From 90321730556fbc30ac133523b71b2a3406125e23 Mon Sep 17 00:00:00 2001 From: Ulthran Date: Tue, 2 Apr 2024 11:50:11 -0400 Subject: [PATCH 1/2] Upload tarball as artifact before adding to release --- .github/workflows/release.yml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index b1b8ab6f..d5785e11 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -58,6 +58,12 @@ jobs: - name: Generate Tarball run: bash dev_scripts/generate_archive.sh + - name: Upload Tarball + uses: actions/upload-artifact@v2 + with: + name: sunbeam.tar.gz + path: sunbeam.tar.gz + - name: Add Tarball to Release uses: irongut/EditRelease@v1.2.0 with: From 0d7f38d35e5279707a88cabddf72d2dbf849eee0 Mon Sep 17 00:00:00 2001 From: Ulthran Date: Tue, 2 Apr 2024 12:16:41 -0400 Subject: [PATCH 2/2] Convert '\n' to '%0A' for release notes --- .github/workflows/dockerhub.yml | 23 +++++++++++++++++------ .github/workflows/release.yml | 2 +- install.sh | 2 +- 3 files changed, 19 insertions(+), 8 deletions(-) diff --git a/.github/workflows/dockerhub.yml b/.github/workflows/dockerhub.yml index a42842ae..7a522a0f 100644 --- a/.github/workflows/dockerhub.yml +++ b/.github/workflows/dockerhub.yml @@ -99,9 +99,12 @@ jobs: - name: Generate image report id: report + # Replace '\n' with '%0A' for embedding into release notes (for somer reason '\n' is not escaped) run: | - echo "package_versions=$(docker run --rm sunbeamlabs/sunbeam:${{ inputs.version }} cat installed_packages.txt)" >> "$GITHUB_OUTPUT" - echo "package_versions_slim=$(docker run --rm sunbeamlabs/sunbeam:${{ inputs.version }}-slim cat installed_packages.txt)" >> "$GITHUB_OUTPUT" + IP=$(docker run --rm sunbeamlabs/sunbeam:${{ inputs.version }} cat installed_packages.txt) + echo "package_versions=${IP//$'\n'/'%0A'}" >> "$GITHUB_OUTPUT" + IP=$(docker run --rm sunbeamlabs/sunbeam:${{ inputs.version }}-slim cat installed_packages.txt) + echo "package_versions_slim=${IP//$'\n'/'%0A'}" >> "$GITHUB_OUTPUT" push-cutadapt-dockerhub: name: Push cutadapt env to Dockerhub @@ -137,7 +140,9 @@ jobs: - name: Generate image report id: report run: | - echo "package_versions=$(docker run --rm sunbeamlabs/cutadapt:${{ inputs.version }} cat installed_packages.txt)" >> "$GITHUB_OUTPUT" + IP=$(docker run --rm sunbeamlabs/cutadapt:${{ inputs.version }} cat installed_packages.txt) + echo $IP + echo "package_versions=${IP//$'\n'/'%0A'}" >> "$GITHUB_OUTPUT" push-komplexity-dockerhub: name: Push komplexity env to Dockerhub @@ -173,7 +178,9 @@ jobs: - name: Generate image report id: report run: | - echo "package_versions=$(docker run --rm sunbeamlabs/komplexity:${{ inputs.version }} cat installed_packages.txt)" >> "$GITHUB_OUTPUT" + IP=$(docker run --rm sunbeamlabs/komplexity:${{ inputs.version }} cat installed_packages.txt) + echo $IP + echo "package_versions=${IP//$'\n'/'%0A'}" >> "$GITHUB_OUTPUT" push-qc-dockerhub: name: Push qc env to Dockerhub @@ -209,7 +216,9 @@ jobs: - name: Generate image report id: report run: | - echo "package_versions=$(docker run --rm sunbeamlabs/qc:${{ inputs.version }} cat installed_packages.txt)" >> "$GITHUB_OUTPUT" + IP=$(docker run --rm sunbeamlabs/qc:${{ inputs.version }} cat installed_packages.txt) + echo $IP + echo "package_versions=${IP//$'\n'/'%0A'}" >> "$GITHUB_OUTPUT" push-reports-dockerhub: name: Push reports env to Dockerhub @@ -245,4 +254,6 @@ jobs: - name: Generate image report id: report run: | - echo "package_versions=$(docker run --rm sunbeamlabs/reports:${{ inputs.version }} cat installed_packages.txt)" >> "$GITHUB_OUTPUT" \ No newline at end of file + IP=$(docker run --rm sunbeamlabs/reports:${{ inputs.version }} cat installed_packages.txt) + echo $IP + echo "package_versions=${IP//$'\n'/'%0A'}" >> "$GITHUB_OUTPUT" \ No newline at end of file diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index d5785e11..051f60c5 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -120,7 +120,7 @@ jobs: with: token: ${{ secrets.GITHUB_TOKEN }} id: ${{ github.event.release.id }} - body: "### sunbeamlabs/sunbeam\n${{ needs.push-dockerhub.outputs.sunbeam_package_versions }}\n### sunbeamlabs/cutadapt\n${{ needs.push-dockerhub.outputs.cutadapt_package_versions }}\n### sunbeamlabs/komplexity\n${{ needs.push-dockerhub.outputs.komplexity_package_versions }}\n### sunbeamlabs/qc\n${{ needs.push-dockerhub.outputs.qc_package_versions }}\n### sunbeamlabs/reports\n${{ needs.push-dockerhub.outputs.reports_package_versions }}" + body: "### sunbeamlabs/sunbeam\n${{ needs.push-dockerhub.outputs.sunbeam_package_versions }}\n### sunbeamlabs/sunbeam:slim\n${{ needs.push-dockerhub.outputs.sunbeam_package_versions_slim }}\n### sunbeamlabs/cutadapt\n${{ needs.push-dockerhub.outputs.cutadapt_package_versions }}\n### sunbeamlabs/komplexity\n${{ needs.push-dockerhub.outputs.komplexity_package_versions }}\n### sunbeamlabs/qc\n${{ needs.push-dockerhub.outputs.qc_package_versions }}\n### sunbeamlabs/reports\n${{ needs.push-dockerhub.outputs.reports_package_versions }}" replacebody: false run-integration-tests: diff --git a/install.sh b/install.sh index 79b014ad..0b7b3f69 100755 --- a/install.sh +++ b/install.sh @@ -1,7 +1,7 @@ #!/usr/bin/env bash __conda_url=https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -__version_tag=$(if git describe --tags >/dev/null 2>&1 ; then git describe --tags; else echo v4.5.2.dev2; fi) # <--- Update this on each version release +__version_tag=$(if git describe --tags >/dev/null 2>&1 ; then git describe --tags; else echo v4.5.2.dev3; fi) # <--- Update this on each version release __version_tag="${__version_tag:1}" # Remove the 'v' prefix read -r -d '' __usage <<-'EOF'