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v2.0.1 Unit Test issues #43

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jraysajulga opened this issue Feb 20, 2021 · 0 comments
Open

v2.0.1 Unit Test issues #43

jraysajulga opened this issue Feb 20, 2021 · 0 comments
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bug Something isn't working

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@jraysajulga
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@jj-umn, I'm having issues with the pandas dependency. Any ideas on how to fix this?

> python -m unittest discover tests
load obo file /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo
/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo: fmt(1.2) rel(2018-10-30) 47,358 GO Terms
load obo file /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/goslim_metagenomics.obo
/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/goslim_metagenomics.obo: fmt(1.2) rel(None) 185 GO Terms
load obo file /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo
/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo: fmt(1.2) rel(2018-10-30) 47,358 GO Terms
load obo file /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/goslim_metagenomics.obo
/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/goslim_metagenomics.obo: fmt(1.2) rel(None) 185 GO Terms
load obo file /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo
/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo: fmt(1.2) rel(2018-10-30) 47,358 GO Terms
load obo file /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/goslim_metagenomics.obo
/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/goslim_metagenomics.obo: fmt(1.2) rel(None) 185 GO Terms
load obo file /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo
/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo: fmt(1.2) rel(2018-10-30) 47,358 GO Terms
load obo file /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/goslim_metagenomics.obo
/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/goslim_metagenomics.obo: fmt(1.2) rel(None) 185 GO Terms
load obo file /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/tmp_go_data_dwnld/go-basic.obo
/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/tmp_go_data_dwnld/go-basic.obo: fmt(1.2) rel(2021-02-01) 47,291 GO Terms
load obo file /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/tmp_go_data_dwnld/goslim_metagenomics.obo
/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/tmp_go_data_dwnld/goslim_metagenomics.obo: fmt(1.2) rel(None) 201 GO Terms
.NCBI database format is outdated. Upgrading
Downloading taxdump.tar.gz from NCBI FTP site (via HTTP)...
Done. Parsing...
Loading node names...
2311792 names loaded.
241707 synonyms loaded.
Loading nodes...
2311792 nodes loaded.
Linking nodes...
Tree is loaded.
Updating database: /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/tmp_test_tax_dwnld/taxa.sqlite ...
 2311000 generating entries...
Uploading to /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/tmp_test_tax_dwnld/taxa.sqlite

Inserting synonyms:      240000
Inserting taxid merges:  60000
Inserting taxids:       2310000
.....300
.load obo file /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo
/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo: fmt(1.2) rel(2018-10-30) 47,358 GO Terms
.load obo file /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo
/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo: fmt(1.2) rel(2018-10-30) 47,358 GO Terms
.load obo file /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo
/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo: fmt(1.2) rel(2018-10-30) 47,358 GO Terms
......Traceback (most recent call last):
  File "metaquantome/cli.py", line 10, in <module>
    from metaquantome.modules.expand import expand
  File "/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/modules/expand.py", line 3, in <module>
    import metaquantome.util.expand_io as expand_io
  File "/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/util/expand_io.py", line 1, in <module>
    import pandas as pd
ModuleNotFoundError: No module named 'pandas'
FTraceback (most recent call last):
  File "metaquantome/cli.py", line 10, in <module>
    from metaquantome.modules.expand import expand
  File "/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/modules/expand.py", line 3, in <module>
    import metaquantome.util.expand_io as expand_io
  File "/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/util/expand_io.py", line 1, in <module>
    import pandas as pd
ModuleNotFoundError: No module named 'pandas'
FTraceback (most recent call last):
  File "metaquantome/cli.py", line 10, in <module>
    from metaquantome.modules.expand import expand
  File "/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/modules/expand.py", line 3, in <module>
    import metaquantome.util.expand_io as expand_io
  File "/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/util/expand_io.py", line 1, in <module>
    import pandas as pd
ModuleNotFoundError: No module named 'pandas'
FTraceback (most recent call last):
  File "metaquantome/cli.py", line 10, in <module>
    from metaquantome.modules.expand import expand
  File "/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/modules/expand.py", line 3, in <module>
    import metaquantome.util.expand_io as expand_io
  File "/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/util/expand_io.py", line 1, in <module>
    import pandas as pd
ModuleNotFoundError: No module named 'pandas'
FTraceback (most recent call last):
  File "metaquantome/cli.py", line 10, in <module>
    from metaquantome.modules.expand import expand
  File "/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/modules/expand.py", line 3, in <module>
    import metaquantome.util.expand_io as expand_io
  File "/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/util/expand_io.py", line 1, in <module>
    import pandas as pd
ModuleNotFoundError: No module named 'pandas'
FTraceback (most recent call last):
  File "metaquantome/cli.py", line 10, in <module>
    from metaquantome.modules.expand import expand
  File "/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/modules/expand.py", line 3, in <module>
    import metaquantome.util.expand_io as expand_io
  File "/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/util/expand_io.py", line 1, in <module>
    import pandas as pd
ModuleNotFoundError: No module named 'pandas'
FTraceback (most recent call last):
  File "metaquantome/cli.py", line 10, in <module>
    from metaquantome.modules.expand import expand
  File "/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/modules/expand.py", line 3, in <module>
    import metaquantome.util.expand_io as expand_io
  File "/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/util/expand_io.py", line 1, in <module>
    import pandas as pd
ModuleNotFoundError: No module named 'pandas'
F........load obo file /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo
/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo: fmt(1.2) rel(2018-10-30) 47,358 GO Terms
...load obo file /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo
/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo: fmt(1.2) rel(2018-10-30) 47,358 GO Terms
.load obo file /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo
/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo: fmt(1.2) rel(2018-10-30) 47,358 GO Terms
load obo file /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo
/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo: fmt(1.2) rel(2018-10-30) 47,358 GO Terms
..load obo file /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo
/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo: fmt(1.2) rel(2018-10-30) 47,358 GO Terms
.load obo file /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo
/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo: fmt(1.2) rel(2018-10-30) 47,358 GO Terms
load obo file /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/goslim_metagenomics.obo
/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/goslim_metagenomics.obo: fmt(1.2) rel(None) 185 GO Terms
..................................................load obo file /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo
/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo: fmt(1.2) rel(2018-10-30) 47,358 GO Terms
load obo file /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/goslim_metagenomics.obo
/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/goslim_metagenomics.obo: fmt(1.2) rel(None) 185 GO Terms
..load obo file /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo
/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo: fmt(1.2) rel(2018-10-30) 47,358 GO Terms
............
======================================================================
FAIL: testFuncBar (travis.testCLI.TestCLI)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rsajulga/Projects/umn/galaxyp/metaquantome/tests/travis/testCLI.py", line 93, in testFuncBar
    self.assertEqual(test_status, 0)
AssertionError: 1 != 0

======================================================================
FAIL: testHeatmapViz (travis.testCLI.TestCLI)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rsajulga/Projects/umn/galaxyp/metaquantome/tests/travis/testCLI.py", line 108, in testHeatmapViz
    self.assertEqual(test_status, 0)
AssertionError: 1 != 0

======================================================================
FAIL: testMultipleInt (travis.testCLI.TestCLI)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rsajulga/Projects/umn/galaxyp/metaquantome/tests/travis/testCLI.py", line 34, in testMultipleInt
    self.assertEqual(exp_status, 0)
AssertionError: 1 != 0

======================================================================
FAIL: testPCABig (travis.testCLI.TestCLI)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rsajulga/Projects/umn/galaxyp/metaquantome/tests/travis/testCLI.py", line 130, in testPCABig
    self.assertEqual(test_status, 0)
AssertionError: 1 != 0

======================================================================
FAIL: testSingleInt (travis.testCLI.TestCLI)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rsajulga/Projects/umn/galaxyp/metaquantome/tests/travis/testCLI.py", line 20, in testSingleInt
    self.assertEqual(status, 0)
AssertionError: 1 != 0

======================================================================
FAIL: testViz (travis.testCLI.TestCLI)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rsajulga/Projects/umn/galaxyp/metaquantome/tests/travis/testCLI.py", line 59, in testViz
    self.assertEqual(test_status, 0)
AssertionError: 1 != 0

======================================================================
FAIL: testVizTabfile (travis.testCLI.TestCLI)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rsajulga/Projects/umn/galaxyp/metaquantome/tests/travis/testCLI.py", line 74, in testVizTabfile
    self.assertEqual(test_status, 0)
AssertionError: 1 != 0

----------------------------------------------------------------------
Ran 101 tests in 243.798s

FAILED (failures=7)
@jraysajulga jraysajulga added the bug Something isn't working label Feb 20, 2021
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