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Merge pull request #394 from kikkomep/build/update-deps-0.14.0
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build: update deps of 0.14.0 version
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kikkomep authored Aug 30, 2024
2 parents 98fb402 + 0437a0c commit 90d4c39
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6 changes: 3 additions & 3 deletions docker/lifemonitor.Dockerfile
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
FROM python:3.10-slim-buster as base
FROM python:3.10-slim-buster AS base

# Install base requirements
RUN apt-get update -q \
Expand Down Expand Up @@ -100,7 +100,7 @@ RUN find /lm/lifemonitor/ -type d -exec chmod a+r {} \;
##################################################################
## Node Stage
##################################################################
FROM node:14.16.0-alpine3.12 as node
FROM node:14.16.0-alpine3.12 AS node


RUN mkdir -p /static && apk add --no-cache bash python3 make g++ \
Expand All @@ -119,7 +119,7 @@ RUN npm run production
##################################################################
## Target Stage
##################################################################
FROM base as target
FROM base AS target

# Set software and build number
ARG SW_VERSION
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7 changes: 4 additions & 3 deletions docker/worker_entrypoint.sh
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Expand Up @@ -41,9 +41,10 @@ export dramatiq_prom_db="${PROMETHEUS_MULTIPROC_DIR}"
log "Starting task queue worker container"
debug_log "PROMETHEUS_MULTIPROC_DIR = ${PROMETHEUS_MULTIPROC_DIR}"

if [[ -n "${DEBUG:-}" ]]; then
verbose=""
if [[ -n "${VERBOSE:-}" ]]; then
verbose='--verbose'
log "Debug Mode Enabled"
echo "Verbose Mode Enabled"
fi

if [[ ${FLASK_ENV} == "development" ]]; then
Expand Down Expand Up @@ -94,4 +95,4 @@ done

log "Worker exiting with exit code ${exit_code}"

exit ${exit_code}
exit ${exit_code}
68 changes: 33 additions & 35 deletions requirements.txt
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@@ -1,61 +1,59 @@
Authlib~=0.15.4
apscheduler==3.10.1
connexion[swagger-ui]~=2.14.2
dramatiq[redis,watch]==1.14.2
email-validator~=1.1.3
boto3~=1.24.80
Authlib~=0.15.6
apscheduler==3.10.4
boto3~=1.35.9
Bcrypt-Flask==1.0.2
giturlparse~=0.10.0
click-option-group~=0.5.5
connexion[swagger-ui]~=2.14.2
cryptography>=41.0.3
dnspython==2.6.1
flask-cors==3.0.10
flask-marshmallow~=0.14.0
flask-restful==0.3.9
dramatiq[redis,watch]==1.14.2
email-validator~=2.2.0
eventlet==0.36.1
flask-cors==4.0.1
flask-login~=0.6.2
flask-marshmallow~=0.14.0
flask-restful==0.3.10
flask-shell-ipython==0.5.1
flask-wtf~=1.1.1
Flask-APScheduler==1.12.4
flask-wtf~=1.2.0
Flask-APScheduler==1.13.1
Flask-Mail~=0.10.0
Flask-Migrate==4.0.7
Flask-SQLAlchemy==2.5.1
Flask-Migrate==3.1.0
Flask-Mail~=0.9.1
Flask~=2.2.5
gunicorn~=20.1.0
itsdangerous~=2.1.0
flask-socketio==5.3.6
gevent-websocket==0.10.1
giturlparse~=0.12.0
gunicorn~=23.0.0
itsdangerous~=2.2.0
jwt==1.3.1
jsonschema==3.2.0
jsonschema==4.23.0
loginpass==0.5
marshmallow-sqlalchemy~=0.28.2
networkx~=3.3
nf-core~=2.5.0
pika~=1.3.2
prometheus-flask-exporter~=0.22
pygit2~=1.12.1
psycopg2-binary~=2.9.6
pyopenssl==23.2.0
pytest-mock~=3.11.1
pygit2~=1.15.1
pyopenssl==24.2.1
pytest~=7.4.0
pytest-mock~=3.11.1
pytest-rerunfailures~=12.0.0
pytest-xdist~=3.3.1
python-dotenv~=0.19.0
python-dotenv~=1.0.1
python-jenkins==1.7.0
python-redis-lock~=4.0.0
PyGithub==1.55
PyYAML~=6.0.1
pika~=1.2.0
redis~=4.5.5
repo2rocrate~=0.1.2
requests~=2.31.0
rich~=13.8.0
rocrate==0.10.0
snakemake==6.13.1
networkx~=3.1.0
rich~=13.4.1
rocrate==0.8.0
SQLAlchemy==1.4.41
wheel~=0.40.0
urllib3==1.26.19
uwsgi==2.0.26
watchdog==4.0.2
wheel~=0.44.0
Werkzeug~=2.2.3
repo2rocrate~=0.1.2
urllib3==1.26.18
flask-socketio==5.3.4
gevent-websocket==0.10.1
eventlet==0.35.2
uwsgi==2.0.22
# watchdog version 2.3 introduces a change that breaks Flask in development mode.
# Don't use watchdog > 2.2.1 until up update Flask to something >= 2.2
watchdog==2.2.1

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