Dannon Baker
03351d2a9f
Apply black to tools as well
2022-02-03 09:12:13 -05:00
John Chilton
54e8d22fa7
Check types of modules without type annotations in the their signatures on new modules.
...
https://mypy.readthedocs.io/en/stable/command_line.html#cmdoption-mypy-check-untyped-defs
> it type checks the body of every function, regardless of whether it has type annotations. (By default the bodies of functions without annotations are not type checked.)
2021-10-11 16:08:26 -04:00
Björn Grüning
1e428e53fa
remove stop_err
2020-10-13 09:55:36 +02:00
Björn Grüning
eb13388ee6
Update velvetg_wrapper.py
2020-10-13 09:53:02 +02:00
Björn Grüning
98e65c5f89
some trick for velvetg
2020-10-12 13:41:57 +02:00
Björn Grüning
43943ffc6a
the byte string is also needed
2020-10-12 13:24:34 +02:00
Björn Grüning
9768cbf8d2
string.join is gone in py3k
2020-10-12 12:32:23 +02:00
Nicola Soranzo
d1bc98dfcb
Python3: fix remaining print statements
...
Remove some debugging prints.
Fix import order.
Consolidate exception logging in ToolShed database migrations.
2017-10-12 18:34:29 +01:00
John Chilton
5a7a15d161
Test and clarifications for composite uploads.
...
- Add an API test for datatype-defined composite uploads - including exercising newline conversion and the space_to_tab parameter.
- Add a test decorator skip_without_datatype to mirror skip_without_tool for this test, improve both decorators.
- The ftype parameter in the composite test tools does nothing - drop it and drop it from the XSD spec.
- Slightly improve the documentation for these composite_data elements in the XSD.
2017-08-31 12:47:40 -04:00
Nicola Soranzo
21b44bf348
Fix all E201 and E202 style errors
...
using the following command:
```
autopep8 -i -r --exclude $(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -sd,) --select E201,E202 .
```
2017-08-17 11:35:39 +01:00
Nicola Soranzo
1d17a29c79
Fixes for pycodestyle 2.2.0
2016-11-15 16:56:50 +00:00
Nicola Soranzo
11b4f3a60c
Fix import order and Python3 compatibility for tools/
...
xref #1715
2016-09-29 19:26:22 +01:00
Nicola Soranzo
ed4132d9c0
Python3: Use open() instead of file()
2016-05-17 23:53:16 +01:00
Nicola Soranzo
39da6c3278
Fix the remaining 2180 flake8 errors in tools/ .
2016-02-10 18:46:03 +00:00
Nicola Soranzo
3c60edfda7
Add Graph2 output dataset when "-read_trkg yes".
2014-10-28 17:15:39 +01:00
Nicola Soranzo
0af9b67d07
Use from_work_dir instead of copying output files line by line. Write velvetg output to stdout.
2014-10-28 18:45:17 +01:00
Gianmauro Cuccuru
333215b750
Add <version_command>.
2013-12-20 10:58:08 +01:00
Nicola Soranzo
7b386b14ed
Fix for "NotFound: cannot find 'cov_cutoff' while searching for 'expected.cov_cutoff'"
2013-10-17 12:46:13 +02:00
Kanwei Li
a037747141
Velvet wrapper: fix typos, tabs -> spaces, spacing
2011-05-27 11:01:46 +02:00
Nate Coraor
e05f11bc73
Convert a bunch of binary requirement tags to package requirements, and change the sputnik tool to call 'sputnik' instead of 'bx-sputnik'.
2010-10-07 16:23:57 -04:00
Greg Von Kuster
ae749436e0
Add support for velvet data types and velveth and velvetg tool wrappers, all contributed by James E Johnson - University of Minnesota.
2010-06-09 11:23:10 -04:00
Dannon Baker