Develop Reference

How to fix Jupyter notebook dependancies? ModuleNotFoundError: No module named 'boto3'

I am running EMR cluster(AWS) but I do not understand how notebook imports packages. I am running PySpark kernel.
import boto3
No module named 'boto3'
Traceback (most recent call last):
ModuleNotFoundError: No module named 'boto3'
print (sys.version) shows
3.7.6 (default, Feb 26 2020, 20:54:15)
[GCC 7.3.1 20180712 (Red Hat 7.3.1-6)]
print(sys.executable) shows
/tmp/1594625399736-0/bin/python
I have both Conda and pip3 install of boto3.
How to solve this?

Are you using pyspark? If yes, then you need to install the packages in the spark context. Refer to this AWS document: https://aws.amazon.com/blogs/big-data/install-python-libraries-on-a-running-cluster-with-emr-notebooks/
similarly install any dependency packages if you see module not found error on import. Make sure the versions are compatible.

sc.list_packages()
Package Version
-------------------------- -------
beautifulsoup4 4.9.0
boto 2.49.0
cycler 0.10.0
jmespath 0.9.5
kiwisolver 1.2.0
lxml 4.5.0
matplotlib 3.2.2
mysqlclient 1.4.2
nltk 3.4.5
nose 1.3.4
numpy 1.19.0
pandas 1.0.5
pip 9.0.1
py-dateutil 2.2
py4j 0.10.9
pyparsing 2.4.7
pyspark 3.0.0
python-dateutil 2.8.1
python37-sagemaker-pyspark 1.3.0
pytz 2020.1
PyYAML 5.3.1
setuptools 28.8.0
six 1.15.0
soupsieve 1.9.5
wheel 0.29.0
windmill 1.6
I have boto.

sc.install_pypi_package("boto3")

Python setup.py: Could not find suitable distribution for Requirement.parse('tensorflow')

I have tensorflow listed as a requirement in the install_requires section of the setup.py of my project.
When I attempt to install my project into a new Anaconda environment I get the following error:
$ python setup.py install
...
Searching for tensorflow
Reading https://pypi.org/simple/tensorflow/
No local packages or working download links found for tensorflow
error: Could not find suitable distribution for Requirement.parse('tensorflow')
I can get past this by installing tensorflow "manually" via conda:
$ conda install tensorflow
Once I do this the install via setup.py works without a hitch.
Am I mistaken in assuming that something is amiss with my environment? If not then what is going on and how can I avoid this issue? (My concern is that users of my package will not be able to install from source using setup.py)
Another oddity that I assume is related or may provide a clue is that the version of TensorFlow listed in my Anaconda environment is 2.0 but if I import it when running Python it appears to instead be using version 1.15. For example:
$ conda list tensorflow
# packages in environment at /home/james/miniconda3/envs/cvdata_test:
#
# Name Version Build Channel
tensorflow 2.0.0 mkl_py37h66b46cc_0
tensorflow-base 2.0.0 mkl_py37h9204916_0
tensorflow-estimator 2.0.0 pyh2649769_0
$ python
Python 3.7.6 | packaged by conda-forge | (default, Jan 7 2020, 22:33:48)
[GCC 7.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import tensorflow as tf
>>> tf.__version__
'1.15.0-rc2'
This is on a Dell laptop running Ubuntu 18.04 without a GPU, so perhaps the version shown in the interpreter is akin to tensorflow-cpu? If I run pip freeze I see tensorflow==2.0.0 and tensorflow-cpu==1.15.0rc2, which is a bit confusing...

This appears to have been caused by using Python version 3.8, which is currently an unsupported version of Python. Once I created a new Anaconda environment with Python version 3.7 this issue went away.
The only remaining issue is this error that I see when I run pip install -e . for my project which includes tensorflow:
ERROR: tensorflow-cpu 1.15.0rc2 has requirement tensorboard<1.16.0,>=1.15.0, but you'll have tensorboard 2.1.0 which is incompatible.
ERROR: tensorflow-cpu 1.15.0rc2 has requirement tensorflow-estimator==1.15.1, but you'll have tensorflow-estimator 2.1.0 which is incompatible.
So the issue of tensorflow-cpu version 1.15.0rc2 actually being installed when version 2.1.0 shows as being the installed version is still a mystery. To wit:
$ conda list tensorflow
# packages in environment at /home/james/miniconda3/envs/cvd:
#
# Name Version Build Channel
tensorflow 2.1.0 pypi_0 pypi
tensorflow-estimator 2.1.0 pypi_0 pypi
$ python -c "import tensorflow as tf; print(tf.__version__)"
1.15.0-rc2

Compiling scikit-image on Windows to run tests

I'm stumped. I'm developing some enhancements to scikit-image which are failing the automated build tests, probably due to rounding errors. I therefore need to get the automated tests running on my Windows system so that I can debug and work out what's wrong. I've so far tried two approaches, neither of which are working:
In my Anaconda Python 3.6 environment, when I try to run the automated tests, I am getting the following error:
RuntimeError: module compiled against API version 0xc but this version of numpy is 0xb
...which I have found reference to in other contexts, but have not been able to eliminate.
Since the automated test do run (but fail) on a Python 3.5-based system, I thought things might work if I tried a local Python 3.5 environment. Here, I am running into the issue that, despite being installed, the environment cannot find the MS C++ compiler cl.exe. It is installed in C:\Program Files (x86)\Microsoft Visual Studio\2017\BuildTools\VC\Tools\MSVC\14.15.26726\bin\HostX86\x64\ and is found and executed by my Python 3.6 environment, but my Python 3.5 environment doesn't find it despite me adding that directory to my PATH. I should add that my Python 3.6 environment finds it without the directory being added to the PATH. I understand that both Python 3.5 and 3.6 use MSVC 14.0.
I would prefer to fix the problem in my Python 3.6 environment if possible. Any assistance much appreciated.
Update
I have made a box-fresh Python 3.6 conda environment as follows:
conda create --name sk36 python=3.6
conda activate sk36
conda install scikit-image --only-deps
conda install cython
git clone https://github.com/scikit-image/scikit-image.git
cd scikit-image
pip install -e .
pytest skimage/feature
The specific error I am getting is as follows:
..\Anaconda3\lib\site-packages\py\_path\local.py:662: in pyimport
__import__(modname)
skimage\__init__.py:135: in <module>
from .data import data_dir
skimage\data\__init__.py:13: in <module>
from ..io import imread, use_plugin
skimage\io\__init__.py:7: in <module>
from .manage_plugins import *
skimage\io\manage_plugins.py:24: in <module>
from .collection import imread_collection_wrapper
skimage\io\collection.py:12: in <module>
from ..external.tifffile import TiffFile
skimage\external\tifffile\__init__.py:1: in <module>
from .tifffile import imsave, imread, imshow, TiffFile, TiffWriter, TiffSequence
skimage\external\tifffile\tifffile.py:292: in <module>
from . import _tifffile
E RuntimeError: module compiled against API version 0xc but this version of numpy is 0xb
...which appears to have something to do with tifffile. Since this package wasn't originally explicitly installed in my new environment, I tried installing various versions of it, including some which downgraded numpy and scipy. Still the same error as above.
Having done some more research it would appear that something is seeing numpy 1.13.x when in fact version 1.15.4 is installed. Here is the full output from conda list:
# Name Version Build Channel
blas 1.0 mkl anaconda
ca-certificates 2018.03.07 0 anaconda
certifi 2018.10.15 py36_0 anaconda
cloudpickle 0.6.1 py36_0 anaconda
cycler 0.10.0 py36h009560c_0 anaconda
cython 0.29 py36ha925a31_0 anaconda
dask-core 0.20.0 py36_0 anaconda
decorator 4.3.0 py36_0 anaconda
freetype 2.9.1 ha9979f8_1 anaconda
icc_rt 2017.0.4 h97af966_0 anaconda
icu 58.2 ha66f8fd_1 anaconda
imageio 2.4.1 py36_0 anaconda
intel-openmp 2019.0 118 anaconda
jpeg 9b hb83a4c4_2 anaconda
kiwisolver 1.0.1 py36h6538335_0 anaconda
libpng 1.6.35 h2a8f88b_0 anaconda
libtiff 4.0.9 h36446d0_2 anaconda
matplotlib 3.0.1 py36hc8f65d3_0 anaconda
mkl 2019.0 118 anaconda
mkl_fft 1.0.6 py36hdbbee80_0 anaconda
mkl_random 1.0.1 py36h77b88f5_1 anaconda
networkx 2.2 py36_1 anaconda
numpy 1.15.4 py36ha559c80_0 anaconda
numpy-base 1.15.4 py36h8128ebf_0 anaconda
olefile 0.46 py36_0 anaconda
openssl 1.0.2p hfa6e2cd_0 anaconda
package_has_been_revoked 1.0 0 enable_revoked
pillow 5.3.0 py36hdc69c19_0 anaconda
pip 18.1 py36_0 anaconda
pyparsing 2.3.0 py36_0 anaconda
pyqt 5.9.2 py36h6538335_2 anaconda
python 3.6.7 h33f27b4_1 anaconda
python-dateutil 2.7.5 py36_0 anaconda
pytz 2018.7 py36_0 anaconda
pywavelets 1.0.1 py36h8c2d366_0 anaconda
qt 5.9.6 vc14h1e9a669_2 anaconda
scikit-image 0.15.dev0 <pip>
scipy 1.1.0 py36h4f6bf74_1 anaconda
setuptools 40.5.0 py36_0 anaconda
sip 4.19.8 py36h6538335_0 anaconda
six 1.11.0 py36_1 anaconda
sqlite 3.25.2 hfa6e2cd_0 anaconda
tifffile 0.15.1 py36h452e1ab_1001 conda-forge
tk 8.6.8 hfa6e2cd_0 anaconda
toolz 0.9.0 py36_0 anaconda
tornado 5.1.1 py36hfa6e2cd_0 anaconda
vc 14.1 h21ff451_3 anaconda
vs2015_runtime 15.5.2 3 anaconda
wheel 0.32.2 py36_0 anaconda
wincertstore 0.2 py36h7fe50ca_0 anaconda
zlib 1.2.11 h8395fce_2 anaconda
Update 2
I've solved the problem for Python 3.6, and I think there's enough information above for the astute to be able to work out what was wrong. I'll put the solution in an answer below.
A cleanly built Python 3.5 environment can't find the compiler, so that issue still remains.

One approach you could try is to upgrade your numpy with
pip install numpy --upgrade
as described here: RuntimeError: module compiled against API version a but this version of numpy is 9
Otherwise (if for some reason you cannot upgrade numpy) I would suggest going with a virtual environment for scikit-image project. I just tried it on Windows 10 and was able to successfully execute tests. My steps (from cmd, inside the project folder):
conda uninstall scikit-image to remove any previously built/installed versions
conda -n scikit-image python=3.6 to create a virtual environment for this project (I used python 3.6, but you can change it to 3.5)
activate scikit-image activated the new virtual env
pip install -r requirements.txt -- installed dependencies (without this step I wasn't getting the dependencies for tests installed)
pip install -e .
pytest

It turns out that pytest wasn't actually installed in the correct environment, it was being invoked from base which did indeed have numpy 1.13.3 installed. Installing it in the cleanly built Python 3.6 environment solved the problem for Python 3.6 at least.

install opencv3 on OSX and use with notebook

I am on OSX el Capitan and doing Data Science.
For this I am using anaconda with Python 2.7
I used various envs successfully and was very happy in general with anaconda.
Now I wanted to do a new env (called tf for tensorflow) and install opencv 3.1 which I succeeded after several trials. So, if I open python, it prompts with
Python 2.7.13 |Continuum Analytics, Inc.| (default, Dec 20 2016, 23:05:08)
[GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.57)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
Anaconda is brought to you by Continuum Analytics.
Please check out: http://continuum.io/thanks and https://anaconda.org
and then I do
import cv2
print(cv2.__version__)
and it prompts me with 3.1.0
So far so good.
All this I do within my environment tf
But now I call a notebook by
jupyter notebook
and open a new notebook, import cv2, it does not like this
ImportError: No module named cv2
I cannot understand this and need help!
When I
conda list
I get all packages (see below partial paste)
jsonschema 2.5.1 py27_0
jupyter 1.0.0 py27_3
jupyter_client 5.0.0 py27_0
jupyter_console 5.1.0 py27_0
jupyter_core 4.3.0 py27_0
libpng 1.6.28 0 conda-forge
libtiff 4.0.6 7 conda-forge
markupsafe 0.23 py27_2
mistune 0.7.4 py27_0
mkl 2017.0.1 0
nbconvert 5.1.1 py27_0
nbformat 4.3.0 py27_0
notebook 4.4.1 py27_0
numpy 1.12.0 py27_0
opencv 3.1.0 np112py27_1 conda-forge
opencv3 3.1.0 py27_0 menpo
openssl 1.0.2k
I also add for info the output of the system when I do
conda info -a
I get
Current conda install:
platform : osx-64
conda version : 4.3.14
conda is private : False
conda-env version : 4.3.14
conda-build version : not installed
python version : 2.7.13.final.0
requests version : 2.12.4
root environment : /Users/peterhirt/anaconda (writable)
default environment : /Users/peterhirt/anaconda/envs/tf
envs directories : /Users/peterhirt/anaconda/envs
/Users/peterhirt/.conda/envs
package cache : /Users/peterhirt/anaconda/pkgs
/Users/peterhirt/.conda/pkgs
channel URLs : https://repo.continuum.io/pkgs/free/osx-64
https://repo.continuum.io/pkgs/free/noarch
https://repo.continuum.io/pkgs/r/osx-64
https://repo.continuum.io/pkgs/r/noarch
https://repo.continuum.io/pkgs/pro/osx-64
https://repo.continuum.io/pkgs/pro/noarch
config file : None
offline mode : False
user-agent : conda/4.3.14 requests/2.12.4 CPython/2.7.13 Darwin/15.6.0 OSX/10.11.6
UID:GID : 501:20
# conda environments:
#
tf * /Users/peterhirt/anaconda/envs/tf
root /Users/peterhirt/anaconda
sys.version: 2.7.13 |Anaconda 4.3.1 (x86_64)| (defaul...
sys.prefix: /Users/peterhirt/anaconda
sys.executable: /Users/peterhirt/anaconda/bin/python
conda location: /Users/peterhirt/anaconda/lib/python2.7/site-packages/conda
conda-build: None
conda-env: /Users/peterhirt/anaconda/bin/conda-env
conda-server: /Users/peterhirt/anaconda/bin/conda-server
user site dirs: ~/.local/lib/python2.7
CIO_TEST: <not set>
CONDA_DEFAULT_ENV: tf
CONDA_ENVS_PATH: <not set>
DYLD_LIBRARY_PATH: <not set>
PATH: /Users/peterhirt/anaconda/envs/tf/bin:/Users/peterhirt/anaconda/bin:/usr/local/bin:/Users/peterhirt/.npm-packages/bin:/Users/peterhirt/anaconda2/bin:/Users/peterhirt/google-cloud-sdk/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin
PYTHONHOME: <not set>
PYTHONPATH: <not set>
License directories:
/Users/peterhirt/.continuum
/Users/peterhirt/Library/Application Support/Anaconda
/Users/peterhirt/anaconda/licenses
License files (license*.txt):
Package/feature end dates:

Using Docker images helps the best in such cases since it encapsulates the environment. You can install Docker from here.
After pulling the image, you can use code like this in the shell:
docker run --rm -it -p 8888:8888 -v d:/Kaggles:/d datmo/kaggle:cpu
Run jupyter notebook inside the container
jupyter notebook --ip=0.0.0.0 --no-browser
This mounts the local directory onto the container having access to it.
Then, go to the browser and hit https://localhost:8888, and when I open a new kernel it's with Python 3.5.
You can find more information from here.
You can also try using datmo in order to easily setup environment and track machine learning projects to make experiments reproducible. You can run datmo task command as follows for setting up jupyter notebook,
datmo task run 'jupyter notebook' --port 8888
It sets up your project and files inside the environment to keep track of your progress.

Miniconda "installs" numpy but Python can't import it

So I have been having some trouble with this. I need to use numpy so that I can use OpenCV and so I installed Miniconda (Not Miniconda3 because we are working in Python 2.7) and I installed numpy with conda install numpy and it worked because when I run conda list I see that it is there:
Microsoft Windows [Version 10.0.10240]
(c) 2015 Microsoft Corporation. All rights reserved.
C:\Users\joe30_000>conda list
# packages in environment at C:\Users\joe30_000\Miniconda:
#
conda 3.17.0 py27_0
conda-env 2.4.2 py27_0
menuinst 1.0.4 py27_0
numpy 1.9.3 py27_0
pip 7.1.2 py27_0
pycosat 0.6.1 py27_0
pycrypto 2.6.1 py27_3
python 2.7.10 0
pyyaml 3.11 py27_2
requests 2.7.0 py27_0
setuptools 18.3.2 py27_0
wheel 0.26.0 py27_1
C:\Users\joe30_000>
And as you can see it is installed for Python 2.7. However, when I go to the python command line and try import numpy I get the error that no module exists:
Python 2.7.10 (default, May 23 2015, 09:40:32) [MSC v.1500 32 bit (Intel)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ImportError: No module named numpy
>>>
Why is this happening? Do I have to somehow sync Conda with Python so that Python is using the modules that Miniconda has installed?

So thanks to #Bubbafat, I found the solution and I want to post it in case anyone else has problems. Like Bubbafat said, conda has its own version of the Python interpreter. It is located in the Miniconda directory (It's called "Python.exe"). If you are using an IDE you need to switch the interpreter to use this version of Python rather than the default one you may have installed on the internet from the Python website itself. I hope this was helpful.