Merge pull request #75 from eunos-1128/master

[eunos-1128]

This pull request updates the io.github.pemsley.coot.yaml file to standardize and improve build configurations across multiple modules. The changes primarily involve adding or modifying compiler flags (cflags and cxxflags) to ensure compatibility and optimization, as well as updating some configuration options for specific modules.

Compiler flag improvements:

• Added -fPIC to cflags and/or cxxflags for modules such as gemmi, fftw, mmdb2, libccp4, clipper, raster3d, and others to improve position-independent code generation. ([[1]](https://github.com/flathub/io.github.pemsley.coot/pull/80/files#diff-55b9e84a877dbbef6cbca71f44f2c253217232100c0d81f840e1abf5346b24efR34-R35), [[2]](https://github.com/flathub/io.github.pemsley.coot/pull/80/files#diff-55b9e84a877dbbef6cbca71f44f2c253217232100c0d81f840e1abf5346b24efR47-R48), [[3]](https://github.com/flathub/io.github.pemsley.coot/pull/80/files#diff-55b9e84a877dbbef6cbca71f44f2c253217232100c0d81f840e1abf5346b24efL60-R64), [[4]](https://github.com/flathub/io.github.pemsley.coot/pull/80/files#diff-55b9e84a877dbbef6cbca71f44f2c253217232100c0d81f840e1abf5346b24efR76-R78), [[5]](https://github.com/flathub/io.github.pemsley.coot/pull/80/files#diff-55b9e84a877dbbef6cbca71f44f2c253217232100c0d81f840e1abf5346b24efL88-R95), [[6]](https://github.com/flathub/io.github.pemsley.coot/pull/80/files#diff-55b9e84a877dbbef6cbca71f44f2c253217232100c0d81f840e1abf5346b24efL114-R121), [[7]](https://github.com/flathub/io.github.pemsley.coot/pull/80/files#diff-55b9e84a877dbbef6cbca71f44f2c253217232100c0d81f840e1abf5346b24efL332-R342))
• Updated cxxflags to include -std=c++11 for modules like mmdb2 and clipper to ensure compatibility with modern C++ standards. ([[1]](https://github.com/flathub/io.github.pemsley.coot/pull/80/files#diff-55b9e84a877dbbef6cbca71f44f2c253217232100c0d81f840e1abf5346b24efL60-R64), [[2]](https://github.com/flathub/io.github.pemsley.coot/pull/80/files#diff-55b9e84a877dbbef6cbca71f44f2c253217232100c0d81f840e1abf5346b24efL88-R95))

Configuration updates:

• Adjusted config-opts for the cmake-ninja build system in the openblas module, including enabling -DDYNAMIC_ARCH=ON, updating -DNUM_THREADS to 64, and setting -DUSE_OPENMP=ON for better performance and multi-threading support. ([io.github.pemsley.coot.yamlL184-R197](https://github.com/flathub/io.github.pemsley.coot/pull/80/files#diff-55b9e84a877dbbef6cbca71f44f2c253217232100c0d81f840e1abf5346b24efL184-R197))

[flathubbot]

🚧 Test build enqueued.

[flathubbot]

🚧 Started test build.

[Copilot]

Pull Request Overview

This PR standardizes and enhances build configurations by adding position-independent code flags and ensuring modern C++ support, as well as tuning the OpenBLAS build for threading and performance.

• Added -fPIC to cflags/cxxflags across modules for PIC compatibility
• Introduced -std=c++11 in C++ modules (mmdb2, clipper)
• Updated OpenBLAS config-opts for threading, OpenMP, and dynamic architecture

Comments suppressed due to low confidence (2)

io.github.pemsley.coot.yaml:34

• [nitpick] There’s repeated duplication of -fPIC and optimization flags in every module. Consider defining a top-level default under a shared build-options block or using YAML anchors to DRY up these common flags.

build-options:

io.github.pemsley.coot.yaml:64

• [nitpick] Instead of embedding -std=c++11 directly in cxxflags, consider using -DCMAKE_CXX_STANDARD=11 in config-opts for CMake-based modules to ensure consistency and better integration with CMake's own standard-checking.

cxxflags: "-g -O2 -fPIC -std=c++11"

[flathubbot]

✅ Test build succeeded. To test this build, install it from the testing repository:

flatpak install --user https://dl.flathub.org/build-repo/191611/io.github.pemsley.coot.flatpakref