mutable arguments removed

[cmorph1]

I have removed the mutable arguments, I haven't touched the Color_scale argument.

[codecov]

Codecov Report

Merging #167 into master will increase coverage by 2.53%.
The diff coverage is 53.84%.

@@            Coverage Diff             @@
##           master     #167      +/-   ##
==========================================
+ Coverage   76.52%   79.05%   +2.53%     
==========================================
  Files          10       10              
  Lines         707      721      +14     
  Branches      141      148       +7     
==========================================
+ Hits          541      570      +29     
+ Misses        140      120      -20     
- Partials       26       31       +5

Impacted Files	Coverage Δ
kmapper/plotlyviz.py	42.76% <50%> (+15.29%)	⬆️
kmapper/kmapper.py	88.88% <66.66%> (-0.23%)	⬇️

---

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update ebe6bda...6dd07ed. Read the comment docs.

[sauln]

Looks good, thanks for doing this!

It looks like there are no tests that use the lens_names property. Would you mind adding one so we can be sure it is working correctly?

Thank you!

[cmorph1]

I get the feeling I am going to sound stupid, but how do you add a test?

[sauln]

not at all! learning about tests is always a hard hurdle.

In the source directory, you can install the test requirements into your environment with the command

pip install -e ".[testing]"

Then, you can run the test suite with the command

pytest test

You should see a summary of all the test runs showing that they've passed.

Then you can add a new test to the file test/test_mapper.py and try running the tests again.

We use pytest for all our tests, you can read more about it on their docs site and look at some of the other tests to see how we structure them.

Let me know if you need anything else!

[cmorph1]

Thanks I'll give it a go

[cmorph1]

When I am trying to run pytest test, I'm being told I need to:
pip install python-igraph plotly ipywidgets
But that fails when I try to install it. I'm not sure what my next move should be

[sauln]

Did running

pip install -e ".[testing]"

result in errors? That command should install those 3 packages. If that did not create errors, you might have a problem with your environments being crossed. Are you using virtual environments?

Compare the output of which pytest and which python, making sure they are both pointing to similar places.

[cmorph1]

I got this error:
'Cannot find the C core of igraph on this system using pkg-config'
I've had workspace issues on this laptop with the virtual environments before. I've pip uninstalled everything on there and try creating another venv tomorrow. Thanks for your help!

[sauln]

Ahh, if you are on Windows you should follow the instructions here: https://igraph.org/python/

Sometimes setting igraph up can be a pain point.

If you still can't get it working, you can specify just running the test file you're extending with the command

pytest test/test_mapper.py

[cmorph1]

Thanks for the help Nathaniel, I'll have a go at this tonight.

[cmorph1]

I think I have done it. Let me know if I need to do anything more.

[sauln]

It looks like you've added a test, but it still has the body of the test you copied above. Maybe you need to make one more commit with the changes to the test?

[cmorph1]

Sorry I'll change this tonight.

[cmorph1]

The test is failing, but I think its down to how I've built it as I am getting this error:
"> if not len(graph["nodes"]) > 0:
E IndexError: only integers, slices (:), ellipsis (...), numpy.newaxis (None) and integer or boolean arrays are valid indices"
I may need to install i-graph and get a better understanding of how it works.

[sauln]

igraph is a dependency for some of the visualization tools we use, but you shouldn't have to use it other than having it installed.

It's hard to diagnose the issue without the code. Feel free to push what you have no and I can make edits if need be.

Thanks!

[cmorph1]

I'll have one last go at it tonight and if I can't work it out I'll push for you to review, thanks Nathaniel

[cmorph1]

Hi Nathaniel,
Unfortunately I'm lost. I tried to install the extra packages and had the following error:
DeprecationWarning: To avoid name collision with the igraph project, this visualization library has been renamed to 'jgraph'. Please upgrade when convenient.

When I try to run test_mapper I get this error:
IndexError: only integers, slices (:), ellipsis (...), numpy.newaxis (None) and integer or boolean arrays are valid indices

I will push my test through to you. It would be a great help if you could explain what I have done wrong so I can learn from it.