Improve requirements

[WillemWybo]

Removes requirements from root dir and moves it to requirements/

Removes dill and pathos from requirements. Applies associated changes to compartmentfitter. Modifies sovtree to not rely on lambda-functions that can only be pickled with dill.

[jakobj]

there are a lot of changes i'm not sure about. are they directly related to improving reqs? do you need them bc you remove pickle?

changes in requirements.txt look good, i like the version tagging. but what's the intention behind creating a separate directory?

[WillemWybo]

@jakobj yes the changes are needed to remove dependency on dill, as with standard pickle we can not use lambda functions. @benelot implemented the separate directory. I presume he wanted a separate file for the doc requirements, but still group all requirements together in a directory

[WillemWybo]

@benelot currently the file requirements/doc.txt still contains all dependencies of the main toolbox:

# documentation
sphinx>=2.4.3
nbsphinx>=0.5.1
sphinx-gallery>=0.6.1
sphinx_rtd_theme>=0.4.3
nb2plots>=0.6
pillow>=7.1.2

numpy>=1.14.1
matplotlib>=2.1.2
cython>=0.27.3
scipy>=1.0.0
sympy>=1.1.1
dill>=0.3.1.1
pathos>=0.2.5
pytest>=4.3.0
scikit_learn>=0.22.2.post1

Can the second part (after the empty line) be removed?

[benelot]

Exactly, I separated them in order to not install all of them just for the documentation part.

[benelot]

I think we can remove the second part from the docs requirements. I mean the following requirements

numpy>=1.14.1
matplotlib>=2.1.2
cython>=0.27.3
scipy>=1.0.0
sympy>=1.1.1
dill>=0.3.1.1
pathos>=0.2.5
pytest>=4.3.0
scikit_learn>=0.22.2.post1

The docs should run through without them. In case it does not, I can fix it afterwards again by checking why it breaks on the docs side. For the release, this will not matter.

[benelot]

This is exactly how I would do the requirements.txt handling. The separate folder is not necessary, but reduces the clutter of the repository base folder. From what I see in other repositories, there are still a lot of standard documents that will reside in the base folder after some years, so it is good to clean up from time to time.