Fix nightly tests (#1182)

* replace "docker-compose" with "docker compose"

* replace more docker-compose calls with docker compose

Author: hotzenklotz

CONTRIBUTING.md

@@ -140,7 +140,7 @@ The `webknossos` folder contains examples, which are not part of the package, bu
 The tests also contain functionality for the WEBKNOSSOS client. There a two modes to run the tests:
 
 1. `./test.sh --refresh-snapshots`, sending network requests to a WEBKNOSSOS instance:
-  This expects a local WEBKNOSSOS setup with specific test data, which is shipped with WEBKNOSSOS. If you're starting and running WEBKNOSSOS manually, please use port 9000 (the default) and run the `tools/postgres/dbtool.js prepare-test-db` script in the WEBKNOSSOS repository (⚠️ this overwrites your local WEBKNOSSOS database). Alternatively, a docker-compose setup is started automatically for the tests, see `./test.sh` and `tests/docker-compose.yml` for details. The network requests & response are recorded as "cassettes" by [vcr.py](https://vcrpy.readthedocs.io), see next point:
+  This expects a local WEBKNOSSOS setup with specific test data, which is shipped with WEBKNOSSOS. If you're starting and running WEBKNOSSOS manually, please use port 9000 (the default) and run the `tools/postgres/dbtool.js prepare-test-db` script in the WEBKNOSSOS repository (⚠️ this overwrites your local WEBKNOSSOS database). Alternatively, a `docker compose` setup is started automatically for the tests, see `./test.sh` and `tests/docker-compose.yml` for details. The network requests & response are recorded as "cassettes" by [vcr.py](https://vcrpy.readthedocs.io), see next point:
 2. `./test.sh` replays responses from previous network snapshots using [vcr.py](https://vcrpy.readthedocs.io) via [pytest-recording](https://github.com/kiwicom/pytest-recording). No additional network requests are allowed in this mode.
 
 `./test.sh --store-durations` updates the durations for
@@ -149,7 +149,7 @@ which is used in the CI to split the tests for different runners.
 
 #### `cluster_tools` package
 
-For testing the `slurm` setup a docker-compose setup is available. Please see the [respective Readme](https://github.com/scalableminds/webknossos-libs/blob/master/cluster_tools/README.md) for details.
+For testing the `slurm` setup a `docker compose` setup is available. Please see the [respective Readme](https://github.com/scalableminds/webknossos-libs/blob/master/cluster_tools/README.md) for details.
 
 For testing the `kubernetes` setup, we recommend a [Kubernetes-in-Docker setup](https://kind.sigs.k8s.io/).
 

cluster_tools/README.md

@@ -76,7 +76,7 @@ If you would like to configure these limits independently, you can do so by sett
 ```
 # See ./dockered-slurm/README.md for troubleshooting
 cd dockered-slurm
-docker-compose up -d
+docker compose up -d
 docker exec -it slurmctld bash
 docker exec -it c1 bash
 ```

cluster_tools/dockered-slurm/README.md

@@ -2,7 +2,7 @@
 
 **Note: Refer to cluster_tools/README.md for how to use this container in the context of testing the cluster_tools**
 
-This is a multi-container Slurm cluster using docker-compose.  The compose file
+This is a multi-container Slurm cluster using `docker compose`.  The compose file
 creates named volumes for persistent storage of MySQL data files as well as
 Slurm state and log directories.
 
@@ -26,10 +26,10 @@ The compose file will create the following named volumes:
 
 ## Starting the Cluster
 
-Run `docker-compose` to instantiate the cluster:
+Run `docker compose` to instantiate the cluster:
 
 ```console
-$ docker-compose up -d
+$ docker compose up -d
 ```
 
 > Note: If you encounter permission errors (`Failed to check keyfile "/etc/munge/munge.key": Permission denied`), follow the steps from the "Deleting the Cluster" section and run the previous command again.
@@ -47,10 +47,10 @@ $ ./register_cluster.sh
 > ready before registering the cluster.  Otherwise, you may get an error such
 > as **sacctmgr: error: Problem talking to the database: Connection refused**.
 >
-> You can check the status of the cluster by viewing the logs: `docker-compose
+> You can check the status of the cluster by viewing the logs: `docker compose
 > logs -f`
 
-> Note: If you encounter an error that the daemon is not running (`Error response from daemon: Container <...> is not running`), the start of the containers was not successful. Check the logs using `docker-compose logs -f` and revisit the last step.
+> Note: If you encounter an error that the daemon is not running (`Error response from daemon: Container <...> is not running`), the start of the containers was not successful. Check the logs using `docker compose logs -f` and revisit the last step.
 
 ## Accessing the Cluster
 
@@ -85,18 +85,18 @@ slurm-2.out
 ## Stopping and Restarting the Cluster
 
 ```console
-$ docker-compose stop
+$ docker compose stop
 ```
 
 ```console
-$ docker-compose start
+$ docker compose start
 ```
 
 ## Deleting the Cluster
 
 To remove all containers and volumes, run:
 
 ```console
-$ docker-compose rm -sf
+$ docker compose rm -sf
 $ docker volume rm dockered-slurm_etc_munge dockered-slurm_etc_slurm dockered-slurm_slurm_jobdir dockered-slurm_var_lib_mysql dockered-slurm_var_log_slurm
 ```

cluster_tools/dockered-slurm/register_cluster.sh

@@ -2,4 +2,4 @@
 set -e
 
 docker exec slurmctld bash -c "/usr/bin/sacctmgr --immediate add cluster name=linux" && \
-docker-compose restart slurmdbd slurmctld
+docker compose restart slurmdbd slurmctld

webknossos/local_wk_setup.sh

@@ -8,12 +8,12 @@ function ensure_local_test_wk {
     export_vars
 
     if ! curl -sf localhost:9000/api/health; then
-        echo "Using docker-compose setup with the docker tag $DOCKER_TAG"
+        echo "Using docker compose setup with the docker tag $DOCKER_TAG"
         echo "  To change this, please update DOCKER_TAG in local_wk_setup.sh"
 
         WK_DOCKER_DIR="tests"
         pushd $WK_DOCKER_DIR > /dev/null
-        docker-compose pull webknossos
+        docker compose pull webknossos
         if [ ! -d binaryData/Organization_X/l4_sample ]; then
             mkdir -p binaryData/Organization_X
             pushd binaryData/Organization_X > /dev/null
@@ -22,19 +22,19 @@ function ensure_local_test_wk {
             rm l4_sample.zip
             popd > /dev/null
         fi
-        USER_UID=$(id -u) USER_GID=$(id -g) docker-compose up -d --no-build webknossos
+        USER_UID=$(id -u) USER_GID=$(id -g) docker compose up -d --no-build webknossos
         stop_wk () {
             ARG=$?
             pushd $WK_DOCKER_DIR > /dev/null
-            docker-compose down
+            docker compose down
             popd > /dev/null
             exit $ARG
         }
         trap stop_wk EXIT
         while ! curl -sf localhost:9000/api/health; do
             sleep 5
         done
-        OUT=$(docker-compose exec -T webknossos tools/postgres/dbtool.js prepare-test-db 2>&1) || echo "$OUT"
+        OUT=$(docker compose exec -T webknossos tools/postgres/dbtool.js prepare-test-db 2>&1) || echo "$OUT"
         popd > /dev/null
     else
         echo "Using the already running local webknossos setup at localhost:9000"
@@ -62,7 +62,7 @@ function ensure_local_test_wk {
 function stop_local_test_wk {
     if [ -n "${WK_DOCKER_DIR-}" ]; then
         pushd $WK_DOCKER_DIR > /dev/null
-        docker-compose down || true
+        docker compose down || true
         popd > /dev/null
     fi
 }