org.pymol.PyMOL.yaml

app-id: org.pymol.PyMOL
runtime: org.kde.Platform
sdk: org.kde.Sdk
runtime-version: 5.15-23.08
base: com.riverbankcomputing.PyQt.BaseApp
base-version: 5.15-23.08
build-options:
  env:
    - BASEAPP_REMOVE_WEBENGINE=1
command: pymol
finish-args:
  - --share=ipc
  - --socket=x11
  - --device=dri
  - --share=network
modules:
  - shared-modules/glew/glew.json

  - name: python-numpy
    buildsystem: simple
    build-commands:
      - python3 setup.py install --prefix=/app --root=/
    sources:
      - type: archive
        url: https://files.pythonhosted.org/packages/65/6e/09db70a523a96d25e115e71cc56a6f9031e7b8cd166c1ac8438307c14058/numpy-1.26.4.tar.gz
        sha256: 2a02aba9ed12e4ac4eb3ea9421c420301a0c6460d9830d74a9df87efa4912010
        x-checker-data:
          type: pypi
          name: numpy

  - name: msgpack
    buildsystem: cmake-ninja
    config-opts:
      - -DBUILD_SHARED_LIBS=ON
      - -DMSGPACK_ENABLE_STATIC=OFF
      - -DCMAKE_INSTALL_LIBDIR=lib
      - -DMSGPACK_BUILD_EXAMPLES=OFF
      - -DMSGPACK_CXX11=ON
    cleanup:
      - /include
      - /lib/cmake
      - /lib/pkgconfig
      - '*.a'
    sources:
      - type: archive
        url: https://github.com/msgpack/msgpack-c/releases/download/cpp-3.3.0/msgpack-3.3.0.tar.gz
        sha256: 6e114d12a5ddb8cb11f669f83f32246e484a8addd0ce93f274996f1941c1f07b
        # x-checker-data:
        #   type: anitya
        #   project-id: 12278
        #   stable-only: true
        #   url-template: https://github.com/msgpack/msgpack-c/releases/download/cpp-$version/msgpack-$version.tar.gz

  - name: hdf5
    buildsystem: cmake-ninja
    builddir: true
    config-opts:
      - -DCMAKE_BUILD_TYPE=Release
      - -DBUILD_TESTING:BOOL=OFF
      - -DHDF5_BUILD_EXAMPLES:BOOL=OFF
      - -DHDF5_ENABLE_Z_LIB_SUPPORT:BOOL=ON
      - -DDEFAULT_API_VERSION:STRING=v18
    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: netcdf
    buildsystem: cmake-ninja
    builddir: true
    config-opts:
      - -DCMAKE_BUILD_TYPE=Release
    sources:
      - type: archive
        url: https://github.com/Unidata/netcdf-c/archive/v4.9.2.tar.gz
        sha256: bc104d101278c68b303359b3dc4192f81592ae8640f1aee486921138f7f88cb7
        x-checker-data:
          type: anitya
          project-id: 10354
          stable-only: true
          url-template: https://github.com/Unidata/netcdf-c/archive/v$version.tar.gz

  - name: mmtf-cpp
    buildsystem: cmake-ninja
    sources:
      - type: archive
        url: https://github.com/rcsb/mmtf-cpp/archive/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/v$version.tar.gz

  - name: python-mmtf-python
    buildsystem: simple
    build-commands:
      - python3 setup.py install --prefix=${FLATPAK_DEST} --root=/ --optimize=1
    sources:
      - type: archive
        url: https://files.pythonhosted.org/packages/d8/0f/f3c132dc9aac9a3f32a0eba7a80f07d14e7624e96f9245eeac5fe48f42cd/mmtf-python-1.1.3.tar.gz
        sha256: 12a02fe1b7131f0a2b8ce45b46f1e0cdd28b9818fe4499554c26884987ea0c32
        x-checker-data:
          type: pypi
          name: mmtf-python

  - name: glm
    buildsystem: simple
    build-commands:
      - cp -r glm /app/include
    sources:
      - type: git
        url: https://github.com/g-truc/glm
        tag: 1.0.1
        commit: 0af55ccecd98d4e5a8d1fad7de25ba429d60e863
        x-checker-data:
          type: git
          tag-pattern: ([\d.]+)$

  #- name: openmpi
    #sources:
      #- type: archive
        #url: https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.1.tar.bz2
        #sha256: e24f7a778bd11a71ad0c14587a7f5b00e68a71aa5623e2157bafee3d44c07cda

    # For VTK-m
  #- name: TBB
    #buildsystem: cmake
    #builddir: true
    #sources:
      #- type: archive
        #url: https://github.com/oneapi-src/oneTBB/archive/refs/tags/v2021.2.0.tar.gz
        #sha256: cee20b0a71d977416f3e3b4ec643ee4f38cedeb2a9ff015303431dd9d8d79854

    #For VTK-m
  #- name: TBB
    #buildsystem: simple
    #build-commands:
      #- make -j $FLATPAK_BUILDER_N_JOBS
      #- install -d /app/lib
      #- install -m755 build/linux_*/*.so* /app/lib
      #- install -d /app/include
      #- cp -a include/tbb /app/include
    #sources:
      #- type: archive
        #url: https://github.com/oneapi-src/oneTBB/archive/refs/tags/2020_U3.tar.gz
        #sha256: 2103cc6238c935664f87680618f6684d57501d4a2fa8ea8f6c97ad6ff7dc722a

    # Enable VTK-m in PyMOL
  #- name: VTK-m
    #buildsystem: cmake
    #builddir: true
    #config-opts:
      #- -DCMAKE_BUILD_TYPE:STRING=Release
      #- -DVTKm_ENABLE_KOKKOS:BOOL=ON
      #- -DVTKm_ENABLE_OPENMP:BOOL=ON
      #- -DVTKm_ENABLE_TBB:BOOL=ON
      #- -DVTKm_ENABLE_RENDERING:BOOL=ON
      #- -DVTKm_ENABLE_MPI:BOOL=ON
    #sources:
      #- type: git
        #url: https://gitlab.kitware.com/vtk/vtk-m/
        #tag: v1.5.1
        #commit: 74ffad9bd0679d061bc87e544a728f1c3c926269
  - name: PyMOL
    buildsystem: simple
    #build-options:
      #env:
        #PREFIX_PATH: "/app:/usr"
    build-commands:
      - python3 setup.py install --prefix=${FLATPAK_DEST} --pymol-path=/app/share/pymol
      - install -Dm644 data/pymol/icons/icon2.svg ${FLATPAK_DEST}/share/icons/hicolor/scalable/apps/${FLATPAK_ID}.svg
      - install -Dm644 ${FLATPAK_ID}.desktop ${FLATPAK_DEST}/share/applications/${FLATPAK_ID}.desktop
      - install -Dm644 ${FLATPAK_ID}.metainfo.xml ${FLATPAK_DEST}/share/metainfo/${FLATPAK_ID}.metainfo.xml
    sources:
      - type: archive
        url: https://github.com/schrodinger/pymol-open-source/archive/v3.0.0.tar.gz
        sha256: 45e800a02680cec62dff7a0f92283f4be7978c13a02934a43ac6bb01f67622cf
        x-checker-data:
          type: anitya
          project-id: 100773
          stable-only: true
          url-template: https://github.com/schrodinger/pymol-open-source/archive/v$version.tar.gz
      - type: file
        path: org.pymol.PyMOL.metainfo.xml
      - type: file
        path: org.pymol.PyMOL.desktop