How can I get dbt working on my Mac targeting Databricks - python

I use my Macbook Pro to develop DBT Models against Databricks. Everything was working well enough, but I couldn't leave well enough alone and recently ran "dbt update" and saw that a bunch of things were outdated. I had run into issues in the past where upgrading my Python (install via Brew) broke things so I avoided upgrading Python, but upgraded SQLite. Apparently, an upgrade Python was a dependency and upgraded Python. So, DBT no longer works.
After lots of searching, I ran
brew remove dbt
brew install dbt
since the brew install dbt told me that installing dbt-labs/dbt/dbt has been deprecated, I instead ran brew install dbt-postgre figuring I will get the core DBT files install this way.
then per https://github.com/databricks/dbt-databricks, I ran
pip install dbt-databricks
All seemed mostly well except for the standard warning about "distutils config files is deprecated", etc...
Now, I run dbt debug and I get
Running with dbt=1.2.2
dbt version: 1.2.2
python version: 3.9.14
python path: /opt/homebrew/Cellar/dbt-postgres/1.2.2/libexec/bin/python
os info: macOS-12.6-arm64-arm-64bit
Using profiles.yml file at /Users/andrewpark/.dbt/profiles.yml
Using dbt_project.yml file at /Users/andrewpark/iCloud Drive (Archive)/Documents/Work >Projects/Github Source/data-platform/transformation/databricks-dbt/dbt_project.yml
18:24:13 target not specified in profile 'databricks_sql', using 'default'
18:24:13 Error importing adapter: No module named 'dbt.adapters.databricks'
Configuration:
profiles.yml file [ERROR invalid]
dbt_project.yml file [OK found and valid]
Required dependencies:
- git [OK found]
1 check failed:
Profile loading failed for the following reason:
Runtime Error
Credentials in profile "databricks_sql", target "default" invalid: Runtime Error
Could not find adapter type databricks!
I haven't touched my profiles.yml file at all so nothing there has changed, but it says the file is invalid. It appears to me that the dbt-databricks adaptor is not being found. How can I resolve this?
OS: MacOS Monterey 12.6
Python Version: 3.10.7
DBT Version (Core): 1.2.2
Also, I had installed dbt-snowflake and dbt-postgres adaptors as well as dbt-databricks, but these adaptors don't appear when I run dbt --version, only the Postgres 1.2.2 plugin.

configure profile.yml
your_profile_name:
target: dev
outputs:
dev:
type: databricks
catalog:
schema:
host:
http_path:
token:

Related

Python python_keyring package - Upgrade of Python has broken keyring

I have upgrade from python 3.9.6 to 3.10.5 and kept thankfully the old version. This is on a Win-64 machine so should be using the WinVault backend (default)
I have copied all the site_packages from 3.9.6 to 3.10.5 (except for those already installed by the newer version)
Running keyring under 3.10.05 the error is
keyring.errors.NoKeyringError: No recommended backend was available. Install a recommended 3rd party backend package; or, install the keyrings.alt package if you want to use the non-recommended backends. See https://pypi.org/project/keyring for details.
I can run the same code under 3.9.6 with no problems.
Running
python -c "import keyring.util.platform_; print(keyring.util.platform_.config_root())"
or
python -c "import keyring.util.platform_; print(keyring.util.platform_.data_root())"
under either version is producing locations that don't really exist. I have created a keyringrc.cfg file with a keyring.backends.Windows.WinVaultKeyring line but it doesn't seem to do anything
I don't mind having to re-enter keyring passwords but would like to get this working under 3.10.5.
Ideas
This has eventually turned out to be needs to upgrade cffi which has fixed the problem.

Install newer version of sqlite3 on AWS Lambda for use with Python

I have a Python script running in a Docker container on AWS Lambda. I'm using the recommended AWS image (public.ecr.aws/lambda/python:3.9), which comes with SQLite version 3.7.17 (from 2013!). When I test the container locally on my M1 Mac, I see this:
$ docker run --env-file .env --entrypoint bash -ti my-image
bash-4.2# uname -a
Linux e9ed14d35cbe 5.10.104-linuxkit #1 SMP PREEMPT Thu Mar 17 17:05:54 UTC 2022 aarch64 aarch64 aarch64 GNU/Linux
bash-4.2# sqlite3 --version
3.7.17 2013-05-20 00:56:22 118a3b35693b134d56ebd780123b7fd6f1497668
However, I use newer SQLite features, so I need to find a way to use a newer version of the library. The most straightforward solution would be to install a binary package as suggested in this answer. The docs say it should be as simple as installing using pip. Unfortunately, when I attempt to use this approach inside the Docker container, I get this:
bash-4.2# pip3 install pysqlite3-binary
ERROR: Could not find a version that satisfies the requirement pysqlite3-binary (from versions: none)
ERROR: No matching distribution found for pysqlite3-binary
And I get the same error when I attempt to install it outside the container using pipenv (which is what I'm actually using for package management):
🕙 01:08:24 ❯ pipenv install pysqlite3-binary
Installing pysqlite3-binary...
Error: An error occurred while installing pysqlite3-binary!
Error text:
ERROR: Could not find a version that satisfies the requirement pysqlite3-binary (from versions: none)
ERROR: No matching distribution found for pysqlite3-binary
✘ Installation Failed
Am I doing something wrong? And if not, how can I get a recent version of SQLite which Python can use in this container? Do I really need to use a separate build stage in the Dockerfile as suggested here and copy the rpm components into place as laid out here? That feels like a lot of work for something that many people presumably need to do all the time.
Update: I tried the rpm approach inside the container using version 3.26 from EPEL8 (IIUC) and it failed with a bunch of dependency errors like this:
bash-4.2# curl --output-dir /tmp -sO https://vault.centos.org/centos/8/BaseOS/aarch64/os/Packages/sqlite-3.26.0-15.el8.aarch64.rpm
bash-4.2# yum localinstall /tmp/sqlite-3.26.0-15.el8.aarch64.rpm
Loaded plugins: ovl
Examining /tmp/sqlite-3.26.0-15.el8.aarch64.rpm: sqlite-3.26.0-15.el8.aarch64
# etc.
--> Finished Dependency Resolution
Error: Package: sqlite-3.26.0-15.el8.aarch64 (/sqlite-3.26.0-15.el8.aarch64)
Requires: libc.so.6(GLIBC_2.28)(64bit)
# Plus 6 other package dependency errors
Error: Package: nss-softokn-3.67.0-3.amzn2.0.1.aarch64 (#amzn2-core)
Requires: libsqlite3.so.0()(64bit)
Removing: sqlite-3.7.17-8.amzn2.1.1.aarch64 (#amzn2-core)
libsqlite3.so.0()(64bit)
Updated By: sqlite-3.26.0-15.el8.aarch64 (/sqlite-3.26.0-15.el8.aarch64)
Not found
Obsoleted By: sqlite-3.26.0-15.el8.aarch64 (/sqlite-3.26.0-15.el8.aarch64)
Not found
Available: sqlite-3.7.17-8.amzn2.0.2.aarch64 (amzn2-core)
libsqlite3.so.0()(64bit)
You could try using --skip-broken to work around the problem
You could try running: rpm -Va --nofiles --nodigest
When I try --skip-broken, it just skips installing the 3.26 package altogether.
Update 2: I've tried downloading the Python 3.9 wheel from pysqlite3-binary manually. However, it looks like that project only produces wheels for x86_64, not the aarch64 platform which Lambda uses. (This is not correct, see answer.) So presumably that's why pip is not finding it.
The problem was that I was running Docker locally to do my testing, on an M1 Mac. Hence the aarch64 architecture. Lambda does allow you to use ARM, but thankfully it still defaults to x86_64. I confirmed that my Lambda function was running x86_64, which is what the binary wheel uses, so that's good:
So I needed to do three things:
Change my Pipfile to conditionally install the binary package only on x86_64:
pysqlite3-binary = { version = "*", platform_machine = "== 'x86_64'" }
Tweak the sqlite import, as described in the original answer:
try:
import pysqlite3 as sqlite3
except ModuleNotFoundError:
import sqlite3 # for local testing because pysqlite3-binary couldn't be installed on macos
print(f"{sqlite3.sqlite_version=}")
Set my Docker container to launch in x86 emulation mode locally.
$ DOCKER_DEFAULT_PLATFORM=linux/amd64 docker build -t my-image .
$ DOCKER_DEFAULT_PLATFORM=linux/amd64 docker run -ti my-image
Et, voilà!
sqlite3.sqlite_version='3.39.2'

How do I resume installing additional node.js tools successfully without starting a duplicate chocolatey installation?

I lost my internet connection while installing additional tools for node.js. using the automatic installation option. I'm new to programming and trying to set up an environment for JavaScript on VS Code. I rebooted my system and tried resuming the installation through the Install Additional Tools for Node.js cmd prompt, but it gives a warning that there is already an existing chocolatey installation detected and thus not continuing installation. Furthermore, 2 packages failed to be upgraded from the initial error when the connection was lost, but now it says one package failed yet still showing 0/2 packages were upgraded? I uninstalled node.js and reinstalled it but it hasn't solved the issue. Is visualstudio2019-workload-vctools the only thing missing? Of which I could maybe try installing it manually? Or are the files now corrupted and I have to start over since installation didn't complete?
I don't want to mess with chocolatey itself (by uninstalling) as I read that it can destroy your pc. If there are still a few more tools or packages to install and files not corrupted, how do I successfully and safely resume the installation of all necessary tools? Python 3.10 looks to be successfully installed.
This is the message on PowerShell and the screenshot is attached as well:
"WARNING: 'choco' was found at 'C:\ProgramData\chocolatey\bin\choco.exe'.
WARNING: An existing Chocolatey installation was detected. Installation will not continue.
For security reasons, this script will not overwrite existing installations.
Please use choco upgrade chocolatey to handle upgrades of Chocolatey itself.
Chocolatey v1.1.0
Upgrading the following packages:
python;visualstudio2019-workload-vctools
By upgrading, you accept licenses for the packages.
python v3.10.5 is the latest version available based on your source(s).
visualstudio2019-workload-vctools is not installed. Installing...
visualstudio2019-workload-vctools not installed. An error occurred during installation:
The remote server returned an error: (524).
visualstudio2019-workload-vctools package files upgrade failed with exit code 1. Performing other installation steps.
The upgrade of visualstudio2019-workload-vctools was NOT successful.
visualstudio2019-workload-vctools not installed. An error occurred during installation:
The remote server returned an error: (524).
Chocolatey upgraded 0/2 packages. 1 packages failed.
See the log for details (C:\ProgramData\chocolatey\logs\chocolatey.log).
Failures
visualstudio2019-workload-vctools (exited 1) - visualstudio2019-workload-vctools not installed. An error occurred during installation:
The remote server returned an error: (524).
Type ENTER to exit:"
PowerShell-chocolatey error
I am thinking the failure is due to the fact that I don't have visual studio 2019? It seems like everything else is fine. I'm setting up using VS Code. It doesn't seem like the issue had anything to do with me losing connection. I have attached a screenshot of the successful vs failed installations.
additional node.js tools

Import ldap in python gives gives "DLL load failed" error

I'm using the "import ldap" in a python code. This is on a windows 10 machine.
I installed the python-ldap module
pip3 install python-ldap
Installed the dependencies based on the instructions at Python Can't install packages
Also resolved all the pip deployment issues based on Installing python-ldap in a virtualenv on Windows
I'm now getting the following error when executing the import ldap statement. am I missing something here? Any ideas to resolve it?
thon39\site-packages\ldap\__init__.py", line 34, in <module>
import _ldap
ImportError: DLL load failed while importing _ldap: The specified module could not be found.
Visit the unofficial Python binaries page:
https://www.lfd.uci.edu/~gohlke/pythonlibs/#python-ldap
Download the appropriate WHL package for your system.
For example, if you're using Python 3.8 on an x64 system, download python_ldap‑3.3.1‑cp38‑cp38‑win_amd64.whl
(hint: do NOT download the +sasl version unless you have the Cyrus SASL code running on your system...)
Start the VirtualEnv for your project, if you're using one (C:\Users\youruser\.virtualenv\YourVirtualEnv\Scripts\activate.bat) -- if you're not, skip this step.
Then run pip3 install C:\Path\To\python_ldap_x.x.x-cpXX-cpXX-winXX.whl and this should install the Python DLL (pyd) file for you.

Error installing Python 2 via Homebrew on MacOS Mojave

I'm having a lot of trouble with installing Python 2.7 on the MacOS 10.14 Mojave Beta.
Yes, I know that Python 2 comes pre-installed on the Mac, but I need a framework build of Python for my task.
I've tried re-installing the command line tools and then installing Python 2.7 as suggested here and here, but am still having issues - below is my output:
NickLaptop:~ nicholasarner$ brew reinstall python#2
==> Reinstalling python#2
==> Downloading https://www.python.org/ftp/python/2.7.15/Python-2.7.15.tar.xz
Already downloaded: /Users/nicholasarner/Library/Caches/Homebrew/python#2-2.7.15.tar.xz
==> ./configure --prefix=/usr/local/Cellar/python#2/2.7.15_1 --enable-ipv6 --datarootdir=/usr/l
==> make
==> make install PYTHONAPPSDIR=/usr/local/Cellar/python#2/2.7.15_1
==> make frameworkinstallextras PYTHONAPPSDIR=/usr/local/Cellar/python#2/2.7.15_1/share/python#
==> Downloading https://files.pythonhosted.org/packages/1a/04/d6f1159feaccdfc508517dba1929eb93a
Already downloaded: /Users/nicholasarner/Library/Caches/Homebrew/python#2--setuptools-39.2.0.zip
==> Downloading https://files.pythonhosted.org/packages/ae/e8/2340d46ecadb1692a1e455f13f75e596d
Already downloaded: /Users/nicholasarner/Library/Caches/Homebrew/python#2--pip-10.0.1.tar.gz
==> Downloading https://files.pythonhosted.org/packages/2a/fb/aefe5d5dbc3f4fe1e815bcdb05cbaab19
Already downloaded: /Users/nicholasarner/Library/Caches/Homebrew/python#2--wheel-0.31.1.tar.gz
==> make html
Last 15 lines from /Users/nicholasarner/Library/Logs/Homebrew/python#2/05.make:
return build_main(argv)
File "/usr/local/Cellar/sphinx-doc/1.7.5_1/libexec/lib/python2.7/site-packages/sphinx/cmd/build.py", line 22, in build_main
from sphinx import cmdline
File "/usr/local/Cellar/sphinx-doc/1.7.5_1/libexec/lib/python2.7/site-packages/sphinx/cmdline.py", line 23, in <module>
from sphinx.application import Sphinx
File "/usr/local/Cellar/sphinx-doc/1.7.5_1/libexec/lib/python2.7/site-packages/sphinx/application.py", line 29, in <module>
from sphinx.config import Config
File "/usr/local/Cellar/sphinx-doc/1.7.5_1/libexec/lib/python2.7/site-packages/sphinx/config.py", line 21, in <module>
from sphinx.util import logging
File "/usr/local/Cellar/sphinx-doc/1.7.5_1/libexec/lib/python2.7/site-packages/sphinx/util/__init__.py", line 33, in <module>
from sphinx.util import logging
File "/usr/local/Cellar/sphinx-doc/1.7.5_1/libexec/lib/python2.7/site-packages/sphinx/util/logging.py", line 106, in <module>
class SphinxLoggerAdapter(logging.LoggerAdapter):
AttributeError: 'module' object has no attribute 'LoggerAdapter'
make: *** [build] Error 1
Do not report this issue to Homebrew/brew or Homebrew/core!
These open issues may also help:
python 3.7.0 https://github.com/Homebrew/homebrew-core/pull/29490
python upgrade failing https://github.com/Homebrew/homebrew-core/issues/29214
app-engine-python 1.9.70 https://github.com/Homebrew/homebrew-core/pull/28858
molecule: Use correct `docker` python package dependency https://github.com/Homebrew/homebrew-core/pull/28635
[root] formula does not link against python#2 correctly. https://github.com/Homebrew/homebrew-core/issues/29377
clingo add support for lua, use python 3 https://github.com/Homebrew/homebrew-core/pull/28057
OSError: [Errno 1] Operation not permitted for python#2 –with-tcl-tk https://github.com/Homebrew/homebrew-core/issues/28168
Error: You are using macOS 10.14.
We do not provide support for this pre-release version.
You may encounter build failures or other breakages.
Please create pull-requests instead of filing issues.
Error: You are using macOS 10.14.
We do not provide support for this pre-release version.
You may encounter build failures or other breakages.
Please create pull-requests instead of filing issues
Any help is appreciated!
EDIT Please don't suggest Anaconda! For what I'm working on, I specifically need a framework built version of Python via Brew.
EDIT 2 - I tried reinstalling Sphinx, which happened with no problems. Upon doing that, I tried running install python#2 again, but had the same issue as before.
Below is the output of running brew doctor
NickLaptop:~ nicholasarner$ brew doctor
Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry or file an issue; just ignore this. Thanks!
Warning: "config" scripts exist outside your system or Homebrew directories.
`./configure` scripts often look for *-config scripts to determine if
software packages are installed, and what additional flags to use when
compiling and linking.
Having additional scripts in your path can confuse software installed via
Homebrew if the config script overrides a system or Homebrew provided
script of the same name. We found the following "config" scripts:
/Library/Frameworks/Python.framework/Versions/2.7/bin/python2-config
/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7-config
/Library/Frameworks/Python.framework/Versions/2.7/bin/python-config
/usr/local/CrossPack-AVR/bin/libusb-config
Warning: Unbrewed dylibs were found in /usr/local/lib.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.
Unexpected dylibs:
/usr/local/lib/libFLAC.8.2.0.dylib
/usr/local/lib/libcdt.5.dylib
/usr/local/lib/libcgraph.6.dylib
/usr/local/lib/libcsnd6.6.0.dylib
/usr/local/lib/libfltk.1.1.dylib
/usr/local/lib/libfltk.1.3.dylib
/usr/local/lib/libfltk_forms.1.3.dylib
/usr/local/lib/libfltk_images.1.1.dylib
/usr/local/lib/libfltk_images.1.3.dylib
/usr/local/lib/libfluidsynth.1.dylib
/usr/local/lib/libgraph.5.dylib
/usr/local/lib/libgvc.6.dylib
/usr/local/lib/libgvpr.2.dylib
/usr/local/lib/liblo.0.dylib
/usr/local/lib/libluajit-5.1.2.0.2.dylib
/usr/local/lib/libmpadec.dylib
/usr/local/lib/libpathplan.4.dylib
/usr/local/lib/libpng12.0.dylib
/usr/local/lib/librealsense.1.12.1.dylib
/usr/local/lib/libsfml-audio.2.0.dylib
/usr/local/lib/libsfml-graphics.2.0.dylib
/usr/local/lib/libsfml-network.2.0.dylib
/usr/local/lib/libsfml-system.2.0.dylib
/usr/local/lib/libsfml-window.2.0.dylib
/usr/local/lib/libsndfile.1.dylib
/usr/local/lib/libwiiuse.dylib
/usr/local/lib/libxdot.4.dylib
Warning: Unbrewed header files were found in /usr/local/include.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.
Unexpected header files:
/usr/local/include/graphviz/arith.h
/usr/local/include/graphviz/cdt.h
/usr/local/include/graphviz/cgraph.h
/usr/local/include/graphviz/color.h
/usr/local/include/graphviz/geom.h
/usr/local/include/graphviz/graph.h
/usr/local/include/graphviz/graphviz_version.h
/usr/local/include/graphviz/gvc.h
/usr/local/include/graphviz/gvcext.h
/usr/local/include/graphviz/gvcjob.h
/usr/local/include/graphviz/gvcommon.h
/usr/local/include/graphviz/gvconfig.h
/usr/local/include/graphviz/gvplugin.h
/usr/local/include/graphviz/gvplugin_device.h
/usr/local/include/graphviz/gvplugin_layout.h
/usr/local/include/graphviz/gvplugin_loadimage.h
/usr/local/include/graphviz/gvplugin_render.h
/usr/local/include/graphviz/gvplugin_textlayout.h
/usr/local/include/graphviz/gvpr.h
/usr/local/include/graphviz/pack.h
/usr/local/include/graphviz/pathgeom.h
/usr/local/include/graphviz/pathplan.h
/usr/local/include/graphviz/textpara.h
/usr/local/include/graphviz/types.h
/usr/local/include/graphviz/usershape.h
/usr/local/include/graphviz/xdot.h
/usr/local/include/jack/control.h
/usr/local/include/jack/intclient.h
/usr/local/include/jack/jack.h
/usr/local/include/jack/jslist.h
/usr/local/include/jack/metadata.h
/usr/local/include/jack/midiport.h
/usr/local/include/jack/net.h
/usr/local/include/jack/ringbuffer.h
/usr/local/include/jack/session.h
/usr/local/include/jack/statistics.h
/usr/local/include/jack/systemdeps.h
/usr/local/include/jack/thread.h
/usr/local/include/jack/transport.h
/usr/local/include/jack/types.h
/usr/local/include/jack/uuid.h
/usr/local/include/jack/weakjack.h
/usr/local/include/jack/weakmacros.h
/usr/local/include/librealsense/rs.h
/usr/local/include/librealsense/rsutil.h
/usr/local/include/runt.h
/usr/local/include/sndfile.h
/usr/local/include/soundpipe.h
/usr/local/include/sporth.h
Warning: Unbrewed .la files were found in /usr/local/lib.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.
Unexpected .la files:
/usr/local/lib/liblo.la
/usr/local/lib/libsndfile.la
Warning: Unbrewed .pc files were found in /usr/local/lib/pkgconfig.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.
Unexpected .pc files:
/usr/local/lib/pkgconfig/jack.pc
/usr/local/lib/pkgconfig/libcdt.pc
/usr/local/lib/pkgconfig/libcgraph.pc
/usr/local/lib/pkgconfig/libgraph.pc
/usr/local/lib/pkgconfig/libgvc.pc
/usr/local/lib/pkgconfig/libgvpr.pc
/usr/local/lib/pkgconfig/libpathplan.pc
/usr/local/lib/pkgconfig/libxdot.pc
/usr/local/lib/pkgconfig/sndfile.pc
Warning: Unbrewed static libraries were found in /usr/local/lib.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.
Unexpected static libraries:
/usr/local/lib/liblua.a
/usr/local/lib/librunt.a
/usr/local/lib/libsndfile.a
/usr/local/lib/libsoundpipe.a
/usr/local/lib/libsporth.a
Warning: You have unlinked kegs in your Cellar
Leaving kegs unlinked can lead to build-trouble and cause brews that depend on
those kegs to fail to run properly once built. Run `brew link` on these:
lua
libsndfile
ruby
Warning: You are using macOS 10.14.
We do not provide support for this pre-release version.
You may encounter build failures or other breakages.
Please create pull-requests instead of filing issues.
Warning: Broken symlinks were found. Remove them with `brew prune`:
/usr/local/bin/git-remote-keybase
/usr/local/bin/keybase
/usr/local/bin/lua
/usr/local/bin/lua-5.2
/usr/local/bin/lua5.2
/usr/local/bin/luac
/usr/local/bin/luac-5.2
/usr/local/bin/luac5.2
/usr/local/bin/luarocks
/usr/local/bin/luarocks-5.2
/usr/local/bin/luarocks-admin
/usr/local/bin/luarocks-admin-5.2
/usr/local/etc/bash_completion.d/_brew_services
/usr/local/etc/fonts/conf.d/10-hinting-slight.conf
/usr/local/etc/fonts/conf.d/10-scale-bitmap-fonts.conf
/usr/local/etc/fonts/conf.d/20-unhint-small-vera.conf
/usr/local/etc/fonts/conf.d/30-metric-aliases.conf
/usr/local/etc/fonts/conf.d/30-urw-aliases.conf
/usr/local/etc/fonts/conf.d/40-nonlatin.conf
/usr/local/etc/fonts/conf.d/45-latin.conf
/usr/local/etc/fonts/conf.d/49-sansserif.conf
/usr/local/etc/fonts/conf.d/50-user.conf
/usr/local/etc/fonts/conf.d/51-local.conf
/usr/local/etc/fonts/conf.d/60-latin.conf
/usr/local/etc/fonts/conf.d/65-fonts-persian.conf
/usr/local/etc/fonts/conf.d/65-nonlatin.conf
/usr/local/etc/fonts/conf.d/69-unifont.conf
/usr/local/etc/fonts/conf.d/80-delicious.conf
/usr/local/etc/fonts/conf.d/90-synthetic.conf
/usr/local/include/lauxlib.h
/usr/local/include/lua.h
/usr/local/include/lua.hpp
/usr/local/include/lua5.2
/usr/local/include/luaconf.h
/usr/local/include/lualib.h
/usr/local/opt/qt5
Warning: Some installed formulae are missing dependencies.
You should `brew install` the missing dependencies:
brew install harfbuzz mono
Run `brew missing` for more details.
This is the output when running brew config:
HOMEBREW_VERSION: 1.6.9-39-g376f67b
ORIGIN: https://github.com/Homebrew/brew.git
HEAD: 376f67bf2c8893a06bf1e42a2375d58e9d8c2670
Last commit: 2 hours ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: 69b99b69ff3a9c686b9d9fb0102927c5dd2f373b
Core tap last commit: 3 hours ago
HOMEBREW_PREFIX: /usr/local
HOMEBREW_DEV_CMD_RUN: 1
CPU: quad-core 64-bit skylake
Homebrew Ruby: 2.3.3 => /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.3_2/bin/ruby
Clang: 10.0 build 1000
Git: 2.17.1 => /usr/local/bin/git
Curl: 7.54.0 => /usr/bin/curl
Java: 1.8.0_131
macOS: 10.14-x86_64
CLT: 10.0.0.0.1.1529074627
CLT headers: 10.0.0.0.1.1529074627
Xcode: 10.0 => /Applications/Xcode-beta.app/Contents/Developer
XQuartz: 2.7.11 => /opt/X11
I had the same problem.
I was able to fix it by completely uninstalling and reinstalling Python after following step by step in this answer: How to fix broken python 2.7.11 after OSx updates
After the reinstallation the problem was gone
As I read you output - this is not a problem with python directly it is a problem with sphinx which builds the docs. I would go for the following steps:
brew update && brew upgrade
brew install sphinx (maybe this gives a better error message or solves the problem if sphinx is installed before)
brew reinstall python#2
If this is not working: Did you reinstalled the commandline tools after upgrading to mac os 10.14? (xcode-select --install). If not installed/updated before do it and retry.
If this all is not working could you please execute brew doctor and post the output so we can better see whats going on with your homebrew instane?
Maybe it could be a option to make an roll back to a stable version of Mac OS (10.13) ?
I'd suggest you used the Anaconda Distribution of python. Anaconda offers both python 2.7 and python 3.6 with easy to use python installers for both versions. The Anaconda page explains how to install and run python on your mac.

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