Hi Liubov,
after uploading q2-types to new I added this to Build-Depends of
q2-alignment and tried to build this package. When doing so I get:
...
test_gap_boundaries (q2_alignment.tests.test_filter.MaskTests) ... ok
test_invalid_conservation_threshold (q2_alignment.tests.test_filter.MaskTests) ... ok
test_invalid_gap_threshold (q2_alignment.tests.test_filter.MaskTests) ... ok
test_N (q2_alignment.tests.test_filter.MostConservedTests) ... ok
test_all_gap (q2_alignment.tests.test_filter.MostConservedTests) ... ok
test_basic (q2_alignment.tests.test_filter.MostConservedTests) ... ok
test_empty (q2_alignment.tests.test_filter.MostConservedTests) ... ok
test_unknown_gap_mode (q2_alignment.tests.test_filter.MostConservedTests) ... ok
test_duplicate_input_ids (q2_alignment.tests.test_mafft.MafftTests) ... FAIL
test_long_ids_are_not_truncated (q2_alignment.tests.test_mafft.MafftTests) ... FAIL
test_mafft (q2_alignment.tests.test_mafft.MafftTests) ... FAIL
test_mafft_parttree_exception (q2_alignment.tests.test_mafft.MafftTests) ... FAIL
test_multithreaded_mafft (q2_alignment.tests.test_mafft.MafftTests) ... FAIL
test_failed_run (q2_alignment.tests.test_mafft.RunCommandTests) ... FAIL
test_failed_run_not_verbose (q2_alignment.tests.test_mafft.RunCommandTests) ... FAIL
======================================================================
FAIL: test_duplicate_input_ids (q2_alignment.tests.test_mafft.MafftTests)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/qiime2/plugin/testing.py", line 63, in setUp
self.fail('%s is not a registered QIIME 2 plugin.' % package)
AssertionError: q2_alignment is not a registered QIIME 2 plugin.
======================================================================
FAIL: test_long_ids_are_not_truncated (q2_alignment.tests.test_mafft.MafftTests)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/qiime2/plugin/testing.py", line 63, in setUp
self.fail('%s is not a registered QIIME 2 plugin.' % package)
AssertionError: q2_alignment is not a registered QIIME 2 plugin.
======================================================================
FAIL: test_mafft (q2_alignment.tests.test_mafft.MafftTests)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/qiime2/plugin/testing.py", line 63, in setUp
self.fail('%s is not a registered QIIME 2 plugin.' % package)
AssertionError: q2_alignment is not a registered QIIME 2 plugin.
...
All the tests are passing now :-)
For this package, there is one more run dependency: SINA [1][2]. Although it was not required
for testing and strangely it is not mentioned in QIIME 2 tutorials as well. Could we upload
the plugin without SINA for the moment and add it later? Maybe it will be useful to leave
a TODO message somewhere not to forget about SINA...
__
Liubov