Merge branch 'main' into version-specification-rtorch

.github/workflows/docker-scout.yaml

@@ -0,0 +1,50 @@
+name: Docker Scout
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: "0 0 1 * *"
+
+env:
+  GH_TOKEN: ${{ github.token }}
+
+jobs:
+  scout:
+    runs-on: ubuntu-latest
+    permissions: write-all
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Login to DockerHub Container Registry
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKERHUB_USER }}
+          password: ${{ secrets.DOCKERHUB_PW }}
+      - name: Install Docker Scout
+        run: |
+          curl -fsSL https://raw.githubusercontent.com/docker/scout-cli/main/install.sh -o install-scout.sh
+          sh install-scout.sh
+      - name: Docker Scout
+        run: |
+          GH_ISSUES=$(gh issue list)
+          for image in *; do
+            if [[ -d "$image" ]] && [[ "$image" != ".github" ]] && [[ $GH_ISSUES != *"$image Vulnerability Analysis"* ]]; then
+              CONTAINER="getwilds/$image:latest"
+              docker scout cves $CONTAINER --only-fixed --format sarif --output cve_check.json
+              NUM_VUL=$(jq '.runs[0].tool.driver.rules | length' cve_check.json)
+              if [[ $NUM_VUL -ge 1 ]]; then
+                docker scout cves $CONTAINER --only-fixed --format markdown --output cve_check.html
+                if [[ $(wc -c cve_check.html) -le 65536 ]]; then
+                  gh issue create --repo getwilds/wilds-docker-library --title "$image Vulnerability Analysis" --body-file cve_check.html
+                else
+                  echo "Significant issues present in bwa, see quickview and recommendations below, but run CVE analysis locally." > qv.txt
+                  echo "\`\`\`" >> qv.txt
+                  docker scout quickview $CONTAINER >> qv.txt
+                  docker scout recommendations $CONTAINER >> qv.txt
+                  echo "\`\`\`" >> qv.txt
+                  gh issue create --repo getwilds/wilds-docker-library --title "$image Vulnerability Analysis" --body-file qv.txt
+                fi
+              fi
+              docker system prune -af
+            fi
+          done

bwa/Dockerfile_0.7.17

@@ -1,6 +1,6 @@
 
 # Using the Ubuntu base image
-FROM ubuntu:noble-20240114
+FROM ubuntu:noble-20241011
 
 # Adding labels for the GitHub Container Registry
 LABEL org.opencontainers.image.title="bwa"
@@ -14,10 +14,10 @@ LABEL org.opencontainers.image.licenses=MIT
 
 # Installing prerequisites
 RUN apt-get update \
-  && apt-get install -y --no-install-recommends build-essential=12.10ubuntu1 wget=1.21.4-1ubuntu4 \
-  zlib1g-dev=1:1.3.dfsg-3.1ubuntu2 autoconf=2.71-3 automake=1:1.16.5-1.3ubuntu1 \
-  libncurses-dev=6.4+20240113-1ubuntu2 libbz2-dev=1.0.8-5.1 liblzma-dev=5.6.1+really5.4.5-1 \
-  libssl-dev=3.0.13-0ubuntu3.1 libcurl4-gnutls-dev=8.5.0-2ubuntu10.1 \
+  && apt-get install -y --no-install-recommends build-essential=12.10ubuntu1 wget=1.21.4-1ubuntu4.1 \
+  zlib1g-dev=1:1.3.dfsg-3.1ubuntu2.1 autoconf=2.71-3 automake=1:1.16.5-1.3ubuntu1 \
+  libncurses-dev=6.4+20240113-1ubuntu2 libbz2-dev=1.0.8-5.1build0.1 liblzma-dev=5.6.1+really5.4.5-1build0.1 \
+  libssl-dev=3.0.13-0ubuntu3.4 libcurl4-gnutls-dev=8.5.0-2ubuntu10.4 gnutls-bin=3.8.3-1.1ubuntu3.2 \
   && rm -rf /var/lib/apt/lists/*
 
 # Pulling and extracting bwa source code

bwa/Dockerfile_latest

@@ -1,6 +1,6 @@
 
 # Using the Ubuntu base image
-FROM ubuntu:noble-20240114
+FROM ubuntu:noble-20241011
 
 # Adding labels for the GitHub Container Registry
 LABEL org.opencontainers.image.title="bwa"
@@ -14,10 +14,10 @@ LABEL org.opencontainers.image.licenses=MIT
 
 # Installing prerequisites
 RUN apt-get update \
-  && apt-get install -y --no-install-recommends build-essential=12.10ubuntu1 wget=1.21.4-1ubuntu4 \
-  zlib1g-dev=1:1.3.dfsg-3.1ubuntu2 autoconf=2.71-3 automake=1:1.16.5-1.3ubuntu1 \
-  libncurses-dev=6.4+20240113-1ubuntu2 libbz2-dev=1.0.8-5.1 liblzma-dev=5.6.1+really5.4.5-1 \
-  libssl-dev=3.0.13-0ubuntu3.1 libcurl4-gnutls-dev=8.5.0-2ubuntu10.1 \
+  && apt-get install -y --no-install-recommends build-essential=12.10ubuntu1 wget=1.21.4-1ubuntu4.1 \
+  zlib1g-dev=1:1.3.dfsg-3.1ubuntu2.1 autoconf=2.71-3 automake=1:1.16.5-1.3ubuntu1 \
+  libncurses-dev=6.4+20240113-1ubuntu2 libbz2-dev=1.0.8-5.1build0.1 liblzma-dev=5.6.1+really5.4.5-1build0.1 \
+  libssl-dev=3.0.13-0ubuntu3.4 libcurl4-gnutls-dev=8.5.0-2ubuntu10.4 gnutls-bin=3.8.3-1.1ubuntu3.2 \
   && rm -rf /var/lib/apt/lists/*
 
 # Pulling and extracting bwa source code

python-dl/Dockerfile_1.0

@@ -0,0 +1,22 @@
+
+# Using a CUDA base image
+FROM nvidia/cuda:11.7.1-cudnn8-devel-ubuntu22.04
+
+# Adding labels for the GitHub Container Registry
+LABEL org.opencontainers.image.title="python-dl"
+LABEL org.opencontainers.image.description="Docker image for the use of Deep Learning Python packages in FH DaSL's WILDS"
+LABEL org.opencontainers.image.version="1.0"
+LABEL org.opencontainers.image.authors="[email protected]"
+LABEL org.opencontainers.image.url=https://hutchdatascience.org/
+LABEL org.opencontainers.image.documentation=https://getwilds.org/
+LABEL org.opencontainers.image.source=https://github.com/getwilds/wilds-docker-library
+LABEL org.opencontainers.image.licenses=MIT
+
+# Installing Python
+RUN apt-get update \
+  && apt-get install -y --no-install-recommends python3=3.10.6-1~22.04.1 python3-pip=22.0.2+dfsg-1ubuntu0.4 \
+  && rm -rf /var/lib/apt/lists/*
+
+# Installing necessary Python modules
+RUN pip install --no-cache-dir numpy==1.26.4 seaborn==0.13.2 matplotlib==3.9.2 pandas==2.2.3 scikit-learn==1.5.2 \
+    scipy==1.14.1 optuna==4.0.0 joblib==1.4.2 keras==3.6.0 tensorflow==2.17.0 torch==2.5.0

python-dl/Dockerfile_latest

@@ -0,0 +1,22 @@
+
+# Using a CUDA base image
+FROM nvidia/cuda:11.7.1-cudnn8-devel-ubuntu22.04
+
+# Adding labels for the GitHub Container Registry
+LABEL org.opencontainers.image.title="python-dl"
+LABEL org.opencontainers.image.description="Docker image for the use of Deep Learning Python packages in FH DaSL's WILDS"
+LABEL org.opencontainers.image.version="latest"
+LABEL org.opencontainers.image.authors="[email protected]"
+LABEL org.opencontainers.image.url=https://hutchdatascience.org/
+LABEL org.opencontainers.image.documentation=https://getwilds.org/
+LABEL org.opencontainers.image.source=https://github.com/getwilds/wilds-docker-library
+LABEL org.opencontainers.image.licenses=MIT
+
+# Installing Python
+RUN apt-get update \
+  && apt-get install -y --no-install-recommends python3=3.10.6-1~22.04.1 python3-pip=22.0.2+dfsg-1ubuntu0.4 \
+  && rm -rf /var/lib/apt/lists/*
+
+# Installing necessary Python modules
+RUN pip install --no-cache-dir numpy==1.26.4 seaborn==0.13.2 matplotlib==3.9.2 pandas==2.2.3 scikit-learn==1.5.2 \
+    scipy==1.14.1 optuna==4.0.0 joblib==1.4.2 keras==3.6.0 tensorflow==2.17.0 torch==2.5.0

star/Dockerfile_2.7.6a

@@ -1,6 +1,6 @@
 
 # Using the Ubuntu base image
-FROM ubuntu:noble-20240114
+FROM ubuntu:oracular-20241009
 
 # Adding labels for the GitHub Container Registry
 LABEL org.opencontainers.image.title="star"
@@ -14,10 +14,10 @@ LABEL org.opencontainers.image.licenses=MIT
 
 # Installing prerequisites
 RUN apt-get update \
-  && apt-get install -y --no-install-recommends build-essential=12.10ubuntu1 wget=1.21.4-1ubuntu4 \
-  zlib1g-dev=1:1.3.dfsg-3.1ubuntu2 autoconf=2.71-3 automake=1:1.16.5-1.3ubuntu1 \
-  libncurses-dev=6.4+20240113-1ubuntu2 libbz2-dev=1.0.8-5.1 liblzma-dev=5.6.1+really5.4.5-1 \
-  libssl-dev=3.0.13-0ubuntu3.1 libcurl4-gnutls-dev=8.5.0-2ubuntu10.1 xxd=2:9.1.0016-1ubuntu7 \
+  && apt-get install -y --no-install-recommends build-essential=12.10ubuntu1 wget=1.24.5-1ubuntu2 \
+  zlib1g-dev=1:1.3.dfsg+really1.3.1-1ubuntu1 autoconf=2.72-3 automake=1:1.16.5-1.3ubuntu1 \
+  libncurses-dev=6.5-2 libbz2-dev=1.0.8-6 liblzma-dev=5.6.2-2 libssl-dev=3.3.1-2ubuntu2 \
+  libcurl4-gnutls-dev=8.9.1-2ubuntu2 xxd=2:9.1.0496-1ubuntu6 \
   && rm -rf /var/lib/apt/lists/*
 
 # Pulling and extracting STAR source code

star/Dockerfile_latest

@@ -1,6 +1,6 @@
 
 # Using the Ubuntu base image
-FROM ubuntu:noble-20240114
+FROM ubuntu:oracular-20241009
 
 # Adding labels for the GitHub Container Registry
 LABEL org.opencontainers.image.title="star"
@@ -14,10 +14,10 @@ LABEL org.opencontainers.image.licenses=MIT
 
 # Installing prerequisites
 RUN apt-get update \
-  && apt-get install -y --no-install-recommends build-essential=12.10ubuntu1 wget=1.21.4-1ubuntu4 \
-  zlib1g-dev=1:1.3.dfsg-3.1ubuntu2 autoconf=2.71-3 automake=1:1.16.5-1.3ubuntu1 \
-  libncurses-dev=6.4+20240113-1ubuntu2 libbz2-dev=1.0.8-5.1 liblzma-dev=5.6.1+really5.4.5-1 \
-  libssl-dev=3.0.13-0ubuntu3.1 libcurl4-gnutls-dev=8.5.0-2ubuntu10.1 xxd=2:9.1.0016-1ubuntu7 \
+  && apt-get install -y --no-install-recommends build-essential=12.10ubuntu1 wget=1.24.5-1ubuntu2 \
+  zlib1g-dev=1:1.3.dfsg+really1.3.1-1ubuntu1 autoconf=2.72-3 automake=1:1.16.5-1.3ubuntu1 \
+  libncurses-dev=6.5-2 libbz2-dev=1.0.8-6 liblzma-dev=5.6.2-2 libssl-dev=3.3.1-2ubuntu2 \
+  libcurl4-gnutls-dev=8.9.1-2ubuntu2 xxd=2:9.1.0496-1ubuntu6 \
   && rm -rf /var/lib/apt/lists/*
 
 # Pulling and extracting STAR source code