layers/meta-opentrons: fix jupyter install in kirkstone

layers/meta-opentrons/recipes-graphics/graphviz/files/0001-Autotools-fix-do-not-put-prefix-based-paths-in-compi.patch

@@ -0,0 +1,43 @@
+From 671e0d091b40ef7deb4a9d43e0dbed2a44edbec8 Mon Sep 17 00:00:00 2001
+From: Matthew Fernandez <matthew.fernandez@gmail.com>
+Date: Sat, 9 Sep 2023 01:03:04 -0700
+Subject: [PATCH] Autotools: fix: do not put '$prefix' based paths in
+ compilation flags
+
+This was causing problems with cross-compilation with a dedicated sysroot,
+because compilation would incorrectly use headers and libraries from the
+`--prefix` path. The `--prefix` path is meant to indicate a target path to
+install to, not a path from which to source dependent libraries.
+
+Gitlab: fixes #2442
+Reported-by: Daniel Klauer
+Suggested-by: Daniel Klauer
+
+Upstream-Status: Backport [https://gitlab.com/graphviz/graphviz/-/commit/012d250a903e13114bce3ba40995fb957fed7848]
+Signed-off-by: Daniel Klauer <daniel.klauer@gin.de>
+---
+ configure.ac | 8 --------
+ 1 files changed, 0 insertions(+), 8 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 573a3ee5d..7d53346de 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -190,14 +190,6 @@ if test "x${prefix}" = "xNONE"; then
+ 	AC_SUBST([prefix])
+ fi
+
+-# automatically check for other dependencies in $prefix first
+-if test "x${prefix}" != "x/usr"; then
+-	CPPFLAGS="$CPPFLAGS -I${prefix}/include"
+-	LDFLAGS="$LDFLAGS -L${prefix}/lib"
+-	PKG_CONFIG_PATH="$prefix/lib/pkgconfig$PATHSEPARATOR$PKG_CONFIG_PATH"
+-	export PKG_CONFIG_PATH
+-fi
+-
+ dnl -----------------------------------
+ # Static/Shared binaries
+
+-- 
+2.34.1
+

layers/meta-opentrons/recipes-graphics/graphviz/graphviz_%.bbappend

@@ -0,0 +1,15 @@
+# apply https://github.com/openembedded/meta-openembedded/commit/883860c40c67544dfe3e2d72732e2d8ef46b6f30 which
+# is in nanbield only
+FILESEXTRAPATHS:prepend := "${THISDIR}/files:"
+SRC_URI:append := " \
+               file://0001-Autotools-fix-do-not-put-prefix-based-paths-in-compi.patch \
+               "
+
+
+# apply https://github.com/openembedded/meta-openembedded/commit/fa616dca0a910aa75565de4988bc7a83102ed17a which
+# is in mickledore only
+
+EXTRA_OECONF:class-native := "\
+                --disable-tcl \
+                "
+

layers/meta-opentrons/recipes-images/images/opentrons-ot3-image.bb

@@ -48,14 +48,15 @@ IMAGE_INSTALL += " \
     weston-xwayland weston weston-init imx-gpu-viv \
     robot-app-wayland-launch opentrons-robot-app \
     opentrons-robot-server opentrons-update-server \
-    opentrons-jupyter-notebook opentrons-usb-bridge \
+    opentrons-usb-bridge \
     opentrons-system-server opentrons-mcu-firmware \
     opentrons-user-environment opentrons-module-firmware \
     opentrons-systemd-units opentrons-ssh-keys \
-    python3 python3-misc python3-modules python3-jupyter \
+    python3 python3-misc python3-modules \
     python3-pip \
     plymouth \
     mosquitto \
+    opentrons-jupyter-notebook \
  "
 
 # We do NOT want the toradex libusbgx packages that autoconfigure the OTG USB

layers/meta-opentrons/recipes-robot/opentrons-jupyter-notebook/files/jupyter-notebook.service

@@ -5,15 +5,15 @@ Description=Jupyter notebook server
 Type=simple
 Restart=always
 RestartSec=1
-ExecStart=/bin/sh -c "jupyter notebook --allow-root --config=%E/jupyter/jupyter_notebook_config.py --notebook-dir=%S/jupyter/notebooks 2>&1"
+ExecStart=/usr/bin/jupyter notebook --allow-root --config=%E/jupyter/jupyter_notebook_config.py --notebook-dir=%S/jupyter/notebooks
 PIDFile=%t/jupyter/jupyter.pid
 SupplementaryGroups=dialout
 StateDirectory=jupyter jupyter/notebooks jupyter/data jupyter/config ipython
 RuntimeDirectory=jupyter
 Environment=RUNNING_ON_VERDIN=true
 Environment=OT_SYSTEM_VERSION=##OT_SYSTEM_VERSION##
 Environment=OT_API_FF_enableOT3HardwareController=true
-Environment=PYTHONPATH=/opt/opentrons-robot-server:/usr/lib/python3.10/site-packages
+Environment=PYTHONPATH=/opt/opentrons-robot-server/:/usr/lib/python3.10/site-packages/:/var/user-packages/usr/lib/python3.10/site-packages/
 Environment=JUPYTER_RUNTIME_DIR=%t/jupyter
 Environment=JUPYTER_CONFIG_DIR=%S/jupyter/config
 Environment=JUPYTER_DATA_DIR=%S/jupyter/data

layers/meta-opentrons/recipes-robot/opentrons-jupyter-notebook/opentrons-jupyter-notebook.bb

@@ -15,16 +15,15 @@ SRC_URI += "file://jupyter_notebook_config.py \
 
 do_install:append() {
         install -d ${D}/${sysconfdir}/jupyter
-        install -d ${D}/${sysconfdir}/systemd/system
         install -m 644 ${WORKDIR}/jupyter_notebook_config.py ${D}/${sysconfdir}/jupyter/jupyter_notebook_config.py
-        install -m 644 ${WORKDIR}/jupyter-notebook.service ${D}/${sysconfdir}/systemd/system/jupyter-notebook.service
-
-	# set the system version env variable
-	sed -i 's/##OT_SYSTEM_VERSION##/${OT_SYSTEM_VERSION}/' ${D}/${sysconfdir}/systemd/system/jupyter-notebook.service
+        install -d ${D}${systemd_system_unitdir}
+        install -m 644 ${WORKDIR}/jupyter-notebook.service ${D}${systemd_system_unitdir}/jupyter-notebook.service
+	    # set the system version env variable
+	    sed -i 's/##OT_SYSTEM_VERSION##/${OT_SYSTEM_VERSION}/' ${D}/${systemd_system_unitdir}/jupyter-notebook.service
 }
 
 FILES:${PN} += "${sysconfdir}/jupyter/jupyter_notebook_config.py \
                 ${sysconfdir}/systemd/system/jupyter-notebook.service \
 "
 
-RDEPENDS:${PN} += "python3-jupyter"
+RDEPENDS:${PN} += " python3-jupyter python3-nbclient python3-jupyterlab-pygments python3-psutil python3-nest-asyncio "