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docker-compose.yaml
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#
Development environment with MySQL and MinIO services
#
#
NOTE: docker-compose is OPTIONAL for running tests.
#
Tests use testcontainers to automatically manage containers.
#
Just run: pytest tests/
#
#
Use docker-compose for development/debugging when you want
#
persistent containers that survive test runs:
#
docker compose up -d db minio # Start services manually
#
pytest tests/ # Tests will use these containers
#
#
Full Docker testing (CI):
#
docker compose --profile test up djtest --build
services
:
db
:
image
:
datajoint/mysql:${MYSQL_VER:-8.0}
environment
:
-
MYSQL_ROOT_PASSWORD=${DJ_PASS:-password}
command
:
mysqld --default-authentication-plugin=mysql_native_password
ports
:
-
"
3306:3306
"
healthcheck
:
test
:
[ "CMD", "mysqladmin", "ping", "-h", "localhost" ]
timeout
:
30s
retries
:
5
interval
:
15s
minio
:
image
:
minio/minio:${MINIO_VER:-RELEASE.2025-02-28T09-55-16Z}
environment
:
-
MINIO_ACCESS_KEY=datajoint
-
MINIO_SECRET_KEY=datajoint
ports
:
-
"
9000:9000
"
command
:
server --address ":9000" /data
healthcheck
:
test
:
-
"
CMD
"
-
"
curl
"
-
"
--fail
"
-
"
http://localhost:9000/minio/health/live
"
timeout
:
30s
retries
:
5
interval
:
15s
app
:
image
:
datajoint/datajoint:${DJ_VERSION:-latest}
build
:
context
:
.
dockerfile
:
Dockerfile
args
:
PY_VER
:
${PY_VER:-3.10}
HOST_UID
:
${HOST_UID:-1000}
depends_on
:
db
:
condition
:
service_healthy
minio
:
condition
:
service_healthy
environment
:
-
DJ_HOST=db
-
DJ_USER=root
-
DJ_PASS=password
-
DJ_TEST_HOST=db
-
DJ_TEST_USER=datajoint
-
DJ_TEST_PASSWORD=datajoint
-
S3_ENDPOINT=minio:9000
-
S3_ACCESS_KEY=datajoint
-
S3_SECRET_KEY=datajoint
-
S3_BUCKET=datajoint.test
-
PYTHON_USER=dja
-
JUPYTER_PASSWORD=datajoint
working_dir
:
/src
user
:
${HOST_UID:-1000}:mambauser
volumes
:
-
.:/src
djtest
:
extends
:
service
:
app
profiles
:
["test"]
command
:
-
sh
-
-c
-
|
set -e
pip install -q -e ".[test]"
pip freeze | grep datajoint
pytest --cov-report term-missing --cov=datajoint tests
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