Commits · dev · vidjil / vidjil

12 Dec, 2018 4 commits
- Merge branch 'feature-g/3656-gitlab-deploy-germlines' into 'dev' · 3425e544
  
  Mathieu Giraud authored Dec 12, 2018
```
Add germline build and deploy on prod server

Closes #3656

See merge request !373
```
  3425e544
- .gitlab-ci.yml: bikeshed date format · 22eb9148
  Mathieu Giraud authored Dec 12, 2018
  
  22eb9148
- .gitlab-ci.yml: Add germline build and deploy on prod server · fcb2d6a2
  Vidjil Team authored Dec 12, 2018
```
Fixes #3656
```
  fcb2d6a2
- Merge branch 'feature-ga/3515-imgt-all' into 'dev' · 0e9493a7
  
  Mikaël Salson authored Dec 12, 2018
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Feature ga/3515 imgt all

See merge request !372
```
  0e9493a7
06 Dec, 2018 4 commits
- tests: check in/outframe genes · 895c9480
  Mathieu Giraud authored Dec 06, 2018
```
See #3515.
```
  895c9480
- germline/split-from-imgt.py: get sequences from several files · ecbdbd2e
  Mathieu Giraud authored Dec 06, 2018
```
See #3515.
```
  ecbdbd2e
- germline/get-germline: gets from IMGT all genes, not only those inframe · 4bd2e72c
  Mathieu Giraud authored Dec 06, 2018
```
Note that we should also keep inframeP, which has gaps.
See #3515.
```
  4bd2e72c
- Merge branch 'feature-c/3641-more-space-for-rotated-labels' into 'dev' · 005d00b0
  
  Mikaël Salson authored Dec 06, 2018
```
js/scatterPlot.js: add 15px to the top margin when the labels are rotated

Closes #3641

See merge request !370
```
  005d00b0
04 Dec, 2018 7 commits
- Merge branch 'feature-ts/3585-fuse-keep-metadata' into 'dev' · d9f0b676
  
  Mikaël Salson authored Dec 04, 2018
```
Feature ts/3585 fuse keep metadata

Closes #3585

See merge request !371
```
  d9f0b676
- tools/fuse.py: keep all interesting clone metadata, even from non-topmost clones · 48ff68af
  Mathieu Giraud authored Dec 04, 2018
```
Closes #3585.
```
  48ff68af
- tests: update · c421fc67
  Mathieu Giraud authored Dec 04, 2018
  
  c421fc67
- tests: fuse should keep clone metadata from non-topmost clones · ec6d38c4
  Mathieu Giraud authored Dec 04, 2018
```
See #3585.
```
  ec6d38c4
- Merge branch 'feature-c/3642-div-data' into 'dev' · e830e520
  
  Mikaël Salson authored Dec 04, 2018
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css: no border on 'data' div

See merge request !369
```
  e830e520
- css: no border for 'data' div · 92449186
  Mathieu Giraud authored Dec 04, 2018
```
See #3642.
```
  92449186
- js/scatterPlot.js: add 15px to the margin when the labels are rotated · 7100e81e
  Mathieu Giraud authored Dec 04, 2018
```
Close #3641.
```
  7100e81e
03 Dec, 2018 1 commit
- Merge branch 'feature-s/3638-no-chown-on-directories' into 'dev' · dac04142
  
  Mathieu Giraud authored Dec 03, 2018
```
Don't chown result/ and upload/

Closes #3638

See merge request !368
```
  dac04142
30 Nov, 2018 2 commits

docker/vidjil-server/scripts/uwsgi-entrypoint.sh: Don't chown result/ and upload/ · f96633bd

Mikaël Salson authored Nov 30, 2018

Those directories may contain sensitive data and may have a huge number of files.
More generally we don't want to modify the external directories

Fixes #3638

f96633bd

.gitlab-ci.yml: Use deploy variables for review · 6137386b

Mikaël Salson authored Nov 30, 2018
```
DEPLOY_SERVER was used for two different things.
We now have REVIEW_SERVER and REVIEW_SERVER_PATH.
```
6137386b

27 Nov, 2018 1 commit
- conf.js: update from browser/js/conf.js · 0a79c79e
  
  Mathieu Giraud authored Nov 27, 2018
  
  0a79c79e
26 Nov, 2018 4 commits
- vidjil-algo: release 2018.10, finally · 31968497
  
  Mathieu Giraud authored Nov 26, 2018
```
See #3571.
```
  31968497
- doc/vidjil-algo: 2018.10 · 22414ad2
  Mathieu Giraud authored Nov 26, 2018
```
Partially reverts 9402d384.
```
  22414ad2
- vidjil-algo: release 2018.10 · c91789fa
  Mikaël Salson authored Nov 23, 2018
  
  c91789fa
- vidjil.cpp: Don't use a pointer for output · 894bb14a
  Mikaël Salson authored Nov 23, 2018
```
This avoids some issue with memory leak when leaving main earlier than expected.

See #3571
```
  894bb14a
24 Nov, 2018 2 commits
- .gitlab-ci.yml: more meaningful name for releases, adjust manual · 4e5a11d9
  
  Mathieu Giraud authored Nov 24, 2018
```
The 'manual' actions concern here 'publish_release' and 'deploy_prod',
the two stages that publish/deploy the release to public places.
```
  4e5a11d9
- Merge branch 'feature-a/should-update' into 'dev' · 06396924
  
  Mathieu Giraud authored Nov 24, 2018
```
tools/should.py: update from upstream

See merge request !366
```
  06396924
23 Nov, 2018 2 commits
- tools/should.py: update from upstream · 336b8051
  Mathieu Giraud authored Nov 23, 2018
```
should@8f711a78
```
  336b8051
- doc/credits.md: update publications · f355173e
  
  Mathieu Giraud authored Nov 20, 2018
  
  f355173e
21 Nov, 2018 5 commits
- Merge branch 'feature-s/cleanup' into 'dev' · 203fb9ee
  
  Mathieu Giraud authored Nov 21, 2018
```
remove unused views and routes

Closes #3076

See merge request !170
```
  203fb9ee
- remove unused views and routes · 1e8a3869
  Ryan Herbert authored Nov 21, 2018
```
See #3076
```
  1e8a3869
- Merge branch 'feature-s/3621-no_fuse_empty_set' into 'dev' · 6ff00141
  
  Mathieu Giraud authored Nov 21, 2018
```
file.py task.py a some fuse failsafes.

Closes #3621

See merge request !359
```
  6ff00141
- Merge branch 'feature-s/docker_gosu' into 'dev' · 8ed8917f
  
  Mathieu Giraud authored Nov 21, 2018
```
vidjil-server/Dockerfile use newer GOSU version

See merge request !358
```
  8ed8917f
- Merge branch 'feature-a/3601-fix-getWarnings' into 'dev' · 8f38936d
  
  Mathieu Giraud authored Nov 21, 2018
```
core/output.cpp: fix Clone.getWarnings()

Closes #3601

See merge request !361
```
  8f38936d
20 Nov, 2018 3 commits
- Merge branch 'feature-s/3619-test_run' into 'dev' · 2fa4434e
  
  Mathieu Giraud authored Nov 20, 2018
```
Feature s/3619 test run

Closes #3619

See merge request !356
```
  2fa4434e
- Merge branch 'feature-c/integrate-vmi-for-prod' into 'dev' · 9e1de6ac
  
  Mathieu Giraud authored Nov 20, 2018
```
Integrate vmi.js, a new framework for a future responsive behavior

See merge request !351
```
  9e1de6ac
- core/output.cpp: fix Clone.getWarnings() · f8127baf
  Mathieu Giraud authored Nov 20, 2018
```
Closes #3601.
Curiously the test introduced in 3af3afbf was passing on gcc even without this 'return'.
```
  f8127baf
19 Nov, 2018 1 commit
- vidjil-server/Dockerfile use newer GOSU version · 2553f69a
  Ryan Herbert authored Nov 19, 2018
```
use a newer version of GOSU because it doesn't seem to work correctly
with the current setup
```
  2553f69a
15 Nov, 2018 1 commit
- Merge branch 'feature/fix-height' into 'dev' · cb474b9f
  
  Mathieu Giraud authored Nov 15, 2018
```
Fix db_table_container height

Closes #3578

See merge request !354
```
  cb474b9f
14 Nov, 2018 3 commits
- test_sample.rb use || instead of or · 0b63ac08
  Ryan Herbert authored Nov 14, 2018
  
  0b63ac08
- test_sample.rb test_run use .present? · 6d5be773
  Ryan Herbert authored Nov 14, 2018
```
include missing boolean functions in boolean expression
See #3619
```
  6d5be773
- test_sample.rb test_run look at all possibilities · 99645a66
  Ryan Herbert authored Nov 14, 2018
```
Just in case the job becoes assigned or completed in the time the test
takes to execute itself.
See #3619
```
  99645a66