Suggested update to installation setup.py

[rppunr]

Hi Bart team,
I installed the command-line version of Bart2 in my Windows 11 laptop in an Anaconda environment yesterday.
Specifics about my environment:

1. Microsoft Windows 11 Home-Version 10.0.22631 Build 22631

2. Anaconda - conda 25.5.1

3. Python 3.13.5

   I received a warning during installation and had some issues getting the Bart2 code to execute from the Anaconda command line after installation because Windows didn't know how to run the Bart2 script file, given it's not a .py extension file.
   This is the warning from Anaconda:

(base) C:\Users\xxx\bart2\bart2-master\bart2-master>python setup.py install
C:\Users\xxx\anaconda3\Lib\site-packages\setuptools\dist.py:289: InformationOnly: Normalizing 'v2.1' to '2.1'
self.metadata.version = self._normalize_version(self.metadata.version)
running install
C:\Users\xxx\anaconda3\Lib\site-packages\setuptools_distutils\cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
!!

    ********************************************************************************
    Please avoid running ``setup.py`` directly.
    Instead, use pypa/build, pypa/installer or other
    standards-based tools.

    See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
    ********************************************************************************

!!
self.initialize_options()
C:\Users\xxx\anaconda3\Lib\site-packages\setuptools_distutils\cmd.py:66: EasyInstallDeprecationWarning: easy_install command is deprecated.
!!

    ********************************************************************************
    Please avoid running ``setup.py`` and ``easy_install``.
    Instead, use pypa/build, pypa/installer or other
    standards-based tools.

    See https://github.com/pypa/setuptools/issues/917 for details.
    ********************************************************************************

!!
self.initialize_options()

I ended up having issues with the bart2 script not being found when I tried to run a genelist simulation:

(base) C:\Users\xxx\bart2\bart2-master\bart2-master>bart2 geneset -i C:\Users\xxx\bart2\bart2-master\bart2-master\genelist\DGE-DAY11.txt -s hg38 --outdir C:\Users\xxx\bart2\bart2-master\bart2-master\outputs
'bart2' is not recognized as an internal or external command,
operable program or batch file.

I reinstalled using pip install. command, but the error persisted without being able to find the bart2 script:

(base) C:\Users\xxx\bart2\bart2-master\bart2-master>pip install -e

Anaconda displayed this warning: Building wheels for collected packages: bart2
DEPRECATION: Building 'bart2' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the --use-pep517 option, (possibly combined with --no-build-isolation), or adding a pyproject.toml file to the source tree of 'bart2'. Discussion can be found at pypa/pip#6334

I finally was able to start the bart2 simulations by adding python to the bart2 command because the bart2 script itself is actually not a .py extension file:

(base) C:\Users\xxx\bart2\bart2-master\bart2-master>python C:\Users\xxx\bart2\bart2-master\bart2-master\bin\bart2 geneset -i C:\Users\xxx\bart2\bart2-master\bart2-master\genelist\DGE-DAY11.txt -s hg38 --outdir C:\Users\xxx\bart2\bart2-master\bart2-master\outputs

Please consider making the suggested updates to the installation. Thank you.