[WIP] Merge PyChaste

Dockerfile

@@ -58,6 +58,16 @@ RUN wget -O /usr/share/keyrings/chaste.asc https://chaste.github.io/chaste.asc \
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
     chaste-dependencies \
+    xvfb \
+    python3-jupyterlab \
+    python3-matplotlib \
+    python3-numpy \
+    python3-petsc4py \
+    python3-pip \
+    python3-venv \
+    python3-vtk9 \
+    python3-xvfbwrapper \
+    castxml \
     clang \
     lldb \
     gdb \
@@ -83,6 +93,7 @@ ARG CHASTE_DIR="/home/${USER}"
 ARG CMAKE_BUILD_TYPE="Debug"
 ARG Chaste_ERROR_ON_WARNING="ON"
 ARG Chaste_UPDATE_PROVENANCE="OFF"
+ARG Chaste_ENABLE_PYCHASTE="ON"
 # RUN source /home/chaste/scripts/set_env_vars.sh
 ENV USER=${USER} \
     GROUP=${USER} \
@@ -93,6 +104,7 @@ ENV USER=${USER} \
     CMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} \
     Chaste_ERROR_ON_WARNING=${Chaste_ERROR_ON_WARNING} \
     Chaste_UPDATE_PROVENANCE=${Chaste_UPDATE_PROVENANCE} \
+    Chaste_ENABLE_PYCHASTE=${Chaste_ENABLE_PYCHASTE} \
     CHASTE_SOURCE_DIR="${CHASTE_DIR}/src" \
     CHASTE_BUILD_DIR="${CHASTE_DIR}/build" \
     CHASTE_TEST_OUTPUT="${CHASTE_DIR}/output" \

Makefile

@@ -7,7 +7,7 @@ help:
 
 
 BASE ?= questing
-GIT_TAG ?= 2024.2
+# GIT_TAG ?= 2024.2
 TEST_SUITE ?= -
 CHASTE_IMAGE ?= chaste/release
 CHASTE_DIR ?= "/home/chaste"
@@ -66,18 +66,21 @@ develop main release: BUILD_ARGS += --build-arg GIT_TAG=$(GIT_TAG) \
 		--build-arg CMAKE_BUILD_TYPE=$(CMAKE_BUILD_TYPE) \
 		--build-arg Chaste_ERROR_ON_WARNING=$(Chaste_ERROR_ON_WARNING) \
 		--build-arg Chaste_UPDATE_PROVENANCE=$(Chaste_UPDATE_PROVENANCE) \
+		--build-arg Chaste_ENABLE_PYCHASTE=${Chaste_ENABLE_PYCHASTE} \
 		--build-arg TEST_SUITE=$(TEST_SUITE)
 
 develop main: CMAKE_BUILD_TYPE="Debug"
 develop main: Chaste_ERROR_ON_WARNING ?= "ON"
 develop main: Chaste_UPDATE_PROVENANCE="OFF"
-develop main: GIT_TAG=$@
+develop main: GIT_TAG?=$@
 
 release: CMAKE_BUILD_TYPE="Release"
 release: Chaste_ERROR_ON_WARNING ?= "OFF"
 release: Chaste_UPDATE_PROVENANCE="ON"
 # release: TEST_SUITE = "Continuous"
+release: GIT_TAG ?= 2024.2
 
+develop main release: Chaste_ENABLE_PYCHASTE="ON"
 base develop main release: CHASTE_IMAGE = chaste/$@
 base develop main release: DOCKER_TAGS = -t $(CHASTE_IMAGE)
 base develop main: DOCKER_TAGS += -t $(CHASTE_IMAGE):$(BASE)

scripts/build_chaste.sh

@@ -42,15 +42,27 @@ else # if [ $VERSION = 'develop' ]; then
         echo "Chaste_ERROR_ON_WARNING=${Chaste_ERROR_ON_WARNING}"
 fi
 
-# Only run if new files have been created
+# # Only run if new files have been created
 cmake -DCMAKE_BUILD_TYPE:STRING=${CMAKE_BUILD_TYPE} \
         -DChaste_ERROR_ON_WARNING:BOOL=${Chaste_ERROR_ON_WARNING} \
         -DChaste_UPDATE_PROVENANCE:BOOL=${Chaste_UPDATE_PROVENANCE} \
+        -DChaste_ENABLE_PYCHASTE:BOOL=${Chaste_ENABLE_PYCHASTE} \
         -H$CHASTE_SOURCE_DIR \
         -B$CHASTE_BUILD_DIR
 
 make --no-print-directory -j$NCORES -C $CHASTE_BUILD_DIR # -f $CHASTE_BUILD_DIR/Makefile
 
+if [ "$Chaste_ENABLE_PYCHASTE" = "ON" ]; then
+    # Install PyChaste
+    echo "Installing PyChaste..."
+    PIP_BREAK_SYSTEM_PACKAGES=1 python3 -m pip install -v --no-cache-dir --user $CHASTE_BUILD_DIR/pychaste/package
+
+    # Test PyChaste
+    # xvfb-run --server-args="-screen 0 1024x768x24" ctest -L pychaste
+else
+    echo "PyChaste is not enabled."
+fi
+
 # Save the build info
 get_chaste_info.sh > "${CHASTE_TEST_OUTPUT}/chaste-info.txt"
 

scripts/get_chaste_info.sh

@@ -1,4 +1,7 @@
 #!/bin/bash
 set -e
 
+cmake -H$CHASTE_SOURCE_DIR -B$CHASTE_BUILD_DIR
+make --no-print-directory -j$(nproc) -C $CHASTE_BUILD_DIR $TEST_SUITE
+#-j$(nproc)
 ( cd $CHASTE_BUILD_DIR && ctest --verbose -R TestChasteBuildInfo$ )