From 3c9b645235fe165213f6421e8157ddc8cfefa393 Mon Sep 17 00:00:00 2001
From: Kwabena Amponsah <kwabenantim@yahoo.com>
Date: Tue, 24 Mar 2026 17:09:00 +0000
Subject: [PATCH 1/6] Attempt to build pychaste on quokka

---
 Dockerfile              | 11 ++++++-----
 scripts/build_chaste.sh | 17 +++++++----------
 2 files changed, 13 insertions(+), 15 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 9a662c5..54f059d 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -59,12 +59,13 @@ RUN apt-get update && \
     apt-get install -y --no-install-recommends \
     chaste-dependencies \
     xvfb \
-    # python3-matplotlib \
-    # python3-notebook \
-    # python3-numpy \
-    # python3-petsc4py \
+    python3-jupyterlab \
+    python3-matplotlib \
+    python3-numpy \
+    python3-petsc4py-real \
     python3-vtk9 \
-    # python3-xvfbwrapper \
+    python3-xvfbwrapper \
+    castxml \
     clang \
     lldb \
     gdb \
diff --git a/scripts/build_chaste.sh b/scripts/build_chaste.sh
index dd63c27..9419a00 100755
--- a/scripts/build_chaste.sh
+++ b/scripts/build_chaste.sh
@@ -50,22 +50,19 @@ cmake -DCMAKE_BUILD_TYPE:STRING=${CMAKE_BUILD_TYPE} \
         -H$CHASTE_SOURCE_DIR \
         -B$CHASTE_BUILD_DIR
 
-# make --no-print-directory -j$NCORES -C $CHASTE_BUILD_DIR # -f $CHASTE_BUILD_DIR/Makefile
+make --no-print-directory -j$NCORES -C $CHASTE_BUILD_DIR # -f $CHASTE_BUILD_DIR/Makefile
 
 if [ "$Chaste_ENABLE_PYCHASTE" = "ON" ]; then
-    # Build and install PyChaste
-    echo "Building PyChaste..."
-    # make --no-print-directory -j$NCORES -C $CHASTE_BUILD_DIR
-    make --no-print-directory -j$NCORES -C $CHASTE_BUILD_DIR pychaste
-    python -m pip install --no-cache-dir --user numpy matplotlib petsc4py jupyterlab xvfbwrapper 
-    # python -m pip install --no-cache-dir --user --no-deps pychaste/package
-    python -m pip install --no-cache-dir --user --no-deps $CHASTE_BUILD_DIR/pychaste/package
+    # Install PyChaste
+    echo "Installing PyChaste..."
+    python3 -m venv --system-site-packages ${CHASTE_DIR}/.venv
+    ${CHASTE_DIR}/.venv/bin/python3 -m pip install --no-cache-dir --upgrade pip
+    ${CHASTE_DIR}/.venv/bin/python3 -m pip install --no-cache-dir ${CHASTE_BUILD_DIR}/pychaste/package
 
     # Test PyChaste
-    # xvfb-run --server-args="-screen 0 1024x768x24" ctest -L pychaste
+    # . ${CHASTE_DIR}/.venv/bin/activate && xvfb-run --server-args="-screen 0 1024x768x24" ctest -L pychaste
 else
     echo "PyChaste is not enabled."
-    make --no-print-directory -j$NCORES -C $CHASTE_BUILD_DIR # -f $CHASTE_BUILD_DIR/Makefile
 fi
 
 # Save the build info

From 555f2b1fcc16fea197396c1990b92a465d1c06c5 Mon Sep 17 00:00:00 2001
From: Kwabena N Amponsah <kwabenantim@yahoo.com>
Date: Mon, 30 Mar 2026 10:55:55 +0000
Subject: [PATCH 2/6] Install PyChaste with --user

---
 Dockerfile              | 4 +++-
 scripts/build_chaste.sh | 5 ++---
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 54f059d..8cb71b2 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -62,7 +62,9 @@ RUN apt-get update && \
     python3-jupyterlab \
     python3-matplotlib \
     python3-numpy \
-    python3-petsc4py-real \
+    python3-petsc4py \
+    python3-pip \
+    python3-venv \
     python3-vtk9 \
     python3-xvfbwrapper \
     castxml \
diff --git a/scripts/build_chaste.sh b/scripts/build_chaste.sh
index 9419a00..0b4c6eb 100755
--- a/scripts/build_chaste.sh
+++ b/scripts/build_chaste.sh
@@ -55,9 +55,8 @@ make --no-print-directory -j$NCORES -C $CHASTE_BUILD_DIR # -f $CHASTE_BUILD_DIR/
 if [ "$Chaste_ENABLE_PYCHASTE" = "ON" ]; then
     # Install PyChaste
     echo "Installing PyChaste..."
-    python3 -m venv --system-site-packages ${CHASTE_DIR}/.venv
-    ${CHASTE_DIR}/.venv/bin/python3 -m pip install --no-cache-dir --upgrade pip
-    ${CHASTE_DIR}/.venv/bin/python3 -m pip install --no-cache-dir ${CHASTE_BUILD_DIR}/pychaste/package
+    python3 -m pip install --no-cache-dir --upgrade pip
+    PIP_BREAK_SYSTEM_PACKAGES=1 python3 -m pip install -v --user pychaste/package
 
     # Test PyChaste
     # . ${CHASTE_DIR}/.venv/bin/activate && xvfb-run --server-args="-screen 0 1024x768x24" ctest -L pychaste

From 429df6fd3ff45be6472739525ca411096928ec50 Mon Sep 17 00:00:00 2001
From: Kwabena N Amponsah <kwabenantim@yahoo.com>
Date: Mon, 30 Mar 2026 10:59:00 +0000
Subject: [PATCH 3/6] Pychaste install without cache

---
 scripts/build_chaste.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/build_chaste.sh b/scripts/build_chaste.sh
index 0b4c6eb..6264df4 100755
--- a/scripts/build_chaste.sh
+++ b/scripts/build_chaste.sh
@@ -56,7 +56,7 @@ if [ "$Chaste_ENABLE_PYCHASTE" = "ON" ]; then
     # Install PyChaste
     echo "Installing PyChaste..."
     python3 -m pip install --no-cache-dir --upgrade pip
-    PIP_BREAK_SYSTEM_PACKAGES=1 python3 -m pip install -v --user pychaste/package
+    PIP_BREAK_SYSTEM_PACKAGES=1 python3 -m pip install -v --no-cache-dir --user pychaste/package
 
     # Test PyChaste
     # . ${CHASTE_DIR}/.venv/bin/activate && xvfb-run --server-args="-screen 0 1024x768x24" ctest -L pychaste

From 49e8c48d5b4fc7dc05a4e8a43262a5cef9bcd3d9 Mon Sep 17 00:00:00 2001
From: Kwabena N Amponsah <kwabenantim@yahoo.com>
Date: Mon, 30 Mar 2026 11:03:09 +0000
Subject: [PATCH 4/6] Pychaste extra venv not required

---
 scripts/build_chaste.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/build_chaste.sh b/scripts/build_chaste.sh
index 6264df4..fa793a3 100755
--- a/scripts/build_chaste.sh
+++ b/scripts/build_chaste.sh
@@ -59,7 +59,7 @@ if [ "$Chaste_ENABLE_PYCHASTE" = "ON" ]; then
     PIP_BREAK_SYSTEM_PACKAGES=1 python3 -m pip install -v --no-cache-dir --user pychaste/package
 
     # Test PyChaste
-    # . ${CHASTE_DIR}/.venv/bin/activate && xvfb-run --server-args="-screen 0 1024x768x24" ctest -L pychaste
+    # xvfb-run --server-args="-screen 0 1024x768x24" ctest -L pychaste
 else
     echo "PyChaste is not enabled."
 fi

From 1482106fc8b4a76d0ba933667bf89d602ee88da7 Mon Sep 17 00:00:00 2001
From: Kwabena N Amponsah <kwabenantim@yahoo.com>
Date: Mon, 30 Mar 2026 12:27:38 +0000
Subject: [PATCH 5/6] Undo pip upgrade

---
 scripts/build_chaste.sh | 1 -
 1 file changed, 1 deletion(-)

diff --git a/scripts/build_chaste.sh b/scripts/build_chaste.sh
index fa793a3..35fa1a6 100755
--- a/scripts/build_chaste.sh
+++ b/scripts/build_chaste.sh
@@ -55,7 +55,6 @@ make --no-print-directory -j$NCORES -C $CHASTE_BUILD_DIR # -f $CHASTE_BUILD_DIR/
 if [ "$Chaste_ENABLE_PYCHASTE" = "ON" ]; then
     # Install PyChaste
     echo "Installing PyChaste..."
-    python3 -m pip install --no-cache-dir --upgrade pip
     PIP_BREAK_SYSTEM_PACKAGES=1 python3 -m pip install -v --no-cache-dir --user pychaste/package
 
     # Test PyChaste

From c638d0b863e4d0b93c2889226614446505751f92 Mon Sep 17 00:00:00 2001
From: Kwabena N Amponsah <kwabenantim@yahoo.com>
Date: Mon, 30 Mar 2026 14:09:55 +0000
Subject: [PATCH 6/6] Fix Pychaste install path

---
 scripts/build_chaste.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/build_chaste.sh b/scripts/build_chaste.sh
index 35fa1a6..b5a9a31 100755
--- a/scripts/build_chaste.sh
+++ b/scripts/build_chaste.sh
@@ -55,7 +55,7 @@ make --no-print-directory -j$NCORES -C $CHASTE_BUILD_DIR # -f $CHASTE_BUILD_DIR/
 if [ "$Chaste_ENABLE_PYCHASTE" = "ON" ]; then
     # Install PyChaste
     echo "Installing PyChaste..."
-    PIP_BREAK_SYSTEM_PACKAGES=1 python3 -m pip install -v --no-cache-dir --user pychaste/package
+    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