Merge pull request #477 from sunbeam-labs/472-452-release

4.5.2.dev5 release

.github/PULL_REQUEST_TEMPLATE.md

@@ -5,4 +5,5 @@
 
 If this is for a release:
 * [ ] I have updated documentation
-* [ ] I have updated the hardcoded version at the top of `install.sh` to match what this release's version will be
+* [ ] I have updated the hardcoded version at the top of `install.sh` to match what this release's version will be
+* [ ] I have created a release archive that will be attached to this release (`bash dev_scripts/generate_archive.sh`)

.github/workflows/dockerhub.yml

@@ -99,12 +99,9 @@ jobs:
 
           - name: Generate image report
             id: report
-            # Replace '\n' with '%0A' for embedding into release notes (for somer reason '\n' is not escaped)
             run: |
-              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"
+              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"
 
     push-cutadapt-dockerhub:
       name: Push cutadapt env to Dockerhub
@@ -140,9 +137,7 @@ jobs:
         - name: Generate image report
           id: report
           run: |
-            IP=$(docker run --rm sunbeamlabs/cutadapt:${{ inputs.version }} cat installed_packages.txt)
-            echo $IP
-            echo "package_versions=${IP//$'\n'/'%0A'}" >> "$GITHUB_OUTPUT"
+            echo "package_versions=$(docker run --rm sunbeamlabs/cutadapt:${{ inputs.version }} cat installed_packages.txt)" >> "$GITHUB_OUTPUT"
 
     push-komplexity-dockerhub:
       name: Push komplexity env to Dockerhub
@@ -178,9 +173,7 @@ jobs:
         - name: Generate image report
           id: report
           run: |
-            IP=$(docker run --rm sunbeamlabs/komplexity:${{ inputs.version }} cat installed_packages.txt)
-            echo $IP
-            echo "package_versions=${IP//$'\n'/'%0A'}" >> "$GITHUB_OUTPUT"
+            echo "package_versions=$(docker run --rm sunbeamlabs/komplexity:${{ inputs.version }} cat installed_packages.txt)" >> "$GITHUB_OUTPUT"
 
     push-qc-dockerhub:
       name: Push qc env to Dockerhub
@@ -216,9 +209,7 @@ jobs:
         - name: Generate image report
           id: report
           run: |
-            IP=$(docker run --rm sunbeamlabs/qc:${{ inputs.version }} cat installed_packages.txt)
-            echo $IP
-            echo "package_versions=${IP//$'\n'/'%0A'}" >> "$GITHUB_OUTPUT"
+            echo "package_versions=$(docker run --rm sunbeamlabs/qc:${{ inputs.version }} cat installed_packages.txt)" >> "$GITHUB_OUTPUT"
 
     push-reports-dockerhub:
       name: Push reports env to Dockerhub
@@ -254,6 +245,4 @@ jobs:
         - name: Generate image report
           id: report
           run: |
-            IP=$(docker run --rm sunbeamlabs/reports:${{ inputs.version }} cat installed_packages.txt)
-            echo $IP
-            echo "package_versions=${IP//$'\n'/'%0A'}" >> "$GITHUB_OUTPUT"
+            echo "package_versions=$(docker run --rm sunbeamlabs/reports:${{ inputs.version }} cat installed_packages.txt)" >> "$GITHUB_OUTPUT"

.github/workflows/release.yml

@@ -44,43 +44,13 @@ jobs:
                     echo "Versions don't match, exiting..."
                     exit 1
                 fi
-
-    generate-tarball:
-        name: Generate Tarball and Add to Release
-        runs-on: ubuntu-latest
-        needs:
-          - run-tests
-          - check-version
-
-        steps:
-          - name: Checkout Code
-            uses: actions/checkout@v4
-
-          - 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/[email protected]
-            with:
-              token: ${{ secrets.GITHUB_TOKEN }}
-              id: ${{ github.event.release.id }}
-              body: "### Sunbeam Tarball\nDownload the Sunbeam tarball from the release page to install Sunbeam locally.\n[Download Sunbeam Tarball](https://github.com/sunbeam-labs/sunbeam/releases/${{ needs.check-version.outputs.version }}/download/sunbeam.tar.gz"
-              replacebody: false
-              files: "sunbeam.tar.gz"
     
     test-tarball:
         name: Test Tarball
         runs-on: ubuntu-latest
         needs:
           - run-tests
           - check-version
-          - generate-tarball
 
         steps:
           - name: setup-conda

Dockerfile

@@ -40,7 +40,7 @@ RUN rm -r projects
 # "Activate" the environment
 SHELL ["conda", "run", "-n", "sunbeam", "/bin/bash", "-c"]
 
-RUN echo "Python: $(python --version)\nSnakemake: $(snakemake --version)\nConda: $(conda --version)" > installed_packages.txt
+RUN echo "Python: $(python --version), Snakemake: $(snakemake --version), Conda: $(conda --version)" > installed_packages.txt
 
 # Run
 CMD "bash"

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=$(if git describe --tags >/dev/null 2>&1 ; then git describe --tags; else echo v4.5.2.dev4; fi) # <--- Update this on each version release
+__version_tag=$(if git describe --tags >/dev/null 2>&1 ; then git describe --tags; else echo v4.5.2.dev5; fi) # <--- Update this on each version release
 __version_tag="${__version_tag:1}" # Remove the 'v' prefix
 
 read -r -d '' __usage <<-'EOF'

slim.Dockerfile

@@ -34,7 +34,7 @@ ENV SUNBEAM_MIN_RUNTIME="60"
 # "Activate" the environment
 SHELL ["conda", "run", "-n", "sunbeam", "/bin/bash", "-c"]
 
-RUN echo "Python: $(python --version)\nSnakemake: $(snakemake --version)\nConda: $(conda --version)" > installed_packages.txt
+RUN echo "Python: $(python --version), Snakemake: $(snakemake --version), Conda: $(conda --version)" > installed_packages.txt
 
 # Run
 CMD "bash"

workflow/envs/cutadapt.Dockerfile

@@ -6,7 +6,7 @@ WORKDIR /home/cutadapt_env
 # Install environment
 RUN pip install cutadapt
 
-RUN echo "Python: $(python --version)\nCutadapt $(pip show cutadapt | grep 'Version: ')" > installed_packages.txt
+RUN echo "Python: $(python --version), Cutadapt $(pip show cutadapt | grep 'Version: ')" > installed_packages.txt
 
 # Run
 CMD ["bash"]

workflow/envs/komplexity.Dockerfile

@@ -8,7 +8,7 @@ RUN apt-get update && apt-get install -y git
 RUN git clone https://github.com/eclarke/komplexity
 RUN cd komplexity && cargo install
 
-RUN echo "Rustc: $(rustc --version)\nKomplexity $(kz --version)" > installed_packages.txt
+RUN echo "Rustc: $(rustc --version), Komplexity $(kz --version)" > installed_packages.txt
 
 # Run
 CMD ["bash"]

workflow/envs/qc.Dockerfile

@@ -13,7 +13,7 @@ ENV PATH="/opt/conda/envs/qc/bin/:${PATH}"
 # "Activate" the environment
 SHELL ["conda", "run", "--no-capture-output", "-n", "qc", "/bin/bash", "-c"]
 
-RUN echo "Python: $(python --version)\nConda: $(conda --version)\nBWA: $(bwa 2>&1 >/dev/null | grep 'Version: ')\nFastQC: $(fastqc --version)\nTrimmomatic: $(trimmomatic -version)" > installed_packages.txt
+RUN echo "Python: $(python --version), Conda: $(conda --version), BWA: $(bwa 2>&1 >/dev/null | grep 'Version: '), FastQC: $(fastqc --version), Trimmomatic: $(trimmomatic -version)" > installed_packages.txt
 
 # Run
 CMD "bash"

workflow/envs/reports.Dockerfile

@@ -6,7 +6,7 @@ WORKDIR /home/reports_env
 # Install environment
 RUN pip install numpy pandas
 
-RUN echo "Python: $(python --version)\nNumpy $(pip show numpy | grep 'Version: ')\nPandas $(pip show pandas | grep 'Version: ')" > installed_packages.txt
+RUN echo "Python: $(python --version), Numpy $(pip show numpy | grep 'Version: '), Pandas $(pip show pandas | grep 'Version: ')" > installed_packages.txt
 
 # Run
 CMD ["bash"]