A large number of test failures on MacOS

[swamidass]

In addition to these failure, two important requirements are not declared: khmer and sphynx.

doc/api-example.rst . sourmash_lib/init.py .. sourmash_lib/logging.py ....... sourmash_lib/test__minhash.py ...................................................................................... sourmash_lib/test_estimators.py .................... sourmash_lib/test_sbt.py ..FF sourmash_lib/test_signature.py ...................... sourmash_lib/test_signature_json.py ..... sourmash_lib/test_sourmash.py .............................FF.FFFF...FFFFFFFFFFF

[swamidass]

Here are the first two errors if it helps trace the bug:

____________________________________________________________________________________________________________ test_tree_save_load _____________________________________________________________________________________________________________

    def test_tree_save_load():
        factory = GraphFactory(31, 1e5, 4)
        tree = SBT(factory)
        for f in glob("demo/*.sig"):
            sig = next(signature.load_signatures(f))
            leaf = SigLeaf(os.path.basename(f), sig)
>           tree.add_node(leaf)

sourmash_lib/test_sbt.py:133: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
sourmash_lib/sbt.py:135: in add_node
    node.update(p.node)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <sourmash_lib.sbtmh.SigLeaf object at 0x10609a090>, parent = <sourmash_lib.sbt.Node object at 0x10609a110>

    def update(self, parent):
        for v in self.data.estimator.mh.get_mins():
>           parent.data.count(v)
E           TypeError: argument 1 must be string, not long

sourmash_lib/sbtmh.py:21: TypeError
___________________________________________________________________________________________________________ test_binary_nary_tree ____________________________________________________________________________________________________________

    def test_binary_nary_tree():
        factory = GraphFactory(31, 1e5, 4)
        trees = {}
        trees[2] = SBT(factory)
        trees[5] = SBT(factory, d=5)
        trees[10] = SBT(factory, d=10)

        for f in glob("demo/*.sig"):
            sig = next(signature.load_signatures(f))
            leaf = SigLeaf(os.path.basename(f), sig)
            for tree in trees.values():
>               tree.add_node(leaf)

sourmash_lib/test_sbt.py:166: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
sourmash_lib/sbt.py:135: in add_node
    node.update(p.node)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <sourmash_lib.sbtmh.SigLeaf object at 0x109aac090>, parent = <sourmash_lib.sbt.Node object at 0x109aac0d0>

    def update(self, parent):
        for v in self.data.estimator.mh.get_mins():
>           parent.data.count(v)
E           TypeError: argument 1 must be string, not long

sourmash_lib/sbtmh.py:21: TypeError

[betatim]

Could you post which version of python you are using? With the following all tests except for test_mash_yaml_to_json pass:

$ make clean && make test
platform darwin -- Python 3.6.0, pytest-3.0.5, py-1.4.32, pluggy-0.4.0
....

[swamidass]

platform darwin -- Python 2.7.13, pytest-3.0.6, py-1.4.32, pluggy-0.4.0

[ctb]

ahh! this is b/c of the version of khmer you have installed, I believe. you'll need the latest master (soon to be khmer 2.1). funny, I thought I'd put in better error messages for that... will revisit.

[ctb]

Note to self: add instructions somewhere for installing latest version of khmer as pip install https://github.com/dib-lab/khmer/archive/master.zip

[betatim]

pip install git+https://github.com/dib-lab/khmer#egg=khmer would be one way of doing that.

[ctb]

(yeah, @luizirber prefers the git-free version, so that you don't have to install git. I amended the comment above.)

[ctb]

Fixed by #117.