Updated docs and requirements for present versions

docs/SETUP.md

@@ -57,16 +57,23 @@ Save the python version of your virtual environment to the global environment fi
 ### Configure your DVC Remote
 
 Choose a [supported storage type](https://dvc.org/doc/command-reference/remote/add#supported-storage-types) and install the required DVC plugin (e.g., for WebDAV):
+
+#### WebDAV
+
 ```sh
 pip install dvc_webdav
 ```
-**Quick configuration**: Uses existing [config](../.dvc/config) file and overwrites only required parts.     
+
+**Quick configuration**: Uses existing [config](../.dvc/config) file and overwrites only required parts.
+
 ```sh
 dvc remote add -d myremote webdavs://example.com/path/to/storage --force
 dvc remote modify --local myremote user 'yourusername'
 dvc remote modify --local myremote password 'yourpassword'
 ```
+
 **Full configuration**: Reinitializes DVC repository and adds all configurations from scratch.
+
 ```sh
 rm -rf .dvc/
 dvc init 
@@ -77,8 +84,23 @@ dvc remote modify myremote timeout 600
 dvc config cache.shared group
 dvc config cache.type symlink
 ```
+
 > **Info:** For detailed information regarding other storage types, refer to the [DVC documentation](https://dvc.org/doc/command-reference/remote).
 
+#### SSH
+
+```sh
+pip install dvc_ssh
+dvc remote add -d myremote ssh://<ssh-alias>:/path/to/storage --force
+# optional:
+dvc remote modify --local myremote keyfile /path/to/keyfile
+# and (if needed)
+dvc remote modify myremote ask_passphrase true
+# or
+dvc remote modify --local myremote passphrase mypassphrase
+```
+
+> **Note**: If you encounter an error while pushing or pulling from the ssh remote with this error code: `ERROR: unexpected error - SSHClientConfig.__init__() missing 2 required positional arguments: 'host' and 'port'`, you need to downgrade the `asyncssh` packjage to version 2.18.0. This is a known [issue](https://github.com/iterative/dvc/issues/10656) that should be fixed soon.
 
 ### Configure Docker Registry  
 
@@ -154,7 +176,7 @@ docker build -t <your_image_name> .
 Run the Docker image locally in an interactive shell to test that everything works as expected:
 
 ```sh
-docker run -it -rm <your_image_name> /bin/bash
+docker run -it --rm <your_image_name> /bin/bash
 ```
 
 ### Automated Image Builds with GitHub Actions
@@ -309,6 +331,11 @@ cp -r /local-ssh/* /root/.ssh/
 # Copying the files will change the ownership to root
 # Check your the files
 ls -la /root/.ssh/
+
+# Optional - in case you have a config file in your dotfiles something similar to this might be needed as well
+docker run -it --rm -v ssh-config:/root/.dotfiles/ssh/.ssh -v $HOME/.ssh:/local-ssh alpine:latest
+# Inside the container
+cp -r /local-ssh/* /root/.ssh/
 ```
 
 > **Info**: This will not change the ownership of the files on your local machine.
@@ -403,6 +430,8 @@ cd <username>
 git clone [email protected]:<github_user>/<repository_name>.git
 ```
 
+> **Info:** On the hpc cluster, the first time you log in a ssh key is generated for you (`~/.ssh/id_rsa`). You can use this key to access your git repository.
+
 Set up a virtual environment:
 
 ```sh

requirements.txt

@@ -1,122 +1,116 @@
-# Fixed versions for example  
 absl-py==2.1.0
-aiohttp==3.9.5
-aiohttp-retry==2.8.3
-aiosignal==1.3.1
-amqp==5.2.0
+aiohappyeyeballs==2.4.4
+aiohttp==3.11.11
+aiohttp-retry==2.9.1
+aiosignal==1.3.2
+amqp==5.3.1
 annotated-types==0.7.0
 antlr4-python3-runtime==4.9.3
-anyio==4.4.0
 appdirs==1.4.4
-asyncssh==2.15.0
-atpublic==4.1.0
-attrs==23.2.0
-billiard==4.2.0
+asyncssh==2.18.0
+atpublic==5.0
+attrs==24.3.0
+bcrypt==4.2.1
+billiard==4.2.1
 celery==5.4.0
-certifi==2024.7.4
-cffi==1.16.0
-charset-normalizer==3.3.2
+certifi==2024.12.14
+cffi==1.17.1
+charset-normalizer==3.4.0
 click==8.1.7
 click-didyoumean==0.3.1
 click-plugins==1.1.1
 click-repl==0.3.0
 colorama==0.4.6
-cryptography==42.0.8
+configobj==5.0.9
+cryptography==44.0.0
 dictdiffer==0.9.0
 diskcache==5.6.3
 distro==1.9.0
 dpath==2.2.0
-dulwich==0.22.1
-dvc==3.51.2
-dvc-data==3.15.1
+dulwich==0.22.7
+dvc==3.58.0
+dvc-data==3.16.7
 dvc-http==2.32.0
 dvc-objects==5.1.0
 dvc-render==1.0.2
+dvc-ssh==4.1.1
 dvc-studio-client==0.21.0
-dvc-task==0.4.0
-dvc-webdav==3.0.0
-dvclive==3.46.1
+dvc-task==0.40.2
 entrypoints==0.4
-filelock==3.15.4
+filelock==3.16.1
 flatten-dict==0.4.2
-flufl.lock==7.1.1
-frozenlist==1.4.1
-fsspec==2024.6.1
+flufl.lock==8.1.0
+frozenlist==1.5.0
+fsspec==2024.12.0
 funcy==2.0
 gitdb==4.0.11
 GitPython==3.1.43
 grandalf==0.8
-grpcio==1.64.1
-gto==1.7.1
-h11==0.14.0
-HiYaPyCo==0.6.0
-httpcore==1.0.5
-httpx==0.27.0
+grpcio==1.68.1
+gto==1.7.2
 hydra-core==1.3.2
-idna==3.7
-iterative-telemetry==0.0.8
+idna==3.10
+iterative-telemetry==0.0.9
 Jinja2==3.1.4
-kombu==5.3.7
-Markdown==3.6
+kombu==5.4.2
+Markdown==3.7
 markdown-it-py==3.0.0
-MarkupSafe==2.1.5
+MarkupSafe==3.0.2
 mdurl==0.1.2
 mpmath==1.3.0
-multidict==6.0.5
-networkx==3.3
-numpy==1.26.4
+multidict==6.1.0
+networkx==3.4.2
+numpy==2.2.0
 omegaconf==2.3.0
-onnx==1.16.1
-orjson==3.10.6
-packaging==24.1
+onnx==1.17.0
+orjson==3.10.12
+packaging==24.2
 pathspec==0.12.1
-pedalboard==0.9.9
-platformdirs==3.11.0
-prompt_toolkit==3.0.47
-protobuf==4.25.3
-psutil==6.0.0
+pedalboard==0.9.16
+platformdirs==4.3.6
+prompt_toolkit==3.0.48
+propcache==0.2.1
+protobuf==5.29.2
+psutil==6.1.1
 pycparser==2.22
-pydantic==2.8.2
-pydantic_core==2.20.1
-pydot==2.0.0
-pygit2==1.15.1
+pydantic==2.10.4
+pydantic_core==2.27.2
+pydot==3.0.3
+pygit2==1.16.0
 Pygments==2.18.0
 pygtrie==2.5.0
-pynvml==11.5.0
-pyparsing==3.1.2
-python-box==7.2.0
+pyparsing==3.2.0
 python-dateutil==2.9.0.post0
-PyYAML==6.0.1
+PyYAML==6.0.2
 requests==2.32.3
-rich==13.7.1
+rich==13.9.4
 ruamel.yaml==0.18.6
-ruamel.yaml.clib==0.2.8
-scmrepo==3.3.6
+ruamel.yaml.clib==0.2.12
+scmrepo==3.3.9
 semver==3.0.2
-setuptools==70.2.0
+setuptools==75.6.0
 shellingham==1.5.4
 shortuuid==1.0.13
 shtab==1.7.1
-six==1.16.0
+six==1.17.0
 smmap==5.0.1
-sniffio==1.3.1
-sqltrie==0.11.0
-sympy==1.12.1
+sqltrie==0.11.1
+sshfs==2024.9.0
+sympy==1.13.1
 tabulate==0.9.0
-tensorboard==2.17.0
+tensorboard==2.18.0
 tensorboard-data-server==0.7.2
-tomlkit==0.12.5
-torch==2.2.2
+tomlkit==0.13.2
+torch==2.5.1
 torchinfo==1.8.0
-tqdm==4.66.4
-typer==0.12.3
+tqdm==4.67.1
+typer==0.15.1
 typing_extensions==4.12.2
-tzdata==2024.1
-urllib3==2.2.2
+tzdata==2024.2
+urllib3==2.2.3
 vine==5.1.0
 voluptuous==0.15.2
 wcwidth==0.2.13
-webdav4==0.9.8
-Werkzeug==3.0.3
-yarl==1.9.4
-zc.lockfile==3.0.post1
+Werkzeug==3.1.3
+yarl==1.18.3
+zc.lockfile==3.0.post1