Merge pull request #223 from sigven/bundle_update_2023

PCGR v.2.0rc - 2024

.bumpversion.cfg

@@ -1,7 +1,11 @@
 [bumpversion]
-current_version = 1.4.1
+current_version = 1.4.1.9021
 commit = True
 tag = False
+parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\.(?P<dev>\d+))?
+serialize = 
+	{major}.{minor}.{patch}.{dev}
+	{major}.{minor}.{patch}
 
 [bumpversion:file:pcgrr/DESCRIPTION]
 search = Version: {current_version}
@@ -15,9 +19,13 @@ replace = {new_version}
 search = __version__ = '{current_version}'
 replace = __version__ = '{new_version}'
 
-[bumpversion:file:setup.py]
-search = version='{current_version}'
-replace = version='{new_version}'
+[bumpversion:file:pyproject.toml]
+search = version = "{current_version}"
+replace = version = "{new_version}"
+
+[bumpversion:file:conda/recipe/pcgr/meta.yaml]
+search = version: {current_version}
+replace = version: {new_version}
 
 [bumpversion:file:conda/recipe/pcgrr/meta.yaml]
 search = version: {current_version}

.dockerignore

@@ -0,0 +1,3 @@
+*
+!conda
+!.dockerignore

.github/workflows/apptainer.yaml

@@ -0,0 +1,65 @@
+name: apptainer
+
+on:
+  push:
+    branches:
+      - patch1
+
+env:
+  VERSION: '1.4.1.9015' # versioned by bump2version
+jobs:
+  docker2apptainer:
+    name: Docker2apptainer
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - name: Free Disk Space
+        uses: jlumbroso/free-disk-space@main
+      - name: Check free space
+        run: |
+          echo "Free space:"
+          df -h
+      - name: Code checkout
+        uses: actions/checkout@v4
+        with:
+          ref: v${{ env.VERSION }}
+      - name: 🏰 QEMU setup
+        uses: docker/setup-qemu-action@v3
+      - name: 🏯 Buildx setup
+        uses: docker/setup-buildx-action@v3
+      - name: DockerHub login
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+      - name: 🐳 Docker img build and push to DockerHub
+        uses: docker/build-push-action@v6
+        with:
+          context: . # yes, dot
+          push: false
+          platforms: linux/amd64
+          tags: |
+            sigven/pcgr:${{ env.VERSION }}
+          outputs: type=docker,dest=pcgr_${{ env.VERSION }}.tar
+
+      - name: Apptainer setup
+        uses: eWaterCycle/setup-apptainer@v2
+
+      - name: Apptainer build
+        run: |
+          docker image ls -a
+          #docker save sigven/pcgr:${VERSION} -o pcgr_${VERSION}.tar
+          ls -la
+          df -h
+          echo "Building Apptainer SIF"
+          echo "---------------------------------"
+          apptainer build pcgr_singularity_${VERSION}.sif docker-archive://pcgr_${VERSION}.tar
+          echo "---------------------------------"
+          ls -la
+          df -h
+     #- name: Upload SIF to GHCR
+     #  run: |
+     #    echo ${{ secrets.GITHUB_TOKEN }} | apptainer registry login -u ${{ github.actor }} --password-stdin oras://ghcr.io
+     #    apptainer push pcgr_${VERSION}.sif oras://ghcr.io/${GITHUB_REPOSITORY}:${VERSION}

.github/workflows/build_conda_recipes.yaml

@@ -4,68 +4,76 @@ on:
   push:
     branches:
       - master
-      - dev
+      - bundle_update_2023
+      - locale
 env:
   atoken: ${{ secrets.ANACONDA_UPLOAD_TOKEN }}
   recipe_path: conda/recipe
   env_yml_path: conda/env/yml
   env_lock_path: conda/env/lock
-  VERSION: '1.4.1' # versioned by bump2version
+  VERSION: '1.4.1.9021' # versioned by bump2version
 jobs:
-  build_conda_pkgs:
+  build_pcgrr_conda_pkg:
     # When merging to one of the branches above and the commit message matches
     if: "startsWith(github.event.head_commit.message, 'Bump version:')"
-    name: Build conda packages
+    name: Build pcgrr conda pkg
     runs-on: ubuntu-latest
     defaults:
       run:
         shell: bash -l {0}
+    steps:
+      - name: Code checkout
+        uses: actions/checkout@v4
+      - name: Micromamba setup
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: ${{ env.env_yml_path }}/condabuild.yml
+      - name: 🐍 Conda pkg build and upload
+        run: |
+          conda mambabuild ${recipe_path}/pcgrr -c conda-forge -c bioconda --token ${atoken}
 
+  build_pcgr_conda_pkg:
+    # When merging to one of the branches above and the commit message matches
+    if: "startsWith(github.event.head_commit.message, 'Bump version:')"
+    name: Build pcgr conda pkg
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
     steps:
       - name: Code checkout
-        uses: actions/checkout@v3
-      - name: Mambaforge setup
-        uses: conda-incubator/setup-miniconda@v2
+        uses: actions/checkout@v4
+      - name: Micromamba setup
+        uses: mamba-org/setup-micromamba@v1
         with:
-          miniforge-variant: Mambaforge
-          miniforge-version: "latest"
-          show-channel-urls: true
-          auto-activate-base: false
-          activate-environment: condabuild
           environment-file: ${{ env.env_yml_path }}/condabuild.yml
-          use-mamba: true
       - name: 🐍 Conda pkg build and upload
         run: |
           conda mambabuild ${recipe_path}/pcgr -c conda-forge -c bioconda --token ${atoken} --quiet
-          conda mambabuild ${recipe_path}/pcgrr -c conda-forge -c bioconda --token ${atoken} --quiet
 
-  # spin up fresh instance since conda-lock
-  # takes ages when run on previous one
+  # spin up fresh instance since conda-lock takes ages when run on previous one
   conda_lock:
     name: Conda lock
     runs-on: ubuntu-latest
-    needs: build_conda_pkgs
+    needs: [build_pcgr_conda_pkg, build_pcgrr_conda_pkg]
     defaults:
       run:
         shell: bash -l {0}
-
     steps:
       - name: Code checkout
-        uses: actions/checkout@v3
-      - name: Set up Mambaforge
-        uses: conda-incubator/setup-miniconda@v2
+        uses: actions/checkout@v4
+      - name: Micromamba setup
+        uses: mamba-org/setup-micromamba@v1
         with:
-          miniforge-variant: Mambaforge
-          miniforge-version: "latest"
-          show-channel-urls: true
-          auto-activate-base: false
-          activate-environment: condabuild
           environment-file: ${{ env.env_yml_path }}/condabuild.yml
-          use-mamba: true
-      - name: Generate conda locks
+      - name: 🔒 Conda lock
         run: |
-          conda-lock lock --mamba --file ${env_yml_path}/pcgr.yml --filename-template 'pcgr-{platform}.lock' -p osx-64 -p linux-64
-          conda-lock lock --mamba --file ${env_yml_path}/pcgrr.yml --filename-template 'pcgrr-{platform}.lock' -p osx-64 -p linux-64
+          # 1. generate a combined lock file
+          # 2. render platform-specific locks
+          conda-lock lock --file ${env_yml_path}/pcgr.yml -p osx-64 -p linux-64
+          conda-lock render --kind explicit -p osx-64 -p linux-64 conda-lock.yml --filename-template 'pcgr-{platform}.lock' && rm conda-lock.yml
+          conda-lock lock --file ${env_yml_path}/pcgrr.yml -p osx-64 -p linux-64
+          conda-lock render --kind explicit -p osx-64 -p linux-64 conda-lock.yml --filename-template 'pcgrr-{platform}.lock' && rm conda-lock.yml
           mv pcgrr-*.lock ${env_lock_path}
           mv pcgr-*.lock ${env_lock_path}
       - name: Commit changes
@@ -77,37 +85,15 @@ jobs:
           git add .
           git commit -m "${MSG}"
           git push
-
-  pkgdown-site:
-    name: Deploy pkgdown website
-    runs-on: ubuntu-latest
-    needs: build_conda_pkgs
-    defaults:
-      run:
-        shell: bash -l {0}
-    steps:
-      - name: Code checkout
-        uses: actions/checkout@v3
-      - name: Set up miniconda
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          miniforge-variant: Mambaforge
-          miniforge-version: "latest"
-          auto-update-conda: true
-          auto-activate-base: true
-          activate-environment: ""
-          channels: "pcgr,conda-forge,bioconda"
-      - name: Install conda packages
-        run: mamba env create -n pkgdown -f ${env_yml_path}/pkgdown.yml
       - name: 🌐 Website publish
+        if: github.ref_name == 'master'
         run: |
-            git config --local user.email "[email protected]"
-            git config --local user.name "GitHub Actions"
-            conda activate pkgdown
-            cp pcgrr/DESCRIPTION . # hack for pkgdown to work
-            printf "pcgrr version:\n"
-            Rscript -e "packageVersion('pcgrr')"
-            Rscript -e "pkgdown::deploy_to_branch(pkg = 'pcgrr', commit_message = paste(pkgdown:::construct_commit_message('.'), '- see https://sigven.github.io/pcgr/'), branch = 'gh-pages', new_process = FALSE)"
+          micromamba env create -n pkgdownenv -f ${env_yml_path}/pkgdown.yml
+          micromamba activate pkgdownenv
+          cp pcgrr/DESCRIPTION . # hack for pkgdown to work
+          printf "pcgrr version:\n"
+          Rscript -e "packageVersion('pcgrr')"
+          Rscript -e "pkgdown::deploy_to_branch(pkg = 'pcgrr', commit_message = 'Built PCGR website: https://sigven.github.io/pcgr/', branch = 'gh-pages', new_process = FALSE)"
 
   docker_deploy:
     name: Build and deploy Docker
@@ -116,10 +102,9 @@ jobs:
     defaults:
       run:
         shell: bash -l {0}
-
     steps:
       - name: Code checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - id: pull_lock_commit
         name: 📥 Pull lock commit
         run: |
@@ -128,7 +113,7 @@ jobs:
             LATEST_COMMIT_HASH="$(git --no-pager log -1 --format='%H')"
             echo "latest_commit_hash=${LATEST_COMMIT_HASH}" >> $GITHUB_OUTPUT
       - name: 🔖 Tag creation
-        uses: actions/github-script@v5
+        uses: actions/github-script@v7
         env:
           LATEST_COMMIT_HASH: ${{ steps.pull_lock_commit.outputs.latest_commit_hash }}
         with:
@@ -142,24 +127,46 @@ jobs:
               sha: the_sha
             })
 
+      - name: 🗑 Free Disk Space
+        uses: jlumbroso/free-disk-space@main
       # work with tag from above
       - name: Code checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           ref: v${{ env.VERSION }}
-      - name: Buildx setup
-        id: buildx
-        uses: docker/setup-buildx-action@v2
+      - name: 🏰 QEMU setup
+        uses: docker/setup-qemu-action@v3
+      - name: 🏯 Buildx setup
+        uses: docker/setup-buildx-action@v3
       - name: DockerHub login
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
-      - name: 🐳 Docker img build and push to DockerHub
-        uses: docker/build-push-action@v4
+      # use the outputs=docker with dest to directly save to tar for apptainer
+      - name: 🐳 Docker img build, tar and push to Docker Hub
+        uses: docker/build-push-action@v6
         with:
-          context: . # yes, dot
+          context: .
           push: true
           platforms: linux/amd64
           tags: |
             sigven/pcgr:${{ env.VERSION }}
+          outputs: type=docker,dest=pcgr_${{ env.VERSION }}.tar
+
+      # Apptainer
+      - name: Apptainer setup
+        uses: eWaterCycle/setup-apptainer@v2
+      - name: 🕹️ Apptainer build
+        run: |
+          ls -lSha
+          df -h
+          echo "Building Apptainer SIF"
+          echo "---------------------------------"
+          apptainer build pcgr_singularity_${VERSION}.sif docker-archive://pcgr_${VERSION}.tar
+          echo "---------------------------------"
+          ls -lSha
+      - name: Upload SIF to GHCR
+        run: |
+          echo ${{ secrets.GITHUB_TOKEN }} | apptainer registry login -u ${{ github.actor }} --password-stdin oras://ghcr.io
+          apptainer push pcgr_singularity_${VERSION}.sif oras://ghcr.io/${GITHUB_REPOSITORY}:${VERSION}.singularity

.gitignore

@@ -17,3 +17,5 @@ docs/_build/
 
 .Rhistory
 *.Rproj
+
+tests

Dockerfile

@@ -1,16 +1,19 @@
 FROM ubuntu:20.04
-LABEL maintainer="https://github.com/pdiakumis"
+LABEL org.opencontainers.image.authors='[email protected], [email protected]' \
+      org.opencontainers.image.description='Personal Cancer Genome Reporter (PCGR)' \
+      org.opencontainers.image.source='https://github.com/sigven/pcgr' \
+      org.opencontainers.image.url='https://github.com/sigven/pcgr' \
+      org.opencontainers.image.documentation='https://sigven.github.io/pcgr' \
+      org.opencontainers.image.licenses='MIT'
 
-ARG MINI_VERSION=4.11.0-0
+ARG MINI_VERSION=24.3.0-0
 ARG MINI_URL=https://github.com/conda-forge/miniforge/releases/download/${MINI_VERSION}/Mambaforge-${MINI_VERSION}-Linux-x86_64.sh
 
 # install core pkgs, mambaforge
 RUN apt-get update && \
     apt-get install --yes --no-install-recommends \
-    bash bzip2 curl git less vim wget zip ca-certificates && \
+    bash bzip2 curl less wget zip ca-certificates && \
     apt-get clean && \
-    rm -r /var/lib/apt/lists/* && \
-    rm -r /var/cache/apt/* && \
     curl --silent -L "${MINI_URL}" -o "mambaforge.sh" && \
     /bin/bash mambaforge.sh -b -p /opt/mambaforge/ && \
     rm mambaforge.sh
@@ -23,6 +26,10 @@ RUN mamba create -n pcgr --file ${PCGR_CONDA_ENV_DIR}/pcgr-linux-64.lock
 RUN mamba create -n pcgrr --file ${PCGR_CONDA_ENV_DIR}/pcgrr-linux-64.lock
 RUN mamba clean --all --force-pkgs-dirs --yes
 
+FROM quay.io/bioconda/base-glibc-debian-bash:3.1
+
+COPY --from=0 /opt/mambaforge/envs/ /opt/mambaforge/envs/
+
 ARG PCGR_ENV_NAME="pcgr"
 # pcgr env is activated by default
 ENV PATH="/opt/mambaforge/envs/${PCGR_ENV_NAME}/bin:${PATH}"

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2017 Sigve Nakken
+Copyright (c) 2024 Sigve Nakken
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal