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This pull request primarily updates the Flatpak build configuration and related documentation for the project, focusing on improving patch management, clarifying installation instructions, and fixing minor issues with the build process. The most important changes are grouped below:

Documentation Updates:

  • Updated Flatpak installation instructions in README.md to use the --user flag, ensuring the remote is added for the current user rather than system-wide. [1] [2]

Patch Management and Build Configuration:

  • Standardized patch file locations in io.github.pemsley.coot.yaml by moving patch paths into a patches/ directory for consistency and clarity. [1] [2] [3]
  • Added a new patch step for Makefile.am in the build process, referencing a specific upstream issue for context. [1] [2]

Build Process Improvements:

  • Renamed the clipper4coot module to clipper in the Flatpak manifest to accurately reflect the dependency.
  • Removed an unnecessary mkdir command from the post-install steps in the Flatpak manifest, as the target directory is already created by the subsequent copy command.

Merge pull request flathub#61 from eunos-1128/beta
Merge pull request flathub#75 from eunos-1128/master
- Replaced `--filesystem=home` with `--filesystem=host`
- Added `--filesystem=xdg-cache` and `--filesystem=xdg-data`
@eunos-1128 eunos-1128 self-assigned this Aug 25, 2025
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🚧 Test build enqueued.

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🚧 Started test build.

@eunos-1128 eunos-1128 requested a review from Copilot August 25, 2025 14:43
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Pull Request Overview

This pull request merges changes from the master branch into the beta branch, focusing on improvements to the Flatpak build configuration and documentation. The changes standardize patch file organization, update installation instructions, and address build process issues.

  • Reorganized patch files into a dedicated patches/ directory for better maintainability
  • Updated Flatpak installation commands to use the --user flag for user-level installations
  • Added a new patch to fix build issues related to the monomers subdirectory

Reviewed Changes

Copilot reviewed 3 out of 6 changed files in this pull request and generated no comments.

File Description
patches/Makefile.am.patch New patch file that adds the missing monomers subdirectory to the build process and removes trailing whitespace
io.github.pemsley.coot.yaml Updated patch paths to use the patches/ directory, renamed module from clipper4coot to clipper, removed unnecessary mkdir command, and added reference to the new Makefile.am patch
README.md Updated Flatpak installation commands to include the --user flag for both stable and beta versions

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

flatpak install --user https://dl.flathub.org/build-repo/206234/io.github.pemsley.coot.flatpakref

@eunos-1128 eunos-1128 merged commit 6537211 into flathub:beta Aug 25, 2025
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2 participants