Add servalcat and acedrg modules #135
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…mline dependency installation
Add `better_enums` of a single header library and prevent `FetchContent_MakeAvailable(better_enums)` in CMakeLists.txt
Updated source type from git to archive for multiple dependencies, including OpenBLAS, gemmi, libgd, boost, glm, bdwgc, swig, Catch2, eigen, and others. Added SHA256 checksums for integrity verification.
Added x-checker-data for several dependencies.
Updated comments for clarity in io.github.pemsley.coot.yaml.
Removed unnecessary cleanup entries from the YAML configuration.
Add workarounds for gcc 15 in library_utils.c
Added notes regarding Guile version compatibility with GTK4.
Updated build options for various dependencies to include -DNDEBUG and changed NUM_THREADS for openblas.
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…mproved accuracy
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Pull request overview
This pull request adds support for the servalcat and acedrg modules by comprehensively overhauling the Python dependency management system. The changes expand both build and runtime dependencies needed for scientific Python packages, update the Flatpak manifest to support acedrg with necessary environment variables, and reorganize module build order.
Key changes include:
- Addition of servalcat and acedrg modules with their full dependency chains
- Expansion of Python build dependencies (flit-core, meson, pybind11, pythran, scikit-build-core, versioneer, Cython)
- Addition of runtime dependencies for scientific computing (networkx, pandas, scipy, omegaconf, pdbecif)
Reviewed changes
Copilot reviewed 4 out of 4 changed files in this pull request and generated 9 comments.
| File | Description |
|---|---|
| io.github.pemsley.coot.yaml | Adds acedrg environment variables, relocates eigen module before servalcat, adds servalcat and acedrg module definitions with build configurations, removes OpenBLAS -DNO_SVE=ON flag |
| deps/requirements.txt | Restructures file with clear build/runtime sections, adds numerous new dependencies with version constraints for scientific Python stack |
| deps/pypi-dependencies.sh | Removes --checker-data flag and updates completion message |
| deps/pypi-dependencies.json | Expands from 5 to 19 Python modules, adds all build and runtime dependencies, removes some x-checker-data configurations |
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✅ Test build succeeded. To test this build, install it from the testing repository: Built for aarch64 and x86_64 architectures. Warnings can be promoted to errors in the future. Please try to resolve them.
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2 participants
This pull request updates the Python dependency management for the project, with a major overhaul of the
deps/pypi-dependencies.jsonanddeps/requirements.txtfiles. It replaces and adds many build and runtime dependencies to support new features and improve compatibility, especially for scientific Python packages. Environment variables are also added to the Flatpak manifest to support theacedrgtool. The changes are grouped below.Dependency Management Overhaul
deps/requirements.txt, including switching frommarkupsafe,meson-python,nanobind, andnumpyto a broader set such asflit-core,meson,meson-python,nanobind,numpy,pybind11,pythran,scikit-build-core,versioneer,wheel, andCython, with specific version constraints for better compatibility.deps/requirements.txtfor scientific and data processing packages, includingnetworkx,pdbecif,antlr4-python3-runtime,omegaconf,packaging,pandas,python_dateutil,pytz,pyyaml,scipy,six, andtzdata.Flatpak Manifest and Build Script Updates
deps/pypi-dependencies.jsonto match the new requirements, removing obsolete packages and adding new ones with correct sources and build commands. This includes adding or updating modules forflit-core,meson-python,nanobind,numpy,pybind11,pythran,scikit-build-core,versioneer,networkx,pdbecif,antlr4-python3-runtime,omegaconf,pandas,python_dateutil,pytz,pyyaml,scipy,six, andtzdata. [1] [2]io.github.pemsley.coot.yaml) to add environment variables required foracedrg(CLIBD_MON,LIBMOL_ROOT,CCP4,CBIN) and clarified comments about dependency management. [1] [2]--checker-dataflag from thedeps/pypi-dependencies.shscript, and updated the completion message for clarity.Minor Build Configuration Changes
-DNO_SVE=ONoption from the OpenBLAS build configuration in the Flatpak manifest, likely for compatibility with newer hardware or builds.