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2944 Commits
Author SHA1 Message Date
Nicola Soranzo 00f7522e7e Merge branch 'release_22.01' into dev 2022-03-19 01:57:33 +00:00
Nicola Soranzo 5114b67902 Merge branch 'release_21.09' into release_22.01 2022-03-18 18:28:15 +00:00
Nicola Soranzo 8e4bdb58e4 Merge branch 'release_21.05' into release_21.09 2022-03-18 18:08:10 +00:00
mvdbeek e2d43806dc Fix `sff_extract` tool, drop type annotation 
I don't think this tool is really used much, but it is loaded in
`tool_conf.xml`.
https://github.com/galaxyproject/galaxy/pull/11877 added type
annotations, and that's a syntax error on 2.7

The alternative would be to fix the rest of the tool for 3.x,
but I think we're just wasting our time there and we shouldn't
touch this again.
 2022-03-16 15:24:55 +01:00
Nicola Soranzo 7f04b5d698 Merge branch 'release_22.01' into dev 2022-03-02 20:08:55 +00:00
Nicola Soranzo 856269b248 Merge branch 'release_21.09' into release_22.01 2022-03-02 19:18:43 +00:00
mvdbeek a9eb669158 Add profile version to ethercalc 
It writes to stderr, so that fails on most job runners (why not all???).
 2022-03-02 14:10:52 +01:00
Dannon Baker 03351d2a9f Apply black to tools as well 2022-02-03 09:12:13 -05:00
Nicola Soranzo dc87e8f38a Help black with placement of noqa comments 2022-02-03 14:07:14 +00:00
Dannon Baker 623a5e165a Apply black formatting. 
Apply isort.
 2022-02-03 07:42:20 -05:00
Alex Ostrovsky f884f9b149 Allow any format in export tool 2022-01-11 13:10:03 -08:00
Nicola Soranzo bd0cefa020 Don't use triple-quoted strings as comments 
They are expressions that get uselessly evaluated.

These were reported as B018 errors by flake8-bugbear 21.11.28 , but B018 for
strings has then been disabled in 21.11.29 since these strings can also be
used as inline attribute doc strings or module variable docstrings (not our
case though).
 2021-11-29 23:02:34 +00:00
mvdbeek 6e01abe4b2 Bump version and add profile 2021-11-26 16:18:31 +01:00
Gianmauro Cuccuru 0cf0b82959 Update interactivetool_pyiron.xml 2021-11-26 15:57:34 +01:00
Nicola Soranzo 1f8ac6c7bb Merge pull request #12965 from common-workflow-lab/type_ignore_narrow 
tighten type ignores
 2021-11-23 16:32:28 +00:00
Nicola Soranzo 30337fbd94 Merge branch 'release_21.09' into dev 2021-11-23 13:30:36 +00:00
Michael R. Crusoe 7819fdc7a6 tighten type ignores 2021-11-23 13:12:07 +01:00
Marius van den Beek 90c2f31cb4 Don't add ca-ceritificates to tool requirements 
ca-certificates is now part of the ncbi-datasets-cli conda package
 2021-11-18 17:17:19 +01:00
Marius van den BeekandHelena f1986a481f Export just once 
Thanks!

Co-authored-by: Helena <hxr@hx42.org>
 2021-11-17 15:28:07 +01:00
mvdbeek 47120ca48f Fix containerized NCBI Datasets Genomes data source tool 2021-11-12 20:17:34 +01:00
John Chilton 4fe7109ab1 Track transformations applied during uploads. 2021-11-12 10:21:55 -05:00
John Chilton 8643daf1dd Attempt to type more upload related things. 2021-11-05 11:58:53 -04:00
mvdbeek 58b2837c7c Merge branch 'release_21.09' into dev 2021-11-01 18:17:54 +01:00
mvdbeek 63e25b20f4 Set profile version of ncbi_datasets so it can run containerized 2021-10-31 16:28:38 +01:00
Dannon Baker c3605c7112 Merge remote-tracking branch 'upstream/release_21.09' into dev 2021-10-19 09:59:21 -04:00
mvdbeek 4dbf235f23 Ignore type in unused function 2021-10-12 15:25:30 +02:00
David López 2ed29639bb Merge pull request #12691 from jmchilton/more_type_fixes 
Check types of modules without type annotations in the their signatures on new modules.
 2021-10-12 13:33:17 +02:00
Nuwan Goonasekera 088c8430d1 Merge pull request #12650 from neoformit/dev-isee 
New interactive tool - iSEE
 2021-10-12 08:37:48 +05:30
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
Cameron Hyde 1fcef64f32 Remove redundant comment 2021-10-06 13:20:18 +10:00
Cameron Hyde c2a395b8db Merge branch 'dev' of https://github.com/neoformit/galaxy into dev-isee 2021-10-06 12:59:09 +10:00
Cameron Hyde 1039c32b72 Add interactive tool iSEE 
------

iSEE is a new interactive tool for visualizing single-cell RNAseq data. It requires a new datatype ``rdata.se`` which allows users to upload an R HDF5SummarizedExperiment object.
 2021-10-06 12:57:52 +10:00
Nate Coraor 6c39e132e7 Modernize sorter (sort1) tool: 
- Don't use shell, pipe with subprocess.PIPE instead
- Switch optparse for argparse
- Add missing coreutils requirement for `sort` command
- Change Python requirement from 2.7 to 3.8
 2021-10-01 12:47:14 -04:00
Dannon 5fac82731f Merge pull request #11738 from mvdbeek/ncbi_datasets_async_tool 
NCBI Datasets data source tool
 2021-09-20 12:17:28 -04:00
mvdbeek a10645d664 Use ncbi_genome_dataset.zip format 2021-09-13 12:05:53 +02:00
mvdbeek 947832541b Use version_command tag, single quotes for paths 2021-09-09 19:15:19 +02:00
Brad Holmes 8b77edbb53 Implement NCBI Datasets Genome Dataset server 2021-09-09 12:28:02 -04:00
Anup Kumar d46c96a63e Add tag version 2021-09-09 11:36:13 +02:00
Anup Kumar 582fb25567 Fix review comments 2021-09-09 10:25:08 +02:00
Anup Kumar 212248b3e2 Merge branch 'galaxyproject:dev' into ml-jupyter-notebook 2021-09-08 18:04:55 +02:00
Brad Holmes 0186289a63 Improve wording and target URL for NCBI Datasets Genomes link tool 2021-09-08 11:00:39 -04:00
Anup Kumar 8fbac0389f Fix review comments 2021-09-08 16:38:10 +02:00
Anup Kumar f3d042e249 Fix review comments 2021-09-08 16:36:19 +02:00
Marius van den Beek 04885b4ae2 Merge pull request #11537 from luke-c-sargent/dev 
Update bam.iobio interactive tool wrapper
 2021-09-08 13:14:53 +02:00
mvdbeek 44ee10e93d Add json_param as possible parameter type 2021-08-31 16:49:54 +02:00
mvdbeek 278b1422fd Replace taxon with generic file parameter 2021-08-31 16:45:56 +02:00
mvdbeek 58e530e65a Use separate dehydrated.zip datatype subclass 2021-08-31 16:45:56 +02:00
mvdbeek e552f79b49 Add dependency on ncbi-datasets-cli 2021-08-31 16:45:55 +02:00
mvdbeek e0855b7d9a Add simple NCBI datasets source tool 2021-08-31 16:45:55 +02:00
Marius van den BeekandNicola Soranzo 94881812a0 Tweak tool options 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2021-08-25 18:03:19 +03:00