0 +1,10 @@
+# Set update schedule for GitHub Actions
+
+version: 2
+updates:
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      # Check for updates to GitHub Actions every weekday
+      interval: "daily"

avogadro-1.102.0/.github/release-drafter.yml

@@ -0,0 +1,58 @@
+name-template: 'Avogadro $RESOLVED_VERSION'
+tag-template: '$RESOLVED_VERSION'
+categories:
+  - title: '✨ Features'
+    labels:
+      - 'feature'
+      - 'enhancement'
+  - title: '🐛 Bug Fixes'
+    labels:
+      - 'fix'
+      - 'bugfix'
+      - 'bug'
+  - title: '🚀 Performance Improvements'
+    labels:
+      - 'speed'
+  - title: '🧰 Maintenance'
+    labels:
+      - 'chore'
+      - 'build'
+  - title: '📚 Translations'
+    labels:
+      - 'i18n'
+autolabeler:
+  - label: 'build'
+    branch:
+      - '/build\/.+/'
+    title:
+      - '/build/i'
+  - label: 'bug'
+    branch:
+      - '/fix\/.+/'
+    title:
+      - '/fix/i'
+  - label: 'i18n'
+    branch:
+      - '/weblate\/.+/'
+change-template: '- $TITLE @$AUTHOR (#$NUMBER)'
+change-title-escapes: '\<*_&' # You can add # and @ to disable mentions, and add ` to disable code blocks.
+version-resolver:
+  major:
+    labels:
+      - 'major'
+  minor:
+    labels:
+      - 'minor'
+  patch:
+    labels:
+      - 'patch'
+  default: minor
+template: |
+  ## Changes
+
+  $CHANGES
+
+  ## Credits
+
+  Thanks to many contributors, including: $CONTRIBUTORS
+  

avogadro-1.102.0/.github/workflows/add_artifact_urls.yml

@@ -0,0 +1,21 @@
+name: add artifact links to pull request
+on:
+  workflow_run:
+    workflows: ['Qt5 Build Matrix']
+    types: [completed]
+
+jobs:
+  artifacts-url-comments:
+    name: add artifact links to pull request job
+    runs-on: windows-latest
+    steps:
+      - name: add artifact links to pull request step
+        uses: tonyhallett/artifacts-url-comments@v1.1.0
+        env:
+            GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+            prefix: Here are the build results
+            suffix: Artifacts will only be retained for 90 days.
+            format: name
+            addTo: pull
+        continue-on-error: true

avogadro-1.102.0/.github/workflows/build_flatpak.yml

@@ -0,0 +1,105 @@
+name: Build Flatpak
+
+on: [push, pull_request, workflow_dispatch]
+
+jobs:
+  flatpak:
+    name: "Flatpak"
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Install dependencies
+      run: sudo apt update -qq && sudo apt install -y -qq flatpak
+
+    - name: Configure flatpak
+      run: flatpak remote-add --if-not-exists --user flathub https://dl.flathub.org/repo/flathub.flatpakrepo
+
+    - name: Install flatpak-builder
+      run: flatpak --user install --or-update --noninteractive flathub org.flatpak.Builder
+
+    - name: Configure git
+      run: git config --global protocol.file.allow always
+      # Have to do this because for a while git's handling of submodules was broken
+      # See https://github.com/flatpak/flatpak-builder/issues/495
+
+    - name: Checkout openchemistry
+      uses: actions/checkout@v5.0.0
+      with:
+        repository: openchemistry/openchemistry
+        submodules: false
+        path: openchemistry
+
+    - name: Checkout avogadroapp
+      uses: actions/checkout@v5.0.0
+      with:
+        repository: openchemistry/avogadroapp
+        path: openchemistry/avogadroapp
+
+    - name: Checkout avogadrolibs
+      uses: actions/checkout@v5.0.0
+      with:
+        path: openchemistry/avogadrolibs
+
+    - name: Checkout i18n
+      uses: actions/checkout@v5.0.0
+      with:
+        repository: openchemistry/avogadro-i18n
+        path: openchemistry/avogadro-i18n
+
+    - name: Checkout avogadrogenerators
+      uses: actions/checkout@v5.0.0
+      with:
+        repository: openchemistry/avogenerators
+        path: openchemistry/avogadrogenerators
+
+    - name: Checkout crystals
+      uses: actions/checkout@v5.0.0
+      with:
+        repository: openchemistry/crystals
+        path: openchemistry/crystals
+
+    - name: Checkout fragments
+      uses: actions/checkout@v5.0.0
+      with:
+        repository: openchemistry/fragments
+        path: openchemistry/fragments
+
+    - name: Checkout molecules
+      uses: actions/checkout@v5.0.0
+      with:
+        repository: openchemistry/molecules
+        path: openchemistry/molecules
+
+    - name: Checkout Flathub shared-modules
+      uses: actions/checkout@v5.0.0
+      with:
+        repository: flathub/shared-modules
+        path: shared-modules
+
+    - name: Set up tmate session
+      if: failure()
+      uses: mxschmitt/action-tmate@v3
+      timeout-minutes: 60
+
+    - name: Move manifest
+      run: mv openchemistry/avogadroapp/flatpak/org.openchemistry.Avogadro2.yaml ./
+
+    - name: Build with flatpak-builder
+      run: dbus-run-session flatpak run org.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 test
+
+    - name: Upload bundle
+      uses: actions/upload-artifact@v4
+      with:
+        path: Avogadro2.flatpak
+
+    - name: Cleanup
+      if: ${{ always() }} # To ensure this step runs even when earlier steps fail
+      shell: bash
+      run: |
+        ls -la ./
+        rm -rf ./* || true
+        rm -rf ./.??* || true
+        ls -la ./

avogadro-1.102.0/.github/workflows/build_linux.yml

@@ -0,0 +1,210 @@
+name: Linux Build Matrix
+# Many thanks to Cristian Adam for examples
+# e.g. https://github.com/cristianadam/HelloWorld/blob/master/.github/workflows/build_cmake.yml
+# https://cristianadam.eu/20191222/using-github-actions-with-c-plus-plus-and-cmake/
+
+on: [push, pull_request, workflow_dispatch]
+
+env:
+  QT_VERSION: 6.8.3
+  FEATURES: -DBUILD_GPL_PLUGINS=ON -DBUILD_MOLEQUEUE=OFF -DWITH_COORDGEN=OFF -DQT_VERSION=6
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build:
+    name: ${{ matrix.config.name }}
+    runs-on: ${{ matrix.config.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+        - {
+            name: "Ubuntu x86", artifact: "",
+            os: ubuntu-latest,
+            cc: "gcc", cxx: "g++",
+            build_type: "Release",
+            cmake_flags: "-G Ninja -DUSE_SYSTEM_EIGEN=TRUE",
+          }
+        #- {
+        #    name: "Ubuntu ARM", artifact: "",
+        #    os: ubuntu-24.04-arm,
+        #    cc: "gcc", cxx: "g++",
+        #    build_type: "Release",
+        #    cmake_flags: "-G Ninja -DUSE_SYSTEM_EIGEN=TRUE",
+        #  }
+        - {
+            name: "AppImage x86", artifact: "Avogadro2-x86_64.AppImage",
+            os: ubuntu-22.04,
+            cc: "gcc", cxx: "g++",
+            build_type: "Release",
+            cmake_flags: "-G Ninja -DUSE_SYSTEM_EIGEN=TRUE -DINSTALL_BUNDLE_FILES=ON -DUSE_YAEHMOP=ON",
+          }
+        #- {
+        #    name: "AppImage ARM", artifact: "Avogadro2-arm64.AppImage",
+        #    os: ubuntu-22.04-arm,
+        #    cc: "gcc", cxx: "g++",
+        #    build_type: "Release",
+        #    cmake_flags: "-G Ninja -DINSTALL_BUNDLE_FILES=ON",
+        #  }
+        - {
+            name: "Ubuntu Address Sanitizer", artifact: "",
+            os: ubuntu-latest,
+            cc: "gcc", cxx: "g++",
+            build_type: "asan",
+            cmake_flags: "-G Ninja -DUSE_SYSTEM_EIGEN=TRUE -DENABLE_TESTING=ON -DTEST_QTGL=OFF -USE_SYSTEM_ZLIB=ON",
+          }
+        - {
+            name: "Ubuntu Undefined Behavior Sanitizer", artifact: "",
+            os: ubuntu-latest,
+            cc: "gcc", cxx: "g++",
+            build_type: "ubsan",
+            cmake_flags: "-G Ninja -DUSE_SYSTEM_EIGEN=TRUE -DENABLE_TESTING=ON -DTEST_QTGL=OFF -USE_SYSTEM_ZLIB=ON",
+          }
+        - {
+            name: "Ubuntu Leak Sanitizer", artifact: "",
+            os: ubuntu-latest,
+            cc: "gcc", cxx: "g++",
+            build_type: "lsan",
+            cmake_flags: "-G Ninja -DUSE_SYSTEM_EIGEN=TRUE -DENABLE_TESTING=ON -DTEST_QTGL=OFF -USE_SYSTEM_ZLIB=ON",
+          }
+        - {
+            name: "Ubuntu Thread Sanitizer", artifact: "",
+            os: ubuntu-latest,
+            cc: "gcc", cxx: "g++",
+            build_type: "tsan",
+            cmake_flags: "-G Ninja -DUSE_SYSTEM_EIGEN=TRUE -DENABLE_TESTING=ON -DTEST_QTGL=OFF -USE_SYSTEM_ZLIB=ON",
+          }
+
+    steps:
+
+    - name: Install Dependencies
+      run: |
+        sudo apt-get -qq update
+        sudo apt-get -qq install ninja-build libeigen3-dev libboost-all-dev libglew-dev libxml2-dev
+        sudo apt-get -qq install libfuse2
+
+    - name: Checkout openchemistry
+      uses: actions/checkout@v5.0.0
+      with:
+        repository: openchemistry/openchemistry
+        submodules: recursive
+        path: openchemistry
+
+    - name: Checkout avogadroapp
+      uses: actions/checkout@v5.0.0
+      with:
+        repository: openchemistry/avogadroapp
+        path: openchemistry/avogadroapp
+
+    - name: Checkout avogadrolibs
+      uses: actions/checkout@v5.0.0
+      with:
+        path: openchemistry/avogadrolibs
+
+    - name: Checkout i18n
+      uses: actions/checkout@v5.0.0
+      with:
+        repository: openchemistry/avogadro-i18n
+        path: openchemistry/avogadro-i18n
+
+    - name: Checkout avogadrogenerators
+      uses: actions/checkout@v5.0.0
+      with:
+        repository: openchemistry/avogenerators
+        path: openchemistry/avogadrogenerators
+
+    - name: Checkout crystals
+      uses: actions/checkout@v5.0.0
+      with:
+        repository: openchemistry/crystals
+        path: openchemistry/crystals
+
+    - name: Checkout fragments
+      uses: actions/checkout@v5.0.0
+      with:
+        repository: openchemistry/fragments
+        path: openchemistry/fragments
+
+    - name: Checkout molecules
+      uses: actions/checkout@v5.0.0
+      with:
+        repository: openchemistry/molecules
+        path: openchemistry/molecules
+
+    - name: Install Qt
+      uses: jurplel/install-qt-action@v4
+      with:
+        version: ${{ env.QT_VERSION }}
+
+    - name: Configure
+      run: |
+        if [ ! -d "${{ runner.workspace }}/build" ]; then mkdir "${{ runner.workspace }}/build"; fi
+        cd "${{ runner.workspace }}/build"
+        CC=${{matrix.config.cc}} CXX=${{matrix.config.cxx}} cmake $GITHUB_WORKSPACE/openchemistry ${{env.FEATURES}} -DCMAKE_BUILD_TYPE=${{matrix.config.build_type}} ${{matrix.config.cmake_flags}}
+      shell: bash
+
+    - name: Build
+      run: |
+        CC=${{matrix.config.cc}} CXX=${{matrix.config.cxx}} cmake --build . --config ${{matrix.config.build_type}} ${{matrix.config.build_flags}}
+      shell: bash
+      working-directory: ${{ runner.workspace }}/build
+
+    - name: Run tests
+      if: (matrix.config.build_type != 'Release')
+      shell: cmake -P {0}
+      run: |
+        include(ProcessorCount)
+        ProcessorCount(N)
+        set(ENV{CTEST_OUTPUT_ON_FAILURE} "ON")
+        set(ENV{ASAN_OPTIONS} "new_delete_type_mismatch=0")
+        execute_process(
+          COMMAND ctest -j ${N}
+          WORKING_DIRECTORY ${{ runner.workspace }}/build/avogadrolibs
+          RESULT_VARIABLE result
+        )
+        if (NOT result EQUAL 0)
+          message(FATAL_ERROR "Running tests failed!")
+        endif()
+
+    - name: Package AppImage
+      if: matrix.config.name == 'AppImage x86'
+      shell: bash
+      run: |
+        mkdir appdir
+        mv prefix appdir/usr
+
+        export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:appdir/usr/lib
+
+        wget -c -nv "https://github.com/linuxdeploy/linuxdeploy/releases/download/continuous/linuxdeploy-x86_64.AppImage"
+        wget -c -nv "https://github.com/linuxdeploy/linuxdeploy-plugin-qt/releases/download/continuous/linuxdeploy-plugin-qt-x86_64.AppImage"
+        wget -c -nv "https://github.com/AppImage/AppImageKit/releases/download/continuous/appimagetool-x86_64.AppImage"
+        chmod a+x *.AppImage
+
+        # get pixi
+        wget -c -nv "https://github.com/prefix-dev/pixi/releases/latest/download/pixi-x86_64-unknown-linux-musl"
+        mv pixi-x86_64-unknown-linux-musl appdir/usr/bin/pixi
+
+        # Though it is not great security practice, bundle libssl and libcrypto
+        ./linuxdeploy-x86_64.AppImage -d appdir/usr/share/applications/*.desktop --plugin qt --library /lib/x86_64-linux-gnu/libssl.so.3 --library /lib/x86_64-linux-gnu/libcrypto.so.3 --appdir appdir
+        # add the custom AppRun
+        rm appdir/AppRun
+        cp ../avogadrolibs/openchemistry/avogadrolibs/scripts/AppImage.sh appdir/AppRun
+        chmod a+x appdir/AppRun
+        ./appimagetool-x86_64.AppImage appdir
+        mv Avogadro*.AppImage avogadroapp/Avogadro2-x86_64.AppImage # for upload
+      working-directory: ${{ runner.workspace }}/build
+
+    - name: Upload
+      if: matrix.config.artifact != 0
+      uses: actions/upload-artifact@v4
+      with:
+        path: ${{ runner.workspace }}/build/avogadroapp/Avogadro2*.*
+        name: ${{ matrix.config.artifact }}
+
+    - name: Setup tmate session
+      if: ${{ failure() }}
+      uses: mxschmitt/action-tmate@v3
+      timeout-minutes: 60