# ropensci-review-bot

Maintenance of `ropensci-review-bot`, built on top of the following Docker containers.

## Docker Containers

### ghcr.io/ropensci-review-tools/pkgcheck:latest

This Docker image contains most of the system libraries required to build the
`roreviewapi` container. These include all libraries contained in the [GitHub
Ubuntu 20.04
runner](https://github.com/actions/virtual-environments/blob/main/images/linux/Ubuntu2004-README.md),
and a selection of R packages. The image is [stored on the GitHub Container
Registry](https://ghcr.io/ropensci-review-tools/pkgcheck), and rebuilt as a
[GitHub
action](https://github.com/ropensci-review-tools/pkgcheck/blob/main/.github/workflows/docker.yaml)
as a weekly cron job (as well as on every push).

The image itself is built on top of the [`rocker/r-bspm`
image](https://github.com/rocker-org/bspm), for reasons explained at length in
[this arXiv manuscript](https://arxiv.org/abs/2103.08069). In short: `bspm` =
Bridge to System Package Manager, and is a system to enable binary installation
of system libraries as properly shared objects. Other system for installation
of binary R packages in Linux, such as `rspm`, do not properly link system
libraries, so that a library required by one package can not be shared by other
packages. `bspm` is both very fast because of binary installation, and very
robust and scalable, because system libraries are only installed once, after
which they are properly shared between any additional packages which require
them.

### roreviewapi

The docker image of the [`roreviewapi`
repository](https://github.com/ropensci-review-tools/roreviewapi/blob/main/Dockerfile)
is mainly used to pull the latest GitHub versions of the R packages contained
in the [`ropensci-review-tools`
organisation](https://github.com/ropensci-review-tools), as well as to
configure the server with the GitHub credentials of `ropensci-review-bot`.

## Digital Ocean Server

All external services called by the bot are hosted on the Digital Ocean server,
and defined in the [`roreviewapi`
package](https://github.com/ropensci-review-tools/roreviewapi). The major
endpoint of that API is the `editor_check`, called both as part of the [Welcome
Responder](https://github.com/ropensci-org/buffy/blob/82dd29bae4aeaa6bf5ca77b27be82cacd3a1ba04/config/settings-production.yml#L18-L32),
and also able to be triggered by the [`check package`
command](https://github.com/ropensci-org/buffy/blob/82dd29bae4aeaa6bf5ca77b27be82cacd3a1ba04/config/settings-production.yml#L92-L106).
The service is built using `docker-compose`, as controlled by the
[`docker-compose.yml`
file](https://github.com/ropensci-review-tools/roreviewapi/blob/main/docker-compose.yml),
in turn built on top of the main
[`Dockerfile`](https://github.com/ropensci-review-tools/roreviewapi/blob/main/Dockerfile),
described above.

### docker-compose

The docker compose actions are all contained within the [`restart.sh`
script](https://github.com/ropensci-review-tools/roreviewapi/blob/main/restart.sh)
within the `roreviewapi` repository. The entire service can be rebuilt and
restarted by calling this script, which is also added to the `crontab` of the
Digital Ocean instance, currently to update once a week.

### Regular Maintenance

The Digital Ocean droplet should be manually updated at regular intervals (at
least every few months). This requires the following two commands:

```
sudo apt-get update
sudo reboot
```

Issuing the latter will automatically close the connection to the droplet.
Reconnection will only be possible after the system has successfully restarted,
generally after a few minutes. Once the system has restarted, the
docker-compose server will need to be restarted with the following command:

```
bash /home/shared/roreviewapi/restart.sh
```

Note that most operations within the `/home/shared` folder require `sudo`,
including editing files and all `git` commands. The docker service itself *does
not* require `sudo`, so the above command just calls `bash`, not `sudo bash`.
Similarly, containers can be run with `docker`, and do not need `sudo docker`.

### Managing and Reducing Disk Usage

On Digital Ocean, docker images are by default stored in
`/var/lib/docker/overlay2`. This directory creates copies of every image
created, and so [grows continuously in
size](https://forums.docker.com/t/some-way-to-clean-up-identify-contents-of-var-lib-docker-overlay/30604/35).
The size of the current container can be seen with `df -h`, where the container
should be `/dev/vda1`. The output has a column (generally second from the
right) of "Use%". As long as this is below 50%, this section may be ignored.
Otherwise, follow the steps described here to manually reduce used disk size.

These images in `/var/lib/docker/overlay2` can not be removed with any `prune`
command, and can only be manually cleaned. This should be done at least once
every few months by manually removing all docker files and rebuilding
everything from scratch. This can be done with the following commands, which
remove the entire current docker installation and rebuild everything anew:

```
COMPOSE_FILE=/home/shared/roreviewapi/docker-compose.yml
docker-compose -f $COMPOSE_FILE down
sudo systemctl stop docker.service
sudo su # Enter super-user mode - be very careful!!!
cd /var/lib/docker
rm -rf *
exit # Exit super-user mode
sudo systemctl start docker.service
bash /home/shared/roreviewapi/restart.sh
```


## Debugging

Error messages in response to package checks can be diagnosed by following the
procedures described in [the "Debugging" 
page](/debugging/debugging).