Add comparison operators to Location object

[godotgildor]

I was writing some unit tests for a tool I wrote which uses DnaChisel. I wanted to assert equality between some Location objects, but found that currently Location only supports < and it looks like it tries to support >=.

This PR does the following:

• Adds in two missing dependencies for DnaChisel that I discovered when I tried to run the DnaChisel test suite. (Feel free to let me know if I missed them and I can remove this part from the PR)
• Adds an __eq__ method to the Location class so that we can test for equality now.
• Removes the __geq__ method - I believe the correct syntax would have been __ge__. However we don't need this method now because I also:
• Added the total_ordering decorator to the definition of the Location class. This decorator will automatically create all comparison operators as long as the class has a definition of __eq__ and one other comparison - in this case we also have __lt__
• Added some unit tests for Location to check that the ==, >= and < comparisons all work.

[veghp]

Thanks for the contribution! Good to hear you found DNA Chisel useful. What is the purpose of your tool / is it public by any chance?

The mentioned extra dependencies are not required for the package, we use it only for testing & development. They're installed during CI:

DnaChisel/.travis.yml

Line 7 in 58321ce

- pip install matplotlib primer3-py genome_collector geneblocks

If you wish to include them, please create a requirements-dev.txt file in root and list them there instead.

I'll try and have a look at the rest sometime but could you please provide context for your feature requirement; also just to confirm >= does not work?

[Zulko]

My bad for __geq__. Regarding test dependencies, another way could be to add a tests section to the extra_requires here so you can do pip install dnachisel[tests]. But a requirements-dev.txt also works.

[godotgildor]

My bad for __geq__. Regarding test dependencies, another way could be to add a tests section to the extra_requires here so you can do pip install dnachisel[tests]. But a requirements-dev.txt also works.

I went ahead and made a tests extra that includes all of the packages installed in the travis ci currently. I also updated the travis CI config to use this extras install.

[godotgildor]

@Zulko - just wanted to check back-in about this PR - anything else I can provide or changes you'd like to see?

[veghp]

I'm merging this today or tomorrow together with the other 2 PRs

[veghp]

Unfortunately the tests fail for EnforceRegionsCompatibility because Location became unhashable due to the changes. Location.__hash__ attribute is now set to None. This means the Counter function doesn't work on a list of Locations:

DnaChisel/dnachisel/builtin_specifications/EnforceRegionsCompatibility.py

Line 32 in 58321ce

counter = Counter(all_locations_with_incompatibility)

Suggestions are welcome. Perhaps a solution is to implement a simple counter, for example https://stackoverflow.com/questions/45955740/counting-occurrences-without-using-collections-counter

https://github.com/Edinburgh-Genome-Foundry/DnaChisel/actions/runs/5164168843/jobs/9302899033

[godotgildor]

I just updated the PR with a commit which adds in a __hash__ method for Location and corresponding tests.

I think this should address the issue with the Counter.

Can you take a look?

[veghp]

Thank you, that was helpful. Tests pass, so I'll make a release by tomorrow after merging the other PR.