Python dependencies and build problems fix (#217)

* add missing jupyter dependencies

* bump pydantic

* add all the missing dependencies

* fix nbformat not versioning

* fix everything but pandas

* Fix pandas building

* rip out some 'optional' dependencies
remove the packages from buildroot, remove the dependencies and write some patches to edit the toml files so pip doesn't complain

* use custom kernel config to rip out unneeded modules

* add some config setting that hopefully get smoothie communication working again

* don't let uboot interrupt startup

* update config.txt

* add gpio tool to debug

* fix the MF ttyAMA0

README.md

@@ -147,6 +147,15 @@ Buildroot includes a TUI application for modifying the defconfig file. Please no
 # 3. save the changes to .config back into configs/ot2_defconfig
 ./opentrons-build.sh -it savedefconfig
 ```
+Buildroot also provides a menuconfig for editing linux kernel options, you need to build the project since the kernel makefiles are downloaded and live in output/build/linux-custom
+
+```shell
+# 1. open the kernel .config file in menuconfig
+./opentrons-build.sh -it linux-menuconfig
+
+# 2. save the changes to board/opentrons/ot2/kernel.config
+./opentrons-build.sh -it linux-savedefconfig
+```
 
 ## Provisioning an SD Card and Booting
 

board/opentrons/ot2/config.txt

@@ -13,8 +13,15 @@ kernel=u-boot.bin
 # If the text shown on the screen disappears off the edge, comment this out
 disable_overscan=1
 
+
 # How much memory in MB to assign to the GPU on Pi models having
 # 256, 512 or 1024 MB total memory
 gpu_mem_256=100
 gpu_mem_512=100
 gpu_mem_1024=100
+
+dtoverlay=ot2-disable-bt
+enable_uart=1
+dtparam=audio=on
+dtoverlay=gpio-revision-bits
+dtoverlay=i2c-rtc-rv3028