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unibe-cns / NEAT

NEAT (NEural Analysis Toolkit)
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Pip installation problem #122

Open WillemWybo opened 3 years ago

WillemWybo commented 3 years ago

A user reported the following issue while trying to install NEAT through pip:

Hi @WillemWybo, I am trying to go through your tutorial for this package.

However, after looking at the link in your main repository I get this error:

(base) $ pip install neatdend ERROR: Could not find a version that satisfies the requirement neatdend (from versions: none) ERROR: No matching distribution found for neatdend

Has the package been published to pypi?

Do you know what the problem might be @jakobj ?

jakobj commented 3 years ago

nope, i've only published it to pypi testing (https://test.pypi.org/project/neatdend/) and pip by default doesn't check there. i can create a proper pypi package. should i do that with the recent release or do you want to create a new one?

WillemWybo commented 3 years ago

I've just created a release for version 0.9.1. Perhaps we upload that one as a proper pypi package?

ZeitgeberH commented 3 years ago

Need to install these three before installing neatdend: neatdend 0.9.5 depends on sphinx>=2.4.3 neatdend 0.9.5 depends on nbsphinx>=0.5.1 neatdend 0.9.5 depends on sphinx-gallery>=0.7

ZeitgeberH commented 3 years ago

Pytest after pip installation results in 13 failures ======platform linux -- Python 3.8.10, pytest-5.3.5, py-1.10.0, pluggy-0.13.1 collected 78 items

tests/test_cnet.py ....F [ 6%] tests/test_compartmentfitter.py ..FFF.FFF [ 17%] tests/test_compartmenttree.py ......... [ 29%] tests/test_greenstree.py .. [ 32%] tests/test_ionchannels.py ... [ 35%] tests/test_morphtree.py ................FF [ 58%] tests/test_net.py ..... [ 65%] tests/test_neurontree.py .FF.... [ 74%] tests/test_phystree.py ..F. [ 79%] tests/test_sovtree.py ... [ 83%] tests/test_stree.py ..........F.. [100%]

while pip install . results in 8 failures: test session starts ============================================================ platform linux -- Python 3.8.10, pytest-5.3.5, py-1.10.0, pluggy-0.13.1 collected 78 items

tests/test_cnet.py ....F [ 6%] tests/test_compartmentfitter.py ..FFF.F.F [ 17%] tests/test_compartmenttree.py ......... [ 29%] tests/test_greenstree.py .. [ 32%] tests/test_ionchannels.py ... [ 35%] tests/test_morphtree.py .................. [ 58%] tests/test_net.py ..... [ 65%] tests/test_neurontree.py .FF.... [ 74%] tests/test_phystree.py .... [ 79%] tests/test_sovtree.py ... [ 83%] tests/test_stree.py .............

WillemWybo commented 3 years ago

@ZeitgeberH A lot of test failures are likely due to the lack of default ion channels compiled for neuron. Try running compilechannels default. It also seems something is wonky with the version, the latest official version is 0.9.1 and this shouldn't depend on sphinx. @jakobj I can't install neat from pip, when running pip install neatdend I get the following error:

ERROR: Could not find a version that satisfies the requirement neatdend (from versions: none)
ERROR: No matching distribution found for neatdend
ZeitgeberH commented 3 years ago

@ZeitgeberH A lot of test failures are likely due to the lack of default ion channels compiled for neuron. Try running compilechannels default. This solved all test failures! Thanks, @WillemWybo It also seems something is wonky with the version, the latest official version is 0.9.1 and this shouldn't depend on sphinx. @jakobj I can't install neat from pip, when running pip install neatdend I get the following error:

ERROR: Could not find a version that satisfies the requirement neatdend (from versions: none)
ERROR: No matching distribution found for neatdend

I was using "pip install -i https://test.pypi.org/simple/ neatdend" as shown in pypi.org website: https://test.pypi.org/project/neatdend/

WillemWybo commented 3 years ago

Ah thanks @ZeitgeberH , seems we still have it only as a test package, perhaps we should change this for v0.9.1 @jakobj