Add extra manifest for third party folder

Avoid softprops

Author: sammysheep

.github/workflows/release.yml

@@ -10,6 +10,7 @@ permissions: {}
 env:
   CARGO_TERM_COLOR: always
   RELEASE_BIN: label
+  RELEASE_BASE: flu-amd
   REGISTRY: ghcr.io
 
 jobs:
@@ -28,33 +29,32 @@ jobs:
         shell: bash
         run: |
           CHANGELOG_CONTENT=$(perl .github/scripts/last_release_notes.pl)
-          echo "changelog<<EOF" >> $GITHUB_OUTPUT
-          echo "$CHANGELOG_CONTENT" >> $GITHUB_OUTPUT
-          echo "EOF" >> $GITHUB_OUTPUT
+          echo -e "changelog<<EOF\n$CHANGELOG_CONTENT\nEOF" >> $GITHUB_OUTPUT
 
       - name: Create Source Code Archive
         id: create_archive
         shell: bash
         run: |
-          ARCHIVE_NAME="${{ env.RELEASE_BIN }}-${{ github.ref_name }}-universal.zip"
-          rm -rf .git* .vscode .docker* .*rc Dockerfile \
-          && zip -r "${ARCHIVE_NAME}" . \
-          && echo "archive_name=${ARCHIVE_NAME}" >> $GITHUB_OUTPUT
+          ARCHIVE_NAME="$RUNNER_TEMP/${{ env.RELEASE_BIN }}-${{ github.ref_name }}-universal.zip"
+          base=${{ env.RELEASE_BASE }}
+
+          cd .. && mv label $base \
+          && zip -r "${ARCHIVE_NAME}" . -x "$base/.git*" "$base/.vscode" "$base/.docker*" "$base/.*rc" "$base/Dockerfile" \
+          && echo "archive_name=${ARCHIVE_NAME}" >> $GITHUB_OUTPUT \
+          && mv $base label
 
       - name: Create Release
         id: create_release
-        uses: softprops/action-gh-release@v2
-        with:
-          body: ${{ steps.extract_changelog.outputs.changelog }}
-          draft: false
-          prerelease: false
-          files: ${{ steps.create_archive.outputs.archive_name }}
+        shell: bash
+        run: |
+          gh release create "${{ github.ref_name }}" "${{ steps.create_archive.outputs.archive_name }}" \
+          --title "${{ github.ref_name }}" \
+          --notes "${{ steps.extract_changelog.outputs.changelog }}"
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
   build-release-images:
     name: Build and Push Release Image
-    needs: [create-release]
     strategy:
       matrix:
         include:

.gitignore

@@ -3,5 +3,5 @@ log.txt
 LABEL_RES/training_data/B_HA-old/
 LABEL_RES/test_data/
 tests
-.*DS_Store
+.DS_Store
 LABEL_RES/training_data/meno-H1

LABEL_RES/scripts/.DS_Store

@@ -0,0 +1,24 @@
+# Third Party Software Manifest
+
+- [GNU Parallel]
+  - Artifacts: `parallel`
+  - Requires: system Perl
+  - Purpose: parallelization
+  - License: [GPL v3]
+- [SHOGUN] version 1.1.0 (2.1+ is not compatible)
+  - Artifacts: `shogun` (cmdline_static)
+  - Provided architectures: linux/x86_64, linux/aarch64, apple/x86_64 (arm64 via Rosetta2)
+  - Purpose: executes the SVM decision phase.
+  - License: [GPL v3]
+- [SAM] version 3.5
+  - Artifacts: `align2model`, `hmmscore`, `modelfromalign`
+  - Provided architectures: linux/x86_64, linux/aarch64, apple/universal (arm64 + intel)
+  - Purpose: build HMM profiles, score sequences for evaluation
+  - License: [Custom][sam-license] academic/government, not-for-profit, redistributed [with permission]
+
+[GNU Parallel]: https://www.gnu.org/software/parallel/
+[with permission]: copyright_and_licenses/sam3.5/SAM%20Redistribution%20Special%20Permissions.pdf
+[GPL v3]: https://www.gnu.org/licenses/gpl-3.0.txt
+[SHOGUN]: https://github.com/shogun-toolbox/
+[sam-license]: https://users.soe.ucsc.edu/~karplus/projects-compbio-html/sam-lic/obj.0
+[SAM]: https://users.soe.ucsc.edu/~karplus/projects-compbio-html/sam2src/