Basic packages for running pnlNipype, luigi-pnlpipe, etc.

[tashrifbillah]

Omitted many packaged from here:
https://github.com/pnlbwh/pnlpipe/blob/master/python_env/environment36.yml

The following seems to be our base packages.

name: pnlpipe9

channels:
  - conda-forge

dependencies:
  - python
  - ipython
  - pytest
  - plumbum
  - pandas
  - nibabel
  - nilearn
  - pyyaml
  - psutil
  - matplotlib
  - luigi
  - sqlalchemy
  - statsmodels
  - scikit-image
  - pip
  - pip:
     - git+https://github.com/dstrohl/Python_log_indenter.git
     - git+https://github.com/mhe/pynrrd.git
     - git+https://github.com/pnlbwh/conversion.git

@RyanZurrin, do you have any comment?

[tashrifbillah]

pip install dipy==1.1.1

[tashrifbillah]

We can probably pip install everything!

[RyanZurrin]

Are you thinking pip installing everything to avoid anaconda license issues?

[tashrifbillah]

Correct.

[tashrifbillah]

pip install -r requirements.txt:

ipython
pytest
plumbum
pandas
nibabel
nilearn
pyyaml
psutil
matplotlib
luigi
sqlalchemy
statsmodels
scikit-image
git+https://github.com/dstrohl/Python_log_indenter.git
git+https://github.com/mhe/pynrrd.git
git+https://github.com/pnlbwh/conversion.git

[RyanZurrin]

Do these install the identical versions that Conda installs? Are the version requirements a bit looser for pnlNipipe then for something like CNN-Masking?

[tashrifbillah]

I like no requirement (soft requirement). But we shall conda export environment for archiving purpose.

[tashrifbillah]

(Self note)

dipy=1.1.1 won't install with Python 3.12 (the latest). Hence, we should make another Python environment for Harmonization.