QGIS cannot import SciPy (QGIS 3.6, Ubuntu 18.04)

Hi everyone,

I’ve submitted this question too to GIS StackExchange. I had been struggling to get QGIS installed because (currently) the ubuntugis repo seems to not be working well (couldn’t load Python at all). I got around that problem by installing QGIS using flatpak.

I neeed to use the ENMAPBox plugin, which requires SciPy, Numpy, and Sklearn modules. Ubuntu came with Python 3.6.8 installed and QGIS brought with it Python 3.7.3. ENMAPBox cannot start because it can’t find either of those modules, and importing them from the console yields the same response. I followed the plugin’s instructions to install those packages using python3 -m pip install.

I’ve verified that the executable used by QGIS python console is /usr/bin/python3, and inspecting sys.path shows that /usr/lib/python3/dis-packages is not in the path (so it would make sense that it can’t find the packages I installed using pip3).

Sys.path looks like this:

[&~~#39~~;/app/share/qgis/python&~~#39~~;, &~~#39~~;/home/nav00a/.var/app/org.qgis.qgis/data/QGIS/QGIS3/profiles/default/python&~~#39~~;, &~~#39~~;/home/nav00a/.var/app/org.qgis.qgis/data/QGIS/QGIS3/profiles/default/python/plugins&~~#39~~;, &~~#39~~;/app/share/qgis/python/plugins&~~#39~~;, &~~#39~~;/usr/lib/python37.zip&~~#39~~;, &~~#39~~;/usr/lib/python3.7&~~#39~~;, &~~#39~~;/usr/lib/python3.7/lib-dynload&~~#39~~;, &~~#39~~;/usr/lib/python3.7/site-packages&~~#39~~;, &~~#39~~;/app/lib/python3.7/site-packages&~~#39~~;, &~~#39~~;/app/lib/python3.7/site-packages/numpy-1.14.3-py3.7-linux-x86_64.egg&~~#39~~;, &~~#39~~;/app/lib/python3.7/site-packages/MarkupSafe-1.0-py3.7-linux-x86_64.egg&~~#39~~;, &~~#39~~;/home/nav00a/.var/app/org.qgis.qgis/data/QGIS/QGIS3/profiles/default/python&~~#39~~;, &~~#39~~;/home/nav00a/.var/app/org.qgis.qgis/data/QGIS/QGIS3/profiles/default/python/plugins/enmapboxplugin/site-packages&~~#39~~;, &~~#39~~;/home/nav00a/.var/app/org.qgis.qgis/data/QGIS/QGIS3/profiles/default/python/plugins/enmapboxplugin/enmapbox&~~#39~~;, &~~#39~~;/usr/lib/python3/dist-packages&~~#39~~;]

Note the last item is there because I appended it, it’s not there by default.

To get QGIS to import SciPy I’ve tried a number of things:

Appending /usr/lib/python3/dist-packages to sys.path

Redirecting pip3 to /usr/lib/python3.7/site-packages

Adding .pth files to /usr/lib/python3.7/site-packages and /home/nav00a/.var/app/org.qgis.qgis/data/QGIS/QGIS3/profiles/default/python/plugins/enmapboxplugin/site-packages with links to /usr/lib/python3/dust-packages and /usr/lib/python3.7/site-packages

Unfortunately the behaviour remains the same. If I import SciPy this is what I get:

Traceback (most recent call last):

File &~~#34~~;/usr/lib/python3.7/code.py&~~#34~~;, line 90, in runcode

exec(code, self.locals)

File &~~#34~~;<input>&~~#34~~;, line 1, in <module>

File &~~#34~~;/app/share/qgis/python/qgis/utils.py&~~#34~~;, line 672, in _import

mod = _builtin_import(name, globals, locals, fromlist, level)

ModuleNotFoundError: No module named &~~#39~~;scipy&~~#39~~;

A user on GIS StackExchange managed to get EnMapBox installed in two minutes using Debian 10 Buster. Changing distros may or may not be an option for me, depends on what my IT department allows me to do.

Any pointers towards a solution will be greatly appreciated

Cheers

Javi

‌

Edit: Just found out the flatpak version of QGIS does not allow for other python modules to be installed, so I’m going back to trying to install QGIS via the normal repository (which is still broken).

Edit2: It is known that (as of 02/09/2019) the ubuntugis repo is broken so installing from there will result in broken dependencies that will not be installed. I was having the exact same issues installing from the Ubuntu LTR release but the nightly release seems to be working just fine.

Comments (10)