udpate/clean docker

doc/howtodocker.doc

@@ -112,10 +112,6 @@ Please adapt the directories to your configuration. In this example, "/home/user
 \endverbatim
 
 Now hack and enjoy!\\
-The sedFoam files will be in /home/sudofoam and the solver is already compiled. Note that the bashrc file from openfoam is here: /openfoam/bash.rc\\
-And if you need python with fluidfoam installed, don't hesitate to use the preconfigured python environment:
-\verbatim
-    source /home/sudofoam/pyenv/bin/activate
-\endverbatim
+The sedFoam files will be in /home/sudofoam and the solver is already compiled. Note that the bashrc file from openfoam is here: /openfoam/bash.rc and the python environment here: /home/sudofoam/pyenv\\
 
 */

docker/Dockerfile

@@ -15,7 +15,7 @@ RUN python3 -m venv /home/sudofoam/pyenv
 RUN /bin/bash -c 'shopt -s expand_aliases && source /home/sudofoam/pyenv/bin/activate && pip3 install --no-cache-dir fluidfoam pandas matplotlib odfpy black'
 
 WORKDIR /root/
-RUN git clone --branch develop --recurse-submodules https://github.com/sedfoam/sedfoam.git
+RUN git clone --branch develop --recurse-submodules https://github.com/sedfoam/sedfoam.git --depth 1
 
 WORKDIR /root
 RUN /bin/bash -c 'hg clone http://hg.code.sf.net/p/openfoam-extend/swak4Foam -b develop && cp sedfoam/docker/Allwmakeswak swak4Foam/Libraries/Allwmake'
@@ -29,13 +29,11 @@ RUN /bin/bash -c 'shopt -s expand_aliases && source /openfoam/bash.rc && export
 WORKDIR /root/sedfoam
 RUN /bin/bash -c 'shopt -s expand_aliases && source /openfoam/bash.rc && export FOAM_USER_LIBBIN=$FOAM_SITE_LIBBIN && ./Allwmake -prefix=group'
 
-WORKDIR /home/sudofoam
-RUN rm -rf swak4Foam sedfoam
-
-USER 1000
+USER 1001
 
 WORKDIR /home/sudofoam
-RUN git clone --branch develop --recurse-submodules https://github.com/sedfoam/sedfoam.git
+RUN sudo cp -r /root/sedfoam sedfoam && sudo chown -R sudofoam: /home/sudofoam && sudo rm -rf /root/*
+RUN echo "source /home/sudofoam/pyenv/bin/activate" >> .bashrc
 
 WORKDIR /home/sudofoam
 ENV HOME=/home/sudofoam

docker/Dockerfile_nb

@@ -4,7 +4,7 @@ ARG WM_NCOMPPROCS=10
 
 
 ARG NB_USER="sudofoam"
-ARG NB_UID="1000"
+ARG NB_UID="1001"
 ARG NB_GID="100"
 
 # Fix DL4006
@@ -65,7 +65,7 @@ RUN sed -i 's/^#force_color_prompt=yes/force_color_prompt=yes/' /etc/skel/.bashr
    # Add call to conda init script see https://stackoverflow.com/a/58081608/4413446
    echo 'eval "$(command conda shell.bash hook 2> /dev/null)"' >> /etc/skel/.bashrc
 
-# Create NB_USER with name jovyan user with UID=1000 and in the 'users' group
+# Create NB_USER with name jovyan user with UID=1001 and in the 'users' group
 # and make sure these dirs are writable by the `users` group.
 RUN echo "auth requisite pam_deny.so" >> /etc/pam.d/su && \
     sed -i.bak -e 's/^%admin/#%admin/' /etc/sudoers && \
@@ -79,7 +79,7 @@ RUN echo "auth requisite pam_deny.so" >> /etc/pam.d/su && \
 # WORKDIR /home/sudofoam
 # RUN rm -rf .cache
 
-USER 1000
+USER 1001
 ARG PYTHON_VERSION=default
 
 
@@ -100,7 +100,7 @@ ARG PYTHON_VERSION=default
 
 # COPY --chown="${NB_UID}:${NB_GID}" /root/sedfoam/docker/docker-stacks/images/docker-stacks-foundation/initial-condarc "${CONDA_DIR}/.condarc"
 RUN /bin/bash -c "sudo cp /root/sedfoam/docker/docker-stacks/images/docker-stacks-foundation/initial-condarc /opt/conda/.condarc"
-RUN /bin/bash -c "sudo chown  1000:100 /opt/conda/.condarc"
+RUN /bin/bash -c "sudo chown  1001:100 /opt/conda/.condarc"
 WORKDIR /tmp
 RUN set -x && \
     arch=$(uname -m) && \

solver/overSedDymFoam/Make/files

@@ -1,2 +1,3 @@
 overSedDymFoam.C
-EXE = $(FOAM_USER_APPBIN)/overSedDymFoam_rbgh
+
+EXE = $(FOAM_MODULE_APPBIN)/overSedDymFoam_rbgh