Remove PyInstaller standalone binary packaging infrastructure#195
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Remove PyInstaller standalone binary packaging infrastructure#195
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Co-authored-by: singjc <32938975+singjc@users.noreply.github.com>
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[WIP] Remove pre-built executables and PyInstaller packaging
Remove PyInstaller standalone binary packaging infrastructure
Mar 3, 2026
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@copilot can you update the README by removing the "Option 2: Pre-built Executables (No Python Required)" section and also update/remove the github actions for building the pyinstalelr release binaries as well as the test build action for testing the pyinstaller binaries |
…E section Co-authored-by: singjc <32938975+singjc@users.noreply.github.com>
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Mar 3, 2026
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Pull request overview
This PR removes the project’s PyInstaller-based standalone binary packaging infrastructure (scripts, hooks, and CI workflows) and updates packaging/docs to reflect Python-package / container distribution only.
Changes:
- Deleted PyInstaller build + installer scripts for Linux/macOS/Windows (and associated hooks/launchers).
- Removed GitHub Actions workflows that built/tested PyInstaller binaries and release assets.
- Updated
pyproject.tomlsetuptools package-discovery exclusions and removed README references/badges for pre-built executables.
Reviewed changes
Copilot reviewed 18 out of 18 changed files in this pull request and generated no comments.
Show a summary per file
| File | Description |
|---|---|
scripts/build/create_windows_installer.ps1 |
Removed Windows installer creation (Inno Setup) for PyInstaller artifacts. |
scripts/build/create_macos_dmg.sh |
Removed macOS DMG creation for the PyInstaller-built executable. |
scripts/build/create_linux_packages.sh |
Removed DEB/RPM packaging flow for the PyInstaller-built executable. |
scripts/build/build_windows.bat |
Removed Windows PyInstaller build script. |
scripts/build/build_macos.sh |
Removed macOS PyInstaller build script. |
scripts/build/build_linux.sh |
Removed Linux PyInstaller build script. |
scripts/build/README.md |
Removed release/build documentation tied to the deleted PyInstaller workflows/scripts. |
pyproject.toml |
Dropped packaging* from setuptools find excludes (now-stale after removing PyInstaller packaging dir). |
packaging/pyinstaller/run_pyprophet.py |
Removed PyInstaller launcher entrypoint. |
packaging/pyinstaller/hooks/hook.pyprophet.py |
Removed PyInstaller hook for collecting pyprophet modules/data. |
packaging/pyinstaller/hooks/hook-xgboost.py |
Removed PyInstaller hook for xgboost libs/data. |
packaging/pyinstaller/hooks/hook-pyopenms.py |
Removed PyInstaller hook for pyopenms native deps. |
packaging/pyinstaller/hooks/hook-duckdb.py |
Removed PyInstaller hook for duckdb metadata. |
dist-scripts/manylinux.patch |
Removed legacy manylinux patch artifact. |
dist-scripts/create-manylinux.sh |
Removed legacy manylinux wheel-building Docker script. |
README.md |
Removed workflow badges and the “Pre-built Executables” installation option; renumbered remaining options. |
.github/workflows/test-build.yml |
Removed CI job that built/tested PyInstaller executables + installers. |
.github/workflows/build-release.yml |
Removed release workflow that built/uploaded PyInstaller binaries and installers. |
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PyInstaller-based standalone binaries are brittle and unnecessary for distribution. Removes all related artifacts.
Removed
packaging/pyinstaller/— launcher script (run_pyprophet.py) and all hooks (duckdb,pyopenms,xgboost,pyprophet)dist-scripts/— manylinux wheel-building Docker scripts (create-manylinux.sh,manylinux.patch).github/workflows/build-release.yml— GitHub Actions workflow for building and releasing PyInstaller binaries.github/workflows/test-build.yml— GitHub Actions workflow for testing PyInstaller binaries on PRs and pushesscripts/build/— PyInstaller build and installer scripts for Linux, Windows, and macOSUpdated
pyproject.toml— dropped stalepackaging*glob from setuptools package discovery exclusionsREADME.md— removed "Option 2: Pre-built Executables (No Python Required)" section, renumbered remaining installation options, and removed stale workflow status badges🔒 GitHub Advanced Security automatically protects Copilot coding agent pull requests. You can protect all pull requests by enabling Advanced Security for your repositories. Learn more about Advanced Security.