Nicola Soranzo
d4662fd952
Merge branch 'release_20.01' into dev
2020-02-19 12:43:07 +00:00
Nicola Soranzo
d40c5ec9f4
Merge branch 'release_19.09' into release_20.01
2020-02-19 12:32:07 +00:00
John Chilton
8e9d6e685e
Merge pull request #9354 from mvdbeek/parent_instance_detached_again_3
...
[19.09] Expunge tool shed repository objects, prevents ParentInstanceDetachedError
2020-02-18 08:54:04 -05:00
Nicola Soranzo
6f0219e883
Merge branch 'release_20.01' into dev
2020-02-13 02:12:03 +00:00
Nicola Soranzo
f16e5cb712
Merge branch 'release_19.09' into release_20.01
2020-02-13 02:11:15 +00:00
mvdbeek
e1780cb20a
Move logic of whether to load a config into can_load_config_file and fix unit tests
2020-02-12 11:53:28 +01:00
mvdbeek
8a8c0990dd
Give ToolShedRepositoryCache.rebuild its own session
2020-02-11 14:57:24 +01:00
mvdbeek
f4e32636e1
Make sure tool dependency relationships are accessibly as well
2020-02-11 12:35:16 +01:00
mvdbeek
82a06af664
Explain why the test does what it does
2020-02-11 12:24:40 +01:00
mvdbeek
098419b9b4
Ensure repository metadata isn't kept in memory
2020-02-11 12:21:39 +01:00
mvdbeek
2a66a39ace
Add test that should provoke https://github.com/galaxyproject/galaxy/issues/9074
2020-02-11 12:09:49 +01:00
Nicola Soranzo
0a26ed38b2
Merge branch 'release_20.01' into dev
2020-02-05 15:26:27 +00:00
Nicola Soranzo
1dc1e5f219
Python3: unicodify the output of `subprocess.check_output()`
...
By default it's a bytestring.
Also:
- don't use `shell=True`
- add a `splitlines()` forgotten in commit 670897ec5c
2020-02-05 12:13:39 +00:00
Dannon Baker
f935c6206b
Clean up old 'blue' style path, update documentation and samples to refer to plain old 'static' now.
2020-02-03 22:41:29 -05:00
Nicola Soranzo
f32ece1e8d
Faster and cleaner set creation
2020-02-03 15:42:09 +00:00
Dannon Baker
947b9eca5b
Merge remote-tracking branch 'upstream/dev' into idp-logout
2020-01-28 14:01:49 -05:00
Dannon Baker
13f4e1e3f1
Merge remote-tracking branch 'upstream/release_20.01' into dev
2020-01-28 13:24:09 -05:00
Dannon
8e16fcb4cc
Merge pull request #9233 from dannon/external-auth-login-refinement
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[20.01] External auth login refinement
2020-01-28 13:22:55 -05:00
Nicola Soranzo
80607164f4
Merge branch 'release_20.01' into dev
2020-01-24 17:13:06 +00:00
Nicola Soranzo
6fbe8c9031
Merge branch 'release_19.09' into release_20.01
2020-01-24 17:08:02 +00:00
Nicola Soranzo
d67295162a
Simplify and refactor
2020-01-23 21:57:54 +00:00
mvdbeek
e227b1473f
Fix unselected select parameter comparison to empty string
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`$wrapper == ""` and `$wrapper == "None"` had been valid ways
to check for unselected / optional select parameters.
This restores the `$wrapper == ""` form as used by gffcompare
https://github.com/galaxyproject/tools-iuc/blob/master/tools/gffcompare/gffcompare.xml#L41
2020-01-23 19:24:52 +00:00
mvdbeek
5d379dc4a5
Fix unselected select parameter comparison to empty string
...
`$wrapper == ""` and `$wrapper == "None"` had been valid ways
to check for unselected / optional select parameters.
This restores the `$wrapper == ""` form as used by gffcompare
https://github.com/galaxyproject/tools-iuc/blob/master/tools/gffcompare/gffcompare.xml#L41
2020-01-23 16:02:56 +01:00
Nicola Soranzo
f5cd88465e
Make str.join()s more efficient
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by using generator expressions and tuples instead of lists.
2020-01-23 11:06:32 +00:00
Dannon Baker
f041eb2190
Fix lint in custos test
2020-01-22 16:43:42 -05:00
Dannon Baker
20a0777a25
Fix custos authnz tests. This should be swapped to use the standard mocked objects?
2020-01-22 11:44:27 -05:00
mvdbeek
ceb214e1d9
Merge branch 'release_20.01' into dev
2020-01-22 16:14:30 +01:00
Dannon Baker
c98c416fa5
Fix custos_authnz tests (allow email kwarg, which does nothing in this case..)
2020-01-21 14:37:50 -05:00
mvdbeek
28277d2b67
Fix unit test
2020-01-21 11:57:20 +01:00
John Chilton
527af29439
Merge remote-tracking branch 'upstream/release_20.01' into dev_merge_2
2020-01-17 12:28:11 -05:00
mvdbeek
5ee23fd52b
Fix mulled-build-files if name_override is not given
2020-01-17 09:35:16 +01:00
Nicola Soranzo
83d52a9e06
Merge branch 'release_20.01' into dev
2020-01-16 15:06:12 +00:00
mvdbeek
b1885b065f
Sort best package by upload time (lowest priority)
...
in addition to version and build number. This is necessary for getting
the extended-base annotation for qiime 1.9.1, which does not contain the
annotation in linux-64/qiime-1.9.1-np110py27_1.tar.bz2 while in the
newer linux-64/qiime-1.9.1-np112py27_1.tar.bz2 it is present. This
depends of course on `conda search` returning packages sorted by upload
time and is a little brittle. It does seem better than always picking
the oldest upload time as we do without this change. Also looks in
meta.yaml for extended base annotation, since sometimes this isn't
present in info/about.json.
2020-01-16 11:52:03 +01:00
Marius van den Beek
ddf6e19a64
Merge pull request #9197 from jmchilton/mixed_object_store
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Allow mixed store_by objectstore configurations.
2020-01-15 17:23:27 +02:00
mvdbeek
6d3b14f9a3
Change any_target_requires_extended_base to base_image_for_targets
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This is easier to use in planemo (we don't need to figure out which
image to use based on the return value of
any_target_requires_extended_base) and leaves open the possibility for
custom base image annotation in conda recipes or other places.
2020-01-14 12:01:31 +02:00
John Chilton
801182c358
Make store_by a true per object store configuration.
2020-01-13 21:22:49 -05:00
Marcus Christie
0792bcd6c0
Merge remote-tracking branch 'upstream/dev' into idp-logout
2020-01-12 14:07:08 -05:00
mvdbeek
c471ab2dde
Add base_image column to mulled-build-files
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This will continue to work for single column files
or files that make use of the second and third column already
(build_number and name_override).
I don't think we should be using name_override,
but given the library nature and not knowing if anyone
except for biocontainers/multi-package-containers uses
this I chose to keep backwards compaitbility.
This does add support for meaningful column headers,
so we can write something like
```
\#base_image targets build_number
extended package 10
```
and not include name_override.
2020-01-10 20:09:09 +02:00
Nicola Soranzo
1e4ec5c843
Use @pytest.mark.skipif decorator
2020-01-09 14:40:48 +01:00
mvdbeek
03e7ea25fb
Fix tool watcher unit tests; sleep needs to happen after watching the file
2020-01-09 14:40:48 +01:00
mvdbeek
d33813c28d
Tweak paramiko missing hostkey policies
2020-01-09 14:40:48 +01:00
mvdbeek
4fd536658d
Merge branch 'release_19.09' into release_20.01
2019-12-27 20:14:21 +01:00
mvdbeek
f12e0844fe
Merge branch 'release_19.05' into release_19.09
2019-12-27 20:12:05 +01:00
Marcus Christie
757cf8cd93
FIx py3 compat and add unit test
2019-12-24 11:02:02 -05:00
mvdbeek
9d1cccd14d
Cast to None for optional params if not comparing strings
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Proposed by @nsroanzo in https://github.com/galaxyproject/galaxy/pull/9149#discussion_r360225247
2019-12-21 17:22:34 +01:00
John Chilton
a2d14be11f
Allow testing command versions in tools - tests, XSD.
2019-12-19 17:34:31 -05:00
John Chilton
738ea0c506
Re-locate version path to a writable directory in containers.
2019-12-19 17:32:40 -05:00
mvdbeek
d12f21d62e
Add test for unset optional parameters
2019-12-19 17:55:00 +01:00
Dannon
84a0ec271a
Merge pull request #8893 from jmchilton/markdown_export
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PDF Export of Galaxy Markdown
2019-12-19 11:21:09 -05:00
mvdbeek
b52b022383
Merge branch 'release_19.09' into dev
2019-12-19 10:36:07 +01:00
Nicola Soranzo