Replacing deprecated "apt-get" with "apt"

Author: CodeByDrescher

.github/workflows/bsts_local.yml

@@ -28,12 +28,12 @@ jobs:
 
       - name: Install Perl # for BioNetGen
         run: |
-          sudo apt-get update -y
-          sudo apt-get install -y --no-install-recommends perl
+          sudo apt update -y
+          sudo apt install -y --no-install-recommends perl
 
       - name: Install XPP
         run: |
-          sudo apt-get install -y --no-install-recommends xppaut
+          sudo apt install -y --no-install-recommends xppaut
 
       - name: Install Go (for Singularity)
         uses: actions/setup-go@v3
@@ -47,7 +47,7 @@ jobs:
           OS: linux
           ARCH: amd64
         run: |
-          sudo apt-get install -y --no-install-recommends \
+          sudo apt install -y --no-install-recommends \
             build-essential \
             libseccomp-dev \
             pkg-config \

.github/workflows/ci_cd.yml

@@ -107,7 +107,7 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Install hdf5 tools needed for testing
-        run: sudo apt-get -y update && sudo apt-get -y install hdf5-tools
+        run: sudo apt -y update && sudo apt -y install hdf5-tools
 
       - name: Set up Python
         uses: actions/setup-python@v5

docker/build/Dockerfile-admin-dev

@@ -16,11 +16,11 @@ ENV PATH "${JAVA_HOME}/bin:${PATH}"
 COPY --from=jre-build /javaruntime $JAVA_HOME
 
 # now we have Java 17
-RUN apt-get -y update && \
-    apt-get install -y curl dnsutils apt-utils libfreetype6 fontconfig fonts-dejavu openssh-client && \
+RUN apt -y update && \
+    apt install -y curl dnsutils apt-utils libfreetype6 fontconfig fonts-dejavu openssh-client && \
     mkdir -p /usr/local/app/lib 
 
-RUN DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends tzdata
+RUN DEBIAN_FRONTEND=noninteractive apt install -y --no-install-recommends tzdata
 RUN unlink /etc/localtime || true
 RUN ln -s /usr/share/zoneinfo/America/New_York /etc/localtime
 

docker/build/Dockerfile-api-dev

@@ -17,11 +17,11 @@ COPY --from=jre-build /javaruntime $JAVA_HOME
 
 # now we have Java 17 and Python 3.9
 
-RUN apt-get -y update && \
-    apt-get install -y --no-install-recommends curl dnsutils apt-utils libfreetype6 fontconfig fonts-dejavu && \
+RUN apt -y update && \
+    apt install -y --no-install-recommends curl dnsutils apt-utils libfreetype6 fontconfig fonts-dejavu && \
     mkdir -p /usr/local/app/lib 
 
-RUN DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends tzdata
+RUN DEBIAN_FRONTEND=noninteractive apt install -y --no-install-recommends tzdata
 RUN unlink /etc/localtime || true
 RUN ln -s /usr/share/zoneinfo/America/New_York /etc/localtime
 

docker/build/Dockerfile-batch-dev

@@ -1,11 +1,11 @@
 FROM ghcr.io/virtualcell/vcell-solvers:v0.8.2
 
-RUN apt-get -y update && \
-    apt-get install -y  curl && \
-	apt-get install -y wget gdebi-core apt-utils libfreetype6 fontconfig fonts-dejavu && \
+RUN apt -y update && \
+    apt install -y  curl && \
+	apt install -y wget gdebi-core apt-utils libfreetype6 fontconfig fonts-dejavu && \
     pip3 install thrift
 
-RUN DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends tzdata
+RUN DEBIAN_FRONTEND=noninteractive apt install -y --no-install-recommends tzdata
 RUN unlink /etc/localtime || true
 RUN ln -s /usr/share/zoneinfo/America/New_York /etc/localtime
 

docker/build/Dockerfile-clientgen-dev

@@ -16,8 +16,8 @@ ENV PATH "${JAVA_HOME}/bin:${PATH}"
 COPY --from=jre-build /javaruntime $JAVA_HOME
 
 RUN mkdir -p /usr/local/app && \
-	apt-get -y update && \
-    apt-get -y install wget apt-utils libfreetype6 fontconfig fonts-dejavu
+	apt -y update && \
+    apt -y install wget apt-utils libfreetype6 fontconfig fonts-dejavu
 
 RUN mkdir /installer && cd /installer && \
     wget --quiet -O install4j_unix_10_0_5.tar.gz \

docker/build/Dockerfile-data-dev

@@ -17,14 +17,14 @@ COPY --from=jre-build /javaruntime $JAVA_HOME
 
 # now we have Java 17 and Python 3.9
 
-RUN apt-get -y update && \
-	apt-get -y install openssh-client screen apt-utils libfreetype6 fontconfig fonts-dejavu && \
+RUN apt -y update && \
+	apt -y install openssh-client screen apt-utils libfreetype6 fontconfig fonts-dejavu && \
     mkdir -p /usr/local/app
 
 RUN python3 -m pip install poetry &&  poetry config cache-dir "/poetry/.cache"
 ENV PATH="/root/.poetry/bin:/root/.local/bin:$PATH"
 
-RUN DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends tzdata
+RUN DEBIAN_FRONTEND=noninteractive apt install -y --no-install-recommends tzdata
 RUN unlink /etc/localtime || true
 RUN ln -s /usr/share/zoneinfo/America/New_York /etc/localtime
 

docker/build/Dockerfile-db-dev

@@ -16,10 +16,10 @@ ENV PATH "${JAVA_HOME}/bin:${PATH}"
 COPY --from=jre-build /javaruntime $JAVA_HOME
 
 RUN mkdir -p /usr/local/app && \
-	apt-get -y update && \
-    apt-get -y install screen apt-utils libfreetype6 fontconfig fonts-dejavu
+	apt -y update && \
+    apt -y install screen apt-utils libfreetype6 fontconfig fonts-dejavu
 
-RUN DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends tzdata
+RUN DEBIAN_FRONTEND=noninteractive apt install -y --no-install-recommends tzdata
 RUN unlink /etc/localtime || true
 RUN ln -s /usr/share/zoneinfo/America/New_York /etc/localtime
 

docker/build/Dockerfile-sched-dev

@@ -17,10 +17,10 @@ COPY --from=jre-build /javaruntime $JAVA_HOME
 
 
 RUN mkdir -p /usr/local/app && \
-	apt-get -y update && \
-    apt-get -y install openssh-client curl screen apt-utils libfreetype6 fontconfig fonts-dejavu
+	apt -y update && \
+    apt -y install openssh-client curl screen apt-utils libfreetype6 fontconfig fonts-dejavu
 
-RUN DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends tzdata
+RUN DEBIAN_FRONTEND=noninteractive apt install -y --no-install-recommends tzdata
 RUN unlink /etc/localtime || true
 RUN ln -s /usr/share/zoneinfo/America/New_York /etc/localtime
 

docker/build/Dockerfile-submit-dev

@@ -16,10 +16,10 @@ ENV PATH "${JAVA_HOME}/bin:${PATH}"
 COPY --from=jre-build /javaruntime $JAVA_HOME
 
 RUN mkdir -p /usr/local/app && \
-	apt-get -y update && \
-    apt-get -y install openssh-client screen apt-utils libfreetype6 fontconfig fonts-dejavu
+	apt -y update && \
+    apt -y install openssh-client screen apt-utils libfreetype6 fontconfig fonts-dejavu
 
-RUN DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends tzdata
+RUN DEBIAN_FRONTEND=noninteractive apt install -y --no-install-recommends tzdata
 RUN unlink /etc/localtime || true
 RUN ln -s /usr/share/zoneinfo/America/New_York /etc/localtime
 

docker/swarm/README_DockerSwarmConfig.md

@@ -25,8 +25,8 @@ install jq (utility for json processing)
 install poetry (for building/installing vcell-admin)
 
 ```bash
-sudo apt-get install -y jq
-sudo apt-get install -y python3-poetry
+sudo apt install -y jq
+sudo apt install -y python3-poetry
 ```
 
 ## Install singularity [more info linux](https://singularity.lbl.gov/install-linux)

pythonCopasiOpt/Dockerfile

@@ -1,7 +1,7 @@
 FROM python:3.10-slim-bullseye
 
 RUN apt -y update && apt -y upgrade &&  \
-    apt-get install -y curl
+    apt install -y curl
 
 RUN mkdir -p /usr/local/app/vcell/installDir && \
     mkdir -p /usr/local/app/vcell/installDir/python/vcell_opt