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In short, my question is, how do I install the latest version of scikit-image into my usr/lib/python3/dist-packages so I can actually use it? I think there is a problem with my understanding of how third-party modules are installed. As a newb, I don’t know how to rectify that, hence this post.

I need help to understand how to install packages in python3 up until now I have used pip/pip3/apt-get/synaptic etc and it has worked fine for many packages. However, I have hit several barriers (Skimage, opencv, plantcv in python3). I must emphasise, the problem I am having is using these packages in python3, not 2.7.

For example, I want to use the latest version of scikit-image (0.14) with python3. (http://scikit-image.org/) I have tried using the installation instructions and have not yet successfully managed to install it. I have navigated to my usr/lib/python3/dist-packages and copied scikit-image into this directory (I have all the dependencies installed in here already). Image of my folder for dist-packages as proof

As you can see, the folder containing skimage is in the directory I want to be installed in, how do I actually install it? Do I have to extract skimage out of the folder into the directory and then run the install command? If I navigate to usr/lib/python3/dist-packages/scikit-image and then run pip install -e . I get an error, stating that I need numpy. If I write a python script using python3 I can clearly see I have it installed (and I have been using it for a long time). So, there must be a problem in how I have this package in my file system. I think a janky workaround would be to copy all the modules into my working directory and Import them that way as if they were modules I have made myself, but this obviously negates the whole point of installing packages.

This has also happened with another package called plantcv. Where I went into the directory usr/lib/python3/dist-packages then cloned the source from git hub and installed as per instructions. When I import plantcv in my python3 script. It Imports fine. But, there is nothing in it, as python cannot see the modules which are inside this folder at usr/lib/python3/dist-packages/plantcv/plantcv.

There is clearly some comprehension here that I am missing, as I have a similar problem for two packages now. Please, Internet. Help me understand what I am missing!

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  • Did you try pip3 install scikit-image as per the installation docs? Commented Feb 10, 2018 at 13:52
  • What did you try? pip3 install -U scikit-image should install it for Python 3. Commented Feb 10, 2018 at 13:52
  • @AshishNitinPatil Yes, This is the message i get pip is configured with locations that require TLS/SSL, however the ssl module in Python is not available. Collecting scikit-image Could not fetch URL pypi.python.org/simple/scikit-image: There was a problem confirming the ssl certificate: Can't connect to HTTPS URL because the SSL module is not available. - skipping Could not find a version that satisfies the requirement scikit-image (from versions: ) No matching distribution found for scikit-image Commented Feb 10, 2018 at 15:35

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You simply need to copy the folder in /usr/lib/python3/dist-packages/package-name

However, there are certain things that are specific to python packages. The folder named package name should be a valid package. A good indicator of that is it will contain a file "__init__.py". It is very likely that every sub-directory inside this package directory will contain a "__init__.py" file. It depends on whether there are modules inside these sub-directories.

In your code simply import the package like the following.

import package-name

where package-name can be skimage

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I have just checked and inside the package-name, there is another folder named package-name as a subdirectory. With the files you mentioned "init.py" Is it this folder only that I need to have in my dist-packages?
Also for plantcv if I use 'import plantcv' It imports fine, however, if I use help('modules') it does not appear in the modules list
both folders should have __init__.py in it. Try taking the inner folder out of the higher folder and paste that into /usr/lib/python3/dist-packages
for example if you have /usr/lib/python3/dist-packages/package-name/package-name/files_inside_package. Then change this scenario to where you will have something like this /usr/lib/python3/dist-packages/package-name/files_inside_package

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