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biolink / ontobio

python library for working with ontologies and ontology associations
https://ontobio.readthedocs.io/en/latest/
BSD 3-Clause "New" or "Revised" License
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Fix dependencies in requirements.txt and setup.py #508

Closed deepakunni3 closed 3 years ago

deepakunni3 commented 3 years ago

This PR addresses the following,

Fixes #506 #482

cmungall commented 3 years ago

Looks good. We should have done the setup.py thing ages ago. Isn't there a version of networkx we need ro exclude?

deepakunni3 commented 3 years ago

Ontobio now would work with all versions of networkx that start with 2.x since there is no use of deprecated/removed methods.

dougli1sqrd commented 3 years ago

Is it normal to to read from requirements like this? Maybe we should unify these by only using setup.py as it's the standard way of installing ontobio anyway. Do we even want people to run requirements.txt by itself? Just feels a little magical.

cmungall commented 3 years ago

I think this PR is a big improvement, both in unpining specific versions, and reducing redundancy

Is there any reason not to merge?

maybe bring up your proposal in a separate ticket @dougli1sqrd ? Whatever solution we choose I want it to be the same across all our python projects

dougli1sqrd commented 3 years ago

I don't know that I have a specific proposal. I think from our convo a few weeks ago about this using setup to read the requirements so that installing in both methods to support people who want to do both seems fine. I was just feeling cautious since I hadn't seen that before in other python projects generally.

@deepakunni3 I think if we fix the conflicts we can just merge.

deepakunni3 commented 3 years ago

Thanks @cmungall @dougli1sqrd !

jLebioda commented 2 years ago

Hi @deepakunni3 ! It looks like you kept marshmallow pinned to 3.0.0b11, and that creates a problem for Python 3.10:

  File "/usr/local/lib/python3.10/site-packages/marshmallow/schema.py", line 5, in <module>
    from collections import defaultdict, Mapping, OrderedDict
ImportError: cannot import name 'Mapping' from 'collections' (/usr/local/lib/python3.10/collections/__init__.py)

This is related to a bug that was already fixed in Marshmallow - https://github.com/marshmallow-code/marshmallow/issues/1174

Could you please bump the marshmallow library in requirements, please?

jLebioda commented 2 years ago

Hi @deepakunni3 ! It looks like you kept marshmallow pinned to 3.0.0b11, and that creates a problem for Python 3.10:

  File "/usr/local/lib/python3.10/site-packages/marshmallow/schema.py", line 5, in <module>
    from collections import defaultdict, Mapping, OrderedDict
ImportError: cannot import name 'Mapping' from 'collections' (/usr/local/lib/python3.10/collections/__init__.py)

This is related to a bug that was already fixed in Marshmallow - marshmallow-code/marshmallow#1174

Could you please bump the marshmallow library in requirements, please?

Ahh, sorry! It looks like it's already been done; I've tested accidentally the previous version (2.7. instead of 2.8). All is fine; my bad!