Update CLI docs (#1299)

* Update docs.

* Remove contribute.md.

* Implement requested changes.

* parse url in download command.

* Apply suggested changes.

* unify args

* Refer to pypi and run format command.

---------

Co-authored-by: Norman Rzepka <[email protected]>

Author: markbader

docs/mkdocs.yml

@@ -282,6 +282,19 @@ nav:
         - Task: api/webknossos/administration/task.md
     - CLI Reference:
       - Overview: cli/index.md
+      - Install and Run: cli/install.md
+      - Environment Variables: cli/environment_variables.md
+      - Distribution Strategies: cli/distribution_strategies.md
+      - CLI Commands:
+        - Convert Images: cli/convert.md
+        - Compress: cli/compress.md
+        - Copy Datasets: cli/copy.md
+        - Download: cli/download.md
+        - Upload: cli/upload.md
+        - Downsample: cli/downsample.md
+        - Upsample: cli/upsample.md
+        - Export as Tiff: cli/export-as-tiff.md
+        - Merge Fallback: cli/merge-fallback.md
     - Version Changelog:
       - webknossos-py/stability_policy.md
       - webknossos-py/changelog.md

docs/src/cli/compress.md

@@ -0,0 +1,72 @@
+# `compress`
+
+The `compress` command allows you to compress a WEBKNOSSOS dataset. It supports compressing specific layers and magnifications (mags) while leveraging parallel execution and customizable distribution strategies.
+
+## Usage
+
+```bash
+compress [OPTIONS] TARGET
+```
+
+### Arguments
+
+- **TARGET**  
+    Path to the WEBKNOSSOS dataset to be compressed.  
+    Example: `/path/to/dataset`.
+
+### Options
+
+- `--layer-name`  
+    Name of the layer to be compressed. If not provided, all layers will be compressed.  
+    Example: `--layer-name segmentation`.
+
+- `--mag`  
+    Magnifications (mags) to be compressed. Specify as a number or a hyphen-separated string (e.g., `2` or `2-2-2`).  
+    For multiple mags, use the option multiple times.  
+    Example: `--mag 1 --mag 2 --mag 4-4-2`.
+
+- `--jobs`  
+    Number of processes to be spawned for parallel execution.  
+    Default: Number of CPU cores.
+
+- `--distribution-strategy`  
+    Strategy to distribute the task across CPUs or nodes.  
+    Options: `multiprocessing`, `slurm`, `kubernetes`, `sequential`. 
+    Default: `multiprocessing`.
+
+- `--job-resources`  
+    Specify resources for jobs when using the SLURM distribution strategy.  
+    Example: `--job-resources '{"mem": "10M"}'`.
+
+## Example Commands
+
+### Compress all layers in a dataset:
+```bash
+compress /path/to/dataset
+```
+This command compresses all layers in the specified dataset.
+
+### Compress a specific layer:
+```bash
+compress --layer-name segmentation /path/to/dataset
+```
+This command compresses only the `segmentation` layer in the dataset.
+
+### Compress specific magnifications:
+```bash
+compress --mag 1 --mag 2 /path/to/dataset
+```
+This command compresses the `1` and `2` magnifications in all layers of the dataset.
+
+### Compress using SLURM with custom job resources:
+```bash
+compress --distribution-strategy slurm --job-resources '{"mem": "10M"}' /path/to/dataset
+```
+This command uses the SLURM distribution strategy with custom memory allocation for each job.
+
+## Notes
+
+- Ensure that the target dataset path is accessible and properly configured.
+- Use the `--layer-name` option to target specific layers for compression.
+- For SLURM distribution, make sure the required resources are specified using the `--job-resources` option.
+- This command is designed to handle large datasets efficiently by leveraging parallel processing and customizable distribution strategies.