Install Monai with all dependencies on windows following the documentation

[bpavie]

Describe the bug
The installation of Monai with all dependecies does not work following the documentation
https://docs.monai.io/en/stable/installation.html#from-github

To Reproduce

git clone https://github.com/Project-MONAI/MONAI.git
cd MONAI/
pip install -e '.[all]'

Get the following error:
ERROR: '.[all]' is not a valid editable requirement. It should either be a path to a local project or a VCS URL (beginning with bzr+http, bzr+https, bzr+ssh, bzr+sftp, bzr+ftp, bzr+lp, bzr+file, git+http, git+https, git+ssh, git+git, git+file, hg+file, hg+http, hg+https, hg+ssh, hg+static-http, svn+ssh, svn+http, svn+https, svn+svn, svn+file).

How it should be run on windows
pip install -e .[all]

However, on windows 10, I still get an error:

from pydantic import BaseModel, ValidationError
      ModuleNotFoundError: No module named 'pydantic'
      [end of output]

[ytl0623]

Hi there, I got the same error when I use command: pip install -e '.[all]'.
But if I tried to use command pip install -r requirements-dev.txt, it looks worked!!!
And I found that there are three requirements file: requirements.txt requirements-dev.txt requirements-min.txt in MONAI directory, maybe you can download all dependencies with those file.

[ytl0623]

For the second question,

from pydantic import BaseModel, ValidationError ModuleNotFoundError: No module named 'pydantic' [end of output]

After I use command pip install pydantic, and it works for me.

[ytl0623]

@wyli @bpavie

Hi there, I found the way install MONAI with all dependencies on Windows.
The command should run pip install -e ".[all]" (double quotation marks), and it works for me(like below).

(monai) C:\Users\User\MONAI>pip install -e ".[all]"
Obtaining file:///C:/Users/User/MONAI
  Installing build dependencies ... done
  Checking if build backend supports build_editable ... done
  Getting requirements to build editable ... done
  Preparing editable metadata (pyproject.toml) ... done

...

Successfully built monai
Installing collected packages: monai
  Attempting uninstall: monai
    Found existing installation: monai 1.3.0+9.gcc20c9be.dirty
    Uninstalling monai-1.3.0+9.gcc20c9be.dirty:
      Successfully uninstalled monai-1.3.0+9.gcc20c9be.dirty
Successfully installed monai-1.3.0+9.gcc20c9be.dirty

So, maybe we can mark the differences between installation on Linux and Windows in the documentation https://docs.monai.io/en/stable/installation.html#from-github.

And the second question, we can add package 'pydantic' in [options.extras_require] section in the setup.cfg file.

(Line 48)
[options.extras_require]
all =
nibabel
ninja
...
pydantic

Hope the above method helps you!

[wyli]

thanks @ytl0623, for the ModuleNotFoundError, could you please share the full error log by any chance? the project's tests currently couldn't detect this error.

[ytl0623]

Hi, @wyli, the error log is like below when running command pip install -e '.[all]' on Windows system.

ERROR: '.[all]' is not a valid editable requirement. It should either be a path to a local project or a VCS URL (beginning with bzr+http, bzr+https, bzr+ssh, bzr+sftp, bzr+ftp, bzr+lp, bzr+file, git+http, git+https, git+ssh, git+git, git+file, hg+file, hg+http, hg+https, hg+ssh, hg+static-http, svn+ssh, svn+http, svn+https, svn+svn, svn+file).

And I found that the way install MONAI with all dependencies should run pip install -e ".[all]" (double quotation marks).
The reason why it works is that the Windows shell doesn't recognize single quotes to delimit a string at all, so on Windows you'll need to use double quotes.

Finally, maybe we can mark the differences between installation on Linux and Windows in the documentation . And maybe this still deserves a PR for Windows users. #7234

Thanks!