Hi Andreas,
On Fri, 29 Mar 2019 at 16:03, Andreas Tille <[email protected]> wrote:
> 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
[1] https://github.com/epruesse/SINA
[2]
https://github.com/qiime2/q2-alignment/blob/ed1d841cddfb47ce6e945d72c0ab106a2c3a6121/ci/recipe/meta.yaml#L26
