trim unused python scripts and unused thrift generated java/python

.github/workflows/CI-full.yml

@@ -57,7 +57,7 @@ jobs:
 
     - name: build vcell-opt package
       run: |
-        cd pythonProject/vcell-opt
+        cd pythonCopasiOpt/vcell-opt
         poetry install
         poetry run python -m pytest
 

.github/workflows/NightlyBMDB_CLI.yml

@@ -49,7 +49,7 @@ jobs:
 
       - name: build vcell-opt package
         run: |
-          cd pythonProject/vcell-opt
+          cd pythonCopasiOpt/vcell-opt
           poetry install
 
       - name: Setup Java for Build

.github/workflows/ci_cd.yml

@@ -41,7 +41,7 @@ jobs:
 
       - name: build vcell-opt package
         run: |
-          cd pythonProject/vcell-opt
+          cd pythonCopasiOpt/vcell-opt
           poetry install
           poetry run python -m pytest
 
@@ -104,7 +104,7 @@ jobs:
 
       - name: build vcell-opt package
         run: |
-          cd pythonProject/vcell-opt
+          cd pythonCopasiOpt/vcell-opt
           poetry install
           poetry run python -m pytest
 
@@ -155,7 +155,7 @@ jobs:
 
       - name: build vcell-opt package
         run: |
-          cd pythonProject/vcell-opt
+          cd pythonCopasiOpt/vcell-opt
           poetry install
           poetry run python -m pytest
 

.github/workflows/nightly-model-testing.yml

@@ -50,7 +50,7 @@ jobs:
           
       - name: build vcell-opt package
         run: |
-          cd pythonProject/vcell-opt
+          cd pythonCopasiOpt/vcell-opt
           poetry install
 
       - name: setup java 17 with maven cache

Dockerfile

@@ -56,12 +56,7 @@ RUN mkdir -p /usr/local/app/vcell/lib && \
     mkdir -p /usr/local/app/vcell/installDir/python/vcell_cli_utils && \
     mkdir -p /usr/local/app/vcell/installDir/bionetgen
 
-# Install Poetry dependency
-#RUN curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py | python3 - && \
-#    echo export PATH="$HOME/.poetry/bin:$PATH" >> /etc/bash.bashrc
-RUN python3 -m pip install wheel fire biosimulators-utils seaborn deprecated python-libsbml-experimental pandas
 RUN python3 -m pip install poetry &&  poetry config cache-dir "/poetry/.cache"
-
 ENV PATH="/root/.poetry/bin:/root/.local/bin:$PATH"
 
 # Copy JAR files
@@ -83,7 +78,9 @@ COPY ./vcell-client/target/vcell-client-0.0.1-SNAPSHOT.jar \
 # Install required python-packages
 COPY ./vcell-cli-utils/ /usr/local/app/vcell/installDir/python/vcell_cli_utils/
 RUN cd /usr/local/app/vcell/installDir/python/vcell_cli_utils/ && \
-     poetry config cache-dir "/poetry/.cache" --local && chmod 755 poetry.toml && poetry install
+    poetry config cache-dir "/poetry/.cache" --local && \
+    chmod 755 poetry.toml && \
+    poetry install
 
 # Add linux local solvers only
 ADD ./localsolvers /usr/local/app/vcell/installDir/localsolvers

docker/build/Dockerfile-batch-dev

@@ -96,7 +96,7 @@ COPY ./docker/build/batch/JavaPreprocessor64 \
      ./docker/build/batch/JavaPostprocessor64 \
      ./docker/build/batch/JavaSimExe64 \
      ./docker/build/batch/entrypoint.sh \
-     ./pythonScripts \
+     ./pythonVtk \
      /vcellscripts/
 
 ENV PATH=/vcellscripts:$PATH \

docker/build/Dockerfile-clientgen-dev

@@ -14,7 +14,6 @@ COPY ./bionetgen      /vcellclient/bionetgen
 COPY ./exampleModels  /vcellclient/exampleModels
 COPY ./localsolvers   /vcellclient/localsolvers
 COPY ./nativelibs     /vcellclient/nativelibs
-COPY ./pythonScripts  /vcellclient/pythonScripts
 
 COPY ./vcell-client/target/vcell-client-0.0.1-SNAPSHOT.jar \
     ./vcell-client/target/maven-jars/*.jar \

docker/build/Dockerfile-data-dev

@@ -75,16 +75,21 @@ RUN mkdir -p /usr/local/app && \
 	apt-get -y update && \
 	apt-get -y install openssh-client screen
 
-RUN pip install vtk
+RUN python3 -m pip install poetry &&  poetry config cache-dir "/poetry/.cache"
+ENV PATH="/root/.poetry/bin:/root/.local/bin:$PATH"
 
 WORKDIR /usr/local/app
 
 COPY ./vcell-server/target/vcell-server-0.0.1-SNAPSHOT.jar \
      ./vcell-server/target/maven-jars/*.jar \
      ./lib/
 
+# Copy and install pythonVtk
+COPY ./pythonVtk/ /usr/local/app/pythonVtk/
+RUN  cd /usr/local/app/pythonVtk && \
+     poetry config cache-dir "/poetry/.cache" --local && \
+     poetry install
 
-COPY ./pythonScripts ./pythonScripts
 COPY ./nativelibs/linux64 ./nativelibs/linux64
 COPY ./docker/build/vcell-data.log4j.xml .
 

docker/build/Dockerfile-web-dev

@@ -23,8 +23,7 @@ COPY ./vcell-web/target/vcell-web-0.0.1-SNAPSHOT.jar \
      ./vcell-web/target/maven-jars/*.jar \
      ./lib/
 
-
-COPY ./pythonScripts ./pythonScripts
+COPY ./pythonVtk ./pythonVtk
 COPY ./nativelibs/linux64 ./nativelibs/linux64
 COPY ./docker/build/vcell-web.log4j.xml .
 

docker/build/build.sh

@@ -188,8 +188,8 @@ build_admin() {
 
 build_opt() {
 	echo "building $repo/vcell-opt:$tag"
-	echo "$SUDO_CMD docker build -f ../../pythonProject/Dockerfile --tag $repo/vcell-opt:$tag ../../pythonProject"
-	$SUDO_CMD docker build -f ../../pythonProject/Dockerfile --tag $repo/vcell-opt:$tag ../../pythonProject
+	echo "$SUDO_CMD docker build -f ../../pythonCopasiOpt/Dockerfile --tag $repo/vcell-opt:$tag ../../pythonCopasiOpt"
+	$SUDO_CMD docker build -f ../../pythonCopasiOpt/Dockerfile --tag $repo/vcell-opt:$tag ../../pythonCopasiOpt
 	if [[ $? -ne 0 ]]; then echo "docker build failed"; exit 1; fi
 	if [ "$skip_push" == "false" ]; then
 		$SUDO_CMD docker push $repo/vcell-opt:$tag

docker/build/installers/VCell.install4j

@@ -18,7 +18,6 @@
       <variable name="vcell5SplashScreenPngFilePath" value="${compiler:mavenRootDir}/vcellSplash.png" />
       <variable name="vcellLocalSolversDirPath" value="${compiler:mavenRootDir}/localsolvers" />
       <variable name="vcellLicenseFilePath" value="${compiler:mavenRootDir}/thirdpartylicenses.txt" />
-      <variable name="vcellPythonPath" value="${compiler:mavenRootDir}/pythonScripts" />
       <variable name="vcellbngPerlPath" value="${compiler:mavenRootDir}/bionetgen" />
       <variable name="macJrePath" value="NO-MAC-JRE-PATH" />
       <variable name="win32JrePath" value="NO-WIN32-JRE-PATH" />
@@ -61,7 +60,6 @@
       <mountPoint id="719" location="lib" />
       <mountPoint id="1473" location="resources" />
       <mountPoint id="1474" location="localsolvers" />
-      <mountPoint id="1748" location="pythonScripts" />
       <mountPoint id="1750" location="bionetgen" />
       <mountPoint id="1348" root="1114" location="nativelibs" />
       <mountPoint id="1349" root="1114" location="nativelibs/mac64" />
@@ -90,7 +88,6 @@
     <entries>
       <dirEntry mountPoint="719" file="${compiler:vcellLibSourcePath}" subDirectory="maven-jars" />
       <fileEntry mountPoint="1473" file="${compiler:vcellLicenseFilePath}" />
-      <dirEntry mountPoint="1748" file="${compiler:vcellPythonPath}" />
       <dirEntry mountPoint="1750" file="${compiler:vcellbngPerlPath}" />
       <dirEntry mountPoint="1349" file="${compiler:vcellNativeLibsDirSourcePath}/mac64" />
       <dirEntry mountPoint="1353" file="${compiler:vcellLocalSolversDirPath}/mac64" fileMode="755" overrideFileMode="true" />

docker/swarm/README_stack_on_mac.md

@@ -5,7 +5,15 @@ pushd ../../
 mvn clean install dependency:copy-dependencies -DskipTests=true
 popd
 
-pushd ../../pythonProject/vcell-opt
+pushd ../../pythonCopasiOpt/vcell-opt
+poetry install
+popd
+
+pushd vcell-admin
+poetry install
+popd
+
+pushd ../../pythonVtk
 poetry install
 popd
 
@@ -28,7 +36,7 @@ on cluster (e.g. xanadu-76) as user vcell build vcell-opt singularity container
 export docker_image=ghcr.io/virtualcell/vcell-opt:dev
 export singularity_file=ghcr.io_virtualcell_vcell-opt_dev.img
 module load singularity
-#singularity remote login -u <github_user> -p <github_token> docker://ghcr.io
+# singularity remote login -u <github_user> -p <github_token> docker://ghcr.io
 singularity build --force ${singularity_file} docker://${docker_image}
 cp ${singularity_file} /state/partition1/singularityImages/
 cp ${singularity_file} /share/apps/vcell3/singularityImages/