Merge pull request #2690 from GaryPWhite/main

docker-compose -> docker compose

.docker-setup.sh

@@ -24,7 +24,6 @@ missingModules=""
 #Check everything that needs to be in the $PATH is in there.
 #Bash doesn't let this work if this is in an if statement for some reason it has to be chained
 type -P "docker" &>/dev/null && echo "docker found..." || missingModules="${missingModules} docker"
-type -P "docker-compose" &>/dev/null && echo "docker-compose found..." || missingModules="${missingModules} docker-compose"
 type -P "ifconfig" &>/dev/null && echo "ifconfig found..." || missingModules="${missingModules} ifconfig (part of net-tools)"
 type -P "psql" &>/dev/null && echo "psql found..." || missingModules="${missingModules} psql"
 type -P "watch" &>/dev/null && echo "watch found..." || missingModules="${missingModules} watch"

Makefile

@@ -139,14 +139,14 @@ docs-view: docs
 
 
 compose-run:
-	@ docker-compose -f docker-compose.yml up --build
+	@ docker compose -f docker-compose.yml up --build
 
 compose-run-database:
 	@ echo "**************************************************************************"
 	@ echo "Make sure there are no database credentials in docker_env.txt!"
 	@ echo "**************************************************************************"
 	@ echo
-	@ docker-compose -f docker-compose.yml -f database-compose.yml up --build
+	@ docker compose -f docker-compose.yml -f database-compose.yml up --build
 
 docker-build: docker-build-backend docker-build-frontend docker-build-database docker-build-rabbitmq
 

docs/8knot.md

@@ -2,7 +2,7 @@
 ## Required Ubuntu Packages
 ```shell
 sudo apt install docker &&
-sudo apt install docker-compose 
+sudo apt install docker compose 
 ```
 
 If you are running Augur on the same computer, you should already have Python3.x installed. If not, for an Ubuntu 22.x Server also issue this command: 
@@ -21,11 +21,11 @@ git checkout redis-remap
 ## Start 8knot
 To see if everything works: 
 ```shell
-sudo docker-compose up --build
+sudo docker compose up --build
 ```
 
 If you want to run 8Knot in the background: 
 ```shell
-(nohup sudo docker-compose up --build &)
+(nohup sudo docker compose up --build &)
 ```
 

docs/dev-osx-install.md

@@ -428,11 +428,11 @@ Note: Augur will run on port 5000 by default (you probably need to change that i
 You can stop augur with `augur backend stop`, followed by `augur backend kill`. We recommend waiting 5 minutes between commands so Augur can shutdown more gently. There is no issue with data integrity if you issue them seconds apart, its just that stopping is nicer than killing. 
 
 ### Docker
-1. Make sure docker, and docker-compose are both installed
+1. Make sure docker, and docker compose are both installed
 2. Modify the `environment.txt` file in the root of the repository to include your GitHub and GitLab API keys.
 3. If you are already running postgresql on your server you have two choices: 
    - Change the port mappings in the `docker-compose.yml` file to match ports for Postgresql not currently in use.
    - Change to variables in `environment.txt` to include the correct values for your local, non-docker-container database.
 4. `sudo docker build -t augur-new -f docker/backend/Dockerfile .`
-5. `sudo docker-compose --env-file ./environment.txt --file docker-compose.yml up` to run the database in a Docker Container or 
-   `sudo docker-compose --env-file ./environment.txt --file docker-compose.yml up` to connect to an already running database. 
+5. `sudo docker compose --env-file ./environment.txt --file docker-compose.yml up` to run the database in a Docker Container or 
+   `sudo docker compose --env-file ./environment.txt --file docker-compose.yml up` to connect to an already running database. 

docs/new-install-ubuntu-python-3.10.md

@@ -368,11 +368,11 @@ Note: Augur will run on port 5000 by default (you probably need to change that i
 You can stop augur with `augur backend stop`, followed by `augur backend kill`. We recommend waiting 5 minutes between commands so Augur can shutdown more gently. There is no issue with data integrity if you issue them seconds apart, its just that stopping is nicer than killing. 
 
 ### Docker
-1. Make sure docker, and docker-compose are both installed
+1. Make sure docker, and docker compose are both installed
 2. Modify the `environment.txt` file in the root of the repository to include your GitHub and GitLab API keys.
 3. If you are already running postgresql on your server you have two choices: 
    - Change the port mappings in the `docker-compose.yml` file to match ports for Postgresql not currently in use.
    - Change to variables in `environment.txt` to include the correct values for your local, non-docker-container database.
 4. `sudo docker build -t augur-new -f docker/backend/Dockerfile .`
-5. `sudo docker-compose --env-file ./environment.txt --file docker-compose.yml up` to run the database in a Docker Container or 
-   `sudo docker-compose --env-file ./environment.txt --file docker-compose.yml up` to connect to an already running database. 
+5. `sudo docker compose --env-file ./environment.txt --file docker-compose.yml up` to run the database in a Docker Container or 
+   `sudo docker compose --env-file ./environment.txt --file docker-compose.yml up` to connect to an already running database. 

docs/new-install.md

@@ -366,11 +366,11 @@ Note: Augur will run on port 5000 by default (you probably need to change that i
 You can stop augur with `augur backend stop`, followed by `augur backend kill`. We recommend waiting 5 minutes between commands so Augur can shutdown more gently. There is no issue with data integrity if you issue them seconds apart, its just that stopping is nicer than killing. 
 
 ### Docker
-1. Make sure docker, and docker-compose are both installed
+1. Make sure docker, and docker compose are both installed
 2. Modify the `environment.txt` file in the root of the repository to include your GitHub and GitLab API keys.
 3. If you are already running postgresql on your server you have two choices: 
    - Change the port mappings in the `docker-compose.yml` file to match ports for Postgresql not currently in use.
    - Change to variables in `environment.txt` to include the correct values for your local, non-docker-container database.
 4. `sudo docker build -t augur-new -f docker/backend/Dockerfile .`
-5. `sudo docker-compose --env-file ./environment.txt --file docker-compose.yml up` to run the database in a Docker Container or 
-   `sudo docker-compose --env-file ./environment.txt --file docker-compose.yml up` to connect to an already running database. 
+5. `sudo docker compose --env-file ./environment.txt --file docker-compose.yml up` to run the database in a Docker Container or 
+   `sudo docker compose --env-file ./environment.txt --file docker-compose.yml up` to connect to an already running database. 

docs/source/docker/docker-compose.rst

@@ -44,18 +44,18 @@ To run Augur **without** the database container:
 
 .. code-block:: bash
 
-    docker-compose -f docker-compose.yml up
+    docker compose -f docker-compose.yml up
 
 To run Augur **with** the database container:
 
 .. code-block:: bash
 
-    docker-compose -f docker-compose.yml -f database-compose.yml up
+    docker compose -f docker-compose.yml -f database-compose.yml up
 
 
 Stopping the containers
 -------------------------
 
-To stop the containers, run ``docker-compose down --remove-orphans``. The flag is necessary to stop the database container if you used one; run the command again to delete them. 
+To stop the containers, run ``docker compose down --remove-orphans``. The flag is necessary to stop the database container if you used one; run the command again to delete them. 
 
 Once you've got your container up and running, checkout out `how to use them <usage.html>`_ 

docs/source/docker/getting-started.rst

@@ -22,7 +22,7 @@ If you are less familiar with Docker, or experience issues you cannot resolve at
 
 Credentials
 ------------
-Before you get started with Docker, you'll need to set up a PostgreSQL instance either locally or using a remote host. Alternatively, you can also set up the database within a docker container either manually or through docker-compose.
+Before you get started with Docker, you'll need to set up a PostgreSQL instance either locally or using a remote host. Alternatively, you can also set up the database within a docker container either manually or through docker compose.
 
 .. note::
 
@@ -58,7 +58,7 @@ First, you'll need to clone the repository. In your terminal, run:
 
 Now that you've got your external database credentials (if you are using one) and your access token, we'll need to set environment variables manually.
 
-Your database credentials and other environment variables used at runtime are stored in a file when running manually and are taken from the active bash session when using docker-compose.
+Your database credentials and other environment variables used at runtime are stored in a file when running manually and are taken from the active bash session when using docker compose.
 
 You can provide your own ``.env`` file to pull from. The file should have the below format and set all the variables to some value.
 

docs/source/docker/quick-start.rst

@@ -45,5 +45,5 @@ Before you get off to such a quick start, go ahead and
   .. code-block:: bash
 
     sudo docker build -t augur-docker -f docker/backend/Dockerfile .
-    sudo docker-compose up
+    sudo docker compose up
 

docs/source/docker/toc.rst

@@ -7,7 +7,7 @@ Docker
    quick-start
    getting-started
    docker
-   docker-compose
+   docker compose
    usage
 
 

docs/source/docker/usage.rst

@@ -35,10 +35,10 @@ By default, the only logs shown by the container are the logs of Augur's main da
 .. code-block:: bash
 
     # to quickly view the most recent logs
-    $ docker-compose logs
+    $ docker compose logs
 
     # to watch the logs in real-time (like tail -f)
-    $ docker-compose logs -f
+    $ docker compose logs -f
 
 
 As for worker logs. They are currently a work in progress to be made easier to view. Shortly, they will automatically populate on the host machine and it will not be necessary to step inside the container.

docs/source/getting-started/dev-osx-install.rst

@@ -603,7 +603,7 @@ killing.
 Docker
 ~~~~~~
 
-1. Make sure docker, and docker-compose are both installed
+1. Make sure docker, and docker compose are both installed
 2. Modify the ``environment.txt`` file in the root of the repository to
    include your GitHub and GitLab API keys.
 3. If you are already running postgresql on your server you have two
@@ -615,7 +615,7 @@ Docker
       values for your local, non-docker-container database.
 
 4. ``sudo docker build -t augur-new -f docker/backend/Dockerfile .``
-5. ``sudo docker-compose --env-file ./environment.txt --file docker-compose.yml up``
+5. ``sudo docker compose --env-file ./environment.txt --file docker-compose.yml up``
    to run the database in a Docker Container or
-   ``sudo docker-compose --env-file ./environment.txt --file docker-compose.yml up``
+   ``sudo docker compose --env-file ./environment.txt --file docker-compose.yml up``
    to connect to an already running database.

docs/source/getting-started/new-install.rst

@@ -503,7 +503,7 @@ killing.
 Docker
 ~~~~~~
 
-1. Make sure docker, and docker-compose are both installed
+1. Make sure docker, and docker compose are both installed
 2. Modify the ``environment.txt`` file in the root of the repository to
    include your GitHub and GitLab API keys.
 3. If you are already running postgresql on your server you have two
@@ -515,7 +515,7 @@ Docker
       values for your local, non-docker-container database.
 
 4. ``sudo docker build -t augur-new -f docker/backend/Dockerfile .``
-5. ``sudo docker-compose --env-file ./environment.txt --file docker-compose.yml up``
+5. ``sudo docker compose --env-file ./environment.txt --file docker-compose.yml up``
    to run the database in a Docker Container or
-   ``sudo docker-compose --env-file ./environment.txt --file docker-compose.yml up``
+   ``sudo docker compose --env-file ./environment.txt --file docker-compose.yml up``
    to connect to an already running database.

docs/source/quick-start.rst

@@ -157,7 +157,7 @@ killing.
 Docker
 ~~~~~~
 
-1. Make sure docker, and docker-compose are both installed
+1. Make sure docker, and docker compose are both installed
 2. Modify the ``environment.txt`` file in the root of the repository to
    include your GitHub and GitLab API keys.
 3. If you are already running postgresql on your server you have two
@@ -169,9 +169,9 @@ Docker
       values for your local, non-docker-container database.
 
 4. ``sudo docker build -t augur-new -f docker/backend/Dockerfile .``
-5. ``sudo docker-compose --env-file ./environment.txt --file docker-compose.yml up``
+5. ``sudo docker compose --env-file ./environment.txt --file docker-compose.yml up``
    to run the database in a Docker Container or
-   ``sudo docker-compose --env-file ./environment.txt --file docker-compose.yml up``
+   ``sudo docker compose --env-file ./environment.txt --file docker-compose.yml up``
    to connect to an already running database.
 
 

scripts/docker/docker-setup-database.sh

@@ -46,21 +46,21 @@ fi
 
 
 echo "Tearing down old docker stack..."
-docker-compose -f docker-compose.yml -f database-compose.yml down --remove-orphans
+docker compose -f docker-compose.yml -f database-compose.yml down --remove-orphans
 
 #Run docker stack in background to catch up to later
 echo "Starting set up of docker stack..."
-nohup docker-compose -f docker-compose.yml -f database-compose.yml up --no-recreate &>/tmp/dockerComposeLog & 
+nohup docker compose -f docker-compose.yml -f database-compose.yml up --no-recreate &>/tmp/dockerComposeLog & 
 PIDOS=$!
 
 #While the containers are up show a watch monitor that shows container status and live feed from logs
 printf "\nNow showing active docker containers:\n"
-watch -n1 --color 'docker-compose -f docker-compose.yml -f database-compose.yml ps && echo && tail -n 30 /tmp/dockerComposeLog && echo "Ctrl+C to Exit"'
+watch -n1 --color 'docker compose -f docker-compose.yml -f database-compose.yml ps && echo && tail -n 30 /tmp/dockerComposeLog && echo "Ctrl+C to Exit"'
 printf "\n"
 
 #Stop the process and clean up dead containers on SIGINT.
 kill -15 $PIDOS
 #Cleaning up dead containers
 echo "Cleaning up dead containers... "
-docker-compose -f docker-compose.yml -f database-compose.yml down --remove-orphans
+docker compose -f docker-compose.yml -f database-compose.yml down --remove-orphans
 bash scripts/docker/cleanup.sh

scripts/docker/docker-setup-external.sh

@@ -59,14 +59,14 @@ then
   fi
   echo "AUGUR_DB_PASSWORD=$dbPassword" >> docker_env.txt
 else
-  #docker_env.txt should always be present in a docker-compose build otherwise it can cause issues for the database.
+  #docker_env.txt should always be present in a docker compose build otherwise it can cause issues for the database.
   if [[ ! -f "docker_env.txt" ]]
   then
     echo "docker_env.txt not found. Please add environment variables in this file or restart the script and choose to prompt db credentials."
     exit 1
   fi
 
-  #Copy host name to docker-compose env file.
+  #Copy host name to docker compose env file.
   cat docker_env.txt | grep AUGUR_DB_HOST >> .env
 fi
 
@@ -122,21 +122,21 @@ else
 fi
 
 echo "Tearing down old docker stack..."
-docker-compose -f docker-compose.yml down --remove-orphans
+docker compose -f docker-compose.yml down --remove-orphans
 
 #Run docker stack in background to catch up to later
 echo "Starting set up of docker stack..."
-nohup docker-compose -f docker-compose.yml up --no-recreate &>/tmp/dockerComposeLog & 
+nohup docker compose -f docker-compose.yml up --no-recreate &>/tmp/dockerComposeLog & 
 PIDOS=$!
 
 #While the containers are up show a watch monitor that shows container status and live feed from logs
 printf "\nNow showing active docker containers:\n"
-watch -n1 --color 'docker-compose ps && echo && tail -n 30 /tmp/dockerComposeLog && echo "Ctrl+C to Exit"'
+watch -n1 --color 'docker compose ps && echo && tail -n 30 /tmp/dockerComposeLog && echo "Ctrl+C to Exit"'
 printf "\n"
 
 #Stop the process and clean up dead containers on SIGINT.
 kill -15 $PIDOS
 #Cleaning up dead containers
 echo "Cleaning up dead containers... "
-docker-compose -f docker-compose.yml down --remove-orphans
+docker compose -f docker-compose.yml down --remove-orphans
 bash scripts/docker/cleanup.sh