Install all dependencies

[t0mdavid-m]

User description

This PR adds portable versions of all dependencies to the windows installations using the cpack routine from the installer.

Note that this required some changes to the OpenMS build configuration and is thus dependent on the following PR in the main repository:

OpenMS/OpenMS#7529

This should fix #67.

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PR Type

enhancement, configuration changes

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Description

• Added a new packaging step using ctest and cpack to both GitHub Actions workflows.
• Replaced separate artifact uploads for bin and share directories with a single package upload.
• Updated artifact download and extraction steps to handle the new package format.
• Removed steps for deleting individual bin and share artifacts, replaced with package artifact deletion.

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Changes walkthrough 📝

Relevant files

Enhancement

build-windows-executable-app-with-pyinstaller.yaml Add packaging step and consolidate artifact handling          .github/workflows/build-windows-executable-app-with-pyinstaller.yaml Added a new packaging step using ctest and cpack. Replaced separate artifact uploads for bin and share directories with a single package upload. Updated artifact download and extraction steps to handle the new package format. Removed steps for deleting individual bin and share artifacts, replaced with package artifact deletion. +28/-26  build-windows-executable-app.yaml Add packaging step and consolidate artifact handling          .github/workflows/build-windows-executable-app.yaml Added a new packaging step using ctest and cpack. Replaced separate artifact uploads for bin and share directories with a single package upload. Updated artifact download and extraction steps to handle the new package format. Removed steps for deleting individual bin and share artifacts, replaced with package artifact deletion. +26/-24

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PR Reviewer Guide 🔍

⏱️ Estimated effort to review [1-5]	3
🧪 Relevant tests	No
🔒 Security concerns	No
⚡ Key issues to review	Possible Bug: Ensure that the new packaging and artifact handling steps are correctly configured and tested. The changes involve significant modifications to the CI/CD pipeline, which could potentially break the build or deployment process if not properly implemented.
	Dependency Check: Verify that the new dependencies and the changes made in the linked PR (https://github.com/OpenMS/OpenMS/pull/7529) are compatible and do not introduce any conflicts or issues in the build process.

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PR Code Suggestions ✨

Category	Suggestion	Score
Enhancement	Improve the specificity of the zip extraction command to ensure only relevant artifacts are processed Consider using a more specific pattern for the zip files to be extracted to avoid unintended file extractions and ensure only relevant artifacts are processed. This can be crucial in a CI environment where multiple jobs might produce different artifacts. .github/workflows/build-windows-executable-app-with-pyinstaller.yaml [180] -unzip "*.zip" -d . +unzip "openms-*.zip" -d . Apply this suggestion Suggestion importance[1-10]: 9 Why: This suggestion improves the robustness of the CI process by ensuring that only relevant artifacts are extracted, which is crucial in environments with multiple jobs producing different artifacts.	9
Best practice	Add error handling to the unzip operation to enhance the robustness of the workflow It's a good practice to check the success of critical operations such as unzipping artifacts. Adding error handling for the unzip operation can prevent subsequent steps from running if the unzip fails, which can save time and resources in the CI process. .github/workflows/build-windows-executable-app-with-pyinstaller.yaml [180] -unzip "*.zip" -d . +unzip "*.zip" -d . || exit 1 Apply this suggestion Suggestion importance[1-10]: 8 Why: Adding error handling to the unzip operation is a good practice that can prevent subsequent steps from running if the unzip fails, saving time and resources in the CI process.	8
	Standardize the version of actions/download-artifact used across the workflow to ensure consistent behavior To maintain consistency and avoid potential issues with different versions of actions, consider using the same version for all instances of actions/download-artifact. This change ensures that all artifact downloads are handled consistently. .github/workflows/build-windows-executable-app-with-pyinstaller.yaml [172] -uses: actions/download-artifact@v4 +uses: actions/download-artifact@v3 Apply this suggestion Suggestion importance[1-10]: 7 Why: Using a consistent version of actions/download-artifact can help avoid potential issues caused by version discrepancies, although the current version (v4) is more recent and likely has improvements over v3.	7
Maintainability	✅ Define environment variables at the job level to ensure consistent access across all steps Suggestion Impact: The suggestion to define environment variables at the job level was implemented. The environment variables OPENMS_VERSION and TOPP_TOOLS were moved to the job level. code diff: +env: + OPENMS_VERSION: 3.0.0 + # Define needed TOPP tools here + TOPP_TOOLS: "FeatureFinderMetabo MetaboliteAdductDecharger SiriusExport" To avoid potential conflicts and ensure that the environment variables are correctly scoped, consider defining SOURCE_DIRECTORY and other related environment variables at the job level instead of within individual steps. This change ensures that all steps within the job have consistent access to these variables. .github/workflows/build-windows-executable-app-with-pyinstaller.yaml [142-147] -SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS" +env: + SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS" + PACKAGE_TYPE: nsis + SEARCH_ENGINES_DIRECTORY: "${{ github.workspace }}/_thirdparty" + CI_PROVIDER: "GitHub-Actions" + PACK_ZIP: 1 + CPACK_PACKAGE_FILE_NAME: "openms-package" Apply this suggestion Suggestion importance[1-10]: 6 Why: Defining environment variables at the job level can improve maintainability and ensure consistent access across all steps, but it is not critical as the current implementation is functional.	6

[t0mdavid-m]

The workflow is currently failing since cipackage.cmake was introduced after the 3.0.0 release. However, until the PR mentioned above is merged and a release is created, there wont be an available release that supports the new workflow. It is working fine for FLASHViewerwhich uses a custom branch of OpenMS with cherry picked commits from the PR.

[t0mdavid-m]

I updated the delete artifact version (see #71)

[t0mdavid-m]

The PR (OpenMS/OpenMS#7529) in the main repository is now merged. We decided on different flags which I just updated for this PR as well.

[Arslan-Siraj]

Thanks for update, Still these files might can arrange (can we try wix or something similar to give one file either .exe or .msi) or we arrange more better for example; .bat outside and then one folder contain all apps files (so user will not need to find .bat file in all files there)? (maybe we can do in the next iteration) @axelwalter

[Arslan-Siraj]

gdpr_consent needed here?

[t0mdavid-m]

Should be able to remove it!

[Arslan-Siraj]

still bin folder which is empty.

[t0mdavid-m]

Removed!

[t0mdavid-m]

Thanks for update, Still these files might can arrange (can we try wix or something similar to give one file either .exe or .msi) or we arrange more better for example; .bat outside and then one folder contain all apps files (so user will not need to find .bat file in all files there)? (maybe we can do in the next iteration) @axelwalter

I also believe this crowded folder is very much not ideal. I think wix sounds like a great solution but its probably best to do it in a separate PR, as this PR has been WIP for forever. I will open an issue!

[t0mdavid-m]

PR would be ready from my side! @Arslan-Siraj