io.github.pemsley.coot.yaml

app-id: io.github.pemsley.coot
runtime: org.gnome.Platform
runtime-version: '49'  # include python 3.13.9
sdk: org.gnome.Sdk
command: coot
finish-args:
  - --socket=x11
  - --socket=pulseaudio
  - --share=ipc
  - --device=dri
  - --filesystem=home
  - --share=network
  - --env=GDK_CORE_DEVICE_EVENTS=1
  - --env=GDK_DEBUG=gl-prefer-gl  # Refer to https://docs.gtk.org/gtk4/running.html#gdk_debug
  - --env=OPENBLAS_MAIN_FREE=1  # Refer to https://github.com/OpenMathLib/OpenBLAS/blob/develop/docs/runtime_variables.md
  - --env=COOT_PREFIX=/app
  - --env=CLIBD_MON=/app/share/coot/lib/data/monomers  # For acedrg
  - --env=LIBMOL_ROOT=/app  # For acedrg
  - --env=CCP4=/app  # For acedrg
  - --env=CBIN=/app/bin  # For acedrg
cleanup:
  - /include
  - /lib/pkgconfig
  - /lib/cmake
  - /share/aclocal
  - /share/doc
  - /share/info
  - /share/man
  - '*.la'
  - '*.a'

modules:
  - name: openblas
    buildsystem: cmake-ninja
    builddir: true
    config-opts:
      - -DCMAKE_BUILD_TYPE=Release
      - -DUSE_OPENMP=ON
      - -DUSE_THREAD=ON
      - -DNO_AFFINITY=ON
      - -DNUM_THREADS=64
      - -DBUILD_SHARED_LIBS=ON
      - -DDYNAMIC_ARCH=ON
    post-install:
      - ln -s /app/lib/libopenblas.so /app/lib/libblas.so
      - ln -s /app/lib/libopenblas.so /app/lib/liblapack.so
    cleanup:
      - /bin
    sources:
      - type: archive
        url: https://github.com/OpenMathLib/OpenBLAS/archive/v0.3.29.tar.gz
        sha256: 38240eee1b29e2bde47ebb5d61160207dc68668a54cac62c076bb5032013b1eb
        x-checker-data:
          type: anitya
          project-id: 2540
          stable-only: true
          url-template: https://github.com/OpenMathLib/OpenBLAS/archive/v$version.tar.gz
          versions:
            <: 0.3.30    # Refer to https://github.com/OpenMathLib/OpenBLAS/issues/5324

  # nanobind, numpy, omegaconf, packaging, pandas, scipy
  - deps/pypi-dependencies.json

  - name: eigen
    buildsystem: cmake-ninja
    builddir: true
    config-opts:
      - -DCMAKE_BUILD_TYPE=Release
      - -DCMAKE_POLICY_VERSION_MINIMUM=3.5
    sources:
      - type: archive
        url: https://gitlab.com/libeigen/eigen/-/archive/3.4.1/eigen-3.4.1.tar.gz
        sha256: b93c667d1b69265cdb4d9f30ec21f8facbbe8b307cf34c0b9942834c6d4fdbe2
        x-checker-data:
          type: anitya
          project-id: 13751
          stable-only: true
          url-template: https://gitlab.com/libeigen/eigen/-/archive/$version/eigen-$version.tar.gz
          versions:
            <: 4.0.0a0

  # Do not update automatically to match the gemmi version used by servalcat
  - name: gemmi
    buildsystem: cmake-ninja
    config-opts:
      - -DCMAKE_BUILD_TYPE=Release
      - -DUSE_PYTHON=ON
      - -DPYTHON_INSTALL_DIR=/app/lib/python3.13/site-packages
    build-options:
      cxxflags: -fPIC -O3
    sources:
      - type: archive
        url: https://github.com/project-gemmi/gemmi/archive/refs/tags/v0.7.4.tar.gz
        sha256: 58ed9023e0f75033ebec1da630461bc6e1af661f29f0c41deed66c20315ebe2a

  - name: servalcat
    buildsystem: simple
    build-commands:
      - |
        pip3 install . \
          --verbose \
          --no-deps \
          --no-index \
          --no-build-isolation \
          --prefix=${FLATPAK_DEST} \
          --config-settings="cmake.args=-Dnanobind_DIR=/app/lib/python3.13/site-packages/nanobind/cmake"
    sources:
      - type: archive
        url: https://files.pythonhosted.org/packages/7c/a9/f3eec5dcbd05385ff9941660c3d4894c643c1ee68d3d20f1fbb52d9c65ee/servalcat-0.4.131.tar.gz
        sha256: d4300bfba939b0f3592c71b905c8d9cb398ed4bdc4069e4f1c3ac0c6bef06eb0
        x-checker-data:
          type: pypi
          name: servalcat
      - type: shell
        commands:
          - rm -rf eigen/  # Use the eigen built above instead of vendorized one

  - name: acedrg
    buildsystem: cmake-ninja
    builddir: true
    config-opts:
      - -DCMAKE_BUILD_TYPE=Release
      - -DCMAKE_CXX_STANDARD=17
      - -DPython_EXECUTABLE=/usr/bin/python3
      - -DPYTHON_VERSION=3
      - -DPython_SITELIB=/app/lib/python3.13/site-packages
    build-options:
      cxxflags: -fPIC -O3
    post-install:
      - ln -sf /app/libexec/libmol /app/bin/libmol
    sources:
      - type: git
        url: https://ccp4forge.rc-harwell.ac.uk/ccp4/acedrg.git
        commit: 8e54f9bdfb21403e4b0b0a12c9abc11576c42094
      - type: shell
        commands:
          - sed -i '/find_package(Python/a set(Python_SITELIB "/app/lib/python3.13/site-packages")'
            CMakeLists.txt
          - grep -rlIZ --exclude-dir=.git 'ccp4-python' . | xargs -0 sed -i 's/ccp4-python/python/g'

  # Note: FFTW3 is NOT compatible with Clipper; use FFTW2 for Coot
  - name: fftw2
    buildsystem: autotools
    config-opts:
      - --enable-float
      - --disable-debug
      - --disable-docs
      - --disable-dependency-tracking
      - --disable-silent-rules
      - --enable-shared
      - --disable-static
      - --disable-Werror
    build-options:
      cflags: -fPIC -O3 -DNDEBUG
    sources:
      - type: archive
        url: https://fftw.org/fftw-2.1.5.tar.gz
        sha256: f8057fae1c7df8b99116783ef3e94a6a44518d49c72e2e630c24b689c6022630
      - type: shell
        commands:
          - cp -f /usr/share/libtool/build-aux/config.sub .
          - cp -f /usr/share/libtool/build-aux/config.guess .

  - name: mmdb2
    buildsystem: autotools
    config-opts:
      - --disable-debug
      - --disable-docs
      - --disable-dependency-tracking
      - --disable-silent-rules
      - --enable-shared
      - --disable-static
      - --disable-Werror
    build-options:
      cxxflags: -O2 -fPIC -fno-strict-aliasing -std=c++11 -DNDEBUG
    sources:
      - type: archive
        url: https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/mmdb2-2.0.22.tar.gz
        sha256: a9646933ce9f34633e1ae4901f2383af0e5318d6490851328f5b6aa06195ab51
        x-checker-data:
          type: html
          url: https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/
          version-pattern: mmdb2-([\d\.]+)\.tar\.gz
          url-template: https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/mmdb2-$version.tar.gz

  - name: libccp4
    buildsystem: autotools
    config-opts:
      - --disable-fortran
      - --disable-debug
      - --disable-docs
      - --disable-dependency-tracking
      - --disable-silent-rules
      - --enable-shared
      - --disable-static
      - --disable-Werror
    build-options:
      cflags: -O2 -fPIC -fno-strict-aliasing -DNDEBUG
      cxxflags: -O2 -fPIC -fno-strict-aliasing -DNDEBUG
    sources:
      - type: archive
        url: https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/libccp4-8.0.0.tar.gz
        sha256: cb813ae86612a0866329deab7cee96eac573d81be5b240341d40f9ad5322ff2d
        x-checker-data:
          type: html
          url: https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/
          version-pattern: libccp4-([\d\.]+)\.tar\.gz
          url-template: https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/libccp4-$version.tar.gz
      - type: shell
        commands:
          # Workarounds for gcc 15
          - cd ccp4 && if ! grep -q '^#include <stdlib.h>' library_utils.c; then sed
            -i '1i \#include <stdlib.h>' library_utils.c; fi
          - cd ccp4 && sed -i -E 's/^[[:space:]]*int[[:space:]]+putenv[[:space:]]*\([^;]*\)[[:space:]]*;/extern
            int putenv(char *);/' library_utils.c

  - name: clipper
    buildsystem: autotools
    config-opts:
      - --enable-mmdb
      - --enable-ccp4
      - --enable-cif
      - --enable-minimol
      - --enable-cns
      - --disable-debug
      - --disable-docs
      - --disable-dependency-tracking
      - --disable-silent-rules
      - --enable-shared
      - --disable-static
      - --disable-Werror
    build-options:
      cxxflags: -O2 -fno-strict-aliasing -Wno-narrowing -fPIC -std=c++11 -DNDEBUG
    sources:
      - type: archive
        url: https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/clipper-2.1.20180802.tar.gz
        sha256: 7c7774f224b59458e0faa104d209da906c129523fa737e81eb3b99ec772b81e0
        x-checker-data:
          type: html
          url: https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/
          version-pattern: clipper-([\d\.]+)\.tar\.gz
          url-template: https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/clipper-$version.tar.gz
      - type: patch
        path: patches/clipper-configure-2.patch
      - type: shell
        commands:
          - sed -i 's|libccp4c|ccp4c|g' configure

  - name: ssm
    buildsystem: autotools
    config-opts:
      - --enable-ccp4
      - --disable-debug
      - --disable-docs
      - --disable-dependency-tracking
      - --disable-silent-rules
      - --enable-shared
      - --disable-static
      - --disable-Werror
    build-options:
      cflags: -fPIC -fno-strict-aliasing -DNDEBUG
    sources:
      - type: archive
        url: https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/ssm-1.4.tar.gz
        sha256: 56e7e64ed86d7d9ec59500fd34f26f881bdb9d541916d9a817c3bfb8cf0e9508
        x-checker-data:
          type: html
          url: https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/
          version-pattern: ssm-([\d\.]+)\.tar\.gz
          url-template: https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/ssm-$version.tar.gz

  - name: libgd
    buildsystem: autotools
    config-opts:
      - --without-x
      - --without-xpm
      - --disable-debug
      - --disable-docs
      - --disable-dependency-tracking
      - --disable-silent-rules
      - --enable-shared
      - --disable-static
      - --disable-Werror
    build-options:
      cflags: -O2 -Wno-error=unused-result -Wno-error=old-style-definition -fPIC -DNDEBUG
      cxxflags: -O2 -Wno-narrowing -fPIC -DNDEBUG
    sources:
      - type: archive
        url: https://github.com/libgd/libgd/releases/download/gd-2.3.3/libgd-2.3.3.tar.xz
        sha256: 3fe822ece20796060af63b7c60acb151e5844204d289da0ce08f8fdf131e5a61
        x-checker-data:
          type: anitya
          project-id: 880
          stable-only: true
          url-template: https://github.com/libgd/libgd/releases/download/gd-$version/libgd-$version.tar.xz
      - type: patch
        path: patches/gd.h.patch

  - name: raster3d
    buildsystem: simple
    build-options:
      cxxflags: -O2 -fno-strict-aliasing -Wno-narrowing -fPIC -DNDEBUG
    build-commands:
      - make linux
      - make all
      - make install
    sources:
      - type: archive
        url: http://www.bmsc.washington.edu/raster3d/Raster3D_3.0-8.tar
        sha256: 4f6999f8d446ed2d7ef32d4f7abaa1d63fa1fa78686e79cecafc06c5ae6b122d
        x-checker-data:
          type: html
          url: http://www.bmsc.washington.edu/raster3d/
          version-pattern: Raster3D_([\d\.-]+)\.tar
          url-template: http://www.bmsc.washington.edu/raster3d/Raster3D_$version.tar
      - type: patch
        path: patches/fix-raster3d-Makefile.template.patch

  - name: boost
    buildsystem: simple
    build-commands:
      - ./bootstrap.sh --without-icu --with-python=python3.13 --with-python-root=/usr
        --with-libraries=python,regex,thread,serialization,iostreams,program_options
        --prefix=/app --libdir=/app/lib
      - ./b2 install --prefix=/app --libdir=/app/lib linkflags=-L/usr/lib python=3.13
        -d2 -j$FLATPAK_BUILDER_N_JOBS threading=multi link=shared,static
    build-options:
      cflags: -fPIC -DNDEBUG
      cxxflags: -fPIC -std=c++14 -DNDEBUG
    cleanup:
      - /share/boost
    sources:
      - type: archive
        url: https://github.com/boostorg/boost/releases/download/boost-1.91.0-1/boost-1.91.0-1-b2-nodocs.tar.xz
        sha256: 7334bb672b9c7aa135da88bcc3111a64a198be9a7d44eb5151d9248e7cfd43ef
        x-checker-data:
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          project-id: 6845
          stable-only: true
          url-template: https://github.com/boostorg/boost/releases/download/boost-$version/boost-$version-b2-nodocs.tar.xz

  - name: libdwarf
    buildsystem: autotools
    config-opts:
      - --disable-debug
      - --disable-docs
      - --disable-dependency-tracking
      - --disable-silent-rules
      - --enable-shared
      - --disable-static
      - --disable-Werror
    build-options:
      cflags: -O2 -fno-strict-aliasing -Wno-narrowing -fPIC -DNDEBUG
    sources:
      - type: archive
        url: https://www.prevanders.net/libdwarf-2.3.1.tar.xz
        sha256: 28cf9a5d27aceff5c1f906244a4fe7ae208e41d20a6d8fc7e091c633a40b6e97
        x-checker-data:
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          stable-only: true
          url-template: https://www.prevanders.net/libdwarf-$version.tar.xz

  - name: gsl
    buildsystem: autotools
    config-opts:
      - --disable-debug
      - --disable-docs
      - --disable-dependency-tracking
      - --disable-silent-rules
      - --enable-shared
      - --disable-static
      - --disable-Werror
    build-options:
      cflags: -O3 -fPIC -DNDEBUG
      ldflags: -L/app/lib -lopenblas
    sources:
      - type: archive
        url: https://ftp.gnu.org/gnu/gsl/gsl-2.8.tar.gz
        sha256: 6a99eeed15632c6354895b1dd542ed5a855c0f15d9ad1326c6fe2b2c9e423190
        x-checker-data:
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          stable-only: true
          url-template: https://ftp.gnu.org/gnu/gsl/gsl-$version.tar.gz

  - name: glm
    buildsystem: cmake-ninja
    config-opts:
      - -DCMAKE_BUILD_TYPE=Release
      - -DGLM_BUILD_TESTS=OFF
      - -DBUILD_SHARED_LIBS=ON
    sources:
      - type: archive
        url: https://github.com/g-truc/glm/archive/refs/tags/1.0.3.tar.gz
        sha256: 6775e47231a446fd086d660ecc18bcd076531cfedd912fbd66e576b118607001
        x-checker-data:
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          project-id: 1181
          stable-only: true
          url-template: https://github.com/g-truc/glm/archive/refs/tags/$version.tar.gz

  - name: bdw-gc
    buildsystem: autotools
    config-opts:
      - --disable-debug
      - --disable-docs
      - --disable-dependency-tracking
      - --disable-silent-rules
      - --enable-shared
      - --disable-static
    build-options:
      cflags: -fPIC -O2 -DNDEBUG
    sources:
      - type: archive
        url: https://github.com/ivmai/bdwgc/archive/refs/tags/v8.2.12.tar.gz
        sha256: d09001f45dabf1c29a5df3e63020a4bab5ad4aad69137bb07100c717e2ecba0b
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  # NOTE: The 'guile-gnome-platform' is currently incompatible with Guile 3.0.
  # Use Guile 2.2.7 until 'guile-gnome-platform' or an alternative (like G-Golf) is ready for Guile 3.0 and GTK4.
  - name: guile
    buildsystem: autotools
    config-opts:
      - --with-libltdl-prefix=/app
      - --with-libreadline-prefix=/app
      - --disable-docs
      - --disable-dependency-tracking
      - --disable-silent-rules
      - --enable-shared
      - --disable-static
    build-options:
      cflags: -fPIC -O2
    sources:
      - type: archive
        url: https://ftp.gnu.org/gnu/guile/guile-2.2.7.tar.xz
        sha256: cdf776ea5f29430b1258209630555beea6d2be5481f9da4d64986b077ff37504

  - name: g-wrap
    buildsystem: autotools
    config-opts:
      - --disable-debug
      - --disable-docs
      - --disable-dependency-tracking
      - --disable-silent-rules
      - --enable-shared
      - --disable-static
      - --disable-Werror
    build-options:
      cflags: -O2 -fPIC -DNDEBUG
    sources:
      - type: archive
        url: https://download.savannah.gnu.org/releases/g-wrap/g-wrap-1.9.15.tar.gz
        sha256: 0ff6e2700e74b457323726f7c2551a466d8ba44339705f6792d7b533145c602a

  - name: guile-cairo
    buildsystem: autotools
    config-opts:
      - --disable-debug
      - --disable-docs
      - --disable-dependency-tracking
      - --disable-silent-rules
      - --enable-shared
      - --disable-static
      - --disable-Werror
    build-options:
      cflags: -O2 -fPIC -DNDEBUG
    sources:
      - type: archive
        url: https://download.savannah.gnu.org/releases/guile-cairo/guile-cairo-1.10.0.tar.gz
        sha256: ae3d7e0f0a8ae93d0a15c692514eb30f2478d407052064976fc59a291cccdd5c

  - name: guile-lib
    buildsystem: autotools
    config-opts:
      - --with-guile-site=yes
      - --disable-debug
      - --disable-docs
      - --disable-dependency-tracking
      - --disable-silent-rules
      - --enable-shared
      - --disable-static
      - --disable-Werror
    build-options:
      cflags: -O2 -fPIC -DNDEBUG
    sources:
      - type: archive
        url: https://download.savannah.nongnu.org/releases/guile-lib/guile-lib-0.2.7.tar.gz
        sha256: e4ef3b845f121882c7c0cf04f81a1cb8fd360c6f64b56b868de5546214f904de

  - name: guile-gnome-platform
    buildsystem: autotools
    config-opts:
      - --disable-debug
      - --disable-docs
      - --disable-dependency-tracking
      - --disable-silent-rules
      - --enable-shared
      - --disable-static
    build-options:
      cflags: -O2 -fPIC -DNDEBUG
    sources:
      - type: archive
        url: https://ftp.gnu.org/gnu/guile-gnome/guile-gnome-platform/guile-gnome-platform-2.16.5.tar.gz
        sha256: 298d8c4f9b567bfe87beda18ed58d047c2e01b88c80895129de5466b921ccebe

  - name: swig
    buildsystem: autotools
    config-opts:
      - --disable-docs
      - --disable-dependency-tracking
      - --disable-silent-rules
      - --enable-shared
      - --disable-static
    sources:
      - type: archive
        url: https://github.com/swig/swig/archive/refs/tags/v4.4.1.tar.gz
        sha256: 8bf32042beb7ee1eeb5c71aa15a62513d964893f84234f2cd77e4a8e2ed41e87
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  - name: Catch2
    buildsystem: cmake-ninja
    builddir: true
    config-opts:
      - -DCMAKE_BUILD_TYPE=Release
      - -DCMAKE_CXX_STANDARD=17
    sources:
      - type: archive
        url: https://github.com/catchorg/Catch2/archive/refs/tags/v3.14.0.tar.gz
        sha256: ba2a939efead3c833c499cf487e185762f419a71d30158cd1b43c6079c586490
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  - name: rdkit
    buildsystem: cmake-ninja
    builddir: true
    config-opts:
      - -DCMAKE_BUILD_TYPE=Release
      - -DCatch2_DIR=/app
      - -DPython_EXECUTABLE=/usr/bin/python3
      - -DPYTHON_INCLUDE_DIR=/usr/include/python3.13
      - -DRDK_BUILD_CAIRO_SUPPORT=ON
      - -DRDK_INSTALL_INTREE=OFF
      - -DRDK_INSTALL_COMIC_FONTS=OFF
      - -DRDK_BUILD_MAEPARSER_SUPPORT=OFF
      - -DRDK_BUILD_CHEMDRAW_SUPPORT=OFF
    build-options:
      cxxflags: -fPIC -O3
    sources:
      - type: git
        url: https://github.com/rdkit/rdkit
        tag: Release_2026_03_2
        commit: 42fe8c952589bb750e27ea7f259a50b36576bfa5
        x-checker-data:
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      - type: archive
        url: https://github.com/schrodinger/maeparser/archive/refs/tags/v1.3.1.tar.gz
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        strip-components: 0
      - type: archive
        url: https://github.com/schrodinger/coordgenlibs/archive/refs/tags/v3.0.2.tar.gz
        sha256: f67697434f7fec03bca150a6d84ea0e8409f6ec49d5aab43badc5833098ff4e3
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      - type: archive
        url: https://github.com/rareylab/RingDecomposerLib/archive/refs/tags/v1.1.3_rdkit.tar.gz
        sha256: 944b5816712a48bbf88aa25d4300ce11871ddf6e971218eac08f90ed2192f715
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      - type: archive
        url: https://github.com/ncbi/pubchem-align3d/archive/daefab3.tar.gz
        sha256: 4871a08104c660890015f27d32a0147fc32df69a8962ca5cd1fe54ef6319c779
        strip-components: 0
      - type: archive
        url: https://github.com/Tencent/rapidjson/archive/858451e.tar.gz
        sha256: 765339356391422ad7f0258f8b746d8010da205762784a84980936e8b38e03ce
        strip-components: 0
      - type: file
        url: https://raw.githubusercontent.com/aantron/better-enums/refs/tags/0.11.3/enum.h  # Single header-only library
        sha256: 43a55c487052cfe068ecf1e4496d52128161bfb82c06c343eea85f177f235e04
      - type: shell
        commands:
          - mkdir -p External/CoordGen/{maeparser,coordgen}
          - mkdir -p External/RingFamilies/RingDecomposerLib
          - mkdir -p External/pubchem_shape/pubchem-align3d
          - mkdir -p External/rapidjson-1.1.0
          - cp -r maeparser-1.3.1/* External/CoordGen/maeparser
          - cp -r coordgenlibs-3.0.2/* External/CoordGen/coordgen
          - cp -r RingDecomposerLib-1.1.3_rdkit/* External/RingFamilies/RingDecomposerLib
          - cp -r pubchem-align3d-daefab3dd0c90ca56da9d3d5e375fe4d651e6be3/* External/pubchem_shape/pubchem-align3d
          - cp -r rapidjson-858451e5b7d1c56cf8f6d58f88cf958351837e53/* External/rapidjson-1.1.0
          - cp enum.h Code/RDGeneral  # Place it in the required location in advance
          - sed -i 's|FetchContent_MakeAvailable(better_enums)||' Code/RDGeneral/CMakeLists.txt  # Prevent downloading

  - name: netcdf
    buildsystem: cmake-ninja
    builddir: true
    config-opts:
      - -DCMAKE_BUILD_TYPE=Release
      - -DENABLE_HDF5=OFF
      - -DENABLE_DAP=OFF
      - -DBUILD_SHARED_LIBS=ON
      - -DENABLE_TESTS=OFF
    sources:
      - type: archive
        url: https://github.com/Unidata/netcdf-c/archive/v4.10.0.tar.gz
        sha256: ce160f9c1483b32d1ba8b7633d7984510259e4e439c48a218b95a023dc02fd4c
        x-checker-data:
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          project-id: 10354
          stable-only: true
          url-template: https://github.com/Unidata/netcdf-c/archive/v$version.tar.gz

  - name: coot
    buildsystem: autotools
    config-opts:
      - --with-boost=/app
      - --with-boost-libdir=/app/lib
      - --with-fftw-prefix=/app
      - --with-gemmi=/app
      - --with-glm=/app
      - --with-rdkit-prefix=/app
      - --with-backward
      - --with-coordgen
      - --with-libdw
      - --with-netcdf
      - --with-guile
      - --with-sound
      - --with-sqlite3
      - --disable-dependency-tracking
      - --disable-silent-rules
      - --enable-shared
      - --disable-static
      - --enable-relocatable-binaries
    build-options:
      cxxflags: -g -O1 -fPIC
      env:
        GLM_CFLAGS: -I/app/include
        GLM_LIBS: -L/app/lib -lglm
    post-install:
      - cp -r python/ ${FLATPAK_DEST}/share/coot/
      - install -Dm644 pixmaps/icons/coot.svg ${FLATPAK_DEST}/share/icons/hicolor/scalable/apps/${FLATPAK_ID}.svg
      - install -Dm644 coot.desktop ${FLATPAK_DEST}/share/applications/${FLATPAK_ID}.desktop
      - desktop-file-edit --set-key=Icon --set-value=${FLATPAK_ID} ${FLATPAK_DEST}/share/applications/${FLATPAK_ID}.desktop
      - install -Dm644 coot.appdata.xml ${FLATPAK_DEST}/share/metainfo/${FLATPAK_ID}.metainfo.xml
    sources:
      - type: git
        url: https://github.com/pemsley/coot.git
        tag: Release-1.2
        commit: 1a5900449e69ea1ef4607882d2f7e15912f7b6ec
        x-checker-data:
          type: git
          tag-pattern: ^Release-([0-9]+(?:\.[0-9]+)*)$