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org.openchemistry.Avogadro2.yaml
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org.openchemistry.Avogadro2.yaml
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app-id: org.openchemistry.Avogadro2
runtime: org.kde.Platform
sdk: org.kde.Sdk
runtime-version: 5.15-23.08
command: avogadro2
rename-desktop-file: avogadro2.desktop
finish-args:
- --share=ipc
# Broke in Wayland
#- --socket=wayland
- --socket=x11
- --device=dri
- --filesystem=home
# Molequeue enjoy its life in the menu tray.
- --talk-name=org.freedesktop.Notifications
- --talk-name=org.kde.StatusNotifierWatcher
# Allow Avogadro to communicate with Molequeue.
- --share=network
- --talk-name=org.freedesktop.DBus
- --talk-name=org.freedesktop.DBus.Proprieties
- --system-talk-name=org.freedesktop.DBus
- --system-talk-name=org.freedesktop.DBus.Proprieties
cleanup:
- /include
- /lib/cmake
- /share/doc
- '*.la'
- '*.a'
modules:
- shared-modules/glew/glew.json
- shared-modules/glu/glu-9.json
- name: OpenBLAS
buildsystem: cmake-ninja
builddir: true
config-opts:
- -DBUILD_TESTING:BOOL=OFF
- -DDYNAMIC_ARCH:BOOL=ON
sources:
- type: archive
url: https://github.com/xianyi/OpenBLAS/archive/v0.3.28.tar.gz
sha256: f1003466ad074e9b0c8d421a204121100b0751c96fc6fcf3d1456bd12f8a00a1
x-checker-data:
type: anitya
project-id: 2540
url-template: https://github.com/xianyi/OpenBLAS/archive/v$version.tar.gz
- name: meson
buildsystem: simple
build-commands:
- python3 setup.py build
- python3 setup.py install --prefix=/app --root=/
sources:
- type: git
url: https://github.com/mesonbuild/meson.git
tag: 1.6.0
commit: 4c6c89ca7afa6244ba888ce08936acb470e126aa
x-checker-data:
type: git
tag-pattern: ^([\d.]+)$
# python3 flatpak-pip-generator tomli packaging pyproject_metadata exceptiongroup meson-python -o python_deps && fb
- python_deps.json
- name: python-numpy
buildsystem: simple
build-options:
ldflags: -lgfortran
build-commands:
- pip3 install --no-index --find-links=file://${PWD} --prefix=${FLATPAK_DEST}
--no-build-isolation .
sources:
- type: archive
url: https://files.pythonhosted.org/packages/65/6e/09db70a523a96d25e115e71cc56a6f9031e7b8cd166c1ac8438307c14058/numpy-1.26.4.tar.gz
sha256: 2a02aba9ed12e4ac4eb3ea9421c420301a0c6460d9830d74a9df87efa4912010
# Don't update to numpy 2.0
# x-checker-data:
# type: pypi
# name: numpy
- name: pybind11
buildsystem: cmake-ninja
builddir: true
config-opts:
- -DPYBIND11_INSTALL:BOOL=ON
- -DPYBIND11_TEST:BOOL=OFF
- -DPYTHON_INCLUDE_DIRS=/usr/include/python3.11
sources:
- type: archive
url: https://github.com/pybind/pybind11/archive/v2.13.6.tar.gz
sha256: e08cb87f4773da97fa7b5f035de8763abc656d87d5773e62f6da0587d1f0ec20
x-checker-data:
type: anitya
project-id: 13384
stable-only: true
url-template: https://github.com/pybind/pybind11/archive/v$version.tar.gz
- name: Eigen3
buildsystem: cmake-ninja
builddir: true
sources:
- type: archive
url: https://gitlab.com/libeigen/eigen/-/archive/3.4.0/eigen-3.4.0.tar.bz2
sha256: b4c198460eba6f28d34894e3a5710998818515104d6e74e5cc331ce31e46e626
x-checker-data:
type: anitya
project-id: 13751
stable-only: true
url-template: https://gitlab.com/libeigen/eigen/-/archive/$version/eigen-$version.tar.bz2
cleanup:
- '*'
- name: hdf5
buildsystem: cmake-ninja
builddir: true
config-opts:
- -DBUILD_TESTING:BOOL=OFF
- -DHDF5_BUILD_EXAMPLES:BOOL=OFF
cleanup:
- /share/hdf5_examples
sources:
- type: archive
url: https://github.com/HDFGroup/hdf5/archive/refs/tags/hdf5-1_14_3.tar.gz
sha256: df5ee33c74d5efb59738075ef96f4201588e1f1eeb233f047ac7fd1072dee1f6
x-checker-data:
type: anitya
project-id: 1303
stable-only: true
url-template: https://github.com/HDFGroup/hdf5/archive/refs/tags/hdf5-$version.tar.gz
- name: libmsym
buildsystem: cmake
config-opts:
- -DMSYM_BUILD_PYTHON:BOOL=ON
- -DBUILD_SHARED_LIBS:BOOL=ON
sources:
- type: archive
url: https://github.com/mcodev31/libmsym/archive/refs/tags/v0.2.3-paper.tar.gz
sha256: 3741ebe163cf40696570d6b62e4834ca587d43dcac9de713994cc5e2960fb8fd
x-checker-data:
type: anitya
project-id: 221475
stable-only: true
url-template: https://github.com/mcodev31/libmsym/archive/refs/tags/v$version.tar.gz
- name: mmtf-cpp
buildsystem: cmake
config-opts:
- -DBUILD_TESTS:BOOL=OFF
- -Dmmtf_build_local:BOOL=OFF
- -Dmmtf_build_examples:BOOL=OFF
sources:
- type: archive
url: https://github.com/rcsb/mmtf-cpp/archive/refs/tags/v1.1.0.tar.gz
sha256: 021173bdc1814b1d0541c4426277d39df2b629af53151999b137e015418f76c0
x-checker-data:
type: anitya
project-id: 221487
stable-only: true
url-template: https://github.com/rcsb/mmtf-cpp/archive/refs/tags/v$version.tar.gz
- name: msgpack
buildsystem: cmake
config-opts:
- -DCMAKE_INSTALL_PREFIX:PATH=/app
- -DBUILD_SHARED_LIBS:BOOL=ON
- -DMSGPACK_ENABLE_STATIC:BOOL=OFF
- -DCMAKE_INSTALL_LIBDIR:PATH=lib
- -DMSGPACK_BUILD_EXAMPLES:BOOL=OFF
- -DMSGPACK_CXX17:BOOL=ON
sources:
- type: archive
url: https://github.com/msgpack/msgpack-c/releases/download/cpp-3.3.0/msgpack-3.3.0.tar.gz
sha256: 6e114d12a5ddb8cb11f669f83f32246e484a8addd0ce93f274996f1941c1f07b
- name: OpenBabel
buildsystem: cmake
builddir: true
config-opts:
- -DENABLE_TESTS:BOOL=OFF
- -DBUILD_GUI:BOOL=OFF
- -DOPTIMIZE_NATIVE:BOOL=OFF
- -DOB_USE_PREBUILT_BINARIES:BOOL=OFF
- -DENABLE_VERSIONED_FORMATS:BOOL=OFF
- -DWITH_JSON:BOOL=OFF
- -DWITH_MAEPARSER:BOOL=OFF
sources:
- type: archive
url: https://github.com/openbabel/openbabel/releases/download/openbabel-3-1-1/openbabel-3.1.1-source.tar.bz2
sha256: a6ec8381d59ea32a4b241c8b1fbd799acb52be94ab64cdbd72506fb4e2270e68
x-checker-data:
type: anitya
project-id: 2539
stable-only: true
url-template: https://github.com/openbabel/openbabel/releases/download/openbabel-3-1-1/openbabel-$version-source.tar.bz2
- type: patch
path: openbabel_time.patch
- name: zeromq
buildsystem: cmake-ninja
builddir: true
sources:
- type: archive
url: https://github.com/zeromq/libzmq/releases/download/v4.3.5/zeromq-4.3.5.tar.gz
sha256: 6653ef5910f17954861fe72332e68b03ca6e4d9c7160eb3a8de5a5a913bfab43
x-checker-data:
type: anitya
project-id: 16245
stable-only: true
url-template: https://github.com/zeromq/libzmq/releases/download/v$version/zeromq-$version.tar.gz
- name: spglib
buildsystem: cmake
builddir: true
config-opts:
- -DSPGLIB_WITH_Fortran=ON
- -DSPGLIB_WITH_Python=ON
- -DSPGLIB_USE_OMP=OFF
- -DSPGLIB_WITH_TESTS=OFF
- -DSPGLIB_SHARED_LIBS=ON
- -DSPGLIB_INSTALL=ON
- -DSPGLIB_TEST_COVERAGE=OFF
- -DPython3_NumPy_INCLUDE_DIR=/app/lib/python3.11/site-packages/numpy/core/include
- -DPython_INSTALL_DIR=/app/lib/python3.11/site-packages/spglib
- -DCMAKE_INSTALL_RPATH=/app/lib
sources:
- type: archive
url: https://github.com/spglib/spglib/archive/refs/tags/v2.5.0.tar.gz
sha256: 80c060b1a606a76b15f2cc708e9fdd4a83479924ebff9ac16ed26a87a0eac1a9
x-checker-data:
type: anitya
project-id: 14891
stable-only: true
url-template: https://github.com/spglib/spglib/archive/refs/tags/v$version.tar.gz
- name: MoleQueue
buildsystem: simple
build-commands:
- install -Dm0644 molequeue/app/icons/molequeue.png /app/share/icons/hicolor/32x32/apps/${FLATPAK_ID}.Molequeue.png
- cmake -DENABLE_TESTING:BOOL=OFF -DBUILD_DOCUMENTATION:BOOL=OFF -DCMAKE_INSTALL_PREFIX:PATH=/app
-Wno-dev .
- cmake --build .
- cmake --install .
- install -Dm0644 ${FLATPAK_ID}.Molequeue.desktop ${FLATPAK_DEST}/share/applications/${FLATPAK_ID}.Molequeue.desktop
- desktop-file-validate ${FLATPAK_DEST}/share/applications/${FLATPAK_ID}.Molequeue.desktop
sources:
- type: archive
url: https://github.com/OpenChemistry/molequeue/releases/download/0.9.0/molequeue-0.9.0.tar.bz2
sha256: 2825fa9645fca707796ad32967c307bec76dab4f6c305befeebeac8c7f7f2ef0
x-checker-data:
type: anitya
project-id: 13839
stable-only: true
url-template: https://github.com/OpenChemistry/molequeue/releases/download/$version/molequeue-$version.tar.bz2
- type: file
path: org.openchemistry.Avogadro2.Molequeue.desktop
# Avogadrolibs does not build with VTK 9.0.1
# https://github.com/OpenChemistry/avogadrolibs/issues/516
- name: VTK
buildsystem: cmake-ninja
builddir: true
config-opts:
- -DBUILD_SHARED_LIBS=ON
- -DOpenGL_GL_PREFERENCE=GLVND
- -DBUILD_TESTING:BOOL=OFF
- -DVTK_GROUP_ENABLE_Qt:BOOL=YES
- -DVTK_BUILD_COMPILE_TOOLS_ONLY:BOOL=OFF
sources:
- type: archive
url: https://www.vtk.org/files/release/9.3/VTK-9.3.0.tar.gz
sha256: fdc7b9295225b34e4fdddc49cd06e66e94260cb00efee456e0f66568c9681be9
- name: avogadrolibs
buildsystem: cmake-ninja
builddir: true
subdir: avogadrolibs
config-opts:
- -DOpenGL_GL_PREFERENCE=GLVND
- -DUSE_SYSTEM_GENXRDPATTERN:BOOL=ON
- -DCMAKE_BUILD_TYPE:STRING=Release
- -DENABLE_TRANSLATIONS:BOOL=ON
- -DUSE_HDF5:BOOL=ON
- -DUSE_PYTHON:BOOL=ON
- -DUSE_QT:BOOL=ON
- -DUSE_LIBMSYM:BOOL=ON
- -DUSE_SPGLIB:BOOL=ON
- -DUSE_MMTF:BOOL=ON
- -DUSE_VTK:BOOL=ON
- -DBUILD_GPL_PLUGINS:BOOL=ON
- -DBUILD_STATIC_PLUGINS:BOOL=ON
- -DENABLE_TESTING:BOOL=OFF
- -DOpenBabel3_INCLUDE_DIR=/app/include/openbabel3
# - -DPython_SITEARCH=/app/lib
sources:
- type: archive
url: https://github.com/OpenChemistry/avogadrolibs/archive/refs/tags/1.99.0.tar.gz
sha256: 34808e3c602b0f60f3c160ff0220832aee777db86e962e3f958c6327fb434063
dest: avogadrolibs
x-checker-data:
type: git
tag-pattern: ^([\d.]+)$
# Fix upstream https://github.com/OpenChemistry/avogadrolibs/pull/1612
- type: patch
path: fix_fragments.patch
- type: patch
path: fix_python_install_dir.patch
- type: archive
url: https://github.com/OpenChemistry/molecules/archive/refs/heads/master.zip
sha256: 18177d79f484e3dc5346b76532e69690f93f2e9e93a0a37fa19edc70bc4ec2df
dest: molecules
dest-filename: molecules.zip
- type: archive
url: https://github.com/OpenChemistry/crystals/archive/refs/heads/master.zip
sha256: fb662b30b3454e68e87002ac59797fc9264b21a65dda78690f627ab02701bf51
dest: crystals
dest-filename: crystals.zip
- type: archive
url: https://github.com/OpenChemistry/molecules/archive/refs/heads/master.zip
sha256: 18177d79f484e3dc5346b76532e69690f93f2e9e93a0a37fa19edc70bc4ec2df
dest: fragments
dest-filename: fragments.zip
- name: Avogadro2
subdir: Avogadro2
buildsystem: cmake-ninja
config-opts:
- -DENABLE_RPATH:BOOL=ON
- -DENABLE_TESTING:BOOL=OFF
- -DBUILD_DOCUMENTATION:BOOL=OFF
- -DCMAKE_BUILD_TYPE:STRING=Release
- -DEIGEN3_INCLUDE_DIR=/app/include/eigen3
build-options:
ldflags: -Wl,--copy-dt-needed-entries
post-install:
- install -Dm644 avogadro/icons/avogadro2_64.png ${FLATPAK_DEST}/share/icons/hicolor/64x64/apps/${FLATPAK_ID}.png
- install -Dm644 avogadro/icons/avogadro2_128.png ${FLATPAK_DEST}/share/icons/hicolor/128x128/apps/${FLATPAK_ID}.png
- install -Dm644 avogadro/icons/avogadro2_256.png ${FLATPAK_DEST}/share/icons/hicolor/256x256/apps/${FLATPAK_ID}.png
- install -Dm644 avogadro/icons/avogadro2_512.png ${FLATPAK_DEST}/share/icons/hicolor/512x512/apps/${FLATPAK_ID}.png
- desktop-file-edit --set-icon=${FLATPAK_ID} ${FLATPAK_DEST}/share/applications/avogadro2.desktop
# Remove Education category fix Avogadro2 not appearing in menu entry, no clue why.
- desktop-file-edit --remove-category=Education ${FLATPAK_DEST}/share/applications/avogadro2.desktop
- install -Dm644 ${FLATPAK_ID}.metainfo.xml ${FLATPAK_DEST}/share/metainfo/${FLATPAK_ID}.metainfo.xml
sources:
- type: archive
url: https://github.com/OpenChemistry/avogadroapp/archive/refs/tags/1.99.0.tar.gz
sha256: 4713faa4e755433947924a381fd1631dfe46a9f27065765cfa04c120ed603189
dest: Avogadro2
x-checker-data:
type: anitya
project-id: 221509
stable-only: true
url-template: https://github.com/OpenChemistry/avogadroapp/archive/refs/tags/$version.tar.gz
- type: archive
url: https://github.com/OpenChemistry/avogadro-i18n/archive/refs/heads/master.zip
dest: avogadro-i18n
sha256: 1cf4b0221abd7e5c33ed8f05066db4424bc3501dccf7d50173623451213f8d36
- type: file
path: org.openchemistry.Avogadro2.metainfo.xml
dest: Avogadro2