Improve docker instructions

Fixes #68

Co-authored-by: Hilmar Lapp <[email protected]>

docs/docker.md

@@ -2,28 +2,48 @@
 
 A docker container for pybioclip is hosted at [ghcr.io](https://github.com/Imageomics/pybioclip/pkgs/container/pybioclip).
 This container has CPU support for Mac, Windows, and Linux. GPU(CUDA) support is only for Windows and Linux.
-In order to access your images the docker container requires you to [mount a volume](https://docs.docker.com/engine/storage/volumes). To avoid redownloading various bioclip files mounting a volume to hold a `.cache` directory is recommended. By default the working and home directories for this container are both set to `/home/bcuser`.
 
-All examples below require an image file named [Ursus-arctos.jpeg](https://huggingface.co/spaces/imageomics/bioclip-demo/blob/main/examples/Ursus-arctos.jpeg) in the current directory.
+### Volumes
+In order to access files the docker container requires you to [mount a volume](https://docs.docker.com/engine/storage/volumes).
+The working and home directories in this container are both set to `/home/bcuser`.
+Minimally you need to mount a volume into this directory so pybioclip can read your images.
+When running pybioclip the software will download various BioCLIP files into a `/home/bcuser/.cache` subdirectory. If you want to store the `.cache` folder in your home directory you will need to mount that directory (`~/.cache`) into the container at `/home/bcuser/.cache`.
+
+### Setup
+The examples below require an image file named [Ursus-arctos.jpeg](https://huggingface.co/spaces/imageomics/bioclip-demo/blob/ef075807a55687b320427196ac1662b9383f988f/examples/Ursus-arctos.jpeg) in the current directory.
 
 ## Mac/Linux CPU Usage
+The following command will create predictions for the `Ursus-arctos.jpeg` image in the current directory.
+The command mounts the current directory into the container at `/home/bcuser`.
+The command mounts the `~/.cache` directory into the container to cache BioCLIP files in your home directory.
 ```console
-docker run --platform linux/amd64 -v $(pwd):/home/bcuser -it ghcr.io/imageomics/pybioclip:1.0.0 bioclip predict Ursus-arctos.jpeg
+docker run --platform linux/amd64 \
+           -v $(pwd):/home/bcuser \
+           -v ~/.cache:/home/bcuser/.cache \
+           --rm ghcr.io/imageomics/pybioclip:1.1.0 \
+           bioclip predict Ursus-arctos.jpeg
 ```
 
 ## Linux GPU Usage
+The following command will create predictions using a GPU for the `Ursus-arctos.jpeg` image in the current directory.
 ```console
-docker run --gpus all --platform linux/amd64 -v $(pwd):/home/bcuser -it ghcr.io/imageomics/pybioclip:1.0.0 bioclip predict --device cuda Ursus-arctos.jpeg
+docker run --gpus all \
+           --platform linux/amd64 \
+           -v $(pwd):/home/bcuser \
+           -v ~/.cache:/home/bcuser/.cache \
+           --rm ghcr.io/imageomics/pybioclip:1.1.0 \
+           bioclip predict --device cuda Ursus-arctos.jpeg
 ```
 
 ## Windows CPU Usage
-
+The following command will create predictions for the `Ursus-arctos.jpeg` image in the current directory.
+Since this command does not mount `/home/bcuser/.cache` in the container the `.cache` directory will be created within the current directory.
 ```console
-docker run -it -v %cd%:/home/bcuser ghcr.io/imageomics/pybioclip:1.0.0 bioclip predict Ursus-arctos.jpeg
+docker run --rm -v %cd%:/home/bcuser ghcr.io/imageomics/pybioclip:1.0.0 bioclip predict Ursus-arctos.jpeg
 ```
 
 ## Windows GPU Usage
-
+The following command will create predictions using a GPU for the `Ursus-arctos.jpeg` image in the current directory.
 ```console
-docker run -it --gpus all -v %cd%:/home/bcuser ghcr.io/imageomics/pybioclip bioclip:1.0.0 predict --device cuda Ursus-arctos.jpeg
+docker run --rm --gpus all -v %cd%:/home/bcuser ghcr.io/imageomics/pybioclip bioclip:1.0.0 predict --device cuda Ursus-arctos.jpeg
 ```