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Turn off docker builds on tags #162

Merged
merged 78 commits into from
Mar 16, 2021
Merged

Turn off docker builds on tags #162

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cef9476
Skip tree build if fewer than 3 samples
Danderson123 Dec 7, 2020
0587c50
Merge branch 'master' into web
Danderson123 Dec 7, 2020
b51f4a2
Move web code into module
johnlees Dec 7, 2020
b639307
Try to set secret key
johnlees Dec 7, 2020
6e89ea6
Move azure CI to github actions
johnlees Dec 7, 2020
39e9707
Merge change for when novel strain assigned
johnlees Dec 7, 2020
cae1011
Update environment.yml
johnlees Dec 7, 2020
6bc4a9c
Add docker action
johnlees Dec 7, 2020
95eb749
Fix yaml syntax
johnlees Dec 7, 2020
d7df86e
More actions changes
johnlees Dec 7, 2020
a9089ce
Add OS to docker action; custom python
johnlees Dec 7, 2020
41c161c
Attempt to activate conda environment
johnlees Dec 7, 2020
c67a6a5
Remove secret from docker
johnlees Dec 7, 2020
8c60469
Missing space in tests
johnlees Dec 7, 2020
796e3d3
Move web code to correct function
johnlees Dec 7, 2020
a46c16f
Use docker version of actions
johnlees Dec 7, 2020
d03fbb7
Fix docker yaml
johnlees Dec 7, 2020
a8a70e8
Point to correct dockerfile
johnlees Dec 7, 2020
818c438
Newline in azure-pipelines
johnlees Dec 7, 2020
9d77b3e
Trigger CI on PR targeting master
johnlees Dec 7, 2020
c2bd44d
Correct name of azure pipelines
johnlees Dec 7, 2020
f19958b
Update dockerfile to actually get code
johnlees Dec 10, 2020
ecddaa9
Try to use default gunicorn port
johnlees Dec 10, 2020
a914a4e
Another attempt to change the port
johnlees Dec 11, 2020
3c8c928
Merge changes from master
johnlees Jan 20, 2021
207529a
Add host IP to gunicorn launch
johnlees Jan 20, 2021
0d78b13
Bind loopback; add test
johnlees Jan 21, 2021
1a0c053
Add ssh to container
johnlees Jan 21, 2021
e693950
Run ssh service; try to optimise gunicorn command
johnlees Jan 21, 2021
81d8e12
Fix apt line
johnlees Jan 21, 2021
2302610
Remove log line from gunicorn launch
johnlees Jan 22, 2021
ce58fa1
Fix syntax error in Dockerfile
johnlees Jan 22, 2021
341ebd4
Add gunicorn logging line
johnlees Jan 22, 2021
3cc7f1e
Remove gunicorn optimisations
johnlees Jan 22, 2021
50bf1a7
Remove ssh access
johnlees Jan 22, 2021
8220fa3
Revert to 207529a09ffd32055ebfaa4c3dc05dbf7c789eaa
johnlees Jan 22, 2021
9e71a13
Bind loopback (again)
johnlees Jan 22, 2021
f983b05
Revert to 341ebd4b6bc466f06c9798762aa4cb7f3aed2f6b
johnlees Jan 22, 2021
cd5d1a4
Revert to 341ebd4b6bc466f06c9798762aa4cb7f3aed2f6b
johnlees Jan 22, 2021
7b07159
Merge branch 'master' into docker
johnlees Jan 31, 2021
c02ce36
Move data locations in web app
johnlees Feb 1, 2021
1dcc7a4
Use flask apscheduler
johnlees Feb 1, 2021
82f088e
make scheduler global
johnlees Feb 1, 2021
9fd4332
Add script to get DB info
johnlees Feb 1, 2021
d6339a2
Increase size of dev shm
johnlees Feb 1, 2021
bb0137d
Remove use of /dev/shm
johnlees Feb 1, 2021
58096c8
Fix db variable name
johnlees Feb 1, 2021
e2725fe
Install extension
johnlees Feb 2, 2021
a789c50
Update include file location for network route
johnlees Feb 2, 2021
4c515fc
Update include file location to check for no of isolates
Danderson123 Feb 2, 2021
ee10f50
remove web arg from visualise
Danderson123 Feb 2, 2021
c91b40d
Move copy to entrypoint; fix path errors in visualise
johnlees Feb 2, 2021
42bba82
Set default for env variable in web
johnlees Feb 2, 2021
b8ceb45
Fix visualise tests
johnlees Feb 2, 2021
33c36ee
Update visualise command in network route
johnlees Feb 2, 2021
c2cf4a2
Update previous clustering argument
johnlees Feb 3, 2021
855db78
Fix path basename in cluster write
johnlees Feb 3, 2021
831d0f3
Fix output location for network route
johnlees Feb 3, 2021
41cd6ce
Update visualise args
johnlees Feb 4, 2021
a1f7f7c
Automated API tests
Danderson123 Feb 4, 2021
40998d0
Remove path insertion
Danderson123 Feb 4, 2021
dc445e2
Force gt v2.35
Danderson123 Feb 4, 2021
3e18607
Merge api routes and set model_dir to reference
Danderson123 Feb 4, 2021
b26a3db
Remove path insert from web test
Danderson123 Feb 4, 2021
2f0e282
Workaround for web query graph
johnlees Feb 5, 2021
0bcb48c
Fix web test
johnlees Feb 5, 2021
2bf46c3
Add assets needed to run web version
johnlees Feb 5, 2021
04c4b1c
Attempt to add ACR action
johnlees Feb 5, 2021
0a281a0
Fix docker build cmd
johnlees Feb 5, 2021
26f75a5
Add path to Dockerfile
johnlees Feb 5, 2021
cb2fefe
Change tag in ACR
johnlees Feb 5, 2021
ee5b0f2
Add check that visualise has enough sequences
johnlees Feb 11, 2021
f222d26
Merge branch 'master' into docker
johnlees Feb 11, 2021
5af6481
Merge branch 'hotfix-tree' into docker
johnlees Feb 11, 2021
30fa3c9
Fix bracket
johnlees Feb 11, 2021
ff64256
Merge branch 'master' into docker
johnlees Mar 16, 2021
d1cea98
Turn off docker push on tags
johnlees Mar 16, 2021
6873f5d
Decrease gworker threads
johnlees Mar 16, 2021
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3 changes: 0 additions & 3 deletions .github/workflows/acr_push.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,9 +4,6 @@ on:
push:
branches:
- docker
create:
tags:
- v*

jobs:
acr-upload:
Expand Down
3 changes: 0 additions & 3 deletions .github/workflows/docker_push.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,9 +4,6 @@ on:
push:
branches:
- docker
create:
tags:
- v*

jobs:
docker-upload:
Expand Down
2 changes: 1 addition & 1 deletion docker/Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -96,6 +96,6 @@ CMD [ "gunicorn", \
"--worker-tmp-dir", "/dev/shm", \
"--log-file=-", \
"--timeout", "600", \
"--workers=2", "--threads=4", "--worker-class=gthread", \
"--workers=2", "--threads=2", "--worker-class=gthread", \
"--chdir", "PopPUNK", \
"web:app" ]